and 62/795,900) submitted by Johns Hopkins University related to cell-free DNA for cancer detecti... more and 62/795,900) submitted by Johns Hopkins University related to cell-free DNA for cancer detection. V.E.V. is a founder of Delfi Diagnostics and Personal Genome Diagnostics, a member of their Scientific Advisory Boards and Boards of Directors, and owns Delfi Diagnostics and Personal Genome Diagnostics stock, which are subject to certain restrictions under university policy. Within the last five years, V.E.V. has been an advisor to Daiichi Sankyo, Janssen Diagnostics, Ignyta, and Takeda Pharmaceuticals. The terms of these arrangements are managed by Johns Hopkins University in accordance with its conflict of interest policies.
Patients with metastatic colorectal cancer (mCRC) have limited benefit from the addition of bevac... more Patients with metastatic colorectal cancer (mCRC) have limited benefit from the addition of bevacizumab to standard chemotherapy. However, a subset probably benefits substantially, highlighting an unmet clinical need for a biomarker of response to bevacizumab. Previously, we demonstrated that losses of chromosomes 5q34, 17q12, and 18q11.2-q12.1 had a significant correlation with progression-free survival (PFS) in patients with mCRC treated with bevacizumab in the CAIRO2 clinical trial but not in patients who did not receive bevacizumab in the CAIRO trial. This study was designed to validate these findings. Materials and Methods Primary mCRC samples were analyzed from two cohorts of patients who received bevacizumab as first-line treatment; 96 samples from the European multicenter study Angiopredict (APD) and 81 samples from the Italian multicenter study, MOMA. A third cohort of 90 samples from patients with mCRC who did not receive bevacizumab was analyzed. Copy number aberrations of tumor biopsy specimens were measured by shallow whole-genome sequencing and were correlated with PFS, overall survival (OS), and response. Results Loss of chromosome 18q11.2-q12.1 was associated with prolonged PFS most significantly in both the cohorts that received bevacizumab (APD: hazard ratio, 0.54; P = .01; PFS difference, 65 days; MOMA: hazard ratio, 0.55; P = .019; PFS difference, 49 days). A similar association was found for OS and overall response rate in these two cohorts, which became significant when combined with the CAIRO2 cohort. Median PFS in the cohort of patients with mCRC who did not receive bevacizumab and in the CAIRO cohort was similar to that of the APD, MOMA, and CAIRO2 patients without an 18q11.2-q12.1 loss. Conclusion We conclude that the loss of chromosome 18q11.2-q12.1 is consistently predictive for prolonged PFS in patients receiving bevacizumab. The predictive value of this loss is substantiated by a significant gain in OS and overall response rate.
Background We evaluated the time to progression (TTP) and survival outcomes of second-line therap... more Background We evaluated the time to progression (TTP) and survival outcomes of second-line therapy for metastatic colorectal cancer among adults aged 70 years and older compared with younger adults following progression on first-line clinical trials. Methods Associations between clinical and disease characteristics, time to initial progression, and rate of receipt of second-line therapy were evaluated. TTP and overall survival (OS) were compared between older and younger adults in first- and second-line trials by Cox regression, adjusting for age, sex, Eastern Cooperative Oncology Group Performance Status, number of metastatic sites and presence of metastasis in the lung, liver, or peritoneum. All statistical tests were 2-sided. Results Older adults comprised 16.4% of patients on first-line trials (870 total older adults aged >70 years; 4419 total younger adults aged ≤70 years, on first-line trials). Older adults and those with Eastern Cooperative Oncology Group Performance Statu...
BackgroundMetastatic colorectal cancer patients with deficient mismatch repair (dMMR mCRC) benefi... more BackgroundMetastatic colorectal cancer patients with deficient mismatch repair (dMMR mCRC) benefit from immunotherapy. Interpretation of the single-arm immunotherapy trials is complicated by insignificant survival data during systemic non-immunotherapy. We present survival data on a large, comprehensive cohort of dMMR mCRC patients, treated with or without systemic non-immunotherapy.MethodsTwo hundred and eighty-one dMMR mCRC patients (n = 54 from three prospective Phase 3 CAIRO trials;n = 227 from the Netherlands Cancer Registry). Overall survival was analysed from diagnosis of mCRC (OS), from initiation of first-line (OS1) and second-line (OS2) systemic treatment. Cox regression analysis examined prognostic factors. As comparison for OS 2746 MMR proficient mCRC patients were identified.ResultsOf 281 dMMR patients, 62% received first-line and 26% second-line treatment. Median OS was 16.0 months (13.8–19.6) with antitumour therapy and 2.5 months (1.8–3.5) in untreated patients. OS1 ...
