U01 CA187956-01 (MPI: A. Goel and D. Wodarz) 9/23/2014 – 8/31/2020
“Aspirin and Cancer Prevention in Lynch Syndrome: From Cell to Population Data”
The major goal of this proposal is to understand how aspirin treatment reduces the incidence of Lynch Syndrome patients and to determine how treatment-induced changes in cellular parameters determine the degree of protection observed at the population level.
DESCRIPTION (provided by applicant): Lynch syndrome patients inherit a germline mutation in one of several DNA mismatch repair (MMR) genes, leading to a significantly earlier onset and a higher penetrance of colorectal cancer than in sporadic cases due to the occurrence of microsatellite instability (MSI). Long term administration of aspirin has been shown to reduce the incidence of colon cancer in Lynch syndrome patients, as documented by epidemiological data. The mechanisms underlying this effect are not fully understood. It is thought that protection is achieved through COX-dependent and independent activities. Basic kinetic parameters, such as the division rate, death rate, and mutation rate of cells have been shown to be affected. In order to better understand how protection is achieved, it is important to find out how changes in cellular parameters determine the degree of protection observed on the population level. The hypothesis is explored that the degree of protection observed on the population level can be predicted from data that quantify how aspirin changes parameters related to the evolutionary dynamics of cells. This hypothesis will be tested with an inter-disciplinary approach that combines experiments with mathematical models and that links data on cellular kinetics with those on incidence in the population. The first two aims will quantify the extent to which aspirin changes a set of key parameters that are related to the growth and evolution of cells. These include the rate of cell division, the rate of ell death, the rate at which genetic changes are incurred, the probability of repair, the mean duration of repair, etc. This will be done with different cell lines exposed to varying levels of inflammation. The investigation starts first in an in vitro setting and is then extended to human tumor xenografts in mice, which represent a more complex growth environment for the cells. Subsequently, the data on cellular kinetics will inform a mathematical model of in vivo carcinogenesis in Lynch Syndrome patients. The model will be used to generate theoretical age-incidence curves for colon cancer in Lynch syndrome patients in the presence and absence of aspirin treatment. It will test whether the model can successfully predict the observed age-incidence curves through model application to epidemiological data. The model will allow us to determine which cellular parameter(s) contribute the most to the protection observed in the population data, and to explore possible avenues to enhance this level of protection. Implications of our results for understanding aspirin-mediated protection against sporadic colorectal cancer will be explored by analyzing appropriate epidemiological data.
R01 CA072851-19 (MPI: A. Goel and C. R. Boland) 8/01/2015 – 07/31/2020
“Familial and early onset colorectal cancer”
This proposal is aimed to study the underlying basis of highly penetrant genetic forms of familial colorectal cancer, which will provide better informaiton for the clinicians managing these patients.
DESCRIPTION (provided by applicant): In spite of all we have learned about the genetic basis of colorectal cancer (CRC) over the past 25 years, a large proportion of patients with some form of familial CRC (FCC) cannot be characterized in a way that the family can be rationally counseled. This proposal is a dual-principal investigator renewal application for a highly productive program that has been ongoing for 18 years. Over the past 5 years, we have made progress in our understanding of how methylation-based silencing of the DNA mismatch repair (MMR) genes play a role in the genesis of CRC; our work has characterized early-onset CRCs that occur in the absence of FCC, and we found that genetic and epigenetic alterations in the tumor tissues of these patients are similar to that of non- Lynch syndrome FCC (or, "FCC-type X"). We characterized how alterations in expression of the MSH3 gene are involved in the genesis of sporadic CRCs. We have provided insights into the role of epigenetics in the genesis and clinical behavior of CRCs. The overarching goal of this program is to move toward a more complete "personalization" of the concepts used in the classification of familiality in CRC. We have four specific aims. Based upon our work on the somatic inactivation of MSH3 in CRCs, we propose to test the hypothesis that germline mutations in the MSH3 gene cause a previously unidentified disease - Lynch syndrome-MSH3 type, which would have a phenotype that would be systematically overlooked because of how we currently screen for Lynch syndrome. Second, we plan to develop an approach for finding balanced inversions in the Lynch syndrome-associated MMR genes to resolve the uncertainty in families where the anticipated germline mutations cannot be identified. Third, we propose that "FCC-type X" is associated with a unique tumor phenotype that will lead us to the germline basis of that disease. Finally, we propose to use whole genome sequencing techniques to test the hypothesis that the serrated polyposis syndrome (SPS) is a rare recessive disease caused by biallelic mutations in a gene involved in the "methylator pathway" of colorectal tumorigenesis. If successful, this work will fill several remaining gaps in the FCC problem, and is likely to have a substantial impact on patient care.
