A Phase II Multi-Center Study of Rapamycin for Treating Kidney Angiomyolipomas in TSC or LAM Patients
Phase: PHASE2
Conditions: Nonmalignant Neoplasm, Tuberous Sclerosis, Lymphangioleimyomatosis, Kidney Angiomyolipoma
Sponsor: Dana-Farber Cancer Institute

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
1
SECTION 1 – Protocol Summary 
 
PRINCIPAL/OVERALL INVESTIGATOR:   
Sandra L. Dabora, M.D., Ph.D. 
Brigham and Women’s Hospital  
 
CO-INVESTIGATORS:   
Judy Garber, M.D., M.P.H. 
 
Dana Farber Cancer Institute 
David Kwiatkowski, M.D., Ph.D. 
Brigham and Women’s Hospital 
 
CLINICAL SITE PRINCIPAL INVESTIGATORS: 
Stephen Ashwal, M.D. 
 
Loma Linda University School of Medicine  
Peter Crino, M.D., Ph.D. 
 
UPENN Medical Center 
Francis DiMario, M.D.  
 
Connecticut Children’s Medical Center 
David Franz, M.D. 
 
 
Cincinnati Children’s Medical Center 
Daniel Miles, M.D.   
 
New York University Medical Center 
Arthur Sagalowsky, M.D. 
 
Univ. of Texas Southwestern 
Elizabeth Thiele M.D., Ph.D.  
Massachusetts General Hospital 
 
STUDY TITLE:  A phase II multi-center study of rapamycin for treating kidney 
angiomyolipomas in TSC or LAM patients 
 
FUNDING:  National Institutes of Health (NCI) and the Tuberous Sclerosis Alliance.   
 
SPECIFIC AIMS:   
 
Specific Aim 1: 
Determine the efficacy of rapamycin (also known as sirolimus and 
Rapamune®;Wyeth-Ayerst) for the treatment of kidney angiomyolipomas in patients with 
tuberous sclerosis (TSC) or lymphangioleiomyomatosis (LAM). 
 
Specific Aim 2: 
Determine the toxicity of using rapamycin in this patient 
population. 
 
Specific Aim 3: 
Collect data on the long term follow up of kidney 
angiomyolipomas for 12 months after treatment with rapamycin is discontinued.  
 
Specific Aim 4: 
Observe changes that occur in other TSC lesions (tubers, 
subependymal giant cell astrocytomas, facial angiofibromas, kidney cysts) and pulmonary 
disease in LAM patients.  Changes in renal and pulmonary function will also be monitored.  
These observations will provide data for future clinical trials for this patient population 
Specific Aim 5:  
Collect blood DNA, serum and urine samples periodically for  
correlative genotype analysis and biomarker studies. 
 
BACKGROUND AND SIGNIFICANCE: 
 
Kidney angiomyolipomas are renal tumors that occur frequently in TSC and LAM 
patients.  These tumors can cause significant morbidity and mortality, and effective systemic 
treatment is not currently available.  There is recent evidence in cell culture experiments, animal 
models, and pathologic specimens from TSC kidney angiomyolipomas, demonstrating that the 
TSC genes (TSC1 and TSC2) normally function to inhibit mTOR in a conserved signaling 
pathway involved in nutrient uptake, cell growth and protein translation.  Rapamycin has a 
similar function and may be able to replace the signaling defect that occurs in TSC and LAM due 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
2
to mutations in the TSC1 or TSC2 gene [1-6].  There is also data in rat and mouse models for 
TSC kidney disease that rapamycin and analogs can normalize the abnormal mTOR signaling 
and decrease severity of kidney tumors.  These data suggest that rapamycin may be a useful 
therapeutic agent for the treatment of TSC lesions such as kidney angiomyolipomas.  
 
RECRUITMENT:   
 
Patients will be recruited from seven TSC specialty clinics in the U.S.  Those who meet 
eligibility criteria for this study will be informed of the study and entered if they wish to 
participate.  Patients will not be directly compensated however they will not be billed for  
medical care related to this study that is not considered standard of care.  We have prepared an 
information sheet that has been IRB approved to use for recruiting participants through the TS 
Alliance newsletters, listservs, e-mail lists, and meetings.  This information may also be mailed 
(or e-mailed) to lists of regional referring physicians at each clinical site. 
 
RESEARCH DESIGN AND METHODS: 
 
This study is a single arm phase II multi-center study and a two-stage design will be 
employed.  Initially 13 patients will be enrolled and if there is at least 1 response among the first 
13 patients, then an additional 63 patients will be enrolled.  Both males and females will be 
included.  Eligibility criteria are:  diagnosis of TSC or LAM, ages 3-65 years old, at least one 
measurable kidney angiomyolipoma larger than 2 cm in diameter, good performance status, 
informed consent, not pregnant or breast feeding, adequate renal, pulmonary and liver function.  
We will exclude individuals with unstable seizures, active infections, coronary artery disease, 
evidence for renal cell cancer and/or impending bleeding from kidney angiomyolipomas.  
Patients who have undergone vascular ablation within six months for kidney angiomyolipomas 
will also be excluded.  Individuals who meet the eligibility criteria and wish to participate will 
undergo baseline evaluation including physical exam, routine baseline blood work and a baseline 
MRI of kidneys.  They will be registered as a participant in this study and then started on 
outpatient treatment with rapamycin.  They will be monitored periodically by physical exam and 
blood work to assess safety of the treatment.  They will undergo kidney MRI evaluation at 16 
weeks, 32 weeks and 52 weeks to assess response of kidney angiomyolipoma(s) to treatment.  
The primary endpoint will be the response of kidney angiomyolipomas to treatment according to 
standard criteria (RECIST criteria, details in section 5.7.2 of protocol, [7]) used for assessing 
response in solid tumors.  Only patients with an overall complete response (CR) or partial 
response (PR) will be considered responders, those with stable disease will not.  The standard of 
care for individuals with angiomyolipomas between 2-5 cm is observation without intervention 
with kidney imaging every 1-3 years [8-10].  At some centers angiomyolipomas larger than 5 cm 
are treated with vascular embolization but this procedure is not widely available.  Patients with 
bleeding kidney angiomyolipomas can be treated with vascular embolization or surgery.  
 
RISKS AND DISCOMFORTS: 
 
Risks of participating in this study include the risks of additional kidney MRI scans 
required for carefully assessing tumor size.  Risks of treatment with rapamycin include elevated 
cholesterol, anemia and thrombocytopenia as well as increased risk of infection.  Participants 
will also undergo additional blood testing and urine sample collection, which is of minimal risk, 
but there is some discomfort associated with blood collection.  There is a risk of disappointment 
if the treatment is not effective or marginally effective. 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
3
 
  
R
E
G
I
S
T
E
R
Rapamycin 
(3-9ng/ml)
K
I
D
N
E
Y
M
R
I
4
M
O
N
T
H
S
CR/PR
Continue
Rapamycin dose
SD/PD
Increase
Rapamycin dose
(9-15 ng/ml)
K
I
D
N
E
Y
M
R
I
8
M
O
N
T
H
S
CR/PR
Continue
Rapamycin dose
SD/PD
Increase
Rapamycin dose
(9-15 ng/ml) 
K
I
D
N
E
Y
M
R
I
12
M
O
N
T
H
S
SECTION 2:  Protocol Schema
CR-Complete Response
PR-Partial Response
SD-Stable Disease
PD-Progression of Disease
 
 
 
 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
4
SECTION 3:  BODY OF PROTOCOL 
 
1.0 
INTRODUCTION 
 
1.1 
Overview 
 
Kidney angiomyolipomas are tumors consisting of blood vessels, smooth muscle cells 
and fat cells.  These tumors are common in patients with tuberous sclerosis (TSC) and are a 
significant cause of morbidity and mortality in children and adults with TSC.  Kidney 
angiomyolipomas occur in approximately 75% of TSC patients over the age of 8 years old [9] 
and there is currently no effective medical therapy for these tumors.  Kidney angiomyolipomas 
often grow and can cause pain, bleeding and/or renal failure.  Although surgical resection or 
vascular embolization is often recommended when kidney angiomyolipomas are large (>5cm) or 
symptomatic, these treatments are not optimal because they are invasive and can contribute to 
further impairment of renal function in patients who may:  1) have other kidney 
angiomyolipomas; 2) have renal cysts (these occur in 30% of TSC patients); 3) develop 
angiomyolipomas or renal cysts in the future.  The standard of care is to observe kidney 
angiomyolipomas with imaging every 1-3 years and if there is evidence of rapid growth, 
suspicion of renal cell cancer, symptoms such as pain or bleeding, or evidence of impending 
bleed, surgical removal or vascular embolization is recommended [8, 9, 11, 12].  Among 
clinicians who care for children and adult patients with TSC, there is general agreement that 
development of medical approaches to treating kidney angiomyolipomas would be useful 
because management of TSC patients with renal disease is often a difficult problem. 
 
  Kidney angiomyolipomas are also common in patients with the related pulmonary 
disorder, lymphangioleiomyomatosis (LAM), occurring in 50% of LAM patients [13].  LAM is 
characterized by the proliferation of smooth muscle cells in the lungs.   TSC gene mutations have 
been found in the lungs and kidney angiomyolipomas of LAM patients so the molecular defect in 
mTOR signaling in LAM is similar to that observed in TSC related tumors (see section 1.3) [2, 
14, 15].  Pulmonary LAM is a progressive disorder that leads to end-stage lung disease and the 
only effective treatment is lung transplantation, so there is a significant need for effective 
systemic therapy for this disease.   
 
