Ignite Creation Date:
2024-05-06 @ 10:05 AM
Last Modification Date:
2024-10-26 @ 12:24 PM
Study NCT ID:
NCT03158571
Status:
COMPLETED
Last Update Posted:
2019-06-17
First Post:
2017-05-16
Brief Title:
Chilean Gastric Cancer Task Force FORCE 1
Sponsor:
Pontificia Universidad Catolica de Chile
Organization:
Pontificia Universidad Catolica de Chile
Study Overview
Official Title:
Chilean Gastric Cancer Task Force FORCE 1 A Study Protocol to Obtain a Clinical and Molecular Classification of a Cohort of Gastric Cancer Patients
Status:
COMPLETED
Status Verified Date:
2019-06
Last Known Status:
None
Delayed Posting:
No
If Stopped, Why?:
Not Stopped
Has Expanded Access:
False
If Expanded Access, NCT#:
N/A
Has Expanded Access, NCT# Status:
N/A
Acronym:
FORCE-1
Brief Summary:
Background Gastric cancer GC is the worlds second leading cause of neoplastic mortality Genetic alterations response to treatments and mortality rates are highly heterogeneous across different regions In Chile GC is the leading cause of cancer death affecting 20 per 100000 people and 3000 deathsyear Clinical outcomes and response to one size fits all therapies are highly heterogeneous and thus a better stratification of patients may aid cancer treatment and response
Study designmethods The Gastric Cancer Task Force GCTF is a Chilean collaborative non-interventional retrospective study that seeks to stratify gastric adenocarcinomas GACs using retrospect clinical outcomes and genomic epigenomic and protein alterations in a cohort of 200 patients Tumor samples from the pathology department and the Cancer Center at UC Christus healthcare network at Pontificia Universidad Católica de Chile will be analyzed using a panel of 143 known cancer genes Oncomine Comprehensive Assay at the Center of Excellence of Precision Medicine CEMP in Santiago Chile Additionally gene promoter methylation will be performed and selected clinically relevant proteins eg PD-L1 Erb-2 VEGFR2 among others will be assessed by Tissue Microarray Epstein-Barr virus EBV status will also be assessed Observations will be correlated to 120 clinical parameters including general patient information cancer history laboratory studies comorbidity index chemotherapy targeted therapies efficacy and follow-up
Discussion The development of a clinically meaningful classification that encompasses comprehensive clinical and molecular parameters may improve patient treatment predict clinical outcomes aid patient selection for clinical trials and offer insights into future preventive andor therapeutic strategies
Study designmethods The Gastric Cancer Task Force GCTF is a Chilean collaborative non-interventional retrospective study that seeks to stratify gastric adenocarcinomas GACs using retrospect clinical outcomes and genomic epigenomic and protein alterations in a cohort of 200 patients Tumor samples from the pathology department and the Cancer Center at UC Christus healthcare network at Pontificia Universidad Católica de Chile will be analyzed using a panel of 143 known cancer genes Oncomine Comprehensive Assay at the Center of Excellence of Precision Medicine CEMP in Santiago Chile Additionally gene promoter methylation will be performed and selected clinically relevant proteins eg PD-L1 Erb-2 VEGFR2 among others will be assessed by Tissue Microarray Epstein-Barr virus EBV status will also be assessed Observations will be correlated to 120 clinical parameters including general patient information cancer history laboratory studies comorbidity index chemotherapy targeted therapies efficacy and follow-up
Discussion The development of a clinically meaningful classification that encompasses comprehensive clinical and molecular parameters may improve patient treatment predict clinical outcomes aid patient selection for clinical trials and offer insights into future preventive andor therapeutic strategies
Detailed Description:
Participating entities The Chilean Gastric Cancer Task Force GCTF is a collective effort between two principal identities 1- The Center of Excellence of Precision Medicine CEMP which was established through a joint funding by the government agency for economic development Corporacion de Fomento de la Produccion CORFO and Pfizer Chile and 2- The Center UC for Investigation in Oncology CITO based at the Pontificia Universidad Católica de Chile Both entities are non-profit research organizations aimed at enhancing public education and implementing strategies to improve clinical outcomes in oncology treatment and cancer prevention
Primary objective To stratify Chilean GC patients into prognostic subgroups and to correlate therapy response according to clinical protein epigenetic and genetic alterations in a cohort of 200 GAC patients
Secondary objectives
To determine the mutation profile in Chilean GC patients
To assess the percentage of Chilean GC patients that could benefit from currently available druggable targets actionable genes
To correlate EBV presence to clinical parameters
To assess the expression levels of proteins associated with molecular stratifications and currently targeted therapies eg PD-L1 and antiangiogenics
To determine the profile of SNPs in the DPYD and TYMS genes in Chilean GC patients and their correlation with adverse events
Study design
