The Translational Research Program in Cancer Differences across Populations

Abstract

Background:

Cancer incidence and mortality vary substantially across populations. The Translational Research Program in Cancer Differences across Populations (TRPCDP) was established in 2020 to address differences in cancer incidence and mortality rates within the United States, with a particular focus on colorectal cancer.

Methods:

The TRPCDP centralized data acquisition and harmonization across three sites in the United States to create a well-annotated resource of colorectal cancer tumors across four populations: African American/Black, Alaska Native, Hispanic/Latino/Latina, and non-Hispanic White. Using a case–control framework, patients with lethal colorectal cancer were matched to two controls with nonlethal colorectal cancer. Formalin-fixed, paraffin-embedded tumor and normal tissue were retrieved and sent for centralized pathology review, followed by DNA and RNA extraction and tissue microarray development. Multiomics and spatial profiling are underway to evaluate the transcriptome, proteome, and microbiome. Patient demographic and clinical data were obtained by medical record review, patient self-report, or linkage to cancer registries. Additional health-related factors were assessed using geospatial linkage.

Results:

The virtual biorepository includes 7,181 patients [African American (n = 1,345), Alaska Native (n = 1,640), Hispanic (n = 1,659), and non-Hispanic White (n = 2,537)]. Tissue blocks (1,594 tumor and 728 normal colon samples) were selected for 938 patients. To date, DNA and RNA have been extracted (n = 831), and tissue microarrays have been constructed (n = 414). Transcriptomic analysis, spatial tumor profiling (multiplex immunofluorescence, PhenoCycler, and GeoMx), and microbiome data (16S rRNA sequencing and digital droplet PCR) are available.

Conclusions:

The TRPCDP has developed a clinically annotated biorepository for future molecular epidemiology studies.

Impact:

The TRPCDP is a unique program that supports collaborative research, community engagement, and pipeline development for the next generation of scientists.

Introduction

Colorectal cancer is a preventable disease, yet it remains a common cancer worldwide. In 2024, colorectal cancer became the leading cause of cancer mortality in men and the second leading cause in women <50 years of age (1) For multifactorial reasons that remain unresolved, colorectal cancer disproportionately affects some communities (2). This is especially true among Alaska Native peoples, who have incidence rates that are more than double US national rates (3). These high rates are a concern for Alaska Native communities, who are working to reduce the burden through increased colorectal cancer screening and prevention. African American/Black individuals (herein referred to as African American) have the second highest incidence and mortality rates for colorectal cancer in the United States (20% and 40% higher than the general US population; ref. 4). Although rates are lower than average among adults in the Hispanic/Latino/Latina (herein referred to as Hispanic) community, this population has experienced the lowest decline in mortality rates over recent decades compared with any other population (5). These communities also experience a high proportion of early-onset colorectal cancer, which has been increasing in incidence since the mid-1990s (2).

Variation in incidence and mortality rates across populations underscores the importance of investigating the complex interplay of environmental and biological factors contributing to cancer-related differences in risk and outcomes. However, few resources exist with sufficient representation from multiple communities (6, 7). Inadequate sample sizes have limited studies published to date but show results that merit further investigation, including differences in the expression of clinically actionable tumor markers when stratified by demographic factors including geography, race, and ethnicity (8–10), reduced treatment efficacy in some genetically defined populations (11, 12), and altered gut microbiota across populations (13) with implications for treatment efficacy (14). These observed differences may reflect underlying genetic diversity, as well as varying environmental exposures and other factors (15, 16). Ongoing innovations in biotechnology and the emergence of novel bioinformatic and machine learning algorithms offer tremendous hope for developing better predictive biomarkers of treatment response and understanding the complex biological contributors that explain differences in the cancer burden.

The Translational Research Program in Cancer Differences across Populations (TRPCDP) was established to provide the necessary infrastructure for applying novel biotechnologies and analytic methods to identify molecular and biological drivers of clinical utility and inform the development of new therapeutic strategies across different populations. Herein, we describe the rationale and development of TRPCDP. By studying population groups with varying cancer rates, we enhance our ability to identify the molecular characteristics and contributing factors driving these differences. Our overarching goal is to meaningfully reduce morbidity and mortality across populations, by (i) discovery and validation of novel molecular, biological, and microbial changes related to response to treatment and risk of lethal cancer and (ii) development of clinical interventions aimed at reducing cancer risk and mortality.  While the current focus of TRPCDP is in on colorectal cancer our long term goal is to expand the work to other cancer types with varying incidence and mortality rates across populations. We describe the organizational structure and methodology of TRPCDP, including the biorepository inventory, current and pending projects, community stakeholder engagement and participation, training of the next generation of cancer researchers, and the creation of an accessible resource for future research.

