Scholars@Duke
Shannon Jones McCall

Shannon Jones McCall

Associate Professor of Pathology
Pathology
Duke Box 3712, Room 309 Davison Bldg, Durham, NC 27710
Dept of Pathology Box 3712, Room 309 Davison Building, Durham, NC 27710
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Selected Publications

Treatment Patterns and Clinical Outcomes Among Patients With Metastatic Prostate Cancer Harboring Homologous Recombination Repair Mutations.

Journal Article Clin Genitourin Cancer · June 2024 BACKGROUND: There is currently limited literature assessing the real-world treatment patterns and clinical outcomes of patients with metastatic castration-resistant prostate cancer (mCRPC) and homologous recombination repair (HRR) mutations. METHODS: Medic ... Full text Link to item Cite

Prevalence of the cagA Virulence Factor Varies by Race Among Helicobacter pylori -Infected Patients Undergoing Upper Endoscopy.

Journal Article Clin Transl Gastroenterol · June 1, 2024 INTRODUCTION: We designed a race-conscious study to assess the presence of Helicobacter pylori v irulence factor cagA in a retrospective cohort of patients with active H. pylori infection. METHODS: We compared cagA status by race in gastric tissue samples ... Full text Link to item Cite

Mediator kinase inhibition impedes transcriptional plasticity and prevents resistance to ERK/MAPK-targeted therapy in KRAS-mutant cancers.

Journal Article NPJ Precis Oncol · May 31, 2024 Acquired resistance remains a major challenge for therapies targeting oncogene activated pathways. KRAS is the most frequently mutated oncogene in human cancers, yet strategies targeting its downstream signaling kinases have failed to produce durable treat ... Full text Link to item Cite

Chromatin Remodeling in Patient-Derived Colorectal Cancer Models.

Conference Adv Sci (Weinh) · April 2024 Patient-Derived Organoids (PDO) and Xenografts (PDX) are the current gold standards for patient-derived models of cancer (PDMC). Nevertheless, how patient tumor cells evolve in these models and the impact on drug response remains unclear. Herein, the trans ... Full text Link to item Cite

Helicobacter pylori testing prior to or at gastric cancer diagnosis and survival in a diverse US patient population.

Journal Article Gastric Cancer · January 2024 BACKGROUND: Gastric cancer (GC) accounts for the greatest disparity in cancer mortality between Black and White Americans. Although clinical trials have shown that Helicobacter pylori (Hp) treatment reduces risk of GC, Hp testing and treatment is not consi ... Full text Link to item Cite

X-ray diffraction imaging of glioblastoma and ductal carcinoma in-situ

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2024 Specimen radiography is critical to cancer diagnostics, but conventional transmission X-ray imaging often lacks the contrast to conclusively differentiate healthy from cancerous tissue. X-ray diffraction (XRD), however, has been shown to be sensitive to st ... Full text Cite

Towards a high-resolution volumetric X-ray diffraction imaging system for biospecimen

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2024 In a surgical pathology setting, the clinical study of tissue specimens is often limited to evaluating an effectively 2D representation of an inherently 3D specimen and disease, most commonly by a several-micron thick hematoxylin and eosin (H&E) stained gl ... Full text Cite

The Cooperative Human Tissue Network of the National Cancer Institute: Supporting Cancer Research for 35 Years.

Journal Article Mol Cancer Ther · October 2, 2023 The Cooperative Human Tissue Network was created by the NCI in 1987 to support a coordinated national effort to collect and distribute high quality, pathologist-validated human tissues for cancer research. Since then, the network has expanded to provide di ... Full text Link to item Cite

Abstract 5519: Biobanking of gastric organoid models from a racially diverse cohort for gastric cancer interception

Conference Cancer Research · April 4, 2023 AbstractPurpose: In the United States, significant disparities exist in gastric cancer incidence and mortality between Black Americans and non-Hispanic White Americans. Helicobacter pylori (HP) infection is ... Full text Cite

Data from A Precision Medicine Drug Discovery Pipeline Identifies Combined CDK2 and 9 Inhibition as a Novel Therapeutic Strategy in Colorectal Cancer

Other · April 3, 2023 <div>Abstract<p>Colorectal cancer is the third most common cancer in the United States and responsible for over 50,000 deaths each year. Therapeutic options for advanced colorectal cancer are limited, and there remains an unmet clinical ... Full text Cite

Data from A Precision Medicine Drug Discovery Pipeline Identifies Combined CDK2 and 9 Inhibition as a Novel Therapeutic Strategy in Colorectal Cancer

Other · April 3, 2023 <div>Abstract<p>Colorectal cancer is the third most common cancer in the United States and responsible for over 50,000 deaths each year. Therapeutic options for advanced colorectal cancer are limited, and there remains an unmet clinical ... Full text Cite

Corrigendum: Psymberin, a marine-derived natural product, induces cancer cell growth arrest and protein translation inhibition.

Journal Article Front Med (Lausanne) · 2023 [This corrects the article DOI: 10.3389/fmed.2022.999004.]. ... Full text Link to item Cite

Treatment Patterns and Clinical Outcomes Among Patients With Metastatic Prostate Cancer Harboring Homologous Recombination Repair Mutations.

Journal Article Clin Genitourin Cancer · June 2024 BACKGROUND: There is currently limited literature assessing the real-world treatment patterns and clinical outcomes of patients with metastatic castration-resistant prostate cancer (mCRPC) and homologous recombination repair (HRR) mutations. METHODS: Medic ... Full text Link to item Cite

Prevalence of the cagA Virulence Factor Varies by Race Among Helicobacter pylori -Infected Patients Undergoing Upper Endoscopy.

Journal Article Clin Transl Gastroenterol · June 1, 2024 INTRODUCTION: We designed a race-conscious study to assess the presence of Helicobacter pylori v irulence factor cagA in a retrospective cohort of patients with active H. pylori infection. METHODS: We compared cagA status by race in gastric tissue samples ... Full text Link to item Cite

Mediator kinase inhibition impedes transcriptional plasticity and prevents resistance to ERK/MAPK-targeted therapy in KRAS-mutant cancers.

Journal Article NPJ Precis Oncol · May 31, 2024 Acquired resistance remains a major challenge for therapies targeting oncogene activated pathways. KRAS is the most frequently mutated oncogene in human cancers, yet strategies targeting its downstream signaling kinases have failed to produce durable treat ... Full text Link to item Cite

Chromatin Remodeling in Patient-Derived Colorectal Cancer Models.

Conference Adv Sci (Weinh) · April 2024 Patient-Derived Organoids (PDO) and Xenografts (PDX) are the current gold standards for patient-derived models of cancer (PDMC). Nevertheless, how patient tumor cells evolve in these models and the impact on drug response remains unclear. Herein, the trans ... Full text Link to item Cite

Helicobacter pylori testing prior to or at gastric cancer diagnosis and survival in a diverse US patient population.