Ethics approval The GCTF is a non-interventional collaborative prospective non-concurrent study that seeks to stratify GAC patients based on their prognosis and therapy response The study will strictly adhere to all legal requirements regulations and general principles established by international agencies governing the ethical conduct in biomedical research on human subjects following the good clinical practices and the declaration of Helsinki The GCTF study protocol has been approved by the Ethics Committee of the University hospital Pontificia Universidad Catolica de Chile CEC MED UC approval number 16-046 resolution dated April 21st 2016
Patient recruitment characteristics Diagnosed GC patients will be recruited from the Red UC Christus network in Santiago Chile Patient recruitment and signing of informed consent forms maintenance and monitoring of patient medical records biological material and sample extractions will be managed by CITO
Patient and treatment history reveals that besides surgery and chemotherapy approximately 10 of patients received Trastuzumab ERBB2 targeted therapy also called Herceptin another 10 received immunotherapy including pembrolizumab and Ipilimumab checkpoint inhibitors Finally approximately 5 of patients received antiangiogenic therapy consisting of VEGFR2 targeted therapy with Ramucirumab Additionally histological analysis showed that approximately 50 of patients were classified as intestinal type 30 as diffuse and 20 were either mixed or undetermined
Inclusion criteria
Adult male or female aged 18 years
Diagnosed with gastric cancer histological or cytological
Attending health centers of the Red UC Christus network for at least 3 months with clinical follow-up
Capable to read and speak Spanish
Willing and able to provide written informed consent to the study that should be dated and signed at the time of enrollment
Exclusion criteria
Patients
With small biopsy samples insufficient for analysis
Whose medical records cannot be collected or are unavailable
Without signed informed consent
Clinical data Clinical data from patients will be obtained by healthcare providers and entered into an online electronic platform Samples will be coded and patient identity known only to the attending physician Clinical variables are divided into sections General Patient Information Cancer History Laboratory Studies Comorbidity Charlson Index Chemotherapy Efficacy Follow Up and Toxicity Patient chemotherapy will be classified by regime number of cycles time of treatment and chemotherapy dose-intensity during the first 6 months Chemotherapy regimens representing the first line chemotherapy prescribed to the patients Full chemotherapy dose intensity during the first 6 months will be obtained through patient interviews and entered directly into the online platform Finally efficacy follow-up and toxicity data obtained from patients
Main clinical outcomes Main outcomes will be inferred from obtained clinical data these include overall survival progression-free and recurrence-free survival rates
Biological samples Oncomine Comprehensive Assay Biological materials obtained at the Red UC Christus will be transported to CEMP in Santiago de Chile under standardized protocols A total of 200 patient tumor samples will be obtained from archived Formalin Fixed Paraffin Embedded FFPE samples Nucleic acids will be extracted using the RecoverAll kit Thermo Fisher Cat AM1975 and analyzed using the commercially available Oncomine Comprehensive Assay kit This assay simultaneously analyzes DNA and RNA from samples allowing the assessment of 73 gene hotspots based on DNA 49 focal copy number variations CNVs DNA based 26 full coding sequences for mutations and CNV loss and 22 gene fusion drivers RNA Notably 72 of these genes are drug targets Genomic raw data obtained vcf and pdf files will be stored and backed up in a local Data Center for subsequent genomic analysis Upon publication of the findings of this study the Oncomine results along with clinical classification of individual tumors will be made publicly available
Tissue Micro Array TMA Analysis The following genes will be further analyzed by a TMA using specific antibodies against PD-L1 Dako Cat SK00521 PD-L2 Thermo Cat B7-DCCD273 Phosphorylated mTOR Abcam CatAB118815 p53 Cat 5278074001 VEGFR2 Abcam Cat AB39256 Phosphorylated Akt Thermo Cat 473 HER2 Roche Cat 05278368001 p16 Roche Cat 06695221001 Met Abcam Cat AB51067 HA-4 Abcam Cat AB24480 and four microsatellite markers all from Roche MLH1 Cat 06472966001 MSH2 Cat 05269270001 MSH6 Cat 5929911001 PMS2 Cat 06419216001 Manual TMA will be prepared as described previously Briefly paraffin blocks will be obtained and cut and stained by Hematoxylin Eosin HE in order to select the best histological area Subsequently selected tissue area will be placed into the TMA by circling the identified area in the corresponding block Cylindrical core biopsies will be extracted from each paraffin block using a 1 mm stylet and placed into a new recipient block Selected adequate cases had tumors that occupied at least 10 of the core area Each case will be processed in triplicate to prevent tissue loss during cutting Sections from each tissue array block will be cut de-paraffinized and dehydrated for HE and immunohistochemical procedures
