A Phase II Trial of Pemetrexed (Alimta [Registered Trademark]) Combined With Sirolimus (Rapamycin, Rapamune [Registered Trademark]) in Subjects With Relapsed or Refractory NSCLC
Phase: PHASE1
Conditions: Carcinoma, Non-Small-Cell Lung
Sponsor: National Cancer Institute (NCI)

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A Phase I/II Trial Of Pemetrexed (Alimta®) Combined With Sirolimus (Rapamycin,
Rapamune®) In Subjects With Relapsed Or Refractory NSCLC.
Abbreviated Title:
Pemetrexed/Sirolimus NSCLC
Principal Investigator: 
Arun Rajan, M.D.
Medical Oncology Branch/CCR/NCI
9000 Rockville Pike
Bldg 10, Room 12N226
Bethesda, MD 20892
Telephone: 301 594-5322
Fax +1 301 402 0172
Email: rajana@mail.nih.gov
Lead Associate Investigator:
Gideon Blumenthal, M.D. 
Special Volunteer, Medical Oncology Branch/CCR/NCI
Bldg. 10, Rm. 12N226
10 Center Drive
Bethesda, MD 20892
Tel: (301) 796-5369
Fax: 301 402-0172
Email: gideon.blumenthal@nih.gov
Associate Investigators:
David Schrump, M.D., SB/CCR/NCI
Stephen Hewitt, M.D., Ph.D.*
William D. Figg, Pharm.D., M.B.A., MOB, CCR/NCI*
Guinevere Chun, R.N., MOB, CCR/NCI *
Takefumi Komiya, M.D., PhD, MOB, CCR/NCI
Statistician:
Seth M. Steinberg, Ph.D., OCD/CCR/NCI*
6116 Executive Blvd, Room 702
Telephone: 301-496-9502
Fax: none 
E-mail address: steinbes@mail.nih.gov
* denotes persons who will not be making clinical decisions
Drug Name: Sirolimus, commercial, (Rapamune®, Wyeth Pharmaceuticals; Philadelphia, 
PA) Pemetrexed, commercial, (Alimta®, Eli Lilly & Co.; Indianapolis, IN)
Version date: November 16, 2012

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PRÉCIS 
Background 
x
Lung cancer is the most deadly cancer due to late stage of diagnosis and intrinsic 
resistance to chemotherapy. 
x
Pemetrexed is a well tolerated FDA-approved second line chemotherapeutic agent 
with a 9% response rate. 
x
Increasing the efficacy of pemetrexed could provide clinical benefit for patients 
with refractory NSCLC.
x
Inhibition of the PI3K/Akt/mTOR pathway may increase response to 
chemotherapy. 
x
Combining sirolimus, an mTOR inhibitor, with pemetrexed could improve patient 
outcomes.
Objectives
x
Determine the safety, tolerability, PKs, and MTD of the combination of sirolimus 
with pemetrexed in subjects with NSCLC.
x
Determine the clinical response rate at the MTD of sirolimus plus pemetrexed in 
NSCLC subjects with activation of the Akt/mTOR pathway. 
x
Determine effects of sirolimus on activation of the PI3K/Akt/mTOR pathway in 
PBMCs and/or tumor tissues, to determine metabolic changes using PET scans, and 
measure PKs. 
Eligibility
x
Adults with refractory or relapsed NSCLC regardless of mTOR pathway 
activation are permitted to enroll in the trial. 
Design
x
Phase I followed by Phase II study
x
For phase I/II subjects, documentation of mTOR pathway activation is not 
mandatory. If accessible, tissue will be obtained at baseline and following two 
cycles of therapy or at time of progression, whichever occurs first. All subjects 
will have pathway analysis using PBMCs at baseline, day 8 and every two cycles 
of therapy or at time of progression, whichever occurs first. Cycle 1 is 28 days in 
length and all others 21 days.
x
Each dose level incorporates a lead-in period of sirolimus alone that will allow for 
correlations of dose level, pharmacokinetics, and biologic effects.

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x
The phase I portion of the study has 5 dose cohorts beginning below the FDA 
approved doses for both agents. There are 3 dose escalations for sirolimus and 2 
for pemetrexed. Up to 30 subjects may enroll in the phase I study.
x
The Phase II portion will utilize the MTD from the Phase I and enroll up to 60
subjects.
x
Sirolimus will be administered by mouth daily, and pemetrexed will be 
administered intravenously every 21 days until unacceptable toxicity or disease 
progression.
x
Clinical imaging (CT or MRI) and a PET CT will be obtained at baseline and 
after two cycles of treatment. Clinical imaging will be performed every two 
cycles until disease progression.

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Schema

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Table of Contents 
1 
INTRODUCTION ............................................................................................................................................ 7 
1.1 
STUDY OBJECTIVES ............................................................................................................................................... 7 
2 
BACKGROUND & RATIONALE ........................................................................................................................ 7 
2.1 
CLINICAL BURDEN OF LUNG CANCER ........................................................................................................................ 7 
3 
ELIGIBILITY ASSESSMENT AND ENROLLMENT ............................................................................................. 21 
3.1 
ELIGIBILITY CRITERIA ........................................................................................................................................... 21 
3.2 
RESEARCH ELIGIBILITY EVALUATION ....................................................................................................................... 23 
3.3 
DOCUMENTING ACTIVATION OF THE MTOR PATHWAY ............................................................................................... 25 
3.4 
PATIENT REGISTRATION ....................................................................................................................................... 27 
4 
STUDY IMPLEMENTATION .......................................................................................................................... 27 
4.1 
STUDY DESIGN ................................................................................................................................................... 27 
4.2 
DRUG ADMINISTRATION ...................................................................................................................................... 29 
4.3 
TREATMENT MODIFICATIONS FOR PHASE I .............................................................................................................. 30 
4.4 
TREATMENT MODIFICATIONS FOR PHASE II ............................................................................................................. 33 
4.5 
PHARMACOKINETIC STUDIES ................................................................................................................................. 33 
4.6 
PERIODIC EVALUATIONS DURING TREATMENT ........................................................................................................... 35 
4.7 
OFF STUDY EVALUATIONS .................................................................................................................................... 39 
4.8 
CONCURRENT THERAPIES ..................................................................................................................................... 39 
4.9 
CORRELATIVE STUDIES ......................................................................................................................................... 39 
4.10 
SURGICAL GUIDELINES .................................................................................................................................... 40 
4.11 
RADIATION THERAPY GUIDELINES ..................................................................................................................... 40 
4.12 
OFF STUDY CRITERIA ...................................................................................................................................... 41 
4.13 
POST STUDY EVALUATION (FOLLOW-UP) ............................................................................................................ 41 
5 
SUPPORTIVE CARE ...................................................................................................................................... 41 
5.1 
MEDICAL CARE .................................................................................................................................................. 41 
5.2 
MANAGEMENT OF HYPERSENSITIVITY REACTIONS ...................................................................................................... 41 
5.3 
FEBRILE NEUTROPENIA ......................................................................................................................................... 42 
5.4 
SYMPTOMATIC ANEMIA ....................................................................................................................................... 42 
5.5 
THROMBOCYTOPENIA .......................................................................................................................................... 42 
5.6 
CENTRAL VENOUS ACCESS ................................................................................................................................... 42 
5.7 
NUTRITIONAL SUPPORT AND PSYCHOSOCIAL SUPPORT ............................................................................................... 42 
5.8 
ANTI-EMETICS ................................................................................................................................................... 42 
5.9 
HYPERCHOLESTEROLEMIA AND HYPERTRIGLYCERIDEMIA ............................................................................................. 42 
5.10 
MONITORING FOR LYMPHOMA ......................................................................................................................... 42 
6 
DATA COLLECTION AND EVALUATION ........................................................................................................ 43 
6.1 
DATA COLLECTION .............................................................................................................................................. 43 
6.2 
RESPONSE CRITERIA ............................................................................................................................................ 43 
6.3 
CONFIRMATORY MEASUREMENT/DURATION OF RESPONSE ........................................................................................ 46 
6.4 
PROGRESSION-FREE SURVIVAL .............................................................................................................................. 47 
6.5 
RESPONSE REVIEW ............................................................................................................................................. 47 
6.6 
TOXICITY CRITERIA .............................................................................................................................................. 47 

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6.7 
STATISTICAL SECTION .......................................................................................................................................... 47 
7 
HUMAN SUBJECTS PROTECTION ................................................................................................................. 51 
7.1 
RATIONALE FOR SUBJECT SELECTION ...................................................................................................................... 51 
7.2 
INCLUSION OF WOMEN AND MINORITIES ................................................................................................................ 51 
7.3 
JUSTIFICATION FOR EXCLUSIONS ............................................................................................................................ 51 
7.4 
PARTICIPATION OF CHILDREN ................................................................................................................................ 52 
7.5 
EVALUATION OF BENEFITS AND RISKS/DISCOMFORTS ................................................................................................ 52 
7.6 
RISK/BENEFITS ANALYSIS ..................................................................................................................................... 52 
7.7 
CONSENT AND ASSENT PROCESS AND DOCUMENTATION ............................................................................................ 52 
8 
SAFETY REPORTING REQUIREMENTS/DATA AND SAFETY MONITORING PLAN ........................................... 53 
8.1 
DEFINITIONS ...................................................................................................................................................... 53 
8.2 
NCI-IRB REPORTING .......................................................................................................................................... 55 
8.3 
DATA AND SAFETY MONITORING PLAN ................................................................................................................... 56 
9 
PHARMACEUTICAL AND INVESTIGATIONAL DEVICE INFORMATION ........................................................... 57 
9.1 
SIROLIMUS ........................................................................................................................................................ 57 
9.2 
PEMETREXED ..................................................................................................................................................... 61 
9.3 
DEXAMETHASONE .............................................................................................................................................. 63 
9.4 
FOLIC ACID ........................................................................................................................................................ 63 
9.5 
CYANOCOBALAMIN ............................................................................................................................................. 63 
10 
REFERENCES ............................................................................................................................................... 64 
11 
APPENDICES ............................................................................................................................................... 68 
11.1 
APPENDIX A: TABLE 3: STUDY CALENDAR ........................................................................................................... 68 
11.2 
APPENDIX B: TABLE 4: PERFORMANCE STATUS CRITERIA....................................................................................... 72 
11.3 
APPENDIX C: STANDARD OPERATING PROCEDURE FOR ISOLATING PBMCS ............................................................... 73 
11.4 
APPENDIX D: STANDARD OPERATING PROCEDURE FOR TUMOR TISSUE ACQUISITION AND STORAGE .............................. 75 
11.5 
APPENDIX E: TABLE 5: DRUGS WITH POTENTIAL CYP3A4 INTERACTIONS ................................................................. 76 

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1
INTRODUCTION
1.1
Study Objectives
1.1.1 Phase I objectives
1.1.1.1 The primary objectives of the phase I component of the study are to determine the safety 
and tolerability of the combination of pemetrexed with sirolimus in human subjects with 
NSCLC, and to determine the maximum tolerated dose (MTD) in this group of subjects.
1.1.1.2 The secondary objectives are to perform PKs, look for early evidence of efficacy of the 
combination, and to define the effects of this combination on mTOR pathway activation 
in PBMC and tumor tissue (optional). PET CT will be used to look for metabolic 
changes in tumors treated with the combination. These changes will be correlated with 
clinical tumor measurements as well as in vitro measures of mTOR pathway activation.
1.1.2 Phase II objectives
1.1.2.1 The primary objective of the phase II component of the study is to determine the efficacy
of the maximal tolerated dose of pemetrexed plus sirolimus in NSCLC patients. The 
primary outcome will be the clinical response rate.
1.1.2.2 The secondary objectives of the phase II component of the study are to determine the 
effects of sirolimus plus pemetrexed on mTOR pathway activation in NSCLC. A series 
of correlative studies will be done to measure biological and clinical effects of this 
combination. These studies will include analyses of tissue and blood samples, as well as 
correlative imaging studies using CT and PET:CT scans.
2
BACKGROUND & RATIONALE
2.1
Clinical Burden of Lung Cancer
Lung cancer is the leading cause of cancer death [1]. 55% of patients will present with 
stage IV or stage IIIB disease that is not amenable to curative resection. With platinum-
based doublets given as first line treatment, the current one-year survival is 34%; moreover, 
12% of patients with a good performance status are alive 2 years after diagnosis [2].
In second line treatment of NSCLC, three agents have been approved. Docetaxel was the 
first to be approved, and pemetrexed, a multi targeted antifolate inhibitor of dihydrofolate 
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(GARFT), was next to be approved. Despite the fact that docetaxel and pemetrexed have 
similar overall response rates (10% and 9.1% respectively) and median survival (7.6 
months and 8.3 months, respectively [3-5]), pemetrexed is preferred because a favorable 
toxicity profile vs. docetaxel. For example, in hematological toxicities, grade 3 and 4 
neutropenia occurred in only 5.3% of patients on pemetrexed vs. 40.2% in patients on
docetaxel. For other toxicities, any grade alopecia occurred in only 6.4% of patients on 
pemetrexed vs. 37.7% of patients on docetaxel. Any grade diarrhea occurred in 12.8% of 
patients on pemetrexed vs. 24.3% of patients on docetaxel [3-5].
Erlotinib is the third agent approved in the second line setting and targets the epidermal 
growth factor receptor (EGFR). The response rate to erlotinib is also ~10%, although there 
may be a subset of patients who benefit from EGFR tyrosine kinase inhibitors more than 
the rest of the population [6]. Clearly, new approaches are needed to increase the efficacy 
of second line chemotherapy in NSCLC, and one possibility is to combine chemotherapy 
with inhibitors of signal transduction pathways such as the PI3K/Akt/mTOR pathway that 
promote survival and chemotherapeutic resistance.
2.1.1 The PI3K/Akt/mTOR pathway and lung cancer biology
Many lines of evidence show that the PI3K/Akt/mTOR pathway is important in lung 
cancer. First, tobacco components increase activation of the PI3K/Akt/mTOR pathway and 
cause a partially transformed phenotype in primary human bronchial epithelial cells [7].
Second, increased activation of Akt and mTOR correlates with phenotypic progression of 
murine lung lesions induced by a tobacco carcinogen, and increased activation of Akt is 
characteristic of human preneoplastic lung lesions [8, 9]. Third, the PI3K/Akt/mTOR 
pathway is constitutively active in NSCLC cells and promotes resistance to chemotherapy 
and radiation [10]. Fourth, pathway activation can be increased further in lung cancer cells 
by exposure to tobacco components or adhesion to specific extracellular matrix proteins. 
This confers increased resistance to traditional and targeted chemotherapies that can be 
reversed by sirolimus [11-13]. Fifth, activation of Akt is a poor prognostic factor for 
NSCLC patients [13].
2.1.2 Sirolimus, the prototypic inhibitor of the 
PI3K/Akt/mTOR pathway
The PI3K/Akt/mTOR pathway is 
activated by many mechanisms relevant to 
cancer such as activation of receptor 
tyrosine kinases (RTKs) or oncogenes 
such as ras (Figure 1). Despite its potential 
importance, few inhibitors of the 
PI3K/Akt/mTOR pathway are available 
Figure 1. Activation and propagation of 
the PI3K/Akt/mTOR pathway.

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for clinical use. The class of agents fully developed for use in patients is inhibitors of 
mTOR such as sirolimus. Sirolimus (Rapamycin) is FDA-approved as an 
immunosuppressant for renal transplant patients and is used in combination with other 
drugs to depress T cell function. mTOR inhibitors cause cell cycle arrest in G1 and/or 
apoptosis by inhibiting phosphorylation of mTOR downstream components such as 4E-
BP1, S6K, and a substrate of S6K, the ribosomal protein S6 (not shown in Figure 1). The 
phosphorylation state of pathway components can be assessed by using phospho-specific 
antibodies in assays such as immunohistochemistry, immunoblotting, and flow cytometry. 
Importantly, mTOR inhibitors are preferentially active in cells that have mutations in 
PTEN or have constitutive activation of mTOR through other mechanisms such as 
activation of growth factor receptors, Ras, or integrins. 
2.1.3 Preclinical Efficacy
Sirolimus is a potent cytostatic 
agent, while at doses above 10 μM, 
it is cytotoxic to virtually all cancer 
cell lines in the NCI 60 cell line 
panel (figure 2). mTOR inhibitors 
can prevent tumorigenesis and 
inhibit tumor growth in vivo. mTOR 
inhibition prevents tumorigenesis in 
transgenic model of breast, prostate 
cells and alveolar epithelial 
neoplasia [14, 15] as well as in a 
carcinogen driven model of lung 
cancer [16]. mTOR inhibitors can 
also inhibit the growth of lung 
tumors in xenograft models when 
given individually or in combination 
with conventional cytotoxic chemotherapy (see below). Sirolimus can also induce 
apoptosis and sensitize cancer cells to induction of apoptosis by DNA-damaging agents 
such as cisplatin in a p53-dependent manner [17].
2.1.4 Clinical Efficacy
In addition to sirolimus, analogs of sirolimus, CCI-779 (Torisel, temsirolimus) and RAD-
001 have under gone testing in renal cancer, breast cancer and glioblastomas [18-20].
Activity has been observed in many tumor types. Partial responses were noted in the phase 
I trials with CCI-779 in one patient with clear-cell renal carcinoma, one patient with breast 
Figure 2. Composite NCI60 panel results for 
sirolimus. Each line represents a single cell line. 
Concentrations of sirolimus range from 10 nM 
to 100μM.

