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Abolhasani M, Mohseni AO, Shakeri R, Khavanin A, Khajehei M, Omidi A, Geramizadeh B, Shafigh E, Naghshvar F, Fathizadeh P, Taghizadehgan L, Gharib A, Gulley ML, Dawsey SM, Malekzadeh R, Rabkin CS, Vasei M. EBV-Associated Gastric Cancer; An In Situ Hybridization Assay on Tissue Microarray: A Multi-Region Study from Four Major Provinces of Iran. Arch Iran Med 2024; 27:191-199. [PMID: 38685845 DOI: 10.34172/aim.2024.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/19/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Gastric cancer is the fourth leading cause of cancer-related deaths in the world. The identification of gastric cancer subtypes related to recognizable microbial agents may play a pivotal role in the targeted prevention and treatment of this cancer. The current study is conducted to define the frequency of Epstein-Barr virus (EBV) infection in gastric cancers of four major provinces, with different incidence rates of gastric cancers, in Iran. METHODS Paraffin blocks of 682 cases of various types of gastric cancer from Tehran, South and North areas of Iran were collected. Twelve tissue microarray (TMA) blocks were constructed from these blocks. Localization of EBV in tumors was assessed by in situ hybridization (ISH) for EBV-encoded RNA (EBER). Chi-squared test was used to evaluate the statistical significance between EBV-associated gastric cancer (EBVaGC) and clinicopathologic tumor characteristics. RESULTS Fourteen out of 682 cases (2.1%) of gastric adenocarcinoma were EBER-positive. EBER was positive in 8 out of 22 (36.4%) of medullary carcinomas and 6 out of 660 (0.9%) of non-medullary type, which was a statistically significant difference (P<0.001). The EBVaGCs were more frequent in younger age (P=0.009) and also showed a trend toward the lower stage of the tumor (P=0.075). CONCLUSION EBV-associated gastric adenocarcinoma has a low prevalence in Iran. This finding can be due to epidemiologic differences in risk factors and exposures, and the low number of gastric medullary carcinomas in the population. It may also be related to gastric tumor heterogeneity not detected with the TMA technique.
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Affiliation(s)
- Maryam Abolhasani
- Oncopathology Research Center, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Ramin Shakeri
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Khavanin
- Emergency Medicine Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mehrdad Khajehei
- Shiraz Medical School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbasali Omidi
- Department of Pathology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Bita Geramizadeh
- Department of Pathology, Transplantation Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ensieh Shafigh
- Department of Pathology, Babol University of Medical Sciences, Babol, Iran
| | - Farshad Naghshvar
- Department of Pathology, Mazandaran University of Medical Sciences, Sari, Iran
| | - Payam Fathizadeh
- Department of Pathology and Laboratory Medicine, Apadana Hospital, Ahvaz, Iran
| | | | - Atoosa Gharib
- Department of Pathology, Modarres Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Margaret L Gulley
- Department of Pathology, University of North Carolina, Chapel Hill, NC, USA
| | - Sanford M Dawsey
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Charles S Rabkin
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Mohammad Vasei
- Gene Therapy Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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Hoerres D, Dai Q, Elmore S, Sheth S, Gupta GP, Kumar S, Gulley ML. Calibration of cell-free DNA measurements by next-generation sequencing. Am J Clin Pathol 2023; 160:314-321. [PMID: 37244060 PMCID: PMC10472744 DOI: 10.1093/ajcp/aqad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/17/2023] [Indexed: 05/29/2023] Open
Abstract
OBJECTIVES Accurate monitoring of disease burden depends on accurate disease marker quantification. Although next-generation sequencing (NGS) is a promising technology for noninvasive monitoring, plasma cell-free DNA levels are often reported in misleading units that are confounded by non-disease-related factors. We proposed a novel strategy for calibrating NGS assays using spiked normalizers to improve precision and to promote standardization and harmonization of analyte concentrations. METHODS In this study, we refined our NGS protocol to calculate absolute analyte concentrations to (1) adjust for assay efficiency, as judged by recovery of spiked synthetic normalizer DNAs, and (2) calibrate NGS values against droplet digital polymerase chain reaction (ddPCR). As a model target, we chose the Epstein-Barr virus (EBV) genome. In patient (n = 12) and mock (n = 12) plasmas, NGS and 2 EBV ddPCR assays were used to report EBV load in copies per mL of plasma. RESULTS Next-generation sequencing was equally sensitive to ddPCR, with improved linearity when NGS values were normalized for spiked DNA read counts (R2 = 0.95 for normalized vs 0.91 for raw read concentrations). Linearity permitted NGS calibration to each ddPCR assay, achieving equivalent concentrations (copies/mL). CONCLUSIONS Our novel strategy for calibrating NGS assays suggests potential for a universal reference material to overcome biological and preanalytical variables hindering traditional NGS strategies for quantifying disease burden.
