Exploratory Study Of The ERCC-1 Gene Expression In Colorectal Cancer Cell Lines And In Patients With Colorectal Cancer
Phase: NA
Conditions: Colon Cancer, Rectal Cancer
Sponsor: Albert Einstein College of Medicine

ERCC-1 CRC study 
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EXPLORATORY STUDY OF THE ERCC-1 GENE EXPRESSION IN COLORECTAL 
CANCER CELL LINES AND IN PATIENTS WITH COLORECTAL CANCER 
 
Principal Investigator:  
 
Sanjay Goel, M.D. 
1695 Eastchester Road 
Montefiore Medical Center Bronx, NY 10461 
Phone: 718-405-8404 
Fax: 
718-405-8433 
sgoel@montefiore.org 
 
Co-Investigators:  
 
Andreas Kaubisch, M.D. 
Montefiore Medical Center 
Hofheimer 100 
111 East 210th Street 
Bronx NY 10467 
Phone: 718-920-4826 
Fax: 
718-798-7474 
akaubisc@montefiore.org 
 
 
Jennifer Chuy, M.D. 
Montefiore Medical Center 
1695 Eastchester Road 
Bronx, NY 10461 
Phone: 718-405-8404 
Fax: 
718-405-8433 
 
 
Lakshmi Rajdev, M.D. 
Montefiore Medical Center 
1695 Eastchester Road 
Bronx, NY 10461 
Phone: 718-405-8404 
Fax: 
718-405-8433 
lrajdev@montefiore.org 
 
Karenza Alexis, M.D. 
Department of Oncology 
Jacobi Medical Center 
Building 1, Room 3N201400 Pelham Parkway South 
Bronx, New York 10461 
Phone: 718-918-5753 
Fax: 
718-918-5578 
Karenza.Alexis@nbhn.net 
 
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Study Coordinator 
 
Imran Chaudhary, M.D. 
Montefiore Medical Park 
1695 Eastchester Road, Oncology 
Phone 718-405-8542 
Fax: 718-405-8527 
ichaudha@montefiore.org 
 
 
 
Biostatistics: 
 
Abdissa Negassa, Ph.D. 
Albert Einstein College of Medicine 
Jack and Pearl Resnick Campus 
1300 Morris Park Avenue 
Belfer Building, Room 1303 
Bronx, NY 10461 
Tel: 
718-430-3575 
Email: anegassa@aecom.yu.edu 
 
Participating Institutions 
Montefiore Medical Center, Bronx, NY 
Jacobi Medical Center, Bronx, NY  
Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 
 
 
 
 
Protocol date: March 17, 2014 
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TABLE OF CONTENTS 
 
1.0 
OBJECTIVES ......................................................................................................................4 
2.0 
BACKGROUND AND RATIONALE ................................................................................4 
3.0 
PRELIMINARY DATA ......................................................................................................7 
4.0 
PATIENT ELIGIBILITY CRITERIA……………………………………………… .........9 
5.0 
REGISTRATION PROCEDURE AND DATA SUBMISSION .......................................10 
6.0 
TREATMENT PLAN AND STUDY DESIGN ................................................................10 
7.0 
SUPPORTIVE THERAPY GUIDELINES .......................................................................13 
8.0 
MONITORING OF PATIENTS ........................................................................................13 
9.0 
STUDY CALENDER ........................................................................................................14 
10.0 
DRUG FORMULATION ..................................................................................................15 
11.0 
RESPONSE CRITERIA ....................................................................................................16 
12.0 
STATISTICAL CONSIDERATIONS...............................................................................19 
13.0 
CRITERIA FOR REMOVAL OF PATIENTS FROM PROTOCOL ...............................20 
14.0 
DURATION OF STUDY ..................................................................................................20 
15.0 
ADVERSE DRUG REACTIONS (ADR) REPORTING ..................................................20 
16.0 
REFERENCES ..................................................................................................................21 
17.0 
LIST OF APPENDICES ....................................................................................................26 
Appendix A: ECOG Performance Status Criteria .......................................................................26 
 
Appendix B: Eligibility Checklist ...............................................................................................27 
 
 
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1 
OBJECTIVES 
1. Determine extent of up regulation in the ERCC-1 gene expression on exposure to 
oxaliplatin in vitro and in vivo.   
1a. The magnitude of ERCC1 up regulation in response to oxaliplatin treatment will be 
correlated with apoptotic and growth inhibitory response in a panel a 30 colon cancer cell 
lines previously screened for response to this agent in the Montefiore laboratory.   
1b. Directly test the link between up regulation of ERCC-1 and oxaliplatin response.  ERCC-1 
gene expression will be silenced in oxaliplatin responsive colon cancer cell lines using 
siRNA, and response to oxaliplatin determined.   
1c. Determine whether changes in ERCC-1 gene expression occur in vivo in patients treated with 
oxaliplatin, and to determine whether the magnitude of ERCC-1 induction correlates with 
patient response.  In addition, whether basal ERCC-1 expression is a determinant of 
oxaliplatin response will also be determined.   
1d. Determine whether changes in ERCC-1 gene expression can be detected in the peripheral 
blood mononuclear cells (PBMC) on exposure to oxaliplatin, and to determine a correlation 
coefficient between the magnitude of change in gene expression in the colorectal cancer 
specimens and the PBMC.   
2 Determine the ERCC-1 C→T polymorphism and determine the association between the 
presence of polymorphism and resistance to oxaliplatin.   
2a. The link between ERCC-1 polymorphism and magnitude of ERCC-1 induction in response 
to oxaliplatin will also be determined.   
2b. Determine whether a specific ERCC-1 polymorphism is linked to objective response to 
oxaliplatin in vivo, and further, to determine whether a specific polymorphism is linked to the 
magnitude of ERCC-1 induction in response to oxaliplatin.  
3 Establish a gene expression pattern that will predict response to oxaliplatin in 
colorectal cancer cell lines.   
3a. This will identify multigene markers as opposed to a single genetic marker.   
3b. Identify genes altered in expression in response to oxaliplatin treatment.  The fresh tumor 
samples will be screened using the array technique.   
 