Materials and Methods

Overview

The foundational work of TRPCDP began with collaborative efforts established more than a decade ago, including forming a consortium with data pooled from the Colon Cancer Family Registry (CCFR; ref. 17), Colorectal Cancer Transdisciplinary Study (CORECT; refs. 18, 19), Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO; refs. 18, 20, 21), ColoCare (22), and the Hispanic Colorectal Cancer Study (HCCS; refs. 23, 24). In 2020, the Fred Hutchinson Cancer Center (FHCC; Seattle, WA), in collaboration with the Alaska Native Tribal Health Consortium (ANTHC; Anchorage, AK), Cedars-Sinai Medical Center (Los Angeles, CA), and Ochsner Health (New Orleans, LA) initiated the TRPCDP (Fig. 1). The TRPCDP is supported by an NCI P20 feasibility and planning grant (P20CA252733) and NCI P50 Specialized Programs of Research Excellence (P50CA285275) and through subsequent support through foundations (V Foundation and Goldman Sachs Foundation), FHCC, Cedars-Sinai, Ochsner Health, ANTHC, and investigator-initiated NCI grants (R01CA155101, R01CA238087, R01CA284732, R01CA248931, R01CA280639, and U01CA290673).

Figure 1.

Organizational structure of the Translational Research Program in Cancer Differences across Populations based on the P20 “mini-SPORE”. Depiction of the population groups included in the TRPCDP and the program organizational structure: executive committee; advisory boards; biospecimen, data and pathology core; research projects; administrative core; and developmental research and career enhancement programs. (Created with BioRender.com.)

The four populations currently represented in TRPCDP are Alaska Native, Hispanic, non-Hispanic White, and African American recruited from the following regions in the United States. The study is conducted in accordance with the Declaration of Helsinki, Council for International Organizations of Medical Sciences (CIOMS) guidelines, the Belmont Report, and the US Common Rule.

Alaska

ANTHC is a nonprofit tribal health organization, owned, managed, and operated by Alaska Native peoples, which provides cancer care and treatment primarily at the Alaska Native Medical Center (ANMC) located in Anchorage, AK, to the approximately 151,000 Alaska Native people living in Alaska. Since 2000, more than 1,600 Alaska Native people living in Alaska have been diagnosed with colorectal cancer (3). American Indian people who have moved to Alaska are able to get care at the ANMC and are included in Surveillance, Epidemiology, and End Results Program (SEER) data. Formalin-fixed, paraffin-embedded (FFPE) tumor blocks going back to the 1970s at the ANMC Pathology Lab Archive were available for TRPCDP use.

This portion of the study was reviewed and approved by the Alaska Area Institutional Review Board (IRB; IRB00000636), which operates under Federalwide Assurance FWA00001138.

California

The HCCS was established in 2010 as a population-based cohort of Hispanic individuals using the California Cancer Registry and direct access to local hospitals. More than 1,600 Hispanic patients with colorectal cancer have been enrolled in the HCCS (24–26). FFPE blocks were retrieved directly from hospitals throughout California. Patient-reported surveys, medical chart abstraction, and data from linkages to the SEER California Cancer Registry and the National Death Index are available. The Cedars-Sinai Medical Center’s IRB (FWA00000468) reviewed and approved this study, and all participants signed informed consent.

Louisiana

Ochsner Health is the largest healthcare provider in Louisiana, serving more than 1.4 million patients per year. It has a long tradition of serving a large African American population, and about one third of its patients identify as African American. Data from medical chart abstraction and linkages with the Louisiana SEER registry/National Death Index for demographic, clinical, outcome, and treatment data are available. Since 2000, Ochsner has diagnosed and treated more than 1,300 African American and more than 2,500 non-Hispanic White patients with colorectal cancer. FFPE blocks were retrieved from their centralized tissue bank and the Department of Pathology. The Ochsner IRB approved this project.

Selection of TRPCDP participants

Patients diagnosed with colorectal cancer at ANMC or Ochsner Health, as well as research participants in the HCCS, were eligible for inclusion. Additional samples were also included from participants in the Seattle Colon Cancer Family Registry (see the Collaborations section). Eligible participants were diagnosed with colon or rectal adenocarcinoma (ICD10 codes: C180 and C182–C189 for colon adenocarcinoma; C199 and C209 for rectal adenocarcinoma; ref. 27) after 2000 and of 18 to 85 years of age at the time of diagnosis. An upper limit of 85 years of age was selected because the outcome of interest was colorectal cancer–specific mortality. Individuals >85 years of age have many competing causes of death and may not receive standard treatment. Focusing on stage I to III also ensured greater homogeneity of first-line therapy. From this, we constructed a virtual biorepository of all participants with colorectal cancer with information on age at diagnosis, sex, tumor stage, and site (Supplementary Table S1).

TRPCDP study design and sample size targets

To optimize statistical power, TRPCDP utilized a nested case–control design in which cases were defined as patients who died of colorectal cancer, and controls were patients with colorectal cancer who survived at least as long as the case to which they were matched. Controls were matched to cases 2:1 on race and ethnicity, age at diagnosis, sex, stage, tumor site, and year of diagnosis. The goal was ∼70 cases of lethal colorectal cancer and ∼140 matched controls for each population group.