3552 Background: Heterogeneity in the biology of colorectal cancer (CRC) is associated with varia... more 3552 Background: Heterogeneity in the biology of colorectal cancer (CRC) is associated with variable responses to standard chemotherapy. We aimed to identify DNA hypermethylated genes as predictive biomarkers for irinotecan treatment of patients with metastatic CRC. Methods: The presence of DNA methylation for a selected panel of 22 genes was assessed by methylation specific PCR (MSP) on primary tumors of 185 patients with metastatic CRC treated with first-line capecitabine (CAP, n=90) or a combination of capecitabine and irinotecan (CAPIRI, n=95) in the phase 3 CAIRO trial. Methylation status of each gene was correlated to progression free survival (PFS) by treatment regimen. Genes for which methylation status associated with response to irinotecan, were validated in 166 patients treated with first-line CAP (n=78) or CAPIRI (n=88). Results: Decoy Receptor 1 (DCR1) was identified as a novel hypermethylated gene in CRC. In CAPIRI treated patients, DCR1 methylation was correlated to a...
Cell-free DNA in the blood provides a non-invasive diagnostic avenue for patients with cancer 1. ... more Cell-free DNA in the blood provides a non-invasive diagnostic avenue for patients with cancer 1. However, characteristics of the origins and molecular features of cell-free DNA are poorly understood. Here we developed an approach to evaluate fragmentation patterns of cell-free DNA across the genome, and found that profiles of healthy individuals reflected nucleosomal patterns of white blood cells, whereas patients with cancer had altered fragmentation profiles. We used this method to analyse the fragmentation profiles of 236 patients with breast, colorectal, lung, ovarian, pancreatic, gastric or bile duct cancer and 245 healthy individuals. A machine learning model that incorporated genome-wide fragmentation features had sensitivities of detection ranging from 57% to more than 99% among the seven cancer types at 98% specificity, with an overall area under the curve value of 0.94. Fragmentation profiles could be used to identify the tissue of origin of the cancers to a limited number of sites in 75% of cases. Combining our approach with mutation-based cell-free DNA analyses detected 91% of patients with cancer. The results of these analyses highlight important properties of cell-free DNA and provide a proof-of-principle approach for the screening, early detection and monitoring of human cancer. Much of the morbidity and mortality of human cancers worldwide results from late diagnosis when therapeutic intervention is less effective 2,3. Unfortunately, clinically proven biomarkers that can be used to broadly diagnose and treat patients are not widely available 4. Recent analyses of circulating cell-free DNA (cfDNA) suggest that approaches using tumour-specific alterations may provide new opportunities for early diagnosis, but not all patients have detectable changes 5-8. Whole-genome sequencing (WGS) of cfDNA can identify chromosomal abnormalities in patients with cancer but detecting such alterations may be challenging owing to the small number of abnormal chromosomal changes 9-12. Analyses of the size of fragments of cfDNA have been contradictory, indicating both increases 13-15 and decreases in the overall distribution of cfDNA 12,16,17-19. Recent studies have suggested that size selection of small cfDNA can increase enrichment of circulating tumour DNA in patients with late-stage cancer 17. Nucleosome positions 18,20 , patterns near transcription start sites 20,21 , and the end positions of cfDNA 22 may be altered in cancer, but the sequencing needed to identify nucleosomes is impractical for routine analyses. Conceptually, the sensitivity of any cfDNA approach depends on the number of alterations examined as well as the technical and biological limitations of detecting such changes. As a typical blood sample contains approximately 2,000 genome equivalents of cfDNA per millilitre of plasma 5 , the theoretical limit of detection of a single alteration can be no better than one in a few thousand mutant to wild-type molecules. We hypothesized that the detection of a larger number of alterations in the genome may be more sensitive for detecting cancer in
European journal of cancer (Oxford, England : 1990), Jan 21, 2018
Patient characteristics and stratification factors are key features influencing trial outcomes. H... more Patient characteristics and stratification factors are key features influencing trial outcomes. However, there is substantial heterogeneity in reporting of patient characteristics and use of stratification factors in phase 3 trials investigating systemic treatment of metastatic colorectal cancer (mCRC). We aimed to develop a minimum set of essential baseline characteristics and stratification factors to include in such trials. We performed a modified, two-round Delphi survey among international experts with wide experience in the conduct and methodology of phase 3 trials of systemic treatment of mCRC. Thirty mCRC experts from 15 different countries completed both consensus rounds. A total of 14 patient characteristics were included in the recommended set: age, performance status, primary tumour location, primary tumour resection, prior chemotherapy, number of metastatic sites, liver-only disease, liver involvement, surgical resection of metastases, synchronous versus metachronous me...
Stage 3a: 88.8% Stage 3b: 67.0% Stage 3c: 63.3% Stage 3a b : 83% Stage 3b b : 64% Stage 3c b : 44... more Stage 3a: 88.8% Stage 3b: 67.0% Stage 3c: 63.3% Stage 3a b : 83% Stage 3b b : 64% Stage 3c b : 44% 80% (all stage 3, with FOLFOX, mean age 60) 40 year-old male, stage 2 colon cancer, MSI +ve Stage 2a a : 93% Stage 2b a : 78% Stage 2c: 57% a Currently not available Stage 2 not supported Not available for MSI +ve 88% (includes stage 2 and 3, without adjuvant chemotherapy) a Without adjuvant chemotherapy. b Mean age 60 years.
