AS553 - Collection and molecular characterization of recurrent and metastatic colorectal tumors

Investigator Names and Contact Information

Ulrike Peters (upeters@fredhutch.org)

Introduction/Intent

Colorectal cancer (CRC) is a biologically heterogeneous disease. Established somatic alterations in colorectal tumors [e.g., BRAF, KRAS, microsatellite instability (MSI), CpG island methylator phenotype (CIMP)] suggest multiple tumor subtypes develop through diverse neoplastic pathways. Comprehensive tumor profiling in large sample sets, made possible by recent advances in next-generation sequencing technologies, is the critical next step to more fully understand tumorigenesis and improve the definition of CRC subtypes—knowledge that can translate into improved CRC prevention and treatment. However, such efforts have largely focused on primary tumors, resulting in a paucity of data that comprehensively characterizes mutations associated with recurrent or metastatic disease, which accounts for the majority of CRC-related deaths. Thus, detailed molecular analysis of both primary and recurrent/metastatic tumors will greatly benefit our understanding of CRC progression and help define tumors predicted to have greater potential for these processes, and, in turn, correspond to poorer prognosis. We propose to collect and extract DNA from recurrent or metastatic tumor tissue for ~250 CRC cases in the WHI Cancer Survivorship Cohort. Using this resource, we will generate a comprehensive somatic mutation profile for recurrent and metastatic colorectal tumors through targeted deep coverage sequencing of ~100 genes informed by existing and ongoing CRC tumor sequencing studies. This profile will be used to perform a comparative analysis of the mutational profiles for recurrent or metastatic colorectal tumors versus their patient-matched primary tumors (construction underway in GECCO as part of an existing WHI AS), and to determine for CRC genes whether mutational concordance between recurrent or metastatic tumors and matched primary tumors is associated with CRC-specific and overall patient survival after accounting for cancer treatment. Beyond establishing an important resource for WHI investigators, this work will provide key insights into CRC etiology and drivers of tumor progression, which can ultimately help inform the development of effective therapeutic strategies.

SPECIFIC AIMS

Established somatic alterations in colorectal tumors [e.g., BRAF, KRAS, microsatellite instability (MSI), CpG island methylator phenotype (CIMP)] suggest multiple tumor subtypes develop through diverse neoplastic pathways^1,2. The increasing availability of next-generation sequencing technology has enabled more comprehensive tumor profiling in large sample sets. The Cancer Genome Atlas (TCGA) Project³, for instance, applied this approach to identify a panel of somatic mutations in genes that highlight key carcinogenic pathways in colorectal cancer (CRC), such as MAPK, Wnt, or TGFβ signaling. This large-scale profiling is critical to understand tumorigenesis and improve the definition of CRC subtypes—knowledge that can translate into improved CRC prevention and treatment^4,5. However, such efforts have largely focused on primary tumors, resulting in a paucity of data that comprehensively characterizes mutations associated with recurrent or metastatic disease^3,6, which accounts for the majority of CRC-related deaths⁷. It is well established that tumors acquire additional mutations in order to metastasize⁸. Thus, detailed molecular analysis of both primary and recurrent/metastatic tumors would greatly benefit our understanding of the CRC progression process^3,6. These data can point to important genetic drivers of recurrence or metastasis by identifying somatic mutations specific to recurrent or metastatic tumor tissue, which can, in turn, help define tumors predicted to have greater potential for these processes^4,6,9. In addition, determining whether somatic mutations in CRC recurrences or metastases influence patient survival would further enhance our biological understanding of tumor progression¹⁰. Such insights can ultimately inform the discovery of novel drug targets, development and application of CRC therapies, and improve patient care^4,5. To this end, we propose to collect, deeply sequence, and comprehensively characterize recurrent and metastatic colorectal tumors; additionally, we will examine these tumors in relation to primary CRC tissue and patient survival.

This work will complement and expand on investigations of primary colorectal tumor tissue underway in the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO, U01CA137088, PI: Peters), conducted in collaboration with the WHI Cancer Survivorship Cohort Life and Longevity After Cancer Study (LILAC) (UM1CA173642, PI: Anderson). GECCO includes CRC cases and controls from well-characterized cohort and population-based case-control studies with extensive data on germline genetics, environmental risk factors, and clinical outcomes. As part of an existing WHI AS characterizing primary colorectal tumor tissue, we are harmonizing existing molecular tumor characteristics data (BRAF, KRAS, MSI, and CIMP) across GECCO studies. Further, to generate a comprehensive profile of somatic tumor DNA mutations and define new molecular subtypes of CRC, we are developing a panel of approximately 100 key CRC genes, which we will target in deep sequencing of primary tumor tissue from approximately 4,200 CRC patients. To fully utilize existing infrastructures and maximize the efficiency of the proposed study, we will focus on CRC patients in GECCO who are participants in the WHI. The ongoing primary tumor collection in WHI will allow for easy implementation of the additional collection of recurrent or metastatic tumor tissue. Further, the WHI has detailed high quality data on clinical factors (e.g., tumor site, treatment, recurrences), outcome information (e.g., CRC-specific and overall survival), and pre-diagnostic environmental risk factors, which will enable proposed and future analyses that fully apply this valuable data from recurrent and metastatic tumors. By leveraging these resources, we will achieve the following aims:

1. Collect and extract DNA from recurrent or metastatic tumor tissue for ~250 CRC cases in the WHI.

2. Generate a comprehensive somatic mutation profile for recurrent and metastatic colorectal tumors through targeted deep coverage sequencing of approximately 100 genes informed by existing and ongoing CRC tumor sequencing studies. This profile will be used to perform the following investigations:

   • a. Comparative analysis of the mutational profiles for recurrent or metastatic colorectal tumors versus their patient-matched primary tumors (which is currently being constructed within GECCO as part of an existing WHI AS).

   • b. For CRC genes, determine whether mutational concordance between recurrent or metastatic tumors and matched primary tumors is associated with CRC-specific and overall patient survival after accounting for cancer treatment.

A more complete understanding of colorectal tumorigenesis requires not only large-scale molecular analysis of primary tumors, but also of advanced disease. To address this knowledge gap, we will collect ~250 recurrent and metastatic colorectal tumor tissues and perform the largest comprehensive characterization of these tumors to date. This proposal will be the first to collect recurrent and metastatic tumor tissue in a large population-based setting. The existing infrastructure, well-characterized WHI study population, and experienced research team optimize the likelihood of success. This work, if successful, will provide critical guidance for expanding these efforts to additional GECCO studies. This resource will enable analyses that provide important insights into CRC etiology and drivers.