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adenocarcinoma, one patient with non small cell lung cancer, and two patients had stable 
disease that lasted 24 weeks [21, 22]. In phase II studies, CCI-779 produced an objective 
response rate of 7% in advanced RCC patients with a median time to tumor progression of 
5.8 months and median survival of 15.0 months [23]. Similar objective response rates were 
observed in a recent Phase III trial in renal cell cancer patients that led to FDA-approval of 
temsirolimus [24]. Galanis et al.[25] enrolled 65 patients with recurrent GBM on 
temsirolimus and observed radiographic improvement in 36% and prolonged time to 
progression of 2.3 months for all participants and 5.4 months for responders. The results of 
many other Phase II trials that demonstrate objective responses have been presented in 
abstract form.
mTOR inhibitors have been combined with traditional chemotherapy as well. Punt et al.,
published a study of temsirolimus and 5FU [26]. Though some responses were seen in this 
trial, the results were overshadowed by the toxicities that forced early closure of the study. 
Pharmacokinetics studies did not indicate increased exposure to either the 5FU or 
temsirolimus as the source of the unexpected toxicity. Unfortunately, like most trials with 
mTOR inhibitors, this one did not use biomarkers to follow modulation of the pathway 
after therapy, so that correlations between mTOR inhibition, efficacy, and/or toxicity could 
not be established. While the results of Punt et al., raise the possibility that pemetrexed and 
sirolimus might be an effective combination against tumors such as NSCLC with marked 
activation of the Akt/mTOR pathway, it emphasizes the need to monitor pathway inhibition 
during clinical trials.
2.1.5 Importance of Biomarkers
Biomarker analysis to confirm modulation of downstream components after mTOR 
inhibition has been performed in a minority studies, but has proved to be illuminating [25, 
27]. In a study of temsirolimus in patients with recurrent glioblastoma by Galanis et al.,
[25] there was a statistically significant correlation between increased mTOR activity, as 
defined by elevated baseline phosphorylated S6 kinase levels in IHC, and radiographic 
improvement. Similarly, Duran et al. showed that the best predictor of response of patients 
with neuroendocrine tumors to temsirolimus was an elevated basal level of phosphorylated 
mTOR S2448, and radiographic response correlated with decreases in levels of phospho-S6 
[27]. These studies are consistent with preclinical data showing that mTOR must be active 
for mTOR inhibitors to be effective and they suggest that measuring the phosphorylation of 
S6 and mTOR has clinical utility. Thus, biomarker assays should be a critical component of 
future studies so that tumor responses or toxicity can be correlated with modulation of 
pathway components after mTOR inhibition therapy. 
Another important application for biomarkers is studying the effect of mTOR inhibitors on 
feedback activation of Akt. This feedback could hypothetically negate any effect of mTOR 

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inhibitors by promoting propagation of the Akt signal to other downstream substrates. Two 
different mechanisms have been described. mTOR can exist in two types of complexes, 
mTORC1 and mTORC2 complexes. Several preclinical studies have shown that mTOR 
inhibitors preferentially decrease the proportion mTORC1 complexes and increase the 
proportion of mTORC2 complexes, which are comprised of mTOR bound to rictor. 
mTORC2 complexes can directly phosphorylate Akt at S473 and lead to its activation [28].
A separate mechanism for feedback activation has also been observed that involves IRS-1,
which normally activates PI3K. S6K, a downstream substrate of mTOR, normally 
phosphorylates and inhibits IRS-1. Inhibition of mTOR by sirolimus decreases S6K 
activity, which indirectly activates IRS-1, prolongs the half-life of IRS-1, and activates 
PI3K [29]. Thus, the inhibition of mTOR could result in two modes of feedback activation 
of Akt, through direct activation of Akt by mTOR-rictor complexes, and through the 
indirect activation of IRS-1 by inhibition of S6K. 
Although either feedback mechanisms could possibly counter the efficacy of an mTOR 
inhibitor, there is no evidence that this occurs in humans, and the clinical relevance of these 
mechanisms is unclear. Nonetheless, this protocol will incorporate evaluation of these 
biomarkers to assess whether such a feedback mechanism occurs in tissues from lung 
cancer patients
2.1.6 Correlating biomarkers with imaging
In addition to monitoring biomarkers such as phospho-S6 or phospho-mTOR in IHC, other 
assays such as immunoblotting and metabolic imaging might also be useful. This has been 
demonstrated recently by our group in analyzing tissues from rare patients with Cowden’s 
syndrome (CS) who were treated with sirolimus as a single agent. CS is a hamartomatous 
tumor syndrome characterized by benign hamartomas and trichilemmomas that occur in 
any organ, and patients with CS are at increased risk for breast, uterine, and thyroid cancer. 
Approximately 80% of CS patients have germline mutations in the PTEN gene, a tumor 
suppressor gene that negatively regulates activation of Akt /mTOR pathway. We have 
recently shown that benign and malignant tumors from CS patients have very high 
endogenous levels of activation of the Akt/mTOR pathway (data not shown). Due to
unusual circumstances, we have had the opportunity to treat two CS patients with cancer 
with sirolimus. At the time sirolimus was initiated, patient #1 had metastatic uterine cancer 
with carcinomatous peritonitis and patient #2 had metastatic NSCLC. After one month of 
sirolimus, we observed inhibition of mTOR by immunoblotting in PBMCs and by 
immunohistochemistry in benign hamartomas (figure 3). Similar results were observed for 
each patient. Based upon the reports from imatinib and GIST trials using PET FDG to 
detect early responses to therapy [30], we obtained PET scans to assess early metabolic 
responses in these two patients. There was 30 to 50% decrease in the SUV uptake in both 
malignant and benign tissues within a month of sirolimus therapy (figure 3). This anecdotal 
data suggests that IHC, immunoblotting, and/or PET scans may be useful to monitor 

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therapy with an mTOR inhibitor.
2.1.7 Combining pemetrexed & sirolimus
We hypothesize that because the PI3K/Akt/mTOR pathway is important in lung cancer 
pathogenesis, the combination of sirolimus and pemetrexed should be more effective than 
either agent alone. Several preclinical studies have shown that inhibition of the Akt/mTOR 
pathway increases the apoptotic response of cancer cell lines to 5FU [31-37] and 
pemetrexed [38, 39]. Moreover, anti-folate agents such as pemetrexed, 5FU, and the 
experimental fluoropyrimidine, S-1, are also capable of decreasing activation of the 
Akt/mTOR pathway as single agents. Thus, there is a rationale to test sirolimus 
sequentially and simultaneously with pemetrexed in lung cancer cell lines to assess additive 
or synergistic effects of the combination.
To assess sequence dependence and demonstrate possible synergistic effects, we combined 
sirolimus and pemetrexed in two human non-small cell cancer lines (figure 4A, 4B). In 
A549 or H157 cells, synergy was observed with combination indices <1.0 for multiple dose 
P-mTOR (S2448)
P-S6K (T389)
P-S6 (S235/6)
Total protein
Before
After 
Figure 3. Biomarkers for mTOR inhibition in clinical 
specimens. Inhibition of mTOR pathway components is 
shown after sirolimus therapy using immunoblotting 
(patient 1), IHC (patient 1), and PET scan results (SUVs 
from patient 2).

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levels (data not shown). There was no difference in cellular responses if sirolimus and 
pemetrexed were administered simultaneously or sequentially. These studies did not 
indicate any antagonistic effects. We did observe, however, that A549 cells were more 
resistant to pemetrexed as a single agent than what has been previously reported in the 
literature [40, 41]. Our IC50 of greater than 1000 μM for A549 cells was higher than the 
2.5±0.3 μM reported by Kano et al. [41] or the 640 nM reported by Smith et al. for the 
same cell line [40]. Because we used different assays to assess proliferation that employed 
different dyes, different serum concentrations, and different types of serum, we repeated 
the experiments exactly as performed by Kano et al. and Smith et al. [40] to confirm that 
the differences in IC50 were due to experimental conditions. We hypothesized that the 
discrepancy might be principally related to the fact that Smith et al. and Kano et al. used 
dialyzed serum, which lacks folate and is devoid of nucleosides and bases capable of 
rescuing pemetrexed treated cells. (Our original experiments followed standard tissue 
culture protocols using undialyzed serum, which contains folate and nucleosides).
Figure 4A
Figure 4B
Sirolimus (μM)
0
250
500
750
1000
30
40
50
60
70
80
90
100
110
Pemetrexed alone
Sirolimus alone
Simutaneous
pemetrexed+sirolimus
Sequential
sirolimus, pemetrexed
Sequential
pemetrexed, sirolimus
0            0.25           0.5            0.75         1.0
Pemetrexed
(nM)
A549 cells
Figure 4: Synergistic effects of comb
lines when cultured with non-dialyze
concentrations shown. Proliferation 
Each condition was assessed in sextu
A: A459 cells B: H157 cells

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We compared responsiveness of A549 cells to pemetrexed in dialyzed or non-dialyzed 
serum (5 %) using the SRB assay as employed by Smith et al. [40] (Figure 5A). The IC50 
in dialyzed serum was <200 nM, yet was not reached in undialyzed serum. This IC50 of 
<200 nM in dialyzed serum is very similar to the IC50 (640 nM) observed by Smith et al.
The IC50 did not significantly differ using 5% or 10% dialyzed serum (data not shown). 
We also tested responsiveness of A549 cells in dialyzed serum to pemetrexed using the 
MTT assay as employed by Kano et al. [41]. The IC50 is these experiments was 1.8 μM, 
consistent with the value of 2.5 μM obtained by Kano et al. (data not shown). 
We also repeated the combination studies shown in Figure 4 in dialyzed serum (Figure 5B, 
5C). The sensitivity to pemetrexed or sirolimus as single agents was increased in dialyzed 
serum. The IC50 of pemetrexed alone decreased about one half log with the simultaneous 
addition of sirolimus. In A549 cells we observed synergy with combination indices (CI) 
<1.0 at concentrations of pemetrexed: sirolimus of 100 nM: 1nM (CI=0.162), 300 nM: 3 
nM (0.082), and 1000 nM: 10 nM (0.29), respectively. In H157 cells, we observed synergy 
with combination indices (CI) <1.0 at the same concentrations of pemetrexed: sirolimus 
100 nM:1nM (0.209), 300 nM:3 nM (0.121), and 1000 nM:10 nM (0.17). Regarding the 
clinical relevance, concentrations of 1 to 10 nM of sirolimus are achievable and safe. The 
Cmax for 2 mg a day dosing per the sirolimus package insert is approximately 15.0 ± 4.9 
Sirolim
0
250
50
30
40
50
60
70
80
90
100
110
0            0.25           0.5 
H157 cells
Pemetr
0
20
40
60
80
100
120
0
2
4
6
Pemetrexed (μM)
10% Non Dialyzed FBS
10% Dialyzed FBS
Figure 5A. Effect of dialyzed 
serum on response to 
pemetrexed. A549 cells grown in 
the presence of 10% dialyzed 
serum have an IC50 of less than 
1μM. The IC50 was not reached 
for cells grown in non dialyzed 

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0
20
40
60
80
100
120
0.1
1
10
100
1000
10000
Pemetrexed (nM)
Pemetrexed
Sirolimus
Sirolimus+Pemetrexed
ng/ml or approximately 11 to 22 nM (MW- 914g). Trough levels, as reported in the 
package insert for 2 mg a day dosing are 8.6 ± 4.0 ng/ml, or approximately 5 to 14 nM. In 
general trough levels < 20 nM are thought to be safe. Again, the concentrations of sirolimus 
at which we observed synergy were 1 to 10 nM, below or within the accepted trough level 
range.
Figure 5B. A549 cells
Figure 5C. H157 cells
.01         .1             1            10                   Sirolimus (nM)                                              .01 
.1             1            10                     Sirolimus (nM)              
.16   .08    .29             Combination Indices (CI)                                                              
.21   .12   .17
CI
Figure 5B and 5C:  Synergistic effects of combining pemetrexed and sirolimus in NSCLC 
cell lines when cultured in 10% dialyzed serum. A549 (5B) and H157 (5C) cells grown in 
the presence of pemetrexed and sirolimus with 10% dialyzed FBS show synergistic effects 
on growth inhibition at the three highest concentrations. Combination indices were 
calculated using Calcusyn Software (Biosoft, Oxford, UK)
In summary, the discrepancy of IC50 doses observed in our in vitro studies and those of 
Smith et al. [40] and Kano et al. [41] was likely due to the presence of dialyzed serum. 
Given that patients treated with pemetrexed receive folate supplementation and their serum 
is replete with nucleosides, the use of undialyzed serum probably represents a more 
physiological situation. In addition, this data suggests that synergy may be most likely to be 
observed at higher doses ranges or dose escalation in a clinical trial.
To extend our in vitro studies, we performed xenograft experiments with sirolimus and 
pemetrexed using H157 cells in nude mice. There are no published xenograft studies using 
this combination of drugs. Published data does suggest, however, that down regulation of 
an activated Akt/mTOR pathway will enhance sensitivity of cell lines to conventional 
0
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chemotherapeutic agents [20]. In an attempt to first inactivate mTOR, we used a lead in 
dose of sirolimus followed by a dose of pemetrexed that has been used previously (100 
mg/kg intraperitoneally administered) [42] (figure 6). This design was intended to be 
similar to the clinical trial design. There was no untoward toxicity experienced by the mice 
and the mice continued to gain weight during the study. In assessing inhibition of NSCLC 
tumor growth, sirolimus alone was effective. In contrast, pemetrexed alone was ineffective, 
which was consistent with in vitro assays performed with H157 cells in undiayzled serum. 
Together, the combination of sirolimus and pemetrexed was more effective than either 
agent alone in a statistically significant manner (p<0.05). These data are consistent with 
data from Teicher et al. who observed a 2 to 4 day delay in tumor growth (H460 cells in 
nude mice) after 7 or 14 days of pemetrexed alone, but up to a 28 day delay with 
pemetrexed in combination with paclitaxel. (Sirolimus was not used in these studies.)
Figure 6
Figure 6: H157 xenograft studies. The schema for administration of sirolimus and 
pemetrexed is shown on the left. The effects of sirolimus and/or pemetrexed on growth of 
H157 tumors in nude mice are shown on the right. Combined sirolimus and pemetrexed 
after a sirolimus lead in had greater inhibition of tumor growth than either agent alone 
(p<0.05).
In addition to the preclinical studies [31-37] showing that inhibition of the Akt pathway 
enhances sensitivity to conventional chemotherapeutic agents, one clinical trial has been 
published that combined a sirolimus analogue with an anti-folate agent. Punt et al. [26]
treated 28 subjects with advanced malignancies with CCI-779, followed by leucovorin, and 
24 hour infusional 5FU. Cycles were repeated weekly. The dose of CCI-779 that was 
Day0
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chosen, 15 mg/m2, was 25% lower than the dose that was being tested in a simultaneously 
running phase I study. This dose was below the maximum tolerated dose and was not 
associated with more than grade 2 toxicity in their phase I study. The study was closed 
early because of toxicity. In addition to serious toxicities such as mucositis, nausea and 
vomiting, thrombocytopenia, and febrile neutropenia, there were two fatal bowel 
perforations unrelated to tumor. 
Pharmacokinetic data did not suggest that CCI-779 treatment resulted in greater exposure 
to 5FU, nor were the sirolimus levels (CCI-779 is metabolized to sirolimus) abnormally 
elevated. Three subjects had confirmed partial responses of 6 to 24 months duration, 
otherwise 11 patients had stable disease. The median time to progression for the entire 
group was 3.2 months and 5.2 months for the responders (partial response and stable 
disease). Notably thirteen subjects had not received prior therapy for their malignancy and 
many subjects had tumors expected to be sensitive to 5FU. The investigators caution that 
future studies should consider the overlapping toxicities and not use the dose/schedule used 
in this trial. No biomarker analyses were employed in this study. 
In summary, our preclinical data demonstrate the importance of tissue culture technique in 
experiments testing efficacy of pemetrexed in H157 and A549 cells. Standard techniques 
using non-dialyzed serum may provide a more physiological setting, but the resistance of 
these cell lines to pemetrexed makes determining an IC50 to that agent impossible. By 
using dialyzed serum, we were able to demonstrate synergy and a threefold decrease in the 
IC50 of pemetrexed when combined with sirolimus. Together our cell line and xenograft 
data provide a rationale to test this combination in patients with refractory NSCLC.
2.1.8
Sirolimus
2.1.8.1 Background
Sirolimus (Rapamycin: Rapamune: Wyeth-Ayerst, PA, USA), first isolated from the soil 
bacteria Streptomyces hygoscopicus in 1975, was approved by the FDA in 1999 as an 
immunosuppressive agent for use in preventing rejection in renal transplant recipients in 
combination with cyclosporine and corticosteroids. The FDA approved dose is a 6 mg 
loading dose on day 1 followed by 2 mg each day starting on day 2. 
2.1.8.2 Pharmacodynamics
Sirolimus is a macrolide that acts as a signal transduction inhibitor of mTOR causing cell 
cycle arrest at G1 [43, 44]. It inhibits the serine-threonine kinase mammalian target of 
Rapamycin (mTOR) by forming a complex with the FK binding protein 12 (FKBP-12). 
mTOR is a member of the evolutionarily conserved phosphatidylinositide 3’-kinase 
(PI3K)-related family and it been shown to be involved in regulating many aspects of 
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membrane trafficking, protein degradation, protein kinase C (PKC) signaling, and 
transcription [45]. The sirolimus/FKBP-12 binding to mTOR leads to dephosphorylation 
and inactivation of the p70S6 kinase (S6K1) and 4E-BP1. In turn, this inhibits the 
translation and production of ribosomal components necessary for protein synthesis and 
thereby Akt activation and causes cell-cycle arrest in G1 phase [46]. This series of events 
effectively forms the rationale for the immunosuppressant role of sirolimus in renal 
transplant patients since IL-2 induced T-cell proliferation is effectively blocked.
2.1.8.3 Pharmacokinetics
Mean time to peak concentration (Tmax) of sirolimus following oral administration is 1 
hour after a single dose in healthy volunteers and 2 hours after multiple daily doses in renal 
transplant recipients. The bioavailability of sirolimus after administration of the tablet is 
approximately 27% higher than that of the oral solution. Clinical equivalence of the two 
formulations has been demonstrated at the 2mg dose level. A high fat meal altered the 
bioavailability characteristics of sirolimus and therefore the drug should be taken 
consistently with or without food. Sirolimus is extensively bound to plasma proteins 
including serum albumin (97%), D1-acid glycoprotein and lipoproteins. Sirolimus is a 
substrate for the cytochrome p450 IIIA4 (CYP3A4) and P-glycoprotein. Inhibitors of 
CYP3A4 may decrease the metabolism of sirolimus and increase sirolimus levels, while 
inducers of CYP3A4 may increase the metabolism of sirolimus and decrease sirolimus 
levels. The majority of sirolimus is excreted in the feces (91%) with only a minor amount 
(2.2% excreted in the urine). Mean whole blood sirolimus trough concentrations achieved 
steady state concentrations within 1 day after the start of dose administration following a 
loading dose of three times the maintenance dose. The pharmacokinetics of sirolimus 
administered with and without pemetrexed will be monitored during the Phase I portion of 
the trial. In the renal transplant setting, adequate therapeutic trough levels are between 16 
to 24 ng/mL for the first year and 12 to 20 ng/mL after that.
2.1.8.4 Toxicology
There are no adequate studies in pregnant women therefore effective contraception must be 
initiated before, during and for 12 weeks following discontinuation of therapy with 
sirolimus. In animal studies, sirolimus was embryo/fetal toxic resulting in mortality and 
reduced fetal weight but no teratogenecity. 
2.1.8.5 Clinical Safety Data
The incidence of adverse reactions was determined utilizing renal transplant patients, who 
were taking sirolimus in combination with cyclosporine and corticosteroids. Two 
randomized, double-blind, multicenter controlled trials were conducted [47, 48]. The first 
study included 558 renal transplant patients and the second 446 renal transplant patients. 
Patients in the sirolimus arm in both trials received Rapamune solution formulation orally
in combination with cyclosporine and corticosteroids. A third study evaluated Rapamune 
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corticosteroids. There was no difference in toxicity between the two formulations except 
for an increased incidence of acne with the oral liquid formulation and an increased 
incidence of tremor with the tablet formulation especially in African American patients. 
Hyperlipidemia and hypercholesterolemia were found to be dose-related effects of 
sirolimus therapy. During clinical trials, renal transplant patients who began sirolimus with 
normal, fasting, total serum triglycerides developed hypertriglyceridemia after treatment 
with sirolimus 2 mg and 5 mg. Treatment of new onset hypercholesterolemia was required 
in 42-52% of renal transplant patients on sirolimus compared to 16% in the placebo arm 
and 22% in the azathioprine arm. Patients treated with sirolimus tended to develop higher 
creatinine and lower glomerular filtration rate compared to the placebo and azathioprine 
arm. During clinical trials, hypophosphatemia occurred in 15% to 23% of patients 
receiving sirolimus, while hypokalemia occurred in 11% to 21% of patients. A negative 
dose adjustment is recommended for patients with mild to moderate hepatic impairment 
since their steady state levels are affected by hepatic function. There is a black box warning 
regarding the increased susceptibility to infection and possibility of developing lymphoma 
secondary to immunosuppression when sirolimus is used in combination with cyclosporine 
and corticosteroids. Further side effects have been reported with sirolimus. CCI-779, a 
sirolimus analogue, was combined with 5-fluorouracil and leucovorin in a phase I study in 
solid tumors. Mucosits, diarrhea, nausea/vomiting, asthenia, rash, anemia, and 
hyperglycemia were the most common grade 2-4 toxicities [26]. When sirolimus was used 
with tacrolimus in liver transplant patients, there were reports of excess mortality, graft 
loss, and in the first 30 days following transplant, hepatic artery thrombosis was reported.
Additionally, the following symptoms were attributed to sirolimus in clinical trials:  
asthenia, fever, chills, malignancy, abnormal healing (including wound dehiscence and 
anastomotic disruption), bacterial infection, viral infection, anaphylactic/anaphylactoid 
reactions, hypertension, tachycardia, congestive heart failure, diarrhea, lymphoproliferative 
disease, lymphoma, lymphadenopathy, anemia, leukopenia, thrombocytopenia, TTP, 
thrombosis, hepatotoxicity, hepatic necrosis, hypercholesterolemia, hyperlipidemia, 
hypokalemia, edema, weight gain, Cushing’s syndrome, diabetes mellitus, arthralgia, bone 
necrosis, insomnia, tremor, headache, interstitial lung disease (pneumonitis, BOOP, 
pulmonary fibrosis), acne, rash, skin cancer, dysuria, and urinary frequency.
Please refer to section 8.1.5 and to FDA labeling for complete description of adverse events
associated with Sirolimus.
2.1.9 Pemetrexed
2.1.9.1 Background
Pemetrexed, (Alimta), for injection, was approved by the FDA in 2004 as an anti-folate 
cancer agent for second line treatment of patients with locally advanced or metastatic non 
small cell lung cancer. It acts by disrupting folate-dependent metabolic pathways causing 

