Rachel Midgley’s research while affiliated with Oxford University Hospitals NHS Trust and other places

Modern developments in molecular genetics have led oncologists not only to define tumors according to their anatomical site, stage, and histological type, but also to appreciate the heterogeneity between tumors according to their specific molecular, genetic, or immunological subtype, empowering oncologists to, ideally, provide more individually tailored treatment to particular patients and their specific tumor subtype by using highly targeted therapies. In this chapter, circulating biomarkers and pharmacodynamics markers for target inhibition, among other markers, will be discussed and exemplified with regard to major oncological entities.

Early clinical trials are pivotal steps in the humanization of a drug development project. Their design has to accomplish both regulatory aspects and scientific gain regarding the drug target, human mechanism of action, and viable biomarkers; they should ultimately support proof-of-concept (PoC) as early as possible. This chapter details the basic characteristics of such trials and shows the opportunities elicited by smart designs of exploratory trials, exploratory investigational new drug filing, microdosing studies, early decision making, adaptive trial design, and the combination of regulatory and exploratory trials. All this aims at accelerating PoC as a major value inflection point of drug development.

Early clinical trials are pivotal steps in the humanization of a drug development project. Their design has to accomplish both regulatory aspects as well as scientific gain regarding the drug target, human mechanism of action, and viable biomarkers; they should ultimately support proof-of-concept as early as possible. This chapter details the basic characteristics of such trials and shows the opportunities elicited by smart designs of exploratory trials, exploratory investigational new drug (eIND) filing, microdosing studies, early decision making, adaptive trial design, and the combination of regulatory and exploratory trials. All this aims at accelerating proof-of-concept as a major value inflection point of drug development.

BRAF mutant colorectal cancer carries a poor prognosis which is thought to be related to poor response to conventional chemotherapy. BRAF mutation is associated with the serrated tumour phenotype. We hypothesised that one of the mechanisms by which BRAF mutant colorectal cancer demonstrate poor outcomes with chemotherapy is abnormal gene methylation. The Cancer Genome Atlas (TCGA) methylation data was analysed using a linear regression model with BRAF mutation as an independent variable. Expression datasets were also obtained to correlate functional changes. Top differentially methylated probes were taken forward for validation by methylation pyrosequencing. These probes were analysed on a cohort of patients enriched for BRAF mutations taken from the VICTOR and QUASAR2 studies. In an analysis of 91 tumours (9 BRAF mutant, 82 wild type), the Illumina probe cg11835197 was the probe identified as top differentially methylated (p = 2.56×10-7, Bayes Factor (BF) =6.54). This probe covered a region -413bp from the promoter region of TFAP2E. We found a complex pattern of CpG specific methylation of this region which was associated with both overall (p=0.044) and disease free (p=0.046) survival. BRAF mutant tumours may attain part of their chemoresistance from abnormal TFAP2E methylation, which has not previously been described.

Aim: The aims of Q2 were to assess whether the addition of BEV 7.5mg/kg q3/52 (12/12) to single agent CAP 1250mg/m², 14 of every 21/7 (6/12), increases disease-free (DFS) and overall survival (OS) in CRC patients after resection of the primary; and to validate suggested, or discover new, biomarkers of BEV efficacy and toxicity. Methods: A phase III international randomised controlled trial, coordinated by the UK and recruiting in 6 countries. In addition to the collection of data on toxicity, DFS and OS, a biobank comprising 1350 FFPE blocks and 1000 germline DNA samples was established. Hypothesis-driven biomarkers (MSI status and epithelial/stromal ratio) and hypothesis-driven biomarkers (chomosomal instabiity, ras, raf, POLE and an 80-gene ion torrent panel) were analysed to assess their prognostic and predictive (BEV) utility. Results: 1941 patients were randomised in a 1:1 ratio and demographics and disease characteristics were well balanced between the two arms. DFS in the whole trial population demonstrates that BEV does not improve outcome in this setting (3 year DFS 75.2% for CAPBEV vs 78.2% for CAP: HR = 1.06; p = 0.54). Similarly OS was not improved (3 year OS 85.5% for CAPBEV vs 87.2% for CAP; p = 0.38; HR = 1.12). There may be a temporal trend in HRs (HRs: 1 year 0.83[0.61-1.13], 2 year 0.87[0.65-1.17], 3 year 1.32 [0.9-1.98]. Biomarker analyses confirm that high tumour stromal content confers a worse prognosis (3 year DFS HR 1.58 [1.22-2.05]; p = 0.001). MSS positivity was associated with a worse DFS in patients treated with CAP/BEV compared to those treated with CAP alone (n = 840; HR 1.43; p = 0.005) suggesting a negative predictive effect for BEV: For MSI positive patients, there was no significant difference in DFS between the two arms (n = 135; HR 0.74; p = 0.42). Conclusions: Q2 supports data from two other trials suggesting no role for BEV in the adjuvant setting of CRC. The Q2 biobank and linked database allows further collaborative biomarker hypotheses to be tested. There is a rationale for meta-analysis of all BEV adjuvant CRC studies to more fully explore the putative temporal effect of BEV administration on DFS. Disclosure: R.S. Midgley and D.J. Kerr: has received research funding in the form of an unrestricted educational grant from Roche. All other authors have declared no conflicts of interest.