 
2.0 
BACKGROUND AND RATIONALE 
 
Colorectal cancer is the second leading cause of cancer death among both men and women, 
accounting for over 56,000 deaths annually [2].  For patients with advanced colon cancer, 
oxaliplatin (trans-L-1, 2-diamino cyclohexane oxalatoplatinum) has been approved for therapy as 
a front line agent [3].  The platinum drugs include the prototype cisplatin, and its analogs, 
carboplatin and oxaliplatin, and have been the mainstay of therapy for lung, ovarian, breast, 
cervical, head and neck, and testicular cancer.  These drugs exert their anti cancer activity by 
forming inter-, and intra- (DNA) strand platinum adducts thereby causing DNA damage and 
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inhibiting cell replication.  In spite of these advances, the benefits that patients derive remain 
dismal with response rates in patients with advanced non-small cell lung cancer in the range of 
15-20%, and median survival of 9 months at best [4].  For patients with metastatic colon cancer, 
with the incorporation of new agents, including oxaliplatin, the median survival has improved to 
24 months with response rates of 50-60% [5].   
DNA damaging agents depend on irreversibly damaging the cell’s DNA in order to exert an anti 
cancer effect.  Successful anti cancer therapy is limited by the cancer cell’s ability to bypass the 
lethal action and subsequent development of drug resistance.  In the case of the platinum 
compounds, the resistance of the cancer cell to the chemotherapy is multifactorial [6,7,8] and 
includes: reduction in drug entry and subsequent accumulation within the cell [6,8]; enhanced 
detoxification by the glutathione and metallothionein systems by sequestration of platinum and 
prevention of formation of DNA adducts [6,9,10,11]; altered patterns of platinum-DNA adduct 
formation [12,13]; prevention of DNA damage after the formation of the DNA-platinum adducts 
by either the ability to rapidly repair the DNA damage [3,4,5,11], or by development of tolerance 
to the DNA damage [12,13].  The repair of DNA damage is made possible by the nucleotide 
excision repair (NER) pathway.  Two major genes involved in this pathway are the excision 
repair cross-complementation group 1 (ERCC-1) and the ERCC-2 (xeroderma pigmentosa - 
XPD) gene.  It has been well established that expression levels of the ERCC-1 gene can 
significantly affect the ability of the drug to influence survival in patients with colon cancer [14].  
The NER reaction is carried out by a multienzyme complex and undergoes a stepwise process of 
recognition, incision, excision, repair synthesis and ligation [15,16].  The ERCC-1 protein forms 
a complex with the XPF product, which leads to development of endonuclease activity [15].  
This then excises DNA-platinum adduct at the 5’ end of the damaged strand [17,18].  Thus far, 
NER is the only known mechanism for the removal and subsequent repair of the damage 
produced by the platinum drugs [19].   
Studies on ovarian and colon cancer cell lines have demonstrated that there is up regulation of 
gene transcription with a rise in both mRNA and protein levels on exposure to cisplatin and 
oxaliplatin, respectively.  We therefore hypothesize that up regulation of ERCC gene expression 
in colorectal cancer cell lines is a reason for the different sensitivity patterns among the 30 colon 
cancer cell lines.  Studies have demonstrated that the extent of DNA damage repair as evidenced 
by the ERCC-1 expression levels is 30-50 times higher in resistant cells as compared to 
hypersensitive cells [20].  Other studies have also proven that in addition to colon cancer, the 
expression of the ERCC-1 gene also predicts for survival and cisplatin resistance in patients with 
lung [21], gastric [22] and ovarian [23] cancer.  Enhanced ERCC expression is directly linked to 
clinical response to cisplatin in ovarian cancer patients [23,24].  It has been clearly established 
that cells that are defective in this pathway are hypersensitive to the platinum [25,26], and those 
overactive in this pathway are resistant [8,27,28].  In a study involving 4 cancer cell lines, 
ovarian and an inherently cisplatin resistant colon (HT-29) cell lines were used.  ERCC-1 mRNA 
levels were measured after exposure to oxaliplatin for 20 hours and were higher than in the 
control, the A2780 (ovarian) cell line [29].  Another group studied the combination of irinotecan 
and oxaliplatin in HCT-8 cell lines and xenograft modes and observed that the ERCC-1 
expression was upregulated on exposure to oxaliplatin.  Addition of irinotecan abrogated this 
effect, with the potential for synergy between the two drugs by the inhibition of DNA repair and 
increased cytotoxicity of the platinum [30]. 
Investigating ERCC-1 gene polymorphisms, DNA was collected from a clinical study evaluating 
the use of oxaliplatin in patients with advanced colorectal cancer and the C→T single nucleotide 
polymorphism in exon 118 was studied.  Patients with the C/C genotype had the most favorable 
survival.  The homozygous TT and the heterozygous CT patients had a relative risk of dying of 
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1.86 and 2.29 (p=0.021); respectively [31]; however there is no evidence that the polymorphism 
bears an association with response.  Similar findings have been observed in lung cancer [32,33].  
In a group of cisplatin treated patients, the C/C homozygous genotype was associated with a 
median survival of 486 days and was significantly (p=0.0058) greater than the T/T genotype with 
a median survival of 281 days.  We also propose to look at polymorphisms in these cell lines and 
establish the presence or absence of an association between the genetic polymorphisms, and the 
cellular sensitivity to the cytotoxicity of oxaliplatin.   
While there is extensive pre-clinical data suggesting the influence of ERCC-1 on platinum 
sensitivity, in vivo data continues to be lacking.  The aim of this proposal is to study changes in 
ERCC-1 gene expression in PBMC and fresh tumor tissue, both before and after oxaliplatin 
therapy.  While it is critical to determine the expression pattern within the malignant cell, 
practically, it is difficult to obtain fresh tumor specimens, especially if one is interested in serial 
sampling to study changes in RNA over time, or on exposure to drugs or toxins.  Some studies 
have demonstrated that in certain circumstances, peripheral blood mononuclear cells (PBMC) 
could serve as a reliable surrogate marker for cancer tissue.  Smoking induced carcinogen-DNA 
adducts were compared and levels from PBMC were found to be a reliable surrogate for levels in 
lung cancer specimens [34].  Patients with renal cancer were treated with the mTOR inhibitor 
CCI-779, and the gene expression profiles from their PBMC reliably identified the expression 
profile with a higher likelihood of a response [35].  Another mTOR inhibitor RAD 0001, was 
looked at in a syngeneic rat pancreatic tumor model, and it was found that long term monitoring 
of PBMC derived S6K1 activity levels could be used for assessing RAD 001 treatment schedules 
in patients with cancer [36].  The PBMC may reflect the events in the cancer cell and it is 
important to make this determination and derive a relationship between the gene expressions in 
the two sources of cells.  The study will look at ERCC-1 gene expression in PBMC and 
determine a correlation between the changes in the expression levels in the PBMC and fresh 
tumor tissue.  If it can be established that the PBMC serves as a surrogate marker for the events 
within the tumor cell, in the future all studies can be readily performed on the peripheral cells 
with confidence.   
Multiple reports have indicated that among patients with colorectal cancer, the survival of 
African Americans is lower than that for Caucasians.  Possible explanations for this disparity is 
lower socio-economic status, lack of screening, delayed diagnoses, and genetic differences that 
possibly render one population to derive less benefit from the available therapy [37,38,39].  
Retrospective data suggests that baseline ERCC-1 expression and the polymorphisms do impact 
on survival of colorectal cancer patients who are treated with oxaliplatin.  We therefore 
hypothesize that one factor accounting for the racial disparity in survival is attributable to 
differences in baseline expression or to a more frequent presence of polymorphism that is 
associated with a poorer survival.   
 