Journal Article Gastric Cancer · January 2024 BACKGROUND: Gastric cancer (GC) accounts for the greatest disparity in cancer mortality between Black and White Americans. Although clinical trials have shown that Helicobacter pylori (Hp) treatment reduces risk of GC, Hp testing and treatment is not consi ... Full text Link to item Cite

X-ray diffraction imaging of glioblastoma and ductal carcinoma in-situ

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2024 Specimen radiography is critical to cancer diagnostics, but conventional transmission X-ray imaging often lacks the contrast to conclusively differentiate healthy from cancerous tissue. X-ray diffraction (XRD), however, has been shown to be sensitive to st ... Full text Cite

Towards a high-resolution volumetric X-ray diffraction imaging system for biospecimen

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2024 In a surgical pathology setting, the clinical study of tissue specimens is often limited to evaluating an effectively 2D representation of an inherently 3D specimen and disease, most commonly by a several-micron thick hematoxylin and eosin (H&E) stained gl ... Full text Cite

The Cooperative Human Tissue Network of the National Cancer Institute: Supporting Cancer Research for 35 Years.

Journal Article Mol Cancer Ther · October 2, 2023 The Cooperative Human Tissue Network was created by the NCI in 1987 to support a coordinated national effort to collect and distribute high quality, pathologist-validated human tissues for cancer research. Since then, the network has expanded to provide di ... Full text Link to item Cite

Abstract 5519: Biobanking of gastric organoid models from a racially diverse cohort for gastric cancer interception

Conference Cancer Research · April 4, 2023 AbstractPurpose: In the United States, significant disparities exist in gastric cancer incidence and mortality between Black Americans and non-Hispanic White Americans. Helicobacter pylori (HP) infection is ... Full text Cite

Data from A Precision Medicine Drug Discovery Pipeline Identifies Combined CDK2 and 9 Inhibition as a Novel Therapeutic Strategy in Colorectal Cancer

Other · April 3, 2023 <div>Abstract<p>Colorectal cancer is the third most common cancer in the United States and responsible for over 50,000 deaths each year. Therapeutic options for advanced colorectal cancer are limited, and there remains an unmet clinical ... Full text Cite

Data from A Precision Medicine Drug Discovery Pipeline Identifies Combined CDK2 and 9 Inhibition as a Novel Therapeutic Strategy in Colorectal Cancer

Other · April 3, 2023 <div>Abstract<p>Colorectal cancer is the third most common cancer in the United States and responsible for over 50,000 deaths each year. Therapeutic options for advanced colorectal cancer are limited, and there remains an unmet clinical ... Full text Cite

Corrigendum: Psymberin, a marine-derived natural product, induces cancer cell growth arrest and protein translation inhibition.

Journal Article Front Med (Lausanne) · 2023 [This corrects the article DOI: 10.3389/fmed.2022.999004.]. ... Full text Link to item Cite

Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis.

Journal Article Sci Rep · November 9, 2022 Patients with non-small cell lung cancer (NSCLC) who have distant metastases have a poor prognosis. To determine which genomic factors of the primary tumor are associated with metastasis, we analyzed data from 759 patients originally diagnosed with stage I ... Full text Link to item Cite

Leveraging patient derived models of FGFR2 fusion positive intrahepatic cholangiocarcinoma to identify synergistic therapies.

Journal Article NPJ Precis Oncol · October 23, 2022 Intrahepatic cholangiocarcinoma (ICC) remains a deadly malignancy lacking systemic therapies for advanced disease. Recent advancements include selective FGFR1-3 inhibitors for the 15% of ICC patients harboring fusions, although survival is limited by poor ... Full text Link to item Cite

Evaluation of tumor microenvironment and biomarkers of immune checkpoint inhibitor response in metastatic renal cell carcinoma.

Journal Article J Immunother Cancer · October 2022 BACKGROUND: Immunotherapy combinations including ipilimumab and nivolumab are now the standard of care for untreated metastatic renal cell carcinoma (mRCC). Biomarkers of response are lacking to predict patients who will have a favorable or unfavorable res ... Full text Open Access Link to item Cite

Characterization of a castrate-resistant prostate cancer xenograft derived from a patient of West African ancestry.

Conference Prostate Cancer Prostatic Dis · September 2022 BACKGROUND: Prostate cancer is a clinically and molecularly heterogeneous disease, with highest incidence and mortality among men of African ancestry. To date, prostate cancer patient-derived xenograft (PCPDX) models to study this disease have been difficu ... Full text Open Access Link to item Cite

Patient-derived micro-organospheres enable clinical precision oncology.

Journal Article Cell Stem Cell · June 2, 2022 Patient-derived xenografts (PDXs) and patient-derived organoids (PDOs) have been shown to model clinical response to cancer therapy. However, it remains challenging to use these models to guide timely clinical decisions for cancer patients. Here, we used d ... Full text Open Access Link to item Cite

A Hybrid Human-Machine Learning Approach for Screening Prostate Biopsies Can Improve Clinical Efficiency Without Compromising Diagnostic Accuracy.

Journal Article Arch Pathol Lab Med · June 1, 2022 CONTEXT.—: Prostate cancer is a common malignancy, and accurate diagnosis typically requires histologic review of multiple prostate core biopsies per patient. As pathology volumes and complexity increase, new tools to improve the efficiency of everyday pra ... Full text Link to item Cite

Automated next-generation profiling of genomic alterations in human cancers.

Journal Article Nat Commun · May 20, 2022 The lack of validated, distributed comprehensive genomic profiling assays for patients with cancer inhibits access to precision oncology treatment. To address this, we describe elio tissue complete, which has been FDA-cleared for examination of 505 cancer- ... Full text Link to item Cite

Pre-existing Castration-resistant Prostate Cancer-like Cells in Primary Prostate Cancer Promote Resistance to Hormonal Therapy.

Journal Article Eur Urol · May 2022 BACKGROUND: Hormonal therapy targeting the androgen receptor inhibits prostate cancer (PCa), but the tumor eventually recurs as castration-resistant prostate cancer (CRPC). OBJECTIVE: To understand the mechanisms by which subclones within early PCa develop ... Full text Open Access Link to item Cite

Psymberin, a marine-derived natural product, induces cancer cell growth arrest and protein translation inhibition.

Journal Article Front Med (Lausanne) · 2022 Colorectal cancer (CRC) is the third most prevalent form of cancer in the United States and results in over 50,000 deaths per year. Treatments for metastatic CRC are limited, and therefore there is an unmet clinical need for more effective therapies. In ou ... Full text Link to item Cite

Plasma cells are essentially absent in the luminal gastrointestinal tract of patients with "complete" 22q11.2 deletion syndrome (DiGeorge syndrome).

Journal Article Hum Pathol · November 2021 Gastrointestinal symptoms are commonly reported in patients with 22q11.2 deletion syndrome or DiGeorge syndrome (DGS) in addition to the dominant cardiac manifestations and immunodeficiency. But literature providing specific morphologic details of the gast ... Full text Link to item Cite

Next-Generation Sequencing Concordance Analysis of Comprehensive Solid Tumor Profiling between a Centralized Specialty Laboratory and the Decentralized Personal Genome Diagnostics elio Tissue Complete Kitted Solution.

Journal Article J Mol Diagn · October 2021 Genomic tumor profiling by next-generation sequencing (NGS) allows for large-scale tumor testing to inform targeted cancer therapies and immunotherapies, and to identify patients for clinical trials. These tests are often underutilized in patients with lat ... Full text Link to item Cite

Expression of X-Linked Inhibitor of Apoptosis Protein (XIAP) in Breast Cancer Is Associated with Shorter Survival and Resistance to Chemotherapy.

