Aging and Colorectal Cancer     |     Translational Biology of Colorectal Adenomas and Sessile Serrated Polyps     |     Biomarkers for Esophageal and Colorectal Cancer | 

Epigenetic Alterations in the Initiation and Progression of Gastrointestinal Cancer     |     Barretts Esophagus and the Microbiome

Aging and Colorectal Cancer

Advanced age is the single most significant risk factor for cancer. Although there are many plausible age-related mechanisms that mediate the increased risk for cancer in the elderly, functional evidence has been lacking for the majority (if not all) of these mechanisms. Our studies focus on the role of the aged microenvironment, particularly senescence, in promoting the formation of colorectal cancer (CRC), which is a common age-related cancer in the U.S. 

CRC has a well characterized normal-to-adenoma-to-cancer histologic and molecular progression sequence. It is well established that the majority of CRCs arise through the serial accumulation of mutations and epigenetic alterations in oncogenes and tumor suppressor genes in colon epithelial stem cells.  However, our group and others have found cells with cancer-causing DNA alterations (e.g. oncogenic KRAS and TP53) in the histologically normal colon mucosa of people, which suggests that the DNA alterations alone are not sufficient to drive the complete CRC formation process.

We have recently shown that a senescent colon tissue microenvironment can promote the neoplastic behavior of colon epithelial cells ex vivo. We found increased cellular senescence, a hallmark age related phenomenon, in the colon fibroblasts from old people and from people at elevated risk for CRC. We have shown that certain senescence associated secretory phenotype (SASP) factors produced by senescent fibroblasts can induce cancer hallmark behaviors through the activation of oncogenic signaling pathways. Based on our preliminary data we hypothesize that senescent fibroblasts in older people and the accompanying specific Senescence Associated Secretory Phenotype (SASP) secreted proteins promote the tumorigenesis of colon epithelial cells that have acquired age-related oncogenic mutations. To test this hypothesis, we are using in vitro engineered tumor organoids, primary adenoma and normal colon organoids, cell lines, and in vivo mouse models of CRC and aging to critically determine the functional role of the senescent tissue microenvironment on the survival, expansion and malignant transformation of mutant colon epithelial cells, which are the cancer-initiating cells in the colon. These studies will provide functional evidence for the role of the aged microenvironment in promoting CRC formation and rationale for the potential use of senolytic and senomorphic drugs as interventions to reduce aging-related CRC.

The Translational Biology of Colorectal Adenomas and Sessile Serrated Polyps

Colon adenomas account for 80-85% of the CRC precancerous lesions (aka early lesions) and can progress to CRC. Yet, due to reasons that are not completely understood, the majority of these early lesions remain in an indolent early state, and only 5-10% are aggressive and progress to CRC. Although the adenoma progression sequence was initially proposed to be driven mainly by the serial accumulation of gene mutations and epigenetic alterations in colon epithelial cells, based on increasingly detailed analyses of the ‘cancer-causing’ alterations that characterize CRC, it has becoming apparent that these same alterations can also be found in indolent adenomas and even in the histologically normal colon epithelium. We propose that the progression of adenomas to cancer is a consequence of complex interactions among various cell types in the colon as well as the host-microbe within the dynamic early lesion ecosystem, which creates autonomous and nonautonomous factors to drive adenoma progression. To study these factors we are performing a multi-omics evaluation of two unique, highly informative adenoma resources: 1) a cohort and biobank of patients with adenomas that were monitored with known progression outcomes; and 2) a cohort and biobank of prospectively recruited CRC screening subjects who have normal colon tissue and matching adenoma tissues to: 1) determine the features of the “primed” colon that enhance adenoma progression and 2) develop biomarkers to predict the risk of advanced adenoma occurrence.

Colon adenomas account for 80-85% of the CRC precancerous lesions (aka early lesions) and can progress to CRC. Yet, due to reasons that are not completely understood, the majority of these early lesions remain in an indolent early state, and only 5-10% are aggressive and progress to CRC. Although the adenoma progression sequence was initially proposed to be driven mainly by the serial accumulation of gene mutations and epigenetic alterations in colon epithelial cells, based on increasingly detailed analyses of the ‘cancer-causing’ alterations that characterize CRC, it has becoming apparent that these same alterations can also be found in indolent adenomas and even in the histologically normal colon epithelium. We propose that the progression of adenomas to cancer is a consequence of complex interactions among various cell types in the colon as well as the host-microbe within the dynamic early lesion ecosystem, which creates autonomous and nonautonomous factors to drive adenoma progression. To study these factors we are performing a multi-omics evaluation of two unique, highly informative adenoma resources: 1) a cohort and biobank of patients with adenomas that were monitored with known progression outcomes; and 2) a cohort and biobank of prospectively recruited CRC screening subjects who have normal colon tissue and matching adenoma tissues to: 1) determine the features of the “primed” colon that enhance adenoma progression and 2) develop biomarkers to predict the risk of advanced adenoma occurrence.

Biomarkers for Esophageal and Colorectal Cancer

The goal of these Early Detection Research Network (EDRN) supported projects is the discovery and validation of biomarkers for reducing mortality from gastrointestinal cancers. These studies are focused on cancers of the colon, the second leading cause of cancer deaths in the U.S and increasing substantially in young people, and adenocarcinoma of the esophagus (EAC), which is one of the fastest increasing causes of cancer deaths (5-fold increased incidence over the last 3 decades) with an 83% mortality rate. 