With the advent of modern micro array technology, it is possible to screen a cell line or tumor 
sample for thousands of genes at one time and using this technique, research groups have 
established specific gene expression profiles that predict for sensitivity to cytotoxic drugs [40].  
The laboratory of Drs. Leonard Augenlicht and John Mariadason has identified the gene 
expression profile in a panel of 30 colon cancer cell lines and that could determine sensitivity 
and resistance patterns to the cytotoxic effects of 5-fluorouracil and irinotecan [41].  They have 
found that the selection of 50 genes correlated with 5-FU responsiveness, but not a random set of 
50 genes.  Also found was that this gene expression was a better predictor of 5-FU response than 
the previous well-established predictors of response, namely, thymidylate synthase, thymidine 
phosphorylase, p53 and mismatch repair status.   
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3.0  
PRELIMINARY DATA 
The cell biology department at the Albert Einstein Cancer Center has studied a panel of 30 colon 
cancer cell lines and determined a sensitivity pattern to various drugs used in the clinic as a 
therapeutic option for patients with advanced disease [55].  The laboratory of Dr. John 
Mariadason has studied a panel of 30 colon cancer cell lines and observed that there is a distinct 
susceptibility pattern with cells ranging from being highly susceptible (GI 50 of 0.5, 95% 
apoptosis) to highly resistant (GI 50 of 11, 10% apoptosis) to oxaliplatin [54].  This pattern is 
hereby displayed below [fig 1].  As is evident, cell lines have been arranged in order of 
increasing sensitivity to oxaliplatin from least sensitive to the most sensitive.  It is this cell lines 
model that will be used for this project to determine ERCC-1 gene expression profiling, to carry 
out the gene silencing experiments, and to determine germline polymorphisms.   
 
KM12
SW1116
LoVo
Caco-2
16E
19A
Lmyc-2
Lmyc-3
HT29
SW837
SW48
Dld-1
LIM2405
HCT-15
Colo201
LIM1215
Colo205
HCT-8
SW480
WiDr
SW620
HCT116
RKO
Colo320
T84
SK-CO-1
RW2982
SW948
HCC2998
RW7213
SW403
LS174T
0
25
50
75
100
Control
Oxaliplatin 100 M
% Apoptosis
 
Fig 1 Apoptotic susceptibility pattern of a panel of 30 colon cancer lines to 
oxaliplatin
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Fig 2: Effect on ERCC-1 gene expression on exposure to oxaliplatin in two colon cancer cell 
lines 
Further, two cell lines were randomly selected and studied for the alteration in the ERCC-1 gene 
expression after exposure to oxaliplatin at 10 μM for 24 hours.  As is evident from this graph, an 
increase in ERCC-1 expression was observed in the HCT116 cell line while a decrease was 
observed in the SW403 cell lines.   
 
 
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4.0 
PATIENT ELIGIBILITY CRITERIA 
 
Inclusion Criteria 
 
3.1 
Histologically confirmed diagnosis of colorectal cancer 
 
3.2 
ECOG Performance Status 0-2 (Appendix A) 
 
3.3 
Patient is a candidate for oxaliplatin based therapy either in the adjuvant or in the 
metastatic setting 
 
3.4 
Consent to donate 9 tubes of PBMC of 7 ml of blood each 
 
3.5 
Willing to consider additional post therapy tumor biopsy if applicable (refusal to 
consent is not an exclusion criteria) 
 
3.6 
Adequate organ function as defined as 
 
 
Neutrophil count > 1500/μl 
 
 
Platelets > 75,000/ μl 
 
 
Hemoglobin > 8 g/dl 
 
 
Bilirubin < 2.0 X upper limit of normal 
 
 
Creatinine < 2 mg% or calculated clearance > 40 ml/mt 
 
3.7 
The patient must have signed a consent form approved by the Albert Einstein 
College of Medicine Cancer Center CCI and Montefiore Medical Center IRB 
 
 
Exclusion Criteria 
 
3.8   
No other significant underlying medical condition that will, in the opinion of the 
principal investigator or designees, make administration of oxaliplatin unusually 
hazardous, such as significant hepatic, bone marrow and/or cardiac disease, requiring 
active medical treatment.   
 
3.9   
Pregnant women or women of child bearing potential not practicing birth control  
or sexually active males unwilling to practice contraception during the study.   
 
3.10   Patients undergoing major surgical procedures (they will be delayed enrollment 
until complete recovery from their surgery - 4 wk for major or 2 wk from minor surgery).  
 