Biospecimen collection and processing

Centralized pathology review and tissue handling

All tissue samples (FFPE blocks and/or unstained slides) were retrieved by staff at the participating sites and subsequently shipped to the FHCC. All tissues were reviewed centrally by a single pathologist (ALK) using a standard operating procedure with additional pathologists available for second opinions as needed. Each FFPE tissue block was evaluated for quality of tissue preservation and processing, histology, confirmation of correct diagnosis, tumor content, and tumor volume using an hematoxylin and eosin (H&E) slide to ensure sufficient material was available for DNA and RNA extraction and annotation of tumor tissue selection for tissue microarray (TMA) generation (Fig. 2).

Figure 2.

Sample sharing and analysis workflow for TRPCDP, 2020–2023. Evaluation of FFPE tumor and normal tissue blocks for quality of tissue preservation and processing, histology, confirmation of correct diagnosis, and tumor content and volume prior to TMA construction. MSI, microsatellite instability. (Created with BioRender.com.)

DNA and RNA extraction

To ensure at least 70% tumor content for DNA and RNA extraction from FFPE tissue sections and unstained slides, tumor areas were marked on the corresponding H&E-stained slide to guide dissection of tumor tissue. All paraffin was removed by treatment with the Deparaffinization Solution (Qiagen). RNA extraction was done using the Qiagen RNeasy FFPE kit (Qiagen) according to the manufacturer’s protocol. Extraction of microbial DNA followed a standard protocol that was adapted for FFPE tissue elsewhere (28, 29) Tumor DNA and RNA and microbial DNA are maintained centrally at the FHCC.

Transcriptomic and microbiome analyses

RNA sequencing (RNA-seq) libraries were generated using the Illumina TruSeq RNA Exome kit (Illumina, Inc.). Libraries were sequenced on NovaSeq 6000 to a minimum depth of 30 million paired reads per sample. Microbial DNA was analyzed using 16S rRNA gene sequencing to classify the relative abundance of different bacterial genera and phyla as well as α and β diversity in both normal and tumor tissue. We developed and applied digital droplet PCR (ddPCR) assays to quantify the following three microbes with putative links to colorectal cancer: Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, polyketide synthase positive Escherichia coli and the human SLCO2A1 gene in FFPE human tissue.

TMA construction

To ensure data robustness, we used three tumor cores per tissue, two collected from the center of the tumor and one from the invasive margin of the tumor. In addition, we collected one core from the normal epithelial tissue. Core selection from FFPE blocks and unstained slides was guided by TRPCDP pathologist (ALK) review of H&E-stained slides. TMAs were constructed using the TMA Grand Master (3DHISTECH). Tissue cores from case–control pairs were distributed throughout a TMA to minimize batch effects. TMAs are maintained centrally at the FHCC.

Multiomics profiling

We profiled a subset of TMAs on various platforms: multiplex immunofluorescence, Akoya PhenoCycler, RNAscope, 10× Visium spatial gene expression, NanoString GeoMx digital spatial profiling and NanoString CosMx.

Covariates

We centralized variable definition and a minimal set of variables for abstraction to ensure uniform collection at each participating site. Across all sites, data were collected using the secure Health Insurance Portability and Accountability Act–compliant Research Electronic Data Capture (REDCap) online data entry system adapted from the ColoCare study (22). The FHCC team, which also oversees the abstraction in ColoCare, provided training to TRPCDP abstractors to ensure a high-quality, standardized approach across sites.

Medical record abstraction

Trained medical abstractors used standardized abstraction forms adapted from the ColoCare Study (22) to manually review medical records for detailed demographic (sex, age, race, and ethnicity), clinical (body mass index, comorbidities, surgical procedures, and treatments), and epidemiologic (smoking and alcohol) data. Patient records were evaluated five years prior to and after colorectal cancer diagnosis including clinic notes, pathology reports, radiology reports, operative/procedure reports, hospital discharge summaries, radiation and medical oncology notes, laboratory results, tumor recurrence, and outpatient summaries (Table 1).

Table 1.

Data elements collected and harmonized in Translational Research Program in Cancer Differences across Populations.

Domain	Variable	Source
Demographic	Age, date of birth, sex, race, and ethnicity	Cancer registries, medical records, patient surveys, and linkage to external databases (geocoding)
Medical history	Family history of cancer, comorbid conditions, prescription medication use, height, weight, smoking history, and pre-CRC surgery antibiotics	Medical records and patient surveys
Tumor characteristics	Grade, histology, clinical/pathologic stage, and lymphovascular and perineural invasion	Cancer registries and medical records
Molecular testing	Microsatellite status, BRAF and KRAS mutations, and other testing	Medical records and molecular profiling
Surgical treatment	Type and dates	Cancer registries and medical records
Radiotherapy	Dates, number of treatments, and dose	Cancer registries and medical records
Chemotherapy	Agents, dose, dates, and number of infusions	Cancer registries and medical records
Immunotherapy	Agents, dose, dates, and number of infusions	Cancer registries and medical records
Treatment side effects	Allergic reactions, fatigue, cardiac/GI/hematologic/neurologic toxicities, and other adverse events	Medical records
Clinical outcomes	CRC recurrences (dates, location, and methods of detection and treatment), progression-free survival, vital status, and cause of death (1°, 2°, and 3° causes)	Cancer registries and medical records
Access to and use of healthcare	Insurance status, insurance type, screening history, and primary care utilization	Cancer registries and medical records