Journal Article Cancers (Basel) · June 4, 2021 XIAP, the most potent inhibitor of cell death pathways, is linked to chemotherapy resistance and tumor aggressiveness. Currently, multiple XIAP-targeting agents are in clinical trials. However, the characterization of XIAP expression in relation to clinico ... Full text Link to item Cite

X-ray fan beam coded aperture transmission and diffraction imaging for fast material analysis.

Journal Article Sci Rep · May 19, 2021 X-ray transmission imaging has been used in a variety of applications for high-resolution measurements based on shape and density. Similarly, X-ray diffraction (XRD) imaging has been used widely for molecular structure-based identification of materials. Co ... Full text Link to item Cite

Reduced MFAP5 expression in stroma of gallbladder adenocarcinoma and its potential diagnostic utility.

Journal Article Virchows Arch · March 2021 The diagnosis of invasive adenocarcinoma of the gallbladder can sometimes be challenging. The presence of true desmoplastic reaction facilitates the diagnosis of invasion. However, desmoplasia-like changes can be observed in benign gallbladder conditions, ... Full text Link to item Cite

RNA splicing and aggregate gene expression differences in lung squamous cell carcinoma between patients of West African and European ancestry.

Journal Article Lung Cancer · March 2021 OBJECTIVES: Despite disparities in lung cancer incidence and mortality, the molecular landscape of lung cancer in patients of African ancestry remains underexplored, and race-related differences in RNA splicing remain unexplored. MATERIALS AND METHODS: We ... Full text Link to item Cite

Results and Clinical Utilization of Foundation Medicine Molecular Tumor Profiling in Uterine and Ovarian Cancers.

Journal Article Target Oncol · January 2021 BACKGROUND: Recent advances in next-generation sequencing have allowed for an increase in molecular tumor profiling. OBJECTIVE: We sought to assess the actionability and clinical utilization of molecular tumor profiling results obtained via Foundation Medi ... Full text Link to item Cite

Implementation of a Molecular Tumor Registry to Support the Adoption of Precision Oncology Within an Academic Medical Center: The Duke University Experience.

Journal Article JCO Precis Oncol · 2021 UNLABELLED: Comprehensive genomic profiling to inform targeted therapy selection is a central part of oncology care. However, the volume and complexity of alterations uncovered through genomic profiling make it difficult for oncologists to choose the most ... Full text Link to item Cite

PD-L1 Assay Concordance in Metastatic Renal Cell Carcinoma and Metastatic Urothelial Carcinoma.

Journal Article Clin Genitourin Cancer · December 2020 BACKGROUND: Immune checkpoint inhibitors are now standard of care for many patients with metastatic renal cell carcinoma (mRCC) and metastatic urothelial carcinoma (mUC). Given real-world limitations in programmed death-ligand 1 (PD-L1) testing, concordanc ... Full text Link to item Cite

A Precision Medicine Drug Discovery Pipeline Identifies Combined CDK2 and 9 Inhibition as a Novel Therapeutic Strategy in Colorectal Cancer.

Journal Article Mol Cancer Ther · December 2020 Colorectal cancer is the third most common cancer in the United States and responsible for over 50,000 deaths each year. Therapeutic options for advanced colorectal cancer are limited, and there remains an unmet clinical need to identify new treatments for ... Full text Link to item Cite

Biobanking in the COVID-19 Era and Beyond: Part 1. How Early Experiences Can Translate into Actionable Wisdom.

Journal Article Biopreserv Biobank · December 2020 The era of COVID-19 has brought about a number of novel challenges for the global biobanking community. To better position the biobanking community to cope with current and future challenges, the International Society for Biological and Environmental Repos ... Full text Link to item Cite

Biobanking in the COVID-19 Era and Beyond: Part 2. A Set of Tool Implementation Case Studies.

Journal Article Biopreserv Biobank · December 2020 The COVID-19 era has brought about a number of novel challenges for the global biobanking community. An array of diverse tools (e.g., standards, best practices, and plans) exists to support quality and fitness-for-purpose in biobank operations. The Interna ... Full text Link to item Cite

A Comparative Oncology Drug Discovery Pipeline to Identify and Validate New Treatments for Osteosarcoma.

Journal Article Cancers (Basel) · November 11, 2020 BACKGROUND: Osteosarcoma is a rare but aggressive bone cancer that occurs primarily in children. Like other rare cancers, treatment advances for osteosarcoma have stagnated, with little improvement in survival for the past several decades. Developing new t ... Full text Link to item Cite

Development of a precision medicine pipeline to identify personalized treatments for colorectal cancer.

Journal Article BMC Cancer · June 24, 2020 BACKGROUND: Metastatic colorectal cancer (CRC) continues to be a major health problem, and current treatments are primarily for disease control and palliation of symptoms. In this study, we developed a precision medicine strategy to discover novel therapeu ... Full text Link to item Cite

Proliferative potential and response to nivolumab in clear cell renal cell carcinoma patients.

Journal Article Oncoimmunology · June 10, 2020 BACKGROUND: Biomarkers predicting immunotherapy response in metastatic renal cell cancer (mRCC) are lacking. PD-L1 immunohistochemistry is a complementary diagnostic for immune checkpoint inhibitors (ICIs) in mRCC, but has shown minimal clinical utility an ... Full text Link to item Cite

Abstract B035: Identification of a tumor cell adaptive stress response signaling pathway, which drives aggressive breast cancer phenotype and therapeutic resistance, in African American patients with locally advanced breast cancer subtypes

Conference Cancer Epidemiology, Biomarkers & Prevention · June 1, 2020 AbstractIntroduction: The higher incidence of biologically aggressive and treatment-resistant breast cancer (BCa) subtypes, which includes triple negative (TN), basal, and inflammatory breast cancer (IBC), c ... Full text Cite

Abstract B071: Genomic differences between non-small cell lung cancer (NSCLC) in African American and white patients

Conference Cancer Epidemiology, Biomarkers & Prevention · June 1, 2020 AbstractBackground: Racial disparities in lung cancer exist, as African Americans (AAs) have the highest incidence of lung cancer and rate of lung cancer-related death and develop lung cancer at an earlier a ... Full text Cite

Abstract A114: Characterization of a metastatic prostate cancer xenograft derived from a patient of African ancestry

Conference Cancer Epidemiology, Biomarkers & Prevention · June 1, 2020 AbstractBackground: Prostate cancer (PCa) is a clinically and molecularly heterogeneous disease, with differences in incidence and mortality among and between racial groups, which grade and stage only partia ... Full text Cite

State of the Art: Toward Improving Outcomes of Lung and Liver Tumor Biopsies in Clinical Trials-A Multidisciplinary Approach.

Journal Article J Clin Oncol · May 10, 2020 PURPOSE: National Cancer Institute (NCI)-sponsored clinical trial network studies frequently require biopsy specimens for pharmacodynamic and molecular biomarker analyses, including paired pre- and post-treatment samples. The purpose of this meeting of NCI ... Full text Link to item Cite

NanoString Gene Expression Profiling in Chronic Lung Allograft Dysfunction (CLAD)

Conference The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation · April 1, 2020 PURPOSE: CLAD, mainly manifest as bronchiolitis obliterans syndrome (BOS), is the leading cause of late death in lung recipients. BOS develops despite routine immunosuppression and its pathogenesis is poorly understood. The histological correlate of BOS is ... Full text Cite

Characterization of tumor mutation burden, PD-L1 and DNA repair genes to assess relationship to immune checkpoint inhibitors response in metastatic renal cell carcinoma.