R01 CA184792-01 (PI: A. Goel) 7/1/2015 – 6/30/2020
“Development of microRNA biomarkers for noninvasive detection of colorectal cancer”
The major goal of this project is to develop blood-based miRNA-based signatures that can be used for the early detection of patients with colorectal neoplasia.
DESCRIPTION (provided by applicant): Colorectal cancer (CRC) is a potentially preventable disease; however, it still ranks as the third most common cancer and second leading cause of cancer-related deaths in the U.S., with an estimated 50,000 deaths annually. Early detection of clinically relevant colorectal neoplasia (CRN), i.e. CRC and advanced CRAs (A-CRA), is the best way to improve survival. However, available screening modalities to diagnose these lesions are impractical due to invasiveness and cost (i.e., colonoscopy) or insufficient diagnostic accuracy (i.e., fecal-based blood tests). A better approach to screening and surveillance, preferably through noninvasive biomarkers that can facilitate earlier diagnosis of CRC would be highly desirable. MicroRNAs (miRNAs), small non-coding RNAs involved in gene regulation and cancer development, are more robust and stable than larger RNAs, being resistant to degradation in tissues, blood, stool, and other body fluids. Previous studies have achieved limited success in developing definitive sets of miRNA biomarkers for CRC screening due non-comprehensive approaches, and a failure to include all CRNs as meaningful targets for clinical discovery. Also, cohorts used in serum-based studies have been insufficiently powered and lacked independent validation sets. In this proposal, innovative strategies that include Next Generation Sequencing (NGS)-based miRNA-Seq will be applied to permit genome-wide miRNA mapping using tissues and matching sera from patients with CRN, and compared with tissues and sera from individuals without CRN. A novel and powerful new approach is being proposed to identify novel miRNA biomarkers with the highest sensitivity and specificity, which will be validated using large, well-characterized sample sets through the following Specific Aims. Aim 1: Candidate miRNA biomarkers will be discovered using genome-wide NGS approaches in matched tissue and serum specimens from patients with CRN and individuals with a normal colon. Aim 2: Candidate non-invasive miRNA biomarkers will be developed that distinguish patients with CRN vs. those without CRN, and validated using quantitative PCR assays. Aim 3: Clinical validation of prioritized non-invasive miRNA biomarkers identified in Aim 2b will be performed in asymptomatic average risk individuals. The innovation of this project is based upon the first use of a novel, NGS-based miRNA-Seq platform for the biomarker discovery of genome-wide profiling of all miRNAs and iso-miRNAs that are linked to colorectal neoplasia, and validating these using a large, well-characterized cohort of patients with CRN and controls. The long-term goal and potential impact of this project is to develop a sensitive, specific, non-invasive and inexpensive diagnostic test for early colorectal neoplasia.
R01CA202797-01 (PI: A. Goel) 09-01-2016 – 07/31/2021
“MicroRNA Biomarkers for Determining Treatment Response in Colorectal Cancer”
The goal of this proposal is to discover microRNA-based markers that will help inform a clinician of the best drugs that might work for specific patients, so that each patient can receive “individualized treatment” based upon the drug that best matches their cancer type, which will help with better care and save health care dollars.