Gene methylation Promoter gene methylation on six selected genes that have previously shown promoter regulation by methylation associated with GC will be assessed Methylation analysis will include the reprimo gene and other mRNAs associated with GC progression Analysis will be performed by bisulfite sequencing as described previously using the EZ DNA methylation Gold kit Zymo Research with minor modifications Briefly bisulfite treated DNA is amplified using specific PCR primers with PCR products subsequently cloned and sequenced
EBV identification EBV subtypes in patient samples will be assessed using the chromogenic in situ hybridization CISH method with minor modifications
Single Nucleotide Polymorphism SNP analysis A significant proportion of GC patients can develop serious toxicity from 5-FU treatment including bone marrow suppression neuropathy low white blood cell numbers fever infections nausea vomiting severe diarrhea mouth and digestive tract inflammation all of which are recorded in the patient history of other cohorts Subtle personal and population changes in DNA called SNPs can account for increases in the risk of 5-FU toxicity 5-FU metabolism is predominantly hepatic where the enzyme DPYD is responsible for metabolizing 80 of the drug producing the inactive metabolite 56 dihydroxy-5-FU It is widely documented that a decreased DPYP activity is associated with severe toxicity Non-metabolised fraction of 5-FU 20 is transformed by a series of enzymes eg TP TK producing the active metabolites that will cause TYMS inhibition thereby promoting DNARNA damage Variations in TYMS and MTHFR genes related to reduced folate synthesis increased 5-FU effect have been associated with toxicity by treatment with 5-FU The approach that was used to select the genetic variants consisted of a search in the database PharmGKB A total of six non-synonymous SNPs will be analyzed four of them comprise the DPYD gene one for TYMS and one for MTHFR Analysis will be performed using TaqMan SNP Genotyping Assay technology Applied Biosystems SNPs will be assessed in DNA isolated from paraffin embedded patient samples
Sample size and statistical analysis
The minimum sample number will be calculated in order to ensure the goals of the project are fully accomplished Considering that approximately 90 of GC cases are indeed GAC at 5 error rate and at 95 confidence interval the investigators originally projected a sample size of 200 patients However the investigators have also considered a 15 rate of sample loss defective samples or patient drop-out which gave a total of 230 patients to be recruited
Standard descriptive statistics will be utilized to analyze qualitative and quantitative variables such as relative and absolute frequencies frequency tables average median standard deviation range and quartiles A 95 confidence will be considered appropriate for analysis Descriptive statistics will also be used to characterize the most relevant clinical parameters measured The association of categorized variables will be performed by chi-square or Fishers exact tests One arm Analysis of Variance will compare continuous variables among groups Survival outcome studies will be accomplished using the Kaplan-Meier method Prognostic factors will be evaluated according to the Cox proportional hazards regression model
Principal component analysis PCA of the genes variants will be conducted and the association of the first principal components with a small pre-defined set of genomic alteration signatures will be assessed To define molecular subgroups the investigators will utilize unsupervised clustering The correlation of the molecular subtypes with clinical data eg age gender Lauren class and clinical outcomes eg overall survival response rate will be assessed Moreover supervised classification will be performed based on clinical outcomes and the resulting groups of both approaches will be compared with other reported molecular subtypes
Patient protectionwritten informed consent forms
All parties guarantee the protection of the patients personal records Patient names are not included in any form in sheet-reports publications or in any type of publishable document derived from the study with the exception of documents required by law Informed consent forms are elaborated strictly following legal and local regulations The written informed consent forms including all changes made throughout the study must be prospectively approved by the Internal Review Boardindependent Ethics Committee and CEMP prior to be incorporated into the study
The investigators representatives or healthcare providers will obtain written informed consent forms from every patient or a legal representative before any specific activity of the study is performed
Primary objective To stratify Chilean GC patients into prognostic subgroups and to correlate therapy response according to clinical protein epigenetic and genetic alterations in a cohort of 200 GAC patients
Secondary objectives
To determine the mutation profile in Chilean GC patients
To assess the percentage of Chilean GC patients that could benefit from currently available druggable targets actionable genes
To correlate EBV presence to clinical parameters