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decreased nucleotides synthesis, and therefore, inhibits cell growth and induces apoptosis.
2.1.9.2 Pharmacodynamics
Pemetrexed acts by disrupting folate-dependent metabolic pathways. It uses both the 
reduced folate carrier and membrane folate binding protein transport systems to cross into 
the cell. Once inside, it undergoes a conversion to polyglutamate forms by 
folylpolyglutamate synthetase, and those glutamate forms inhibit thymidylate synthase 
dihydrofolate reductase (DHFR), and glycinamide ribonucleotide formyltransferase 
(GARFT). Both of these enzymes are essential in the de novo biosynthesis of thymidine 
and purine nucleotides. Lack of these nucleotides inhibits cell growth and induces 
apoptosis. Poly-glutamated metabolites have an increased half-life and are synthesized 
predominantly in malignant cells.
2.1.9.3 Pharmacokinetics
Pemetrexed as a single agent is 81% bound to plasma proteins. Pemetrexed is not 
metabolized significantly and is eliminated in the urine with 70-90% of the dose recovered 
unchanged within the first 24 hours following administration. The elimination half-life of 
Pemetrexed is 3.5 hours in patients with normal renal function (creatinine clearance of 90 
mL/min). The clearance decreases as renal function decreases. Pemetrexed’s total systemic 
exposure (AUC) and maximum plasma concentration (Cmax) increase proportionally with 
dose. Additionally, the pharmacokinetics do not change over multiple treatment cycles. 
Pemetrexed must be co-administrated with oral folic acid and intramuscular vitamin B12,
which does not affect its pharmacokinetics. No studies were conducted to determine the 
cytochrome P450 isoenzyme induction potential of Pemetrexed, because used as 
recommended, once every 21 days; it would not be expected to cause any significant 
enzyme induction.
2.1.9.4 Toxicology
Pemetrexed was fetotoxic and teratogenic in mice at i.p. doses of 0.2 mg/kg (0.6 mg/m2). 
Embryotoxicity was characterized by increased embryo-fetal deaths. There are no studies 
of pemetrexed in pregnant women. No carcinogenicity studies have been conducted with 
Pemetrexed.
2.1.9.5 Clinical safety data
Patients treated with Pemetrexed must take folic acid and vitamin B12. In clinical studies, 
there was less overall toxicity and reductions in Grade 3/4 hematologic and non-
hematologic toxicities such as neutropenia, febrile neutropenia, and infection when 
pretreatment with folic acid and vitamin B12 was administered. Leucovorin was permitted 
for rescue from CTC Grade 4 leukopenia lasting >3 days, CTC Grade 4 neutropenia lasting 
>3 days, and immediately for CTC Grade 4 thrombocytopenia, bleeding associated with 
Grade 3 thrombocytopenia, or Grade 3 or 4 mucositis [4].

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Pemetrexed is excreted via the kidneys and decreased renal function will result in reduced 
clearance and greater exposure (AUC). No dose modifications are required for creatinine 
clearance >45 mL/min. The incidence of CTC Grade 3/4 hypertension was the only finding 
demonstrating an age difference in patients treated with Pemetrexed and was greater in 
patients >=65 years as compared to younger patients.
3
ELIGIBILITY ASSESSMENT AND ENROLLMENT
3.1
Eligibility Criteria
3.1.1 Inclusion Criteria
3.1.1.1 Histologically documented NSCLC that is confirmed by the Laboratory of Pathology at 
the Clinical Center/NIH or the Laboratory of Pathology at NNMC (see section 2.2.13). 
3.1.1.2 Tumor biopsy will be requested from all study subjects unless the procedure poses too 
great a risk. If the subject declines, he or she may still participate in the study. We will 
ask subjects not undergoing biopsy to provide 6 unstained slides or a tissue block of 
archived tissue for immunohistochemistry (IHC) evaluation. Tumors from subjects 
enrolling in the phase II portion of the study will be analyzed retrospectively to 
demonstrate mTOR activation as assessed by immunohistochemistry in a fresh biopsy. 
mTOR activation will be defined using distribution and intensity of staining for 
phosphorylation of mTOR, or its downstream substrates S6K, and S6, as defined in 
section 2.2.13. SOPs describing the acquisition and handling of PBMCs and tissues are 
outlined in appendix 10.3 and 10.4. At a minimum, a total score (sum of intensity and 
distribution scores, see 2.2.13) of 2 for phospho-S6 or phospho-mTOR (S2448) mTOR 
will be required to determine that mTOR is active. Either measurement will be 
sufficient to ascertain that mTOR is active. Measurement of phosphorylation of Akt, 
4E-BP1, and total levels of thymidylate synthase (TS) will also be measured, but are not 
part of the eligibility requirements. In the event of limited tissue availability, the stains 
will be prioritized as follows: S6, mTOR, S6K, Akt (S473), Akt (T308), and TS. 
Phosphorylation of S6 correlates most closely with mTOR activity [49], while 
phosphorylation of mTOR at S2448 best predicts response to sirolimus [27].
3.1.1.3 Tissue from the time of original diagnosis will be adequate for enrollment on study.
Optional fresh tissue biopsy must be obtained AFTER their most recent chemotherapy 
(including small molecule or targeted therapy) or radiation therapy. Tumors that can be 
biopsied percutaneously (with or without CT/ultrasound guidance) or via bronchoscopy 
will be considered accessible if there are no other competing risk factors such as 
coagulopathy, hypoxemia, unstable cardiovascular disease, uncontrolled pain, or 
inability to give informed consent.
3.1.1.4 Individuals with relapsed NSCLC who have received at least one standard 

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chemotherapeutic regimen are eligible. Patients who received adjuvant chemotherapy 
and then relDSVHRUUHFXUPRQWKVDIWHUFRPSOHWLRQRIFKHPRWKHUDS\ZLOOEHHOLJLEOH
Patients who received adjuvant chemotherapy and relapse > 12 months after completion 
of chemotherapy should receive frontline therapy for metastatic disease before 
enrollment, as should individuals who initially present with incurable disease that is 
chemotherapy naive. Individuals unwilling to receive standard front line therapy for 
metastatic lung cancer may enroll.
3.1.1.5 Patients must have not received any chemotherapy, biological, or radiation therapy in the 
21 days prior to protocol enrollment. All previous chemo and radiation therapy induced 
toxicities must have resolved to grade 1 or less prior to enrollment.
3.1.1.6 Because sirolimus may affect the efficacy of hormonal birth control via CYP 3A4, study 
subjects of child bearing potential must be willing to use barrier birth control while 
receiving sirolimus therapy and for 12 weeks after discontinuation of sirolimus. 
3.1.1.7 Patients must have measurable disease for the phase II portion of the study. 
3.1.1.8 Age t 18 years of age 
3.1.1.9 ECOG performance score of 0-2
3.1.1.10 Expected survival of at least 3 months
3.1.1.11 Patients must have the capacity to provide informed consent and demonstrate 
willingness to comply with an oral regimen.
3.1.1.12 Patients must have normal organ and marrow function as defined below:
• Absolute neutrophil count t1,500/mL
• Platelets t100,000/mL
• Total bilirubin <1.5 X upper limit of institutional normal
• AST (SGOT) <2.5 X upper limit of institutional normal
• ALT (SGPT) <2.5 X upper limit of institutional normal
• Creatinine Estimated creatinine clearance as calculated using the MDRD equation
must be >60 ml/min/1.73m2. The formula to be used is MDRD: 186 x (Scr) -1.154 x (Age) 
-0.203 x (0.742 if female) x (1.212 if African American)
6HUXPWULJO\FHULGHV;XSSHUOLPLWRIQRUPDOVHUXPFKROHVWHUROPJGO
(includes subjects with familial and acquired hyperlipidemia).
3.1.1.12 6XEMHFWVRQVWHURLGVPXVWEHRQDVWDEOHRUWDSHULQJGRVHRIPJGD\RISUHGQLVRQH
(or equivalent dose of another glucocorticoid) for at least one week prior to study entry. 

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3.1.2 Exclusion Criteria
3.1.2.1 HIV positive patients
3.1.2.2 Pregnant or lactating women
3.1.2.3 Patients who received pemetrexed previously for Phase 1 only.  Patients with prior 
pemetrexed are eligible for Phase 2.
3.1.2.4 Patients who have had prior therapy with mTOR inhibitors such as sirolimus or its 
analogues within six months
3.1.2.5 Any concurrent therapy with chemotherapeutic agents or biologic agents or radiation 
therapy
3.1.2.6 Subjects with brain metastases may participate if the metastases are asymptomatic. 
Subjects are ineligible if brain metastases are symptomatic.
3.1.2.7 Patients who are on the following drugs that modulate CYP3A4 and cannot replace these 
medications with other equivalent medications for the period of the study: amprenavir, 
atazanavir, bromocriptine, cimetidine, clarithromycin, clotrimazole, cyclosporine, 
danazol, diltiazem, erythromycin, fluconazole, fosamprenavir, other HIV protease 
inhibitors, indinavir, itraconazole, ketoconazole, metoclopramide, nefazodone, 
nelfinavir, nicardipine, nifedipine, ritonavir, saquinavir, telithromycin, troleandomycin 
(TAO), verapamil, voriconazole, nevirapine, rifampicin, rifampin, rifabutin, rifapentin, 
phenytoin, carbamazepine, phenobarbital, and St. John’s Wort. Please see appendix 
10.5 (Table 5) for a list of relevant agents.
3.1.2.8 Subjects taking non steroidal anti-inflammatory agents who are unable to stop or replace 
the agents for the 5 days prior to and the 2 days after pemetrexed will not be eligible.
3.1.2.9 Patients who have received live vaccines in the past 21 days.
3.2
Research Eligibility Evaluation
3.2.1 History and Physical
History and physical examination including vital signs, ECOG performance status (Table 4 
Section 10), narcotic use, and medication review. If examination is done within 17 days of 
initiation of study treatment, it may be used as baseline. 

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3.2.2 Laboratory evaluation
CBC with differential, PT, APTT, electrolytes, BUN, creatinine, albumin, calcium, 
magnesium, phosphorus, LDH, SGOT, SGPT, total bilirubin, alkaline phosphatase, 
amylase, lipase, vitamin B12, folate, fasting cholesterol (HDL, LDL) and triglycerides If 
tests are done within 17 days of initiation of study treatment, they may be used as baseline.
3.2.3 Lymphocyte subsets
If done within 17 days prior to the initiation of study treatment, this may be used as 
baseline.
3.2.4 Urinanalysis 
If test is done within 17 days prior to the initiation of study treatment, it may be used as 
baseline.
3.2.5 Clinical tumor measurements
Clinical tumor measurements; i.e., skin lesions, subcutaneous nodules, palpable masses, 
within 4 weeks for purposes of screening. If measurements are done within 17 days prior to 
the initiation of study treatment, they may be used as baseline. 
3.2.6 Clinical imaging 
Clinical imaging (CT or MRI) for tumor measurements: These do not need to be repeated 
for screening if performed within the previous 28 days. If scans are done within 28 days 
prior to the initiation of study treatment, they may be used as baseline. 
3.2.7 Chest x-ray
Chest x-ray - Required only if there are no plans to obtain a chest CT. This does not need to 
be repeated for screening if performed within the previous 28 days. If done within 28 days 
prior to the initiation of study treatment, it may be used as baseline.
3.2.8 EKG
This does not need to be repeated for screening if performed within the previous 28 days. If 
done within 28 days prior to the initiation of study treatment, it may be used as baseline.
3.2.9 Pregnancy test
Pregnancy test:  Performed within 7 days prior to the initiation of study treatment in 
women of childbearing potential.
3.2.10 BMC 
BMC for storage to assess baseline mTOR pathway activation.

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3.3
Documenting activation of the mTOR pathway
Documentation of the activation of the mTOR pathway will be done retrospectively.  
Activation of mTOR pathway will be assessed using immunoblotting and/or IHC. The use 
of commercially available antibodies against components of the mTOR pathway in 
immunoblotting has been used extensively in hundreds of published studies. Because 
documentation of activation of the Akt/mTOR pathway is an inclusion criteria in the study, 
the IHC will be performed in a CLIA approved laboratory. In collaboration with Dr. 
Stephen Hewitt, Dr. Mark Raffeld is developing assays which will meet CLIA standards by 
the time the phase II study begins accruing. IHC has been performed previously in paraffin-
embedded, formalin-fixed tissues [13]. The methods that will be employed are as follows. 
Staining of slides from patients’ biopsies will be compared with staining of slides from cell 
blocks of NSCLC cells that have high levels of pathway activation (H157) and cells that 
have low levels of pathway activation (H1355). Sections will be deparaffinized with xylene 
and rehydrated through graded alcohols into buffer. A Decloaking chamber (Biocare 
Medical, Walnut Creek, CA) will be used for antigen retrieval with high pH citrate buffer 
(Dako cytomation, Carpinteria, CA) for 30 minutes. Endogenous peroxidase will be 
blocked with 3% H2O2 in PBS for 10 minutes, followed by washing twice in PBS. Tissues 
will be placed in a humidity chamber and incubated with 1.5% goat serum in PBS for 30
minutes. Slides will be incubated overnight with phospho-specific antibodies or antibodies 
that measure total levels of pathway components (Cell Signaling Technology, Beverly, 
0$DWDGLOXWLRQDWÛ&7KHDQWLERGLHVWREHHPSOR\HGDUHDVIROORZVphospho-Akt 
(Ser473) (736E11) rabbit mAb (IHC Specific), phospho-Akt (Thr308) (244F9) rabbit mAb, 
phospho-mTOR (Ser2448) (49F9) rabbit mAb (IHC Specific), phospho-p70 S6 kinase 
(Thr389) (1A5) mouse mAb, and phospho-S6 ribosomal protein (Ser235/236) (91B2) 
rabbit mAb, and phospho 4E-BP1 (Thr37/46) (236B4) rabbit mAb (IHC Preferred). These 
antibodies have been widely used in immunohistochemistry and are specific (see data 
sheets at http://www.cellsignal.com). After washing three times with PBS, each series of 
sections will be incubated for 30 minutes with biotinylated secondary antibodies (Vector 
Laboratories) diluted to 1:200 by the blocking agent described above, washed three times 
in PBS, and then incubated for 30 minutes with avidin-biotin complex method reagent 
(Vectstatin Elite ABC kit; Vector Laboratories). The reaction products will be washed 
twice with PBS, placed in 0.05 M Tris-HCl buffer (pH 7.5) for 5 minutes, and then 
developed in liquid 3,3'-diaminobenzidine (DAKO) for 3 minutes. After development, 
sections will be washed twice with distilled water, lightly counter-stained with Mayer's 
hematoxylin, dehydrated, cleared, and mounted with resinous mounting medium [13].
Scoring will be based on intensity and distribution, as previously described [49]. Briefly, 
staining will be based on the coexistence of both positive and negative cells in the same 
tissue sample. Signals will be considered positive when reaction products were localized in 
the expected cellular component. The criteria for the staining will be scored as follows: 
distribution score will be scored as 0 (0%), 1 (1–50%), and 2 (51–100%) to indicate the 
percentage of positive cells in all tumor cells present in one tissue. The intensity of the 
signal (intensity score) will be scored as 0 (no signal), 1 (weak), 2 (moderate), and 3

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(marked). This protocol can detect a wide spectrum of mTOR activity (Figure 7).
The distribution score and intensity score will then be summed into a total score (TS) of 
TS0 (sum=0), TS1 (sum=2), TS2 (sum=3), and TS3 (sum=4–5). TS0 or TS1 will be 
regarded as negative, whereas TS2 or TS3 will regarded as positive. Internal controls for 
IHC analysis will include slides made from cell blocks of lung cancer cell lines that have 
wide variation of pathway activation, which will assist assessment of staining intensity. 
Specimens with questionable signals due to insufficient tumor cells, tumor cells that are 
difficult to distinguish from other inflammatory or interstitial cells, or tissues with 
homogenously weak signals will be excluded from further evaluation. Tissue sections with 
only necrotic tumor cells or tissues with high homogenous background will also be 
excluded. In the event of limited tissue availability, the stains will be prioritized as follows: 
phospho-S6, phospho-mTOR, phospho-S6K, phospho-Akt, and TS. Modulation of S6 
phosphorylation correlates most closely with administration mTOR activation [49], and 
serine 2448 phosphorylation mTOR best predicts response to sirolimus [27]. For the phase 
II portion of the trial where activation of the mTOR is required for enrollment, we will 
UHTXLUHDSRVLWLYHVFRUH76LQHLWKHUSKRVSKR-S6 or phospho serine 2448 mTOR as a 
minimum requirement for protocol enrollment. 
Figure 7: Immunohistochemical staining of lung carcinoma tissue to demonstrate 
mTOR pathway activation. Panels A and C are low and high power views, 
respectively, of a NSCLC specimen stained for phosphorylated S2448 mTOR with a 
distribution score of 2 and an intensity score of 3. Panels B and D are low and high 
power views, respectively, of a NSCLC specimen stained for phosphorylated S2448 
mTOR with a distribution score of 2, and an intensity score of 1.

