Publications by authors named "Mary P Bronner"

106 Publications

Histologic mimics and diagnostic pitfalls of gastrointestinal endoscopic lifting media, ORISE™ gel and Eleview®.

Hum Pathol 2021 Oct 1;119:28-40. Epub 2021 Oct 1.

Department of Pathology, University of Utah and ARUP Laboratories, 2000 Circle of Hope, HCI, 3161, Salt Lake City, UT, USA. Electronic address:

Synthetic lifting media, ORISE™ gel and Eleview®, are increasingly used in gastrointestinal endoscopy, but neither comparative features nor pitfalls are well-established. Media histopathology, morphologic mimics, and complications are described, along with helpful stains and endoscopist media preference. A 3-year retrospective search was performed. A total of 123 cases (108 endoscopies and 15 subsequent surgeries) were identified. ORISE gel was used in 86 (79.6%), Eleview in 20 (13.9%), and others in 7 (6.5%). ORISE gel was histologically identified in 58.1% (n = 50) of endoscopic specimens and all 15 resections. Eleview media were not detected histologically. ORISE gel mimicked mucin in hematoxylin and eosin-stained biopsies, concerning for adenocarcinoma misdiagnosis and/or upstaging, but did not stain for mucin. Acid-fast bacterial staining highlights ORISE gel for specific and definitive identification. In resections, ORISE evolves into an amorphous eosinophilic material, often with exuberant giant cell reaction and transmural bowel penetration. Polyp formation leads to polypectomy in one patient, and operative lesions concerning for adenocarcinoma resulted in frozen sections in two patients. ORISE gel mimics mucin, malignant masses, amyloid, pulse granulomata, elastofibromas, and infectious granulomata. No significant endoscopist media preference was identified. Recognition of ORISE gel in tissues eliminates multiple pitfalls. Eleview was not detectable, yielded none of the pitfalls seen with ORISE gel, and, on our survey, has equivalent endoscopist acceptance. In this largest published series to date, Eleview is clearly preferable to ORISE gel.
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http://dx.doi.org/10.1016/j.humpath.2021.09.008DOI Listing
October 2021

Detection of circulating tumor DNA without a tumor-informed search using next-generation sequencing is a prognostic biomarker in pancreatic ductal adenocarcinoma.

Neoplasia 2021 09 21;23(9):859-869. Epub 2021 Jul 21.

Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah; Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah; Department of Radiology, University of Utah, Salt Lake City, Utah. Electronic address:

The confounding effects of next-generation sequencing (NGS) noise on detection of low frequency circulating tumor DNA (ctDNA) without a priori knowledge of solid tumor mutations has limited the applications of circulating cell-free DNA (ccfDNA) in clinical oncology. Here, we use a 118 gene panel and leverage ccfDNA technical replicates to eliminate NGS-associated errors while also enhancing detection of ctDNA from pancreatic ductal adenocarcinomas (PDACs). Pre-operative ccfDNA and tumor DNA were acquired from 14 patients with PDAC (78.6% stage II-III). Post-operative ccfDNA was also collected from 11 of the patients within 100 days of surgery. ctDNA detection was restricted to variants corresponding to pathogenic mutations in PDAC present in both replicates. PDAC-associated pathogenic mutations were detected in pre-operative ccfDNA in four genes (KRAS, TP53, SMAD4, ALK) from five patients. Of the nine ctDNA variants detected (variant allele frequency: 0.08%-1.59%), five had a corresponding mutation in tumor DNA. Pre-operative detection of ctDNA was associated with shorter survival (312 vs. 826 days; χ=5.4, P = 0.021). Guiding ctDNA detection in pre-operative ccfDNA based on mutations present in tumor DNA yielded a similar survival analysis. Detection of ctDNA in the post-operative ccfDNA with or without tumor-informed guidance was not associated with outcomes. Therefore, the detection of PDAC-derived ctDNA during a broad and untargeted survey of ccfDNA with NGS may be a valuable, non-invasive, prognostic biomarker to integrate into the clinical assessment and management of patients prior to surgery.
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http://dx.doi.org/10.1016/j.neo.2021.06.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8322473PMC
September 2021

Circulating Folate and Folic Acid Concentrations: Associations With Colorectal Cancer Recurrence and Survival.

JNCI Cancer Spectr 2020 Oct 7;4(5):pkaa051. Epub 2020 Jul 7.

Department of Surgery, Hospital Group Twente ZGT, Almelo, the Netherlands.

Background: Folates, including folic acid, may play a dual role in colorectal cancer development. Folate is suggested to be protective in early carcinogenesis but could accelerate growth of premalignant lesions or micrometastases. Whether circulating concentrations of folate and folic acid, measured around time of diagnosis, are associated with recurrence and survival in colorectal cancer patients is largely unknown.

Methods: Circulating concentrations of folate, folic acid, and folate catabolites p-aminobenzoylglutamate and p-acetamidobenzoylglutamate were measured by liquid chromatography-tandem mass spectrometry at diagnosis in 2024 stage I-III colorectal cancer patients from European and US patient cohort studies. Multivariable-adjusted Cox proportional hazard models were used to assess associations between folate, folic acid, and folate catabolites concentrations with recurrence, overall survival, and disease-free survival.

Results: No statistically significant associations were observed between folate, p-aminobenzoylglutamate, and p-acetamidobenzoylglutamate concentrations and recurrence, overall survival, and disease-free survival, with hazard ratios ranging from 0.92 to 1.16. The detection of folic acid in the circulation (yes or no) was not associated with any outcome. However, among patients with detectable folic acid concentrations (n = 296), a higher risk of recurrence was observed for each twofold increase in folic acid (hazard ratio = 1.31, 95% confidence interval = 1.02 to 1.58). No statistically significant associations were found between folic acid concentrations and overall and disease-free survival.

Conclusions: Circulating folate and folate catabolite concentrations at colorectal cancer diagnosis were not associated with recurrence and survival. However, caution is warranted for high blood concentrations of folic acid because they may increase the risk of colorectal cancer recurrence.
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http://dx.doi.org/10.1093/jncics/pkaa051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7583160PMC
October 2020

Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches.

Genome Med 2020 07 14;12(1):62. Epub 2020 Jul 14.

Department of Human Genetics, University of Utah, 15 S 2030 E, Salt Lake City, UT, 84112, USA.

Background: When interpreting sequencing data from multiple spatial or longitudinal biopsies, detecting sample mix-ups is essential, yet more difficult than in studies of germline variation. In most genomic studies of tumors, genetic variation is detected through pairwise comparisons of the tumor and a matched normal tissue from the sample donor. In many cases, only somatic variants are reported, which hinders the use of existing tools that detect sample swaps solely based on genotypes of inherited variants. To address this problem, we have developed Somalier, a tool that operates directly on alignments and does not require jointly called germline variants. Instead, Somalier extracts a small sketch of informative genetic variation for each sample. Sketches from hundreds of germline or somatic samples can then be compared in under a second, making Somalier a useful tool for measuring relatedness in large cohorts. Somalier produces both text output and an interactive visual report that facilitates the detection and correction of sample swaps using multiple relatedness metrics.

