Identifying Stage II Colorectal Cancer Recurrence Associated Genes by Microarray Meta-Analysis and Building Predictive Models with Machine Learning Algorithms

Background

Stage II colorectal cancer patients had heterogeneous prognosis, and patients with recurrent events had poor survival. In this study, we aimed to identify stage II colorectal cancer recurrence associated genes by microarray meta-analysis and build predictive models to stratify patients' recurrence-free survival.

Methods

We searched the GEO database to retrieve eligible microarray datasets. The microarray meta-analysis was used to identify universal recurrence associated genes. Total samples were randomly divided into the training set and the test set. Two survival models (lasso Cox model and random survival forest model) were trained in the training set, and AUC values of the time-dependent receiver operating characteristic (ROC) curves were calculated. Survival analysis was performed to determine whether there was significant difference between the predicted high and low risk groups in the test set.

Results

Six datasets containing 651 stage II colorectal cancer patients were included in this study. The microarray meta-analysis identified 479 recurrence associated genes. KEGG and GO enrichment analysis showed that G protein-coupled glutamate receptor binding and Hedgehog signaling were significantly enriched. AUC values of the lasso Cox model and the random survival forest model were 0.815 and 0.993 at 60 months, respectively. In addition, the random survival forest model demonstrated that the effects of gene expression on the recurrence-free survival probability were nonlinear. According to the risk scores computed by the random survival forest model, the high risk group had significantly higher recurrence risk than the low risk group (HR = 1.824, 95% CI: 1.079-3.084, p = 0.025).

Conclusions

We identified 479 stage II colorectal cancer recurrence associated genes by microarray meta-analysis. The random survival forest model which was based on the recurrence associated gene signature could strongly predict the recurrence risk of stage II colorectal cancer patients.

Exploring and modelling colon cancer inter-tumour heterogeneity: opportunities and challenges

Colon cancer inter-tumour heterogeneity is installed on multiple levels, ranging from (epi)genetic driver events to signalling pathway rewiring reflected by differential gene expression patterns. Although the existence of heterogeneity in colon cancer has been recognised for a longer period of time, it is sparingly incorporated as a determining factor in current clinical practice. Here we describe how unsupervised gene expression-based classification efforts, amongst which the consensus molecular subtypes (CMS), can stratify patients in biological subgroups associated with distinct disease outcome and responses to therapy. We will discuss what is needed to extend these subtyping efforts to the clinic and we will argue that preclinical models recapitulate CMS subtypes and can be of vital use to increase our understanding of treatment response and resistance and to discover novel targets for therapy.

Novel digital signatures of tissue phenotypes for predicting distant metastasis in colorectal cancer

Distant metastasis is the major cause of death in colorectal cancer (CRC). Patients at high risk of developing distant metastasis could benefit from appropriate adjuvant and follow-up treatments if stratified accurately at an early stage of the disease. Studies have increasingly recognized the role of diverse cellular components within the tumor microenvironment in the development and progression of CRC tumors. In this paper, we show that automated analysis of digitized images from locally advanced colorectal cancer tissue slides can provide estimate of risk of distant metastasis on the basis of novel tissue phenotypic signatures of the tumor microenvironment. Specifically, we determine what cell types are found in the vicinity of other cell types, and in what numbers, rather than concentrating exclusively on the cancerous cells. We then extract novel tissue phenotypic signatures using statistical measurements about tissue composition. Such signatures can underpin clinical decisions about the advisability of various types of adjuvant therapy.

Comparative economics of a 12-gene assay for predicting risk of recurrence in stage II colon cancer

BACKGROUND

Prior economic analysis that compared the 12-gene assay to published patterns of care predicted the assay would improve outcomes while lowering medical costs for stage II, T3, mismatch-repair-proficient (MMR-P) colon cancer patients. This study assessed the validity of those findings with real-world adjuvant chemotherapy (aCT) recommendations from the US third-party payer perspective.

METHODS

Costs and quality-adjusted life-years (QALYs) were estimated for stage II, T3, MMR-P colon cancer patients using guideline-compliant, state-transition probability estimation methods in a Markov model. A study of 141 patients from 17 sites in the Mayo Clinic Cancer Research Consortium provided aCT recommendations before and after knowledge of the 12-gene assay results. Progression and adverse events data with aCT regimens were based on published literature. Drug and administration costs for aCT were obtained from 2014 Medicare Fee Schedule. Sensitivity analyses evaluated the drivers and robustness of the primary outcomes.

RESULTS

After receiving the 12-gene assay results, physician recommendations in favor of aCT decreased 22 %; fluoropyrimidine monotherapy and FOLFOX recommendations each declined 11 %. Average per-patient drugs, administration, and adverse events costs decreased $US2,339, $US733, and $US3,211, respectively. Average total direct medical costs decreased $US991. Average patient well-being improved by 0.114 QALYs. Savings are expected to persist even if the cost of oxaliplatin drops by >75 % due to generic substitution.