NOTE: Data from cancer registry and linkage to external databases (geocoding) are available for all patients in the virtual repository (Supplementary Table S1), survey data for all Hispanic patients (Supplementary Table S1), and medical record collection is ongoing for all patients in the physical repository (Table 2).

Abbreviations: CRC, colorectal cancer; GI, gastrointestinal.

Linkage to cancer registries

We obtained data from SEER cancer registries on the following clinical variables: age at diagnosis, sex, tumor site, stage, surgery, chemotherapy, radiation, recurrence, overall colorectal cancer–specific death, and age of death. We compared data obtained from medical records and adjudicated discrepancies.

Patient-reported surveys

HCCS participants completed demographic, lifestyle, and medical history questionnaires including colorectal cancer–specific outcomes like recurrence. Data were used to verify and augment information from medical records and cancer registries as needed.

Other health-related factors

Where available, we leveraged data from SEER cancer registries and geospatial linkage that assessed factors such as rurality or geographic access to care based on the patients’ geocoded addresses at the time of diagnosis (30–36).

Collaborations

The TRPCDP is actively engaging with international collaborators to pool additional data on participants with colorectal cancer.

Seattle Colon Cancer Family Registry

The Seattle Colon Cancer Family Registry (SCCFR) is a population-based case–control study in Washington State, one of seven centers forming the Colon Cancer Family Registry (www.coloncfr.org). Recruitment of cases and controls began in 1998 and ended in 2012. The SCCFR collected information on demographics, risk factors, family, medical, and reproductive histories, physical activity, diet, survival, and tumor characteristics. Through an ongoing ancillary study within the SCCFR, data were also collected to characterize the tumor-associated microbiome in colorectal cancer, using 16S rRNA-seq and ddPCR assays for F. nucleatum on paired tumor and adjacent normal colon tissue samples. From within this data resource, a sample of 146 non-Hispanic White participants meeting eligibility for TRPCDP analyses was selected and pooled with other included populations for analysis.

Administration

TRPCDP administration functions were centralized at the FHCC to provide programmatic support; coordinate activities within the biospecimen and pathology core to provide sample processing and data management services, coordinate laboratory analyses, and establish future collaborations; build a development research program to support pilot studies; and coordinate activities of the community, internal, and external advisory boards (Fig. 1). We established standard protocols, material transfer agreements, and data transfer agreements between the TRPCDP partners and the FHCC to facilitate the secure transfer of samples and related data.

Community Advisory Board

Given the focus on colorectal cancer differences in incidence and mortality by race and ethnicity and our primary goal of conducting translational research that meaningfully reduces cancer rates, our Community Advisory Board consisted of African American, Alaska Native, and Hispanic patient advocates and key community stakeholders. These individuals shared their lived experience with colorectal cancer, patient advocacy work, and provided critical feedback to inform research priorities, research design, implementation, and dissemination of study results.

Scientific internal and external advisory boards

Internal and External Advisory Board members were chosen to provide experience in leading large program grants and scientific expertise in the areas of colorectal cancer research, clinical medicine, cancer disparity research, and community-based participatory research. Board members represented a range of backgrounds, including current NCI P20 Cancer Disparities principal investigators, NCI P50 Specialized Programs of Research Excellence principal investigators, FHCC institutional leadership, and researchers from TRPCDP-participating institutions.

Data availability

We developed a framework for sharing data in accordance with the FAIR principles: Findable, Accessible, Interoperable, and Reusable (37). Biospecimens and data collected as part of TRPCDP were available to all TRPCDP pilot project awardees. After prioritizing TRPCDP projects and pilots, biospecimen and data will be made available through non-TRPCDP investigators after appropriate approvals are in place. Data will also be made publicly available via controlled access, such as the NIH Database of Genotypes and Phenotypes. As TRPCDP involves samples from Alaska Native peoples who have tribal sovereignty over their data and biospecimens, we developed a rigorous review and approval process for requesting data (including via the NIH Database of Genotypes and Phenotypes data repository) in collaboration with the NCI, the Alaska Area IRB, and Alaska tribal research review committees. Data from Alaska Native peoples are subject to tribal sovereignty and have additional review and approval requirements for their use (Supplemental Fig. S1).