1.2  
Review of morbidity and mortality associated with kidney angiomyolipomas. 
Kidney angiomyolipomas cause significant morbidity and mortality in TSC patients. 
Although these are generally slow growing tumors, they can cause bleeding, pain and renal 
failure.  The risk of hemorrhage is a particularly difficult problem because, although this can 
often be successfully managed using either nephron sparing surgery or vascular embolization, 
there are also reports of shock, death or need for nephrectomy in the setting of bleeding kidney 
angiomyolipomas [10, 16-24].  There is evidence that kidney angiomyolipomas and other renal 
manifestations of TSC are an important cause of mortality in TSC patients.  Shepherd  et al. 
(1991) investigated the causes of death in a group of 355 TSC patients seen at least once at the 
Mayo Clinic.  In this group there were 40 deaths attributable to TSC.  Of these, kidney pathology 
(renal failure, bleeding kidney angiomyolipoma, or renal cell carcinoma) was the cause of death 
in 31% (11/40) of all patients and in 35% of adult patients >19 years old [25].   This study also 
showed a decreased life expectancy in the TSC population compared to the normal population.   
Two recent studies of kidney angiomyolipomas in cohorts of TSC patients showed that 
that most kidney angiomyolipomas grow and there was no evidence of spontaneous regression.  
In a prospective study of kidney lesions in 60 children with TSC ages 1-18, kidney 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
5
angiomyolipomas occurred in 75% of cases.  Growth of kidney angiomyolipomas was common 
and occurred in 47% of cases (median follow-up was 10.5 years).  Spontaneous regression was 
not observed [9].  In a retrospective review of renal imaging (using ultrasound, CT, or MRI) on 
59 TSC patients (ages 3 days to 36 yrs, mean age 11.4 years), kidney angiomyolipomas occurred 
in 80% and renal cysts occurred in 47% of patients.  In this study, there were a total of 80 follow-
up renal imaging studies.  This included 18 studies with no angiomyolipomas, 30 with 
unchanged kidney angiomyolipomas, and 32 with angiomyolipomas that increased in size and/or 
number.  Of these, there was an increase in both size and number of kidney angiomyolipomas in 
28/32, and increase in size only in 1/32, and and increase in number in 3/32.   No cases of 
spontaneous regression were reported [15].  Observations on tumor growth and lack of tumor 
regression were consistent between these two studies.  
There are three recent reviews in the urology and nephrology literature that summarize 
additional clinical features associated with kidney angiomyolipomas.  Nelson et al. (2002) 
reviewed the surgical literature from 1986-2001 to summarize clinical findings from 336 cases of 
kidney angiomyolipomas.  Of this group, 19% had TSC and 59% were symptomatic.  Patients 
with TSC were younger, more likely to have multiple tumors, and more likely to hemorrhage 
than patients with sporadic kidney angiomyolipomas.  This review also included a summary of 
76 patients who underwent embolization for treatment of angiomyolipomas.  Of these 76, 17% 
had recurrent hemorrhage, 14% required repeat embolization, and 16% underwent surgery [16].  
Lendvay and Marshall (2003) reviewed clinical manifestations of TSC reported in 75 articles on 
TSC identified using Medline to search “ tuberous sclerosis”.  They report that renal pathology is 
significant and includes kidney angiomyolipomas, renal cysts, renal cell carcinoma, oncocytoma, 
perirenal cysts, and polycystic kidney disease.  Renal disease is the primary cause of TSC related 
death in patients older than 30 years and kidney angiomyolipomas are the most common renal 
manifestation of TSC.  Two-thirds of angiomyolipomas grow over time and 60% are 
asymptomatic.  Morbidity of hemorrhage from kidney angiomyolipomas is significant as 
symptoms of shock were observed in 10-20%  of cases in some reports [10].  In a review by two 
nephrologists with an interest in TSC kidney disease, Bissler and Kingswood (2004) estimate 
that there are 10 million people world wide with kidney angiomyolipomas and an estimated 1 
million of these also have TSC.  They note that although the disease can be benign, it can also be 
associated with life-threatening hemorrhage.  Estimates of the risk of hemorrhage are variable 
with 3%, 8-18%, 25-50% reported in the literature.  Bleeding risk is associated with large size 
(>4-5 cm) and/or aneurysm formation.  Renal failure can occur and about 1% of TSC patients 
develop end-stage renal disease [12, 26, 27].  Regarding management, these authors comment 
that in the case of pain, hemorrhage or suspicion of malignancy, nephron sparing surgery is a 
useful treatment.  This is preferred over nephrectomy because angiomyolipomas are usually 
benign and renal function should be maximized.  Unfortunately, even nephron sparing surgery is 
associated with hemorrhage requiring nephrectomy and loss of some adjacent normal kidney.  
Embolization is also useful in cases of symptoms from a single identifiable angiomyolipoma.  A 
common complication of embolization is post embolization syndrome (PES) resulting in fever 
and/or pain after the procedure.  Although PES can be significant, this complication may be 
reduced by treating with a course of prednisone [11].  Embolization is less useful for more 
diffuse disease, treating multiple lesions, or in cases where it is difficult to identify the source of 
bleeding.  Because of the invasive nature of these treatment options, the current recommendation 
for asymptomatic angiomyolipomas that are <5cm is to observe without treatment.   

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
6
There are several key reasons why effective therapy for kidney angiomyolipomas would 
be beneficial:  1)  Kidney angiomyolipomas are common in TSC and LAM.  Patients often have 
multiple and/or bilateral tumors; 2) Although many are asymptomatic, many tumors grow, 
patients are at risk for developing new angiomyolipomas, and there is a risk for bleeding and/or 
renal impairment;  3)  Hemorrhage from kidney angiomyolipomas is problematic because 
bleeding is unpredictable and can be life threatening; 4)  Although there are invasive treatment 
options such as nephron sparing surgery, nephrectomy and vascular embolization for kidney 
angiomyolipomas in specific clinical situations, all of these have risks of complications.  In 
addition, because they are local therapies, they only treat target angiomyolipomas; 5) Treatment 
is not currently recommended for small and asymptomatic lesions because partial nephrectomy 
and embolization are invasive and involve some risks.  Furthermore, because these are local 
treatments, these treatment interventions will not prevent the development of new 
angiomyolipomas.   
In TSC patients, it is not possible to predict which angiomyolipomas will grow, form 
aneurysms, hemorrhage, or cause other symptoms.  In addition, patients who develop an acute 
problem away from a tertiary center may not get medical care where nephron sparing partial 
nephrectomy or embolization is available.  LAM patients are eager for systemic therapy because 
of the progressive nature of this disease.  Because TSC mutations have been found in both the 
lungs and kidney angiomyolipomas from LAM patients, effective treatment of kidney 
angiomyolipomas will have significant implications for developing treatments for the devastating 
pulmonary manifestations of LAM.  Given these issues, there is significant interest in the 
development of effective systemic therapy of kidney angiomyolipomas in TSC and LAM 
patients.  If a well-tolerated medical therapy were available that effectively treated this tumor, it 
is likely that both TSC and LAM patients would consider this a desirable treatment option.  It 
would also be an important step towards effective therapy for other manifestations of TSC and 
pulmonary manifestations of LAM.  
 
 
 
1.3 
Background:  preclinical data demonstrate potential efficacy of  rapamycin 
for the treatment of kidney angiomyolipomas 
 
There has been recent progress in the understanding of the molecular defect that occurs in 
TSC lesions such as kidney angiomyolipomas.  The genes for TSC have been identified [28, 29] 
and several recent studies have demonstrated a role for tuberin and hamartin (gene products of 
TSC2 and TSC1 genes respectively) in a highly conserved signal transduction pathway involving 
PI3 kinase, Akt, mTOR and S6 kinase [30, 31].  This has been demonstrated in a variety of 
organisms including humans, rats, mice and drosophila.  This pathway is involved in the 
regulation of nutrient uptake, cell growth and protein translation; a schematic illustration of this 
pathway is illustrated in Figure 1.  The particular abnormality seen in hamartin and/or tuberin 
deficient cells is the hyperphosphorylation of the downstream targets S6 kinase and S6 
(ribosomal subunit).  This suggests that the hamartin/tuberin complex is an inhibitor of mTOR 
and this finding has been confirmed in a variety of organisms in several independent labs [1, 3, 5, 
6, 32, 33]. Because these studies demonstrate that the abnormality in cells lacking tuberin or 
hamartin is the lack of inhibition of mTOR, it is possible that restoring the inhibition of mTOR 
within this pathway could be a useful strategy for treating TSC. 
Rapamycin is an FDA approved immunosuppressive agent that is known to inhibit 
mTOR [34, 35].  Because of this biochemical similarity in the function of rapamycin and the 
tuberin/hamartin complex, there is great interest in investigating the potential therapeutic benefit 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
7
of rapamycin (or other mTOR inhibitors) in TSC related tumors.  There is strong evidence in 
preclinical rodent models of TSC that pharmacologic inhibition of mTOR kinase may be a useful 
anti-tumor approach in TSC.  There is one recent report demonstrating that a short course of 
rapamycin not only leads to normalization of phosphorylated S6, but also stimulates apoptosis 
within kidney tumors in the Eker rat model of TSC [4].  We have also observed that treatment of 
a transgenic mouse model for TSC with a rapamycin analog decreases the severity of kidney and 
liver tumors in these animals and we observed similar results in a nude mouse model for 
Tsc2null tumors [36].  It is important to note that tumors from rodent models for TSC have 
similar abnormalities in mTOR signaling (hyperphosphorylated S6 kinase and S6) as kidney 
angiomyolipomas from TSC patients [37] and lung tissue from LAM patients [2].   Early 
evidence that this targeted therapeutic approach may be effective in patients with LAM and TSC 
is demonstrated by a recent case report in which a 27 year old patient with relapsed LAM in a 
transplanted lung responded to rapamycin that was being used for immunosuppression [38].  In 
addition, there were two cases of partial responses of kidney angiomyolipomas from two 
ongoing single institution trials [39, 40]. 
Because rapamycin is an approved drug, there is significant information on the safety of 
this drug in humans and there is significant practical experience using this drug in the organ 
transplant population  [34, 41-44].  There is now some limited experience using rapamycin in 
TSC and/or LAM patients that shows that it is well tolerated in this population [39, 40]. 
 
RECEP  TOR
PI3K
Akt
mTOR
S6K
S6
4E-BP1
PROTEIN
TRANSLATION
TSC2
TUBERIN
GAP
Rheb-GDP
Rheb-GTP
TSC1 and TSC2 are normal 
Rheb-GDP form is favored 
mTOR kinase activity is low
Downstream targets are not phosphorylated
TSC1
HAMARTIN
A
RECEP  TOR
PI3K
Akt
mTOR
S6K
S6
4E-BP1
PROTEIN
TRANSLATION
TSC2
TUBERIN
GAP
Rheb-GDP
Rheb-GTP
TSC1 or TSC2 is defective  
Rheb-GTP form is favored 
mTOR kinase activity is high
Downstream targets are highly phosphorylated
TSC1
HAMARTIN
B
P
P
P
RECEP  TOR
PI3K
Akt
mTOR
S6K
S6
4E-BP1
PROTEIN
TRANSLATION
TSC2
TUBERIN
GAP
Rheb-GDP
Rheb-GTP
TSC1 or TSC2 is defective  
Rheb-GTP form is favored 
Inhibitor keeps mTOR kinase activity low
Downstream targets are not phosphorylated
TSC1
HAMARTIN
C
CCI-779 or
RAPAMYCIN
 
 
 
Figure 1.  Schematic diagram of the mTOR signaling pathway.  A, When hamartin (TSC1 gene 
product)  and tuberin (TSC2 gene product) are normal, they form a complex, TSC2 functions as 
a GAP for Rheb favoring the Rheb-GDP form, and mTOR kinase activity is low.  B, When 
TSC1 or TSC2 is defective, the Rheb-GTP form is favored, mTOR kinase activity is high, and 
abnormal hyperphosphorylated downstream targets can be detected (such as pS6k, pS6, p4E-
BP1). C,  Disregulated mTOR signaling is normalized in the presence of mTOR kinase inhibitors 
(CCI-779 or rapamycin).   
 