Results: We introduce the tool and demonstrate its utility on a cohort of five glioma samples each with a normal, tumor, and cell-free DNA sample. Applying Somalier to high-coverage sequence data from the 1000 Genomes Project also identifies several related samples. We also demonstrate that it can distinguish pairs of whole-genome and RNA-seq samples from the same individuals in the Genotype-Tissue Expression (GTEx) project.

Conclusions: Somalier is a tool that can rapidly evaluate relatedness from sequencing data. It can be applied to diverse sequencing data types and genome builds and is available under an MIT license at github.com/brentp/somalier .
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http://dx.doi.org/10.1186/s13073-020-00761-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7362544PMC
July 2020

The stochastic nature of errors in next-generation sequencing of circulating cell-free DNA.

PLoS One 2020 21;15(2):e0229063. Epub 2020 Feb 21.

Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America.

Challenges with distinguishing circulating tumor DNA (ctDNA) from next-generation sequencing (NGS) artifacts limits variant searches to established solid tumor mutations. Here we show early and random PCR errors are a principal source of NGS noise that persist despite duplex molecular barcoding, removal of artifacts due to clonal hematopoiesis of indeterminate potential, and suppression of patterned errors. We also demonstrate sample duplicates are necessary to eliminate the stochastic noise associated with NGS. Integration of sample duplicates into NGS analytics may broaden ctDNA applications by removing NGS-related errors that confound identification of true very low frequency variants during searches for ctDNA without a priori knowledge of specific mutations to target.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229063PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7034809PMC
May 2020

Smooth muscle tumors of the gastrointestinal tract: an analysis of prognostic features in 407 cases.

Mod Pathol 2020 07 12;33(7):1410-1419. Epub 2020 Feb 12.

Washington University School of Medicine, St. Louis, MO, USA.

Smooth muscle tumors represent the second most common mural mesenchymal neoplasm in the gastrointestinal tract, but established criteria for prognostic assessment of these tumors are lacking. A large cohort of surgically resected intramural gastrointestinal smooth muscle tumors from 31 institutions was analyzed to identify potential prognostic features. Pathologic features were assessed by expert gastrointestinal and/or soft tissue pathologists at each center. Immunohistochemical confirmation was required. A total of 407 cases from the esophagus (n = 97, 24%), stomach (n = 180, 44%), small bowel (n = 74, 18%), and colorectum (n = 56, 14%) were identified. Patients ranged in age from 19 to 92 years (mean 55 years), with a slight female predominance (57%). Mean tumor size was 5.4 cm, with the largest tumor measuring 29 cm. Disease progression following surgery, defined as local recurrence, metastasis, or disease-related death, occurred in 56 patients (14%). Colorectal tumors were most likely to progress, followed by small bowel and gastric tumors. None of the esophageal tumors in this series progressed. Receiver operator characteristic analysis identified optimal cutoffs of 9.8 cm and 3 mitoses/5 mm for discriminating between progressive and non-progressive tumors. Histologic features strongly associated with progression by univariate analysis included moderate-to-severe atypia, high cellularity, abnormal differentiation (defined as differentiation not closely resembling that of normal smooth muscle), tumor necrosis, mucosal ulceration, lamina propria involvement, and serosal involvement (P < 0.0001 for all features). Age, sex, and margin status were not significantly associated with progression (P = 0.23, 0.82, and 0.07, respectively). A risk assessment table was created based on tumor site, size, and mitotic count, and Kaplan-Meier plots of progression-free survival for each subgroup revealed progression-based tiers. Based on our findings, it appears that nonesophageal gastrointestinal smooth muscle tumors measuring >10 cm and/or showing ≥3 mitoses/5 mm may behave aggressively, and therefore close clinical follow-up is recommended in these cases.
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http://dx.doi.org/10.1038/s41379-020-0492-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8405135PMC
July 2020

Extensive subclonal mutational diversity in human colorectal cancer and its significance.

Proc Natl Acad Sci U S A 2019 Dec 5. Epub 2019 Dec 5.

Department of Oncology, Georgetown University Medical Center, Washington, DC 20007.

Human colorectal cancers (CRCs) contain both clonal and subclonal mutations. Clonal driver mutations are positively selected, present in most cells, and drive malignant progression. Subclonal mutations are randomly dispersed throughout the genome, providing a vast reservoir of mutant cells that can expand, repopulate the tumor, and result in the rapid emergence of resistance, as well as being a major contributor to tumor heterogeneity. Here, we apply duplex sequencing (DS) methodology to quantify subclonal mutations in CRC tumor with unprecedented depth (10) and accuracy (<10). We measured mutation frequencies in genes encoding replicative DNA polymerases and in genes frequently mutated in CRC, and found an unexpectedly high effective mutation rate, 7.1 × 10 The curve of subclonal mutation accumulation as a function of sequencing depth, using DNA obtained from 5 different tumors, is in accord with a neutral model of tumor evolution. We present a theoretical approach to model neutral evolution independent of the infinite-sites assumption (which states that a particular mutation arises only in one tumor cell at any given time). Our analysis indicates that the infinite-sites assumption is not applicable once the number of tumor cells exceeds the reciprocal of the mutation rate, a circumstance relevant to even the smallest clinically diagnosable tumor. Our methods allow accurate estimation of the total mutation burden in clinical cancers. Our results indicate that no DNA locus is wild type in every malignant cell within a tumor at the time of diagnosis (probability of all cells being wild type, 10).
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http://dx.doi.org/10.1073/pnas.1910301116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936702PMC
December 2019

Molecular Biomarkers of Sessile Serrated Adenoma/Polyps.

Clin Transl Gastroenterol 2019 12;10(12):e00104

Department of Gastroenterology, University of Utah, Salt Lake City, Utah, USA.

Objectives: Sessile serrated adenoma/polyps (SSA/Ps) contribute up to 30% of all colon cancers. There is considerable histological overlap between SSA/Ps and hyperplastic polyps. Inadequate consensus exists among pathologists, and no molecular biomarkers exist to differentiate these lesions with high accuracy. Lack of reliable diagnosis adversely affects clinical care. We previously defined a novel 7-gene panel by RNA sequencing that differentiates SSA/Ps from hyperplastic polyps. Here, we use the 7-gene panel as a molecular approach to differentiate SSA/Ps and HPs with higher sensitivity and specificity in a large sample set from a tertiary health care center.

Methods: Reverse transcription quantitative polymerase chain reaction of the 7-gene panel was performed on 223 formalin-fixed, paraffin-embedded serrated polyp and normal colon samples. We compare the sensitivity and specificity of the 7-gene panel with the BRAF and KRAS mutation incidence in differentiating SSA/Ps and HPs. We also evaluate the clinical data of patients with SSA/Ps showing high and low expression of the gene panel.