Results

Characteristics of TRPCDP study participants

Currently, data and biospecimens from a total of 938 (African American: 214; Alaska Native: 319; Hispanic: 185; and non-Hispanic White: 220) patients with colorectal cancer are available for molecular assessments in the TRPCDP physical repository (Table 2; Supplementary Table S2). Study characteristics are reflective of the selection criteria (see Selection of TRPCDP participants) and, as such, vary from those in the virtual repository. The mean age at diagnosis (64.1 years ± 11.9) was similar across population groups, except for the Hispanic cohort, which had a lower mean age at diagnosis (57.8 ± 12.3). A nearly equal representation of females to males is available across all population groups (48%). Approximately one fifth of patients had rectal cancers (17%), with a higher proportion in the Hispanic population (31%). There were more patients with colorectal cancer tumors at more advanced stage of diagnosis [stage I: 190 (20%); stage II: 351 (37%); stage III: 397 (42%)]; however, the distribution varies by ethnicity and race [African American: stage I: 36 (17%), stage II: 82 (38%), and stage III: 96 (45%); Alaska Native: stage I: 56 (18%), stage II: 126 (39%), and stage III: 137 (43%); Hispanic: stage I: 43 (23%), stage II: 56 (30%), and stage III: 86 (46%); and non-Hispanic White: stage I: 25 (25%), stage II: 40 (40%), and stage III: 35 (35%)]. Per the case–control design, one third of all patients had lethal colorectal cancer. The physical repository will continue to grow based on ongoing and future funding. For instance, current efforts will increase the number of patients with early-onset colorectal cancer and patients undergoing immune checkpoint inhibitor treatment.

Table 2.

Summary of Translational Research Program in Cancer Differences across Populations current physical repository stratified by population group.

​	African American		Alaska Native		Hispanic		Non-Hispanic White
	N	%	N	%	N	%	N	%
Patients with colorectal cancer	214		319		185		220
Diagnosis years	2000–2015		2000–2017		2008–2016		2000–2015
Age at diagnosis (years)
Mean	64.2		65.2		57.8		67.9
<50	21	10%	34	11%	45	24%	14	6%
50–60	52	24%	71	22%	62	34%	45	21%
>60	141	66%	214	67%	78	42%	161	73%
Female	107	50%	195	61%	77	42%	78	35%
Tumor stage	​	​	​	​	​	​	​	​
I	36	17%	56	18%	43	23%	55	25%
II	82	38%	126	39%	56	30%	87	40%
III	96	45%	137	43%	86	47%	78	35%
IV	NA
Tumor site	​	​	​	​	​	​	​	​
Proximal colon	101	47%	161	50%	60	32%	109	50%
Distal colon	87	41%	124	39%	63	34%	61	28%
Rectum	24	11%	33	10%	57	31%	47	21%
Unspecified	2	1%	1	1%	7	3%	3	1%
Tumor tissue # of blocks	401		537		248		408
Normal tissue # of blocks	204		245		79		200
Extracted DNA and RNA	206		258		153		214
TMA	113		111		69		121

TRPCDP biorepository

As of August 2024, the biorepository includes 2,322 FFPE tissue blocks (1,594 tumor and 728 normal tissues from the surgical margin). Due to funding for additional research projects, the largest number of tissue blocks is available for the Alaska Native group: 554 tumor and 253 normal blocks with DNA/RNA extracted for 217 patients with colorectal cancer and TMAs constructed for 112 patients with colorectal cancer. In the African American cohort, there are 421 tumor and 212 normal blocks available, with DNA/RNA extracted for 212 patients with colorectal cancer and TMAs constructed for 118 patients with colorectal cancer. The non-Hispanic White cohort contains 412 tumor and 201 normal blocks with DNA/RNA extraction for 218 patients with colorectal cancer and TMAs for 120 patients with colorectal cancer. The Hispanic cohort is the smallest with 248 tumor and 66 normal blocks and DNA/RNA extracted for 151 patients with colorectal cancer and TMAs constructed for 62 patients with colorectal cancer.

TRPCDP projects and pilot studies

Starting in 2020, there were multiple projects which used biospecimens from TRPCDP for risk prediction, tumor sequencing, transcriptomics, tumor microbiome analysis, spatial profiling, and treatment response studies, including comparison of population groups in terms of colorectal cancer–specific survival as well as gene expression of tumor tissues and aspects of the microbial community in tumors (Table 3). Specimens from 782 patients with colorectal cancer underwent RNA-seq, and 715 underwent microbiome assessments. A total of 10 TMAs, representing 123 patients, have undergone GeoMx and PhenoCycler analyses so far. Another funded ancillary study will develop a cohort of Alaska Native individuals undergoing colorectal cancer screening to examine risk factors for colorectal cancer in this population and build an additional biorepository for future research (U01CA290673).

Table 3.

Translational Research Program in Cancer Differences across Populations Projects, 2020–2023.