In recent years, the high heterogeneity of colorectal cancer (CRC) has become evident. Hence, bio... more In recent years, the high heterogeneity of colorectal cancer (CRC) has become evident. Hence, biomarkers need to be developed that enable the stratification of patients with CRC into different prognostic subgroups and in relation to response to therapies, according to the distinctive tumour biology. Currently, only RAS-mutation status is used routinely as a negative predictive marker to avoid treatment with anti-EGFR agents in patients with metastatic CRC, and mismatch-repair status can guide the use of adjuvant chemotherapy in patients with early stage colon cancer. Advances in molecular biology over the past decade have enabled a better understanding of the development of CRC, as well as the more-precise use of innovative targeted therapies for this disease, and include three fundamental achievements. First, the availability of large databases to capture and store the genomic landscape of patients with CRC, providing information on the genes that are frequently deregulated in CRC....
Patients with peritoneal metastatic colorectal cancer have reduced overall survival compared with... more Patients with peritoneal metastatic colorectal cancer have reduced overall survival compared with patients with metastatic colorectal cancer without peritoneal involvement. Here we further investigated the effect of the number and location of metastases in patients receiving first-line systemic chemotherapy. We analysed individual patient data for previously untreated patients enrolled in 14 phase 3 randomised trials done between 1997 and 2008. Trials were included if protocols explicitly pre-specified and solicited for patients with peritoneal involvement in the trial data collection process or had done a formal peritoneum-focused review of individual pre-treatment scans. We used stratified multivariable Cox models to assess the prognostic associations of peritoneal metastatic colorectal cancer with overall survival and progression-free survival, adjusting for other key clinical-pathological factors (age, sex, Eastern Cooperative Oncology Group (ECOG) performance score, primary tum...
Clinical cancer research : an official journal of the American Association for Cancer Research, Jan 26, 2016
Recent transcriptomic analyses have identified four distinct molecular subtypes of colorectal can... more Recent transcriptomic analyses have identified four distinct molecular subtypes of colorectal cancer (CRC) with evident clinical relevance. However, the requirement for sufficient quantities of bulk tumor and difficulties in obtaining high quality genome-wide transcriptome data from formalin-fixed paraffin-embedded tissue are obstacles towards widespread adoption of this taxonomy. Here, we develop an immunohistochemistry-based classifier to validate the prognostic and predictive value of molecular CRC subtyping in a multi-center study. Tissue microarrays from 1076 CRC patients from four different cohorts were stained for five markers (CDX2, FRMD6, HTR2B, ZEB1 and KER) by immunohistochemistry and assessed for microsatellite instability. An automated classification system was trained on one cohort using quantitative image analysis or semi-quantitative pathologist scoring of the cores as input, and applied to three independent clinical cohorts. This classifier demonstrated 87% concorda...
Clinical cancer research : an official journal of the American Association for Cancer Research, Jan 27, 2016
WRN promoter CpG island hypermethylation in colorectal cancer (CRC) has been reported to increase... more WRN promoter CpG island hypermethylation in colorectal cancer (CRC) has been reported to increase sensitivity to irinotecan-based therapies. We aimed to characterize methylation of the WRN promoter; determine the effect of WRN promoter hypermethylation upon expression; and validate a previous report that WRN promoter hypermethylation predicts improved outcomes for metastatic colorectal cancer (mCRC) patients treated with irinotecan-based therapy. WRN methylation status was assessed using methylation-specific PCR and bisulfite sequencing assays. WRN expression was determined using qRT-PCR and Western blotting. WRN methylation status was correlated with overall survival (OS) and progression-free survival (PFS) in 183 patients with mCRC. Among these patients 90 received capecitabine monotherapy (CAP) as first line therapy and 93 received capecitabine plus irinotecan (CAPIRI) therapy as part of the CAIRO Phase III clinical trial. WRN mRNA and WRN protein expression levels were low in CR...
Microsatellite instability (MSI) has been associated with favourable survival in early stage colo... more Microsatellite instability (MSI) has been associated with favourable survival in early stage colorectal cancer (CRC) compared to microsatellite stable (MSS) CRC. The BRAF V600E mutation has been associated with worse survival in MSS CRC. This mutation occurs in 40% of MSI CRC and it is unclear whether it confers worse survival in this setting. The prognostic value of KRAS mutations in both MSS and MSI CRC remains unclear. We examined the effect of BRAF and KRAS mutations on survival in stage II and III MSI colon cancer patients. BRAF exon 15 and KRAS exon 2–3 mutation status was assessed in 143 stage II (n = 85) and III (n = 58) MSI colon cancers by high resolution melting analysis and sequencing. The relation between mutation status and cancer‐specific (CSS) and overall survival (OS) was analyzed using Kaplan–Meier and Cox regression analysis. BRAF V600E mutations were observed in 51% (n = 73) and KRAS mutations in 16% of cases (n = 23). Patients with double wild‐type cancers (dWT;...