 
2.0 
OBJECTIVES 
 
2.1: 
Determine the efficacy of rapamycin for the treatment of kidney 
angiomyolipomas in patients with tuberous sclerosis (TSC) or lymphangioleiomyomatosis 
(LAM) in a multicenter phase II trial. 
 
2.2: 
Determine the toxicity of using rapamycin in this patient population. 
 
2.3: 
Collect data on long term follow up of kidney angiomyolipomas for 12 months 
after treatment on this study is discontinued. 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
8
 
2.4: 
Observe changes that occur to other TSC lesions (tubers, subependymal giant cell 
astrocytomas, facial angiofibromas, kidney cysts) and pulmonary disease in LAM patients.  
Changes in renal and pulmonary function will also be monitored.  These observations will 
provide data for future clinical trials for this patient population.   
2.5:  
Collect blood DNA, serum and urine samples periodically during this study for 
genotype analysis and biomarker studies. 
 
 
3.0 
ELIGIBILITY 
 
3.1 
Eligibility Criteria 
3.1.1    Age 3-65 years old (females of reproductive age must not be pregnant or breast-
feeding)  
3.1.2        Kidney ANGIOMYOLIPOMA 2 cm or greater on baseline MRI (a CT scan 
may be used for patients who cannot undergo MRI imaging)  
 
3.1.3        No evidence of severe LAM (not on continuous oxygen)  
3.1.4      Informed consent, including consent for submission of blood, urine and tissue  
samples as described in the appendix.   
 
3.1.5        Adequate renal and liver function (eGFR of 30 or higher, SGOT, SGPT, TBili, 
Alk Phos all<2x normal) 
 
3.1.6        HCT>27% 
3.1.7 
ANC > 1500 and platelet count >100,000   
3.1.8   Diagnosis of TSC or LAM (diagnosis of TSC using revised diagnostic criteria 
[45], diagnosis of LAM made by chest CT scan and reviewed by a pulmonologist). 
3.1.9  Fertility/Reproductive issues:  The effects of rapamycin on the developing fetus at 
the doses used in this study are unknown.  For this reason, rapamycin should not be taken 
during pregnancy.  Participants who are fertile must maintain adequate contraception 
while they are taking rapamycin and for twelve weeks after stopping the drug. Acceptable 
contraceptive measures include prior hysterectomy, oophorectomy or tubal ligation, 
complete abstinence, barrier methods which include both a cervical diaphram and 
spermicidal jelly, and progestin based contraceptives. Pregnancy tests will be obtained at 
enrollment and during study visits at 8 weeks, 16 weeks, 24 weeks, 32 weeks, 40 weeks, 
and 52 weeks.  
 
 
Note: Eligibility requirement of ECOG PS of 0 or 1 has been removed to allow 
participation of those subjects with TSC who are classified as ECOG PS of 2,3, or 4 
because of cognitive impairment rather than progressive disease. This change allows site 
PI's to individualize decision making on whether or not to enroll such subjects after 
discussing details of the study with prospective participant and legal guardian. The 
decision to enroll individuals with ECOG PS of 2,3, or 4 will be at the discretion of the 
Principal Investigator.  
 
3.2 
Exclusion criteria 
 
3.2.1       Unstable seizures (defined as changes in anti-epileptics OR increase in 
frequency and/or severity or seizures in the 60 days prior to study entry) 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
9
 
3.2.3       Significant bleed associated with kidney angiomyolipoma(s) (defined as bleed 
associated with shock OR requiring a blood transfusion in the 30 days prior to study entry)  
 
3.2.3       Severe LAM (defined as dependent on continuous supplemental oxygen) 
 
3.2.4       Evidence for accelerating renal dysfunction or acute renal failure  
 
3.2.5       Diagnosis of Renal Cell Cancer that has not been treated (additional 
clarification:  individuals with a prior history of renal cancer who have had appropriate surgery 
and have no evidence of metastatic disease can be enrolled) 3.2.6       Active infection 
3.2.7       Patients will be excluded if they have been treated with any investigational  
   agent in the 30 days prior to study entry 
3.2.8    Patients may not be treated with other investigational agents while on study 
 
3.2.9    Prior history of coronary artery disease 
3.2.10 
Vascular embolization for treatment of kidney angiomyolipoma(s) within 6 
months 
3.2.11 
Patients who must take diltiazem, ketoconazole or rifampin chronically will be 
excluded because of known drug interactions.  Both diltiazem and ketoconazole 
are strong inhibitors of CYP3A4 and are known to increase rapamycin levels.  
Rifampin is a known CYP3A4 and P-glycoprotein inducer and is known to 
significantly reduce rapamycin levels.     
 
 
4.0 
PATIENT ENTRY 
 
At the time of enrollment, patients will be registered by contacting the DFCI Quality 
Assurance Center for Clinical Trials (QACT) at 454 Brookline Ave in Boston (phone-617-632-
3761, fax-617-632-2295) during business hours Monday-Friday before treatment begins.  The 
QACT will ask for the following information:   
-Name, telephone and pager number of investigator or study coordinator registering patient. 
-Protocol name and number 
-Date treatment begins 
-Patient ID name, address, date of birth, Social Security number, and diagnosis 
-Patient ID number 
-Treating physician and institution 
-Confirmation of eligibility 
-Copies of Consent Form signature pages (separate consent forms for treatment and specimen 
collection) 
-Verify that treatment and specimen collection Consent Forms are signed 
 
 
 
5.0 
TREATMENT PROGRAM 
 
5.1  Introduction 
 
This protocol is a single arm phase II efficacy study with a two-stage design.  All patients 
will receive rapamycin.  This study is designed to determine the response rate of kidney 
angiomyolipomas to rapamycin.  We have selected a two-stage design because although the in 
vitro and animal model data is very promising and is a targeted therapy based on the molecular 
defect, there is no published data on using this drug in TSC and/or LAM patients.  Although 
there is one case report in a LAM patient of response with no significant toxicity [38], the two 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
10
stage design allows us to enroll 13 patients initially.  If there is evidence for response and no 
severe toxicity, an additional 22 patients will be enrolled. 
   
 
5.2  Prerequisites 
 
 
5.2.1 Timing - All pretreatment baseline blood tests will be performed within 
 
60 days of initiating treatment on this protocol.  The baseline kidney MRI imaging  
 
 
documenting measurable disease will be performed within 30 days of initiating  
 
 
treatment. 
    
 
 
5.2.2 Lab Parameters –  
 
 
Stable renal function (with eGFR 30 or higher), no evidence of acute renal failure 
 
 
Adequate liver function (SGOT, SGPT, TBili, Alk Phos all<2x normal 
 
 
ANC > 1500 and platelet count >100,000 
 
 
HCT>27% 
 
5.2.3   Pretreatment diagnostic Tests-Baseline kidney MRI according to protocol 
methods documenting at least 1 kidney angiomyolipoma >2cm and measuring all 
lesions according to protocol methods. 
 
 
 
5.2.4 Baseline lab work and other tests- (all should be completed within 60 days 
of initiating  
 
 
treatment) 
 
 
Fasting cholesterol profile 
 
 
Triglycerides 
 
 
Chest X-Ray 
 
 
Urine Analysis 
 
 
Urine B-HCG (in fertile females) 
 
 
Pulmonary Function Testing in females 18 years and older 
 
 
High-resolution chest CT in females 18 years and older 
 
 
Brain MRI 
 
 
EKG 
 
 
EEG on all patients with abnormal brain scans, history of seizures, or on anti- 
 
 
 
 
epileptic medication 
 
 
 
5.2.5   Pretreatment Research lab work  
 
 
Blood sample (10 cc) for DNA extraction 
 
 
Blood sample (10 cc) for serum analysis of biomarkers 
 
 
Urine sample (10 cc) for DNA extraction 
 
 
Urine sample (10 cc) for analysis of biomarkers 
See protocol section 7.2 for additional details on collection and processing of 
blood and urine samples for correlative research studies. 
 
 
 
5.2.6   History and Physical exam 
 
 
Document skin exam (including grade of facial angiofibromas) 
 
 
Detailed neurologic exam 
 
 
 
5.3  Additional Requirements 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
11
5.3.1  Rapamycin levels will be checked for monitoring purposes periodically 
during the 12-month treatment period.  Details on timing of rapamycin level 
monitoring can be found in protocol sections 5.5 and 7.0.  If the rapamycin dose is 
adjusted or changes are made in medications that are CYP3A4 inhibitors or 
inducers (see protocol appendix), rapamycin levels will be checked 7-14 days 
after each change until an appropriate trough level is achieved.   Rapamycin levels 
will either be sent to the reference lab at Children’s Hospital (Boston, MA) or 
locally if available at the site PI’s institution or a local Quest Diagnostics lab. 
Additional details regarding logistics of rapamycin monitoring can be found in 
section 7.1.     
 
5.3.2 Fasting cholesterol and triglyceride profile (week 1, then every 8-12 
weeks until rapamycin discontinued (see section 7.0).  Treatment with dietary 
modification and a lipid lowering agent will be considered for LDL > 200. 
 
5.3.3 CBC and chemistry 12 panel for toxicity monitoring (1 week, 2 weeks,  
then every 8-12 weeks until rapamycin discontinued.  Chemistry 12 panel 
includes electrolytes, BUN/creatinine, bilirubin (total and direct), SGOT, SGPT.  
Urine analysis for toxicity monitoring will be done every 8-12 weeks.  Urine B-
HCG will be done in females of reproductive potential every 8-12 weeks until 
rapamycin is discontinued.  See section 7.0 for schedule of tests in table format. 
 
 
 
5.3.4 Kidney MRI at 16 weeks, 32 weeks and 52 weeks during treatment.  For  
 
 
long term follow up, kidney MRIs will also be obtained  at 18 months and 24  
months.  
 
5.3.5 Skin and General Neurologic exam will be documented at 16 weeks, 32 
weeks, 52 weeks, 18 months and 24 months. 
 
 
 
5.3.6 If clinically indicated, follow up brain MRI will be obtained at 12 months   
 
 
 
5.3.7 If baseline PFTs or high resolution chest CT are abnormal at the start of  
 
 
treatment, they will be obtained again at 12 months or if clinically indicated. 
 