Project	Technology	Population	Number of samples
Main P20 projects
Identifying novel molecular predictors of lethal CRC	RNA-seq	AA, AN, Hispanic, and NHW	840
Examine the CRC-associated microbiome using candidate and agnostic approaches	16S rRNA-seq and ddPCR	AA, AN, Hispanic, and NHW	840
Developmental pilot projects
Predictive factors in CRC progression and treatment response	mIF	AA and NHW	30
Metabolic dependencies in obesity-associated CRCs	CRISPR/Cas-9, in vivo mouse studies, and mass spectrometry	Not applicable (animal study)	​
Developing single-cell omics from colorectal mucosa biopsies	10X Single Cell Multiome	NHW	4
Characterizing the CRC tumor microenvironment	PhenoCycler	AN	13
Testing a microbiome-modulating fiber supplement in rectal cancer	ddPCR, 16S rRNA-seq, and RNAscope	AA and NHW	12
Gene-level correlates of the gut microbiome and colorectal neoplasia	Shotgun sequencing	AN	30
Prognostic biomarker evaluation in patients with pancreatic cancer	RNA ISH and multiplex IHC	AA and NHW	40
Measuring the CRC intratumoral mycobiome in diverse racial and ethnic populations	18S rRNA-seq	AA, AN, Hispanic, and NHW	40
A DNA microarray approach to characterize the intratumoral microbiome	DNA microarray	AA, AN, Hispanic, and NHW	40
Technical feasibility studies
NanoString GeoMx digital spatial profiler  10X Genomics Visium spatial transcriptomics  PhenoCycler for senescence markers	GeoMx Visium PhenoCycler	AN	​

Abbreviations: AA, African American; AN, Alaska Native; CRC, colorectal cancer; mIF, multiplex immunofluorescence; NHW, non-Hispanic White.

Discussion

The overarching goal of TRPCDP is to use molecular epidemiology studies to identify biological factors that drive colorectal cancer incidence and mortality, which may explain observed population differences. By examining population groups with distinct colorectal cancer rates, we can increase the range of molecular characteristics affecting colorectal cancer development and mortality and thereby increase the statistical power. We developed an organizational infrastructure representative of four populations with stark differences in colorectal cancer incidence and mortality rates, built a rich annotated biorepository, initiated collaborative research projects, established a process for community engagement and participation in research, and created the resources and a training environment for the next generation of cancer researchers. Our major scientific priorities center around clinically relevant questions in colorectal cancer differences in outcomes. The main themes and how our program is designed to advance our major scientific priorities are discussed below:

• 1. Inclusion of communities rarely studied in cancer research: Most of the focus in cancer research has been on investigating factors driving non-Hispanic White and African American differences (10, 38–41). The TRPCDP addresses a critical gap in knowledge for both admixed populations including the Hispanic community and Alaska Native peoples. Studies of Alaska Native populations are particularly scarce, and most have focused on implementation research aimed at improving screening (42–49). These studies successfully illustrated increases in screening utilization among Alaska Native peoples to a level that now mirrors rates in the general US population (42–51), leading us to consider how to make similar progress in addressing the high mortality rates in this less studied population. Similarly, for the Hispanic community, our group has led efforts to investigate genetic susceptibility and the somatic and immune landscape of colorectal tumors (15, 19–21, 23, 52–55). TRPCDP is poised to make significant strides in dissecting the underlying biological drivers of colorectal cancer mortality across multiple populations, as this is a first-of-its-kind infrastructure that has centralized data/biospecimens across four populations.

• 2. Identification and validation of biological drivers influencing and reflecting differences in colorectal cancer mortality across populations: The Cancer Genome Atlas revolutionized the field of cancer genomics but was constrained by a significant gap in representation across populations, which may mean missing the full spectrum of variation. To date, we and others have demonstrated that tumors from African American patients exhibit distinct mutational frequencies in several key colorectal cancer genes, including PIK3CA, KRAS, and BRAF, as well as differences in the expression of genes associated with inflammation and immune response (41). Fewer than 20% of those included in the Human Tumor Atlas Network identify as African American or Hispanic, and the number of Alaska Native and American Indian patients with cancer is too small to be listed separately. Consequently, The Cancer Genome Atlas and Human Tumor Atlas Network have limited ability to provide accurate tumor characterization for the full breadth of populations affected by colorectal cancer. The TRPCDP aims to fill this gap by investigating population-based differences in colorectal cancer incidence and mortality. Through this research, we aim to create a comprehensive profile of the colorectal cancer tumor transcriptome and microbiome across four distinct populations. Comparing data across groups with vastly different incidence and mortality rates may advance our understanding of molecular and biological drivers and markers of differences in colorectal cancer rates. We will also increase the predictive performance of molecular and microbial markers and the identification of novel therapeutic targets/approaches, through the inclusion of more individuals of varying background and exposures. Given observed differences in disease burden across these population groups, such inclusion can also inform the development of novel strategies, particularly among populations with reduced access to medical services. Published work in other cancers demonstrates the effectiveness of this approach in identifying novel, clinically meaningful prognostic and predictive tumor features (56–60). By expanding this methodology to colorectal cancer, we aim to uncover critical insights that can lead to significant improvements in patient outcomes across populations.