Background: Mucinous carcinoma (MC) is found in 10%-15% of colorectal cancer (CRC) patients. It d... more Background: Mucinous carcinoma (MC) is found in 10%-15% of colorectal cancer (CRC) patients. It differs from the common adenocarcinoma (AC) in histopathological appearance and clinical behavior. Methods: Genome-wide DNA copy number and survival data from MC and AC primary CRC samples from patients from two phase III trials (CAIRO and CAIRO2) was compared. Chromosomal copy number data from The Cancer Genome Atlas (TCGA) was used for validation. Altogether, 470 ACs were compared to 57 MCs. Results: MC showed a reduced amount of copy number aberrations (CNAs) compared with AC for the CAIRO/CAIRO2 cohort, with a median amount of CNAs that was 1.5-fold lower (P = 0.002). Data from TCGA also showed a reduced amount of CNAs for MC. MC samples in both cohorts displayed less gain at chromosome 20q and less loss of chromosome 18p. A high rate of chromosomal instability was a strong negative prognostic marker for survival in MC patients from the CAIRO cohorts (hazard ratio 15.60, 95% CI 3.24-75.05). Conclusions: Results from this study indicate that the distinct MC phenotype is accompanied by a different genetic basis when compared with AC and show a strong association between the rate of chromosomal instability and survival in MC patients.
American Society of Clinical Oncology Educational Book, 2015
With the currently available cytotoxic and targeted drugs, metastatic colorectal cancer (mCRC) ma... more With the currently available cytotoxic and targeted drugs, metastatic colorectal cancer (mCRC) may be controlled by systemic treatment for a substantial period of time. However, many questions remain about the optimal use of drugs and duration of treatment. The feasibility of chemotherapy-free intervals has been studied in patients with mCRC treated with chemotherapy alone, but the results are conflicting. Current data show that oxaliplatin may be safely interrupted, but they do not allow a firm conclusion on the safety of a full treatment break of chemotherapy. For targeted therapy, continuous inhibition of intracellular signaling by prolonged administration would theoretically be beneficial for efficacy of treatment. Recent data support the use of maintenance treatment with chemotherapy and bevacizumab. No data on the optimal duration of treatment with anti-epidermal growth factor receptor (EGFR) agents are currently available.
With the currently available cytotoxic and targeted drugs, metastatic colorectal cancer (mCRC) ma... more With the currently available cytotoxic and targeted drugs, metastatic colorectal cancer (mCRC) may be controlled by systemic treatment for a significant period of time. However, many questions remain about the optimal use of drugs and duration of treatment. We reviewed the data from clinical trials on the optimal duration of systemic treatment with chemotherapy and targeted therapy in mCRC patients. The feasibility of chemotherapy-free intervals has been studied in mCRC patients treated with chemotherapy alone, but the results are conflicting. Current data show that oxaliplatin may be safely interrupted, but do not allow a firm conclusion on the safety of a full treatment break of chemotherapy. For targeted therapy, continuous inhibition of intracellular signalling by prolonged administration would theoretically be beneficial for efficacy of treatment, and has been suggested by retrospectively collected data. Recent data from a prospective study show a clinical benefit for maintenan...
Clinical cancer research : an official journal of the American Association for Cancer Research, Jan 15, 2014
To determine the prevalence and prognostic value of mismatch repair (MMR) status and its relation... more To determine the prevalence and prognostic value of mismatch repair (MMR) status and its relation to BRAF mutation (BRAF(MT)) status in metastatic colorectal cancer (mCRC). A pooled analysis of four phase III studies in first-line treatment of mCRC (CAIRO, CAIRO2, COIN, and FOCUS) was performed. Primary outcome parameter was the hazard ratio (HR) for median progression-free survival (PFS) and overall survival (OS) in relation to MMR and BRAF. For the pooled analysis, Cox regression analysis was performed on individual patient data. The primary tumors of 3,063 patients were analyzed, of which 153 (5.0%) exhibited deficient MMR (dMMR) and 250 (8.2%) a BRAF(MT). BRAF(MT) was observed in 53 (34.6%) of patients with dMMR tumors compared with 197 (6.8%) of patients with proficient MMR (pMMR) tumors (P < 0.001). In the pooled dataset, median PFS and OS were significantly worse for patients with dMMR compared with pMMR tumors [HR, 1.33; 95% confidence interval (CI), 1.12-1.57 and HR, 1.3...
Background KRAS mutation is a negative predictive factor for treatment with anti-epidermal growth... more Background KRAS mutation is a negative predictive factor for treatment with anti-epidermal growth factor receptor (EGFR) antibodies in metastatic colorectal cancer (mCRC). Novel predictive markers are required to further improve the selection of patients for this treatment. We assessed the influence of modification of KRAS by gene copy number aberration (CNA) and microRNAs (miRNAs) in correlation to clinical outcome in mCRC patients treated with cetuximab in combination with chemotherapy and bevacizumab. Methods Formalin-fixed paraffin-embedded primary tumour tissue was used from 34 mCRC patients in a phase III trial, who were selected based upon their good (n = 17) or poor (n = 17) progression-free survival (PFS) upon treatment with cetuximab in combination with capecitabine, oxaliplatin, and bevacizumab. Gene copy number at the KRAS locus was assessed using high resolution genome-wide array CGH and the expression levels of 17 miRNAs targeting KRAS were determined by real-time PCR....
and 62/795,900) submitted by Johns Hopkins University related to cell-free DNA for cancer detecti... more and 62/795,900) submitted by Johns Hopkins University related to cell-free DNA for cancer detection. V.E.V. is a founder of Delfi Diagnostics and Personal Genome Diagnostics, a member of their Scientific Advisory Boards and Boards of Directors, and owns Delfi Diagnostics and Personal Genome Diagnostics stock, which are subject to certain restrictions under university policy. Within the last five years, V.E.V. has been an advisor to Daiichi Sankyo, Janssen Diagnostics, Ignyta, and Takeda Pharmaceuticals. The terms of these arrangements are managed by Johns Hopkins University in accordance with its conflict of interest policies.