Results: The 7-gene RNA expression panel differentiates SSA/Ps and HPs with 89.2% sensitivity and 88.4% specificity. The gene panel outperforms BRAF mutation in identification of SSA/Ps. Clinical data suggest that expression of the 7-gene panel correlates with the development of SSA/Ps in the future.

Discussion: This study describes a novel 7-gene panel that identifies SSA/Ps with improved accuracy. Our data show that RNA markers of SSA/Ps advance the distinction of serrated lesions and contribute to the study of the serrated pathway to colon cancer.
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http://dx.doi.org/10.14309/ctg.0000000000000104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6970553PMC
December 2019

Small RNA sequencing of sessile serrated polyps identifies microRNA profile associated with colon cancer.

Genes Chromosomes Cancer 2019 01 18;58(1):23-33. Epub 2018 Nov 18.

Division of Gastroenterology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah.

Sessile serrated adenoma/polyps (SSA/Ps) of the colon account for 20-30% of all colon cancers. Small non-coding RNAs, including microRNAs (miRNAs), may function as oncogenes or tumor suppressor genes involved in cancer development. Small RNA sequencing (RNA-seq) was used to characterize miRNA profiles in SSA/Ps, hyperplastic polyps (HPs), adenomatous polyps and paired uninvolved colon. Our 108 small RNA-seq samples' results were compared to small RNA-seq data from 212 colon cancers from the Cancer Genome Atlas. Twenty-three and six miRNAs were differentially expressed in SSA/Ps compared to paired uninvolved colon and HPs, respectively. Differential expression of MIR31-5p, MIR135B-5p and MIR378A-5p was confirmed by RT-qPCR. SSA/P-specific miRNAs are similarly expressed in colon cancers containing genomic aberrations described in serrated cancers. Correlation of miRNA expression with consensus molecular subtypes suggests more than one subtype is associated with the serrated neoplasia pathway. Canonical pathway analysis suggests many of these miRNAs target growth factor signaling pathways.
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http://dx.doi.org/10.1002/gcc.22686DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6437779PMC
January 2019

Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing.

PLoS One 2018 25;13(7):e0197333. Epub 2018 Jul 25.

Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah, United States of America.

Circulating tumor-derived cell-free DNA (ctDNA) enables non-invasive diagnosis, monitoring, and treatment susceptibility testing in human cancers. However, accurate detection of variant alleles, particularly during untargeted searches, remains a principal obstacle to widespread application of cell-free DNA in clinical oncology. In this study, isolation of short cell-free DNA fragments is shown to enrich for tumor variants and improve correction of PCR- and sequencing-associated errors. Subfractions of the mononucleosome of circulating cell-free DNA (ccfDNA) were isolated from patients with melanoma, pancreatic ductal adenocarcinoma, and colorectal adenocarcinoma using a high-throughput-capable automated gel-extraction platform. Using a 128-gene (128 kb) custom next-generation sequencing panel, variant alleles were on average 2-fold enriched in the short fraction (median insert size: ~142 bp) compared to the original ccfDNA sample, while 0.7-fold reduced in the fraction corresponding to the principal peak of the mononucleosome (median insert size: ~167 bp). Size-selected short fractions compared to the original ccfDNA yielded significantly larger family sizes (i.e., PCR duplicates) during in silico consensus sequence interpretation via unique molecular identifiers. Increments in family size were associated with a progressive reduction of PCR and sequencing errors. Although consensus read depth also decreased at larger family sizes, the variant allele frequency in the short ccfDNA fraction remained consistent, while variant detection in the original ccfDNA was commonly lost at family sizes necessary to minimize errors. These collective findings support the automated extraction of short ccfDNA fragments to enrich for ctDNA while concomitantly reducing false positives through in silico error correction.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0197333PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6059400PMC
December 2018

Context-Dependent Requirements for FimH and Other Canonical Virulence Factors in Gut Colonization by Extraintestinal Pathogenic Escherichia coli.

Infect Immun 2018 03 20;86(3). Epub 2018 Feb 20.

University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, Utah, USA

Extraintestinal pathogenic (ExPEC) acts as a commensal within the mammalian gut but can induce pathology upon dissemination to other host environments such as the urinary tract and bloodstream. ExPEC genomes are likely shaped by evolutionary forces encountered within the gut, where the bacteria spend much of their time, provoking the question of how their extraintestinal virulence traits arose. The principle of coincidental evolution, in which a gene that evolved in one niche happens to be advantageous in another, has been used to argue that ExPEC virulence factors originated in response to selective pressures within the gut ecosystem. As a test of this hypothesis, the fitness of ExPEC mutants lacking canonical virulence factors was assessed within the intact murine gut in the absence of antibiotic treatment. We found that most of the tested factors, including cytotoxic necrotizing factor type 1 (CNF1), Usp, colibactin, flagella, and plasmid pUTI89, were dispensable for gut colonization. The deletion of genes encoding the adhesin PapG or the toxin HlyA had transient effects but did not interfere with longer-term persistence. In contrast, a mutant missing the type 1 pilus-associated adhesin FimH displayed somewhat reduced persistence within the gut. However, this phenotype varied dependent on the presence of specific competing strains and was partially attributable to aberrant flagellin expression in the absence of These data indicate that FimH and other key ExPEC-associated factors are not strictly required for gut colonization, suggesting that the development of extraintestinal virulence traits is not driven solely by selective pressures within the gut.
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http://dx.doi.org/10.1128/IAI.00746-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5820936PMC
March 2018

Intramucosal lipomas of the colon implicate Cowden syndrome.

Mod Pathol 2018 04 1;31(4):643-651. Epub 2017 Dec 1.

Department of Pathology and ARUP Laboratories, University of Utah Health Sciences Center, Salt Lake City, UT, USA.