Journal Article J Immunother Cancer · March 2020 BACKGROUND: Immune checkpoint inhibitors (ICIs) have expanded treatment options for metastatic renal cell carcinoma (mRCC); however, there are limited predictive biomarkers for response to ICIs in this indication, with programmed death-ligand 1 (PD-L1) sta ... Full text Link to item Cite

The Project Baseline Health Study: a step towards a broader mission to map human health.

Journal Article NPJ Digit Med · 2020 The Project Baseline Health Study (PBHS) was launched to map human health through a comprehensive understanding of both the health of an individual and how it relates to the broader population. The study will contribute to the creation of a biomedical info ... Full text Open Access Link to item Cite

Prior tonsillectomy is associated with an increased risk of esophageal adenocarcinoma.

Journal Article PLoS One · 2020 BACKGROUND: Esophageal cancer is a deadly cancer with 5-year survival <20%. Although multiple risk factors for esophageal adenocarcinoma (EAC) including obesity, GERD and smoking have been identified, these risk factors do not fully explain the rising inci ... Full text Link to item Cite

Targeting cellular heterogeneity with CXCR2 blockade for the treatment of therapy-resistant prostate cancer.

Journal Article Sci Transl Med · December 4, 2019 Hormonal therapy targeting androgen receptor (AR) is initially effective to treat prostate cancer (PCa), but it eventually fails. It has been hypothesized that cellular heterogeneity of PCa, consisting of AR+ luminal tumor cells and AR- neuroendocrine (NE) ... Full text Link to item Cite

The Immune Landscape of Cancer.

Journal Article Immunity · August 20, 2019 Full text Link to item Cite

X-Ray Diffraction for Breast Cancer Imaging

Conference MEDICAL PHYSICS · June 1, 2019 Link to item Cite

Characterization of tumor mutational burden (TMB), PD-L1, and DNA repair genes to assess correlation with immune checkpoint inhibitors (ICIs) response in metastatic renal cell carcinoma (mRCC).

Conference Journal of Clinical Oncology · May 20, 2019 e16079 Background: ICIs have revolutionized treatment for mRCC; however there are limited predictive biomarkers for response to ICIs. PD-L1 status is still controversial, demonstrating little predictive utility in mRCC. TMB is pr ... Full text Cite

Evaluation of tumor microenvironment and biomarkers of immune checkpoint inhibitor (ICI) response in metastatic renal cell carcinoma (mRCC).

Conference Journal of Clinical Oncology · May 20, 2019 2595 Background: ICIs are now standard of care for mRCC; however, there are few biomarkers to predict ICI response. Recent data from atezolizumab/bevacizumab trials in mRCC suggest tumors with high Teff Full text Cite

Concordance between PD-L1 assays for metastatic renal cell carcinoma (mRCC) and metastatic urothelial carcinoma (mUC).

Conference Journal of Clinical Oncology · May 20, 2019 e14259 Background: Immune checkpoint inhibitors (ICIs) are standard of care for mRCC and mUC patients (pts). PD-L1 status is gaining importance as a predictive biomarker, particularly for cisplatin-ineligible mUC. PD-L1 positivit ... Full text Cite

Cell proliferation as a biomarker for response to immune checkpoint inhibitors in highly inflamed renal cell carcinoma.

Conference Journal of Clinical Oncology · March 10, 2019 61 Background: Cell proliferation is an important marker of survival in many tumors and we hypothesized that this attribute could be related to response to immune checkpoint inhibitors in RCC. Previously we reported (SITC 2018) m ... Full text Cite

Cell proliferation as a biomarker for response to immune checkpoint inhibitors in PD-L1 negative renal cell carcinoma.

Conference Journal of Clinical Oncology · March 10, 2019 62 Background: Cell proliferation is an important marker of survival in many tumors, and we hypothesized that this attribute could be related to response to immune checkpoint inhibitors (ICIs) in RCC. Previously we reported (SITC ... Full text Cite

Evaluation of tumor microenvironment and biomarkers of immune checkpoint inhibitor (ICI) response in metastatic renal cell carcinoma (mRCC).

Conference Journal of Clinical Oncology · March 10, 2019 63 Background: ICIs are now standard of care for mRCC; however, there are few biomarkers to predict ICI response. Recent data from atezolizumab/bevacizumab trials in mRCC suggest tumors with high Teff Full text Cite

Characterization of tumor mutational burden (TMB), PD-L1, and DNA repair genes to assess correlation with immune checkpoint inhibitors (ICIs) response in metastatic renal cell carcinoma (mRCC).

Conference Journal of Clinical Oncology · March 1, 2019 589 Background: ICIs have revolutionized treatment for mRCC; however there are limited predictive biomarkers for response to ICIs. PD-L1 status is still controversial demonstrating little predictive utility in mRCC. TMB is predic ... Full text Cite

Characterization of genomic alterations as biomarkers of immune checkpoint inhibitor (ICI) response in metastatic urothelial carcinoma (mUC).

Conference Journal of Clinical Oncology · March 1, 2019 400 Background: ICIs have expanded therapeutic options for mUC patients (pts); however, biomarkers such as PD-L1 have not served as reliable predictors of treatment efficacy. High tumor mutation burden (TMB) has been previously d ... Full text Cite

Concordance between PD-L1 assays for metastatic renal cell carcinoma (mRCC) and metastatic urothelial carcinoma (mUC).

Conference Journal of Clinical Oncology · March 1, 2019 577 Background: Immune checkpoint inhibitors (ICIs) are now standard of care for mRCC and mUC patients (pts). PD-L1 status is gaining importance as a predictive biomarker, particularly for cisplatin-ineligible mUC. Four different ... Full text Cite

Evaluation of tumor microenvironment and biomarkers of immune checkpoint inhibitor (ICI) response in metastatic renal cell carcinoma (mRCC).

Conference Journal of Clinical Oncology · March 1, 2019 607 Background: ICIs are now standard of care for mRCC; however, there are few biomarkers to predict ICI response. Recent data from atezolizumab/bevacizumab trials in mRCC suggest tumors with high Teff Full text Cite

Proliferative potential and resistance to immune checkpoint blockade in lung cancer patients.

Journal Article J Immunother Cancer · February 1, 2019 BACKGROUND: Resistance to immune checkpoint inhibitors (ICIs) has been linked to local immunosuppression independent of major ICI targets (e.g., PD-1). Clinical experience with response prediction based on PD-L1 expression suggests that other factors influ ... Full text Link to item Cite

Next generation sequencing of PD-L1 for predicting response to immune checkpoint inhibitors.

Journal Article J Immunother Cancer · January 24, 2019 BACKGROUND: PD-L1 immunohistochemistry (IHC) has been traditionally used for predicting clinical responses to immune checkpoint inhibitors (ICIs). However, there are at least 4 different assays and antibodies used for PD-L1 IHC, each developed with a diffe ... Full text Link to item Cite

Perspectives on Inflammatory Breast Cancer (IBC) Research, Clinical Management and Community Engagement from the Duke IBC Consortium.

Journal Article J Cancer · 2019 Inflammatory breast cancer (IBC) is an understudied and aggressive form of breast cancer with a poor prognosis, accounting for 2-6% of new breast cancer diagnoses but 10% of all breast cancer-related deaths in the United States. Currently there are no ther ... Full text Open Access Link to item Cite

Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer.