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3.4
Patient Registration
3.4.1 Patient Registration
Authorized staff must register an eligible candidate with NCI Central Registration Office 
(CRO) within 24 hours of signing consent. A registration Eligibility Checklist from the 
web site (http://camp.nci.nih.gov/ccr/welcome.htm) must be completed and faxed to 301-
480-0757. After confirmation of eligibility at Central Registration Office, CRO staff will 
call pharmacy to advise them of the acceptance of the patient on the protocol prior to the 
release of any investigational agents. Verification of Registration will be forwarded 
electronically via e-mail. Please note, it is very important for all registrars to acquire 
encrypted e-mail from NIH Help Desk, since the verification of registration includes 
patient’s information. A recorder is available during non-working hours. 
3.4.2 Off-Study Procedure
Authorized staff must notify Central Registration Office (CRO) when a patient is taken off-
study. An off-study form from the web site (http://camp.nci.nih.gov/ccr/welcome.htm)
main page must be completed and faxed to 301-480-0757.
3.4.3 Dose Level
For dose level, contact the protocol chair or the principal investigator.
4
STUDY IMPLEMENTATION
4.1
Study Design
Treatment will be administered on an outpatient basis except when admission is required 
for tumor biopsy/research samples or side effects of treatment. No other investigational 
agents or therapies other than those described below may be administered with the intent to 
treat the patient’s malignancy. Treatment is outlined as follows: 
All eligible patients will receive sirolimus orally for 7 days prior to the initiation of 
pemetrexed. The starting dose is 3 mg load followed by 1 mg each day continuously. 
Patients are to swallow the sirolimus tablets with approximately 250 ml of water each 
morning on an empty stomach. Tablets should not be taken with food, but patients may eat 
after 1 hr. On day 8, pemetrexed will be administered in an IV infusion on a 21-day cycle 
at an initial dose level of 375 mg/m2. As recommended by the FDA, folic acid 1mg orally 
every day and vitamin B12 1000 μg subcutaneously or intramuscularly every 63 days will 
be administered during the week preceding the first dose of pemetrexed. Folic acid will be 
continued for 21 days following the last dose of pemetrexed. Dexamethasone 4 mg is to be 
given by mouth twice daily the day before, the day of, and the day after pemetrexed 

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administration. Because of the effects of non steroidal anti inflammatory (NSAIDS) agents 
on renal blood flow, study subjects will be required to stop use of all NSAIDS beginning 5 
days before and for two days after receiving pemetrexed.
For the phase I portion of the study, the doses of sirolimus and pemetrexed will be based on 
cohort assignment (table 1). Cohort 1 receives sirolimus at a 3 mg load, followed by 1 mg a 
day maintenance. The loading dose of sirolimus is administered on day 1; the maintenance 
dose is administered day 2 and every day thereafter. Pemetrexed starts day 8 at 375 mg/m2.
The starting dose for both pemetrexed and sirolimus are below the usual FDA-approved 
doses. These doses were chosen because of the potential for increased toxicity with the 
combination as described by Punt et al. If two of six subjects experience a dose limiting 
toxicity in dose level 1, dose level -1 will be opened. If two of six subjects experience a 
dose limiting toxicity in dose level -1, enrollment will be suspended. If an MTD is not 
reached after the fifth dose level, that dose level will be used for the phase II study. No 
further dose escalation of either drug will be performed.
Table 1: Dose escalation scheme for SIROLIMUS and PEMETREXED
Once the phase I portion of the protocol is completed, the data will be analyzed and an 
addendum will be made to address any modifications required and applicable to the phase 
II portion of the protocol. The data from the phase I part of the protocol will be analyzed 
and reported in a peer reviewed journal as soon as possible, regardless of the progress of 
the phase II portion of the protocol.
The MTD determined in the phase I portion of the study will be used for the phase II study. 
As many as 6 phase I subjects may enroll in the phase II study provided they met all 
eligibility requirements, including biopsy documenting Akt pathway activation, for the 
phase II study at the time of enrollment in the phase I study. Subjects who experienced 
toxicity while enrolled in the phase I study may enroll in the phase II study provided they
recover to grade 2 neutropenia and grade 1 all other toxicities, within 21 days. In order to 
roll in to the phase II study, phase I subjects must have no signs or symptoms of 
progressive malignancy. Subjects who were receiving the dose level above the MTD in 
phase I will begin treatment at the MTD on day 1 of the first cycle, within the phase II 
 Dose Level
Sirolimus  (mg)
Pemetrexed (mg/m2)
-1
1.5 mg load/0.5 mg/day 
186 mg/m2
1
3 mg load/1 mg/day 
375 mg/m2
2
6 mg load/2 mg /day 
375 mg/m2
3
6 mg load/2 mg /day 
500 mg/m2
4
10 mg load/3 mg/day
500 mg/m2
5
15 mg load/5 mg/day 
500 mg/m2

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study. PKs will be repeated in the first phase II cycle for all phase I participants who were 
treated at the dose above the MTD. Subjects who were receiving the MTD on phase I will 
not have PKs repeated in the phase II study. Subjects on the phase I study who completed 
at least one cycle of therapy at the MTD but came off study because of progressive disease 
or unacceptable toxicity may be counted as a phase II subject provided they were treated 
for at least 3 weeks and met all the enrollment criteria for the phase II study.
There is a lead-in period for sirolimus alone in the phase II portion just like in the phase I 
study. Repeated cycles will be administered indefinitely provided there are no dose-
limiting toxicities or clinical deterioration. During the 7th week of treatment and every two 
cycles thereafter, patients undergo clinical and radiographic tumor restaging. 
Patients enrolled in both phases of the study will undergo a baseline imaging (CT or MRI) 
to establish baseline disease burden and sites of measurable disease. A PET CT will be 
performed prior to starting treatment on day 1 to establish baseline metabolic activity in the 
tumor. Patients will undergo a follow up PET CT scan if baseline was positive, defined as 
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study. Clinical CT or MRI will be performed for restaging process after 2 cycles or at the 
time of disease progression, whichever occurs first. They will undergo additional clinical 
imaging (CT or MRI) scans every 2 cycles as long as they remain on the protocol and until 
they meet off-study criteria.
mTOR activation will be studied in peripheral blood mononuclear cells (PBMCs) and 
tumor tissue. PBMCs will be evaluated at baseline, day 8 and after every two treatment 
cycles in all subjects of the phase I and phase II portions of the study. Patient consent will 
be obtained by the physician obtaining the biopsy, who in turn, will detail the risks of that 
procedure. Patients have the right to refuse any biopsy.
Patients will be monitored for compliance with sirolimus through pill count to be done at 
about the end of each cycle. We will use the NCI CCR Pill Count Form found on the 
NCI/CCR intranet, Policies/SOP section (http://ccrintra.nci.nih.gov/).
4.2
Drug Administration
4.2.1 Administration of Pemetrexed
Pemetrexed will be administered by intravenous infusion on day 8 of cycle 1 and day 1 of 
all subsequent cycles. The dose escalation scheme is outlined in Table 1. Each dose level 
will have a cohort of 3 to 6 subjects depending upon toxicity. There will be no intrapatient 
dose escalation. All patients will receive standard concurrent FDA required pemetrexed 
therapy consisting of vitamin B12, folate, and dexamethasone in the below mentioned 
doses to ameliorate the side effects of pemetrexed. Vitamin B12 is to be given 

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subcutaneously or intra-muscularly at 1000 μg approximately every 63 days. Folic acid 
tablets are to be administered at 1mg orally on a daily basis and will be continued for 21 
days following the last dose of pemetrexed. Both agents are to be initiated five to seven 
days before the first dose of pemetrexed. Dexamethasone 4 mg is to be given by mouth 
twice daily the day before, the day of, and the day after pemetrexed administration.
4.2.2 Administration of Sirolimus
Sirolimus tablets will be administered to all eligible study subjects once daily by mouth on 
an empty stomach with 250 cc water beginning day 1 cycle 1. Sirolimus Oral Solution will 
be administered when dose reduction requires a fractional dose. The solution is drawn from 
the bottle with the accompanying syringe. The dose is placed in a glass or plastic cup 
containing at least 2 ounces (60 cc) of water or orange juice, then stirred vigorously for one 
minute and consumed immediately. The container is then refilled with at least 4 ounces 
(120 cc) of water or orange juice, stirred vigorously again, and consumed immediately. No 
other liquids are to be used. Only glass or plastic cups should be used.  Sirolimus will be 
taken every day of the 28 (cycle 1 only) or 21 day cycle (because of the 7 day lead in for 
the first cycle, cycle 1 is 28 days in duration). Subjects may eat one hour after taking the 
sirolimus. The sirolimus should be taken at the same time each day, preferably in the 
morning around 0900 to 1000 EST to facilitate pharmacokinetics and periodic sirolimus 
trough levels performed at clinic visits. Sirolimus trough levels will be checked weekly in 
cycle 1, on day 1 of each subsequent cycle, at the time of any grade 3 toxicity, and as 
needed for follow up of that toxicity. 
4.3
Treatment Modifications for Phase I
4.3.1 MTD
4.3.1.1 The MTD will be based on the tolerability observed during the first 4 weeks of treatment 
only. Escalations of sirolimus and pemetrexed are planned in groups of three patients, 
with an additional three patients to be added at the first indication of Dose Limiting 
Toxicity (DLT). The MTD of sirolimus will be the highest dose at which less than two 
out of six patients experience DLT, as defined in section 3.3.2. If dose level 5 is reached 
and the MTD has not been established, there will be no further dose escalation.
4.3.1.2 Up to three patients may be enrolled simultaneously at each dose level specified in Table 
1. These patients should be observed for DLT for at least 4 weeks from the first day of 
treatment before new patients are enrolled at the next higher dose level. If patients are 
not fully evaluable for toxicity in cycle 1, patients will be replaced.
4.3.2 The following dose escalation rules will be used:

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4.3.2.1 Three patients are studied at the first dose level.
4.3.2.2 If none of these three patients experience DLT, then the dose is escalated to the next 
higher level in the three subsequent patients.
4.3.2.3 If one of the three patients experiences a DLT at a given dose level, then three more 
patients are accrued at the same dose. If none of these three additional patients 
experience a DLT, then the dose is escalated to the next level in subsequent patients. If 
one or more of these three additional patients experiences DLT, the MTD has been 
exceeded and three more patients are treated at the next lower dose (if only three 
patients were previously treated at that prior dose).
4.3.2.4 The MTD is the dose level at which 0/6 or 1/6 patients experience DLT with the next 
higher dose level having at least 2/6 patients experiencing DLT.
4.3.3 Dose Limiting Toxicity (DLT)
Toxicities will be graded according to the NCI Common Terminology Criteria for Adverse 
Events (CTCAE Version 3.0) scale. If multiple toxicities are seen, the presence of DLT 
should be based on the most severe toxicity experienced. DLT will be defined as any of the 
following events occurring during the first 4 week course of treatment as is deemed to be 
from a possible, probable, or definite effect of the study drugs. Attributions will be made 
for both drugs.
4.3.3.1 Any grade 4 hematologic toxicity (except grade 4 lymphopenia, orgrade 4 neutropenia 
with duration of days) or febrile neutropenia (ANC <1000 cells/mm3 and 
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4.3.3.2 Grade 3 hypercholesterolemia (defined as >400 mg/dL or 10.34 mmol/L) or 
hypertriglyceridemia (defined as > 5X ULN) in spite of treatment with HMG-CoA 
reductase inhibitors. 
4.3.3.3 Grade 3 diarrhea (defined as >7 stools per day over baseline; incontinence; 
hospitalization, need for IV fluids for 24 hours, severe increase in ostomy output, or 
interfering with ADL) that has not resolved to grade 2 diarrhea within 24 hours and 
grade 1 within 48 hours of starting fibercon or metamucil and diphenoxylate or 
loperamide. 
4.3.3.4 Grade 3 pneumonitis (defined as symptomatic, interfering with ADL, oxygen required). 
4.3.3.5 Grade 3 or 4 mucositis

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4.3.3.6 Any other non-hematologic grade 3 and grade 4 toxicity. Grade 3 or 4 nausea and 
vomiting will be defined as grade 3 or grade 4 nausea and vomiting that has not 
resolved to grade 2 within 24 hours and grade 1 within 48 hours of starting of starting 
ondansetron, granisetron, emend, dexamethasone, and or ativan.
4.3.4 Dose Adjustments
4.3.4.1 If a subject experiences a DLT as defined in Section 4.3.2, the treatment will be 
immediately stopped for a minimum of 1 week. Both drugs will be held until the patient 
recovers to a grade 2 neutropenia and grade 1 all other toxicities. If the patient recovers 
within 21 days, treatment may be resumed using the dosing guidelines in Table 2. When 
the patient resumes therapy, the sirolimus dose will be immediately adjusted per Table 2 
guidelines. Those patients requiring fractional doses upon resumption of therapy will be 
placed on the commercially available oral solution of sirolimus. In patients with resting 
tremor or who are otherwise unable to self-administer the oral solution, the patient 
should take the next lowest pill form of sirolimus even if it is a greater dose reduction 
than that specified in table 2.  Pemetrexed will be adjusted at the beginning of the next 
cycle. 
4.3.4.2 If the subject fails to recover to a grade 2 neutropenia and grade 1 all other toxicity within 
21 days, she/he will be removed from the study. 
4.3.4.3 Subject will be allowed a maximum of two dose reductions before being taken off study. 
If subject experiences a life threatening toxicity at any time, she/he will be removed 
from the study.
4.3.4.4 For patients who had their dose reduced in any prior cycle for the drug related toxicity, 
their dose will not be re-escalated, even if there is minimal or no toxicity with the 
reduced dose. Patients whose dose has been reduced in prior cycles for adverse events 
that are subsequently not felt to be related to the drug combination may have the dose 
re-escalated after completion of one cycle with toxicities less than or equal to grade 1.
4.3.4.5 Patients will have sirolimus trough levels drawn on day 8±1 day, 15±1 day, 22±1 day of 
cycle 1 then day 1 of subsequent cycles. In addition sirolimus levels will be obtained 
any time the patient experiences a grade 3 or higher toxicity. Dose modification will be 
based upon the toxicity and not the sirolimus level.