CONCLUSIONS

This study provides evidence that real-world changes in aCT recommendations due to the 12-gene assay are likely to reduce direct medical costs and improve well-being for stage II, T3, MMR-P colon cancer patients.

Value of primary tumor gene signatures in colon cancer when national quality standards are adhered to: preliminary results of an international prospective multicenter trial

BACKGROUND

The purpose of this study was to determine if gene signatures are informative in colon cancer (CC) when National Quality Standards (NQS) are adhered to. Several studies have demonstrated the prognostic potential of gene signatures in primary CC. This has never been evaluated prospectively with adherence to NQS.

METHODS

This was a prospective, international, multicenter trial. Eligibility criteria were: no distant metastasis, ≥12 lymph nodes (LNs), and no adjuvant chemotherapy for LN-negative CC. RNA from frozen tumor samples was considered reliable if RNA Integrity Number >9. Using an Agilent whole human genome array, 44,000 genes were analyzed in primary tumors for differential gene expression (DGE). ANOVA applied at 2-fold expression level was performed in at least 8 experiments to obtain the DGEs.

RESULTS

Molecular analysis was completed in 113 of 128 patients. With median follow-up of 27 months, 11.5 % recurred within 3 years after surgery. Significant DGE was identified in recurrent tumors reflected by upregulation (UR) in cellular proliferation and by downregulation (DR) in prodifferentiating panel of 9 genes, independent of T or N classification. By multivariate analysis 3-year disease-free survival was 12.5 % in the UR/DR group versus 93.4 % in the non-UR/DR group (p < .0001; HR = 24.2; 95 % CI 4.8-120.4).

CONCLUSIONS

This is the first prospective trial to evaluate gene signatures in CC with adherence to a 12-node minimum quality standard. Certain molecular pathways may be prognostically relevant if both surgery and pathology are standardized, regardless of T or N classification. Careful consideration should be made to include surgical quality measures when planning clinical trials to evaluate the true effect of molecular markers in CC.

Clinicopathological risk factors of Stage II colon cancer: results of a prospective study

AIM

Adjuvant 5-fluorouracil based chemotherapy has demonstrated benefit in Stage III colon cancer but still remains controversial in Stage II. The aim of this study was to analyse the prognostic impact of clinicopathological factors that may help guide treatment decisions in Stage II colon cancer.

METHOD

Between 1996 and 2006 data from patients diagnosed with colorectal cancer at Hospital Universitari Bellvitge and its referral comprehensive cancer centre Institut Català d'Oncologia/L'Hospitalet were prospectively included in a database. We identified 432 patients with Stage II colon cancer operated on at Hospital Universitari Bellvitge. The 5-year relapse-free survival (RFS) and colon-cancer-specific survival (CCSS) were determined.

RESULTS

The 5-year RFS and CCSS were 83% and 88%, respectively. Lymphovascular or perineural invasion was associated with RFS [hazard ratio (HR) 1.84; 95% CI 1.01-3.35]. Gender (women, HR 0.48; 95% CI 0.23-1) and lymphovascular or perineural invasion (HR 3.51; 95% CI 1.86-6.64) together with pT4 (HR 2.79; 95% CI 1.44-5.41) influenced CCSS. In multivariate analysis pT4 and lymphovascular or perineural invasion remained significantly associated with CCSS. We performed a risk index with these factors with prognostic impact. Patients with pT4 tumours and lymphovascular or perineural invasion had a 5-year CCSS of 61%vs the 93% (HR 5.87; 95 CI 2.46-13.97) of those without any of these factors.

CONCLUSION

pT4 and lymphatic, venous or perineural invasion are confirmed as significant prognostic factors in Stage II colon cancer and should be taken into account in the clinical validation process of new molecular prognostic factors.

Deficient mismatch repair phenotype is a prognostic factor for colorectal cancer in elderly patients

OBJECTIVE

About 15% of colorectal adenocarcinomas have a deficient DNA mismatch repair phenotype. The frequency of deficient DNA mismatch repair tumours increases with age due to the hypermethylation of hMLH1 promoter. The study aimed to determine the prognostic value of deficient DNA mismatch repair phenotype in elderly patients.

DESIGN

Mismatch repair phenotype was retrospectively determined by molecular analysis in consecutive resected colorectal adenocarcinoma specimens from patients over 75 years of age from 4 Oncology centres.