Journal Article Cell Rep · October 30, 2018 Hippo signaling has been recognized as a key tumor suppressor pathway. Here, we perform a comprehensive molecular characterization of 19 Hippo core genes in 9,125 tumor samples across 33 cancer types using multidimensional "omic" data from The Cancer Genom ... Full text Link to item Cite

A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily.

Journal Article Cell Syst · October 24, 2018 We present an integromic analysis of gene alterations that modulate transforming growth factor β (TGF-β)-Smad-mediated signaling in 9,125 tumor samples across 33 cancer types in The Cancer Genome Atlas (TCGA). Focusing on genes that encode mediators and re ... Full text Link to item Cite

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.

Journal Article Cancer Cell · August 13, 2018 Our comprehensive analysis of alternative splicing across 32 The Cancer Genome Atlas cancer types from 8,705 patients detects alternative splicing events and tumor variants by reanalyzing RNA and whole-exome sequencing data. Tumors have up to 30% more alte ... Full text Link to item Cite

Targeting the human epidermal growth factor receptor 2 (HER2) oncogene in colorectal cancer.

Journal Article Ann Oncol · May 1, 2018 Human epidermal growth factor receptor 2 (HER2) is an oncogenic driver, and a well-established therapeutic target in breast and gastric cancers. Using functional and genomic analyses of patient-derived xenografts, we previously showed that a subset (approx ... Full text Link to item Cite

The Immune Landscape of Cancer.

Journal Article Immunity · April 17, 2018 We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we identified six immune subtypes-wound healing, IFN-γ dominant, inflammatory, lymphocyt ... Full text Link to item Cite

Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas.

Journal Article Cancer Cell · April 9, 2018 We analyzed 921 adenocarcinomas of the esophagus, stomach, colon, and rectum to examine shared and distinguishing molecular characteristics of gastrointestinal tract adenocarcinomas (GIACs). Hypermutated tumors were distinct regardless of cancer type and c ... Full text Link to item Cite

lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer.

Journal Article Cancer Cell · April 9, 2018 We characterized the epigenetic landscape of genes encoding long noncoding RNAs (lncRNAs) across 6,475 tumors and 455 cancer cell lines. In stark contrast to the CpG island hypermethylation phenotype in cancer, we observed a recurrent hypomethylation of 1, ... Full text Link to item Cite

Genomic and Functional Approaches to Understanding Cancer Aneuploidy.

Journal Article Cancer Cell · April 9, 2018 Aneuploidy, whole chromosome or chromosome arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic mutation rate, and expression of pro ... Full text Link to item Cite

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers.

Journal Article Cancer Cell · April 9, 2018 We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. We f ... Full text Link to item Cite

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.

Journal Article Cell · April 5, 2018 The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 tumors from 33 cancer types, we pr ... Full text Link to item Cite

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.

Journal Article Cell · April 5, 2018 We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chr ... Full text Link to item Cite

Pathogenic Germline Variants in 10,389 Adult Cancers.

Journal Article Cell · April 5, 2018 We conducted the largest investigation of predisposition variants in cancer to date, discovering 853 pathogenic or likely pathogenic variants in 8% of 10,389 cases from 33 cancer types. Twenty-one genes showed single or cross-cancer associations, including ... Full text Link to item Cite

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.

Journal Article Cell · April 5, 2018 The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 892 ... Full text Link to item Cite

Oncogenic Signaling Pathways in The Cancer Genome Atlas.

Journal Article Cell · April 5, 2018 Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tu ... Full text Link to item Cite

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

Journal Article Cell · April 5, 2018 Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic dedifferentiation. We used an innovative one ... Full text Link to item Cite

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics.

Journal Article Cell · April 5, 2018 For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features represe ... Full text Link to item Cite

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Journal Article Cell · April 5, 2018 Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report a PanCancer and PanSoftware analy ... Full text Link to item Cite

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma.

Journal Article Cell Rep · April 3, 2018 Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, includ ... Full text Link to item Cite

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context.

Journal Article Cell Rep · April 3, 2018 Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles in cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling th ... Full text Link to item Cite

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Journal Article Cell Rep · April 3, 2018 Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation ra ... Full text Link to item Cite

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.

Journal Article Cell Rep · April 3, 2018 Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumor-infiltrating lymphocytes (TILs) based on H&E images from 13 TCGA t ... Full text Link to item Cite

Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers.

Journal Article Cell Rep · April 3, 2018 Metabolic reprogramming provides critical information for clinical oncology. Using molecular data of 9,125 patient samples from The Cancer Genome Atlas, we identified tumor subtypes in 33 cancer types based on mRNA expression patterns of seven major metabo ... Full text Link to item Cite

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.

Journal Article Cell Rep · April 3, 2018 This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recu ... Full text Link to item Cite

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types.

Journal Article Cell Rep · April 3, 2018 Protein ubiquitination is a dynamic and reversible process of adding single ubiquitin molecules or various ubiquitin chains to target proteins. Here, using multidimensional omic data of 9,125 tumor samples across 33 cancer types from The Cancer Genome Atla ... Full text Link to item Cite

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas.

Journal Article Cell Rep · April 3, 2018 Precision oncology uses genomic evidence to match patients with treatment but often fails to identify all patients who may respond. The transcriptome of these "hidden responders" may reveal responsive molecular states. We describe and evaluate a machine-le ... Full text Link to item Cite

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types.

Journal Article Cell Rep · April 3, 2018 Hotspot mutations in splicing factor genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of RNA splicing in cancer. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome ... Full text Link to item Cite

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

Journal Article Cell Rep · April 3, 2018 For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creat ... Full text Link to item Cite

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas.

Journal Article Cell Rep · April 3, 2018 DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heter ... Full text Link to item Cite

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas.

Journal Article Cell Syst · March 28, 2018 Although the MYC oncogene has been implicated in cancer, a systematic assessment of alterations of MYC, related transcription factors, and co-regulatory proteins, forming the proximal MYC network (PMN), across human cancers is lacking. Using computational ... Full text Link to item Cite

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.

Journal Article Cell Syst · March 28, 2018 The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Can ... Full text Link to item Cite

The College of American Pathologists Biorepository Accreditation Program: Results from the First 5 Years.

Journal Article Biopreserv Biobank · February 2018 The College of American Pathologists (CAP) developed the Biorepository Accreditation Program (BAP) in 2012. This program integrates best practices from the International Society for Biological and Environmental Biorepositories, the National Cancer Institut ... Full text Link to item Cite

Metastatic Renal Cell Carcinoma as Solitary Subcentimeter Polypoid Gastric Mucosal Lesions: Clinicopathologic Analysis of Five Cases.

Journal Article Gastroenterology Res · February 2018 BACKGROUND: The stomach is an uncommon site for metastatic carcinoma. Approximately 6% of renal cell carcinomas (RCCs) may metastasize to the stomach. The majority of the reported metastatic RCCs in the stomach presented as large masses or ulcers greater t ... Full text Open Access Link to item Cite

Standardization of the histopathology cancer report: An ontological approach

Conference CEUR Workshop Proceedings · January 1, 2018 Cite

Overexpression of SOX11 and TFE3 in Solid-Pseudopapillary Neoplasms of the Pancreas.