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Affiliation(s)
- Derek Hoerres
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Qunsheng Dai
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
| | - Sandra Elmore
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
| | - Siddharth Sheth
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
- Division of Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Sunil Kumar
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Margaret L Gulley
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
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3
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Karachaliou GS, Alkallas R, Carroll SB, Caressi C, Zakria D, Patel NM, Trembath DG, Ezzell JA, Pegna GJ, Googe PB, Galeotti JP, Ayvali F, Collichio FA, Lee CB, Ollila DW, Gulley ML, Johnson DB, Kim KB, Watson IR, Moschos SJ. The clinical significance of adenomatous polyposis coli (APC) and catenin Beta 1 (CTNNB1) genetic aberrations in patients with melanoma. BMC Cancer 2022; 22:38. [PMID: 34986841 PMCID: PMC8734243 DOI: 10.1186/s12885-021-08908-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 10/12/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Melanoma-intrinsic activated β-catenin pathway, the product of the catenin beta 1 (CTNNB1) gene, has been associated with low/absent tumor-infiltrating lymphocytes, accelerated tumor growth, metastases development, and resistance to anti-PD-L1/anti-CTLA-4 agents in mouse melanoma models. Little is known about the association between the adenomatous polyposis coli (APC) and CTNNB1 gene mutations in stage IV melanoma with immunotherapy response and overall survival (OS). METHODS We examined the prognostic significance of somatic APC/CTNNB1 mutations in the Cancer Genome Atlas Project for Skin Cutaneous Melanoma (TCGA-SKCM) database. We assessed APC/CTNNB1 mutations as predictors of response to immunotherapies in a clinicopathologically annotated metastatic patient cohort from three US melanoma centers. RESULTS In the TCGA-SKCM patient cohort (n = 434) presence of a somatic APC/CTNNB1 mutation was associated with a worse outcome only in stage IV melanoma (n = 82, median OS of APC/CTNNB1 mutants vs. wild-type was 8.15 vs. 22.8 months; log-rank hazard ratio 4.20, p = 0.011). APC/CTNNB1 mutation did not significantly affect lymphocyte distribution and density. In the 3-melanoma institution cohort, tumor tissues underwent targeted panel sequencing using two standards of care assays. We identified 55 patients with stage IV melanoma and APC/CTNNB1 genetic aberrations (mut) and 169 patients without (wt). At a median follow-up of more than 25 months for both groups, mut compared with wt patients had slightly more frequent (44% vs. 39%) and earlier (66% vs. 45% within six months from original diagnosis of stage IV melanoma) development of brain metastases. Nevertheless, time-to-development of brain metastases was not significantly different between the two groups. Fortunately, mut patients had similar clinical benefits from PD-1 inhibitor-based treatments compared to wt patients (median OS 26.1 months vs. 29.9 months, respectively, log-rank p = 0.23). Less frequent mutations in the NF1, RAC1, and PTEN genes were seen in the mut compared with wt patients from the 3-melanoma institution cohort. Analysis of brain melanoma tumor tissues from a separate craniotomy patient cohort (n = 55) showed that melanoma-specific, activated β-catenin (i.e., nuclear localization) was infrequent (n = 3, 6%) and not prognostic in established brain metastases. CONCLUSIONS APC/CTNNB1 mutations are associated with a worse outcome in stage IV melanoma and early brain metastases independent of tumor-infiltrating lymphocyte density. However, PD1 inhibitor-based treatments provide comparable benefits to both mut and wt patients with stage IV melanoma.
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Affiliation(s)
- Georgia Sofia Karachaliou
- Department of Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Rached Alkallas
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Sarah B Carroll
- Department of Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Chongshan Caressi
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Danny Zakria
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Nirali M Patel
- Department of Pathology & Laboratory Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dimitri G Trembath
- Department of Pathology & Laboratory Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Jennifer A Ezzell
- Department of Cell Biology & Physiology, Histology Research Core Facility, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Guillaume J Pegna
- Department of Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Paul B Googe
- Department of Dermatology, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan P Galeotti
- Department of Pathology & Laboratory Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Fatih Ayvali
- Department of Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Frances A Collichio
- Department of Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Carrie B Lee
- Department of Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David W Ollila
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Surgery, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Margaret L Gulley
- Department of Pathology & Laboratory Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Kevin B Kim
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Ian R Watson
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Stergios J Moschos
- Department of Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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4
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Tasoulas J, Lenze NR, Farquhar D, P Schrank T, Shen C, Shazib MA, Singer B, Patel S, Grilley Olson JE, Hayes DN, Gulley ML, Chera BS, Hackman T, Olshan AF, Weiss J, Sheth S. The addition of chemotherapy to adjuvant radiation is associated with inferior survival outcomes in intermediate-risk HPV-negative HNSCC. Cancer Med 2021; 10:3231-3239. [PMID: 33934525 PMCID: PMC8124130 DOI: 10.1002/cam4.3883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/13/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Only high-risk tumors with extranodal extension (ENE) and/or positive surgical margins (PSM) benefit from adjuvant therapy (AT) with concurrent chemoradiation (CRT) compared to radiation therapy (RT) in locally advanced head and neck squamous cell carcinoma (HNSCC). Optimal treatment for intermediate-risk tumors remains controversial. We categorized patients based on their surgical pathologic risk factors and described AT treatment patterns and associated survival outcomes. METHODS Patients were identified from CHANCE, a population-based study, and risk was classified based on surgical pathology review. High-risk patients (n = 204) required ENE and/or PSM. Intermediate-risk (n = 186) patients had pathological T3/T4 disease, perineural invasion (PNI), lymphovascular invasion (LVI), or positive lymph nodes without ENE. Low-risk patients (n = 226) had none of these features. RESULTS We identified 616 HPV-negative HNSCC patients who received primary surgical resection with neck dissection. High-risk patients receiving AT had favorable OS (HR 0.50, p = 0.013) which was significantly improved with the addition of chemotherapy compared to RT alone (HR 0.47, p = 0.021). When stratified by node status, the survival benefit of AT in high-risk patients persisted only among those who were node-positive (HR: 0.17, p < 0.0005). On the contrary, intermediate-risk patients did not benefit from AT (HR: 1.26, p = 0.380) and the addition of chemotherapy was associated with significantly worse OS compared to RT (HR: 1.76, p = 0.046). CONCLUSION In high-risk patients, adjuvant chemoradiotherapy improved OS compared to RT alone. The greatest benefit was in node-positive cases. In intermediate-risk patients, the addition of chemotherapy to RT increased mortality risk and therefore should only be used cautiously in these patients.