3.11     Patients with grade 2 neuropathy will not be eligible for the study 
 
3.12     The patient must not have received chemotherapy within 4 weeks of beginning 
oxaliplatin treatment.  At least 6 weeks must elapse if prior therapy included 
mitomycin C or nitrosoureas.  At least 2 weeks must have elapsed since the end of 
prior palliative radiation therapy.   
 
 
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5.0 
REGISTRATION PROCEDURE AND DATA SUBMISSION 
 
All patients will be registered with Milagros Rodriquez in the Cancer Clinical Trials Data 
Management Office of the Montefiore-Einstein Center for Cancer Care  
1521 Jarret Place 
Bronx, NY 10461  
Phone (718) 379-6861  
Fax 
(718) 822-0335 
 
 
6.0  
TREATMENT PLAN AND STUDY DESIGN 
The 30 colon cancer cell lines panel that has been described in the preliminary data section of the 
protocol will be used.  Total ERCC-1 mRNA will be extracted using the RNeasy RNA extraction 
kit from Qiagen and converted to cDNA using an anchored oligo dT primer and reverse 
transcriptase.  Quantitative real time PCR will be used to quantify ERCC1 mRNA and results 
expressed relative to GAPDH levels.  Total cellular protein will be extracted and ERCC-1 
protein level quantified by Western Blotting using an anti ERCC-1 antibody.   
Forty patients (20 patients/year) will be enrolled to collect four tubes of 7 ml of blood for PBMC 
analysis.  This will be used to collect cells for ERCC expression.  mRNA will be measured by 
quantitative PCR [22,44] and protein by Western Blotting [45].  This tube of blood will be drawn 
before commencement of any chemotherapy (0 hours/baseline), at the end of infusion (2 hours), 
and at 48 hours (this is typically when patients return to the infusion unit to discontinue the 5-FU 
infusional pump).  Another tube will be collected when the patient returns on the first day of the 
next cycle.  The PBMC samples will be processed within 60 minutes of collection.   
In addition, patients will be identified before a diagnostic procedure such as an endoscopy, or a 
CT guided biopsy.  The patients will be asked to sign a consent form before the diagnostic 
procedure that will allow the use their biopsy or resection specimens as a source of tissue.  The 
gastroenterologist performing the endoscopies will biopsy two specimens, of which one 
specimen will be formalin fixed and sent to pathology for the establishment of a diagnosis.  The 
second will be handed to me my designee and this will be immediately placed in dry ice in the 
operating/procedure room.  The sample will be transported out of the procedure room 
immediately and then placed in liquid nitrogen.  This tissue will be studied for ERCC-1 mRNA 
expression.  For patients from whom we will be unable to obtain fresh tumor samples, only the 
formalin fixed, paraffin embedded tissue block will be used to estimate ERCC-1 protein content 
in a semi-quantitative manner using the immune-histochemistry (IHC) analysis using a 
commercially available antibody to the protein [42].  The IHC staining will be performed using 
antibodies from biomeda, and analyses using standard techniques described previously [43].  
Appropriate positive and negative controls will be used.  The IHC will be graded as positive or 
negative and will be independently verified by a pathologist blinded to the identity of the sample.  
It is estimated that close to 22%, of patients with unresectable metastatic colorectal cancer are 
able to undergo curative resection of the metastases after therapy with the FOLFOX regimen [5].  
The surgeon performing the liver resection will hand over a piece of the resected specimen to my 
designee or me and this will be handled in a manner described previously.  This will facilitate 
gene expression study over time after a 2-hour exposure to oxaliplatin.  Both, the fresh tissue and 
the PBMC will be analyzed for semi-quantitative ERCC-1 by IHC staining, and by quantitative 
mRNA and protein analyses.  Analyses to estimate the degree of correlation between the 
magnitude of change in the ERCC-1 gene expression in PBMC and the fresh tumor samples will 
be performed.   
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All patients will undergo serial radiological testing (CT scans) every 2 cycles (each cycle 
consisting of 4 weeks of therapy in case of FOLFOX or 3 weeks in case of XELOX).  The 
patients will be evaluated for response using the response evaluation criteria in solid tumors 
(RECIST) as described previously [46].   
 
Silencing of ERCC-1 
 
To directly determine the role of ERCC-1 in mediating cellular response to oxaliplatin in colon 
cancer cells, we will transfect 2 oxaliplatin-resistant cell lines with siRNAs that specifically 
target ERCC-1.  siRNAs will be purchased from Dharmacon, and transfected into cell lines using 
lipofectamine 2000 at a final siRNA concentration of 100 nM.  As a control, cells will also be 
transfected with a non-targeting siRNA.  The silencing efficiency of the siRNAs will be 
validated 24 hours post transfection by their ability to inhibit basal and oxaliplatin-induced 
ERCC-1 expression at the mRNA (QPCR) and protein level (western blot).  Once silencing 
efficiency has been confirmed, apoptotic response of ERCC-1-silenced colon cancer cells treated 
with 1, 10 and 100 μM oxaliplatin for 72 hours will be compared to cells transfected with non-
targeting siRNA.  Apoptosis will be assessed by propidium iodide staining followed by FACS 
analysis.  Experiments will be performed in triplicate on 3 independent occasions.  In addition to 
apoptosis assays, we will further test the role of ERCC-1 silencing on oxaliplatin response by 
clonogenic assay.  Cells transfected with ERCC-1 or non-targeting siRNA will be treated with 1, 
10 or 100 mM oxaliplatin for 9 hours, following which time the drug will be removed, cells 
trypsinized, and reseeded in fresh medium at a density of 500 cells per well.  Colony formation 
will be monitored over the following 2 weeks and visualized by staining with crystal violet.   
From the panel of 30 colon cancer cell lines, genomic DNA will be extracted and studied for 
germline polymorphisms as described below.  Similarly, from the baseline PBMC from all 
patients, DNA will be extracted to determine germline polymorphisms.  The genomic DNA will 
be prepared from PBMC using the Puregene blood DNA kit (Gentra Inc.) following the 
manufacturer’s protocol.  The ERCC-1 C→T polymorphism will be detected using modified 
PCR-RFLP methods, using primer sequences described previously [33].  It is well established 
that certain germline polymorphisms in the ERCC-1 gene predicts for increased survival, 
however, no such association has been established with clinical response.  This proposal will 
determine an association between the presence of a particular polymorphism with changes in 
ERCC gene expression, and of the ERCC-1 gene polymorphisms with clinical response.   
 