 
5.3.8 Research blood work (10 cc) will be obtained at 16 weeks, 32 weeks, and  
52 weeks for serum biomarker studies.  
 
5.3.9 Research Urine samples will also be obtained at 16 weeks, 32 weeks, and  
52 weeks for biomarker studies.  
 
 
 
 
5.4 Drug Formulation and Procurement  
5.4.1-Rapamycin (Sirolimus, Rapamune) 
      Mode of action: Rapamycin is a macrocylic lactone produced by Streptomyces 
hygroscopicus. It is an immunosuppressive agent. It inhibits T lymphocyte activation 
and proliferation that occurs in response to antigenic and cytokine (Interleukins 2,4, 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
12
and 15) stimulation by a mechanism that is distinct from that of the other 
immunosuppressants. Rapamycin  also inhibits the activation of mTOR (mammalian 
Target of Rapamycin), a key regulatory kinase. 
How supplied: Rapamycin is available as a white, triangular-shaped tablet containing 
1 mg per tablet, as a yellow/beige triangular-shaped tablet containing 2 mg per tablet, 
and also as an oral solution containing 1mg/ml. 
Preparation and Administration: See section 5.5.1 
Storage and Stability: Tablets-protect from light and store at controlled room 
temperature (20ºC to 25ºC). 
Oral Solution-protect from light and refrigerate at 2ºC-8ºC. Once the bottle is 
opened, the contents should be used within one month. 
Route of adminstration:  oral 
Availability:  Rapamycin (sirolimus) is commercially available (Wyeth 
Pharmaceuticals) and will be stored according to the manufacturers recommendation.  
The overall PI will seek a free supply of sirolimus for this study  
 
 
Treatment with  rapamycin will be administered on an outpatient basis.  Although there is 
more than minimal risk in this study, there are substantial preclinical data suggesting a potential 
benefit.  Because rapamycin is an approved drug, there is substantial safety data from completed 
phase I-III trials and the overall experience is that rapamycin is well tolerated by most patients.   
Expected adverse events and dose modification are described in Section 6.   
 
 
5.5  Drug Administration 
 
 
 
This study uses rapamycin, which is commercially available and will be  
 
administered according to standard guidelines and instructions found in the package 
 
inserts with modifications according to recent studies in the organ transplant population.   
Patients will be started on the tablet form.  The oral suspension will be available to 
patients who are unable to tolerate the tablet form.  An updated Rapamune package insert 
is in the protocol appendix.    
  
5.5.1 In adults and children who are 13 years of age and older and weigh at least 
40 kilograms, rapamycin treatment will be initiated with a loading dose of 
6 mg PO on the day that the patient is enrolled followed by a dose of 2 mg 
PO QD.  Dosing will be adjusted to maintain a target level of 3-9 ng/ml.  
This is the FDA approved dose for adults and children 13 years of age and 
older weighing 40 kilograms or more.  Dosing adjustments will be made 
as described in section 5.6.2.  Patients will be maintained at a trough level 
of 3-9 ng/ml for the first 16 weeks of the study.  Rapamycin levels will be 
checked weekly until a stable target trough level is achieved.  Rapamycin 
levels will also be checked at 8 weeks and 16 weeks.  See section 7.0 for 
schedule of rapamycin level monitoring and protocol section 7.1 for 
details regarding the logistics of rapamycin level monitoring. 
5.5.2 In children younger than 13 years of age or weighing less than 40 
kilograms, treatment will be initiated with a loading dose of 3mg/m2 PO 
on the day the patient is enrolled followed by a dose of 1.5mg/m2/day PO 
(rounding up to the nearest milligram) [46]   

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
13
 
5.5.3 The dose of rapamycin will be increased to a target level of 9-15 ng/ml 
after 16 weeks unless there is evidence for a PR or CR by kidney MRI.  
This will be done by increasing the dose by 25-100% increments until a 
stable trough level of 9-15 ng/ml is achieved.  Rapamycin levels will be 
checked every 1-3 weeks (7-14 days after each dose change) until the 
higher target trough level is achieved.  The rapamycin dose will not be 
increased in patients with a PR or CR at 16 weeks.  In these patients, 
rapamycin levels will be maintained at the lower target level of 3-9 ng/ml 
for weeks 16-52 of the study.  Rapamycin levels will be checked every 8-
12 weeks (at 24 weeks, 32 weeks, 40 weeks, and 52 weeks) in all patients 
until the 12-month treatment period has been completed (see section 7.0 
for schedule of rapamycin monitoring and other monitoring details in table 
format). 
 
5.5.4 The dose of rapamycin will be replaced if the patient vomits within 15 
minutes of taking a dose.  Premedication with antiemetics is acceptable if 
there is recurrent vomiting associated with taking rapamycin dose. 
 
5.5.5 A missed dose of rapamycin can be taken up to 12 hours late.  For doses 
up to 6 hours late, no change is needed in the timing of the dose on the 
following day.  If a dose is 6-12 hours late, the dose on the following day 
should be delayed for 3-6 hours.    
 
            5.5.6 Concomitant Therapy with CYP3A4 inhibitors or inducers 
Rapamycin is extensively metabolized by the CYP3A4 isoenzyme, thus drugs 
which are inhibitors or inducers of this enzyme should be avoided if possible or 
used with caution.  The following drugs are contraindicated: diltiazem, 
ketoconazole and rifampin.  Patients who are on these  chronically will be 
excluded because of known drug interactions.  Both diltiazem and ketoconazole 
are strong inhibitors of CYP3A4 and are known to increase rapamycin levels.  
Rifampin is a known CYP3A4 and P-glycoprotein inducer and is known to 
significantly reduce rapamycin levels.  Because grapefruit juice and St. John’s 
wort are CYP3A4 inhibitors, they may increase levels.  Therefore patients will be 
instructed to avoid grapefruit,grapefruit juice, and St. John’s wort during 
rapamycin treatment.  The appendix contains a list of additional drugs that are 
known CYP3A4 inhibitors or inducers.  These medicines will be used with 
caution.  Since this population often has epilepsy, we will pay particular attention 
to potential interactions with anti-epileptic medications.  Carbamazepine and 
phenobarbital are examples of anti-epileptic agents that are known CYP3A4 
inducers.  Because of known drug interactions, rapamycin will be held in patients 
who require a course of the following macrolide antibiotics:  erythromycin, 
clarithromycin and telithromycin.  
 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
14
5.5.7 Rapamycin is known to impair wound healing.  In patients who require 
surgery,rapamycin treatment will be held for 7-14 days prior to elective surgery 
and for 14 days after surgery.   
 
 
 
5.5.8  If patients miss more than 10 consecutiverapamycin doses because of 
surgery or treatment with macrolide antibiotics (erythromycin, clarithromycin and 
telithromycin), additional days of rapamycin treatment will be added so total 
duration of rapamycin treatment is 12 months (365 days).  If this occurs, the date 
of the week 52 visit will be adjusted according to number of missed doses.  The 
18 month and 24 month follow up dates will be based on the revised week 52 visit 
date. 
 
 
 
5.6  Adverse Events 
 
 
5.6.1  Anticipated Toxicities and Management 
5.6.1.1 Rapamycin 
 
Phase III clinical trials in organ transplant patients indicate that the 
primary toxicities are hypertriglyceridemia, hypercholesterolemia, 
thrombocytopenia, anemia, and leukopenia.  Other toxicities include 
hypokalemia, arthralgia, epistaxis, edema, and infections.     
Similar to other immunosuppresant agents, rapamycin may increase the 
risk of opportunistic infections and lymphoproliferative disorders but these 
toxicities have been seen in the transplant population that generally is 
treated with other immunosuppresant agents together with rapamycin.  
There have been also several rare cases of pneumonitis reported that could 
be related to rapamycin treatment.  As stated above in section 5.5.3, 
rapamycin is metabolized by CYP3A4 so other drugs that are CYP3A4 
inducers or inhibitors may affect rapamycin blood levels.  There is now 
preliminary data in TSC and LAM patients demonstrating that rapamycin 
is well tolerated.  The most common toxicities observed so far in TSC and 
LAM patients are mouth ulcers (in 7/27 patients) and 
hypercholesterolemia (in 4/27 patients) [39]. 
 
 
 
5.6.2  Dose Modifications 
 
 
 
5.6.2.1  Rapamycin 
The dose of rapamycin will be held and reduced if the trough level 
exceeds 15 ng/ml at any dose level.  For patients with rapamycin trough 
levels higher than the target range, the dose will be reduced according to 
trough level as follows: 
9-15 ng/ml   
Reduce dose by 25-50% 
 
 
16-24 ng/ml 
Hold dose for 24 hours then resume at 50% of prior dose 
 
 
25-33 ng/ml  Hold dose for 48 hours then resume at 25% of prior dose 
 
 
over 33 ng/ml Hold dose for 72 hours then resume at 10% of prior dose 
 
 
 
 
 
 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
15
 
 
If trough levels are low at the 2 mg PO QD dose, the dose will  
 
 
 
be increased by 25-100% increments until the target dose level is  
achieved.    
 
 
 
5.7  Therapy Duration 
 
5.7.1  Objective responses- Patients will be evaluated for response to 
therapy at 16 weeks, 32 weeks and 52 weeks.  Response criteria will be 
determined based on the standardized criteria used to assess response of solid 
tumors treatment (RECIST criteria; see protocol appendix or 
http:/cancer.gov/bip/RECIST.htm) [7] and applied to this protocol as summarized 
below.  Only those patients with an overall complete or partial response will be 
considered a responder. 
 
Measurable disease - the presence of at least one measurable lesion.  
 
Measurable lesions - lesions that can be accurately measured in at least 
one dimension with longest diameter >20 mm using conventional techniques. 
 
Non-measurable lesions - all other lesions, including small lesions 
(longest diameter <20 mm). 
* 
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 4 weeks before the 
beginning of the treatment.  
* 
The same method of assessment and the same technique should be 
used to characterize each identified and reported lesion at baseline and during 
follow-up.  
 
Baseline documentation of “Target” and “Non-Target” lesions 
* 
All measurable lesions up to a maximum of five lesions per kidney 
and 10 lesions in total, 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. 
* 
All other lesions should be identified as non-target lesions and 
should also be recorded at baseline. Measurements of these lesions are not 
required, but the presence or absence of each should be noted throughout follow-
up.  
 
 
5.7.2  Response Criteria 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
16
  
 
 
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 LD of 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 
  
 
 
Evaluation of non-target lesions 
* Complete Response (CR):  Disappearance of all non-target lesions  
* 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 (1)  
 
 
 
 
 
Overall response (from Therasse et al., 2000)  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
5.7.3   
Therapy Duration- In the original version of this protocol, we planned to treat all  
 
subjects with rapamycin for 12 months and then follow them off therapy during months 
 
12-24.   
 