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Affiliation(s)
- Jason Tasoulas
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas R Lenze
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Douglas Farquhar
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Travis P Schrank
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Colette Shen
- Department of Radiation Oncology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Ali Shazib
- Division of Diagnostic Sciences, Adams School of Dentistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bart Singer
- Department of Pathology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shetal Patel
- Division of Medical Oncology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Juneko E Grilley Olson
- Division of Medical Oncology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David N Hayes
- Division of Hematology-Oncology, Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Margaret L Gulley
- Department of Pathology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bhishamjit S Chera
- Department of Radiation Oncology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Trevor Hackman
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jared Weiss
- Division of Medical Oncology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Siddharth Sheth
- Division of Medical Oncology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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5
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Aversa JG, Song M, Hu N, Goldstein AM, Hewitt SM, Gulley ML, Dawsey S, Camargo MC, Taylor PR, Rabkin CS. Low Epstein-Barr Virus Prevalence in Cardia Gastric Cancer Among a High-Incidence Chinese Population. Dig Dis Sci 2021; 66:1220-1226. [PMID: 32367248 PMCID: PMC7685001 DOI: 10.1007/s10620-020-06288-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/18/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Epstein-Barr virus (EBV) positivity is associated with better gastric cancer prognosis and is found in a relatively fixed 9% of tumors worldwide. AIM We aimed to examine the EBV status of gastric adenocarcinomas in a very high-incidence population and to compare prevalence between cardia and non-cardia anatomic subsites. METHODS We evaluated 1035 adult gastric adenocarcinoma cases presenting during 1997-2005 to the Shanxi Cancer Hospital in Taiyuan, Shanxi Province, China. EBV-encoded RNA was detected in alcohol-fixed paraffin-embedded tumor specimens by in situ hybridization. Associations were assessed in case-case comparisons using the Chi-squared test for categorical variables and the Mann-Whitney U test for continuous variables, with p values < 0.05 considered statistically significant. Adjusted odds ratios were calculated using logistic regression, and mortality hazard ratios (HRs) were estimated by Cox proportional hazards regression. RESULTS Sixty-four percent of the evaluated cancers were found in the cardia. Cardia tumor localization was associated with male sex, advanced primary tumor stage, better differentiated histology, and intestinal-type Lauren classification. Four percent of the non-cardia and only 0.9% of cardia cancers were EBV-positive. EBV positivity was associated with better overall survival (adjusted HR 0.30, 95% CI 0.14-0.63). CONCLUSIONS Our study highlights unusually low EBV prevalence in gastric adenocarcinoma among a high-incidence population, particularly for cardia cancers. These findings suggest a unique risk factor profile for the high incidence of gastric cancer in this population.