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4.4
Treatment Modifications for Phase II
Based on safety and efficacy analysis from the Phase I study, the dose of sirolimus and 
pemetrexed used in the phase II portion of the study will be that of dose level 4 from the 
Phase I portion of the study (pemetrexed 500mg/m2 IV every 21 days and sirolimus 10mg 
load on day 1 and 3 mg daily thereafter). If trough sirolimus levels exceed 15 ng/mL at any 
point, sirolimus will be held for 48 hours and will resume at 2 mg/po/qd.  
To account for safety in the Phase II portion, if 2 of the first 6 subjects encounter a DLT as 
defined in the Phase I portion, we will amend the protocol to use dose level 3 (500 mg/m2
IV every 21 days and sirolimus 6 mg load on day 1 and 2 mg daily thereafter) for new 
subject enrollments. Phase II study subjects who experience a DLT while on dose level 4 
will be reduced to dose level 3. If a phase II study subject on dose level 3 experiences a 
DLT as defined in section 3.3.2 we will follow the same procedures outlined in section 
3.3.3.1 using Table 2 for guidance. If the subject does not recover in 21 days, he/she will be 
taken off study. Any subject requiring more than two dose reductions will be taken off 
study.
4.5
Pharmacokinetic Studies
Pharmacokinetic sampling will be performed during cycle 1, on days 7 and 8 to allow for 
comparison of steady state sirolimus pharmacokinetics in the absence and presence of 
pemetrexed.  
On cycle 1 day 7, a single venous blood samples (5ml) will be obtained in an 
Table 2: Dose Modifications for Pemetrexed and Sirolimus
Toxicity
Pemetrexed Dose (mg/m2)
Sirolimus (mg)
Nadir ANC <500/mm3 and
nadir platelets ³50,000/mm 3
75% of previous dose
75% of previous dose
Nadir platelets <50,000/ mm3
regardless of nadir ANC
50% of previous dose
50% of previous dose
Grade 3 or 4 non-hematologic 
toxicities except mucositis and 
pneumonitis
75% of previous dose
75% of previous dose
Any diarrhea requiring 
hospitalization         
(irrespective of grade)
75% of previous dose
75% of previous dose
Grade 3 pneumonitis
No dose reduction 
50% of previous dose
Grade 3 or 4 mucositis
50% of previous dose
50% of previous dose
Grade 3 nausea, vomiting
75% of previous dose
75% of previous dose

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ethylenediamine-tetra-acetic (EDTA) tube, at each of the following time points: 
immediately pre dose and at 20 min, 40 min, 1 hour, 2 hours, 3 hours, 4 hours, 6 hours, 12 
after the administration of sirolimus and will be analyzed for sirolimus levels. On cycle 1 
day 8, the blood will be drawn in two EDTA tubes pre dose, then 20 min, 40 min, 1 hour, 2 
hours, 3 hours, 4 hours, 6 hours, 12 hours, and 24 hours after administration of sirolimus, 
but will be analyzed for both sirolimus and pemetrexed levels. Sirolimus ingestion and 
pemetrexed infusion will be administered at the same time. The time each drug was 
administered will be noted. Patients will be admitted to the in-patient oncology unit, if 
necessary, in order to obtain the 12 and 24 hour post drug administration. The samples will 
be drawn using the following guidelines:
PK samples should not be drawn through the drug administration line/port. Residual drug 
in the line or port distorts PK data obtained from specimens drawn at the same site as drug 
administration. PK data is collected on drug concentrations in plasma after it has traveled 
through the body. This is not possible if specimens are drawn at the same site as 
administration.
The patient name and exact draw time will be provided on all specimens. The exact draw 
time – not just the ideal time – for PK samples will be recorded even if they are drawn late. 
Also, for PK samples, cycle information will be provided on the specimen container (e.g. 
C1D1 - 5 hr post infusion – 12:30pm May 15, 2006). 
Immediately after collection, sample will be placed on ice and stored in the refrigerator. 
(Especially important with PK samples, as it prevents drug degradation.) Dr. Figg’s lab, 
Gareth Peters/Kathy Compton at 102-11964 will be paged for sample pickup.
The Clinical Pharmacology Program (Dr. William D. Figg, 5A-01, 301-402-3622) will 
coordinate rapid acquisition and processing of blood samples. HPLC-MS analytical method 
will be used to quantify sirolimus and pemetrexed whole blood concentrations. The 
pharmacokinetic characteristics of sirolimus and its interactions with pemetrexed will be 
evaluated using the WinNonLin pharmacokinetic software (Pharisight, Mountain View, 
CA). The maximum plasma concentration, time to maximum concentration, area under the 
curve extrapolated to infinity, and apparent terminal half-life will be calculated by non-
compartmental analysis. Pharmacodynamic analysis will attempt to correlate any 
correlation in sirolimus concentration with disease response and/or toxicities. 
All samples will be barcoded, with data entered and stored in the Patient Sample Data 
Management System (PSDMS) utilized by the Clinical Pharmacology Program (CPP). This 
is a secure program, with access to the PSDMS limited to defined CPP personnel, who are 
issued individual user accounts. The program creates a unique barcode ID for every sample 
and sample box, which cannot be traced back to patients without PSDM System access. 
The data recorded for each sample includes the patient ID, name, trial name/protocol 
number, time drawn, cycle time point, dose, material type, as well as box and freezer 

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location. Patient demographics associated with the clinical center patient number are 
provided in the system. For each sample, there are notes associated with the processing 
method (delay in sample processing, storage conditions on the ward, etc.). In addition to 
the barcode, the sample label contains an abbreviation for the clinical study, along with an 
abbreviation for the sample type, followed by the sample and aliquot number, i.e. ETT-PL-
0001-001. As such, these labels are coded and the sample number does not specifically 
denote the patient or patient ID.
Barcoded samples are stored in barcoded boxes in a locked freezer at either -20 or -80qC
according to stability requirements. These freezers are located onsite in the CPP and offsite 
at NCI Frederick Central Repository Services (Fisher Bioservices) in Frederick, MD. 
Samples will be stored until requested by a researcher on the protocol. All requests are 
monitored and tracked in the PSDM System. All researchers are required to sign a form 
stating that the samples are only to be used for research purposes associated with this trial 
(as per the IRB approved protocol) and that any unused samples must be returned to the 
CPP.
Following completion of this study, samples will remain in storage as detailed above. 
Access to these samples will only be granted following IRB approval of an additional 
protocol, granting the rights to use the material. 
If, at any time, a patient withdraws from the study and does not wish for their existing 
samples to be utilized, the individual must provide a written request. Following receipt of 
this request, the samples will be destroyed  (or returned to the patient, if so requested), and 
reported as such to the IRB. Any samples lost (in transit or by a researcher) or destroyed 
due to unknown sample integrity (i.e. broken freezer allows for extensive sample thawing, 
etc.) will be reported as such to the IRB.
Sample barcodes are linked to patient demographics and limited clinical information. This 
information will only be provided to investigators listed on this protocol, via registered use 
of the PSDMS. It is critical that the sample remains linked to patient information such as 
race, age, dates of diagnosis and death, and histological information about the tumor, in 
order to correlate genotype with these variables.
4.6
Periodic evaluations during treatment 
(See Table 3, section 10)
4.6.1 Cycle 1 Day 1
4.6.1.1 History and Physical examination (including vital signs, ECOG performance status 
(Table 4 Section 10), narcotic use, medication review).  If performed within 17 days, 

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the baseline History and Physical is acceptable.  
4.6.1.2 Adverse events. If performed within 17 days, the baseline Adverse Events is acceptable.  
4.6.1.3 Laboratory evaluation: CBC with differential, PT, APTT, electrolytes, BUN, creatinine, 
albumin, calcium, magnesium, phosphorus, LDH, SGOT, SGPT, total bilirubin, 
alkaline phosphatase, amylase, lipase, fasting cholesterol (HDL, LDL) and triglycerides, 
vitamin B12 and folate.  If performed within 17 days, the baseline laboratory results are 
acceptable.  
4.6.1.4 Lymphocyte subsets. If performed within 17 days, the baseline lymphocyte subsets are 
acceptable.   
4.6.1.5 EKG: within 28 days prior to initiation of treatment
4.6.1.6 CXR: within 28 days prior to initiation of treatment, only required if there are no plans to 
perform chest CT. 
4.6.1.7 Clinical tumor measurements, i.e. skin lesions, subcutaneous nodules, palpable masses 
within 17 days of treatment
4.6.1.8 Clinical imaging (CT or MRI) for tumor measurement: within 28 days prior to initiation 
of treatment
4.6.1.9 Pregnancy test for women of childbearing potential within 72 hours of starting study 
drug. 
4.6.1.10 PET CT: within 28 days prior to initiation of treatment. Inability to accomplish study 
will not disqualify subject
4.6.1.11 PBMC for mTOR pathway activation within 17 days prior to starting study drug. 
4.6.2 Day 1 all subsequent cycles
These studies may be performed up to 72 hours prior to day 1 of subsequent cycles unless 
otherwise specified.
4.6.2.1 History and Physical examination (including vital signs, ECOG performance status 
(Table 4 Section 10), narcotic use, medication review and adverse events).
4.6.2.2 Adverse events

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4.6.2.3 Clinical tumor measurements, i.e. skin lesions, subcutaneous nodules, palpable masses
4.6.2.4 Laboratory evaluation: CBC with differential, PT, APTT, electrolytes, BUN, creatinine, 
albumin, calcium, magnesium, phosphorus, LDH, SGOT, SGPT, total bilirubin, 
alkaline phosphatase, amylase, lipase, PT, APTT, fasting cholesterol (HDL, LDL) and 
triglycerides.
4.6.2.5 Lymphocyte subsets
4.6.2.6 Imaging (CT or MRI); within 72 hours of day 1 cycle 3 and every 2 cycles thereafter
4.6.2.7 PET CT: within 72 hours of day 1 cycle 3 only, provided baseline scan was positive 
(maximum 2 PET CT scans).
4.6.2.8 Tissue for follow up on mTOR pathway activation – optional for phase I subjects, 
required for phase II - within 7 days of day 1 cycle 3 only. If subject progresses before 
cycle 3, then tissue will be obtained at time of progression.
4.6.2.9 PBMC for mTOR pathway activation – all subjects phase I and phase II within 7 days of 
day 1 cycle 3 and every 2 cycles thereafter. If subject progresses before cycle 3, then 
PBMC will be studied at the time of progression.
4.6.2.10 Pregnancy test for women of childbearing potential within 72 hours 
4.6.2.11 Trough sirolimus levels within 72 hours
4.6.3 Day 8 evaluations will be performed in cycle 1 for every patient.
The following will be included:
4.6.3.1 History and physical examination (including vital signs, ECOG performance status 
(Table 4 Section 10), narcotic use, and medication review)
4.6.3.2 Adverse events
4.6.3.3 Laboratory evaluation: CBC with differential, PT, APTT, electrolytes, BUN, creatinine, 
albumin, calcium, magnesium, phosphorus, LDH, SGOT, SGPT, total bilirubin, 
alkaline phosphatase, amylase, lipase, fasting cholesterol (HDL, LDL) and triglycerides
4.6.3.4 Pharmacokinetics for sirolimus and pemetrexed

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4.6.3.5 PBMC for mTOR pathway activation, day 8 cycle 1 only
4.6.3.6 Trough sirolimus level
4.6.4 Day 15 evaluation will be performed in cycle 1 for every patient. 
4.6.4.1 Adverse events
4.6.4.2 CBC with differential 
4.6.4.3 Trough sirolimus level
4.6.5 Day 22 evaluation will be performed in cycle 1 only (cycle 1 is 28 days all other cycles are 
21 days) for every patient
4.6.5.1 Adverse events
4.6.5.2 CBC with differential
4.6.5.3 Trough sirolimus level
4.6.6 Unexpected evaluations 
If a dose adjustment is made in any cycle following cycle 1, evaluations will be performed 
on day 8 and or day 15 depending upon when in the cycle the dose adjustment is made. 
Subjects will always have at least 2 weekly follow up evaluations following dose
modification. If medically indicated, more frequent evaluations will take place. If, 
following dose modification, the cycle is completed without further adverse events, weekly 
visits may be omitted in subsequent cycles. The weekly visits will include the following if 
indicated:
4.6.6.1 History and physical examination (including vital signs, ECOG performance status 
(Table 4 Section 10), narcotic use, and medication review)
4.6.6.2 Adverse events
4.6.6.3 CBC with differential
4.6.6.4 Laboratory evaluation: PT, APTT, electrolytes, BUN, creatinine, albumin, calcium, 
magnesium, phosphorus, LDH, SGOT, SGPT, total bilirubin, alkaline phosphatase, 
amylase, lipase, fasting cholesterol (HDL, LDL) and triglycerides

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4.6.6.5 Trough sirolimus level
4.7
Off Study Evaluations
4.7.1 History and Physical
The history and physical examination (including vital signs, ECOG performance status, 
adverse events, narcotic use, and medication review) will be performed at the off study 
visit. 
4.7.2 Follow-up PET CT and tissue for mTOR pathway determination
If the subject comes off study after cycle 1 but prior to cycle 3, then off study evaluation 
will include follow up PET CT (if baseline was positive) and tissue for mTOR pathway 
determination (optional for phase I subjects).
4.7.3 CBC with differential 
4.7.4 Laboratory evaluation
Laboratory evaluation: PT, APTT, electrolytes, BUN, creatinine, albumin, calcium, 
magnesium, phosphorus, LDH, SGOT, SGPT, total bilirubin, alkaline phosphatase, 
amylase, lipase, fasting cholesterol (HDL, LDL) and triglycerides
4.8
Concurrent Therapies
As recommended by the FDA for the amelioration of toxicity associated with the 
administration of pemetrexed, all patient will receive folic acid, vitamin B12, and 
dexamethasone. Vitamin B12 is to be given subcutaneously or intra-muscular at 1000 μg 
approximately every 63 days. Folic acid tablets are to be administered at 1mg orally on a 
daily basis. Both agents are to begin five to seven days before the initial dose of 
pemetrexed. Dexamethasone 4 mg is to be given by mouth twice daily the day before, the 
day of, and the day after pemetrexed administration. Because of the effects of non steroidal 
anti inflammatory (NSAIDS) agents on renal blood flow, study subjects will be required to 
stop use of all NSAIDS beginning 5 days before and for two days after receiving 
pemetrexed.
4.9
Correlative Studies
4.9.1 Measurement of mTOR pathway activation in PBMCs and tumor tissue
A total of 16 ml of blood will be collected from each patient in blue/black speckled (CPT)
tubes at baseline (within 17 days) and day 8 of cycle 1 and every 2 cycles (within 72 hours) 
thereafter to study inhibition of the pathway by sirolimus in peripheral blood mononuclear 

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cells (PBMC) and to correlate pathway inhibition with sirolimus levels. Activation of 
mTOR, S6K1, 4E-BP1, S6, and Akt will be assessed by immunoblotting of PBMC lysates 
from each patient. Paired specimens will be run simultaneously and band intensity will be 
quantified using densitometry. This technique has been successfully employed in other 
protocols using sirolimus analogues [50]. Additionally, fixed tumor biopsies will be 
assessed for activation of p-S6K, p-S6, p-4E-BP1, pS473-Akt, and TS levels using
immunohistochemical techniques [13]. Internal controls for IHC analysis will include 
slides made from cell blocks of lung cancer cell lines that have wide variation of pathway 
activation, which will assist assessment of staining intensity. Scoring of tumor biopsies will 
incorporate distribution and intensity of staining, and will be scored as being positive or 
negative as previously described [49].
4.9.2 Tissue Biopsy
Any residual samples will be stored permanently in the laboratory of Dr. Giuseppe 
Giaccone. The IRB will be updated in the continuing review regarding the status of the 
specimen and any use beyond this protocol. We will report destroyed samples to the IRB if 
samples become unsalvageable because of environmental factors (ex. broken freezer or 
lack of dry ice in a shipping container) or if a patient withdraws consent. Samples will also 
be reported as lost if they are lost in transit between facilities or misplaced by a researcher. 
4.9.3 Stored Tissue
Blood and tissue specimens collected in the course of this research project may be banked 
and used in the future to investigate new scientific questions related to this study. However, 
this research may only be done if the risks of the new questions were covered in the 
consent document. If new risks are associated with the research (e.g. analysis of germ line 
genetic mutations), the principal investigator or the protocol chairperson must amend the 
protocol and obtain informed consent from all research subjects.
4.10 Surgical Guidelines
If the primary tissue is not appropriate because of intervening therapy, if the tissue 
provided does not confirm the NSCLC diagnosis, or is deemed inadequate to test for 
mTOR pathway activation, biopsies will be obtained by the NNMC or NIH Clinical Center 
staff via the least invasive and least risky method. A separate informed consent will be 
obtained by the physician performing the procedure. 
4.11 Radiation Therapy Guidelines
There is no radiation therapy component in this study.

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4.12 Off Study Criteria
4.12.1 Progression of disease (as defined in 6.2)
4.12.1.1 Subjects must be followed with the same types of clinical imaging (CT or MRI) that 
were used for baseline tumor measurements. 
4.12.1.2 Subjects will be removed from study 4 weeks after disease progression is documented.
4.12.2 The patient may withdraw from the study at any time for any reason if he/she wishes.
4.12.3 Subjects may be removed for medical or psychiatric illness, which in the investigator's 
judgment renders the patient incapable of further therapy.
4.12.4 Subjects may be removed for non-compliance with the oral regimen as judged by missing 
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and coordinated with the principal investigator and/or study chairperson.
4.12.5 All reasons for discontinuation of treatment must be documented in the medical record 
and Central Registration Office must be notified.
4.13 Post Study Evaluation (Follow-up)
Patients will be followed for 4 weeks after the patients are taken off therapy or until death, 
whichever occurs first.  No studies are required.  The follow-up can be performed by the 
patient’s primary oncologist.  Patients removed from study for unacceptable adverse events 
will be followed until resolution or stabilization of the adverse event. 
5
SUPPORTIVE CARE
5.1
Medical Care
All cancer related care will be provided during and following protocol administration for 
cancer related complication including any treatments for drug-related complications such 
as tumor lysis syndrome, development of organ dysfunction (e.g., renal dysfunction), 
infections/ fever and neutropenia, blood product support and cytokine support. Care will be 
taken to avoid agents that are strong CYP3a4 inhibitors.
5.2
Management of hypersensitivity reactions
Hypersensitivity reactions will be managed with slowing or stopping the infusion and/or 
diphenhydramine with or without dexamethasone. Patients experiencing life-threatening 
hypersensitivity reaction to pemetrexed in the setting of steroid pre-medication will not be 
rechallenged with pemetrexed.