 
However, based on recent published data (Bissler et al., 2008) and our own 
 
observations, we know there is a high frequency of kidney angiomyolipoma regrowth 
 
after rapamycin is discontinued, so we are amending the protocol to allow re-treatment 
 
after completing the first 12 months of rapamycin.  Bissler and colleagues reported 13/18 
 
had tumor regrowth after discontinuation of rapamycin (Bissler et al., 2008).  As of 
 
12/2008, we have observed tumor regrowth at 18 months in 9/12 subjects.  We anticipate 
 
that approximately 12 subjects will be candidates for additional rapamycin treatment.  
Target lesions 
Nontarget lesions 
New lesions 
Overall Response 
CR 
CR 
No 
CR 
CR 
Incomplete response/SD 
No 
PR 
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 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
17
 
Additional treatment can be offered from 12-24 months to subjects who reach the 18 
 
month time point in October 2008 or later.  Any additional treatment after 12 months will 
 
be considered optional.  The final decision regarding offering additional rapamycin 
 
treatment will be made by the site PI after a careful consideration of the potential benefits 
 
and risks of additional treatment.  All subjects who are treated after month 12 will be re-
 
consented.  The target trough rapamycin level will be 3-15ng/ml.  The site PI will be 
 
responsible for drug level and toxicity monitoring.  The site PI will notify Dr. Sandra 
 
Dabora regarding duration of treatment, dose, and drug levels from months 12-24.  
 
Wyeth has agreed to provide rapamycin at no cost for this additional treatment.  This 
 
change will not affect the primary endpoints (response & toxicity at 1 year) or most of the 
 
secondary endpoints.  Because this affects only a subset of participants, we plan to 
 
describe the details of this subset when second year results are published but will not be 
 
adding or changing any statistical analyses.  This change will allow us to collect 
 
important pilot data on tumor regression and tolerability with a longer duration of 
 
treatment.   
 
 
Treatment will be stopped early if unacceptable toxicity develops or if the patient 
 
requests to withdraw from the study. 
 
 
 
 
6.0 
ADVERSE EVENT REPORTING 
 
According to FDA and institutional criteria, serious adverse events will be reported for all 
side effects that are both serious (life-threatening or fatal) and unexpected.  These events will be 
reported by phone within 24 hours to the overall PI and the members of the Data and Safety  
Monitoring Committee.  The overall PI will immediately notify all co-investigators and clinical 
site principal investigators of such events.  A written report of such events will follow within 10 
working days.  All such events will be reported to the DFCI Human Protection Committee by the 
overall PI.  The conduct of the study will comply with all FDA safety reporting requirements and 
the safety reporting requirements of all participating institutions.  

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
18
 
7.0  REQUIRED DATA  
 
 
On study wk1
wk 2-
4 
wk 8
wk 16
wk 17-
19 
wk 24 wk 32  wk 40 wk 52
18 mos 24 mos
  
  
 
  
  
  
 
  
  
  
  
 
 
Informed consent (pt or guardian) 
X 
 
  
  
  
 
  
  
  
  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
History 
X 
 
 
X 
X 
 
X 
X 
X 
X 
X 
X 
Physical Exam 
X 
 
 
 
X 
 
 
X 
 
X 
X 
X 
documentation of skin exam a  
X 
 
 
 
X 
 
 
X 
 
X 
X 
X 
Renal MRI (or CT k size and # angiomyolipomas 
&cysts) 
X 
 
  
  
X 
 
 
X 
 
X 
X 
X 
rapamycin level (trough)b 
  
X 
X c 
X 
X 
X d 
X 
X 
X 
X 
 
 
Chem 12 
X 
X 
X e 
X 
X 
X f 
X 
X 
X 
X 
 
 
CBC 
X 
X 
X e 
X 
X 
X f 
X 
X 
X 
X 
 
 
Fasting cholesterol profile 
X 
X 
 
X 
X 
X 
X 
X 
X 
X 
 
 
Triglycerides 
X 
X 
  
X 
X 
X 
X 
X 
X 
X 
 
 
Baseline EEG g 
X g 
 
 
 
 
 
 
 
 
 
 
 
CXR 
X 
 
  
  
  
 
  
  
  
  
 
 
Urine Analysisl 
X 
 
 
X 
X 
 
X 
X 
X 
X 
X 
X 
Urine B-HCG h 
X 
 
 
X 
X 
 
X 
X 
X 
X 
 
 
high res. Chest CT (females only) 
X 
 
  
  
  
 
  
  
 
X 
  
 
recent brain MRI (within 3 months) 
X 
 
  
  
  
 
  
  
 
X 
  
 
PFTs (females only) 
X 
 
  
  
  
 
  
  
 
X 
  
  
EKG 
X 
 
  
  
  
 
  
  
 
  
  
  
Research Blood for DNA sample i  
X 
 
  
  
 
 
 
 
 
 
 
 
Research Blood for serum-bank j 
X 
 
  
 
X 
 
 
X 
 
X 
 
X 
Research Urine, bankl 
X 
 
  
 
X 
 
 
X 
 
X 
 
X 
Review eligibility checklist 
X 
 
  
  
  
 
  
  
  
  
 
 
 
 
a Including photograph of face for patients with facial angiofibromas 
b If there are changes in medications metabolized by CYP3A4, rapamycin levels will be checked 
weekly until appropriate stable trough level is achieved  
c Rapamycin levels will be checked again every 1-3 weeks until a trough level of 3-9 ng/ml is 
achieved (see additional details in section 7.1).  Levels will be checked 7-14 days after 
each dose change. 
d For patients with SD or PD, rapamycin levels will be checked again every 1-3 weeks as dose is 
adjusted until stable trough level of 9-15 ng/ml is achieved.  Levels will be checked 7-14 
days after each dose change.  
e Chem 12 and CBC every 1-3 weeks as rapamycin dose is adjusted until rapamycin level of 3-9 
ng/ml achieved  
f Chem 12 and CBC every 1-3 weeks as rapamycin dose is adjusted until rapamycin level of 9-15 
ng/ml achieved (for patients with SD or PD at 16 weeks)   
g EEG in patients with a history of seizures or abnormal brain MRI at baseline and during 
rapamycin treatment as clinically indicated 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
19
h Urine B-HCG only in females with reproductive potential 
i For TSC1 and TSC2 mutation analysis and genotype studies (additional details in section 7.2 
and appendix) 
j For  biomarker studies (additional details in section 7.2 and appendix) 
kAlthough MRI is preferred, a CT can be used if unable to obtain MRI 
lBecause it may be difficult to obtain urine specimens for children ages 3-5 years old who are not 
toilet trained, urine analysis and urine for research studies will be considered optional 
 
 
7.0.1  Additional Notes about Required Data: 
Scheduled visit dates will be determined based on the date participants start treatment.  Visits 
occuring within 14 days of scheduled visit dates will be considered acceptable.   
 
Study visits at enrollment, week 16, week 32, week 52, 18 months, 24 months must occur at the 
site PIs institution. 
 
Blood and urine tests at 8 weeks, 24 weeks, 40 weeks, and other times during rapamycin dose 
adjustments can be done at a local Quest Diagnostics lab and results faxed immediately to the 
site PI.  If this is done, there must be phone contact between the patient and the study team so 
toxicity history can be obtained and appropriate lab, rapamycin treatment, and toxicity forms 
submitted to Dr. Sandra Dabora.   
 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
20
 
7.1 
Rapamcyin level monitoring 
Whole blood will be collected in 10 ml EDTA tubes (purple cap).  For sample tracking purposes, 
all blood samples for rapamycin levels will be shipped by express mail to  
Dr. Dabora’s lab: 
 
Attn:  Sandra Dabora, Nancy Lee, Chelsey Woodrum or Alison Nobil 
 
Division of Hematology, Brigham and Women’s Hospital 
 
One Blackfan Circle, CHRB 6th Floor 
 
Boston, MA  02115 
 
Phone: 617-355-9033 or 617-355-9004 
 
Upon arrival, samples will be hand delivered by Sandra Dabora, Nancy Lee, Chelsey Woodrum 
or Alison Nobil to the lab of Dr. Nader Rifai at the following address at Children’s Hospital 
where rapamycin levels will be measured.       
Nader Rifai Ph.D., Lab Director 
Lab Medicine, FA 755 
Children's Hospital Boston 
300 Longwood Ave, 
     
Boston MA 02115 
Phone:  617-355-6733 
All samples arriving at Children’s Hospital prior to 11 AM will be run the same day and those 
arriving after 11AM will be run the next day.  Including time for shipping, the anticipated turn 
around time for rapamycin levels will be within 2 days for samples drawn Monday-Wednesday 
and within 4 days for samples drawn on Thursdays-Fridays.  Results will be reported on the day 
they are available to the clinical site PI by e-mail and fax.  Alternatively, if a rapamycin level test 
is available locally (at site PI institution or local Quest Diagnostics Lab), a rapamycin level test 
may be done locally.  If a rapamycin level is measured locally, the result must be reported to 
Sandra Dabora via fax and email immediately (by the next business day is considered 
acceptable). 
 
 
 
7.2  COLLECTION OF BLOOD, URINE AND TISSUE SAMPLES FOR 
RESEARCH STUDIES   
7.2.1 Genetic and biomarker analyses 
Several blood and urine samples will be collected for correlative genetic and biomarker  
studies.  Tissue samples will be collected only if patients require surgery for a TSC or LAM 
related lesion.  Potential genetic studies on blood, urine and tissue samples may include  
TSC mutation analysis, interferon-gamma (IFN-g) genotyping, genotyping polymorphisms in 
candidate modifier genes, genotyping polymorphisms in genes relevant to drug metabolism.   
Biomarker studies may include the analysis of vascular endothelial growth factor (VEGF) levels 
and other possible secreted biomarkers.  There are additional details regarding statistical issues 
for correlative studies in section 9.3.        

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
21
 
7.2.2 Blood sample collection 
Blood samples for research will be collected at the time of enrollment .  At the time of 
enrollment, two 10 ml tubes of blood will be drawn into EDTA containing tubes.  An additional 
10 ml tube of blood will be collected (also in EDTA containing tubes) four additional times (at 
weeks 16, 32, 52 and at 24 months).  Samples will be shipped by overnight mail to: 
Dr. Sandra Dabora 
Hematology Division 
Brigham and Women’s Hospital 
One Blackfan Circle, CHNRB 6th Floor 
Boston, MA  02115 
 
Plasma will be separated from the cellular components by centrifugation and allocated 
into plastic freezing tubes at clinical sites.  Upon arrival research samples will be catalogued, and 
frozen at –80 °C for biomarker analyses.  DNA will be extracted from the appropriate tube for 
genotype analysis relevant to TSC and LAM, including modifier genes and genes relevant to 
drug metabolism.   
 
7.2.3 Urine sample collection 
Patients will be also be asked to give 5 urine specimens for research studies (at 
enrollment, week 16, week 32, week 52, and at 24 months).  Samples will be shipped by 
overnight mail to Dr. Dabora’s Lab (address above). 
Upon arrival in Dr. Dabora’s lab, urine will be allocated into plastic freezing tubes, 
catalogued, and frozen at –70 °C for VEGF analyses and future studies.   
 
