Ulcerative colitis (UC) is a chronic inflammatory disease that elevates an individual's risk of colon cancer. After 30 years, ten to twenty percent of patients with chronic ulcerative colitis have developed colon cancer. The current recommendations for patient management entail annual endoscopic surveillance with procurement of multiple biopsies, which are histologically assessed by a pathologist for signs of neoplasia. For cancer detection to be useful, it must occur during a narrow window of time between when a local tumor becomes large enough to have a high probability of being sampled but before it has spread to elsewhere in the body and become untreatable. Because of this limitation, endoscopy must be relatively frequent and sampling relatively extensive, making current surveillance techniques, expensive, time consuming and impractical for many individuals. We have recently demonstrated that DNA sequence alterations at mutational hotspots can be used to track abnormal patterns of clonal cell growth in normal-appearing tissues throughout the entire colon of UC patients harboring localized cancers, but not in those with similarly inflamed colons without cancer or precancerous lesions. In a blinded pilot study, in which we screened for clonal mutations at polyguanine tracts in random biopsies from UC patients'colons, we were able to distinguish UC patients with cancer and precancerous lesions (11 patients, 61 mutations) from age and disease-duration matched patients who were cancer/dysplasia free (8 patients 2 mutations) with 100% sensitivity and 92% specificity using only five samples per patient. Our proposed studies will further characterize and validate the association between mutations in polyguanine tracts in DNA with the development of colon cancer in UC. We will enhance our assay throughput and sensitivity through optimal selection of genomic mutational hotspots and technical improvements using both conventional and next-generation sequencing technology. We will determine if our mutational markers can be detected in biopsies prior to the histological detection of precancerous lesions or tumors by histology. In addition, we will determine the changes that occur in colon cells that generate mutations in polyguanine tracts. These cellular alterations may provide new targets to prevent the emergence of colon cancers in ulcerative colitis. Our studies should reduce the cost and the number of patients requiring extensive cancer surveillance and ultimately may be applicable for the early detection of a variety of inflammation-driven cancers.
Many chronic inflammatory diseases increase a patient's risk of cancer, requiring these individuals to be closely monitored for emerging tumors. Current techniques for cancer surveillance are insufficiently sensitive, time-consuming and costly. We propose to develop better methods for identifying early cancers with greater ease and at less cost using state-of-the-art DNA sequencing technology that can be rapidly commercialized for translation to patient care settings.
|Baker, Kathryn T; Salk, Jesse J; Brentnall, Teresa A et al. (2018) Precancer in ulcerative colitis: the role of the field effect and its clinical implications. Carcinogenesis 39:11-20|
|Nachmanson, Daniela; Lian, Shenyi; Schmidt, Elizabeth K et al. (2018) Targeted genome fragmentation with CRISPR/Cas9 enables fast and efficient enrichment of small genomic regions and ultra-accurate sequencing with low DNA input (CRISPR-DS). Genome Res 28:1589-1599|
|Reid-Bayliss, Kate S; Loeb, Lawrence A (2017) Accurate RNA consensus sequencing for high-fidelity detection of transcriptional mutagenesis-induced epimutations. Proc Natl Acad Sci U S A 114:9415-9420|
|Beckman, Robert A; Loeb, Lawrence A (2017) Evolutionary dynamics and significance of multiple subclonal mutations in cancer. DNA Repair (Amst) 56:7-15|
|Chawanthayatham, Supawadee; Valentine 3rd, Charles C; Fedeles, Bogdan I et al. (2017) Mutational spectra of aflatoxin B1 in vivo establish biomarkers of exposure for human hepatocellular carcinoma. Proc Natl Acad Sci U S A 114:E3101-E3109|
|Fox, Edward J; Salk, Jesse J; Loeb, Lawrence A (2016) Exploring the implications of distinct mutational signatures and mutation rates in aging and cancer. Genome Med 8:30|
|Ahn, Eun Hyun; Lee, Seung Hyuk; Kim, Joon Yup et al. (2016) Decreased Mitochondrial Mutagenesis during Transformation of Human Breast Stem Cells into Tumorigenic Cells. Cancer Res 76:4569-78|
|Loeb, Lawrence A (2016) Human Cancers Express a Mutator Phenotype: Hypothesis, Origin, and Consequences. Cancer Res 76:2057-9|
|Schmitt, Michael W; Loeb, Lawrence A; Salk, Jesse J (2016) The influence of subclonal resistance mutations on targeted cancer therapy. Nat Rev Clin Oncol 13:335-47|
|Schmitt, Michael W; Fox, Edward J; Prindle, Marc J et al. (2015) Sequencing small genomic targets with high efficiency and extreme accuracy. Nat Methods 12:423-5|
Showing the most recent 10 out of 20 publications