Journal Article Am J Clin Pathol · December 20, 2017 OBJECTIVES: To characterize the expression of SOX11 and TFE3 proteins in solid-pseudopapillary neoplasms (SPNs) and their histologic mimickers. METHODS: Immunohistochemistry for SOX11, TFE3, and β-catenin was performed on 31 cases of surgically resected SP ... Full text Link to item Cite

Immune Activation in Early-Stage Non-Small Cell Lung Cancer Patients Receiving Neoadjuvant Chemotherapy Plus Ipilimumab.

Journal Article Clin Cancer Res · December 15, 2017 Purpose: To determine the immunologic effects of neoadjuvant chemotherapy plus ipilimumab in early-stage non-small cell lung cancer (NSCLC) patients.Experimental Design: This is a single-arm chemotherapy plus phased ipilimumab phase II study of 24 treatmen ... Full text Link to item Cite

Melanoma Therapeutic Strategies that Select against Resistance by Exploiting MYC-Driven Evolutionary Convergence.

Journal Article Cell Rep · December 5, 2017 Diverse pathways drive resistance to BRAF/MEK inhibitors in BRAF-mutant melanoma, suggesting that durable control of resistance will be a challenge. By combining statistical modeling of genomic data from matched pre-treatment and post-relapse patient tumor ... Full text Link to item Cite

Porcine Esophageal Submucosal Gland Culture Model Shows Capacity for Proliferation and Differentiation.

Journal Article Cell Mol Gastroenterol Hepatol · November 2017 BACKGROUND & AIMS: Although cells comprising esophageal submucosal glands (ESMGs) represent a potential progenitor cell niche, new models are needed to understand their capacity to proliferate and differentiate. By histologic appearance, ESMGs have been as ... Full text Link to item Cite

Ductular and proliferative response of esophageal submucosal glands in a porcine model of esophageal injury and repair.

Journal Article Am J Physiol Gastrointest Liver Physiol · September 1, 2017 Esophageal injury is a risk factor for diseases such as Barrett's esophagus (BE) and esophageal adenocarcinoma. To improve understanding of signaling pathways associated with both normal and abnormal repair, animal models are needed. Traditional rodent mod ... Full text Link to item Cite

A Landscape of Therapeutic Cooperativity in KRAS Mutant Cancers Reveals Principles for Controlling Tumor Evolution.

Journal Article Cell Rep · July 25, 2017 Combinatorial inhibition of effector and feedback pathways is a promising treatment strategy for KRAS mutant cancers. However, the particular pathways that should be targeted to optimize therapeutic responses are unclear. Using CRISPR/Cas9, we systematical ... Full text Link to item Cite

Professional Practice Evaluation for Pathologists: The Development, Life, and Death of the Evalumetrics Program.

Journal Article Arch Pathol Lab Med · April 2017 CONTEXT: - In 2008, the Joint Commission (JC) implemented a standard mandating formal monitoring of physician professional performance as part of the process of granting and maintaining practice privileges. OBJECTIVE: - To create a pathology-specific manag ... Full text Link to item Cite

Integrated genomic characterization of oesophageal carcinoma.

Journal Article Nature · January 12, 2017 Oesophageal cancers are prominent worldwide; however, there are few targeted therapies and survival rates for these cancers remain dismal. Here we performed a comprehensive molecular analysis of 164 carcinomas of the oesophagus derived from Western and Eas ... Full text Link to item Cite

Coded aperture coherent scatter spectral imaging for assessment of breast cancers: An ex-vivo demonstration

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2017 A Coded Aperture Coherent Scatter Spectral Imaging (CACSSI) system was developed in our group to differentiate cancer and healthy tissue in the breast. The utility of the experimental system was previously demonstrated using anthropomorphic breast phantoms ... Full text Cite

Biobanking-Budgets and the Role of Pathology Biobanks in Precision Medicine.

Journal Article Acad Pathol · 2017 Biobanks have become an important component of the routine practice of pathology. At the 2016 meeting of the Association of Pathology Chairs, a series of presentations covered several important aspects of biobanking. An often overlooked aspect of biobankin ... Full text Link to item Cite

PIK3CA mutations enable targeting of a breast tumor dependency through mTOR-mediated MCL-1 translation.

Journal Article Sci Transl Med · December 14, 2016 Therapies that efficiently induce apoptosis are likely to be required for durable clinical responses in patients with solid tumors. Using a pharmacological screening approach, we discovered that combined inhibition of B cell lymphoma-extra large (BCL-XL) a ... Full text Open Access Link to item Cite

Radiographic and endoscopic regression of metastatic gastric cancer to the colon in the setting of 5-aminosalicylic acid use.

Journal Article J Gastrointest Oncol · December 2016 Colonic metastases from gastric cancer are a rare phenomenon and sparsely reported in the literature. We report a case of a 59-year-old woman who presented with vague abdominal symptoms and initial computer tomography (CT) imaging suggestive of a colonic a ... Full text Link to item Cite

TGF-β-induced stromal CYR61 promotes resistance to gemcitabine in pancreatic ductal adenocarcinoma through downregulation of the nucleoside transporters hENT1 and hCNT3.

Journal Article Carcinogenesis · November 1, 2016 Pancreatic ductal adenocarcinoma (PDAC) is a lethal cancer in part due to inherent resistance to chemotherapy, including the first-line drug gemcitabine. Although low expression of the nucleoside transporters hENT1 and hCNT3 that mediate cellular uptake of ... Full text Link to item Cite

Physician Satisfaction With Clinical Laboratory Services: A College of American Pathologists Q-Probes Study of 81 Institutions.

Journal Article Arch Pathol Lab Med · October 2016 CONTEXT: -Assessment of customer satisfaction is a vital component of the laboratory quality improvement program. OBJECTIVE: -To survey the level of physician satisfaction with hospital clinical laboratory services. DESIGN: -Participating institutions prov ... Full text Link to item Cite

TH-AB-209-10: Breast Cancer Identification Through X-Ray Coherent Scatter Spectral Imaging.

Journal Article Med Phys · June 2016 PURPOSE: We have previously described the development and testing of a coherent-scatter spectral imaging system for identification of cancer. Our prior evaluations were performed using either tissue surrogate phantoms or formalin-fixed tissue obtained from ... Full text Link to item Cite

Mixed Adenoneuroendocrine Carcinoma, Amphicrine Type, of the Small Bowel.

Journal Article Am J Clin Pathol · May 2016 OBJECTIVES: Amphicrine-type mixed adenoneuroendocrine carcinomas are exceedingly rare lesions of the gastrointestinal tract, comprising tumor cells simultaneously demonstrating both neuroendocrine and exocrine features. To date, only 14 cases of amphicrine ... Full text Link to item Cite

Primary high-grade neuroendocrine carcinoma emerging from an adenomatous polyp in the setting of familial adenomatous polyposis.

Journal Article BMJ Case Rep · February 16, 2016 Familial adenomatous polyposis (FAP) is a rare inherited syndrome that is characterised by innumerable adenomas of the colon and rectum, a high risk of colorectal cancer and a variety of extracolonic manifestations. FAP presents as hundreds to thousands of ... Full text Link to item Cite

Validation of coded aperture coherent scatter spectral imaging for normal and neoplastic breast tissues via surgical pathology

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2016 This study intends to validate the sensitivity and specificity of coded aperture coherent scatter spectral imaging (CACSSI) by comparison to standard histological preparation and pathologic analysis methods used to differentiate normal and neoplastic breas ... Full text Cite

Ductal metaplasia in oesophageal submucosal glands is associated with inflammation and oesophageal adenocarcinoma.