7.2.4 Tissue sample collection 
If surgical resection of any lesions relevant to TSC and/or LAM occurs while patient is 
enrolled, frozen and/or fixed tissue will be obtained for biomarker analyses.  If the lesion is 
sufficiently large, both frozen and fixed tissue will be obtained. 
 
Additional details regarding collection of specimens can be found in the appendix.  
 
 
 8.0 
MODALITY REVIEW 
 
Response to therapy will be measured by kidney MRI imaging.  To ensure consistency in 
tumor measurements from scan to scan in individual patients, kidney MRIs will be reviewed by 
the Dana-Farber radiology department.  Because there will be some delays in getting the central 
review done, all clinical decisions will be made based on the measurements made at the clinical 
site.  Results of measurements from clinical sites and by the central reviewer will be reported.  
The central review will be done in all subjects enrolled in Boston.  Central review at other sites 
will depend on the availability of adequate funding.    
 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
22
 
9.0 
STATISTICAL PLAN 
9.1 Primary Objectives 
The primary endpoint is the proportion of patients exhibiting objective response 
according to RECIST criteria  (see appendix or http:/cancer.gov/bip/RECIST.htm) [7].  For each 
arm, a true but unobserved underlying response rate of 20% would be considered worthy of 
further study, while a response rate of 5% would be considered not promising. 
A two-stage design will be employed.  First, 13 eligible patients will be registered.  If 
there are no responses among the 13 eligible patients, the study will be discontinued and the 
regimen declared unpromising.  If there is at least 1 response among the 13 eligible patients, then 
an additional 22 eligible patients will be enrolled. If 4 or more responses are observed among 35 
total eligible patients on a given arm, the regimen will be considered worthy of further study.  
Alternatively, if 3 or fewer responses are observed, the regimen will be declared unpromising.  A 
study with this design has 51% probability of stopping early if the true response rate is 5%, 8.4% 
probability of declaring the treatment effective at the end of the study if the response rate is 5%, 
and 90% probability of declaring the treatment effective if the response rate is 20%.  If 4 
responses are observed, the 90% exact two-stage binomial confidence interval on the response 
rate will be (4.2, 25.6%). 
As of 1/31/08, six responses have been observed among 21 patients with follow-up 
disease evaluations, which exceeds the success criterion in the study design.  With the 
amendment of 1/31/08, we propose to enroll 40 additional patients.  The purpose of expanding 
accrual is to better define the response rate, given that the success criterion has been met, to 
provide adequate power for correlative endpoints, and to provide a mechanism for collecting 
additional information on adverse events in a clinical trial setting.  The higher response rate 
means that more patients will be needed to form a similarly sized confidence interval on the 
response rate.  Without the amendment patients are likely to be treated off protocol, as there are 
limited clinical trials options in this rare disease.  Given 40 additional patients and assuming 16 
responses, the 90% exact conditional confidence interval on the response rate will be (14.0% - 
33.3%). 
With the changes of amendment 20 submitted to the DFCI IRB in 2/2009, a subset of 12 
out of the first 36 participants are eligible for additional rapamycin treatment between 12 and 24 
months on study.  This will allow collection of response and toxicity data on rapamycin 
treatment extending beyond 12 months.  The analysis of data from this group of participants on 
extended therapy will be exploratory. 
Toxicity is another important endpoint of the study.  NCI Common Toxicity Criteria will 
be used to assess toxicity (see appendix or http://ctep.cancer.gov/reporting/ctc.html).  With 76 
treated patients, the maximum width of the 90% confidence interval on the rate of severe 
toxicities will be no wider than 20%.  The probability of observing at least 1 severe toxicity with 
a true rate of 5% is approximately 98%.  If the true rate of severe toxicity is 1%, the probability 
of observing at least 1 patient with severe (grade 3 or 4 toxicity) is 17.6%. 
Added power for the correlative analysis is described in Section 9.3.  
 
9.2 Secondary objectives - Response of other disease manifestations to  rapamycin 
TSC is a multisystem disorder so there is great interest in determining whether 
manifestations of these diseases other than kidney angiomyolipomas respond to 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
23
rapamycin.  LAM is a progressive pulmonary disorder so we are interested in evaluating 
pulmonary endpoints in these patients.   
 
9.2.1  Neurologic 
To assess neurologic manifestations of TSC, a brain MRI and detailed neurologic 
exam will be obtained at baseline and again at 52 weeks. The neurologic exam will 
include a general assessment of cognitive status.  This assessment will be individualized 
given the range of neuropsychiatric issues in this population. Qualitative changes of brain 
lesions by MRI will be assessed by site PI's.  The proportion of patients with change in 
cognitive status and the proportion with changes in brain lesions will be reported, along 
with a 95% confidence interval. 
 
9.2.2 Skin 
A detailed skin examination will be performed on all patients at baseline and 
again at 52 weeks.  Using the TSC Clinical Features Grading Form (see appendix), 
investigators will assess the status of hypomelanotic macules, shagreen patch, forehead 
plaque, and facial angiofibromas.  Investigators will also photograph facial 
angiomyolipomas and other skin lesions at baseline and again at 52 weeks.  Facial 
angiofibromas will be graded according to Dabora et al (2001) [47]:  
Grade 0:  None 
Grade 1:  macular (flat) lesions 
Grade 2:  papular lesions < 3 mm diameter 
Grade 3:  papular lesions > 3 mm diameter and/or extending below mouth 
 
The grade at baseline and 52 weeks will be tabulated. Changes from baseline to 
best grade post-baseline and from baseline to 52 weeks will be evaluated for each patient.  
The hypothesis of no change will be examined using the Wilcoxon signed rank test. 
 
9.2.3  Renal cysts and renal function 
Renal cysts will be evaluated qualitatively by kidney MRI at baseline, 16 weeks, 
32 weeks, and 52 weeks.  The proportion of patients with improvement by week 52 will 
be reported, along with a 95% confidence interval.  Levels of serum creatinine and BUN 
will be assessed over time at the same intervals.  Based on the observed distribution of 
values, either a linear or non-linear model will be fit for each patient.  If a linear model is 
adequate to provide good fit, the null hypothesis that there is no change over time will be 
tested by evaluating slopes. 
 
9.2.4  Pulmonary 
Because pulmonary disease associated with TSC and LAM affects only women, 
spiral CT and pulmonary function tests will be used in women only to assess the impact 
of rapamycin therapy.  Differences from baseline in FEV1, FVC, and DLCO will be 
examined using the Wilcoxon signed rank test.  The proportion of patients with 
qualitative change in the number or size of pulmonary lesions by spiral CT will be 
reported, along with a 95% confidence interval. 
 
9.3 Secondary objectives - genotype and biomarker analyses 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
24
VEGF levels will be assessed using ELISA at 16 weeks, 32 weeks, and 52 weeks.  
The feasibility of capturing and analyzing this information is the primary endpoint of 
interest.  We will consider this correlative analysis to be feasible if VEGF levels can be 
successfully characterized in at least half of the patients at each time point.  The 
proportion with assessable VEGF levels will be described along with 95% confidence 
intervals. 
Differences in the pattern of change between responders and non-responders will 
also be examined using mixed effects model with a time-by-response interaction term.  
Statistical power will be limited for this analysis and will depend on the proportion of 
patients classified as responders.  As an illustration of statistical power that will exist, we 
consider a simpler model that uses only baseline and 52-week values.  For each patient, a 
change score will be calculated.  The difference in change scores between responders and 
non-responders will be examined using a t-test.  Use of this test assumes that change 
scores are normally distributed.  In a study by Heymach et al., (2004), change in urine 
VEGF from baseline was measured after 2 cycles of chemotherapy among 12 sarcoma 
patients [48]. The mean change was 41.6 pg/ml and the standard deviation of change was 
131.0 in this small sample.  The within-patient correlation between measurements was 
0.56.  Assuming baseline levels of 70 pg/ml and standard deviation of change= 50 pg/ml 
in both groups, 50% response rate (35 responders, 35 non-responders) and an intra-
patient correlation of 0.5, the study will have good power (90%) to detect a difference in 
change between 45 pg/ml in responders and 10 pg/ml in non-responders. 
 
 
9.4  Accrual  
We anticipate that after IRB approval is obtained at all  sites and contracts for 
rapamycin distribution are in place for all 6 sites, the expected accrual rate to the study 
will be 1 - 4 patients per month.  Given this rate, we expect the first 13 patients to be 
enrolled within 3-12 months.  If there is at least one response, we anticipate the accrual of 
the additional 22 patients will occur within months 12-30.  We anticipate that by month 
42, all enrolled patients will have completed the 12-month course of treatment and the 
primary endpoint data will be collected.  We expect accrual of all 35 patients to the study 
to be completed in approximately 2.5 years (30 months).  
Note on accrual: enrollment for cases 1-36 was completed in 4/2008.  There has 
been a delay in accrual of cases 37-76 (per amendment 17) because of a delay in 
obtaining funding for this additional enrollment. 
 