RESULTS

231 patients (median age: 81, range: 75-100) were enrolled from 2005 to 2008. Mean prevalence of deficient DNA mismatch repair phenotype was 22.5%, and 36% for patients over 85 years. Deficient DNA mismatch repair status was significantly associated with older age, female sex, proximal colon primary and high grade tumour. For stage II tumours no deficient DNA mismatch repair tumours had a recurrence at end of follow-up compared to 17% for tumours with proficient phenotype. The proficient phenotype status was significantly associated with worse age-adjusted overall survival [HR 2.60; 95% CI 1.05-6.44; p=0.039]. For stage III tumours a trend for less recurrence was observed for deficient DNA mismatch repair phenotype (16%) compared to proficient phenotype (36%).

CONCLUSION

deficient DNA mismatch repair phenotype is a prognostic factor in stage II colorectal tumour in elderly patients. Our results suggest that mismatch repair phenotype should be taken in consideration for adjuvant chemotherapy decision in elderly patients.

Therapeutic implications of DNA mismatch repair in adjuvant colorectal cancer chemotherapy

SUMMARY Microsatellite instability (MSI) is a molecular marker of defective DNA mismatch repair (MMR) and constitutes an important oncogenic molecular pathway in colorectal cancer that is present in approximately 12–15% of all colorectal malignant tumors. Defective MMR status in colorectal cancer occurs as a result of germline mutations in MMR genes (less than one third of cases) or, more commonly, from somatic hypermethylation of the MLH1 promoter (more than two thirds). MMR deficiency accelerates colorectal oncogenesis by accumulation of secondary mutations in specific target genes. Patients with defective MMR tumors have distinct clinicopathologic characteristics and have been associated with a better stage-adjusted prognosis than patients with proficient MMR tumors. MMR deficiency may predict tumor chemoresistance to adjuvant 5-fluorouracil treatment. Preliminary clinical data suggested that adding oxaliplatin to 5-fluorouracil could restore the benefit of adjuvant chemotherapy in MSI patients. Further studies are needed to clarify the differential chemosensitivity of MSI patients depending on the mechanism of MMR deficiency and the adjuvant chemotherapeutic regimen used.

Comparative clinical benefits of systemic adjuvant therapy for paradigm solid tumors

Adjuvant therapy employing cytotoxic chemotherapy, molecularly targeted agents, immunologic, and hormonal agents has shown a significant impact upon a variety of solid tumors. The principles that guide adjuvant therapy differ among various tumor types and specific modalities, but generally indicate a greater impact of therapy in the postsurgical setting of micrometastatic disease, for which adjuvant therapy is commonly pursued, vs. the setting of gross unresectable disease. This review of adjuvant therapies in current use for five major solid tumors highlights the rationale for current effective adjuvant therapy, and draws comparisons between the adjuvant regimens that have found application in solid tumors.

Integrated analysis of molecular and clinical prognostic factors in stage II/III colon cancer

BACKGROUND

The prognostic potential of individual clinical and molecular parameters in stage II/III colon cancer has been investigated, but a thorough multivariable assessment of their relative impact is missing.

METHODS

Tumors from patients (N = 1404) in the PETACC3 adjuvant chemotherapy trial were examined for BRAF and KRAS mutations, microsatellite instability (MSI), chromosome 18q loss of heterozygosity (18qLOH), and SMAD4 expression. Their importance in predicting relapse-free survival (RFS) and overall survival (OS) was assessed by Kaplan-Meier analyses, Cox regression models, and recursive partitioning trees. All statistical tests were two-sided.

RESULTS

MSI-high status and SMAD4 focal loss of expression were identified as independent prognostic factors with better RFS (hazard ratio [HR] of recurrence = 0.54, 95% CI = 0.37 to 0.81, P = .003) and OS (HR of death = 0.43, 95% CI = 0.27 to 0.70, P = .001) for MSI-high status and worse RFS (HR = 1.47, 95% CI = 1.19 to 1.81, P < .001) and OS (HR = 1.58, 95% CI = 1.23 to 2.01, P < .001) for SMAD4 loss. 18qLOH did not have any prognostic value in RFS or OS. Recursive partitioning identified refinements of TNM into new clinically interesting prognostic subgroups. Notably, T3N1 tumors with MSI-high status and retained SMAD4 expression had outcomes similar to stage II disease.

CONCLUSIONS

Concomitant assessment of molecular and clinical markers in multivariable analysis is essential to confirm or refute their independent prognostic value. Including molecular markers with independent prognostic value might allow more accurate prediction of prognosis than TNM staging alone.

ColoGuidePro: a prognostic 7-gene expression signature for stage III colorectal cancer patients

PURPOSE

Improved prognostic stratification of patients with stage II and III colorectal cancer is warranted for postoperative clinical decision making. This study was conducted to develop a clinically feasible and robust prognostic classifier for these patients independent of adjuvant treatment.