Colorectal cancer (CRC) is a common malignancy, and remains the second leading cause of cancer-related deaths in the United States. The present guidelines for CRC treatment recommend that patients with stage III and IV colon cancers (with lymph node or distant metastasis) should be treated with adjuvant or palliative chemotherapy using cytotoxic drugs such as 5-fluorouracil (5-FU) and oxaliplatin after surgical resection of the primary cancer.In spite of our best intentions, a significant proportion of patients treated with chemotherapy derive no clinical benefit, though all are exposed to toxic and expensive therapeutic regimens. Therefore, there is a clear need to develop biomarkers that can help predict which subset of patients will or will not benefit from these treatment regimens. Currently there are no biomarkers available for determining response for oxaliplatin-based chemotherapy (FOLFOX) which serves as standard-of-care for treating patients with advanced CRC. The significance of the current proposal stems from the huge unmet clinical need for the lack of availability of a single established predictive/prognostic biomarker for stage III or IV CRC patients treated with oxaliplatin-based chemotherapy, which is the standard-of-care treatment for such patients. This gap in knowledge encouraged us to undertake systematic and comprehensive microRNA (miRNA) biomarker discovery using next generation sequencing approaches, rigorous biomarker prioritization and validation of candidate markers in multiple, independent patient cohorts, and potential translation of some of these aberrantly methylated genes/loci as blood-based, noninvasive biomarkers. To achieve these goals, we will pursue the following 3 specific aims: Aim #1: MiRNA biomarkers will be “discovered” using miRNA-Seq in matched tumor and normal mucosa tissues from advanced CRC patients with and without response to FOLFOX chemotherapy. Aim #2: Candidate miRNA biomarkers will be “clinically validated” and their “performance evaluated” in primary tumor tissues from independent cohorts of stage III (adjuvant treatment) and stage IV (palliative treatment) CRC patients treated with FOLFOX. Aim #3: Determine the feasibility of translating “tissue-based” miRNAs into “plasma-based” predictive biomarkers in metastatic CRC patients treated with FOLFOX. This project will be undertaken by a team of investigators who have longstanding experience and track record in the field of cancer epigenetics and biomarker discovery. Our findings will have an important clinical impact in identifying patients who will benefit from current chemotherapeutic regimens, and those who are likely to experience adverse outcomes without benefit. The ability to identify such biomarkers will help reduce the overall healthcare cost burden associated with such treatments, and will provide a significant step forward into the era of personalized or precision medicine. 1
U01 CA214254-01 (MPI: A. Goel and D. Von Hoff) 9/1/2017 – 8/31/2022
“Noncoding RNA Biomarkers for Noninvasive and Early Detection of Pancreatic Cancer”
The major goal of this project is to develop blood-based miRNA and exosomal biomarkers that can facilitate early detection of pancreatic cancer.
PROJECT SUMMARY: Pancreatic cancer is the fourth leading cause of adult cancer deaths in the U.S., and will become the second leading cause of cancer-related deaths by 2030. The lack of reliable and cost-effective assays impedes wide-spread pancreatic cancer diagnostics. Clearly, early diagnostic procedures will improve the prognosis of patients with pancreatic ductal adenocarcinoma (PDAC), but will require novel methods of development. MicroRNAs (miRNAs) are small noncoding RNAs that are implicated in the tumorigenesis of every human cancer, including PDAC. Importantly, miRNAs are robust and resistant to degradation in tissues and body fluids, making them ideal candidates as non-invasive biomarkers. The recent discovery of cancers that actively excrete specific miRNAs in small vesicles, called “exosomes”, has brought additional enthusiasm to the cancer biomarker arena. Previous attempts to define blood-based miRNA biomarkers that can discriminate between non-invasive, early-stage and late-stage PDAC were insufficiently sensitive or specific because of improperly designed cohorts and the narrow dynamic ranges of technologies used. Furthermore, candidate markers were non-comprehensively selected, studies lacked important controls, and the cohorts were insufficiently powered or validated, or did not represent the average risk population. These factors stifled the discovery of miRNA biomarkers that could identify