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Affiliation(s)
- John G. Aversa
- Surgical Oncology Program, Center for Cancer Research,
National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Minkyo Song
- Division of Cancer Epidemiology and Genetics, National
Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National
Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alisa M. Goldstein
- Division of Cancer Epidemiology and Genetics, National
Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen M. Hewitt
- Laboratory of Pathology, Center for Cancer Research,
National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Margaret L. Gulley
- Department of Pathology and Laboratory Medicine, University
of North Carolina, Chapel Hill, NC, USA
| | - Sanford Dawsey
- Division of Cancer Epidemiology and Genetics, National
Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - M. Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National
Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Philip R. Taylor
- Division of Cancer Epidemiology and Genetics, National
Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles S. Rabkin
- Division of Cancer Epidemiology and Genetics, National
Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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6
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Lopez EM, Tanner AM, Du E, Patel SN, Weiss J, Weissler MC, Hackman T, Gupta GP, Zevallos J, Elmore S, Betancourt R, Thorne L, Sheth S, Gulley ML. Decline in circulating viral and human tumor markers after resection of head and neck carcinoma. Head Neck 2020; 43:27-34. [PMID: 32860343 DOI: 10.1002/hed.26444] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/12/2020] [Accepted: 08/14/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND DNA sequencing panels can simultaneously quantify human and viral tumor markers in blood. We explored changes in levels of plasma tumor markers following surgical resection of head and neck carcinoma. METHODS In preresection and postresection plasmas, targeted DNA sequencing quantified variants in 28 human cancer genes and levels of oncogenic pathogens (human papillomavirus [HPV], Epstein-Barr virus [EBV], Helicobacter pylori) from 21 patients with head and neck squamous cell carcinoma. RESULTS Preresection, 11 of 21 patients (52%) had detectable tumor markers in plasma, most commonly TP53 mutation or HPV genome. Several days postresection, levels fell to undetectable in 8 of 10 evaluable patients, while two high-stage patients retained circulating tumor markers. CONCLUSIONS Modern sequencing technology can simultaneously quantify human gene variants and oncogenic viral genomes in plasma. Falling levels of cancer-specific markers upon resection can help identify viral and human markers to track at subsequent timepoints as a means to evaluate efficacy of interventions.
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Affiliation(s)
- Erin M Lopez
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - April Michelle Tanner
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Eugenie Du
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Samip N Patel
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jared Weiss
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Medicine, Oncology Division, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark C Weissler
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Trevor Hackman
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jose Zevallos
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sandra Elmore
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Renee Betancourt
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Leigh Thorne
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Siddharth Sheth
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Medicine, Oncology Division, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Margaret L Gulley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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7
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Camargo MC, Kim KM, Matsuo K, Torres J, Liao LM, Morgan D, Michel A, Waterboer T, Song M, Gulley ML, Dominguez RL, Yatabe Y, Kim S, Cortes-Martinez G, Lissowska J, Zabaleta J, Pawlita M, Rabkin CS. Circulating Antibodies against Epstein-Barr Virus (EBV) and p53 in EBV-Positive and -Negative Gastric Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:414-419. [PMID: 31719065 PMCID: PMC8272980 DOI: 10.1158/1055-9965.epi-19-0790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/01/2019] [Accepted: 11/04/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Epstein-Barr virus (EBV)-positive gastric cancers have clinicopathologic differences from EBV-negative tumors and lack TP53 mutation. Serologic profiles may inform viral contribution to carcinogenesis. METHODS We compared humoral responses of EBV-positive (n = 67) and EBV-negative (n = 137) patients with gastric cancer from the International EBV-Gastric Cancer Consortium. Serum antibodies against four EBV proteins, nuclear (EBNA), viral capsid (VCA), early-diffuse (EA-D), and Zta replication activator (ZEBRA), and to p53 were assessed by multiplex assays. OR of antibody level tertiles (T1-T3) were adjusted by logistic regression. We also conducted a meta-analysis of reported anti-p53 seropositivity in gastric cancer. RESULTS Consistent with EBV's ubiquity, 99% of patients were seropositive for anti-EBNA and 98% for anti-VCA, without difference by tumor EBV status. Seropositivity varied between patients with EBV-positive and EBV-negative tumors for anti-EA-D (97% vs. 67%, respectively, P < 0.001) and anti-ZEBRA (97% vs. 85%, respectively, P = 0.009). Adjusted ORs (vs. T1) for patients with EBV-positive versus EBV-negative tumors were significantly elevated for higher antibodies against EBNA (2.6 for T2 and 13 for T3), VCA (1.8 for T2 and 2.4 for T3), EA-D (6.0 for T2 and 44 for T3), and ZEBRA (4.6 for T2 and 12 for T3). Antibodies to p53 were inversely associated with EBV positivity (3% vs. 15%; adjusted OR = 0.16, P = 0.021). Anti-p53 prevalence from the literature was 15%. CONCLUSIONS These serologic patterns suggest viral reactivation in EBV-positive cancers and identify variation of p53 seropositivity by subtype. IMPACT Anti-EBV and anti-p53 antibodies are differentially associated with tumor EBV positivity. Serology may identify EBV-positive gastric cancer for targeted therapies.
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Affiliation(s)
- M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland.