EXPERIMENTAL DESIGN

Global gene expression profiles from altogether 387 stage II and III colorectal cancer tissue samples from three independent patient series were included in the study. ColoGuidePro, a seven-gene prognostic classifier, was developed from a selected Norwegian learning series (n = 95; no adjuvant treatment) using lasso-penalized multivariate survival modeling with cross-validation.

RESULTS

The expression signature significantly stratified patients in a consecutive Norwegian test series, in which patients were treated according to current standards [HR, 2.9 (1.1-7.5); P = 0.03; n = 77] and an external validation series [HR, 3.7 (2.0-6.8); P < 0.001; n = 215] according to survival. ColoGuidePro was also an independent predictor of prognosis in multivariate models including tumor stage in both series (HR, ≥ 3.1; P ≤ 0.03). In the validation series, which consisted of patients from other populations (United States and Australia), 5-year relapse-free survival was significantly predicted for stage III patients only (P < 0.001; n = 107). Here, prognostic stratification was independent of adjuvant treatment (P = 0.001).

CONCLUSIONS

We present ColoGuidePro, a prognostic classifier developed for patients with stage II and III colorectal cancer. The test is suitable for transfer to clinical use and has best prognostic prediction potential for stage III patients.

Recommendations and expert opinion on the adjuvant treatment of colon cancer in Spain

Adjuvant chemotherapy is the current standard in the management of patients with localised colon cancer (CC) following curative resection. The use of oxaliplatin plus 5 fluorouracil/leucovorin (FOLFOX) or oxaliplatin plus capecitabine-based (XELOX) regimens, both approved in Europe as adjuvant treatment for stage III CC, has improved prognosis in this stage, but questions on their usefulness in high-risk stage II or elderly CC patients and on the role of some prognostic biomarkers are still pending. In April 2010, a consensus meeting on adjuvant CC treatment based on a revision of the most recent literature was held in Spain. The panel considered the use of adjuvant chemotherapy for high-risk stage II CC patients to be justified. Additionally, the more convenient administration of oral fluoropyrimidines vs. IV continuous infusion 5-FU would make XELOX a more suitable alternative for the patient. A more cautious decision should be taken when prescribing oxaliplatin treatment in patients aged ≥70.

The evolution of adjuvant therapy in the treatment of early-stage colon cancer

Adjuvant treatment of colon cancer, one of the most common malignancies, is an important issue in oncology. This article describes the development of adjuvant therapy and how the 2 major evolution steps, the successes of fluoropyrimidines, and then of oxaliplatin, have been achieved, Problems and failures, such as those of targeted therapies, also are addressed to help us to overcome their limitations. Special situations, such as stage II disease and an elderly population in which adjuvant chemotherapy is still controversial, are reviewed from the clinician perspective. The synthesis of these data allows us to conceive a future development focused on translational research.

Personalized treatment of colorectal cancer

In the last 15 years, significant progress in the management of colorectal cancer (CRC) has been achieved with several new agents licensed extending median overall survival for stage IV disease to about 2 years. Treatment of CRC is stage-specific, multidisciplinary, and based on patient and tumor characteristics. Although especially early stages (0-III, according to Union for International Cancer Control) are treated with curative intent, patients with limited stage IV disease (liver and/or lung or localized peritoneal metastases) might still be curable in a multimodality approach including surgery, perioperative chemotherapy and/or radiotherapy. Despite the broad variety of prognostic factors, treatment decisions and selection of drugs are mainly based on clinicopathologic variables for early stage CRC, extent of disease, potential resectability, patients' eligibility to receive aggressive treatments including chemotherapy, surgery, and very few molecular markers such as KRAS mutational status for advanced disease. However, a tailored approach for the treatment of CRC taking into account all mentioned factors is currently recommended by national and international guidelines and will be discussed in this review.

Design of clinical trials for biomarker research in oncology

The developmental pathway from discovery to clinical practice for biomarkers and biomarker-directed therapies is complex. While several issues need careful consideration, two critical issues that surround the validation of biomarkers are the choice of clinical trial design (which is based on the strength of the preliminary evidence and marker prevalence) and the biomarker assay related issues surrounding the marker assessment methods such as the reliability and reproducibility of the assay. This review focuses on trial designs for marker validation, both in the setting of early phase trials for initial validation, as well as in the context of larger definitive trials. Designs for biomarker validation are broadly classified as retrospective (i.e., using data from previously well-conducted, randomized, controlled trials) or prospective (enrichment, allcomers or adaptive). We believe that the systematic evaluation and implementation of these design strategies are essential to accelerate the clinical validation of biomarker-guided therapy, thereby taking us a step closer to the goal of personalized medicine.

Development and independent validation of a prognostic assay for stage II colon cancer using formalin-fixed paraffin-embedded tissue

PURPOSE

Current prognostic factors are poor at identifying patients at risk of disease recurrence after surgery for stage II colon cancer. Here we describe a DNA microarray-based prognostic assay using clinically relevant formalin-fixed paraffin-embedded (FFPE) samples.