asymptomatic patients before metastatic disease had developed, or distinguish early stage, radiographically occult PDAC from noninvasive pancreatic precancerous neoplasms (PNs). In this proposal, innovative strategies including Next Generation Sequencing (NGS)-based miRNA-Seq will be applied to the genome-wide and systematic discovery of comprehensive and highly specific blood-based miRNAs by analyzing tissues and matching plasma that discern different stages of invasive PDAC and PN. A novel and powerful new approach is being proposed to identify biomarkers with the highest sensitivity and specificity, which will be validated in a prospective, large, well-characterized samples through the following Specific Aims. Aim #1: Discover candidate cell-free and exosomal-miRNA biomarkers using small RNA-Seq in matched tissue and plasma from patients with PDAC, PNs, pancreatitis and normal pancreas. Aim #2: Develop a cell-free and exosomal-miRNA biomarker panel that distinguishes patients with PDAC from those with PNs or pancreatitis. Aim #3: Clinically validate the optimized panel of non-invasive miRNA biomarkers (identified in Aim #2) in prospective cohorts of patients with PDAC and PNs. This project is innovative as it will use NGS-based miRNA-Sequencing for discovery of cell-free and exosomal miRNA biomarkers in matched tissue and plasma samples, and validate these in multiple, well-characterized cohorts of patients with PNs and PDAC vs. controls. If successful, this proposal will profoundly transform early- detection of pancreatic cancer using a non-invasive, robust and inexpensive clinical assay.
R01 CA181572-01A1 (PI: A. Goel) 05/21/2014 – 04/20/2020
“Methylation biomarker development for noninvasive detection of colorectal cancer”
The major goal of this project was to develop blood-based DNA methylation biomarkers that can be used for screening of patients with adenomatous polyps and cancers in their colon.
DESCRIPTION (provided by applicant): Colorectal carcinoma (CRC) is the third most common cancer in the United States, with an estimated 150,000 new cases occurring annually. Early detection of clinically relevant colorectal neoplasia (CRN), i.e., CRC and advanced colorectal adenomas (A-CRA), is the best way to improve survival. However, available screening modalities are impractical due to invasiveness and cost (i.e., colonoscopy) or insufficient diagnostic accuracy (i.e., fecal-based blood tests). A better approach to screening and surveillance would be highly desirable. Abnormal DNA methylation is an important epigenetic mechanism that has been strongly implicated in the pathogenesis and progression of colorectal neoplasia. Aberrant DNA methylation is detectable in serum making it an ideal candidate biomarker species for non-invasive screening. Previous studies have achieved limited success in developing definitive sets of methylation biomarkers for CRC screening due non-comprehensive approaches, and a failure to include all CRNs as meaningful targets for clinical discovery. Also, cohorts used in serum-based studies have been insufficiently powered and lacked independent validation sets. In this proposal, innovative strategies will be applied to permit genome-scale methylation mapping using tissues and sera from patients with CRN, and compared with tissues and sera from individuals without CRN. A novel and powerful new approach is being proposed to identify new biomarkers and methylation targets with the highest sensitivity and specificity, and will be validated using large, well- characterized sample sets through the following Specific Aims. Aim 1: Candidate DNA methylation biomarkers will be discovered using next generation bisulfite sequencing in matched tissue and serum from patients with CRN and individuals with a normal colon. Aim 2: Candidate serum methylation biomarkers will be discovered that distinguish patients with CRN vs. those without CRN, and validated biomarkers using quantitative PCR assays. Aim 3: Clinical validation of prioritized serum methylation biomarkers identified in Aim 2b will be performed in asymptomatic average risk individuals. The innovation of this project is based upon the first use of a novel, next generation sequencing-based approach for identifying methylation-based biomarkers using a genome-scale assay for methylation sites linked to colorectal neoplasia, and validating these newly discovered biomarkers using a large, well-characterized cohort of patients with CRN and controls. The long-term goal and potential impact of this project is to develop a sensitive, specific, non-invasive and inexpensive diagnostic test for early colorectal neoplasia.