To assess the expression levels of proteins associated with molecular stratifications and currently targeted therapies eg PD-L1 and antiangiogenics
To determine the profile of SNPs in the DPYD and TYMS genes in Chilean GC patients and their correlation with adverse events
Study design
Ethics approval The GCTF is a non-interventional collaborative prospective non-concurrent study that seeks to stratify GAC patients based on their prognosis and therapy response The study will strictly adhere to all legal requirements regulations and general principles established by international agencies governing the ethical conduct in biomedical research on human subjects following the good clinical practices and the declaration of Helsinki The GCTF study protocol has been approved by the Ethics Committee of the University hospital Pontificia Universidad Catolica de Chile CEC MED UC approval number 16-046 resolution dated April 21st 2016
Patient recruitment characteristics Diagnosed GC patients will be recruited from the Red UC Christus network in Santiago Chile Patient recruitment and signing of informed consent forms maintenance and monitoring of patient medical records biological material and sample extractions will be managed by CITO
Patient and treatment history reveals that besides surgery and chemotherapy approximately 10 of patients received Trastuzumab ERBB2 targeted therapy also called Herceptin another 10 received immunotherapy including pembrolizumab and Ipilimumab checkpoint inhibitors Finally approximately 5 of patients received antiangiogenic therapy consisting of VEGFR2 targeted therapy with Ramucirumab Additionally histological analysis showed that approximately 50 of patients were classified as intestinal type 30 as diffuse and 20 were either mixed or undetermined
Inclusion criteria
Adult male or female aged 18 years
Diagnosed with gastric cancer histological or cytological
Attending health centers of the Red UC Christus network for at least 3 months with clinical follow-up
Capable to read and speak Spanish
Willing and able to provide written informed consent to the study that should be dated and signed at the time of enrollment
Exclusion criteria
Patients
With small biopsy samples insufficient for analysis
Whose medical records cannot be collected or are unavailable
Without signed informed consent
Clinical data Clinical data from patients will be obtained by healthcare providers and entered into an online electronic platform Samples will be coded and patient identity known only to the attending physician Clinical variables are divided into sections General Patient Information Cancer History Laboratory Studies Comorbidity Charlson Index Chemotherapy Efficacy Follow Up and Toxicity Patient chemotherapy will be classified by regime number of cycles time of treatment and chemotherapy dose-intensity during the first 6 months Chemotherapy regimens representing the first line chemotherapy prescribed to the patients Full chemotherapy dose intensity during the first 6 months will be obtained through patient interviews and entered directly into the online platform Finally efficacy follow-up and toxicity data obtained from patients
Main clinical outcomes Main outcomes will be inferred from obtained clinical data these include overall survival progression-free and recurrence-free survival rates
Biological samples Oncomine Comprehensive Assay Biological materials obtained at the Red UC Christus will be transported to CEMP in Santiago de Chile under standardized protocols A total of 200 patient tumor samples will be obtained from archived Formalin Fixed Paraffin Embedded FFPE samples Nucleic acids will be extracted using the RecoverAll kit Thermo Fisher Cat AM1975 and analyzed using the commercially available Oncomine Comprehensive Assay kit This assay simultaneously analyzes DNA and RNA from samples allowing the assessment of 73 gene hotspots based on DNA 49 focal copy number variations CNVs DNA based 26 full coding sequences for mutations and CNV loss and 22 gene fusion drivers RNA Notably 72 of these genes are drug targets Genomic raw data obtained vcf and pdf files will be stored and backed up in a local Data Center for subsequent genomic analysis Upon publication of the findings of this study the Oncomine results along with clinical classification of individual tumors will be made publicly available
Tissue Micro Array TMA Analysis The following genes will be further analyzed by a TMA using specific antibodies against PD-L1 Dako Cat SK00521 PD-L2 Thermo Cat B7-DCCD273 Phosphorylated mTOR Abcam CatAB118815 p53 Cat 5278074001 VEGFR2 Abcam Cat AB39256 Phosphorylated Akt Thermo Cat 473 HER2 Roche Cat 05278368001 p16 Roche Cat 06695221001 Met Abcam Cat AB51067 HA-4 Abcam Cat AB24480 and four microsatellite markers all from Roche MLH1 Cat 06472966001 MSH2 Cat 05269270001 MSH6 Cat 5929911001 PMS2 Cat 06419216001 Manual TMA will be prepared as described previously Briefly paraffin blocks will be obtained and cut and stained by Hematoxylin Eosin HE in order to select the best histological area Subsequently selected tissue area will be placed into the TMA by circling the identified area in the corresponding block Cylindrical core biopsies will be extracted from each paraffin block using a 1 mm stylet and placed into a new recipient block Selected adequate cases had tumors that occupied at least 10 of the core area Each case will be processed in triplicate to prevent tissue loss during cutting Sections from each tissue array block will be cut de-paraffinized and dehydrated for HE and immunohistochemical procedures