PATIENTS AND METHODS

A gene signature was developed from a balanced set of 73 patients with recurrent disease (high risk) and 142 patients with no recurrence (low risk) within 5 years of surgery.

RESULTS

The 634-probe set signature identified high-risk patients with a hazard ratio (HR) of 2.62 (P < .001) during cross validation of the training set. In an independent validation set of 144 samples, the signature identified high-risk patients with an HR of 2.53 (P < .001) for recurrence and an HR of 2.21 (P = .0084) for cancer-related death. Additionally, the signature was shown to perform independently from known prognostic factors (P < .001).

CONCLUSION

This gene signature represents a novel prognostic biomarker for patients with stage II colon cancer that can be applied to FFPE tumor samples.

From chemotherapy to targeted therapy in adjuvant treatment for stage III colon cancer

Colorectal cancer represents a major public health problem due to its frequency and mortality rate. Adjuvant chemotherapy has improved the prognosis of colon cancer. Six months of oxaliplatin and fluoropyrimidine in combination is the standard adjuvant treatment in stage III patients. Ongoing trials are evaluating the optimal duration of chemotherapy. A critical issue, which needs to be specifically addressed, is the role of adjuvant therapy in elderly patients. Preliminary results of trials evaluating targeted therapies in combination with chemotherapy have shown disappointing results. The monoclonal antibodies bevacizumab, targeting vascular endothelial growth factor (VEGF) and cetuximab, targeting epidermal growth factor receptor (EGFR)/HER1, which improved survival in patients with metastatic colorectal cancer, could even induce chemotherapy resistance in a significant number of patients in the adjuvant setting. A major challenge is emerging to understand the mechanism leading to this effect and to multi-target the tumor cell proliferation and survival network. Clarity regarding the clinical signal needed before launching a phase III study and optimized designs adapted to multiple agents are urgently needed for new trials.

Biomarker-based selection of therapy for colorectal cancer

Colorectal cancer (CRC) has been re-classified based on molecular analyses of various genes and proteins capable of separating morphologic types of tumors into molecular categories. The diagnosis and management of CRC has evolved with the discovery and validation of a wide variety of biomarkers designed to facilitate a personalized approach for the treatment of the disease. In addition, a number of new prognostic and predictive individual genes and proteins have been discovered that are designed to reflect the sensitivity and/or resistance of CRC to existing therapies. Multigene predictors have also been developed to predict the risk of relapse for intermediate-stage CRC after completion of surgical resection. Finally, a number of biomarkers have been proposed as specific predictors of chemotherapy and radiotherapy response and, in some instances, drug toxicity. In this article, a series of novel biomarkers are considered and compared with standard-of-care markers for their potential use as pharmacogenomic and pharmacogenetic predictors of disease outcome.

Tumour Genetics and Genomics to Personalise Cancer Treatment

Personalising cancer treatment to optimise therapeutic efficacy while minimising exposure to the toxicities of ineffective drugs is the holy grail of medical oncology. Clinical parameters and conventional histopathological characterisations of cancers are no longer adequate to guide the practising oncologists in treatment planning. The explosion of knowledge in cancer molecular biology has led to the availability of tumour-specific molecules that serve as predictive and prognostic markers. In breast cancer, HER-2 positivity is a good predictor for success of anti-HER-2 trastuzumab monoclonal antibody therapy. K-ras mutational status predicts the likelihood of response to anti-EGFR monoclonal antibodies in advanced colorectal cancers. Similarly, EGFR mutational status in pulmonary adenocarcinoma is highly predictive for responses or otherwise to tyrosine kinase inhibitors. Notwithstanding our deeper understanding of tumour biology and the availability of predictive and prognostic laboratory tools, we are still far from achieving our dream of the perfect personalised cancer treatment, as each tumour in a particular patient is unique to itself. A much coveted, real-time, anti-tumour drug sensitivity testing in the future may one day pave the way for truly treating the right tumour with the right drug in the right patient. Key words: Personalised cancer treatment, Predictive markers, Prognostic markers