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5.3
Febrile neutropenia
Febrile neutropenia is potentially life threatening and requires hospitalization and urgent 
broad-spectrum antibiotics.
5.4
Symptomatic Anemia
Symptomatic anemia should be treated with appropriate red blood cell or erythropoietin 
support.
5.5
Thrombocytopenia
Thrombocytopenia should be treated conservatively. In the absence of bleeding or a 
planned invasive procedure, platelet transfusions should be given for a platelet count below 
10,000/mm3. If invasive procedures are planned or the patient develops bleeding, platelet 
transfusions should be administered in accordance with standard of practice, usually 
maintaining a platelet count of >50,000/mm3.
5.6
Central Venous Access
Placement of central venous access will be at the discretion of protocol chair and/or the 
primary investigator. Possible lines include mediport implantable devices, HICKMAN or 
GROSHONG catheters.
5.7
Nutritional Support and Psychosocial support
During cancer treatments it is sometimes difficult for patients to maintain good nutrition. If 
it is deemed necessary, or it could benefit the patient, the patient will be referred for a 
nutritional consult. Patients who are having emotional difficulty coping with their disease 
and/or their treatment will be referred to a social worker for evaluation and support.
5.8
Anti-emetics
Anti-emetics will be prescribed by the treating physician as necessary and as used 
traditionally in cancer patients. 
5.9
Hypercholesterolemia and hypertriglyceridemia
Patients will be given HMG-CoA reductase inhibitors as anti-hyperlipidemic medications 
according to National Cholesterol Education Program (Adult Treatment panel III) (NCEP 
ATIII) guidelines, if their cholesterol and triglycerides levels require  
(http://www.nhlbi.nih.gov/guidelines/cholesterol/atglance.pdf). 
Pravastatin and rosuvastatin are the preferred agents since they are not metabolized by 
CYP3A4.
5.10 Monitoring for lymphoma
To address the increased incidence of lymphoma in patients on sirolimus when it was used 
in combination with cyclosporine and corticosteroids, all patients on this study will be 

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monitored with physical exam every scheduled visit for any new lymph node enlargement 
and with complete blood count every cycle for any abnormality in cell differential. 
Lymphadenopathy that develops after enrollment that persists for 4 wk will be biopsied.
6
DATA COLLECTION AND EVALUATION
6.1
Data Collection
The NCI investigators will be responsible for the collection, maintenance, security and 
quality control of all study data. Meetings chaired by the principal investigator and/or 
protocol chairperson will be held on a biweekly basis to review the study data for quality, 
completeness, and interim analysis (see section 5.9). Data will be captured on the NCI C3D 
database. Research records will be maintained to include but not limited to the following:
• Signed, dated consent form.
• Completed eligibility checklist
• Source documents verifying eligibility criteria such as path reports and pathway 
activation
• Interim monitoring test results
• PK collection forms
• Response evaluations
• Off study summary
6.2
Response Criteria
6.2.1 Criteria Determination
For the purposes of this study, patients should be reevaluated for response after about 6 
weeks (or 2 cycles, except for the first two cycles which are 7 weeks). In addition to a 
baseline scan, confirmatory scans should also be obtained 6 weeks following initial 
documentation of objective response, (which refers to complete response, or partial 
response as defined in section 5.2). Response and progression will be evaluated in this 
study using the new international criteria proposed by the Response Evaluation Criteria in 
Solid Tumors (RECIST) Committee [51]. Changes in only the largest diameter (uni-
dimensional measurement) of the tumor lesions are used in the RECIST criteria. Note:  
Lesions are either measurable or non-measurable using the criteria provided below. The 
term “evaluable,” in reference to measurability, will not be used because it does not 
provide additional meaning or accuracy.
6.2.2 Definitions of Disease State
6.2.2.1 Measurable disease
Measurable lesions are defined as those that can be accurately measured in at least one 
dimension (longest diameter to be recorded) as >20 mm with conventional techniques (CT, 
MRI, x-ray) or as >10 mm with spiral CT scan. All tumor measurements must be recorded 
in millimeters (or decimal fractions of centimeters). 

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6.2.2.2 Evaluation of Measurable Disease
All measurements should be taken and recorded in metric notation using a ruler or calipers. 
All baseline evaluations should be performed as closely as possible to the beginning of 
treatment and never more than four weeks before the beginning of the treatment.
Note: Tumor lesions that are situated in a previously irradiated area might or might not be 
considered measurable. Tumor lesions that have been biopsied previously might or might 
not be considered measurable. 
6.2.2.3 Non-measurable disease
All other lesions (or sites of disease), including small lesions (longest diameter <20 mm 
with conventional techniques or <10 mm using spiral CT scan), are considered non-
measurable disease. Bone lesions, leptomeningeal disease, ascites, pleural/pericardial 
effusions, lymphangitis cutis/pulmonis, abdominal masses (not followed by CT or MRI), 
and cystic lesions are all non-measurable.
6.2.2.4 Target lesions
All measurable lesions up to a maximum of five lesions per organ and 10 lesions in total, 
representative of all involved organs, should be identified as target lesions and recorded 
and measured at baseline. Target lesions should be selected on the basis of their size 
(lesions with the longest diameter) and their suitability for accurate repeated measurements 
(either by imaging techniques or clinically). A sum of the longest diameter (LD) for all 
target lesions will be calculated and reported as the baseline sum LD. The baseline sum LD 
will be used as reference by which to characterize the objective tumor response.
6.2.2.5 Non-target lesions
All other lesions (or sites of disease) should be identified as non-target lesions and should 
also be recorded at baseline. Non-target lesions include measurable lesions that exceed the 
maximum numbers per organ or total of all involved organs as well as non-measurable 
lesions. Measurements of these lesions are not required, but the presence or absence of 
each should be noted throughout follow-up.
6.2.2.6 Clinical lesions 
Clinical lesions will only be considered measurable when they are superficial (e.g., skin 
nodules and palpable lymph nodes). In the case of skin lesions, documentation by color 
photography, including a ruler to estimate the size of the lesion, is recommended.
6.2.2.7 Evaluation of Target Lesions
Complete Response (CR): Disappearance of all target lesions
Partial Response (PR):At least a 30% decrease in the sum of the longest diameter (LD) of 

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target lesions, taking as reference the baseline sum LD
Progressive Disease (PD): At least a 20% increase in the sum of the LD of target lesions, 
taking as reference the smallest sum LD recorded since the treatment started or the 
appearance of one or more new lesions
Stable Disease (SD): Neither sufficient shrinkage to qualify for PR nor sufficient increase 
to qualify for PD, taking as reference the smallest sum LD since the treatment started
6.2.2.8 Evaluation of non-target lesions
Complete Response (CR): Disappearance of all non-target lesions and normalization of 
tumor marker level
Incomplete Response/Stable Disease (SD): Persistence of one or more non-target lesion(s) 
and/or maintenance of tumor marker level above the normal limits
Progressive Disease (PD): Appearance of one or more new lesions and/or unequivocal 
progression of existing non-target lesions
Although a clear progression of “non-target” lesions only is exceptional, in such 
circumstances the opinion of the treating physician should prevail and the progression 
status should be confirmed at a later time by the principal investigator or the study 
chairperson.
6.2.2.9 Evaluation of best overall response:
The best overall response is the best response recorded from the start of the treatment until 
disease progression/recurrence (taking as reference for progressive disease the smallest 
measurements recorded since the treatment started). The patient's best response assignment 
will depend on the achievement of both measurement and confirmation criteria.
Target 
Lesions
Non-Target 
Lesions
New 
Lesions
Overall 
Response
CR
CR
No
CR
CR
Incomplete 
response/S
D
No
PR

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PR
Non-PD
No
PR
SD
Non-PD
No
SD
PD
Any
Yes or No
PD
Any
PD
Yes or No
PD
Any
Any
Yes
PD
Note: Patients with a global deterioration of health status requiring discontinuation of 
treatment without objective evidence of disease progression at that time should be 
classified as having “symptomatic deterioration.”  Every effort should be made to 
document the objective progression, even after discontinuation of treatment.
In some circumstances it may be difficult to distinguish residual disease from normal 
tissue. When the evaluation of complete response depends on this determination, it is 
recommended that the residual lesion be investigated (fine needle aspirate/biopsy) before 
confirming the complete response status.
6.3
Confirmatory Measurement/Duration of Response
6.3.1 Confirmation
To be assigned a status of PR or CR, changes in tumor measurements must be confirmed 
by repeat assessments that should be performed four weeks after the criteria for response 
are first met. In the case of SD, follow-up measurements must have met the SD criteria at 
least once after study entry and at a minimum interval of eight weeks (see section 6.2.2).
6.3.2 Duration of overall response
The duration of overall response is measured from the time measurement criteria are met 
for CR or PR (whichever is first recorded) until the first date that recurrent or progressive 
disease is objectively documented (taking as reference for progressive disease the smallest 
measurements recorded since the treatment started).
6.3.3 Duration of overall CR
The duration of overall CR is measured from the time measurement criteria are first met for 
CR until the first date that recurrent disease is objectively documented.
6.3.4 Duration of Stable Disease
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are met, taking as reference the smallest measurements recorded since the treatment started. 
6.4
Progression-Free Survival
Progression free survival will be determined from the date treatment began until 
radiographic evidence of progressive disease is noted.
6.5
Response Review
Patients with measurable disease will be assessed by standard criteria. The purpose of 
tumor measurements will be to assess benefit to the patients from treatment and to 
determine appropriateness for continuing on study. For the purposes of this study, patients 
should be re-evaluated every cycle and undergo imaging studies every two cycles. 
Following documentation of an objective response, confirmatory scans will also be 
obtained four weeks after. The response will be evaluated by Dr Peter Choyke from the 
NCI at the Clinical Center.
6.6
Toxicity Criteria
This study will utilize the CTCAEv3 (http://ctep.cancer.gov/forms/CTCAEv3.pdf) for 
toxicity and adverse event reporting. 
6.7
Statistical Section
6.7.1 Statistical considerations for Phase I portion of the trial
6.7.1.1 Baseline characteristics will be summarized across all enrolled patients. An accounting 
will be done of all patients registered in the study. The number of patients who died or 
withdrew before treatment began will be specified. Patients who did not meet all 
eligibility criteria will be described. Patients who were evaluated separately due to first-
cycle non-drug-related death or cessation of first-cycle therapy prior to DLT will be 
characterized. Patients not fully evaluable for toxicity in cycle 1 will be replaced.
6.7.1.2 Treatment administration will be described for all cycles. Doses administered, dose 
modifications or delays, and duration of therapy will be evaluated.
6.7.1.3 Safety variables will be summarized at each dose level using descriptive statistics. 
Adverse events that occur will be reported for each dose level and described in terms of 
incidence and severity. Laboratory data will be presented by dose level at each 
observation time. Values outside of normal limits will be identified and their frequency 
calculated. Parameters will be described based on the CTCAE version 3.0 severity 
grading. Distribution by CTC severity grade (when applicable) and clinical relevance 
will be given.

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6.7.1.4 A descriptive analysis of evidence of anti-tumor activity at each dose level, focusing on
the MTD, will be provided based on clinical, radiographic, and biologic assessments of 
efficacy.
6.7.1.5 Bioanalytical and Pharmacokinetic Analysis: The whole blood concentration of sirolimus 
and pemetrexed will be quantified by LCMS/MS method.
6.7.1.6 Whole blood concentration of sirolimus will be evaluated and analysis will determine 
concentration ranges that may be used for allowable dose adjustments in phase II study.
6.7.1.7 The anticipated rate of accrual for the phase I portion of the trial will be approximately 1 
subject/month. Depending on the dose level identified as the MTD, up to 30 subjects 
maybe required for this portion of the trial (5 levels with a maximum of 6 patients per 
level). If dose level 5 is reached and the MTD has not been established, dose level 5
will be used as the dose for subjects enrolling on the phase II portion of the study. 
6.7.2 Statistical considerations for phase II portion of the trial
6.7.2.1 The primary objective of this study is to determine if the combination of sirolimus and 
pemetrexed, at the MTD for the combination, on a standard schedule, is able to result in 
an enhanced clinical response rate compared to that of pemetrexed alone. 
6.7.2.2 Based on a prior published study, the response rate (CR+PR) to Pemetrexed in a 
population similar to that for this study is approximately 9%. It would be desirable to 
determine if the combination could be associated with a clinical response rate consistent 
with a 15% improvement, to 24%. 
6.7.2.3 Prior to Amendment G, the study was planned to be conducted using a phase II optimal 
design [52] as follows. The study was to have been designed to determine if the 
combination of agents is able to be associated with a response rate (CR+PR) that can 
rule out 9% (p0=0.09) in favor of a 24% response rate (p1=0.24). Using alpha=0.10
(10% probability of accepting a poor therapy) and beta=0.10 (10% probability of 
rejecting a good therapy), 17 evaluable patients were to be enrolled onto the trial. If 0 to 
1 of the 17 patients experiences a response, then enrollment was to be terminated. A
pause in the accrual of patients may have been required until it could have been 
determined that there were adequate patients with a response to justify accrual to the 
second stage.
This pause in accrual may have been up to 13 weeks in duration following enrollment of 
the 17th subject if 2 responses had not been previously been documented. If 2 or more of 

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the first 17 evaluable patients enrolled would have had a response, then accrual would have 
continued until a total of 46 evaluable patients would have been enrolled. If 2 to 6 of the 46 
were to have a response, then this would have been considered inadequate for further 
investigation. If 7 or more of 46 patients were to have had a response, then this would have 
indicated that this strategy provided a new approach that may be worthy of further 
consideration as it is consistent with 24%. Under the null hypothesis (9% response rate), 
the probability of early termination is 54%. 
6.7.2.4 For patients who are pemetrexed-naïve, the study will be conducted using a phase II 
optimal design [52]. The study will be designed to determine if the combination of 
agents is able to be associated with a response rate (CR+PR) that can rule out 9% 
(p0=0.09) in favor of a 34% response rate (p1=0.34). Using alpha=0.10 (10% 
probability of accepting a poor therapy) and beta=0.10 (10% probability of rejecting a 
good therapy), 7 evaluable patients will be enrolled onto the trial. If 0 of the 7 patients 
experience a response, then enrollment will be terminated. A pause in the accrual of 
patients may be required until it can be determined that there are adequate patients with 
a response to justify accrual to the second stage. This pause in accrual may be up to 13 
weeks in duration following enrollment of the 7th subject if 1 response has not 
previously been documented. If 1 or more of the first 7 evaluable patients enrolled have 
a response, then accrual will continue until a total of 20 evaluable patients have been 
enrolled. If 1 to 3 of the 20 patients has a response, then this will be considered 
inadequate for further investigation. If 4 or more of 20 patients have a response, then 
this will indicate that this strategy provides a new approach that may be worthy of 
further consideration as it is consistent with 34%. Under the null hypothesis (9% 
response rate), the probability of early termination is 52%.
6.7.2.5 For patients who had prior pemetrexed, the study will also be conducted using a phase II 
optimal design [52]. In this stratum, the study will be designed to determine if the 
combination of agents is able to be associated with a response rate (CR+PR) that can 
rule out 5% (p0=0.05) in favor of a 20% response rate (p1=0.20). Using alpha=0.10 
(10% probability of accepting a poor therapy) and beta=0.10 (10% probability of 
rejecting a good therapy), 12 evaluable patients will be enrolled onto the trial. If 0 of the 
12 patients experience a response, then enrollment will be terminated. A pause in the 
accrual of patients may be required until it can be determined that there are adequate 
patients with a response to justify accrual to the second stage. This pause in accrual may 
be up to 13 weeks in duration following enrollment of the 12th subject if 1 response has 
not previously been documented. If 1 or more of the first 12 evaluable patients enrolled
have a response, then accrual will continue until a total of 37 evaluable patients have 
been enrolled. If 1 to 3 of the 37 patients has a response, then this will be considered
inadequate for further investigation. If 4 or more of 37 patients have a response, then 
this will indicate that this strategy provides a new approach that may be worthy of 

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further consideration as it is consistent with 20%. Under the null hypothesis (5% 
response rate), the probability of early termination is 54%.
6.7.2.6 Twenty-two patients were enrolled on this protocol in the phase I portion. The phase II 
portion for both strata requires up to 57 evaluable patients. We will allow up to 60 
patients to be accrued to the phase II portion to allow for the possibility of a small 
number of in-evaluable patients. Thus, the accrual ceiling for Phase II will be set at 
22+60 for a total of 82 patients.
6.7.3 Secondary statistical Analysis of biological data
6.7.3.1 Tumor Tissue Assays
A variety of markers will be evaluated at baseline as well as after the conclusion of 
treatment. Changes from baseline will be determined in either absolute or relative terms as 
appropriate, and evaluated for statistical significance, as well as to determine if the changes 
or the actual values at a time point are associated with clinical response. Paired 
comparisons with baseline will be done using a paired t-test or Wilcoxon signed rank test 
as appropriate, and the changes will be compared between responders (CR +PR) and non-
responders (PD) using a two sample t-test (adequate numbers of subjects with normally 
distributed data in both groups) or a Wilcoxon rank sum test, if enough patients respond for 
this to be appropriate. Changes in PET scan SUVs will also be compared in a similar 
fashion with respect to any association with clinical response.
6.7.3.2 In all such cases, these secondary analyses will be considered exploratory and not 
formally adjusted for multiple comparisons. However, to ensure proper interpretation in 
the context of a potentially large number of explorations being performed, only p-values 
<0.01 will be interpretable as being associated with statistical significance.
6.7.3.3 The phase I portion of the study will enroll 12 to 30 patients depending upon the number 
of dose levels needed to reach the MTD, and therefore will require anywhere from 12 to 
30 months to complete accrual. A review of the literature reveals a median prevalence 
rate for mTOR pathway activation of approximately 60% [13]. In the past 6 months we 
have received 13 lung cancer referrals for a phase 1 study. About half of these potential 
study subjects are ineligible for a number of reasons (other than mTOR pathway 
activation). Using our current accrual rate and the prevalence rate of mTOR activation 
from the literature, we would predict an accrual rate of 7 – 8 subjects/year 
(60%[50%(13)/6mos]). Up to 6 patients treated in the phase I study may enroll in the 
phase II study. As we are a young group we hope that through increased awareness and 
recruiting efforts we will be able to accrue at a faster rate in the near future.