| | - Kyoung-Mee Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center, Nagoya, Japan
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, CMN SXXI, Instituto Mexicano del Seguro Social, México City, México
| | - Linda M Liao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Douglas Morgan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, Vanderbilt University, Nashville, Tennessee
- Division of Gastroenterology and Hepatology, Department of Medicine, School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Angelika Michel
- Infections and Cancer Epidemiology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Minkyo Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Margaret L Gulley
- Department of Pathology and Laboratory Medicine and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Ricardo L Dominguez
- Department of Medicine, Western Regional Hospital, Santa Rosa de Copan, Honduras
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Sung Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Gustavo Cortes-Martinez
- Servicio de Cirugía, Hospital de Oncología, CMN SXXI, Instituto Mexicano del Seguro Social, México City, México
| | - Jolanta Lissowska
- Division of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland
| | - Jovanny Zabaleta
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Michael Pawlita
- Infections and Cancer Epidemiology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
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8
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Gasenko E, Isajevs S, Camargo MC, Offerhaus GJA, Polaka I, Gulley ML, Skapars R, Sivins A, Kojalo I, Kirsners A, Santare D, Pavlova J, Sjomina O, Liepina E, Tzivian L, Rabkin CS, Leja M. Clinicopathological characteristics of Epstein-Barr virus-positive gastric cancer in Latvia. Eur J Gastroenterol Hepatol 2019; 31:1328-1333. [PMID: 31569122 PMCID: PMC8560222 DOI: 10.1097/meg.0000000000001521] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Epstein-Barr virus (EBV)-associated gastric cancer has been proposed to be a distinct gastric cancer molecular subtype. The prognostic significance of EBV infection in gastric cancer remains unclear and needs further investigation. Our study aimed to analyze EBV-positive and EBV-negative gastric cancer patients regarding their personal and tumor-related characteristics, and compare their overall survival. METHODS Gastric cancer patients consecutively treated at the Riga East University Hospital during 2009-2016 were identified retrospectively. Tumor EBV status was determined by in-situ hybridization for EBV-encoded RNA (EBER). Information about clinicopathological characteristics was obtained from patient questionnaires, hospital records. Overall survival was ascertained through 30 July 2017. Cox proportional hazard regression models adjusted for personal and tumor-related covariates compared survival between EBV-positive and EBV-negative patients. RESULTS There were a total of 302 gastric cancer patients (61% males) with mean and SD age 63.6 ± 11.5 years. EBER positivity was present in 8.6% of tumors. EBV-positive gastric cancer patients had better survival at 80 months [adjusted hazard ratio = 0.37, 95% confidence interval (CI) = 0.19-0.72] compared to EBV-negative patients. Worse survival was observed for patients with stage III (hazard ratio = 2.76, 95% CI = 1.67-4.56) and stage IV (hazard ratio = 10.02, 95% CI = 5.72-17.57) compared to stage I gastric cancer, and overlapping and unspecified subsite (hazard ratio = 1.85; 95% CI = 1.14; 3.00) compared to distal tumors. CONCLUSION Tumor EBV positivity is a favorable prognostic factor in gastric cancer.
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Affiliation(s)
- Evita Gasenko
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
- Riga East University Hospital, Riga, Latvia
| | - Sergejs Isajevs
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
- Riga East University Hospital, Riga, Latvia
- Academic Histology Laboratory, Riga, Latvia
| | - M. Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Inese Polaka
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
- Institute of Information Technology, Riga Technical University, Riga, Latvia
| | - Margaret L. Gulley
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Roberts Skapars
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
- Riga East University Hospital, Riga, Latvia
| | - Armands Sivins
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
- Riga East University Hospital, Riga, Latvia
| | - Ilona Kojalo
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
- Riga East University Hospital, Riga, Latvia
| | - Arnis Kirsners
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
- Riga East University Hospital, Riga, Latvia
- Institute of Information Technology, Riga Technical University, Riga, Latvia
| | - Daiga Santare
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
- Riga East University Hospital, Riga, Latvia
| | - Jelizaveta Pavlova
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
| | - Olga Sjomina
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
| | - Elina Liepina
- Riga East University Hospital, Riga, Latvia
- The Centre of Disease Prevention and Control of Latvia, Riga, Latvia
| | - Liliana Tzivian
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Charles S. Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Marcis Leja
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
- Riga East University Hospital, Riga, Latvia
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9
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Dominguez RL, Cherry CB, Estevez-Ordonez D, Mera R, Escamilla V, Pawlita M, Waterboer T, Wilson KT, Peek RM, Tavera G, Williams SM, Gulley ML, Emch M, Morgan DR. Geospatial analyses identify regional hot spots of diffuse gastric cancer in rural Central America. BMC Cancer 2019; 19:545. [PMID: 31174492 PMCID: PMC6554991 DOI: 10.1186/s12885-019-5726-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 05/16/2019] [Indexed: 12/12/2022] Open
Abstract
Background Geospatial technology has facilitated the discovery of disease distributions and etiology and helped target prevention programs. Globally, gastric cancer is the leading infection-associated cancer, and third leading cause of cancer mortality worldwide, with marked geographic variation. Central and South America have a significant burden, particularly in the mountainous regions. In the context of an ongoing population-based case-control study in Central America, our aim was to examine the spatial epidemiology of gastric cancer subtypes and H. pylori virulence factors. Methods Patients diagnosed with gastric cancer from 2002 to 2013 in western Honduras were identified in the prospective gastric cancer registry at the principal district hospital. Diagnosis was based on endoscopy and confirmatory histopathology. Geospatial methods were applied using the ArcGIS v10.3.1 and SaTScan v9.4.2 platforms to examine regional distributions of the gastric cancer histologic subtypes (Lauren classification), and the H. pylori CagA virulence factor. Getis-Ord-Gi hot spot and Discrete Poisson SaTScan statistics, respectively, were used to explore spatial clustering at the village level (30–50 rural households), with standardization by each village’s population. H. pylori and CagA serologic status was determined using the novel H. pylori multiplex assay (DKFZ, Germany). Results Three hundred seventy-eight incident cases met the inclusion criteria (mean age 63.7, male 66.3%). Areas of higher gastric cancer incidence were identified. Significant spatial clustering of diffuse histology adenocarcinoma was revealed both by the Getis-Ord-GI* hot spot analysis (P-value < 0.0015; range 0.00003–0.0014; 99%CI), and by the SaTScan statistic (P-value < 0.006; range 0.0026–0.0054). The intestinal subtype was randomly distributed. H. pylori CagA had significant spatial clustering only in association with the diffuse histology cancer hot spot (Getis-Ord-Gi* P value ≤0.001; range 0.0001–0.0010; SaTScan statistic P value 0.0085). In the diffuse gastric cancer hot spot, the lowest age quartile range was 21–46 years, significantly lower than the intestinal cancers (P = 0.024). Conclusions Geospatial methods have identified a significant cluster of incident diffuse type adenocarcinoma cases in rural Central America, suggest of a germline genetic association. Further genomic and geospatial analyses to identify potential spatial patterns of genetic, bacterial, and environmental risk factors may be informative.