Intramucosal lipomas are rare and easily overlooked by pathologists, despite their diagnostic significance for Cowden syndrome (PTEN hamartoma tumor syndrome), an inherited multiorgan cancer syndrome. Only 25-35% of patients harbor identifiable PTEN mutations, thus clinical features, like intramucosal lipomas, remain the mainstay of diagnosis. The significance and diagnostic approach to intramucosal lipomas have not been thoroughly addressed in the literature. Intramucosal lipomas are mimicked by pseudolipomatosis coli, an artifactual mucosal gas infiltration from endoscopic insufflation. This differential was investigated by morphology and S-100 immunohistochemistry. Twenty-five colonic intramucosal lipomas were identified from 176 archival gastrointestinal lipomas from 1998 to 2017. Controls included 40 submucosal lipomas and 30 pseudolipomatoses. S-100 immunohistochemistry on all 95 lesions confirmed delicate fat vacuole membranous and nuclear S-100 staining in lipomas absent from pseudolipomatoses. Differentiating morphology between intramucosal lipoma and pseudolipomatosis, respectively, included consistently large, regular fat vacuoles (92% vs 7%), associated spindle cells (80% vs 0%), and mucosal lymphoid aggregate involvement (12% vs 80%). Of the 25 intramucosal lipomas, five patients (20%) had confirmed Cowden syndrome (four with PTEN mutations). In four of these Cowden patients, the intramucosal lipoma was the index diagnostic lesion. Three (12%) intramucosal lipoma patients had additional clinical features associated with Cowden syndrome, but did not meet the diagnostic criteria. Sporadic-type intramucosal lipomas were identified in 17 patients (68%) without evidence of Cowden syndrome, including three with normal PTEN genetic testing. No distinguishing endoscopic or pathologic polyp features were identified between sporadic and syndromic intramucosal lipomas. These data provide evidence that intramucosal lipomas are important harbingers of Cowden syndrome, making up approximately one-third of this series, the largest in the literature. We also show for the first time that two-thirds of intramucosal lipomas are sporadic. Gastrointestinal pathologists, gastroenterologists, and geneticists should increase their awareness of this subtle but diagnosable lesion strongly associated with Cowden syndrome.
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http://dx.doi.org/10.1038/modpathol.2017.161DOI Listing
April 2018

Control of intestinal stem cell function and proliferation by mitochondrial pyruvate metabolism.

Nat Cell Biol 2017 Sep 14;19(9):1027-1036. Epub 2017 Aug 14.

Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.

Most differentiated cells convert glucose to pyruvate in the cytosol through glycolysis, followed by pyruvate oxidation in the mitochondria. These processes are linked by the mitochondrial pyruvate carrier (MPC), which is required for efficient mitochondrial pyruvate uptake. In contrast, proliferative cells, including many cancer and stem cells, perform glycolysis robustly but limit fractional mitochondrial pyruvate oxidation. We sought to understand the role this transition from glycolysis to pyruvate oxidation plays in stem cell maintenance and differentiation. Loss of the MPC in Lgr5-EGFP-positive stem cells, or treatment of intestinal organoids with an MPC inhibitor, increases proliferation and expands the stem cell compartment. Similarly, genetic deletion of the MPC in Drosophila intestinal stem cells also increases proliferation, whereas MPC overexpression suppresses stem cell proliferation. These data demonstrate that limiting mitochondrial pyruvate metabolism is necessary and sufficient to maintain the proliferation of intestinal stem cells.
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http://dx.doi.org/10.1038/ncb3593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6137334PMC
September 2017

PD-L1 protein expression in tumour cells and immune cells in mismatch repair protein-deficient and -proficient colorectal cancer: the foundation study using the SP142 antibody and whole section immunohistochemistry.

J Clin Pathol 2018 Jan 30;71(1):46-51. Epub 2017 Jun 30.

Anatomic Pathology, Albany Medical College, Albany, NY, USA.

Aims: Routine application of PD-L1 immunohistochemistry (IHC) in colorectal cancer (CRC) is limited due to lack of standardized scoring criteria, antibody clones, and intratumoral staining heterogeneity. We assessed PD-L1 protein expression on full face CRC tissue sections and applied two algorithms based on the published clinical trials that support the recent FDA approval for immune checkpoint inhibitors (ICPI) therapy in non-small cell lung cancer (NSCLC).

Methods: PD-L1/CD274 IHC (Roche/Ventana, clone SP142) was performed on representative tumour blocks from 52 mismatch repair-deficient (MMR-D) and 52 MMR-proficient (MMR-P) CRCs. Membranous PD-L1 expression was scored for the tumour cell (TC) and tumour-infiltrating immune cell (IC) components. PD-L1 positivity status was determined based on the published NSCLC clinical trials that utilized the Ventana SP142 assay. Hybrid capture-based comprehensive genomic profiling (CGP) was performed on a separate set of 2268 clinically advanced CRCs and the frequency of PD-L1/PD-L2 amplification was determined.

Results: PD-L1 expression in the TC and IC correlated with MMR-D (p=0.013, p<0.0001), T stage (p=0.036, p=0.0036) and clinical stage (p=0.022, p=0.0037). PD-L1 positivity status correlated with MMR-D by two algorithms. Five of 2268 (<1%) advansced CRCs demonstrated amplification of either the or genes by CGP.

Conclusions: PD-L1 expression in TC and IC is associated with advanced stage and MMR-D. PD-L1 positivity status by the published algorithm is associated with MMR-D. amplification is extremely uncommon in CRC. Evaluation of whole tissue section and incorporation of IC staining enhance the sensitivity to screen patients who may benefit from ICPI therapy.
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http://dx.doi.org/10.1136/jclinpath-2017-204525DOI Listing
January 2018

A Clinicopathologic Evaluation of Incidental Fundic Gland Polyps With Dysplasia: Implications for Clinical Management.

Am J Gastroenterol 2017 Jul 2;112(7):1094-1102. Epub 2017 May 2.

Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, Utah, USA.

Objectives: Fundic gland polyps (FGPs) can rarely exhibit dysplasia of the surface epithelium. Based on retrospective data, FGPs with dysplasia (FGPDs) are thought to be a strong marker for familial adenomatous polyposis (FAP), although sporadic, non-syndromic FGPDs also occur. Owing to the significant syndromic association, diagnosis of an apparently sporadic FGPD may prompt clinical evaluation for FAP, especially its attenuated variant. We sought to evaluate the positive predictive value of incidental FGPDs for FAP. We also characterized the clinicopathologic features of incidental FGPDs to advance clinical management.

Methods: Incidental FGPDs were identified from 2004 to 2015 in patients without FAP at biopsy. All clinical follow-up data were reviewed, and germline analysis for APC and MUTYH mutations was performed in consenting patients.

Results: We identified 25 incidental FGPDs in patients not known to have FAP (11.6% of FGPDs, 1.0% of all FGPs). Four patients had a family history of gastric polyps or gastrointestinal cancers. Clinical management included completion polypectomy and gastric endoscopic surveillance (44%), endoscopic surveillance alone (32%), no follow-up (24%), colonoscopy referral (12%), and genetic counseling (4%). Colonoscopies on record revealed 0-7 cumulative adenomas. Follow-up averaged 4.4 years (range 0.3-10.6). No clinical evidence of FAP, gastric cancer, death, or surgery occurred. None of the 11 patients consenting to germline APC and MUTYH testing had genomic alterations.

Conclusions: Incidental FGPDs in this series were all found to be sporadic (25/25) by endoscopic, clinical, and molecular findings, and thus FGPDs were not harbingers of FAP. As isolated findings, FGPDs do not appear to warrant follow-up genetic counseling or testing.
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http://dx.doi.org/10.1038/ajg.2017.125DOI Listing
July 2017

Novel MicroRNA Signature to Differentiate Ulcerative Colitis from Crohn Disease: A Genome-Wide Study Using Next Generation Sequencing.

Microrna 2016 ;5(3):222-229

Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States.