Challenges in the management of stage II colon cancer

Approximately one third of patients diagnosed with early-stage colon cancer will present with lymph node involvement (stage III) and about one quarter with transmural bowel wall invasion but negative lymph nodes (stage II). Adjuvant chemotherapy targets micrometastatic disease to improve disease-free (DFS) and overall survival (OS). While beneficial for stage III patients, the role of adjuvant chemotherapy is unestablished in stage II disease. This likely relates to the improved outcome of these patients, and the difficulties in developing studies with sufficient power to document benefit in this patient population. However, recent investigation also suggests that molecular differences may exist between stage II and III cancers and within stage II patients. Validated pathologic prognostic markers are useful at identifying stage II patients at high risk for recurrence for whom the benefit from adjuvant chemotherapy may be greater. Such high-risk features include higher T stage (T4 v T3), suboptimal lymph node retrieval, presence of lymphovascular invasion, bowel obstruction, or bowel perforation, and poorly differentiated histology. However, for the majority of patients who do not carry any of these adverse features and are classified as "average-risk" stage II patients, the benefit of adjuvant chemotherapy remains unproven. Emerging understanding of the underlying biology of stage II colon cancer has identified molecular markers that may change this paradigm and improve our risk assessment and treatment choices for stage II disease. Assessment of microsatellite stability (MSI), which serves as a marker for DNA mismatch repair (MMR) system function, has emerged as a useful tool for risk stratification of patients with stage II colon cancer. Patients with high frequency of MSI have been shown to have increased OS and limited benefit from 5-fluorouracil (5-FU)-based chemotherapy. Additional research is necessary to clearly define the most appropriate way to use this marker and others in routine clinical practice.

Prognostic and predictive impact of DNA mismatch repair in the management of colorectal cancer

Colorectal cancers develop via two major pathways that include chromosomal instability and microsatellite instability. Microsatellite instability occurs due to deficient DNA mismatch repair (MMR), which can be caused by epigenetic silencing of the MLH1 MMR gene in sporadic colorectal cancers or germline mutations in MMR genes that result in Lynch syndrome. While the molecular origin of deficient MMR differs, sporadic and Lynch syndrome tumors share similar pathological features and have a more favorable stage-adjusted prognosis compared with MMR-proficient cases. While controversy remains, there is evidence to suggest that deficient MMR may predict a lack of benefit from 5-fluorouracil-based adjuvant chemotherapy. The focus of this article is on the MMR phenotype and its prognostic and predictive implications for the management of patients with colorectal cancer.

Microsatellite instability and loss of heterozygosity at chromosomal location 18q: prospective evaluation of biomarkers for stages II and III colon cancer--a study of CALGB 9581 and 89803

PURPOSE

Colorectal cancer (CRC) develops as a result of a series of accumulated genomic changes that produce oncogene activation and tumor suppressor gene loss. These characteristics may classify CRC into subsets of distinct clinical behaviors.

PATIENTS AND METHODS

We studied two of these genomic defects-mismatch repair deficiency (MMR-D) and loss of heterozygosity at chromosomal location 18q (18qLOH)-in patients enrolled onto two phase III cooperative group trials for treatment of potentially curable colon cancer. These trials included prospective secondary analyses to determine the relationship between these markers and treatment outcome. A total of 1,852 patients were tested for MMR status and 955 (excluding patients with MMR-D tumors) for 18qLOH.

RESULTS

Compared with stage III, more stage II tumors were MMR-D (21.3% v 14.4%; P < .001) and were intact at 18q (24.2% v 15.1%; P = .001). For the combined cohort, patients with MMR-D tumors had better 5-year disease-free survival (DFS; 0.76 v 0.67; P < .001) and overall survival (OS; 0.81 v 0.78; P = .029) than those with MMR intact (MMR-I) tumors. Among patients with MMR-I tumors, the status of 18q did not affect outcome, with 5-year values for patients with 18q intact versus 18qLOH tumors of 0.74 versus 0.65 (P = .18) for DFS and 0.81 versus 0.77 (P = .18) for OS.

CONCLUSION

We conclude that MMR-D tumor status, but not the presence of 18qLOH, has prognostic value for stages II and III colon cancer.

Critical comments for roles of biomarkers in the diagnosis and treatment of cancer

A biomarker is defined as "a characteristic that is objectively measured and evaluated as an indicator of normal biologic processes, pathogenic processes, or pharmacologic/pharmacodynamic responses to a therapeutic intervention". Various assays, including immunohistochemistry, gene constitution such as amplification, mutation, and rearrangement, gene and protein expression analysis such as single gene or protein expression, exhaustive analysis and gene or protein signature and single nucleotide polymorphism have been used to identify biomarkers in recent years. No therapeutic effects have yet been predicted based on the results of such exhaustive gene analysis because of low reproducibility although some correlate with the prognosis of patients. Biomarkers such as HER2 for breast cancer or EGFR mutation for lung cancer and KRAS mutation in colon cancer have contributed to identify a patient population that might show a good and bad treatment response, respectively. On the other hand, other biomarkers such as bcr-abl, c-kit gene mutation and CD20 expression, which are positive for CML, GIST and B cell lymphoma, respectively, have crucial biological significance but have not necessarily been used for practical clinical screening since pathological diagnosis coincide with finding of biomarkers. Hence, much work remains to be done in many areas of biomarker research.