Patients with metastatic colorectal cancer (mCRC) have limited benefit from the addition of bevac... more Patients with metastatic colorectal cancer (mCRC) have limited benefit from the addition of bevacizumab to standard chemotherapy. However, a subset probably benefits substantially, highlighting an unmet clinical need for a biomarker of response to bevacizumab. Previously, we demonstrated that losses of chromosomes 5q34, 17q12, and 18q11.2-q12.1 had a significant correlation with progression-free survival (PFS) in patients with mCRC treated with bevacizumab in the CAIRO2 clinical trial but not in patients who did not receive bevacizumab in the CAIRO trial. This study was designed to validate these findings. Materials and Methods Primary mCRC samples were analyzed from two cohorts of patients who received bevacizumab as first-line treatment; 96 samples from the European multicenter study Angiopredict (APD) and 81 samples from the Italian multicenter study, MOMA. A third cohort of 90 samples from patients with mCRC who did not receive bevacizumab was analyzed. Copy number aberrations of tumor biopsy specimens were measured by shallow whole-genome sequencing and were correlated with PFS, overall survival (OS), and response. Results Loss of chromosome 18q11.2-q12.1 was associated with prolonged PFS most significantly in both the cohorts that received bevacizumab (APD: hazard ratio, 0.54; P = .01; PFS difference, 65 days; MOMA: hazard ratio, 0.55; P = .019; PFS difference, 49 days). A similar association was found for OS and overall response rate in these two cohorts, which became significant when combined with the CAIRO2 cohort. Median PFS in the cohort of patients with mCRC who did not receive bevacizumab and in the CAIRO cohort was similar to that of the APD, MOMA, and CAIRO2 patients without an 18q11.2-q12.1 loss. Conclusion We conclude that the loss of chromosome 18q11.2-q12.1 is consistently predictive for prolonged PFS in patients receiving bevacizumab. The predictive value of this loss is substantiated by a significant gain in OS and overall response rate.
Background We evaluated the time to progression (TTP) and survival outcomes of second-line therap... more Background We evaluated the time to progression (TTP) and survival outcomes of second-line therapy for metastatic colorectal cancer among adults aged 70 years and older compared with younger adults following progression on first-line clinical trials. Methods Associations between clinical and disease characteristics, time to initial progression, and rate of receipt of second-line therapy were evaluated. TTP and overall survival (OS) were compared between older and younger adults in first- and second-line trials by Cox regression, adjusting for age, sex, Eastern Cooperative Oncology Group Performance Status, number of metastatic sites and presence of metastasis in the lung, liver, or peritoneum. All statistical tests were 2-sided. Results Older adults comprised 16.4% of patients on first-line trials (870 total older adults aged >70 years; 4419 total younger adults aged ≤70 years, on first-line trials). Older adults and those with Eastern Cooperative Oncology Group Performance Statu...
BackgroundMetastatic colorectal cancer patients with deficient mismatch repair (dMMR mCRC) benefi... more BackgroundMetastatic colorectal cancer patients with deficient mismatch repair (dMMR mCRC) benefit from immunotherapy. Interpretation of the single-arm immunotherapy trials is complicated by insignificant survival data during systemic non-immunotherapy. We present survival data on a large, comprehensive cohort of dMMR mCRC patients, treated with or without systemic non-immunotherapy.MethodsTwo hundred and eighty-one dMMR mCRC patients (n = 54 from three prospective Phase 3 CAIRO trials;n = 227 from the Netherlands Cancer Registry). Overall survival was analysed from diagnosis of mCRC (OS), from initiation of first-line (OS1) and second-line (OS2) systemic treatment. Cox regression analysis examined prognostic factors. As comparison for OS 2746 MMR proficient mCRC patients were identified.ResultsOf 281 dMMR patients, 62% received first-line and 26% second-line treatment. Median OS was 16.0 months (13.8–19.6) with antitumour therapy and 2.5 months (1.8–3.5) in untreated patients. OS1 ...