Background: The diagnosis of ulcerative colitis (UC) or Crohn disease (CD) can be challenging given the overlapping features. Knowledge of microRNAs in IBD has expanded recently and supports that microRNAs play an important role. This study aimed to identify novel microRNA biomarkers through comprehensive genome-wide sequencing to distinguish UC from CD.

Design: Illumina next generation sequencing was performed on nondysplastic fresh-frozen colonic mucosa of the distal-most colectomy from 19 patients (10 UC and 9 CD) and 18 patients with diverticular disease serving as controls.

Results: USeq software package identified 44 microRNAs with altered expression (fold change ≥2 and false discovery rate ≤0.10) compared to controls. Among them, a panel of 11 microRNAs was aberrantly expressed between UC and CD. qRT-PCR validation assays performed on frozen tissue from additional samples of UC (n=20) and CD (n=10) confirmed specific differential expression of miR-147b, miR-194-2, miR-383, miR-615 and miR-1826 (P<0.05). In addition, pathway analysis identified target genes of epithelial adhesion junction, integrin, glycolysis and cell cycle that involve in signaling pathways of TGF-β, STAT3, IL-8 and PI3L/AKT/mTOR.

Conclusion: Identification of differentially expressed microRNAs in UC and CD supports the hypothesis that UC and CD are regulated by distinct pathophysiologic mechanisms. MicroRNA panels show promise as diagnostic biomarkers for the subtyping of inflammatory bowel disease.
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http://dx.doi.org/10.2174/2211536605666161117113031DOI Listing
July 2017

Gastrointestinal Polyposis in Cowden Syndrome.

J Clin Gastroenterol 2017 Aug;51(7):e60-e67

*Department of Pathology, Soroka Medical Center, Ben-Gurion University of the Negev, Beer Sheva, Israel †Department of Pathology & ARUP Laboratories ∥Department of Internal Medicine ‡Huntsman Cancer Institute §Genetic Counseling ¶Division of Gastroenterology #Division of Epidemiology, University of Utah, Salt Lake City, UT.

Goals: To further characterize the gastrointestinal manifestations of Cowden syndrome in clinically well-annotated patients to improve the diagnosis of this syndrome.

Background: The gastrointestinal manifestations of Cowden Syndrome, an important heritable and multiorgan cancer syndrome, are not well defined. Proper diagnosis is essential for effective cancer surveillance and prevention in these patients.

Study: Cowden patients with gastrointestinal polyps were selected for medical record and pathologic slide review.

Results: Of 19 total patients, genetic testing revealed pathogenic PTEN mutations in 12. Pan-colonic (11-patients, 58%) and pan-gastrointestinal (8-patients, 42%) polyp distributions were common. Inflammatory (juvenile) polyps were the most common of the hamartomatous polyp (18 patients, 95%), along with expansive lymphoid follicle polyps (12 patients, 63%), ganglioneuromatous polyps (10 patients, 53%), and intramucosal lipomas (5 patients, 26%). The findings of 2 or more hamartomatous polyp types per patient emerged as a newly described and highly prevalent (79%) feature of Cowden syndrome. Ganglioneuromatous polyps, rare in the general population, and intramucosal lipomas, which may be unique to Cowden syndrome, should both prompt further evaluation. Colonic adenomas and adenocarcinomas were common; 10 patients (53%) had single and 3 (16%) had ≥3 adenomas, whereas 2 (11%) had colonic adenocarcinoma, strengthening the emerging association of colorectal cancer with Cowden syndrome.

Conclusions: The clinical phenotypes and gastrointestinal manifestations in Cowden syndrome are quite variable but this series adds the following new considerations for this syndromic diagnosis: multiple gastrointestinal hamartomas, especially 2 or more hamartoma types, and any intramucosal lipomas or ganglioneuromas. These features should warrant consideration of Cowden syndrome.
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http://dx.doi.org/10.1097/MCG.0000000000000703DOI Listing
August 2017

Fragment Length of Circulating Tumor DNA.

PLoS Genet 2016 07 18;12(7):e1006162. Epub 2016 Jul 18.

Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.

Malignant tumors shed DNA into the circulation. The transient half-life of circulating tumor DNA (ctDNA) may afford the opportunity to diagnose, monitor recurrence, and evaluate response to therapy solely through a non-invasive blood draw. However, detecting ctDNA against the normally occurring background of cell-free DNA derived from healthy cells has proven challenging, particularly in non-metastatic solid tumors. In this study, distinct differences in fragment length size between ctDNAs and normal cell-free DNA are defined. Human ctDNA in rat plasma derived from human glioblastoma multiforme stem-like cells in the rat brain and human hepatocellular carcinoma in the rat flank were found to have a shorter principal fragment length than the background rat cell-free DNA (134-144 bp vs. 167 bp, respectively). Subsequently, a similar shift in the fragment length of ctDNA in humans with melanoma and lung cancer was identified compared to healthy controls. Comparison of fragment lengths from cell-free DNA between a melanoma patient and healthy controls found that the BRAF V600E mutant allele occurred more commonly at a shorter fragment length than the fragment length of the wild-type allele (132-145 bp vs. 165 bp, respectively). Moreover, size-selecting for shorter cell-free DNA fragment lengths substantially increased the EGFR T790M mutant allele frequency in human lung cancer. These findings provide compelling evidence that experimental or bioinformatic isolation of a specific subset of fragment lengths from cell-free DNA may improve detection of ctDNA.
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http://dx.doi.org/10.1371/journal.pgen.1006162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4948782PMC
July 2016

Low miR-187 expression promotes resistance to chemoradiation therapy in vitro and correlates with treatment failure in patients with esophageal adenocarcinoma.

Mol Med 2016 05 23;22. Epub 2016 May 23.

University of Dublin Trinity College, Dublin, Ireland.

Esophageal adenocarcinoma (EAC) has a poor prognosis and is increasing in incidence in many western populations. Neoadjuvant chemoradiation therapy (CRT) followed by surgery is increasingly the standard of care for locally advanced EAC; however, resistance to treatment is a significant clinical problem. The identification of both novel biomarkers predicting response to treatment and novel therapeutic targets to enhance the efficacy of CRT are key to improving survival rates in EAC. In this study we performed global microRNA (miRNA) profiling of pre-treatment EAC biopsies and identified 67 miRNA significantly altered in patients who are resistant to CRT. One of these miRNA, miR-187, was significantly decreased in pre-treatment EAC tumors from patients having a poor response to neoadjuvant CRT, highlighting downregulation of miR-187 as a potential mechanism of treatment resistance in EAC. In vitro, miR-187 was demonstrated to play a functional role in modulating sensitivity to X-ray radiation and cisplatin in EAC and its dysregulation was demonstrated to be due to chromosomal alterations. In vitro, miR-187 altered expression of a diverse array of pathways, including the immune regulator complement component 3 (C3), serum levels of which we have previously demonstrated to predict patient response to CRT. In vivo, expression of C3 was significantly increased in tumors from patients having a poor response to CRT. This study highlights for the first time a role for miR-187 as a novel biomarker of response to CRT and a potential therapeutic target for enhancing the efficacy of CRT in EAC.
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http://dx.doi.org/10.2119/molmed.2016.00020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5072404PMC
May 2016

Gene Signature in Sessile Serrated Polyps Identifies Colon Cancer Subtype.