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7
HUMAN SUBJECTS PROTECTION
7.1
Rationale for Subject Selection
This study will be open to all individual with relapsed or refractory NSCLC regardless of 
gender, ethnicity, or race provided that the aforementioned inclusion and exclusion criteria 
are met. For safety reasons, pregnant women and children are excluded from this study. 
This study will be recruited through internal referral, our local physician referral base, and 
through various cancer information hotlines (i.e., Clinical Studies Support Center, 1-800-
4Cancer). Patients should realize that we are hopeful that they may gain benefit from this 
study, but there is no objective evidence to support our optimism at this time. Patients must 
have failed or be unable or unwilling to be treated with front line therapy (platinum or non 
platinum containing regimens) of proven efficacy for NSCLC. To date, there is no 
information that suggests that differences in drug metabolism or disease response would be 
expected in one ethnic group compared to another. Efforts will be made to extend accrual 
to each representative population, but in this preliminary study, a balance must be struck 
between patient safety considerations and limitations on the number of individuals exposed 
to potentially toxic and/or ineffective treatments on the one hand and the need to explore 
racial/ethnic aspects of clinical research on the other hand. If differences in outcome that 
correlate to ethnic identity are noted, accrual may be expanded or a follow-up study may be 
written to investigate those differences more fully.
7.2
Inclusion of Women and Minorities
Both men and women and members of all races and ethnic groups are eligible for this trial. 
Every effort will be made to recruit women and minorities in this study.
7.3
Justification for Exclusions
Due to lack of knowledge of the effects of sirolimus and pemetrexed on the fetus or on 
infants, as well as the possibility of teratogenic effects, pregnant and nursing women will 
be excluded from this trial. Some animal studies have shown fetal malformations and fetal 
toxicity. 
HIV-positive patients receiving anti-retroviral therapy are excluded from this study due to 
pharmacokinetic interactions between anti-retroviral medications such as protease 
inhibitors, which are CYP3A4 inhibitors, and sirolimus. HIV positive patients not receiving 
antiretroviral therapy are excluded due to the possibility that sirolimus may worsen their 
condition secondary to the immunosuppression of sirolimus and the likelihood that their 
underlying condition may obscure the attribution of adverse events with respect to 
sirolimus. Appropriate studies should be undertaken in this subgroup of patients in the 
future. Patients with unstable or serious medical or psychiatric conditions are excluded due 

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to the possibility that the underlying condition may obscure the attribution of adverse
events with respect to sirolimus and pemetrexed.
7.4
Participation of Children
Patients under the age of 18 will be excluded from study because of the relative 
infrequence of NSCLC in this group. The effect of sirolimus and pemetrexed in children 
may be investigated in studies that exclusively enroll children.
7.5
Evaluation of Benefits and Risks/Discomforts
The potential benefit to a patient who enters study is a reduction in the bulk of his/her 
tumor, which may or may not have a favorable impact on symptoms and/or survival. 
Potential risks include the possible occurrence of any of a range of side effects that are 
listed in the pharmaceutical section and the consent document. Subjects will receive an 
effective radiation dose of 3.7 rem from the PET CT scans. Subjects who undergo a CT 
directed biopsy will receive an additional 0.1 rem per biopsy procedure. For subjects who 
complete both PET scans and undergo two CT directed biopsies, the total effective dose of 
radiation will be 3.9 rem which falls within the 5 rem/year allowed by the radiation safety 
committee. The procedure for protecting against or minimizing risks will be to medically 
evaluate patients on a regular basis as described earlier.
7.6
Risk/Benefits Analysis
All care will be taken to minimize risks that may be incurred by tumor sampling. However, 
there are procedure-related risks (such as bleeding, infection and visceral injury) that will 
be explained fully during informed consent. If patients suffer any physical injury as a result 
of the biopsies, immediate medical treatment is available at the National Naval Medical 
Center in Bethesda and Clinical Research Center at NIH in Bethesda, Maryland. Although 
no compensation is available, any injury will be fully evaluated and treated in keeping with 
the benefits or care to which patients are entitled under applicable regulations.
7.7
Consent and Assent Process and Documentation
An associate or principal investigator or the protocol chairperson on the trial will inform 
patients of the purpose, alternatives, treatment plan, research objectives and follow-up of 
this trial. The patient will be provided an IRB-approved consent for review and signature 
and his/her questions will be answered. After a decision is made to enroll into the study, a 
signature will be obtained from the patient at a subsequent visit. The original copy of the 
signed informed consent will be placed in the patient's medical record and a copy will be 
stored in the Research Record.
All patients must have a signed informed consent form and an on-study (confirmation of 
eligibility) form filled out and signed by a participating investigator before entering on 

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study.
8
SAFETY REPORTING REQUIREMENTS/DATA AND SAFETY MONITORING
PLAN
8.1
Definitions
8.1.1 Adverse Event
An adverse event is defined as any reaction, side effect, or untoward event that occurs 
during the course of the clinical trial associated with the use of a drug in humans, whether 
or not the event is considered related to the treatment or clinically significant. For this 
study, AEs will include events reported by the patient, as well as clinically significant 
abnormal findings on physical examination or laboratory evaluation. A new illness, 
symptom, sign or clinically significant laboratory abnormality or worsening of a pre-
existing condition or abnormality is considered an AE.  All AEs must be recorded on the 
AE case report form.  
All AEs, including clinically significant abnormal findings on laboratory evaluations, 
regardless of severity, will be followed until satisfactory resolution. AEs should be reported 
up to 30 days following the last dose of study drug.  AEs that are considered treatment 
related, expected, continuing, but not resolvable by 30 days after treatment completion 
(e.g., alopecia) will not be followed after the 30-day period. 
An abnormal laboratory value will be considered an AE if the laboratory abnormality is 
characterized by any of the following:
x
Results in discontinuation from the study
x
Is associated with clinical signs or symptoms 
x
Requires treatment or any other therapeutic intervention
x
Is associated with death or another serious adverse event, including 
hospitalization. 
x
Is judged by the Investigator to be of significant clinical impact
x
If any abnormal laboratory result is considered clinically significant, the 
investigator will provide details about the action taken with respect to the test 
drug and about the patient’s outcome.
8.1.2 Suspected adverse reaction
Suspected adverse reaction means any adverse event for which there is a reasonable 
possibility that the drug caused the adverse event.  For the purposes of IND safety 
reporting, ‘reasonable possibility’ means there is evidence to suggest a causal relationship 
between the drug and the adverse event.  A suspected adverse reaction implies a lesser 
degree of certainty about causality than adverse reaction, which means any adverse event 
caused by a drug.

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8.1.3 Unexpected adverse reaction
An adverse event or suspected adverse reaction is considered “unexpected” if it is not listed 
in the investigator brochure or is not listed at the specificity or severity that has been 
observed; or, if an investigator brochure is not required or available, is not consistent with 
the risk information described in the general investigational plan or elsewhere in the current 
application. "Unexpected”, also refers to adverse events or suspected adverse reactions that 
are mentioned in the investigator brochure as occurring with a class of drugs or as 
anticipated from the pharmacological properties of the drug, but are not specifically 
mentioned as occurring with the particular drug under investigation.
8.1.4 Serious 
An adverse event or suspected adverse reaction is considered serious if in the view of the 
investigator or the sponsor, it results in any of the following:
x
Death,
x
A life-threatening adverse drug experience
x
Inpatient hospitalization or prolongation of existing hospitalization
x
Persistent or significant incapacity or substantial disruption of the ability to 
conduct normal life functions
x
A congenital anomaly/birth defect.
x
Important medical events that may not result in death, be life-threatening, or 
require hospitalization may be considered a serious adverse drug experience 
when, based upon appropriate medical judgment, they may jeopardize the patient 
or subject and may require medical or surgical intervention to prevent one of the 
outcomes listed in this definition.
8.1.5 Disability
A substantial disruption of a person’s ability to conduct normal life functions.
8.1.6 Life-threatening adverse drug experience
Any adverse event or suspected adverse reaction that places the patient or subject, in the 
view of the investigator or sponsor, at immediate risk of death from the reaction as it 
occurred, i.e., it does not include a reaction that had it occurred in a more severe form, 
might have caused death.
8.1.7 Protocol Deviation (NIH Definition)
Any change, divergence, or departure from the IRB approved study procedures in a 
research protocol that does not have a major impact on the subject’s rights, safety or well-

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being, or the completeness, accuracy and reliability of the study data.
8.1.8 Protocol Violation (NIH Definition)
Any change, divergence, or departure from the IRB-approved study procedures in a 
research protocol that does have a major impact on the subject’s rights, safety, or well-
being and/or the completeness, accuracy and reliability of the study data.
8.1.9 Unanticipated Problem
Any incident, experience, or outcome that:
Is unexpected in terms of nature, severity, or frequency in relation to 
(a) the research risks that are described in the IRB-approved research protocol and 
informed consent document; Investigator’s Brochure or other study documents, AND
(b) the characteristics of the subject population being studied; AND
Is related or possibly related to participation in the research; AND
Places subjects or others at a greater risk of harm (including physical, psychological, 
economic, or social harm) than was previously known or recognized.
8.2
NCI-IRB Reporting
8.2.1 NCI-IRB Expedited Reporting of Adverse Events, Unanticipated Problems, and Deaths 
The Protocol PI will report to the NCI-IRB:
x
All unexpected serious adverse events that are possibly, probably, or definitely 
related to the research.
x
All deaths, except deaths due to progressive disease
x
All Protocol Violations or Deviations
x
All Unanticipated Problems
Reports must be received by the NCI-IRB within 7 working days of PI awareness via iRIS.
8.2.2 NCI-IRB Requirements for PI Reporting of Adverse Events at Continuing Review
For reporting of adverse events at time of continuing review, the NCI-IRB requires a 
summary report of adverse events that have occurred on the protocol since the previous 
continuing review and in aggregate. The method of presentation should provide the NCI-
IRB with the information necessary to clearly identify risks to participants and to make a 
risk:benefit determination. The summary report is based on the following guidance: any 

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unexpected severity and/or unexpected frequency of expected events needs to be reported 
and interpreted in relation to the risk:benefit of study participants in the narrative. 
The protocol PI will report to the NCI-IRB: 
x
All Grade 2 unexpected events that are possibly, probably or definitely related to 
the research; 
x
All Grade 3 and 4 events that are possibly, probably or definitely related to the 
research; 
x
All Grade 5 events regardless of attribution; 
x
All Serious Events regardless of attribution. 
NOTE: Grade 1 events are not required to be reported.
8.2.3 NCI-IRB Reporting of IND Safety Reports
Only IND Safety Reports that require a sponsor recommended change to the protocol or the 
consent form or in the opinion of the PI increases risks to study participants will need to be 
reported to the NCI IRB.
8.3
Data and Safety Monitoring Plan
The principal investigator will review adverse event and response data on each patient to 
ensure safety and data accuracy. The principal investigator will personally conduct or 
supervise the investigation and provide appropriate delegation of responsibilities to other 
members of the research staff. 
The clinical research team will meet on a regular basis when patients are being actively 
treated on the trial to discuss each patient. Decisions about dose level enrollment and dose 
escalation if applicable will be made based on the toxicity data from prior patients. 
Data will be monitored regularly by the principal investigator and/or the study chairperson 
in order to identify significant toxicity trends. This will be done in biweekly meetings that 
review the treatment course of all the patients on the protocol at that point in time. 
All new significant findings that may affect the patient’s willingness to continue in the 
study will be shared with patients. All patients receiving study agents will be evaluated for 
safety. The safety parameters include all laboratory tests and hematological abnormalities, 
CNS observations, physical examination findings, and spontaneous reports of adverse 
events reported to the investigator by patients. All toxicities encountered during the study
will be evaluated according to the Common Terminology Criteria Adverse Events version 
3.0 and recorded prior to each course of therapy. Life-threatening toxicities should be 
reported immediately to the Principal Investigator or study chairperson and the Institutional 

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Review Board (IRB).
All data will be collected in a timely manner and reviewed by the principal investigator or a 
lead associate investigator. Adverse events will be reported as required above. Any safety 
concerns, new information that might affect either the ethical and or scientific conduct of 
the trial, or protocol deviations and violations will be immediately reported to the IRB 
using iRIS. These reports will be reviewed, entered into the protocol database, circulated 
and reviewed at the next scheduled IRB meeting, and then filed in the IRB protocol file. 
For confidentiality reasons, PIs should remove names, addresses and social security 
numbers from any supplemental information submitted with the AE/SAE form. Medical 
record numbers and/or study ID numbers are the only identifiers that should be used.
Confidentiality will be maintained as much as possible, consistent with applicable 
regulations. Names of participants or identifying material will not be released without 
patient permission, except when such release is required by law. No patient’s name or 
identifying information will be released in any publication or presentation. Records are 
maintained according to current legal requirements, and are made available for review 
according to the requirements of the Food and Drug Administration (FDA) or other 
authorized user, only under guidelines established by the Federal Privacy Act. 
9
PHARMACEUTICAL AND INVESTIGATIONAL DEVICE INFORMATION
9.1
Sirolimus
9.1.1 Product Description
9.1.1.1 Other Names: Sirolimus, Rapamycin, Rapamune®
9.1.1.2 Classification: Immunosuppressive agent.
9.1.1.3 Mechanism of Action: Sirolimus binds to the FK Binding Protein-12 (FKBP-12). This 
complex binds to and inhibits the activation of the mammalian regulatory kinase, Target 
Of Rapamycin (mTOR). This inhibition suppresses cytokine-driven T-cell proliferation, 
inhibiting the progression from the G1 to the S phase of the cell cycle.
9.1.1.4 Molecular Weight: 914.2
9.1.2 Storage Requirements

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Sirolimus tablets should be stored at USP Controlled Room Temperature (68° to 77°F). 
Cartons should be used to protect blister cards and strips from light. Dispense tablets in a 
tight, light-resistant container as defined in the USP. Sirolimus (Rapamune) Oral Solution 
bottles should be stored protected from light and refrigerated at 2°C to 8°C (36°F to 46°F). 
Once the bottle is opened, the contents should be used within one month. If necessary, the 
patient may store the bottles at room temperatures up to 25°C (77°F) for a short period of 
time (e.g., not more than 15 days for the bottles). An amber syringe and cap are provided 
for dosing and the product may be kept in the syringe for a maximum of 24 hours at room 
temperatures up to 25°C (77°F) or refrigerated at 2°C to 8°C (36°F to 46°F). The syringe 
should be discarded after one use. After dilution, the preparation should be used 
immediately. Rapamune Oral Solution provided in bottles may develop a slight haze when 
refrigerated. If such a haze occurs allow the product to stand at room temperature and 
shake gently until the haze disappears. The presence of this haze does not affect the quality 
of the product.
9.1.3 Stability
Sirolimus tablets are stable through the manufacturer’s expiration date imprinted on the 
product container.
9.1.4 Administration
Sirolimus is to be administered orally consistently without food, at a dose and schedule 
defined by the protocol dose escalation schema. Study patients are not to ingest grapefruit, 
grapefruit juice or grapefruit juice containing products while on sirolimus therapy.
9.1.5 Toxicity
Refer to FDA labeling for complete description of adverse events associated with 
Sirolimus. The most frequent adverse effects of sirolimus include peripheral edema, 
lymphocele, hyperlipidemia, hypercholesterolemia, tachycardia, venous thromboembolism, 
gastrointestinal disturbances, stomatitis, epistaxis, acne, rash, bone necrosis, arthralgia, 
hypokalaemia, and pyelonephritis. Please see the FDA labeling for complete description of 
adverse events associated with sirolimus.
9.1.5.1 Body as a Whole: abdomen enlarged, abscess, ascites, cellulitis, chills, face edema, flu 
syndrome, generalized edema, hernia, Herpes zoster infection, lymphocele, malaise, 
pelvic pain, peritonitis, sepsis, asthenia, fever, chills, malignancy, delayed wound 
healing has been reported in transplant patients with bronchial anastomotic dehiscence 
has occurred in lung transplant and in some cases fatal , bacterial infection, viral 
infection, anaphylactic/anaphylactoid reactions.

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9.1.5.2 Cardiovascular: atrial fibrillation, hemorrhage, hypervolemia, hypotension, palpitation, 
postural hypotension, peripheral vascular disorder, syncope, thrombophlebitis, 
thrombosis, vasodilatation, venous thromboembolism, hypertension, tachycardia, 
congestive heart failure.
9.1.5.3 Digestive: anorexia, dysphagia, eructation, esophagitis, flatulence, gastritis, 
gastroenteritis, gingivitis, gum hyperplasia, ileus, liver function tests abnormal, mouth 
ulceration, oral moniliasis, stomatitis, diarrhea.
9.1.5.4 Heme and Lymphatic: ecchymosis, leukocytosis, lymphadenopathy, polycythemia, 
thrombotic thrombocytopenic purpura (hemolytic-uremic syndrome),. 
lymphoproliferative disease, lymphoma, lymphadenopathy, anemia, leukopenia, 
thrombocytopenia, especially at higher doses, TTP.
9.1.5.5 Hepatic: hepatotoxicity, hepatic necrosis 
9.1.5.6 Metabolic: acidosis, alkaline phosphatase increased, BUN increased, creatine 
phosphokinase increased, dehydration, healing abnormal, hypercalcemia, 
hyperglycemia, hyperphosphatemia, hypocalcemia, hypoglycemia, hypomagnesemia, 
hyponatremia, lactic dehydrogenase increased, AST/SGOT increased, ALT/SGPT 
increased, weight loss. hypercholesterolemia, hyperlipidemia, hypokalemia, edema, 
weight gain, Cushing’s syndrome, diabetes mellitus, glycosuria.
9.1.5.7 Musculoskeletal: arthralgia, bone necrosis arthrosis, leg cramps, myalgia, osteoporosis, 
and tetany.
9.1.5.8 Nervous: anxiety, confusion, depression, dizziness, emotional lability, hypertonia, 
hypesthesia, hypotonia, insomnia, neuropathy, paresthesia, somnolence insomnia, 
tremor, and headache.
9.1.5.9 Respiratory: interstitial lung disease (pneumonitis, BOOP, pulmonary fibrosis) asthma, 
atelectasis, bronchitis, cough increased, epistaxis, hypoxia, lung edema, pleural 
effusion, pneumonia, rhinitis, and sinusitis.
9.1.5.10 Skin: acne, rash, skin cancer fungal dermatitis, hirsutism, pruritus, skin hypertrophy, 
skin ulcer, sweating.
9.1.5.11 Urinary: dysuria, urinary frequency albuminuria, bladder pain, hematuria, 
hydronephrosis, impotence, kidney pain, kidney tubular necrosis, nocturia, oliguria, 
pyelonephritis, pyuria, scrotal edema, testis disorder, toxic nephropathy, urinary 
frequency, urinary incontinence, urinary retention

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9.1.5.12 Special Senses: abnormal vision, cataract, conjunctivitis, deafness, ear pain, otitis 
media, tinnitus.
9.1.5.13 Serious Toxicities include: Cases of interstitial lung disease (including pneumonitis, and 
infrequently bronchiolitis obliterans organizing pneumonia [BOOP] and pulmonary 
fibrosis), some fatal, with no identified infectious etiology have occurred in patients 
receiving immunosuppressive regimens including sirolimus. In some cases, the 
interstitial lung disease has resolved upon discontinuation or dose reduction of 
sirolimus. Alveolar hemorrhage has also been reported. Hepatotoxicity has been 
reported, including fatal hepatic necrosis with elevated sirolimus trough concentrations. 
Abnormal healing following transplant surgery has been reported, including fascial 
dehiscence and anastomotic disruption (e.g., wound, vascular, airway, ureteral, biliary).
9.1.5.14 Less frequently occurring adverse events included: mycobacterial infections, Epstein-
Barr virus infections, and pancreatitis.
9.1.6 Drug interactions
9.1.6.1 Sirolimus is a substrate for P-glycoprotein and gut and liver CYP3A4. The co-
administration of a potent inhibitor or inducer of CYP3A4 may respectively increase or 
decrease sirolimus AUC. Inhibitors of CYP3A4 include (but are not limited to): 
amprenavir, atazanavir, bromocriptine, cimetidine, clarithromycin, clotrimazole, 
cyclosporine, danazol, diltiazem, erythromycin, fluconazole, fosamprenavir, other HIV 
protease inhibitors, indinavir, itraconazole, ketoconazole, metoclopramide, nefazodone, 
nelfinavir, nicardipine, nifedipine, ritonavir, saquinavir, telithromycin, troleandomycin 
(TAO), verapamil, and voriconazole. Inducers of CYP3A4 include: nevirapine, 
rifampicin, rifampin, rifabutin, rifapentin, phenytoin, carbamazepine, phenobarbital and 
St. John’s Wort.
9.1.6.2 The use of live vaccines should be avoided in patients receiving sirolimus.
9.1.6.3 Grapefruit juice inhibits CYP3A4. Patients should not ingest grapefruit juice while on 
sirolimus therapy.
9.1.6.4 Angioneurotic edema-type reactions have been observed when sirolimus and an ACE 
inhibitor are given concurrently.
9.1.7 Agent Ordering/Availability
9.1.7.1 Agent Ordering: Sirolimus will be procured via commercial mechanisms.