• 3. Spotlight on the intratumoral microbiota across populations: A growing body of evidence has implicated the gut microbiota’s role in colorectal cancer progression through multiple mechanisms that include enhancement of host pro-inflammatory genes and cytokines (61–63), induction of oxidative stress (64, 65), affecting the immune system, and via the action of bacteria-derived genotoxins (66–69). However, to date, studies of the tumor microbiome in colorectal cancer have been conducted mainly in non-Hispanic White populations. However, the microbiome could play an important role in observed differences in colorectal cancer rates across population groups given differences in lifestyle and environmental exposures (e.g., diet and antibiotic use). Although a growing number of studies are exploring the gut microbiome using stool samples (61, 70–73), less data are available on the tumor microbiome (74–76). Identifying aspects of, and patterns in, the intratumoral microbiome may provide avenues to enhance prediction of incident colorectal cancer and adverse outcomes that ultimately lead to improvements in colorectal cancer survival. In the TRPCDP, we propose using discovery-based, agnostic, and targeted candidate approaches to identify differences and similarities in the tumor-associated microbiome across populations. To agnostically compare patterns of tumor-associated microbial community structure, we sequence bacterial 16S rRNA gene segments from tumor tissue specimens and matched normal tissue specimens. Furthermore, we developed and applied highly sensitive and quantitative ddPCR assays to compare the quantities of candidate bacteria in tumors across populations. This approach aims to identify potential novel microbial biomarkers and pathways that may be associated with or contribute to differences in colorectal cancer outcomes.

• 4. Tumor tissue–based spatially resolved predictors of treatment response across populations: We propose a highly innovative colorectal cancer tumor molecular profiling strategy. Specifically, spatial proteomic analyses enable deep characterization of the tumor microenvironment and immune response, which in other cancers has been shown to be of high translational relevance (77–79). Few studies, however, have applied this powerful approach to colorectal cancer or advanced our understanding of cancer by studying patients from multiple populations. It is critical to identify new biomarkers, given that carcinoembryonic antigen (CEA), the most commonly used biomarker clinically to assess disease progression, has only moderate sensitivity and specificity for detecting recurrent colorectal cancer. Its use remains controversial as a Cochrane review of CEA’s utility concluded that “CEA is insufficiently sensitive to be used alone” and that it is “essential to augment CEA monitoring with another diagnostic modality in order to avoid missed cases (recurrences; ref. 80).” Thus, there is an urgent need for novel biomarkers that can be used to guide clinical decision-making and that perform well among populations of patients that experience the greatest colorectal cancer burden. Through this initiative, we aim to develop biomarkers that are not only more sensitive and specific than current options but that perform optimally in all individuals. This will enhance personalized treatment strategies, reduce differences in colorectal cancer outcomes, and ultimately lead to improved survival and quality of life.

• 5. Bi-directional partnership with community stakeholders: For the successful translation of our research, community engagement is key, as it can result in higher-quality, more generalizable, and more acceptable research. Our Community Advisory Board, comprising patient advocates, is a key TRPCDP partner, providing critical feedback and actively engaging in the execution of our research and the dissemination of study results. Community engagement improves the effectiveness of our communication with diverse audiences (81), improving our ability to disseminate information across various health literacy levels and cultural preferences (82).

• 6. Preparing a new generation of cancer researchers: TRPCDP plans to mentor and support early career investigators and established faculty members interested in careers on translational cancer research through research support, leadership development, and enhanced recruitment and retention strategies at TRPCDP-participating institutions.

Our study has strengths and limitations. Most importantly, our program represents multiple groups across the United States that experience high as well as low colorectal cancer incidence rates. None of the studies harmonized in the TRPCDP include individuals who self-identify as Asian or other combinations of race and ethnicity beyond the four described above; however, there exists several notable resources including the International Cancer Genome Consortium and Accelerating Research in Genomic Oncology, 100,000 Genomes Project (83, 84), and others (85–88) that will allow opportunities for collaboration in the future. When faced with the need to develop a well-powered study with sufficient follow-up time in a timely and cost-effective manner, reliance on archival specimens and data is crucial. Archival FFPE tissue blocks have become increasingly valuable for research, given that a growing number of molecular profiling platforms can utilize FFPE tissue, allowing for detailed tumor profiling at the single-cell level. All patient recruitment areas are covered by SEER cancer registries, which have enabled us to start with a well-harmonized virtual repository of key patient characteristics. This allowed us to select the most informative patients and design a well-balanced and matched set of patients for downstream analysis. Enriching our analysis for patients who died of colorectal cancer substantially increases the power for our primary outcome of colorectal cancer–specific death. However, not all patients selected from the virtual repository have usable tumor tissue; for approximately 20% of patients, the tissue blocks are either unavailable or have too low tumor content for extraction and analysis. To account for this and the case–control sampling approach, we use inverse probability weighting to their sampling fractions derived from available SEER data, which provides complete information on the underlying patient population. Another limitation is the lack of comprehensive risk factor data, including dietary variables, in the TRPCDP, given limitations of electronic medical records. Linkage to other databases and leveraging geospatial data will help increase data on various health-related factors (89).