3552 Background: Heterogeneity in the biology of colorectal cancer (CRC) is associated with varia... more 3552 Background: Heterogeneity in the biology of colorectal cancer (CRC) is associated with variable responses to standard chemotherapy. We aimed to identify DNA hypermethylated genes as predictive biomarkers for irinotecan treatment of patients with metastatic CRC. Methods: The presence of DNA methylation for a selected panel of 22 genes was assessed by methylation specific PCR (MSP) on primary tumors of 185 patients with metastatic CRC treated with first-line capecitabine (CAP, n=90) or a combination of capecitabine and irinotecan (CAPIRI, n=95) in the phase 3 CAIRO trial. Methylation status of each gene was correlated to progression free survival (PFS) by treatment regimen. Genes for which methylation status associated with response to irinotecan, were validated in 166 patients treated with first-line CAP (n=78) or CAPIRI (n=88). Results: Decoy Receptor 1 (DCR1) was identified as a novel hypermethylated gene in CRC. In CAPIRI treated patients, DCR1 methylation was correlated to a...
Cell-free DNA in the blood provides a non-invasive diagnostic avenue for patients with cancer 1. ... more Cell-free DNA in the blood provides a non-invasive diagnostic avenue for patients with cancer 1. However, characteristics of the origins and molecular features of cell-free DNA are poorly understood. Here we developed an approach to evaluate fragmentation patterns of cell-free DNA across the genome, and found that profiles of healthy individuals reflected nucleosomal patterns of white blood cells, whereas patients with cancer had altered fragmentation profiles. We used this method to analyse the fragmentation profiles of 236 patients with breast, colorectal, lung, ovarian, pancreatic, gastric or bile duct cancer and 245 healthy individuals. A machine learning model that incorporated genome-wide fragmentation features had sensitivities of detection ranging from 57% to more than 99% among the seven cancer types at 98% specificity, with an overall area under the curve value of 0.94. Fragmentation profiles could be used to identify the tissue of origin of the cancers to a limited number of sites in 75% of cases. Combining our approach with mutation-based cell-free DNA analyses detected 91% of patients with cancer. The results of these analyses highlight important properties of cell-free DNA and provide a proof-of-principle approach for the screening, early detection and monitoring of human cancer. Much of the morbidity and mortality of human cancers worldwide results from late diagnosis when therapeutic intervention is less effective 2,3. Unfortunately, clinically proven biomarkers that can be used to broadly diagnose and treat patients are not widely available 4. Recent analyses of circulating cell-free DNA (cfDNA) suggest that approaches using tumour-specific alterations may provide new opportunities for early diagnosis, but not all patients have detectable changes 5-8. Whole-genome sequencing (WGS) of cfDNA can identify chromosomal abnormalities in patients with cancer but detecting such alterations may be challenging owing to the small number of abnormal chromosomal changes 9-12. Analyses of the size of fragments of cfDNA have been contradictory, indicating both increases 13-15 and decreases in the overall distribution of cfDNA 12,16,17-19. Recent studies have suggested that size selection of small cfDNA can increase enrichment of circulating tumour DNA in patients with late-stage cancer 17. Nucleosome positions 18,20 , patterns near transcription start sites 20,21 , and the end positions of cfDNA 22 may be altered in cancer, but the sequencing needed to identify nucleosomes is impractical for routine analyses. Conceptually, the sensitivity of any cfDNA approach depends on the number of alterations examined as well as the technical and biological limitations of detecting such changes. As a typical blood sample contains approximately 2,000 genome equivalents of cfDNA per millilitre of plasma 5 , the theoretical limit of detection of a single alteration can be no better than one in a few thousand mutant to wild-type molecules. We hypothesized that the detection of a larger number of alterations in the genome may be more sensitive for detecting cancer in
European journal of cancer (Oxford, England : 1990), Jan 21, 2018
Patient characteristics and stratification factors are key features influencing trial outcomes. H... more Patient characteristics and stratification factors are key features influencing trial outcomes. However, there is substantial heterogeneity in reporting of patient characteristics and use of stratification factors in phase 3 trials investigating systemic treatment of metastatic colorectal cancer (mCRC). We aimed to develop a minimum set of essential baseline characteristics and stratification factors to include in such trials. We performed a modified, two-round Delphi survey among international experts with wide experience in the conduct and methodology of phase 3 trials of systemic treatment of mCRC. Thirty mCRC experts from 15 different countries completed both consensus rounds. A total of 14 patient characteristics were included in the recommended set: age, performance status, primary tumour location, primary tumour resection, prior chemotherapy, number of metastatic sites, liver-only disease, liver involvement, surgical resection of metastases, synchronous versus metachronous me...
Stage 3a: 88.8% Stage 3b: 67.0% Stage 3c: 63.3% Stage 3a b : 83% Stage 3b b : 64% Stage 3c b : 44... more Stage 3a: 88.8% Stage 3b: 67.0% Stage 3c: 63.3% Stage 3a b : 83% Stage 3b b : 64% Stage 3c b : 44% 80% (all stage 3, with FOLFOX, mean age 60) 40 year-old male, stage 2 colon cancer, MSI +ve Stage 2a a : 93% Stage 2b a : 78% Stage 2c: 57% a Currently not available Stage 2 not supported Not available for MSI +ve 88% (includes stage 2 and 3, without adjuvant chemotherapy) a Without adjuvant chemotherapy. b Mean age 60 years.