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Affiliation(s)
| | - Charlotte B Cherry
- Office of Public Health Informatics & Analytics, Tennessee Department of Public Health, Nashville, TN, USA
| | - Dago Estevez-Ordonez
- Vanderbilt Ingram Cancer Center (VICC), Vanderbilt University Medical Center, Nashville, USA
| | - Robertino Mera
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, USA
| | - Veronica Escamilla
- Carolina Population Center, University of North Carolina, Chapel Hill, USA
| | - Michael Pawlita
- Division of Molecular Diagnostics of Oncogenic Infections, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tim Waterboer
- Division of Molecular Diagnostics of Oncogenic Infections, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, USA
| | - Richard M Peek
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, USA
| | - Gloria Tavera
- Department of Population and Quantitative Health Sciences and Institute of Computational Biology, Case Western Reserve University, Cleveland, USA
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences and Institute of Computational Biology, Case Western Reserve University, Cleveland, USA
| | - Margaret L Gulley
- Department of Pathology, University of North Carolina, Chapel Hill, USA
| | - Michael Emch
- Department of Geography, University of North Carolina, Chapel Hill, USA
| | - Douglas R Morgan
- Vanderbilt Ingram Cancer Center (VICC), Vanderbilt University Medical Center, Nashville, USA. .,Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, USA. .,Division of Gastroenterology and Hepatology, The University of Alabama at Birmingham (UAB), 1808 7th Avenue South, BDB 373, Birmingham, AL, 35233, USA.
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10
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Camargo MC, Sivins A, Isajevs S, Folkmanis V, Rudzīte D, Gulley ML, Offerhaus GJ, Leja M, Rabkin CS. Associations of Epstein-Barr Virus-Positive Gastric Adenocarcinoma with Circulating Mediators of Inflammation and Immune Response. Cancers (Basel) 2018; 10:cancers10090284. [PMID: 30142953 PMCID: PMC6162799 DOI: 10.3390/cancers10090284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/16/2018] [Accepted: 08/20/2018] [Indexed: 12/30/2022] Open
Abstract
Epstein-Barr virus (EBV)-positive gastric adenocarcinoma exhibits locally intense inflammation but systemic manifestations are uncertain. Our study examined whether circulating mediators of inflammation and immune response differ by tumor EBV status. From a Latvian series of 302 gastric cancer cases, we measured plasma levels of 92 immune-related proteins in the 28 patients with EBV-positive tumors and 34 patients with EBV-negative tumors. Eight markers were statistically significantly higher with tumor EBV positivity: chemokine C-C motif ligand (CCL) 20 (Odds Ratio (OR) = 3.6; p-trend = 0.001), chemokine C-X-C motif ligand 9 (OR = 3.6; p-trend = 0.003), programmed death-ligand 1 (PD-L1; OR = 3.4; p-trend = 0.004), interleukin (IL)-10 (OR = 2.4; p-trend = 0.019), CCL19 (OR = 2.3; p-trend = 0.019), CCL11 (OR = 2.2; p-trend = 0.026), IL-17A (OR = 2.0; p-trend = 0.038) and CCL8 (OR = 1.9; p-trend = 0.049). Systemic responses to EBV-positive gastric cancer are characterized by alterations in chemokines and PD-L1. Profiling of these molecules may enable non-invasive diagnosis of EBV status when tumor tissue is unavailable. Our findings provide theoretical justification for clinical evaluations of immune checkpoint therapy for EBV-positive gastric cancer.