Cancer Prev Res (Phila) 2016 06 29;9(6):456-65. Epub 2016 Mar 29.

Department of Gastroenterology, University of Utah, Salt Lake City, Utah.

Sessile serrated colon adenoma/polyps (SSA/P) are found during routine screening colonoscopy and may account for 20% to 30% of colon cancers. However, differentiating SSA/Ps from hyperplastic polyps (HP) with little risk of cancer is challenging and complementary molecular markers are needed. In addition, the molecular mechanisms of colon cancer development from SSA/Ps are poorly understood. RNA sequencing (RNA-Seq) was performed on 21 SSA/Ps, 10 HPs, 10 adenomas, 21 uninvolved colon, and 20 control colon specimens. Differential expression and leave-one-out cross-validation methods were used to define a unique gene signature of SSA/Ps. Our SSA/P gene signature was evaluated in colon cancer RNA-Seq data from The Cancer Genome Atlas (TCGA) to identify a subtype of colon cancers that may develop from SSA/Ps. A total of 1,422 differentially expressed genes were found in SSA/Ps relative to controls. Serrated polyposis syndrome (n = 12) and sporadic SSA/Ps (n = 9) exhibited almost complete (96%) gene overlap. A 51-gene panel in SSA/P showed similar expression in a subset of TCGA colon cancers with high microsatellite instability. A smaller 7-gene panel showed high sensitivity and specificity in identifying BRAF-mutant, CpG island methylator phenotype high, and MLH1-silenced colon cancers. We describe a unique gene signature in SSA/Ps that identifies a subset of colon cancers likely to develop through the serrated pathway. These gene panels may be utilized for improved differentiation of SSA/Ps from HPs and provide insights into novel molecular pathways altered in colon cancer arising from the serrated pathway. Cancer Prev Res; 9(6); 456-65. ©2016 AACR.
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http://dx.doi.org/10.1158/1940-6207.CAPR-15-0363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941619PMC
June 2016

Morphologic characterization of hamartomatous gastrointestinal polyps in Cowden syndrome, Peutz-Jeghers syndrome, and juvenile polyposis syndrome.

Hum Pathol 2016 Mar 31;49:39-48. Epub 2015 Oct 31.

Department of Pathology & ARUP Laboratories, University of Utah, Salt Lake City, UT 84112; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112.

The morphologic features of the gastrointestinal polyps in hamartomatous polyposis syndromes are poorly defined. Our aim was to better characterize the gastrointestinal hamartomas in these syndromes. A blinded review was performed regarding many histologic features for every polyp. The study included 15 Cowden syndrome, 13 Peutz-Jeghers (PJS), 12 juvenile polyposis (JuvPS) patients, and 32 cases of sporadic hamartomatous polyps. A total of 375 polyps were examined. Cowden syndrome polyps were characteristically colonic, sessile, small, without surface erosion, and showing mildly inflamed fibrotic lamina propria with smooth muscle proliferation and lymphoid follicles. They showed the least degree of cystic glands and had no thick mucin. Uncommon but specific features were ganglion cells and nerve fibers within the lamina propria and mucosal fat. PJS polyps were typically of small or large bowel origin, often exophytic, seldom eroded, with inflamed edematous and fibrotic lamina propria and dilated cystic glands filled with often thick mucin. All PJS polyps showed smooth muscle proliferation, frequently widespread. The polyps of JuvPS were typically colonic, large, exophytic, eroded, with strikingly edematous, fibrotic markedly inflamed lamina propria, cystic glands filled with frequently thick mucin, and the least degree of smooth muscle proliferation. Nonsyndromic hamartomatous polyps were similar to JuvPS polyps; however, they were more often colonic, were smaller, showed more widespread smooth muscle proliferation, and were less likely to contain thick mucin. In conclusion, we were able to define the characteristic hamartomatous polyp for each hamartomatous polyposis syndrome. Awareness to these features may aid in the diagnosis of these rare syndromes.
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http://dx.doi.org/10.1016/j.humpath.2015.10.002DOI Listing
March 2016

MicroRNA-146a constrains multiple parameters of intestinal immunity and increases susceptibility to DSS colitis.

Oncotarget 2015 Oct;6(30):28556-72

Host-microbial interactions within the mammalian intestines must be properly regulated in order to promote host health and limit disease. Because the microbiota provide constant immunological signals to intestinal tissues, a variety of regulatory mechanisms have evolved to ensure proper immune responses to maintain homeostasis. However, many of the genes that comprise these regulatory pathways, including immune-modulating microRNAs (miRNAs), have not yet been identified or studied in the context of intestinal homeostasis. Here, we investigated the role of microRNA-146a (miR-146a) in regulating intestinal immunity and barrier function and found that this miRNA is expressed in a variety of gut tissues in adult mice. By comparing intestinal gene expression in WT and miR-146a-/- mice, we demonstrate that miR-146a represses a subset of gut barrier and inflammatory genes all within a network of immune-related signaling pathways. We also found that miR-146a restricts the expansion of intestinal T cell populations, including Th17, Tregs, and Tfh cells. GC B cells, Tfh ICOS expression, and the production of luminal IgA were also reduced by miR-146a in the gut. Consistent with an enhanced intestinal barrier, we found that miR-146a-/- mice are resistant to DSS-induced colitis, a model of Ulcerative Colitis (UC), and this correlated with elevated colonic miR-146a expression in human UC patients. Taken together, our data describe a role for miR-146a in constraining intestinal barrier function, a process that alters gut homeostasis and enhances at least some forms of intestinal disease in mice.
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http://dx.doi.org/10.18632/oncotarget.5597DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4745677PMC
October 2015

The acinar differentiation determinant PTF1A inhibits initiation of pancreatic ductal adenocarcinoma.

Elife 2015 Jul 7;4. Epub 2015 Jul 7.

Department of Human Genetics, University of Utah, Salt Lake City, United States.