The angiogenic capability of colorectal carcinomas (CRC), and their susceptibility to anti-angiogenic therapy, is determined by expression of vascular endothelial growth factor (VEGF) isoforms. The intracellular protein T-cell Intracellular Antigen (TIA-1) alters post-transcriptional RNA processing and binds VEGF-A mRNA. We therefore tested the hypothesis that TIA-1 could regulate VEGF-A isoform expression in colorectal cancers. TIA-1 and VEGF-A isoform expression was measured in colorectal cancers and cell lines. We discovered that an endogenous splice variant of TIA-1 encoding a truncated protein, short TIA-1 (sTIA-1) was expressed in CRC tissues and invasive K-Ras mutant colon cancer cells and tissues but not in adenoma cell lines. sTIA-1 was more highly expressed in CRC than in normal tissues and increased with tumour stage. Knockdown of sTIA-1 or over-expression of full length TIA-1 (flTIA-1) induced expression of the anti-angiogenic VEGF isoform VEGF-A165b. Whereas flTIA-1 selectively bound VEGF-A165 mRNA and increased translation of VEGF-A165b, sTIA-1 prevented this binding. In nude mice, xenografted colon cancer cells over-expressing flTIA-1 formed smaller, less vascular tumours than those expressing sTIA-1, but flTIA-1 expression inhibited the effect of anti-VEGF antibodies. These results indicate that alternative splicing of an RNA binding protein can regulate isoform specific expression of VEGF providing an added layer of complexity to the angiogenic profile of colorectal cancer and their resistance to anti-angiogenic therapy.

Colorectal cancer is the third most common cancer in the UK, and represents a significant burden of disease. While there have been few recent advances with traditional therapies, the last few years have seen a rapid expansion of targeted agents, most notably those targeting VEGF, in particular bevacizumab, as treatments providing significant improvements in outcome, particularly in the setting of metastatic disease. However, results in adjuvant therapy have been disappointing and cost remains a major barrier to more widespread use. Many agents are now in varying stages of development as the field continues to expand. The potential benefits of antiangiogenics in colorectal cancer will be improved greatly by the development of methods for stratifying the population and identification of appropriate biomarkers, currently a key area of investigation.

Fluourouracil (FU) is a mainstay of chemotherapy, although toxicities are common. Genetic biomarkers have been used to predict these adverse events, but their utility is uncertain. We tested candidate polymorphisms identified from a systematic literature search for associations with capecitabine toxicity in 927 patients with colorectal cancer in the Quick and Simple and Reliable trial (QUASAR2). We then performed meta-analysis of QUASAR2 and 16 published studies (n = 4,855 patients) to examine the polymorphisms in various FU monotherapy and combination therapy regimens. Global capecitabine toxicity (grades 0/1/2 v grades 3/4/5) was associated with the rare, functional DPYD alleles 2846T>A and *2A (combined odds ratio, 5.51; P = .0013) and with the common TYMS polymorphisms 5`VNTR2R/3R and 3`UTR 6bp ins-del (combined odds ratio, 1.31; P = 9.4 × 10(-6)). There was weaker evidence that these polymorphisms predict toxicity from bolus and infusional FU monotherapy. No good evidence of association with toxicity was found for the remaining polymorphisms, including several currently included in predictive kits. No polymorphisms were associated with toxicity in combination regimens. A panel of genetic biomarkers for capecitabine monotherapy toxicity would currently comprise only the four DPYD and TYMS variants above. We estimate this test could provide 26% sensitivity, 86% specificity, and 49% positive predictive value-better than most available commercial kits, but suboptimal for clinical use. The test panel might be extended to include additional, rare DPYD variants functionally equivalent to *2A and 2846A, though insufficient evidence supports its use in bolus, infusional, or combination FU. There remains a need to identify further markers of FU toxicity for all regimens.

Aspirin and other nonsteroidal anti-inflammatory drugs (NSAIDs) protect against colorectal cancer (CRC) and are associated with reduced disease recurrence and improved outcome after primary treatment. However, toxicities of NSAIDs have limited their use as antineoplastic therapy. Recent data have suggested that the benefit of aspirin after CRC diagnosis is limited to patients with PIK3CA-mutant cancers. We sought to determine the predictive utility of PIK3CA mutation for benefit from both cyclooxygenase-2 inhibition and aspirin. We performed molecular analysis of tumors from 896 participants in the Vioxx in Colorectal Cancer Therapy: Definition of Optimal Regime (VICTOR) trial, a large randomized trial comparing rofecoxib with placebo after primary CRC resection. We compared relapse-free survival and overall survival between rofecoxib therapy and placebo and between the use and nonuse of low-dose aspirin, according to tumor PIK3CA mutation status. We found no evidence of a greater benefit from rofecoxib treatment compared with placebo in patients whose tumors had PIK3CA mutations (multivariate adjusted hazard ratio [HR], 1.2; 95% CI, 0.53 to 2.72; P = .66; PINTERACTION = .47) compared with patients with PIK3CA wild-type cancers (HR, 0.87; 95% CI, 0.64 to 1.16; P = .34). In contrast, regular aspirin use after CRC diagnosis was associated with a reduced rate of CRC recurrence in patients with PIK3CA-mutant cancers (HR, 0.11; 95% CI, 0.001 to 0.832; P = .027; PINTERACTION = .024) but not in patients lacking tumor PIK3CA mutation (HR, 0.92; 95% CI, 0.60 to 1.42; P = .71). Although tumor PIK3CA mutation does not predict benefit from rofecoxib treatment, it merits further evaluation as a predictive biomarker for aspirin therapy. Our findings are concordant with recent data and support the prospective investigation of adjuvant aspirin in PIK3CA-mutant CRC.