 
10.0 
REFERENCES   
1. 
Gao, X., Y. Zhang, P. Arrazola, O. Hino, T. Kobayashi, R.S. Yeung, B. Ru, and D. Pan. 
Tsc tumour suppressor proteins antagonize amino-acid#150;TOR signalling. Nat Cell 
Biol, 2002. 4(9): p. 699-704. 
2. 
Goncharova, E.A., D.A. Goncharov, A. Eszterhas, D.S. Hunter, M.K. Glassberg, R.S. 
Yeung, C.L. Walker, D. Noonan, D.J. Kwiatkowski, M.M. Chou, R.A. Panettieri, Jr., and 
V.P. Krymskaya. Tuberin regulates p70 S6 kinase activation and ribosomal protein S6 
phosphorylation. A role for the TSC2 tumor suppressor gene in pulmonary 
lymphangioleiomyomatosis (LAM). J Biol Chem, 2002. 277(34): p. 30958-67. 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
25
3. 
Inoki, K., Y. Li, T. Zhu, J. Wu, and K.L. Guan. TSC2 is phosphorylated and inhibited by 
Akt and suppresses mTOR signalling. Nat Cell Biol, 2002. 4(9): p. 648-57. 
4. 
Kenerson, H.L., L.D. Aicher, L.D. True, and R.S. Yeung. Activated Mammalian target of 
rapamycin pathway in the pathogenesis of tuberous sclerosis complex renal tumors. 
Cancer Res, 2002. 62(20): p. 5645-50. 
5. 
Kwiatkowski, D.J., H. Zhang, J.L. Bandura, K.M. Heiberger, M. Glogauer, N. el-
Hashemite, and H. Onda. A mouse model of TSC1 reveals sex-dependent lethality from 
liver hemangiomas, and up-regulation of p70S6 kinase activity in Tsc1 null cells. Hum 
Mol Genet, 2002. 11(5): p. 525-34. 
6. 
Tee, A.R., D.C. Fingar, B.D. Manning, D.J. Kwiatkowski, L.C. Cantley, and J. Blenis. 
Tuberous Sclerosis Complex-1 and 2 gene products function together to inhibit 
mammalian target of Rapamycin- (mTOR) mediated downstream signalling. Proc Natl 
Acad Sci U S A, 2002. 99: p. 13571-6. 
7. 
Therasse, P. New guidelines to evaluate the response to treatment in solid tumors. 
European Organization for Research and Treatment of Cancer, National Cancer Institute 
of the United States, National Cancer Institute of Canada. 2000. 92: p. 205-216. 
8. 
Roach, E.S., F.J. DiMario, R.S. Kandt, and H. Northrup. Tuberous sclerosis consensus 
conference: recommendations for diagnostic evaluation. J Child Neurol, 1999. 14(6): p. 
401-7. 
9. 
Ewalt, D.H., E. Sheffield, S.P. Sparagana, M.R. Delgado, and E.S. Roach. Renal lesion 
growth in children with tuberous sclerosis complex. J Urol, 1998. 160(1): p. 141-5. 
10. 
Lendvay, T.S. and F.F. Marshall. The TS Complex and its highly variable manifestations. 
J. Urol., 2003. 169: p. 1635-1642. 
11. 
Bissler, J.J., J. Racadio, L.F. Donnelly, and N.D. Johnson. Reduction of postembolization 
syndrome after ablation of renal angiomyolipoma. American Journal of Kidney Diseases 
[Online], 2002. 39(5): p. 966-71. 
12. 
Bissler, J.J. and J.C. Kingswood. Renal angiomyolipomata. Kidney Int, 2004. 66(3): p. 
924-34. 
13. 
Sullivan, E.J. Lymphangioleiomyomatosis: a review. Chest, 1998. 114(6): p. 1689-703. 
14. 
Astrinidis, A., L. Khare, T. Carsillo, T. Smolarek, K.S. Au, H. Northrup, and E.P. 
Henske. Mutational analysis of the tuberous sclerosis gene TSC2 in patients with 
pulmonary lymphangioleiomyomatosis. J Med Genet, 2000. 37(1): p. 55-7. 
15. 
Casper, K.A., L.F. Donnelly, B. Chen, and J.J. Bissler. Tuberous sclerosis complex: renal 
imaging findings. Radiology, 2002. 225(2): p. 451-6. 
16. 
Nelson, C.P. and M.G. Sanda. Contemporary diagnosis and management of renal 
angiomyolipoma. J Urol, 2002. 168(4 Pt 1): p. 1315-25. 
17. 
Mouded, I.M., B.M. Tolia, J.E. Bernie, and H.R. Newman. Symptomatic renal 
angiomyolipoma: report of 8 cases, 2 with spontaneous rupture. J Urol, 1978. 119(5): p. 
684-8. 
18. 
Takigawa, H., M. Yano, and S. Kagawa. [Management of hemorrhage secondary to renal 
angiomyolipoma]. Hinyokika Kiyo, 1985. 31(10): p. 1767-71. 
19. 
Martinez-Pecino, M., F. Camacho Ortuno, J.L. Madrid Rondon, E. Sanchez Rodriguez, 
M. Rodriguez Ramos, S. Vazquez Navarrette, J.M. Rodriguez Santamaria, and E. Garcia 
Romero. [Intraperitoneal hemorrhage after labor as manifestation of renal 
angiomyolipoma]. Arch Esp Urol, 1989. 42(1): p. 25-8. 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
26
20. 
Rapp, N., G. Audibert, P.F. Gerbaud, G. Grosdidier, and M.C. Laxenaire. [Spontaneous 
retroperitoneal hematoma: a rare cause of hemorrhagic shock]. Ann Fr Anesth Reanim, 
1994. 13(6): p. 853-6. 
21. 
Lee, J.D., H.C. Chang, S.H. Chu, S. Hsueh, and Y.K. Soong. Massive retroperitoneal 
hemorrhage from spontaneous rupture of a renal angiomyolipoma during pregnancy. A 
case report. J Reprod Med, 1994. 39(6): p. 477-80. 
22. 
Daskalopoulos, G., I. Karyotis, I. Heretis, P. Anezinis, E. Mavromanolakis, and D. 
Delakas. Spontaneous perirenal hemorrhage: a 10-year experience at our institution. Int 
Urol Nephrol, 2004. 36(1): p. 15-9. 
23. 
Shiba, M. and H. Takatera. [Retroperitoneal angiomyolipoma with rapidly progressing 
intracystic hemorrhage and lymph node involvement: a case report]. Hinyokika Kiyo, 
2003. 49(10): p. 611-3. 
24. 
Benjelloun, M., R. Rabii, M.H. Mezzour, A. Joual, S. Bennani, and M. el Mrini. 
[Hemorrhagic bilateral renal angiomyolipoma]. Prog Urol, 2003. 13(4): p. 683-5. 
25. 
Shepherd, C.W., M.R. Gomez, J.T. Lie, and C.S. Crowson. Causes of death in patients 
with tuberous sclerosis. Mayo Clin Proc, 1991. 66(8): p. 792-6. 
26. 
Clarke, A., E. Hancock, C. Kingswood, and J.P. Osborne. End-stage renal failure in 
adults with the tuberous sclerosis complex. Nephrol Dial Transplant, 1999. 14(4): p. 988-
91. 
27. 
Schillinger, F. and R. Montagnac. Chronic renal failure and its treatment in tuberous 
sclerosis. Nephrol Dial Transplant, 1996. 11(3): p. 481-5. 
28. 
Consortium, E.C.T.S. Identification and characterization of the tuberous sclerosis gene on 
chromosome 16. Cell, 1993. 75(7): p. 1305-15. 
29. 
van Slegtenhorst, M., R. de Hoogt, C. Hermans, M. Nellist, B. Janssen, S. Verhoef, D. 
Lindhout, A. van den Ouweland, D. Halley, J. Young, M. Burley, S. Jeremiah, K. 
Woodward, J. Nahmias, M. Fox, R. Ekong, J. Osborne, J. Wolfe, S. Povey, R.G. Snell, 
J.P. Cheadle, A.C. Jones, M. Tachataki, D. Ravine, and D.J. Kwiatkowski. Identification 
of the tuberous sclerosis gene TSC1 on chromosome 9q34. Science, 1997. 277(5327): p. 
805-8. 
30. 
Gao, X. and D. Pan. TSC1 and TSC2 tumor suppressors antagonize insulin signaling in 
cell growth. Genes Dev, 2001. 15(11): p. 1383-92. 
31. 
Potter, C.J., H. Huang, and T. Xu. Drosophila Tsc1 functions with Tsc2 to antagonize 
insulin signaling in regulating cell growth, cell proliferation, and organ size. Cell, 2001. 
105(3): p. 357-68. 
32. 
Manning, B.D., A.R. Tee, M.N. Logsdon, J. Blenis, and L.C. Cantley. Identification of 
the tuberous sclerosis complex-2 tumor suppressor gene product tuberin as a target of the 
phosphoinositide 3-kinase/akt pathway. Mol Cell, 2002. 10(1): p. 151-62. 
33. 
Potter, C.J., L.G. Pedraza, and T. Xu. Akt regulates growth by directly phosphorylating 
Tsc2. Nat Cell Biol, 2002. 4(9): p. 658-65. 
34. 
Garber, K. Rapamycin's resurrection: a new way to target the cancer cell cycle. J Natl 
Cancer Inst, 2001. 93(20): p. 1517-9. 
35. 
Hidalgo, M. and E.K. Rowinsky. The rapamycin-sensitive signal transduction pathway as 
a target for cancer therapy. Oncogene, 2000. 19(56): p. 6680-6. 
36. 
Lee, L., P. Sudentas, B. Donohue, K. Asrican, A. Worku, V. Walker, Y. Sun, K. Schmidt, 
M.S. Albert, N. El Hashemite, A.S. Lader, H. Onda, H. Zhang, D.J. Kwiatkowski, and 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
27
S.L. Dabora. Efficacy of a rapamycin anaolog (CCI-779) and IFN-g in tuberous sclerosis 
mouse models. submitted: p. submitted. 
37. 
El-Hashemite, N., H. Zhang, E.P. Henske, and D.J. Kwiatkowski. Mutation in TSC2 and 
activation of mammalian target of rapamycin signalling pathway in renal 
angiomyolipoma. Lancet, 2003. 361(9366): p. 1348-9. 
38. 
Niedermeyer, J. Rapamycin for recurrent LAM following lung transplantation-a first 
experience. Abstract at LAM foundation research conference, April 2003, 2003. 
39. 
Bissler, J., D. Franz, F.X. McCormack, G. Chuck, J. Leonard, L. Young, and J. Elwing. 
Rapamycin therapy of AMLs in patients with TSC and sporadic LAM. p. Unpublished 
data presented at TSC Conference, Cambridge, UK, Sept. 2004. 
40. 
Wienecke, R., I. Fackler, N. Akdeli, U. Linsenmaier, M. Vogeser, K. Mayer, T. Licht, 
and M. Kretzler. Effective treatment of TSC with rapamycin. p. Unpublished data 
presented at TSC Conference, Cambridge, UK, Sept. 2004. 
41. 
Brattstrom, C., J. Sawe, B. Jansson, A. Lonnebo, J. Nordin, J.J. Zimmerman, J.T. Burke, 
and C.G. Groth. Pharmacokinetics and safety of single oral doses of sirolimus 
(rapamycin) in healthy male volunteers. Therapeutic Drug Monitoring, 2000. 22(5): p. 
537-44. 
42. 
MacDonald, A.S. and e. al. A worldwide, phase III, randomized, controlled, safety and 
efficacy study of a sirolimus/cyclosporine regimen for prevention of acute rejection in 
recipients of primary mismatched renal allografts. Transplantation, 2001. 71(2): p. 271-
80. 
43. 
Mahalati, K. and B.D. Kahan. Clinical pharmacokinetics of sirolimus. Clinical 
Pharmacokinetics, 2001. 40(8): p. 573-85. 
44. 
Yatscoff, R.W. Pharmacokinetics of rapamycin. Transplantation Proceedings, 1996. 
28(2): p. 970-3. 
45. 
Roach, E.S., M.R. Gomez, and H. Northrup. Tuberous sclerosis complex consensus 
conference: revised clinical diagnostic criteria. J Child Neurol, 1998. 13(12): p. 624-8. 
46. 
Franz, D.N., J. Leonard, C. Tudor, G. Chuck, M. Care, G. Sethuraman, A. Dinopoulos, 
G. Thomas, and K.R. Crone. Rapamycin causes regression of astrocytomas in tuberous 
sclerosis complex. Ann Neurol, 2006. 59(3): p. 490-8. 
47. 
Dabora, S.L., S. Jozwiak, D.N. Franz, P.S. Roberts, A. Nieto, J. Chung, Y.S. Choy, M.P. 
Reeve, E. Thiele, J.C. Egelhoff, J. Kasprzyk-Obara, D. Domanska-Pakiela, and D.J. 
Kwiatkowski. Mutational Analysis in a Cohort of 224 Tuberous Sclerosis Patients 
Indicates Increased Severity of TSC2, Compared with TSC1, Disease in Multiple Organs. 
Am J Hum Genet, 2001. 68(1): p. 64-80. 
48. 
Heymach, J.V., J. Desai, J. Manola, D.W. Davis, D.J. McConkey, D. Harmon, D.P. Ryan, 
G. Goss, T. Quigley, A.D. Van den Abbeele, S.G. Silverman, S. Connors, J. Folkman, 
C.D. Fletcher, and G.D. Demetri. Phase II study of the antiangiogenic agent SU5416 in 
patients with advanced soft tissue sarcomas. Clin Cancer Res, 2004. 10(17): p. 5732-40. 
 