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9.1.7.2 Availability: Sirolimus is available commercially as 1mg mg white triangular shaped 
tablets and 2 mg yellow to beige tablets, supplied in bottles of 100 tablets and cartons of 
100 tablets (10 blister cards of 10 tablets each). Sirolimus is also available 
commercially as an oral solution, supplied at a concentration of 1 mg/mL in cartons 
which contain a 2 oz (60 mL fill) amber glass bottle. In addition to the bottles, each 
carton is supplied with an oral syringe adapter for fitting into the neck of the bottle, 
sufficient disposable amber oral syringes and caps for daily dosing, and a carrying case.
9.2
Pemetrexed
9.2.1 Product Description
9.2.1.1 Other Names: Alimta®
9.2.1.2 Classification: Antifolate antineoplastic.
9.2.1.3 Mechanism of Action: Pemetrexed inhibits the folate-dependent enzymes involved in the 
de novo biosynthesis of thymidine and purine nucleotides, thymidylate synthase, 
dihydrofolate reductase, and glycinamide ribonucleotide formyltransferase.
9.2.1.4 Molecular Weight: 597.49
9.2.2 Storage Requirements
Pemetrexed for injection should be stored at 25°C with excursions permitted to 15-30°C 
(USP Controlled Room Temperature).
9.2.3 Stability
Reconstituted and infusion solutions of pemetrexed are stable for up to 24 hours following 
initial reconstitution, when stored refrigerated at 2-8°C (36-46°F), or at USP Controlled 
Room Temperature under ambient lighting.
9.2.4 Preparation
Infusion solutions of pemetrexed are to be prepared aseptically, following precautions 
recommended for the preparation of antineoplastic agents which limit exposure of the 
preparer to the drug. Each 500-mg vial of pemetrexed for injection is to be reconstituted 
with 20ml of 0.9% Sodium Chloride Injection (preservative free) to yield a solution 
containing 25mg/ml pemetrexed per ml. The desired dose of pemetrexed is to be further 

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diluted to 100ml with 0.9% Sodium Chloride Injection (preservative free). Unused 
pemetrexed is to be discarded.
9.2.5 Administration
Pemetrexed is to be administered as an intravenous infusion over 10 minutes. Patients 
receiving pemetrexed must receive premedication with a corticosteroid, folic acid, and 
cyanocobalamin. Dexamethasone 4mg shall be taken twice daily for 3 days beginning the 
day prior to pemetrexed. Folic acid 1mg shall be taken by mouth every day, with least 5 
daily doses taken during the 7-day period preceding the first dose of pemetrexed. Folic acid 
dosing shall continue during the full course of therapy and for 21 days after the last dose of 
pemetrexed. The patient shall receive one intramuscular injection of vitamin B12 1000mcg 
during the week preceding the first dose of pemetrexed, and day 1 of all subsequent cycles.  
9.2.6 Toxicity
Refer to the FDA-approved package insert provided with the drug for a complete 
description of adverse events associated with Pemetrexed.
9.2.6.1 Body as a Whole: Fatigue, fever, allergic reaction, and hypersensitivity.
9.2.6.2 Cardiovascular:  Hypertension, edema, thromboembolism, and cardiac ischemia.
9.2.6.3 Digestive: Nausea, vomiting, stomatitis, constipation, diarrhea, anorexia.
9.2.6.4 Heme and Lymphatic: Myelosuppression.
9.2.6.5 Hepatic: Elevated hepatic enzymes.
9.2.6.6 Musculoskeletal: arthralgia, myalgia,
9.2.6.7 Nervous: Sensory Neuropathy, depression/mood alteration.
9.2.6.8 Renal: Decreased creatinine clearance.
9.2.6.9 Respiratory: Dyspnea
9.2.6.10 Skin: Rash, desquamation, alopecia
9.2.7 Drug interactions

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9.2.7.1 Daily ibuprofen doses of 400 mg qid reduce pemetrexed clearance by 20% and increase 
pemetrexed AUC by 20% in patients with normal renal function. Patients will be 
counseled to avoid all NSAIDS for 5 days prior to pemetrexed and 2 days afterward. 
Longer acting NSAIDS will be avoided for 5 days prior and 2 days afterward
9.2.7.2 Aspirin 325mg qid does not affect pemetrexed pharmacokinetics
9.2.8 Agent Ordering/Availability
9.2.8.1 Availability: Pemetrexed for injection is available commercially as a sterile lyophilized 
powder for reconstitution containing 500mg pemetrexed per vial.
9.2.8.2 Agent Ordering: Pemetrexed will be procured via commercial mechanisms.
9.3
Dexamethasone 
Dexamethasone will be obtained from commercial sources. The FDA approved package 
insert provides information on the storage and administration of the agent. Possible side 
effects include euphoria or mood changes, headache, insomnia, edema, hypertension, 
glucose intolerance, acne, may be observed with dexamethasone given intermittently as in 
this protocol. Other side effects associated with longer chronic administration of 
dexamethasone include adrenal insufficiency, muscle weakness, Cushingoid state, and 
osteoporosis. This medication should be taken with food.
9.4
Folic acid
Folic acid will be obtained from commercial sources. The FDA approved package insert 
provides information on the storage and administration of the agent. Side effects from folic 
acid are not common. Allergic reaction manifested by rash, itching, swelling, dizziness, 
trouble breathing have all been reported.
9.5
Cyanocobalamin
Cyanocobalamin will be obtained from commercial sources. The FDA approved package 
insert provides information on the storage and administration of the agent. Side effects are 
generally rare but the following have been reported: Dermatologic: itching, rash, transitory 
exanthema, and urticaria have been reported. Gastrointestinal: diarrhea has been reported. 
Hematologic: peripheral vascular thrombosis has been reported. Treatment of vitamin B12
deficiency can unmask polycythemia vera, which is characterized by an increase in blood 
volume and the number of red blood cells. There may also be pain or redness associated 
with the injection.

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transformation, invasion, and metastasis. Mol Cell Biol, 2004. 24(12): p. 5565-76.
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11 APPENDICES
11.1 Appendix A: Table 3: Study Calendar
Evaluation
Baseline
Cycle 1 Day 
1
Cycle 1 Day 
7
Cycle 1 Day 
8
Day          14 
& 21
C2 D1
C3 D1
Day1 Every 
cycle
Every two 
cycles
Off study
Informed consent
X
Medical History/ 
Demographics   
Xa
Inclusion/Exclusion 
Criteria         
Xa
PE (VS, Ht, Wt, 
Performance status, 
narcotic use, meds) 
Xa
X
Xk,
l
Xk, l
Xk,
l
X
Adverse Events
X
X
X
X
X
X
X
X
X
EKG
Xb
CXR
Xb
Hematology profile      
CBC with 
differentialn
Xa
X
X
Xk,l
Xk,l
Xk,l
X
Biochemical Profilec
Xa
X
Xk,l
Xk,l
Xk,l
X
Coagulation Profile      
(PT, APTT)          
Xa
X
Xk,l
Xk,l
Xk,l
X
Lipid Profile                 
(fasting chol panel & 
Xa
X
Xk,l
Xk,l
Xk,l
X

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Evaluation
Baseline
Cycle 1 Day 
1
Cycle 1 Day 
7
Cycle 1 Day 
8
Day          14 
& 21
C2 D1
C3 D1
Day1 Every 
cycle
Every two 
cycles
Off study
triglycerides)
Vitamin Profile    
(B12 and folate)
Xa
Xk,l
Xk, l
Xk,l 
Urinanalysis
Xa
Xk
Xk,l
Xk, l
Xk,
l
pregnacy test
Xa
Xk,l
Xk, l
Xk,l
Lymphocyte subsets
Xa
Xk,l
Xk,l
Xk,l
Trough sirolimus 
levels
X
X
Xk,l
Xk,l
Xk,l
CT scans: Chest Abd 
Pelvis
Xb
Xk,m
Xk
PET/ CT scan
Xh
Xk
Akt/mTOR pathway 
activation    Tumor 
(T) or PBMC (P)
X
T, 
P,
d
X
P
X
T,P,m
X
P
Pharmacokinetics         
Xj
Xj
Start daily sirolimus     
e
X
Start Pemetrexed 
infusions        Q 21 
days
X
X
X
X

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Evaluation
Baseline
Cycle 1 Day 
1
Cycle 1 Day 
7
Cycle 1 Day 
8
Day          14 
& 21
C2 D1
C3 D1
Day1 Every 
cycle
Every two 
cycles
Off study
Start vitamin B12 
folate  f
X
Start folate                    
g
X
a = if done within 17 days of initiation of therapy may count as baseline (pregnancy test 
within 7 days)
b = if done within 28 days of initiation of therapy may count as baseline
c = incudes Mg, Na, K, Cl, HCO3, Ca, PO4, Cr, BUN, Glu, AST, ALT, T bili, Alk phos, 
alb, T protein, LDH, amylase, lipase
d = Akt activation in tumor determines eligibility for phase II subjects (testing required)
e = administerd once a day every day of the cycle on an empty stomach
f = 1000μg first dose within 7 days before pemetrexed initiated then q 63 days
g = 1mg starting within 7 days before pemetrexed initiated, then administered 
continuously
h = must be performed within 28 days of day 1 cycle 1 
i = for sirolimus pre dose, 20min, 40min, 1h, 2, 3h, 4h, 6h, 12h, 24h AFTER 
SIROLIMUS

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j = for both sirolimus and pemetrexed, pre dose 20min, 40min, 1h, 2, 3h, 4h, 6h, 12h, 24h
AFTER PEMETREXED
k = within 72 hours of the start of each cycle
l = repeated for toxcity follow up on day 7 or day 14 of any cycle in which dose 
reduction took place on day 1
m = after two cycles of treatment or at time of progression, which ever occurs first
n = CBC twice weekly for subjects with Grade 3 or 4 neutropenia, until resolution

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11.2 Appendix B: Table 4: Performance Status Criteria
Grade
Description
Percent
Description
100
Normal, no complaints, no 
evidence of disease.
90
Able to carry on normal activity; 
minor signs or symptoms of 
disease.
80
Normal activity with effort; some 
signs or symptoms of disease.
70
Cares for self, unable to carry on 
normal activity or do active work.
60
Requires occasional assistance, but
is able to care for most of his/her 
needs.
50
Reqires considerable assistance 
and frequent medical care.
40
Disabled, requires special care and 
assistance.
30
Severely disabled, hospitalization 
indicated. Death is not imminent.
20
Very sick, hospitalization indicated.
Death is not imminent.
10
Moribund, fatal processes 
progressing rapidly.
5
Dead
0
Dead
ECOG Performance Status Scale
Normal activity Fully active, able to 
carry on all pre-disease performance 
without restriction.
Symptoms, but ambulaory. 
Restricted in pysically strenuous 
activity, but ambulatory and able to 
carry out work of a light or sedenary 
nature (e.g. light housework, office 
work).
In bed <50% of the time. 
Amublatory and capable of all self 
care, but unable to carry out any 
work activities. Up and about more 
than 50% of waking hours.
In bed >50% of the time. Capable of
only limited self-care, confined to 
bed or chair more than 50% of 
waking hours.
100% bedridden. Completely 
disabled. Cannot carry on any self-
care. Totally confined to bed or chair
0
1
Karnofsky Performance Scale
2
3
4

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11.3 Appendix C: Standard Operating Procedure for Isolating PBMCs
The following protocol will be used to isolate PBMCs
Using Vacutainer CPT collection tube (BD), with sodium heparin
Note: This tube contains a Ficoll gradient that will separate cell layers upon centrifugation.  
The cell layers are as follows..
Collect blood in CPT tube.  Spin tube down at ROOM TEMP (18-25qC) @ 3000 rpm (6th
floor centrifuge) for 30 min.
To calculate rpm: Measure radius of centrifuge/rotor.  Desired RCF (relative centrifugal 
force) is ~ 1500-1800.  Enter these values on BD website and it will calculate for you what 
the corresponding rpm is.
http://www.bd.com/vacutainer/products/molecular/heparin/procedure.asp
PBMC layer will be a cloudy layer (~0.5-1 inches tall) right above the polyester gel plug.  
The height and density of the layer will vary depending on the WBC count of each patient.
If plasma is desired- remove the TOP few mls of plasma carefully, and store at  -80C in 
several eppendorf tubes. 
To isolate PBMCs- Remove the remaining plasma (including the PBMC layer) and place in 
a 15 ml conical tube.  Fill the tube to the top with 1X PBS.  Be careful not to aspirate any 
of the polyester gel, as this will pellet with the PBMCs.
Pellet PBMCs by spinning at 1500-2000 rpm for 5-10 minutes.

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Aspirate PBS from pellet. Lyse in 2X LSB with protease inhibitors. Store @ -80qC.

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11.4 Appendix D: Standard Operating Procedure for Tumor Tissue Acquisition and 
Storage
After OR specimen is obtained, it should be divided in half. One sample is sent to 
Pathology for routine histopathologic examination, the other is for research.  
One half will be fixed in formalin and processed for immunohistochemistry. Plastic jar 
containing 10mL formalin (Sigma) will be provided.
Processing for IHC includes paraffin-embedding of tissue specimen, and subsequent 
sectioning onto charged glass slides.  Approximately 20 sections will be obtained for each 
specimen, and the remainder saved in paraffin-embedded blocks.  Histoserv® 
(Germantown, MD) will perform these processes.
Blocks and slides will be stored at NNMC, Building 8, 4th floor, Room 4151 in cabinets 
marked “clinical specimens”.  Samples will have numbers corresponding to protocol and 
patient ID #.  
One half will be flash-frozen in a bath of dry ice and 100% ethanol, and transported back to 
NNMC to be stored at -135qC.
Sample will remain frozen until it is processed for immunoblotting.  Processing includes 
thawing sample and immersing in 2X LSB (lysis buffer), and using a standard Tissue 
Tearor ® (tissue homogenizer) to make a lysate.
Lysates obtained from each sample will be aliquoted and stored in Eppendorf microfuge 
tubes (1.5mL), labeled with protocol and patient ID #.
Lysates will be stored at NNMC, Building 8, 6th floor, freezer room (at end of hall, no 
room #), in freezer # 4 (open-top freezer, -135qC), box will be labeled with protocol #.

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11.5 Appendix E: Table 5: Drugs with potential CYP3A4 interactions
CYP3A4 Substrates
Albuterol
Alfentanil
Alprazolam
Amiodarone
Amlodipine
Amprenavir
Aprepitant
Aripiprazole
Atazanavir
Atorvastatin
Benzphetamine
Bisoprolol
Bortezomib
Bosentan
Bromazepam
Bromocriptine
Budesonide
Buprenorphine
Buspirone
Busulfan
Carbamazepine
Cerivastatin
Chlordiazepoxid
e
Chloroquine
Chlorphenirami
ne
Cilostazol
Cisapride
Citalopram
Clarithromycin
Clobazam
Clonazepam
Clorazepate
Cocaine
Colchicine
Conivaptan
Cyclophosphami
Dihydroergotami
ne 
Diltiazem 
Disopyramide 
Docetaxel
Doxepin
Doxorubicin
Doxycycline
Efavirenz
Eletriptan
Enalapril
Eplerenone
Ergoloid 
mesylates
Ergonovine
Ergotamine
Erythromycin
Escitalopram
Estradiol
Estrogens, conj., 
synthetic
Estrogens, conj., 
equine
Estrogens, conj., 
esterified
Estrone
Estropipate
Ethinyl estradiol
Ethosuximide
Etoposide
Exemestane
Felbamate
Felodipine
Fentanyl
Flurazepam
Flutamide
Fluticasone
Fosamprenavir
Isradipine 
Itraconazole
Ketamine 
Ketoconazole
Lansoprazole
Letrozole
Levonorgestrel
Lidocaine
Losartan
Lovastatin
Medroxyprogester
one Mefloquine
Mestranol
Methadone
Methylergonovine
Methysergide
Miconazole
Midazolam
Miglustat
Mirtazapine
Modafinil
Montelukast
Moricizine
Nateglinide
Nefazodone
Nelfinavir
Nevirapine
Nicardipine
Nifedipine
Nimodipine
Nisoldipine
Norethindrone
Norgestrel
Ondansetron
Paclitaxel
Pergolide
Phencyclidine
Pimozide
Quinidine
Rabeprazole 
Ranolazine
Repaglinide
Rifabutin
Ritonavir
Salmeterol
Saquinavir
Sibutramine
Sildenafil
Simvastatin
Sirolimus
Spiramycin
Sufentanil
Sunitinib
Tacrolimus
Tamoxifen
Tamsulosin
Telithromycin
Teniposide
Tetracycline
Theophylline
Tiagabine
Ticlopidine
Tipranavir
Tolterodine
Toremifene
Trazodone
Triazolam
Trimethoprim
Trimipramine
Troleandomy
cin
Vardenafil

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de
Cyclosporine
Dantrolene
Dapsone
Dasatinib (1)
Delavirdine
Diazepam
Gefitinib
Haloperidol
Ifosfamide
Imatinib
Indinavir
Irinotecan
Isosorbide
Isosorbide 
dinitrate
Isosorbide 
mononitrate
Pipotiazine
Primaquine
Progesterone
Quetiapine
Venlafaxine
Verapamil
Vinblastine
Vincristine
Vinorelbine
Zolpidem
Zonisamide
Zopiclone