Gene methylation Promoter gene methylation on six selected genes that have previously shown promoter regulation by methylation associated with GC will be assessed Methylation analysis will include the reprimo gene and other mRNAs associated with GC progression Analysis will be performed by bisulfite sequencing as described previously using the EZ DNA methylation Gold kit Zymo Research with minor modifications Briefly bisulfite treated DNA is amplified using specific PCR primers with PCR products subsequently cloned and sequenced
EBV identification EBV subtypes in patient samples will be assessed using the chromogenic in situ hybridization CISH method with minor modifications
Single Nucleotide Polymorphism SNP analysis A significant proportion of GC patients can develop serious toxicity from 5-FU treatment including bone marrow suppression neuropathy low white blood cell numbers fever infections nausea vomiting severe diarrhea mouth and digestive tract inflammation all of which are recorded in the patient history of other cohorts Subtle personal and population changes in DNA called SNPs can account for increases in the risk of 5-FU toxicity 5-FU metabolism is predominantly hepatic where the enzyme DPYD is responsible for metabolizing 80 of the drug producing the inactive metabolite 56 dihydroxy-5-FU It is widely documented that a decreased DPYP activity is associated with severe toxicity Non-metabolised fraction of 5-FU 20 is transformed by a series of enzymes eg TP TK producing the active metabolites that will cause TYMS inhibition thereby promoting DNARNA damage Variations in TYMS and MTHFR genes related to reduced folate synthesis increased 5-FU effect have been associated with toxicity by treatment with 5-FU The approach that was used to select the genetic variants consisted of a search in the database PharmGKB A total of six non-synonymous SNPs will be analyzed four of them comprise the DPYD gene one for TYMS and one for MTHFR Analysis will be performed using TaqMan SNP Genotyping Assay technology Applied Biosystems SNPs will be assessed in DNA isolated from paraffin embedded patient samples
Sample size and statistical analysis
The minimum sample number will be calculated in order to ensure the goals of the project are fully accomplished Considering that approximately 90 of GC cases are indeed GAC at 5 error rate and at 95 confidence interval the investigators originally projected a sample size of 200 patients However the investigators have also considered a 15 rate of sample loss defective samples or patient drop-out which gave a total of 230 patients to be recruited
Standard descriptive statistics will be utilized to analyze qualitative and quantitative variables such as relative and absolute frequencies frequency tables average median standard deviation range and quartiles A 95 confidence will be considered appropriate for analysis Descriptive statistics will also be used to characterize the most relevant clinical parameters measured The association of categorized variables will be performed by chi-square or Fishers exact tests One arm Analysis of Variance will compare continuous variables among groups Survival outcome studies will be accomplished using the Kaplan-Meier method Prognostic factors will be evaluated according to the Cox proportional hazards regression model
Principal component analysis PCA of the genes variants will be conducted and the association of the first principal components with a small pre-defined set of genomic alteration signatures will be assessed To define molecular subgroups the investigators will utilize unsupervised clustering The correlation of the molecular subtypes with clinical data eg age gender Lauren class and clinical outcomes eg overall survival response rate will be assessed Moreover supervised classification will be performed based on clinical outcomes and the resulting groups of both approaches will be compared with other reported molecular subtypes
Patient protectionwritten informed consent forms
All parties guarantee the protection of the patients personal records Patient names are not included in any form in sheet-reports publications or in any type of publishable document derived from the study with the exception of documents required by law Informed consent forms are elaborated strictly following legal and local regulations The written informed consent forms including all changes made throughout the study must be prospectively approved by the Internal Review Boardindependent Ethics Committee and CEMP prior to be incorporated into the study
The investigators representatives or healthcare providers will obtain written informed consent forms from every patient or a legal representative before any specific activity of the study is performed
Study Oversight
Has Oversight DMC:
None
Is a FDA Regulated Drug?:
False
Is a FDA Regulated Device?:
False
Is an Unapproved Device?:
None
Is a PPSD?:
None
Is a US Export?:
None
Is an FDA AA801 Violation?:
None