In recent years, the high heterogeneity of colorectal cancer (CRC) has become evident. Hence, bio... more In recent years, the high heterogeneity of colorectal cancer (CRC) has become evident. Hence, biomarkers need to be developed that enable the stratification of patients with CRC into different prognostic subgroups and in relation to response to therapies, according to the distinctive tumour biology. Currently, only RAS-mutation status is used routinely as a negative predictive marker to avoid treatment with anti-EGFR agents in patients with metastatic CRC, and mismatch-repair status can guide the use of adjuvant chemotherapy in patients with early stage colon cancer. Advances in molecular biology over the past decade have enabled a better understanding of the development of CRC, as well as the more-precise use of innovative targeted therapies for this disease, and include three fundamental achievements. First, the availability of large databases to capture and store the genomic landscape of patients with CRC, providing information on the genes that are frequently deregulated in CRC....
Patients with peritoneal metastatic colorectal cancer have reduced overall survival compared with... more Patients with peritoneal metastatic colorectal cancer have reduced overall survival compared with patients with metastatic colorectal cancer without peritoneal involvement. Here we further investigated the effect of the number and location of metastases in patients receiving first-line systemic chemotherapy. We analysed individual patient data for previously untreated patients enrolled in 14 phase 3 randomised trials done between 1997 and 2008. Trials were included if protocols explicitly pre-specified and solicited for patients with peritoneal involvement in the trial data collection process or had done a formal peritoneum-focused review of individual pre-treatment scans. We used stratified multivariable Cox models to assess the prognostic associations of peritoneal metastatic colorectal cancer with overall survival and progression-free survival, adjusting for other key clinical-pathological factors (age, sex, Eastern Cooperative Oncology Group (ECOG) performance score, primary tum...
Clinical cancer research : an official journal of the American Association for Cancer Research, Jan 26, 2016
Recent transcriptomic analyses have identified four distinct molecular subtypes of colorectal can... more Recent transcriptomic analyses have identified four distinct molecular subtypes of colorectal cancer (CRC) with evident clinical relevance. However, the requirement for sufficient quantities of bulk tumor and difficulties in obtaining high quality genome-wide transcriptome data from formalin-fixed paraffin-embedded tissue are obstacles towards widespread adoption of this taxonomy. Here, we develop an immunohistochemistry-based classifier to validate the prognostic and predictive value of molecular CRC subtyping in a multi-center study. Tissue microarrays from 1076 CRC patients from four different cohorts were stained for five markers (CDX2, FRMD6, HTR2B, ZEB1 and KER) by immunohistochemistry and assessed for microsatellite instability. An automated classification system was trained on one cohort using quantitative image analysis or semi-quantitative pathologist scoring of the cores as input, and applied to three independent clinical cohorts. This classifier demonstrated 87% concorda...
Clinical cancer research : an official journal of the American Association for Cancer Research, Jan 27, 2016
WRN promoter CpG island hypermethylation in colorectal cancer (CRC) has been reported to increase... more WRN promoter CpG island hypermethylation in colorectal cancer (CRC) has been reported to increase sensitivity to irinotecan-based therapies. We aimed to characterize methylation of the WRN promoter; determine the effect of WRN promoter hypermethylation upon expression; and validate a previous report that WRN promoter hypermethylation predicts improved outcomes for metastatic colorectal cancer (mCRC) patients treated with irinotecan-based therapy. WRN methylation status was assessed using methylation-specific PCR and bisulfite sequencing assays. WRN expression was determined using qRT-PCR and Western blotting. WRN methylation status was correlated with overall survival (OS) and progression-free survival (PFS) in 183 patients with mCRC. Among these patients 90 received capecitabine monotherapy (CAP) as first line therapy and 93 received capecitabine plus irinotecan (CAPIRI) therapy as part of the CAIRO Phase III clinical trial. WRN mRNA and WRN protein expression levels were low in CR...
Microsatellite instability (MSI) has been associated with favourable survival in early stage colo... more Microsatellite instability (MSI) has been associated with favourable survival in early stage colorectal cancer (CRC) compared to microsatellite stable (MSS) CRC. The BRAF V600E mutation has been associated with worse survival in MSS CRC. This mutation occurs in 40% of MSI CRC and it is unclear whether it confers worse survival in this setting. The prognostic value of KRAS mutations in both MSS and MSI CRC remains unclear. We examined the effect of BRAF and KRAS mutations on survival in stage II and III MSI colon cancer patients. BRAF exon 15 and KRAS exon 2–3 mutation status was assessed in 143 stage II (n = 85) and III (n = 58) MSI colon cancers by high resolution melting analysis and sequencing. The relation between mutation status and cancer‐specific (CSS) and overall survival (OS) was analyzed using Kaplan–Meier and Cox regression analysis. BRAF V600E mutations were observed in 51% (n = 73) and KRAS mutations in 16% of cases (n = 23). Patients with double wild‐type cancers (dWT;...