To gain further insights into the mechanisms of oxaliplatin response and to identify novel 
molecular determinants for differential cellular response to this agent, we will undertake a non-
hypothesis driven microarray-based screening strategy.  Based on our preliminary data, we will 
select the 5 most oxaliplatin-sensitive (LS174T, SW403, RW7213, HCC2998, SW948) and 5 
most oxaliplatin-resistant cell lines (KM12, SW1116, LoVo, Caco-2, 16E) for further analysis 
(10 cell lines in total).  Each of these cell lines will be treated with 10 μM oxaliplatin for 24 
hours.  Total RNA will be isolated from treated and untreated cells using the RNeasy kit 
(Qiagen, Valencia, CA).  For microarray hybridizations, 50 μg of RNA from oxaliplatin treated 
cells will be labeled with Cy5 dUTP, and 50 μg of RNA from untreated cells labeled with Cy3 
dUTP.  Probe preparation, hybridization conditions, and array scanning procedure were as 
previously described and as routinely performed in our laboratory [47,48].  Labeled probes will 
be hybridized to 27,000 feature cDNA microarrays generated by the Albert Einstein College of 
Medicine microarray facility [49].  Images will be analyzed using Genepix Pro software (Axon 
Instruments, Union City, CA), and lowess normalized.  For each cell line, two independent 
oxaliplatin treatment experiments will be performed, and the mean value (ratio) for each gene 
computed.   
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Genes differentially expressed between oxaliplatin sensitive and resistance cell lines will be 
determined using a students t test, with a P value of <0.05 considered to be statistically 
significant.  To reduce the number of false positive discoveries, the mean value across the 5 
sensitive and 5 resistant cell lines will be computed, and genes that are differently expressed 2-
fold or greater between sensitive and resistant cell lines determined.  Genes that satisfy both of 
these criteria will be considered differentially expressed between oxaliplatin sensitive and 
resistant cell lines.  To gain mechanistic insights into differentially expressed gene lists, we 
routinely perform enrichment analyses to identify functionally related categories of genes 
enriched for differential expression.  For this analysis we will take advantage of our prior 
classification of all genes on the AECOM cDNA microarrays into 150 biologically related 
categories, including cell cycle progression mediators, apoptosis mediators, transcription factors 
and signaling mediators.  We will utilize a Fisher exact test to identify biologically related 
categories of genes enriched for altered expression in response to oxaliplatin treatment and 
differentially expressed between oxaliplatin sensitive and resistant cell lines.  Differentially 
expressed genes will be validated by RT-PCR and whether specific candidate genes play a direct 
role in oxaliplatin response tested by siRNA-mediated silencing experiments followed by 
reassessment of oxaliplatin response.   
 
The same biopsy material described in aim 1 that will be obtained from patients pre- and post-
oxaliplatin treatment will be used to determine the changes in gene expression induced by this 
agent in vivo.  RNA will be extracted from biopsies by homogenization of biopsy tissue in Trizol 
followed by further purification using an RNeasy column (Qiagen).  From previous studies we 
envision obtaining between 2-5 micrograms of total RNA from patient biopsies [50].  RNA will 
be linearly amplified by T7 bacteriophage RNA polymerase driven in vitro transcription 
(Arcturus, KIT 0201).  For colon cancer cell lines, this procedure typically yields approximately 
30 μg of polyU mRNA from 5 μg of total starting RNA.  5 μg of polyU/polyA mRNA from pre 
and post treatment specimens will be labeled with Cy5 dUTP and compared to 5 μg of Cy3 
dUTP-labeled reference RNA routinely utilized in the Augenlicht laboratory [55].  Comparison 
of the pre and post treatment samples to a reference RNA will enable additional analyses to be 
performed in the future, including the identification of genes / signatures whose basal level of 
expression may be predictive of oxaliplatin response.  Patient with good and bad response to 
oxaliplatin will be separated and genes differentially expressed in response to oxaliplatin 
identified as described in previously.  In addition, genes altered in expression in response to 
oxaliplatin treatment in vitro and in vivo will be identified.   
 
Oxaliplatin and other chemotherapy will be delivered as is standard of care.  However, doses 
may be modified per treating physician and patient tolerance 
 
FOLFOX (q 14 days) 
Oxaliplatin at 85 mg/m2 over 2 hours on day 1 
5-FU at 400 mg/m2 bolus on day 1 
Leucovorin 400 mg/m2 over 2 hours on day 1 
5-FU at 2400 mg/m2 over 46 hours via infusion pump 
Bevacizumab 5 mg/kg on day 1 
 
XELOX (q 21 days) 
Oxaliplatin 130 mg/m2 over 2 hours on day 1 
Capecitabine 1000 mg/m2 q 12 hours on days 1-14 
Bevacizumab 7.5 mg/kg on day 1 
 
 
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7.0 
SUPPORTIVE THERAPY GUIDELINES 
 
Use of supportive therapy including antiemetic therapy will be at the discretion of the 
treating physician.  However, it is suggested that patients receive a 5-HT3 antagonist, 
decadron and lorazepam prior to oxaliplatin dosing.   
Use of colony stimulating factors (such as Procrit, Aranesp, Neupogen, Neulasta) is 
allowed and is at the discretion of the treating physician.   
For patients with bony metastases, use of bisphosphanate therapy is allowed and is at the 
discretion of the treating physician.   
 
8.0        MONITORING OF PATIENTS 
 
Patients will be evaluated as is standard of care for a patient receiving oxaliplatin based 
therapy either alone or in combination with 5-FU (FOLFOX) or with capecitabine 
(Xeloda® - XELOX).  It is suggested that they at least be evaluated once every other 
week by the treating physician.   
 
All patients will have imaging studies for tumor evaluation at baseline and at the end of 
two cycles (each cycle consisting of 4 weeks with FOLFOX or 3 weeks of XELOX).   
 