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Affiliation(s)
- M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Dr., BG 9609/6E338, Bethesda, MD 20892, USA.
| | - Armands Sivins
- Institute of Clinical and Preventive Medicine and Faculty of Medicine, University of Latvia, LV1586 Riga, Latvia.
| | - Sergejs Isajevs
- Institute of Clinical and Preventive Medicine and Faculty of Medicine, University of Latvia, LV1586 Riga, Latvia.
| | - Valdis Folkmanis
- Institute of Clinical and Preventive Medicine and Faculty of Medicine, University of Latvia, LV1586 Riga, Latvia.
| | - Dace Rudzīte
- Institute of Clinical and Preventive Medicine and Faculty of Medicine, University of Latvia, LV1586 Riga, Latvia.
| | - Margaret L Gulley
- Department of Pathology, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - G Johan Offerhaus
- Department of Pathology, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands.
| | - Marcis Leja
- Institute of Clinical and Preventive Medicine and Faculty of Medicine, University of Latvia, LV1586 Riga, Latvia.
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Dr., BG 9609/6E338, Bethesda, MD 20892, USA.
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11
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Montgomery ND, Parker JS, Eberhard DA, Patel NM, Weck KE, Sharpless NE, Hu Z, Hayes DN, Gulley ML. Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next-generation Sequencing. Appl Immunohistochem Mol Morphol 2017; 24:490-5. [PMID: 26371432 DOI: 10.1097/pai.0000000000000215] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Human papillomaviruses (HPV) are oncogenic DNA viruses implicated in squamous cell carcinomas of several anatomic sites, as well as endocervical adenocarcinomas. Identification of HPV is an actionable finding in some carcinomas, potentially influencing tumor classification, prognosis, and management. We incorporated capture probes for oncogenic HPV strains 16 and 18 into a broader next-generation sequencing (NGS) panel designed to identify actionable mutations in solid malignancies. A total of 21 head and neck, genitourinary, and gynecologic squamous cell carcinomas and endocervical adenocarcinomas were sequenced as part of the UNCSeq project. Using p16 immunohistochemical results as the gold standard, we set a cutoff for proportion of aligned HPV reads that maximized performance of our NGS assay (92% sensitive, 100% specific for HPV). These results suggest that sequencing of oncogenic pathogens can be incorporated into targeted NGS panels, extending the clinical utility of genomic assays.
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Affiliation(s)
- Nathan D Montgomery
- *Department of Pathology and Laboratory Medicine †Lineberger Comprehensive Cancer Center ‡Department of Medicine, Division of Medical Oncology, The University of North Carolina, Chapel Hill, NC
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12
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Leal SM, Gulley ML. Current and Emerging Molecular Tests for Human Papillomavirus-Related Neoplasia in the Genomic Era. J Mol Diagn 2017; 19:366-377. [PMID: 28325688 DOI: 10.1016/j.jmoldx.2017.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/30/2017] [Indexed: 12/14/2022] Open
Abstract
Laboratory tests have a key role in preventing human papillomavirus (HPV)-driven carcinomas and in guiding therapeutic interventions. An understanding of the virology, immunology, and carcinogenesis of HPV is essential for choosing appropriate diagnostic test modalities and developing new and even more effective cancer prevention strategies. HPV infects basal epithelial cells on multiple surfaces and induces carcinoma primarily in the cervix and the oropharynx. HPV types are stratified as high risk or low risk based on their carcinogenic potential. During oncogenesis, HPV interferes with cell cycle regulation and incites DNA damage responses that thwart apoptosis and enable mutations to accumulate. Such mutations are an adverse effect of innate and adaptive antiviral immune responses that up-regulate DNA-editing enzymes, with natural selection of cells having a chromosomally integrated viral genome lacking expression of viral proteins targeted by the immune system. Infected cancers share a similar mutation signature, reflecting the effect of apolipoprotein B mRNA-editing catalytic polypeptide enzyme DNA-editing enzymes. It is feasible that genomic tests for characteristic mutations or methylation signatures, along with tests for dysregulated HPV gene expression, add value in predicting behavior of premalignant lesions. Furthermore, these tumor markers in cell-free DNA of plasma or body fluids may one day assist in early detection or monitoring cancer burden during treatment.
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Affiliation(s)
- Sixto M Leal
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Margaret L Gulley
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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13
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Treece AL, Gulley ML, Vasalos P, Paquette C, Lindeman NI, Jennings LJ, Bartley AN. Reporting Results of Molecular Tests: A Retrospective Examination of BRAF Mutation Reporting. Arch Pathol Lab Med 2017; 141:658-665. [PMID: 28447902 DOI: 10.5858/arpa.2016-0280-cp] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - With enormous growth in the field of molecular pathology, the reporting of results gleaned from this testing is essential to guide patient care. OBJECTIVE - To examine molecular reports from laboratories participating in proficiency testing for required elements to convey molecular laboratory test results to clinicians and patients. DESIGN - Molecular laboratories participating in the College of American Pathologists (CAP) proficiency testing program for BRAF mutation analysis were solicited to submit examples of final reports from 2 separate proficiency testing reporting cycles. Reports were reviewed for the presence or absence of relevant components. RESULTS - A total of 107 evaluable reports were received (57 demonstrating a positive result for the BRAF V600E mutation and 50 negative). Methods for BRAF testing varied, with 95% (102 of 107) of reports adequately describing their assay methods and 87% (93 of 107) of reports adequately describing the target(s) of their assays. Information on the analytic sensitivity of the assay was present in 74% (79 of 107) of reports and 83% (89 of 107) reported at least 1 assay limitation, though only 34% (36 of 107) reported on variants not detected by their assays. Analytic and clinical interpretive comments were included in 99% (106 of 107) and 90% (96 of 107) of reports, respectively. Of participants that perform a laboratory-developed test, 88% (88 of 100) included language addressing the development of the assay. CONCLUSIONS - Laboratories participating in BRAF proficiency testing through the CAP are including most of the required reporting elements to unambiguously convey molecular results. Laboratories should continue to strive to report these results in a concise and comprehensive manner.