Understanding the initiation and progression of pancreatic ductal adenocarcinoma (PDAC) may provide therapeutic strategies for this deadly disease. Recently, we and others made the surprising finding that PDAC and its preinvasive precursors, pancreatic intraepithelial neoplasia (PanIN), arise via reprogramming of mature acinar cells. We therefore hypothesized that the master regulator of acinar differentiation, PTF1A, could play a central role in suppressing PDAC initiation. In this study, we demonstrate that PTF1A expression is lost in both mouse and human PanINs, and that this downregulation is functionally imperative in mice for acinar reprogramming by oncogenic KRAS. Loss of Ptf1a alone is sufficient to induce acinar-to-ductal metaplasia, potentiate inflammation, and induce a KRAS-permissive, PDAC-like gene expression profile. As a result, Ptf1a-deficient acinar cells are dramatically sensitized to KRAS transformation, and reduced Ptf1a greatly accelerates development of invasive PDAC. Together, these data indicate that cell differentiation regulators constitute a new tumor suppressive mechanism in the pancreas.
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http://dx.doi.org/10.7554/eLife.07125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4536747PMC
July 2015

Overdiagnosis of high-grade dysplasia in Barrett's esophagus: a multicenter, international study.

Mod Pathol 2015 Jun 13;28(6):758-65. Epub 2015 Feb 13.

1] Department of Pathology, Schulich School of Medicine and London Health Sciences Centre, London, Ontario, Canada [2] Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, USA.

Numerous histological mimics of high-grade dysplasia in Barrett's esophagus predispose to overdiagnosis and potential serious mismanagement, including unnecessary esophagectomy. This study investigates the prevalence and sources of this problem. Biopsies from 485 patients diagnosed with Barrett's high-grade dysplasia were screened for a multi-institutional, international Barrett's endoscopic ablation trial. Screening included review of the original diagnostic slides and an additional protocol endoscopy with an extensive biopsy sampling. Observer variability by the study pathologists was assessed through two blinded diagnostic rounds on 437 biopsies from 26 random study endoscopies. Study diagnostic reassessments revealed significantly lower rates of high-grade dysplasia. Only 248 patients (51%) were confirmed to have high-grade dysplasia. The remaining patients had inflamed gastric cardia without Barrett's (n=18; 7%), Barrett's without dysplasia (n=35; 15%), indefinite change (n=61; 26%), low-grade dysplasia (n=79; 33%), adenocarcinoma (n=43; 18%), and other (n=1; <1%), yielding an alarming total of 194 or 40% of patients who were overdiagnosed with Barrett's high-grade dysplasia. Study pathologists achieved a high-level agreement (90% three-way inter-observer agreement per biopsy, Kappa value 0.77) for high-grade dysplasia. Confounding factors promoting overdiagnosis included Barrett's inflammatory atypia (n=182), atypia limited to the basal metaplastic glands (n=147), imprecise criteria for low grade neoplasia (n=102), tangential sectioning artifact (n=59), and reactive gastric cardiac mucosa (n=38). A total of 194 patients (40%) were overdiagnosed with Barrett's high-grade dysplasia, as affirmed by the extensive screening process and high-level study pathologist agreement. The multiple diagnostic pitfalls uncovered should help raise pathologists' awareness of this problem and improve diagnostic accuracy.
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http://dx.doi.org/10.1038/modpathol.2015.2DOI Listing
June 2015

Up-regulation of mitochondrial chaperone TRAP1 in ulcerative colitis associated colorectal cancer.

World J Gastroenterol 2014 Dec;20(45):17037-48

Ru Chen, Sheng Pan, Lisa A Lai, David A Crispin, Teresa A Brentnall, Department of Medicine, University of Washington, Seattle, WA 98195, United States.

Aim: To characterize tumor necrosis factor receptor-associated protein 1 (TRAP1) expression in the progression of ulcerative colitis (UC)-associated colorectal cancer.

Methods: Chronic UC is an inflammatory bowel disease that predisposes to colorectal cancer. Immunohistochemical analysis was used to evaluate TRAP1 expression on tissue microarrays containing colonic tissues from 42 UC progressors (patients with cancer or dysplasia) and 38 non-progressors (dysplasia/cancer free patients). Statistical analyses of the TRAP1 immunohistochemistry staining were performed using GraphPad Prism. Differences in the TRAP1 level between non-progressors and progressors were tested for statistical significance using the Mann-Whitney test. Receiver operating characteristic curve method was used to quantify marker performance in distinguishing diseased cases from controls.

Results: TRAP1 was up-regulated in the colon tissues from UC progressors, but not in the colon tissues from UC non-progressors. Moreover, up-regulation of TRAP1 preceded the neoplastic changes: it was present in both the dysplastic and non-dysplastic tissues of UC progressors. When TRAP1 staining in rectal tissue was used as a diagnostic marker, it could distinguish progressors from non-progressors with 59% sensitivity and 80% specificity. Our study further showed that the increase of TRAP1 expression positively correlated with the degree of inflammation in the colorectal cancer tissues, which could be related to the increased oxidation present in the colonic mucosa from UC progressors. We then investigated the cellular proteome changes underlying oxidative stress, and found that oxidative stress could induce up-regulation of TRAP1 along with several other negative modulators of apoptosis.

Conclusion: These results suggest that oxidative stress in long standing UC could lead to the increase of cytoprotective protein TRAP1, which in turn could promote cancer progression by preventing or protecting the oxidative damaged epithelial cells from undergoing apoptosis. TRAP1 could be a potential diagnostic marker for UC associated colorectal cancer.
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http://dx.doi.org/10.3748/wjg.v20.i45.17037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4258572PMC
December 2014

RNA sequencing of sessile serrated colon polyps identifies differentially expressed genes and immunohistochemical markers.

PLoS One 2014 12;9(2):e88367. Epub 2014 Feb 12.

Department of Medicine, University of Utah, Salt Lake City, Utah, United States of America ; Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America ; Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America ; University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America ; The Central Arkansas Veterans Healthcare System, Little Rock, Arkansas, United States of America.

Background: Sessile serrated adenomas/polyps (SSA/Ps) may account for 20-30% of colon cancers. Although large SSA/Ps are generally recognized phenotypically, small (<1 cm) or dysplastic SSA/Ps are difficult to differentiate from hyperplastic or small adenomatous polyps by endoscopy and histopathology. Our aim was to define the comprehensive gene expression phenotype of SSA/Ps to better define this cancer precursor.

Results: RNA sequencing was performed on 5' capped RNA from seven SSA/Ps collected from patients with the serrated polyposis syndrome (SPS) versus eight controls. Highly expressed genes were analyzed by qPCR in additional SSA/Ps, adenomas and controls. The cellular localization and level of gene products were examined by immunohistochemistry in syndromic and sporadic SSA/Ps, adenomatous and hyperplastic polyps and controls. We identified 1,294 differentially expressed annotated genes, with 106 increased ≥10-fold, in SSA/Ps compared to controls. Comparing these genes with an array dataset for adenomatous polyps identified 30 protein coding genes uniquely expressed ≥10-fold in SSA/Ps. Biological pathways altered in SSA/Ps included mucosal integrity, cell adhesion, and cell development. Marked increased expression of MUC17, the cell junction protein genes VSIG1 and GJB5, and the antiapoptotic gene REG4 were found in SSA/Ps, relative to controls and adenomas, were verified by qPCR analysis of additional SSA/Ps (n = 21) and adenomas (n = 10). Immunohistochemical staining of syndromic (n≥11) and sporadic SSA/Ps (n≥17), adenomatous (n≥13) and hyperplastic (n≥10) polyps plus controls (n≥16) identified unique expression patterns for VSIG1 and MUC17 in SSA/Ps.