Personalized colon cancer care in 2010

Colon cancer (CC) therapies have improved patient outcomes significantly over the last decades in both the adjuvant and metastatic settings. With the introduction of a number of novel agents, both traditional chemotherapies and biologically targeted agents, the need to identify subgroups that are likely and not likely to respond to a particular treatment regimen is paramount. This will allow patients who are likely to benefit to receive optimal care, while sparing those unlikely to benefit from unnecessary toxicity and cost. With the identification of several novel biomarkers and a variety of technologies to interrogate the genome, we already are able to rapidly study patient tumor or blood samples and normal tissues to generate a large dataset of aberrations within the cancer. How to digest this complex information to obtain accurate, reliable, and meaningful results that will allow us to provide truly personalized care for CC patients is just starting to be addressed. In this article, we briefly review the history of CC treatment, with an emphasis on current clinical standards that incorporate a "personalized medicine" approach. We then review strategies that will potentially improve our ability to individualize therapy in the future.

Prognostic and predictive markers in stage II colon cancer: is there a role for gene expression profiling?

Conventional clinical and pathologic risk factors in stage II colon cancer provide limited prognostic information and do not predict response to adjuvant 5-fluorouracil-based chemotherapy. New prognostic and predictive biomarkers are needed to identify patients with highest recurrence risk who will receive the greatest absolute risk reduction from adjuvant chemotherapy. We review below the evidence for conventional risk factors in patients with node-negative colon cancer, followed by a discussion of promising new molecular and genetic markers in this malignancy. Gene expression profiling is an emerging tool with both prognostic and predictive potential in oncology. For patients with stage II colon cancer, the Oncotype DX Colon Cancer test is now commercially available as a prognostic marker, and the ColoPrint assay is expected to be released later this year. Current evidence for both of these assays is described below, concluding with a discussion of potential future directions for gene expression profiling in colon cancer risk stratification and treatment decision making.

Circulating tumor cells in colorectal cancer: past, present, and future challenges

Recent advances in immunomagnetic separation and flow cytometry have made the detection and characterization of circulating tumor cells (CTC) a reality. This technology has already demonstrated prognostic significance in breast and prostate cancer. In the current review, we will review the historical and current data regarding the enumeration and identification of CTC in colorectal cancer. With immunomagnetic separation techniques, CTC can reliably and reproducibly be identified within 1 to 2 cells in a 7.5 mL sample of peripheral blood. Prospective studies have demonstrated a significant adverse impact on survival with the presence of > or = 3 CTC per 7.5 mL blood. Approximately one quarter of patients with metastatic disease will be categorized in this poor prognosis group. In addition, change in number of cells on treatment has prognostic significance. While CTC enumerated through immunomagnetic separation are a clear prognostic factor for patients with mCRC, the future challenge is to study whether treatment decision-making should be impacted by their level. Low cell yield in mCRC is a potential hinderance to answering these important clinical questions at present. CTC can also be isolated and studied with flow cytometry, FISH, and RT-PCR, allowing real-time assessment of tumor biology. Future advances in this field will improve both the detection and manipulation of these cells. Improvements in detection and characterization of CTC will hopefully lead to refinement of the surgical and chemotherapeutic treatment of colorectal cancer.

Gene expression signature to improve prognosis prediction of stage II and III colorectal cancer

PURPOSE

This study aims to develop a robust gene expression classifier that can predict disease relapse in patients with early-stage colorectal cancer (CRC).

PATIENTS AND METHODS

Fresh frozen tumor tissue from 188 patients with stage I to IV CRC undergoing surgery was analyzed using Agilent 44K oligonucleotide arrays. Median follow-up time was 65.1 months, and the majority of patients (83.6%) did not receive adjuvant chemotherapy. A nearest mean classifier was developed using a cross-validation procedure to score all genes for their association with 5-year distant metastasis-free survival.

RESULTS

An optimal set of 18 genes was identified and used to construct a prognostic classifier (ColoPrint). The signature was validated on an independent set of 206 samples from patients with stage I, II, and III CRC. The signature classified 60% of patients as low risk and 40% as high risk. Five-year relapse-free survival rates were 87.6% (95% CI, 81.5% to 93.7%) and 67.2% (95% CI, 55.4% to 79.0%) for low- and high-risk patients, respectively, with a hazard ratio (HR) of 2.5 (95% CI, 1.33 to 4.73; P = .005). In multivariate analysis, the signature remained one of the most significant prognostic factors, with an HR of 2.69 (95% CI, 1.41 to 5.14; P = .003). In patients with stage II CRC, the signature had an HR of 3.34 (P = .017) and was superior to American Society of Clinical Oncology criteria in assessing the risk of cancer recurrence without prescreening for microsatellite instability (MSI).