For details, refer to study calender.  
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9.0 
STUDY CALENDAR 
All radiological tests and disease assessments have to be within 4 weeks of starting treatment 
The consent date is within four weeks of registration for study 
All blood tests and physical exam have to be done within 2 weeks of starting treatment 
 
 
Pre-study 
 
D 1 
D 3 
D15 
q 2 wk 
(q 3 wk)d 
q 3 wk 
(q 4 wk) d 
wk 8 
(Day  
-28 to 
start) 
(Day  
-14 to 
start) 
Informed consent 
X 
 
 
 
 
 
 
 
History and Physical 
 
X 
 
 
 
 
X 
 
Vital Signs 
 
X 
 
 
 
 
X 
 
Weight 
 
X 
 
 
 
 
X 
 
Height 
 
X 
 
 
 
 
 
 
BSA 
 
X 
 
 
 
 
X 
 
PS 
 
X 
 
 
 
 
X 
 
AE/SAE Monitoring 
 
 
X 
 
 
 
X 
 
CT scans a 
X 
 
 
 
 
 
 
X 
Tumor Measurements a 
X 
 
 
 
 
 
 
 
CBC 
 
X 
 
 
X 
X 
X 
 
Chemistry-7 
 
X 
 
 
 
 
 
 
LFT 
 
X 
 
 
 
 
 
 
Beta-hCG b 
 
X 
 
 
 
 
 
 
CEA 
 
X 
 
 
 
 
X 
 
Oxaliplatin dosing 
 
 
X 
 
X 
X 
 
 
PBMC collection c 
 
 
X 
X 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Index for Study Calender 
 
Xa 
If a patient has a clearly defined palpable mass or on an X-ray, a CT may be avoided 
 
After every two cycles (4 doses)of therapy  
 
Xb 
In women of childbearing potential (can be serum or urine). 
 
Xc 
PBMC will be collected at baseline, 2 hr (EOI), 48 hr and at D 15 
 
Xd 
Bracketed time interval is for XELOX while non bracketed is for FOLFOX 
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10.0 
DRUG FORMULATION 
 
Oxaliplatin is available in two different dose vials containing 50 mg and 100 mg of active 
drug at a concentration of 5 mg/ml.  It is stored at 25*C.  It must be diluted prior to 
infusion in 250-500 ml of 5% dextrose [under no circumstance should 0.9% sodium 
chloride (NS) be used].   
 
The drug will be prepared and infused, as is standard practice.   
 
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11.0 
RESPONSE CRITERIA 
 
Determination of response rate is a secondary objective of this study and any responses 
will be documented and reported. The RECIST criteria to determine treatment status 
(2000) will be followed.  
 
11.1 
Response Evaluation Criteria in Solid Tumors (RECIST)  
 
Eligibility 
 
 
Measurable disease - the presence of at least one measurable lesion. If the measurable disease is 
restricted to a solitary lesion, its neoplastic nature should be confirmed by cytology/histology.  
 
Measurable lesions - lesions that can be accurately measured in at least one dimension with 
longest diameter >20 mm using conventional techniques or >10 mm with spiral CT scan. 
 
Non-measurable lesions - all other lesions, including small lesions (longest diameter <20 mm 
with conventional techniques or <10 mm with spiral CT scan), i.e., bone lesions, leptomeningeal 
disease, ascites, pleural/pericardial effusion, inflammatory breast disease, lymphangitis 
cutis/pulmonis, cystic lesions, and also abdominal masses that are not confirmed and followed by 
imaging techniques; and. 
 
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.  
Clinical lesions will only be considered measurable when they are superficial (e.g., skin nodules 
and palpable lymph nodes). For the case of skin lesions, documentation by color photography, 
including a ruler to estimate the size of the lesion is recommended.  
 
Methods of Measurement -  
 
CT and MRI are the best currently available and reproducible methods to measure target lesions 
selected for response assessment. Conventional CT and MRI should be performed with cuts of 
10 mm or less in slice thickness contiguously. Spiral CT should be performed using a 5 mm 
contiguous reconstruction algorithm.  
 
Baseline documentation of "Target" and "Non-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. All other lesions (or sites of disease) should be 
identified as non-target lesions and should also be recorded at baseline. Measurements of these 
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lesions are not required, but the presence or absence of each should be noted throughout follow-
up. 
 
Response Criteria 
 
Evaluation of target lesions 
1. Complete Response (CR): Disappearance of all target lesions 
2. Partial Response (PR): At least a 30% decrease in the sum of the LD of target lesions, taking 
as reference the baseline sum LD 
3. 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 
4. 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 
1.Complete Response (CR): Disappearance of all non-target lesions and normalization of tumor 
marker level 
2.Incomplete Response/Stable Disease (SD): Persistence of one or more non-target lesion(s) 
or/and maintenance of tumor marker level above the normal limits 
3.Progressive Disease (PD): Appearance of one or more new lesions and/or unequivocal 
progression of existing non-target lesion.  
 
(1) 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 later on by the review panel (or study chair). 
 
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 PD the smallest measurements recorded 
since the treatment started). In general, the patient's best 
response assignment will depend on the achievement of both measurement and confirmation 
criteria  
 
Target lesions 
Non-target lesions 
Evaluation of NTL 
Overall Response 
CR 
CR 
No 
CR 
CR 
Incomplete Resp./ 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 
 
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 
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the residual lesion be investigated (fine needle aspirate/biopsy) to confirm the complete response 
status.  
 
Duration of overall response 
 
The duration of overall response is measured from the time measurement criteria are met for CR 
or PR (whichever status is recorded first) until the first date that recurrence or PD is objectively 
documented, taking as reference for PD the measurements recorded since the treatment started.  
 
Duration of stable disease 
 
SD is measured from the start of the treatment until the criteria for disease progression are met, 
taking as reference the smallest measurements recorded since the treatment started.  
 
 
11.2 
Time to Disease Progression - From date of registration to date of progressive 
disease. 
 
11.3   
Duration of Response - Time from documentation of complete or partial response 
to documentation of disease progression. 
 