Journal Article Histopathology · December 2015 Featured Publication AIMS: Recent studies have suggested that oesophageal submucosal gland (ESMG) ducts harbour progenitor cells that may contribute to oesophageal metaplasia. Our objective was to determine whether histological differences exist between the ESMGs of individual ... Full text Link to item Cite

The Molecular Taxonomy of Primary Prostate Cancer.

Journal Article Cell · November 5, 2015 Featured Publication There is substantial heterogeneity among primary prostate cancers, evident in the spectrum of molecular abnormalities and its variable clinical course. As part of The Cancer Genome Atlas (TCGA), we present a comprehensive molecular analysis of 333 primary ... Full text Link to item Cite

Metastatic gallbladder cancer masquerading as primary colon malignancy.

Journal Article Clinical Medicine Review Case Reports · June 1, 2015 Featured Publication Cite

Error Reduction and Prevention in Surgical Pathology

Chapter · March 3, 2015 Featured Publication Diagnostic musculoskeletal surgical pathology. Philadelphia: Elsevier; 2004. pp. 1–18. Suriawinata AA, Antonio LB, Thung SN. Liver tissue processing and normal histology. In: Odze RD, Goldblum JR, editors. Surgical pathology of the GI tract, ... ... Cite

Mismatch repair gone awry: Management of Lynch syndrome.

Journal Article Crit Rev Oncol Hematol · March 2015 Featured Publication The hallmark of Lynch syndrome involves germline mutations of genes important in DNA mismatch repair. Affected family kindreds will have multiple associated malignancies, the most common of which is colorectal adenocarcinoma. Recently, evidence has shown t ... Full text Link to item Cite

Endogenous elevation of plasma cholecystokinin does not prevent gallstones.

Journal Article Eur J Clin Invest · March 2015 Featured Publication BACKGROUND: Regular gall bladder contraction reduces bile stasis and prevents gallstone formation. Intraduodenal administration of exogenous pancreatic secretory trypsin inhibitor-I (PSTI-I, also known as monitor peptide) causes cholecystokinin (CCK) secre ... Full text Link to item Cite

Patterns of failure for stage I ampulla of Vater adenocarcinoma: a single institutional experience.

Journal Article J Gastrointest Oncol · December 2014 Featured Publication BACKGROUND: Ampullary adenocarcinoma is a rare malignancy associated with a relatively favorable prognosis. Given high survival rates in stage I patients reported in small series with surgery alone, adjuvant chemoradiotherapy (CRT) has traditionally been r ... Full text Link to item Cite

Radiosensitive orbital metastasis as presentation of occult colonic adenocarcinoma.

Journal Article BMJ Case Rep · September 19, 2014 Featured Publication An 82-year-old man presented with progressive right frontal headaches. The patient's history was significant for benign polyps on surveillance colonoscopy 2 years prior, without high-grade dysplasia or carcinoma. MRI revealed an enhancing lesion arising wi ... Full text Link to item Cite

Comprehensive molecular characterization of gastric adenocarcinoma.

Journal Article Nature · September 11, 2014 Featured Publication Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric ... Full text Link to item Cite

Q-Probes studies in anatomic pathology: quality improvement through targeted benchmarking.

Journal Article Arch Pathol Lab Med · September 2014 Featured Publication CONTEXT: The Q-Probes program is a peer-comparison quality assurance service offered by the College of American Pathologists that was created in 1989. OBJECTIVE: To establish national benchmarks around a specific quality metric at a specific point in time ... Full text Link to item Cite

Identification and validation of actionable mutations in solid tumors.

Conference Journal of Clinical Oncology · May 20, 2014 Featured Publication Full text Cite

Phase I study of dasatinib in combination with capecitabine, oxaliplatin and bevacizumab followed by an expanded cohort in previously untreated metastatic colorectal cancer.

Journal Article Invest New Drugs · April 2014 Featured Publication PURPOSE: Dasatinib inhibits src family kinases and has anti-angiogenic properties. We conducted a phase I study of dasatinib, capecitabine, oxaliplatin, and bevacizumab (CapeOx/bevacizumab), with an expansion cohort in metastatic colorectal cancer (CRC). M ... Full text Link to item Cite

TTF-1 Is Expressed in a Subset of Esophageal Adenocarcinomas

Conference MODERN PATHOLOGY · February 1, 2014 Featured Publication Link to item Cite

TTF-1 Is Expressed in a Subset of Esophageal Adenocarcinomas

Conference LABORATORY INVESTIGATION · February 1, 2014 Link to item Cite

Delayed Specimen Collection May Artifactually Damage the Mucosal Surface in Barrett's EMR Specimens

Conference LABORATORY INVESTIGATION · February 1, 2014 Featured Publication Link to item Cite

The role of local excision in invasive adenocarcinoma of the ampulla of Vater.

Journal Article J Gastrointest Oncol · March 2013 Featured Publication BACKGROUND: Ampulla of Vater carcinomas are rare malignancies that have been traditionally treated with radical surgical resection. Given the mortality associated with pancreaticoduodenectomy, some patients may benefit from local resection. A single-instit ... Full text Link to item Cite

Patterns of Failure for Stage I Ampulla of Vater Adenocarcinoma: A Single Institutional Experience

Conference INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS · 2013 Featured Publication Full text Cite

Costaining for keratins 8/18 plus ubiquitin improves detection of hepatocyte injury in nonalcoholic fatty liver disease.

Journal Article Hum Pathol · June 2012 Featured Publication Nonalcoholic fatty liver disease is a global health dilemma. The gold standard for diagnosis is liver biopsy. Ballooned hepatocytes are histologic manifestations of hepatocellular injury and are characteristic of steatohepatitis, the more severe form of no ... Full text Link to item Cite

A phase I/II study of capecitabine (Cape), oxaliplatin (Ox), panitumumab (Pmab), and external beam radiation therapy (RT) for patients with esophagogastric carcinoma (EC).

Journal Article J Clin Oncol · February 2012 68 Background: EC is commonly managed with concurrent chemoradiotherapy, with or without surgical resection. The optimal combination and dose of agents is the subject of continued investigation. This study examines chemotherapeutic agents with known effica ... Link to item Cite

A phase I/II study of capecitabine (Cape), oxaliplatin (Ox), panitumumab (Pmab), and external beam radiation therapy (RT) for patients with esophagogastric carcinoma (EC).

Conference Journal of Clinical Oncology · February 1, 2012 68 Background: EC is commonly managed with concurrent chemoradiotherapy, with or without surgical resection. The optimal combination and dose of agents is the subject of continued investigation. This study examines chemotherapeut ... Full text Cite

Histological and molecular evaluation of patient-derived colorectal cancer explants.

Journal Article PLoS One · 2012 Featured Publication Mouse models have been developed to investigate colorectal cancer etiology and evaluate new anti-cancer therapies. While genetically engineered and carcinogen-induced mouse models have provided important information with regard to the mechanisms underlying ... Full text Link to item Cite

Hedgehog activity, epithelial-mesenchymal transitions, and biliary dysmorphogenesis in biliary atresia.