Background: Mucinous carcinoma (MC) is found in 10%-15% of colorectal cancer (CRC) patients. It d... more Background: Mucinous carcinoma (MC) is found in 10%-15% of colorectal cancer (CRC) patients. It differs from the common adenocarcinoma (AC) in histopathological appearance and clinical behavior. Methods: Genome-wide DNA copy number and survival data from MC and AC primary CRC samples from patients from two phase III trials (CAIRO and CAIRO2) was compared. Chromosomal copy number data from The Cancer Genome Atlas (TCGA) was used for validation. Altogether, 470 ACs were compared to 57 MCs. Results: MC showed a reduced amount of copy number aberrations (CNAs) compared with AC for the CAIRO/CAIRO2 cohort, with a median amount of CNAs that was 1.5-fold lower (P = 0.002). Data from TCGA also showed a reduced amount of CNAs for MC. MC samples in both cohorts displayed less gain at chromosome 20q and less loss of chromosome 18p. A high rate of chromosomal instability was a strong negative prognostic marker for survival in MC patients from the CAIRO cohorts (hazard ratio 15.60, 95% CI 3.24-75.05). Conclusions: Results from this study indicate that the distinct MC phenotype is accompanied by a different genetic basis when compared with AC and show a strong association between the rate of chromosomal instability and survival in MC patients.
American Society of Clinical Oncology Educational Book, 2015
With the currently available cytotoxic and targeted drugs, metastatic colorectal cancer (mCRC) ma... more With the currently available cytotoxic and targeted drugs, metastatic colorectal cancer (mCRC) may be controlled by systemic treatment for a substantial period of time. However, many questions remain about the optimal use of drugs and duration of treatment. The feasibility of chemotherapy-free intervals has been studied in patients with mCRC treated with chemotherapy alone, but the results are conflicting. Current data show that oxaliplatin may be safely interrupted, but they do not allow a firm conclusion on the safety of a full treatment break of chemotherapy. For targeted therapy, continuous inhibition of intracellular signaling by prolonged administration would theoretically be beneficial for efficacy of treatment. Recent data support the use of maintenance treatment with chemotherapy and bevacizumab. No data on the optimal duration of treatment with anti-epidermal growth factor receptor (EGFR) agents are currently available.
With the currently available cytotoxic and targeted drugs, metastatic colorectal cancer (mCRC) ma... more With the currently available cytotoxic and targeted drugs, metastatic colorectal cancer (mCRC) may be controlled by systemic treatment for a significant period of time. However, many questions remain about the optimal use of drugs and duration of treatment. We reviewed the data from clinical trials on the optimal duration of systemic treatment with chemotherapy and targeted therapy in mCRC patients. The feasibility of chemotherapy-free intervals has been studied in mCRC patients treated with chemotherapy alone, but the results are conflicting. Current data show that oxaliplatin may be safely interrupted, but do not allow a firm conclusion on the safety of a full treatment break of chemotherapy. For targeted therapy, continuous inhibition of intracellular signalling by prolonged administration would theoretically be beneficial for efficacy of treatment, and has been suggested by retrospectively collected data. Recent data from a prospective study show a clinical benefit for maintenan...
Clinical cancer research : an official journal of the American Association for Cancer Research, Jan 15, 2014
To determine the prevalence and prognostic value of mismatch repair (MMR) status and its relation... more To determine the prevalence and prognostic value of mismatch repair (MMR) status and its relation to BRAF mutation (BRAF(MT)) status in metastatic colorectal cancer (mCRC). A pooled analysis of four phase III studies in first-line treatment of mCRC (CAIRO, CAIRO2, COIN, and FOCUS) was performed. Primary outcome parameter was the hazard ratio (HR) for median progression-free survival (PFS) and overall survival (OS) in relation to MMR and BRAF. For the pooled analysis, Cox regression analysis was performed on individual patient data. The primary tumors of 3,063 patients were analyzed, of which 153 (5.0%) exhibited deficient MMR (dMMR) and 250 (8.2%) a BRAF(MT). BRAF(MT) was observed in 53 (34.6%) of patients with dMMR tumors compared with 197 (6.8%) of patients with proficient MMR (pMMR) tumors (P < 0.001). In the pooled dataset, median PFS and OS were significantly worse for patients with dMMR compared with pMMR tumors [HR, 1.33; 95% confidence interval (CI), 1.12-1.57 and HR, 1.3...
Background KRAS mutation is a negative predictive factor for treatment with anti-epidermal growth... more Background KRAS mutation is a negative predictive factor for treatment with anti-epidermal growth factor receptor (EGFR) antibodies in metastatic colorectal cancer (mCRC). Novel predictive markers are required to further improve the selection of patients for this treatment. We assessed the influence of modification of KRAS by gene copy number aberration (CNA) and microRNAs (miRNAs) in correlation to clinical outcome in mCRC patients treated with cetuximab in combination with chemotherapy and bevacizumab. Methods Formalin-fixed paraffin-embedded primary tumour tissue was used from 34 mCRC patients in a phase III trial, who were selected based upon their good (n = 17) or poor (n = 17) progression-free survival (PFS) upon treatment with cetuximab in combination with capecitabine, oxaliplatin, and bevacizumab. Gene copy number at the KRAS locus was assessed using high resolution genome-wide array CGH and the expression levels of 17 miRNAs targeting KRAS were determined by real-time PCR....
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Papers by Miriam Koopman