CONCLUSION

ColoPrint significantly improves the prognostic accuracy of pathologic factors and MSI in patients with stage II and III CRC and facilitates the identification of patients with stage II disease who may be safely managed without chemotherapy.

Stage II and stage III colon cancer: treatment advances and future directions

Because of its frequency and mortality rate, colorectal cancer represents a major public health problem. Adjuvant chemotherapy has improved the prognosis. Six months of oxaliplatin and fluoropyrimidine in combination is the standard adjuvant treatment in stage III patients. Two monoclonal antibodies, bevacizumab targeting vascular endothelial growth factor and cetuximab targeting epidermal growth factor receptor 1, are being assessed in addition to chemotherapy in the adjuvant setting. Preliminary results of 2 trials have shown disappointing results. Duration of therapy is another other critical issue for the future. Adjuvant chemotherapy in patients with stage II colon cancer is still a subject of controversy. The potential biomarkers that can accurately select patients with stage II or III cancer who are at risk for recurrence to individualize therapy from microsatellite instability to gene signature are reviewed. Adjuvant therapy in elderly patients is another matter of debate due to the lack of survival advantage in the recent trials.

Defective mismatch repair as a predictive marker for lack of efficacy of fluorouracil-based adjuvant therapy in colon cancer

PURPOSE

Prior reports have indicated that patients with colon cancer who demonstrate high-level microsatellite instability (MSI-H) or defective DNA mismatch repair (dMMR) have improved survival and receive no benefit from fluorouracil (FU) -based adjuvant therapy compared with patients who have microsatellite-stable or proficient mismatch repair (pMMR) tumors. We examined MMR status as a predictor of adjuvant therapy benefit in patients with stages II and III colon cancer.

METHODS

MSI assay or immunohistochemistry for MMR proteins were performed on 457 patients who were previously randomly assigned to FU-based therapy (either FU + levamisole or FU + leucovorin; n = 229) versus no postsurgical treatment (n = 228). Data were subsequently pooled with data from a previous analysis. The primary end point was disease-free survival (DFS).

RESULTS

Overall, 70 (15%) of 457 patients exhibited dMMR. Adjuvant therapy significantly improved DFS (hazard ratio [HR], 0.67; 95% CI, 0.48 to 0.93; P = .02) in patients with pMMR tumors. Patients with dMMR tumors receiving FU had no improvement in DFS (HR, 1.10; 95% CI, 0.42 to 2.91; P = .85) compared with those randomly assigned to surgery alone. In the pooled data set of 1,027 patients (n = 165 with dMMR), these findings were maintained; in patients with stage II disease and with dMMR tumors, treatment was associated with reduced overall survival (HR, 2.95; 95% CI, 1.02 to 8.54; P = .04).

CONCLUSION

Patient stratification by MMR status may provide a more tailored approach to colon cancer adjuvant therapy. These data support MMR status assessment for patients being considered for FU therapy alone and consideration of MMR status in treatment decision making.

Combination therapy in high-risk stage II or stage III colon cancer: current practice and future prospects

Colon cancer represents the second leading cause of cancer-related deaths. For patients who have undergone curative surgery, adjuvant therapy can reduce the risk of recurrence and death from relapsed or metastatic disease. Postoperative chemotherapy with a 5-fluorouracil-based regimen combined with oxaliplatin is the current standard of care for stage III patients. However, there is still controversy in stage II disease about the real impact of adjuvant monotherapy or combined therapy on survival. Better identification of a subgroup of patients with a higher risk of recurrence can select patients who might benefit from adjuvant therapy. For the elderly population, there is a well-established role for postoperative therapy, although the most appropriate regimen remains to be defined. Targeted agents for combined adjuvant therapy in stage II and III colon cancer is a promising area, but to date, there is no evidence supporting its use in this setting. Results from large prospective trials with targeted therapy have been disappointing and new drugs and strategies are needed to define the role of these types of agents in the adjuvant scenario of colon cancer.

DNA mismatch repair and adjuvant chemotherapy in sporadic colon cancer

Defective DNA mismatch repair (MMR) occurs in approximately 15% of sporadic colorectal cancers (CRCs). Multiple retrospective studies have shown that patients with MMR-deficient CRCs have a more favorable stage-adjusted prognosis compared with those who have MMR-proficient tumors. Evidence also indicates that patients with MMR-deficient colon cancers do not benefit from treatment with adjuvant 5-fluorouracil chemotherapy. Furthermore, recent studies, including a pooled analysis, have validated the prognostic and predictive impact of MMR status in patients with stage II and III colon cancer who were treated in adjuvant chemotherapy trials. Given these data, it can be recommended that MMR status be determined and used to inform clinical decision-making for adjuvant chemotherapy in patients with stage II colon cancer.