1R01CA227602-01A1 (PI: A. Goel) 8/20/2019-7/31/2024
“Exosomal Biomarkers for the Noninvasive Detection of Colorectal Cancer”
PROJECT SUMMARY: Colorectal cancer (CRC) is the second leading cause of cancer-related deaths in the United States. Yet, unlike other cancers, the majority of early stage CRCs are surgically curable. Therefore, early detection of CRCs and removal of precursor lesions, particularly advanced colorectal adenomas (A-CRA), is considered as the best approach in reducing CRC-associated mortality. However, current available screening procedures are impractical. In spite of the efficacy of colonoscopy as a screening tool, its invasive nature and expense often dissuade individuals to follow CRC screening guidelines; and inaccuracy of fecal-based tests remains insufficient as a diagnostic modality. Accumulating evidence indicates that dysregulation of microRNAs (miRNAs) occurs in all human cancers. As biomarkers, miRNAs are more resilient than mRNAs as they are less prone to degradation, and are frequently deregulated even in the earliest stages of neoplasia compared to genetic alterations. Furthermore, the recent discovery that cancers actively excrete small extracellular vesicles, called “exosomes”, into systemic circulation, has brought additional enthusiasm to the field of translational biomarker research. Even though exosomes are considered promising due to their structural stability and molecular profiles reflecting their cell-of-origin, utilization of exosomes in biomarker research has been hampered due to multiple reasons, including: i) lack of standardized protocols for their isolation and purification; ii) use of cell line-derived, not patient-derived specimens for biomarker discovery; iii) lack of molecular profiling studies on cancer-derived exosomes from matched tissues and plasma specimens to establish their cancer specificity; iv) albeit the perception that exosomal-miRNAs (exo-miRNAs) may be superior to circulating cell-free miRNAs (cf-miRNAs), no studies have undertaken an effort to directly compare these two types, in order to support or negate the superiority of either type, as clinically-relevant disease biomarkers. In this proposal, we will address these concerns by undertaking the following Specific Aims. Aim 1: Optimization of patient-derived exosome isolation, followed by RNA-Seq based discovery of circulating cell-free (cf-miRNAs) and exosomal miRNAs (exo- miRNAs) in matched tissue and plasma specimens collected from patients with A-CRAs, CRCs and individuals with normal colon. Aim 2: Development of circulating cell-free and exosomal miRNA biomarker panels that distinguish patients with A-CRAs and CRCs from healthy individuals. Aim 3: Clinical validation and performance evaluation of optimized cf-miRNAs and exo-miRNAs in large, independent patient cohorts with colorectal neoplasia. If successful, this proposal will provide much needed molecular characterization of cell-free and exosomal miRNA biomarkers as liquid biopsy biomarkers, which may transform early-detection of CRC into a robust, non- invasive, and inexpensive clinical assay.
The Hilton-City of Hope Nutrition Initiative for Cancer Prevention 10/1/2019-9/30/2020
“Cell-free DNA methylation biomarkers for non-invasive early-detection of pancreatic cancer”
In this proposal, we will overcome some of these challenges by undertaking 2 specific aims. In Specific Aim-1, an innovative strategy (developed by our team) that permits genome-wide profiling of methylation patterns - TAPS (TET-assisted pyridine borane sequencing) – will be used for a systematic and comprehensive discovery of cfDNA biomarkers to discern PDACs and PNs from controls (non-neoplastic conditions and healthy individuals). In Specific Aim-2, the prioritized biomarkers will be validated using qPCR-based assays in an independent, patient cohort for the early and non-invasive detection of pancreatic cancer.
The Hilton-City of Hope Nutrition Initiative for Cancer Prevention initiative is a comprehensive cancer prevention initiative that will target poor diet and obesity as key risk factors for disease. City of Hope, in partnership with the Conrad N. Hilton Foundation, will bring a diverse coalition of stakeholders to promote increased access to healthy foods, adoption of good nutritional practices and an environment that is supportive of healthy lifestyles. This will be accomplished through strategic research exploring links between cancer and nutrition, interventions focused on implementing and sustaining healthy lifestyles and advocacy efforts.
The Hilton-COH pilot award program supports innovative nutritional studies with practical applications.