In summary, high-dimensional molecular and microbiome data in large, well-characterized patients derived from different population groups are urgently needed. These data are essential to improve statistical power and to develop better prediction models to inform prognosis. It could also help guide the selection of therapeutic agents and the development of novel strategies. Through this integrated effort, we envision realizing our goal of a sustained translational research program dedicated to eliminating differences in colorectal cancer incidence and mortality rates across populations and, more broadly, reducing colorectal cancer–related morbidity and mortality in the Unites States.

Supplementary Material

Supplemental Figure 1

Supplemental Figure 1. Shows the process for requesting data from Alaska Native peoples from the Alaska Native Tribal Health Consortium and accessible via the NIH dbGaP data repository.

Supplemental Table 1

Supplemental Table 1 shows a Summary of Translational Research Program in Colorectal Cancer Disparities virtual repository of colorectal cancer patients.

Supplemental Table 2

Supplemental Table 2 Shows a summary of Translational Research Program in Colorectal Cancer Disparities physical repository of colorectal cancer patients stratified by case-control status

Authors’ Disclosures

J.C. Figueiredo reports grants from NIH during the conduct of the study. D. Redwood reports grants from NIH during the conduct of the study. W.M. Grady reports personal fees from Guardant Health and Karius outside the submitted work. M. Matrana reports personal fees from Merck, Eisai, AstraZeneca, Johnson and Johnson/Janssen, Exelixis, EMD Serono, Pfizer, Astellas Pharma, Bristol Myers Squibb, Seagen, and Genentech outside the submitted work. J.D. Mizrahi reports personal fees from Seagen, Daiichi Sankyo, AstraZeneca, Exelixis, Amgen, Bristol Myers Squibb, and Intera Oncology outside the submitted work. S. Thomas reports grants from NIH during the conduct of the study. C.C.S. Yeung reports personal fees from TwinStrand, Thermo Fisher Scientific, and Beckman Coulter and grants from Sensei Bio, OBI Pharma, and Kineta outside the submitted work. U. Peters reports other support from AbbVie during the conduct of the study; reports being a consultant for AbbVie; and reports that her husband is holding individual stocks for the following companies: Amazon, ARM Holdings plc, BioNTech, BYD Company Limited, CrowdStrike Holdings, Inc., CureVac, Google/Alphabet, Microsoft Corporation, NVIDIA Corporation, and Stellantis. No disclosures were reported by the other authors.

Authors’ Contributions

J.C. Figueiredo: Conceptualization, resources, investigation, methodology, writing–original draft, writing–review and editing. D. Redwood: Conceptualization, resources, investigation, methodology, writing–original draft, project administration, writing–review and editing. L. Li: Resources, methodology, writing–review and editing. E. Donato: Writing–review and editing. D. Fort: Methodology, writing–original draft, writing–review and editing. E.E. Fox: Methodology, writing–review and editing. W.M. Grady: Methodology, writing–review and editing. H. Green: Methodology, writing–review and editing. T.A. Harrison: Writing–review and editing. C. Haupt: Writing–review and editing. L. Hsu: Methodology, writing–review and editing. M.A.J. Hullar: Methodology, writing–review and editing. J.R. Huyghe: Methodology, writing–review and editing. W. Johnson: Writing–review and editing. A.L. Koehne: Methodology, writing–review and editing. S.D. LaBrie: Writing–review and editing. M.A. Lakey: Resources, project administration, writing–review and editing. M. Lin: Resources, project administration, writing–review and editing. N.C. Loroña: Writing–review and editing. G.A. Maresh: Resources, writing–review and editing. M. Matrana: Writing–review and editing. J.D. Mizrahi: Resources, writing–review and editing. S.H. Nash: Writing–review and editing. N.T. Nguyen: Resources, project administration, writing–review and editing. J.L. Paruch: Writing–review and editing. A.I. Phipps: Resources, writing–review and editing. C. Qu: Writing–review and editing. T.W. Randolph: Writing–original draft, writing–review and editing. S. Romo: Resources, project administration, writing–review and editing. C.E. Thomas: Writing–review and editing. S. Thomas: Resources, project administration, writing–review and editing. J. Tiesinga: Writing–review and editing. C. Whitlow: Resources, writing–review and editing. C.C.S. Yeung: Resources, writing–review and editing. H. Yin: Writing–review and editing. C.M. Zibilich: Writing–original draft, writing–review and editing. C.I. Li: Conceptualization, resources, funding acquisition, methodology, project administration, writing–review and editing. T.K. Thomas: Conceptualization, resources, funding acquisition, methodology, project administration, writing–review and editing. U. Peters: Resources, supervision, funding acquisition, investigation, writing–original draft, project administration, writing–review and editing.