For colorectal cancers (CRC), we are developing markers to identify individuals who are at high risk of CRC, and for whom CRC screening that starts at a younger age and is done at more frequent intervals is lifesaving. We are conducting phase 1 and 2 EDRN studies to interrogate a class of molecular markers whose detection in normal colon mucosa we have implicated as identifying individuals at increased CRC risk. These risk markers include a novel set of genomic loci whose methylation in normal colonic mucosa we have found associate with the risk of recurrent colon adenomas in follow-up colonoscopies.

For esophageal adenocarcinomas, we are using an approach: 1) to identify biomarkers that will accurately detect high grade dysplasia (HGD) and EAC but not BE at a clinically meaningful sensitivity and specificity, thus identifying surveillance biomarkers for detecting early BE progression to HGD or early EAC that requires therapy for cancer mortality prevention; and 2) to identify biomarkers that predict the risk of BE progressing to HGD or early EAC.  Ongoing studies are also assessing candidate HGD and early EAC detection biomarkers in phase 2 EDRN trials.   Early detection HGD and early EAC detection biomarker assays based on esophageal brushing samples have the potential to be developed into inexpensive non-endoscopic tests, using devices, like the Esocheck device (Lucid Technologies).

These studies are based on past research developing biomarkers and on unique and essential cohorts for risk predication biomarker development and validation including:1) the world’s only prospective natural history study of BE patients, who had progressive or stable disease; 2) a retrospective cohort study of BE patients who progressed to EAC or had stable disease; and 3) 2 prospective cohorts of colonoscopy based CRC screening patients with 5 to 15 years follow-up data.

Epigenetic Alterations in the Initiation and Progression of Gastrointestinal Cancer

The field of epigenetic alterations in cancer has undergone rapid development in the last 2 decades and has been the subject of intense investigation during this time. Our group provided one of the first studies that demonstrated a causal role for aberrant gene methylation in the formation of cancer. We have also demonstrated the role of aberrant gene methylation in the polyp-cancer progression sequence in both sporadic and familial colorectal cancer and has discovered several novel genes that are aberrantly methylated in colorectal cancer. This has not only led to publications in high-impact journals,(e.g. Nature Genetics, Cancer Research, Clinical Cancer Research, Gastroenterology, etc) but also to patented assays for methylated MLH1 and EVL/miR-324 (patent pending). Our group has also revealed the functional role of specific methylated genes in colorectal cancer and esophageal adenocarcinoma. Studies in our lab have demonstrated that methylated genes can be used as blood and stool based biomarkers for colorectal cancer and esophageal cancer and have provided novel advances in technical performance of these assays. We are currently conducting studies of the molecular subtypes of colon adenomas, CRC, Barretts esophagus, and esophageal adenocarcinoma; of the epigenetic alterations driving cancer initiation and progression; and of the interactions of genetic alterations and epigenetic alterations in gastrointestinal tract carcinogenesis.

Barretts Esophagus and the Microbiome

Barrett’s esophagus (BE), the precursor lesion for esophageal adenocarcinoma, and esophageal adenocarcinoma (EAC) have increased dramatically in the US and other western countries since the 1970s for unclear reasons.  Although there are epidemiological factors associated with the risk of BE and EAC, such as chronic esophageal reflux of stomach and bile acids due to gastroesophageal reflux disease (GERD), smoking, and obesity, these are not the sole factors responsible for promoting the BEEAC progression sequence and only affect subsets of patients with BE and EAC. A modeling study that analyzed the temporal trends of EAC suggested that environmental changes in the 1940’s and 50’s, when antibiotic use became widespread and presumably resulted in widespread alterations in the gastrointestinal tract microbiome, may explain the increasing incidence of EAC.

Preliminary published studies suggest that microbiome alterations, potentially from antibiotics or diet changes, are an additional causative factor in BE and EAC. These studies have assessed the microbiome of the esophagus in patients with BE and EAC and have shown differences between these patients and healthy study subjects, suggesting that dysbiotic microbiomes of the lower esophagus may mediate the initiation of BE or progression of BE to EAC. There are also studies that have shown candidate BE and EAC associated bacterial species associate with BE and/or EAC; however, their role in the pathogenesis of BE->EAC as oncogenic driver bacterial species is not known. This is a significant knowledge gap that has significant implications on our understanding of EAC causation, as it has been well shown that the tumorigenic effects of bacterial species, such as H. pylori in the stomach and F. nucleatum in the colon, make them oncogenic drivers of cancer.

In order to address the innovative hypothesis that dysbiotic esophageal microbiomes have a causal role in the pathogenesis of BE and EAC, we are using state-of-the-art methods to identify and characterize both candidate dysbiotic esophageal microbiomes and candidate oncogenic driver bacterial species in the only existing well characterized prospective cohort of patients with BE that progressed or did not progress to EAC over time. The results of these studies will provide the bases for larger, definitive studies to investigate the utility of microbiome composition as a biomarker of EAC risk. The potential clinical impact of this study would be identification of easily assayed targets for determining cancer progression risk in patients with BE, as well as suggesting means of modulating EAC risk through elimination of the oncogenic microbe(s) or introduction of tumor suppressive microbe(s) through antibiotic or probiotic treatments.