Conclusion: A subset of genes and pathways are uniquely increased in SSA/Ps, compared to adenomatous polyps, thus supporting the concept that cancer develops by different pathways in these phenotypically distinct polyps with markedly different gene expression profiles. Immunostaining for a subset of these genes differentiates both syndromic and sporadic SSA/Ps from adenomatous and hyperplastic polyps.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0088367PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3922809PMC
January 2015

Clonal expansions and short telomeres are associated with neoplasia in early-onset, but not late-onset, ulcerative colitis.

Inflamm Bowel Dis 2013 Nov;19(12):2593-602

*Department of Pathology, †Department of Medicine, ‡Department of Biostatistics, and §Division of Gastroenterology, University of Washington, School of Medicine, Seattle, Washington; ‖Division of Anatomic Pathology, University of Utah, Salt Lake City, Utah; and ¶Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, Washington.

Background: Patients with ulcerative colitis (UC) are at risk of developing colorectal cancer. We have previously reported that cancer progression is associated with the presence of clonal expansions and shorter telomeres in nondysplastic mucosa. We sought to validate these findings in an independent case-control study.

Methods: This study included 33 patients with UC: 14 progressors (patients with high-grade dysplasia or cancer) and 19 nonprogressors. For each patient, a mean of 5 nondysplastic biopsies from proximal, mid, and distal colon were assessed for clonal expansions, as determined by clonal length altering mutations in polyguanine tracts, and telomere length, as measured by quantitative PCR. Both parameters were compared with individual clinicopathological characteristics.

Results: Clonal expansions and shorter telomeres were more frequent in nondysplastic biopsies from UC progressors than nonprogressors, but only for patients with early-onset of UC (diagnosis at younger than 50 years of age). Late-onset progressor patients had very few or no clonal expansions and longer telomeres. A few nonprogressors exhibited clonal expansions, which were associated with older age and shorter telomeres. In progressors, clonal expansions were associated with proximity to dysplasia. The mean percentage of clonally expanded mutations distinguished early-onset progressors from nonprogressors with 100% sensitivity and 80% specificity.

Conclusions: Early-onset progressors develop cancer in a field of clonally expanded epithelium with shorter telomeres. The detection of these clones in a few random nondysplastic colon biopsies is a promising cancer biomarker in early-onset UC. Curiously, patients with late-onset UC seem to develop cancer without the involvement of such fields.
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http://dx.doi.org/10.1097/MIB.0b013e3182a87640DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3885330PMC
November 2013

Novel specific microRNA biomarkers in idiopathic inflammatory bowel disease unrelated to disease activity.

Mod Pathol 2014 Apr 20;27(4):602-8. Epub 2013 Sep 20.

Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, USA.

The diagnosis of idiopathic inflammatory bowel disease can be challenging. MicroRNAs (miRNAs) are small, non-coding RNAs that regulate protein synthesis through post-transcriptional suppression. This study is to identify new miRNA markers in inflammatory bowel disease, and to examine whether miRNA biomarkers might assist in the diagnosis of inflammatory bowel disease. Illumina small RNA sequencing was performed on non-dysplastic fresh-frozen colonic mucosa samples of the distalmost colectomy tissue from 19 patients with inflammatory bowel disease (10 ulcerative colitis and 9 Crohn disease) and 18 patients with diverticular disease serving as controls. To determine differentially expressed miRNAs, the USeq software package identified 44 miRNAs with altered expression (fold change ≥ 2 and false discovery rate ≤ 0.10) compared with the controls. Among them, a panel of nine miRNAs was aberrantly expressed in both ulcerative colitis and Crohn disease. Validation assays performed using quantitative reverse transcription PCR (qRT-PCR) on additional frozen tissue from ulcerative colitis, Crohn disease, and control groups confirmed specific differential expression in inflammatory bowel disease for miR-31, miR-206, miR-424, and miR-146a (P<0.05). The expression of these four miRNAs was further evaluated on formalin-fixed, paraffin-embedded tissue of the distalmost colectomy mucosa from cohorts of diverticular disease controls (n=29), ulcerative colitis (n=36), Crohn disease (n=26), and the other diseases mimicking inflammatory bowel disease including infectious colitis (n=12) and chronic ischemic colitis (n=19), again confirming increased expression specific to inflammatory bowel disease (P<0.05). In summary, we demonstrate that miR-31, miR-206, miR-424, and miR-146a are novel specific biomarkers of inflammatory bowel disease. Furthermore, miR-31 is universally expressed in both ulcerative colitis and Crohn disease not only in fresh-frozen but also in formalin-fixed, paraffin-embedded tissues.
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http://dx.doi.org/10.1038/modpathol.2013.152DOI Listing
April 2014

BRAF V600E mutation detection by immunohistochemistry in colorectal carcinoma.

Genes Chromosomes Cancer 2013 Aug 7;52(8):748-52. Epub 2013 May 7.

University of Utah Health Sciences Center, Department of Pathology, Salt Lake City, UT, USA.

The serine/threonine-protein kinase B-raf (BRAF) is an oncogene mutated in various neoplasms, including 5-15% of colorectal carcinomas. The T1799A point mutation, responsible for a large majority of these alterations, results in an amino acid substitution (V600E) causing the constitutive activation of a protein kinase cascade. BRAF V600E in MLH1 deficient tumors implicates somatic tumor-only methylation of the MLH1 promoter region instead of a germline MLH1 mutation. BRAF V600E also predicts poor prognosis in microsatellite stable colorectal cancers and may be a marker of resistance to anti-EGFR therapy in metastatic disease. Currently, only molecular methods are available for assessing BRAF mutational status. An immunohistochemical approach is evaluated here. Colon cancers from 2008 to 2012 tested by pyrosequencing for BRAF V600E mutation were selected. A total of 31 tumors with (n = 14) and without (n = 17) the BRAF V600E mutation were analyzed by immunohistochemistry using a commercially available antibody specific to the V600E-mutated protein. All 14 colorectal carcinomas with the BRAF V600E mutation demonstrated cytoplasmic positivity in tumor cells with the anti-BRAF antibody. In a minority of cases, staining intensity for the mutated tumor samples was weak (n = 2) or heterogeneous (n = 4); however, the majority of cases showed diffuse, strong cytoplasmic positivity (8 of 14 cases). None of the 17 BRAF wild-type colorectal cancers showed immunoreactivity to the antibody. The overall sensitivity and specificity of the immunohistochemical BRAF V600E assay was 100%. Detection of the BRAF V600E mutation in colorectal cancer by immunohistochemistry is a viable alternative to molecular methods.
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http://dx.doi.org/10.1002/gcc.22070DOI Listing
August 2013
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