R01 CA202797 (PI: A. Goel) 9/01/2016-7/31/2023 (NCE) NIH/NCI

"MicroRNA biomarkers for determining response in colorectal cancer"

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 primary cancer. Despite 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, no biomarkers are 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 knowledge gap 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 three 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 with longstanding experience and track records in 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 likely to experience adverse outcomes without benefit. Identifying such biomarkers will help reduce the overall healthcare cost burden associated with such treatments and will provide a significant step forward in the era of personalized or precision medicine.
   

U01 CA214254 (PI: A. Goel) 9/01/2017-7/31/2023 (NCE) NIH/NCI

Noncoding RNA biomarkers for noninvasive and early detection of pancreatic cancer"

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. Unfortunately, the lack of reliable and cost-effective assays impedes widespread pancreatic cancer diagnostics. Early diagnostic procedures will improve the prognosis of patients with pancreatic ductal adenocarcinoma (PDAC) but will require novel development methods. MicroRNAs (miRNAs) are small noncoding RNAs implicated in every human cancer's tumorigenesis, including PDAC. Importantly, miRNAs are robust and resistant to degradation in tissues and body fluids, making them ideal candidates as noninvasive 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 discriminate between noninvasive, 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 the metastatic disease had developed or distinguished 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 discerns different stages of invasive PDAC and PN. A novel, powerful new approach is being proposed to identify biomarkers with the highest sensitivity and specificity, which will be validated in 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 noninvasive 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 to discover 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 the early detection of pancreatic cancer using a noninvasive, robust and inexpensive clinical assay.
   

R01 CA227602-01-A1 (PI: A. Goel) 8/20/2019-7/31/2024 NIH

"Exosomal biomarkers for the noninvasive detection of colorectal cancer"

Colorectal cancer (CRC) is the second leading cause of cancer-related deaths in the United States. However, unlike other cancers, most early-stage CRCs are surgically curable. Therefore, early detection of CRCs and removal of precursor lesions, particularly advanced colorectal adenomas (A-CRA), is considered the best approach to reducing CRC-associated mortality. However, the currently available screening procedures are impractical. Despite the efficacy of colonoscopy as a screening tool, its invasive nature and expense often dissuade individuals from following CRC screening guidelines; the inaccuracy of fecal-based tests remains insufficient as a diagnostic modality. Accumulating evidence indicates that microRNA (miRNA) dysregulation 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. However, 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:

• Lack of standardized protocols for their isolation and purification
• Use of cell line-derived, not patient-derived specimens for biomarker discovery.
• Lack of molecular profiling studies on cancer-derived exosomes from matched tissues and plasma specimens to establish their cancer specificity.
• 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 to support or negate the superiority of either type, as clinically-relevant disease biomarkers.

This proposal 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 a 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 a 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, noninvasive, and inexpensive clinical assay.
   

Susan E. Riley Foundation 3/01/2022-2/28/2025

"Development of a DNA methylation-based, liquid biopsy, assay for the early detection of pancreatic cancer"

Dr. Goel's lab is seeking funding to develop a blood test for the early detection of pancreatic cancer. This noninvasive test would be used for early detection of pancreatic cancer, particularly in high-risk populations, long before patients show symptoms of this deadly disease. The test would use abnormal DNA methylation patterns specific to pancreatic ductal adenocarcinoma (PDAC) tumors. Healthy DNA methylation is a biological process essential for normal cell function; in cancer cells, however, this process is altered, leading to abnormal patterns that induce chromosomal instability and other changes that are a hallmark of cancer cells. These patterns have emerged as a significant marker enabling us to target tumor cells because methylated DNA is a highly stable and cancer tissue-specific change that can be measured in bodily fluids such as blood (e.g., plasma or serum), urine, and stool. In the last ten years, such liquid biopsy assays have gained attention in the scientific community, leading to several tests approved by the FDA for the early detection of other cancers. No such test yet exists, however, for pancreatic cancer. Dr. Goel's project aims to produce a test of this kind for pancreatic cancer.
 

Stupid Strong 5/01/2022-4/30/2025

"Transcriptomic signatures for diagnosis and prognosis of gastric cancer"

Stomach cancer, also known as gastric cancer, is one of the most frequently diagnosed cancers and the second leading cause of cancer-related deaths worldwide. Most gastric cancer cases are diagnosed at an advanced stage because they rarely show symptoms in the earlier stages, and consequently, a significant number of patients experience disease recurrence following surgery. Although chemotherapy has reduced tumor recurrence rates and improved patient survival, the overall benefit from these interventions is approximately 10%, and the prognosis of a majority of patients remains unsatisfactory. A major clinical challenge is a diversity in response to the various treatments, even within the same disease stage, as some patients can be effectively cured through surgery alone, while others do not benefit. There is an unmet need for clinical biomarkers that can allow the identification of patients at a higher risk for disease recurrence and determine the likelihood of treatment benefit. Thus, Dr. Goel's team undertook a comprehensive discovery and validation effort to identify recurrence prediction biomarkers by analyzing the genetic profiles of 157 patients with gastric cancer, followed by validation of these biomarkers in 254 patients. A seven-gene panel was identified, and these genes have been reported to play an essential role in cancer development. Dr. Goel's study further indicated that patients with diffuse-type gastric cancer, one of the two main types of gastric cancer, comprise a subset of individuals with different disease prognoses. This study, published in the prestigious journal of Gastric Cancer, classifies high- and low-risk patients vulnerable to disease recurrence. Since these patients most likely will not respond to current treatments, novel therapies must be explored to target these genes to help cure their cancer.