11.4   
Time to Death - From date of registration to date of death. 
  
 
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12.0 
STATISTICAL CONSIDERATIONS  
 
The main objective of the study is to determine extent of up regulation in the ERCC-1 gene 
expression on exposure to oxaliplatin in vivo.  Specifically, in comparing PBMC with pre and 
post exposure to oxaliplatin (end of infusion – 2 hour sample), we hypothesize that ERCC-1 
expression will be significantly increased after exposure.  The baseline expression is relative to a 
standard protein, beta actin, and has been found to be 50%.  Samples will be analyzed for ERCC-
1 protein relative to beta-actin.  A level of < 50% will be coded as negative (-), and that of > 50% 
will be coded as positive (+).  A sample size of 40 pairs of observations (pre and post exposure) 
will give us 80% power to detect an odds ratio of 3.0 using a one-sided McNemar test with an 
alpha level of 0.025.  This odds ratio is equivalent to a difference between paired proportions of 
0.41 which assumes the proportion of samples with (+,-) pattern to be 0.20 and the proportion of 
(-,+)pattern to be 0.61.  The proportion of discordant pairs is assumed to be 0.81.  The study will 
accrue upto 80 patients to ensure enough yield for the 40 pairs of observations.   
 
Comparison of before and after treatment ERCC-1 expression level will be compared using 
McNemar test. Response rate will be summarized as percentage with associated 95% exact 
confidence intervals. Time-to-event outcomes will be summarized using KM estimator as 
appropriate. Other continuous outcomes will be summarized using descriptive summaries such as 
mean, median, inter-quartile range, as appropriate. 
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13.0 
CRITERIA FOR REMOVAL OF PATIENTS FROM PROTOCOL 
 
When a patient is removed from study, the Principal investigator should be notified, and 
the reason for withdrawal noted in the flow sheets. 
 
12.1 
Progressive disease 
 
12.2 
Patient desire to withdraw 
 
12.3 
At the discretion of the Principal Investigator 
 
 
14.0 
DURATION OF STUDY 
 
The study will last until the first tumor evaluation post treatment will be performed, at the end of 
2 cycles [28 day cycle (2 doses of FOLFOX), or 21 day cycle, XELOX].  This will enable 
documentation of best response.   
 
15.0 
ADVERSE DRUG REACTION (ADR) REPORTING 
 
Reports of adverse reactions will be made using the Modified NCI Common Toxicity 
Criteria for Adverse Events version 3.0 for reference according to the guidelines 
published by the NCI.   
 
 
 
Report the following by telephone to the principal investigator or study 
coordinator at (718) 405-8404 or 718-405-8515, available 24 hours, [recorder 
after working hours]: 
 
1. 
All unexpected grade 3 events 
2. 
All life-threatening (Grade 4) events  
3. 
All fatal events. 
 
A full report to the PI is to be made within 10 days of the event.  
 
The Institution Review Board of the Montefiore Medical Center will be notified of any 
SAE within 48 business hours of the time that the PI was informed of the event, by 
phone, fax or e-mail.  A full report will be submitted within 10 business days of the time 
that the PI was informed of the event.  If the event is ongoing, a follow up report will be 
made at the end of the event.  All deaths within 6 months of discontinuation of study 
drugs will be reported.  All SAE within 30 days of discontinuation of study drugs will be 
reported.   
 
All serious adverse experiences/events (SAEs) that are unexpected and possibly related to 
use of the Study Drug (s) will also be reported directly to Sanofi-Aventis.  The U.S. 
Package Insert shall be used to define expectedness.   
 
See Appendix C for SAE form  
 
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colorectal cancer improves with the availability of fluorouracil-leucovorin, irinotecan, 
and oxaliplatin in the course of treatment. J Clin Oncol. 22:1209-14, 2004.  
52. Wu XM, Zhou YK, Xu SQ, Hao QL, Ren S. [Antisense ERCC1 RNA decreases the 
repair capability of damaged DNA in lung cancer cells induced by benzo[a]pyrene]. 
Zhonghua Yu Fang Yi Xue Za Zhi. 37:167-70, 2003. 
53. Chang IY, Kim MH, Kim HB, Lee do Y, Kim SH, Kim HY, You HJ. Small interfering 
RNA-induced suppression of ERCC1 enhances sensitivity of human cancer cells to 
cisplatin. Biochem Biophys Res Commun. 327:225-33, 2005. 
54. Youn CK, Kim MH, Cho HJ, Kim HB, Chang IY, Chung MH, You HJ. Oncogenic H-
Ras up-regulates expression of ERCC1 to protect cells from platinum-based anticancer 
agents. Cancer Res. 64:4849-57, 2004.  
 
 
IRB NUMBER: 07-10-376
IRB APPROVAL DATE: 09/04/2015
IRB NUMBER: 07-10-376
IRB APPROVAL DATE: 09/04/2015

ERCC-1 CRC study 
26
 
 
16.0 
LIST OF APPENDICES 
 
Appendix A: 
 
ECOG PERFORMANCE STATUS SCALE 
 
 
0 
Normal activity 
 
1 
Symptoms of disease, but ambulatory and able to 
carry out activities of daily living 
 
2 
Out of bed more than 50% of the time.  
Occasionally needs assistance 
 
3 
In bed more than 50% of the time, needs nursing 
care  
 
4 
Bedridden, may need hospitalization 
 
 
IRB NUMBER: 07-10-376
IRB APPROVAL DATE: 09/04/2015
IRB NUMBER: 07-10-376
IRB APPROVAL DATE: 09/04/2015

ERCC-1 CRC study 
27
Appendix B 
 
ELIGIBILITY CHECKLIST 
 
Patient Name:  _________________________ 
 
 
Patient Medical Record #_______________ 
 
All questions must be “yes” for patient to be eligible 
 
1. Does the patient have a histological confirmed diagnosis of colon  
or rectal cancer?   
 
 
 
 
 
 
 
______ 
 
2. Is the patient a candidate for oxaliplatin therapy  
 
 
 
______ 
 
3. Is the patient > 18 years of age?  
 
 
 
 
 
______ 
 
4. Is the Performance Status 0-2 ?  
 
 
 
 
 