 
10.1 INTERNET RESOURCES 
RECIST Criteria, http://cancer.gov/bip/RECIST.htm 
 
NCI Common Terminology Criteria for Adverse Events v3.0 (CTCAE), 
http://ctep.cancer.gov/reporting/ctc.html 
 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
28
Statistical power calculation program, http://hedwig.mgh.harvard.edu/sample_size/size.html 
 
 
11.0 
REGULATORY REQUIREMENTS 
11.1  Declaration of Helsinki – The overall principal investigator along with co-
investigators and clinical site principal investigators will ensure that this study is 
conducted in full conformity with the current revision of the Declaration of Helsinki and 
with the US FDA Regulations, whichever affords the greater protection to the patient. 
 
11.2 Informed Consent – In accordance with US FDA Regulations all participating 
clinical site principal investigators will be responsible for obtaining written informed 
consent from the patient or patient’s legally authorized guardian/representative after 
adequate explanation of the aims, methods, anticipated benefits, and potential hazards of 
the study and before any study medications are administered.  The patient (or guardian) 
will be given a copy of the informed consent documentation that is labeled “PATIENT’S 
REFERENCE COPY”. The original signed copy of the informed consent will be retained 
in the Institution’s medical records.   
 
11.3 Patient Confidentiality – All participating investigators will ensure that the patient’s 
anonymity is maintained.    
 
In compliance with US FDA Regulations regarding the monitoring of clinical trials, the 
institute shall permit US FDA representatives to review the portion of the patient’s 
medical record that is directly related to the study.  As part of the required content of 
informed consent, the patient must be informed that his/her records may be reviewed by a 
representative of the US FDA.   
 
 
 
 
12.0 
LIST OF APPENDIX DOCUMENTS 
 
TSC clinical features grading form   
 
 
 
 
 
(Appendix 1) 
 
Cytochrome P450 3A4 substrates, inhibitors and inducers 
(Appendix 2) 
 
Response Evaluation Criteria in Solid Tumors (RECIST) Quick Reference 
(Appendix 3) 
 
NCI Common Terminology Criteria for Adverse Events v3.0 (CTCAE) Quick Reference 
(Appendix 4) 
 
Rapamune Product Information (annotated version, updated on 1/21/04)  
(Appendix 5) 

Protocol # 04-298 
 
 
 
 
                   Principal Investigator:  Sandra L. Dabora 
Rapamycin for treating kidney angiomyolipomas (1/30/09 version) 
 
 
29
 
Collection of blood, urine and tissue specimens from patients with TSC or LAM 
(Appendix 6) 
 
 

 
 
 
 
The TSC Multicenter Clinical Trial is Now Enrolling Study Participants 
 
Adults with TSC who have one or more  
kidney angiomyolipomas are eligible for the study 
 
 
Treatment:  rapamycin (sirolimus) for 12 months 
 
 
We are currently open for enrollment at the following sites: 
Doctor 
 
 
 
Clinical Site 
 
 
 
 
 
        City 
Dr. Elizabeth Thiele  
Mass. General Hospital  
 
 
    Boston 
Dr. Daniel Miles 
 
New York University 
 
 
 
New York 
Dr. David Franz 
 
Cincinnati Children's Hosp.  Med. Ctr. 
Cincinnati 
Dr. Arthur Sagalowsky 
Univ. of Texas, Southwestern  
 
      Dallas 
Dr. Francis DiMario  
Connecticut Children's Med. Ctr.  
           Hartford 
Dr. Peter Crino 
 
UPENN Medical Center  
 
    Philadelphia 
 
 
ADDITIONAL INFORMATION IS ATTACHED (INCLUDING PHONE NUMBERS OF 
PARTICIPATING CLINICS).  IF YOU ARE INTERESTED IN PARTICIPATING, 
PLEASE CONTACT THE CLOSEST SITE. 
 
If you have any questions about this study, please contact Dr. Sandra Dabora (study 
organizer) at sdabora@partners.org or 617-355-9004. 
 
 
 
YOU CAN FIND GENERAL INFORMATION ABOUT CLINICAL TRIALS AT: 
http://www.clinicaltrials.gov   
 
 
 
 
 
 
 
 
 
 

 
 
 
 
Home 
Search 
Listings 
Resources 
Help 
What's New 
About 
Sirolimus in Treating Patients With Angiomyolipoma of the Kidney 
This study is currently recruiting patients. 
Verified by National Cancer Institute (NCI) April 2006 
Sponsors and Collaborators: Dana-Farber Cancer Institute  
National Cancer Institute (NCI) 
Information provided by: National Cancer Institute (NCI) 
ClinicalTrials.gov Identifier: NCT00126672 
 
Purpose  
RATIONALE: Drugs used in chemotherapy, such as sirolimus, work in different ways to stop the growth 
of tumor cells, either by killing the cells or by stopping them from dividing.  
PURPOSE: This phase II trial is studying how well sirolimus works in treating patients with 
angiomyolipoma of the kidney. 
Condition  
Intervention 
Phase 
Angiomyolipoma 
 Drug: sirolimus 
 Procedure: chemotherapy 
 Procedure: enzyme inhibitor therapy 
Phase II 
MedlinePlus related topics:  Cancer;   Cancer Alternative Therapies 
Genetics Home Reference related topics:  Cancer 
Study Type: Interventional 
Study Design: Treatment  
Official Title: Phase II Study of Sirolimus in Patients With Angiomyolipoma of the Kidney Secondary to 
Tuberous Sclerosis or Lymphangioleiomyomatosis 
Further study details as provided by National Cancer Institute (NCI): 
 
Primary Objectives: 
• 
Determine the efficacy of sirolimus, in terms of objective response rate, in patients with 
angiomyolipoma of the kidney secondary to tuberous sclerosis (TSC) or 
lymphangioleiomyomatosis (LAM).  
• 
Determine the toxicity of this drug in these patients.  
 

Secondary Objectives: 
• 
Determine changes in other TSC lesions (e.g., tubers, subependymal giant cell 
astrocytomas, facial angiofibromas, or kidney cysts) in patients with TSC treated with this 
drug.  
• 
Determine changes in pulmonary disease in patients with LAM treated with this drug.  
OUTLINE: This is a multicenter study. 
Patients receive oral sirolimus once daily for 12 months in the absence of unacceptable toxicity. 
After completion of study treatment, patients are followed at 6 months and 1 year. 
PROJECTED ACCRUAL: A total of 13-35 patients will be accrued for this study within 3-30 
months. 
Eligibility  
Ages Eligible for Study:  18 Years   -   65 Years,  Genders Eligible for Study:  Both  
Criteria 
DISEASE CHARACTERISTICS: 
• Diagnosis of angiomyolipoma of the kidney secondary to tuberous sclerosis (TSC) or 
lymphangioleiomyomatosis (LAM) 
• Tumor ≥ 2 cm by MRI NOTE: *Diagnosis of LAM by chest CT scan  
• No angiomyolipoma-related bleeding or impending bleed  
• No evidence of severe LAM, defined as either of the following:  
• Oxygen-dependent disease  
• Poor performance status  
• No suspicion of or known renal cell carcinoma  
PATIENT CHARACTERISTICS: 
• Age 
18 to 65  
• Renal 
Creatinine < 4.1 mg/dL , no evidence of acute renal failure  
 
OTHER: 
• Not pregnant or nursing  
• Negative pregnancy test  
• Fertile patients must use effective barrier contraception  
• No unstable seizures, defined as a recent change in seizure pattern or change in antiepileptic drug 
regimen  
• No active infection  
• More than 30 days since prior investigational agents  
• More than 6 months since prior vascular embolization therapy for treatment of kidney 
angiomyolipomas  
• No concurrent chronic use of diltiazem, ketoconazole, or rifampin  
• No other concurrent investigational agents  
 
 

Location and Contact Information  
Please refer to this study by ClinicalTrials.gov identifier  NCT00126672  
 
Connecticut 
      Connecticut Children's Medical Center, Hartford,  Connecticut,  06106,  United States; Recruiting  
Francis J. DiMario, MD  860-545-9460   
 
Massachusetts 
      Massachusetts General Hospital, Boston,  Massachusetts,  02114,  United States; Recruiting  
Elizabeth Thiele, MD, PhD  617-726-6540   
 
New York 
      New York University Medical Center, New York,  New York,  10016,  United States; Recruiting  
Daniel K. Miles, MD  212-263-8318   
 
Ohio 
      Cincinnati Children's Hospital Medical Center, Cincinnati,  Ohio,  45229-3039,  United 
States; Recruiting  
David Franz, MD  513-636-4222    david.franz@chmcc.org   
 
Pennsylvania 
      University of Pennsylvania Medical Center, Philadelphia,  Pennsylvania,  19104-4283,  United 
States; Recruiting  
Peter Crino, MD, PhD  215-349-5312   
 
Texas 
      University of Texas Southwestern Medical Center at Dallas, Dallas,  Texas,  75390,  United 
States; Recruiting  
Arthur I. Sagalowsky, MD  214-645-8797    arthur.sagalowsky@utsouthwestern.edu   
 
Study chairs or principal investigators  
 
Sandra Dabora, MD, PhD,  Study Chair,  Brigham and Women's Hospital  617-355-9004 
    
More Information  
Clinical trial summary from the National Cancer Institute's PDQ® database 
Study ID Numbers:  CDR0000440080; DFCI-04298; WYETH-C-0468H1-101899 
Last Updated:  May 3, 2006 
Record first received:  August 2, 2005 
ClinicalTrials.gov Identifier:  NCT00126672 
Health Authority: United States: Federal Government 
ClinicalTrials.gov processed this record on 2006-05-24  
 
 
U.S. National Library of Medicine, Contact NLM Customer Service 
National Institutes of Health, Department of Health & Human Services 
Copyright, Privacy, Accessibility, Freedom of Information Act