Journal Article Hepatology · April 2011 Featured Publication UNLABELLED: Biliary atresia (BA) is notable for marked ductular reaction and rapid development of fibrosis. Activation of the Hedgehog (Hh) pathway promotes the expansion of populations of immature epithelial cells that coexpress mesenchymal markers and ma ... Full text Link to item Cite

Rho GTPase activity modulates Wnt3a/beta-catenin signaling.

Journal Article Cell Signal · November 2009 Featured Publication Wnt proteins constitute a family of secreted signaling molecules that regulate highly conserved pathways essential for development and, when aberrantly activated, drive oncogenesis in a number of human cancers. A key feature of the most widely studied Wnt ... Full text Link to item Cite

Analysis of Hepatic Progenitor Populations in Methyl Deficient Liver Injury

Journal Article ANNALS OF SURGICAL ONCOLOGY · 2009 Featured Publication Cite

Fructose consumption as a risk factor for non-alcoholic fatty liver disease.

Journal Article J Hepatol · June 2008 Featured Publication BACKGROUND/AIMS: While the rise in non-alcoholic fatty liver disease (NAFLD) parallels the increase in obesity and diabetes, a significant increase in dietary fructose consumption in industrialized countries has also occurred. The increased consumption of ... Full text Link to item Cite

Pharmacologic disruption of TRPV1-expressing primary sensory neurons but not genetic deletion of TRPV1 protects mice against pancreatitis.

Journal Article Pancreas · May 2008 Featured Publication OBJECTIVES: Transient receptor potential subtype vanilloid 1 (TRPV1) is an ion channel that is primarily expressed by primary sensory neurons where it mediates pain and heat sensation and participates in neurogenic inflammation. In this study, we examined ... Full text Link to item Cite

Diacylglycerol acyltranferase 1 anti-sense oligonucleotides reduce hepatic fibrosis in mice with nonalcoholic steatohepatitis.

Journal Article Hepatology · February 2008 Featured Publication UNLABELLED: Retinyl ester (RE) stores decrease during hepatic stellate cell (HSC) activation and liver fibrosis. Although retinol esterification is mostly catalyzed by lecithin:retinol acyltransferase (LRAT), diacylglycerol acyltransferase (DGAT)1 also doe ... Full text Link to item Cite

Effectiveness of Glycerol Mono-oleate as a Biosealant.

Journal Article J Invasive Cardiol · January 2008 Featured Publication BACKGROUND: The number of femoral artery catheterizations will increase over the next decade to more than 9 million worldwide. Accordingly, a new era of access site management with vascular closure techniques utilizing biologics are being developed and imp ... Link to item Cite

Inhibiting triglyceride synthesis improves hepatic steatosis but exacerbates liver damage and fibrosis in obese mice with nonalcoholic steatohepatitis.

Journal Article Hepatology · June 2007 Featured Publication UNLABELLED: In the early stages of nonalcoholic fatty liver disease (NAFLD), triglycerides accumulate in hepatocytes. Diacylglycerol acyltransferase 2 (DGAT2) catalyzes the final step in hepatocyte triglyceride biosynthesis. DGAT2 antisense oligonucleotide ... Full text Link to item Cite

Hedgehog-mediated mesenchymal-epithelial interactions modulate hepatic response to bile duct ligation.

Journal Article Lab Invest · May 2007 Featured Publication In bile duct-ligated (BDL) rodents, as in humans with chronic cholangiopathies, biliary obstruction triggers proliferation of bile ductular cells that are surrounded by fibrosis produced by adjacent myofibroblastic cells in the hepatic mesenchyme. The prox ... Full text Link to item Cite

Bile ductules and stromal cells express hedgehog ligands and/or hedgehog target genes in primary biliary cirrhosis.

Journal Article Hepatology · May 2007 Featured Publication UNLABELLED: Indian Hedgehog (Ihh) regulates tissue morphogenesis. Hedgehog (Hh) activity has been demonstrated in human cholangiocarcinoma and hepatocellular carcinoma lines, and in myofibroblasts and progenitors from adult rodent livers. We evaluated Hh p ... Full text Link to item Cite

Aminoaciduria and altered renal expression of luminal amino acid transporters in mice lacking novel gene collectrin.

Journal Article Am J Physiol Renal Physiol · February 2007 Featured Publication Defects in renal proximal tubule transport manifest in a number of human diseases. Although variable in clinical presentation, disorders such as Hartnup disease, Dent's disease, and Fanconi syndrome are characterized by wasting of solutes commonly recovere ... Full text Link to item Cite

Evidence for epithelial-mesenchymal transitions in adult liver cells.

Journal Article Am J Physiol Gastrointest Liver Physiol · October 2006 Featured Publication Both myofibroblastic hepatic stellate cells (HSC) and hepatic epithelial progenitors accumulate in damaged livers. In some injured organs, the ability to distinguish between fibroblastic and epithelial cells is sometimes difficult because cells undergo epi ... Full text Link to item Cite

Development and cardiac contractility: cardiac troponin T isoforms and cytosolic calcium in rabbit.

Journal Article Pediatr Res · September 2006 Featured Publication Cardiac contractility depends on calcium sensitivity of the myofilaments and cytosolic free calcium concentration ([Ca(2+)](i)) during activation. During development, the cardiac troponin T isoform cTnT(1) is replaced by shorter cTnT isoforms, including cT ... Full text Link to item Cite

Interleukin-15 increases hepatic regenerative activity.

Journal Article J Hepatol · September 2006 Featured Publication BACKGROUND/AIMS: Interleukin-15 (IL-15) is expressed in many organs. It generally inhibits apoptosis and increases cellular proliferation and differentiation. However, IL-15's roles in liver are unknown. We aimed to determine if IL-15 influences hepatic in ... Full text Link to item Cite

Loss of heterozygosity of M6P/IGF2R gene is an early event in the development of prostate cancer.

Journal Article Prostate Cancer Prostatic Dis · 2006 Featured Publication BACKGROUND: The genetic events leading to initiation and/or progression of prostate cancer are not well characterized. The gene coding for the mannose 6-phosphate/insulin-like growth factor 2 receptor (M6P/IGF2R) has recently been identified as a tumor sup ... Full text Link to item Cite

Pulmonary embolization of microcrystalline cellulose in a lung transplant recipient.

Journal Article J Heart Lung Transplant · May 2005 Featured Publication Intravenous injection of drugs that contain insoluble foreign material can lead to pulmonary embolization of the material and can have devastating results, including pulmonary hypertension and death. Most cases are detected after the onset of extensive, ir ... Full text Link to item Cite

Loss of heterozygosity in the M6P/IFG2R gene is an early event in the development of prostate cancer

Conference International Journal of Radiation OncologyBiologyPhysics · September 2004 Featured Publication Full text Cite

Prognostic significance of microvascular thrombosis in donor kidney allograft biopsies.

Journal Article Transplantation · June 15, 2003 Featured Publication BACKGROUND: With a continuing demand for donor kidneys for organ transplantation, it is important to understand the significance of pathologic findings in the donor organ before transplantation. Microvascular thrombosis is sometimes encountered in associat ... Full text Link to item Cite

Hepatic veno-occlusive disease in primary humoral immunodeficiency

Conference LABORATORY INVESTIGATION · 2003 Featured Publication Cite