______ 
 
5. Does the patient have adequate organ function as defined? 
(all blood tests done within 14 days of registration) 
 
 
Parameter 
Criteria 
Date 
Patient value 
 
 
 
 
 
 
WBC 
> 3,000/L 
 
 
 
ANC 
> 1500/L 
 
 
 
Platelet 
> 75,000/L 
 
 
 
Creatinine 
clearance 
OR Creatinine 
> 40 ml/mt  
< 2 mg% 
 
 
 
Bilirubin 
< 2 mg/dl 
 
 
 
SGOT/SGPT 
< 3 X N 
 
 
 
6. Has the patient given informed consent?  
 
 
 
 
_______ 
 
7. Has she had a negative pregnancy test?  
 
 
 
 
_______ 
 
8. Is the patient at least 4 weeks out of major surgery, chemotherapy and  
2 wk from radiation therapy and at least a week out of minor surgery?  
_______ 
 
 
IRB NUMBER: 07-10-376
IRB APPROVAL DATE: 09/04/2015
IRB NUMBER: 07-10-376
IRB APPROVAL DATE: 09/04/2015

E R C C- 1 C R C st u d y 
2 8  
A p pe n di x C 
 
s a n ofi -a v e nti s U. S. I n c.  
Gl o b al P h ar m a c o vi gil a n c e a n d E pi d e mi ol o g y  
2 0 0  Cr o s si n g B o ul e v ar d, P. O. B o x 6 8 9 0  
M ail st o p B X 4 -4 1 2 -i 
Bri d g e w at er, N J 0 8 8 0 7  
s a n ofi -a v e nti s U. S. 
I n c. 
F ax  S A E R E P O R T              I N V E S TI G A T O R S P O N S O R E D T RI A L S 
Please  √  o ne:   El o x ati n 
 T a x ot er e     R e p ort e d t o 
F D A ?  
 
Y e s   
 N o  
F a x:  
9 0 8 -2 3 1 -4 8 2 7  
9 0 8 -2 3 1 -4 8 2 7  
 
 
D at e:  
 
P a g e s:    
Fr o m:   
P h o n e:   
I S T #: 
 
St u d y Title:  
 
PI Na me:  
 
Re p orta bilit y:  
All seri o us a d verse/e ve nts ( S A Es) u ne x pecte d a n d p ossi bl y relate d t o t h e use  of t h e St u d y 
Dr u g(s) are re p orte d directl y t o t h e F D A i n acc or da nce wit h a p plica ble la w, r e g ulati o ns a n d 
St u d y pr ot o c ol wit h a c o p y s u b mitte d t o sa n ofi -a ve ntis.  If t h e F D A d oes n ot re q uire t he s p o ns or 
(i n vesti gat or) t o s u b mit S A Es t h at are u ne x pecte d a n d relate d, S A E re p orts s h o ul d be se nt t o 
sa n ofi-a ve ntis w he n disc o vere d.   
T he U. S. P ac ka ge I nsert  s hall be use d t o defi n e e x pecte d ness.  All S A Es will be e val u ate d b y 
t h e i n vesti gat or f or re p orta bilit y.  Relate d ness is assesse d usi n g t h e defi niti o ns bel o w. 
F or C o m parat or Dr u gs / Sec o n dar y S us pects  ( C o nc o mita nt Me dicati o ns), all seri o us a d verse 
e x perie nces will be f or war de d t o t he pr o d uct ma n ufa ct urer. 
Please  √  o ne:  
 
 
U nli kel y :   T he e ve nt is cle arl y d ue t o ca uses disti nct fr o m t h e use of t h e st u d y dr u g, s uc h as a 
d oc u me nte d pre -e xisti n g c o n diti o n, t he effect of a c o nc o mita nt me dicati o n, a ne w c o n diti o n 
w hic h, base d u p o n t h e pat h o p h ysi ol o g y of t h e c o n diti o n, a n d t he p har mac ol o g y of t h e st u d y 
dr u g, w o ul d be u nli kel y relate d t o t h e use of t h e st u d y dr u g.   
 
P ossi ble :  T he e ve nt f oll o ws a re as o na ble te m p oral se q ue nce fr o m a d mi nistrati o n of t h e st u d y 
dr u g or t h e e ve nt f oll o ws a k n o w n res p o nse patter n t o t h e st u d y dr u g B U T  t h e e ve nt c o ul d ha ve 
bee n pr o d uce d b y a n i nterc urre nt me dical c o n diti o n w hic h, base d o n t h e pat h o p h ysi ol o g y of t h e 
c o n diti o n, a n d t he p har mac ol o g y of t h e st u d y dr u g, w o ul d be u nli kel y r elate d t o t h e use of t h e 
st u d y dr u g or t he e ve nt c o ul d be t he effect of a c o nc o mita nt me dicati o n.    
 
Pr o ba ble :  T he e ve nt f oll o ws a r eas o na ble te m p oral se q uence fr o m a d mi nistrati o n of t h e st u d y 
dr u g a n d t he e ve nt f oll o ws a k n o w n res p o nse patter n t o t he st u d y dr u g A N D  t h e e ve nt ca n n ot 
ha ve bee n reas o na bl y e x plai ne d b y a n i nterc urre nt me dical c o n diti o n or  t h e e ve nt ca n n ot be t h e 
effect of a c o nc o mita nt me dicati o n.  
 
Defi nite :  T he e ve nt f oll o ws a r e as o na ble te m p oral se q ue nce fr o m a d mi nistrati o n of t h e st u d y 
dr u g, t he e ve nt f oll o ws a k n o w n res p o nse patter n t o t h e st u d y dr u g a n d base d o n t h e k n o w n 
p har mac ol o g y of t h e st u d y dr u g, t h e e ve nt is clearl y relate d t o t h e effe ct of t h e st u d y dr u g.  
 
 
 
I R B N U M B E R: 0 7- 1 0- 3 7 6
I R B A P P R O V A L D A T E: 0 9/ 0 4/ 2 0 1 5
I R B N U M B E R: 0 7- 1 0- 3 7 6
I R B A P P R O V A L D A T E: 0 9/ 0 4/ 2 0 1 5