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Affiliation(s)
| | | | | | | | | | | | - Angela N Bartley
- From the Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora (Dr Treece); the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Gulley); College of American Pathologists, Northfield, Illinois (Ms Vasalos); the Department of Pathology, Warren Alpert Medical School of Brown University, Providence, Rhode Island (Dr Paquette); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Lindeman); the Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois (Dr Jennings); and the Department of Pathology and Laboratory Medicine, St. Joseph Mercy Hospital, Ann Arbor, Michigan (Dr Bartley)
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14
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Glaser SL, Canchola AJ, Keegan THM, Clarke CA, Longacre TA, Gulley ML. Variation in risk and outcomes of Epstein-Barr virus-associated breast cancer by epidemiologic characteristics and virus detection strategies: an exploratory study. Cancer Causes Control 2017; 28:273-287. [PMID: 28229344 DOI: 10.1007/s10552-017-0865-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/03/2017] [Indexed: 02/04/2023]
Abstract
PURPOSE A relationship of Epstein-Barr virus (EBV) and breast cancer etiology and outcome may have clinical utility and potential to enhance understanding of tumor biology. Research to date has yielded variable results, likely reflecting differing virus detection assays and unaddressed epidemiologic heterogeneity across studies. METHODS Applying our novel, five-target assay detection strategy in an exploratory study, we examined demographic, clinical, and tumor characteristics, and overall survival, associated with EBV positivity in breast adenocarcinomas from 59 non-Hispanic white and 68 Hispanic women sampled by age (<50, 50+) and stage (localized, regional/remote) and examined associations based on single assay targets. RESULTS EBV was localized only to lymphocytes. Nevertheless, viral prevalence, although low, varied across patient subgroups. Adjusted odds ratios (OR) for EBV positivity were lower for younger Hispanic than white women (p interaction = 0.05), and marginally higher for larger [OR (95% confidence intervals) 1.03 (1.00-1.05) per mm increase] and right-sided [2.8 (0.97-7.8)] tumors. In whites, ORs were marginally higher for larger tumors [1.04 (1.00-1.07)] and marginally lower for age 50+ [0.24 (0.06-1.03)]; in Hispanics, ORs were higher for ER negative [5.6 (1.1-30.5)], and marginally higher for right-sided, tumors [5.8 (0.94-36.2)]. Survival was suggestively poorer for EBV-positive than EBV-negative tumors in older women with localized disease. EBV associations differed across single assay targets, indicating variation in prior findings likely due to assay performance. CONCLUSIONS The differing EBV associations by age and race/ethnicity suggest a non-random role of EBV in breast cancer and support further study using multi-target assays, relevant epidemiologic design, and a larger study sample.
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Affiliation(s)
- Sally L Glaser
- Cancer Prevention Institute of California, 2201 Walnut Avenue, Suite 300, Fremont, CA, 94538, USA. .,Department of Health Research and Policy (Epidemiology), Stanford Medicine, Stanford, CA, 94306, USA.
| | - Alison J Canchola
- Cancer Prevention Institute of California, 2201 Walnut Avenue, Suite 300, Fremont, CA, 94538, USA
| | - Theresa H M Keegan
- Cancer Prevention Institute of California, 2201 Walnut Avenue, Suite 300, Fremont, CA, 94538, USA.,Division of Hematology and Oncology, Department of Internal Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, CA, 95817, USA
| | - Christina A Clarke
- Cancer Prevention Institute of California, 2201 Walnut Avenue, Suite 300, Fremont, CA, 94538, USA.,Department of Health Research and Policy (Epidemiology), Stanford Medicine, Stanford, CA, 94306, USA
| | - Teri A Longacre
- Department of Pathology, Stanford Medicine, Stanford, CA, 94305, USA
| | - Margaret L Gulley
- Department of Pathology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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15
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Bartley AN, Washington MK, Colasacco C, Ventura CB, Ismaila N, Benson AB, Carrato A, Gulley ML, Jain D, Kakar S, Mackay HJ, Streutker C, Tang L, Troxell M, Ajani JA. HER2 Testing and Clinical Decision Making in Gastroesophageal Adenocarcinoma: Guideline From the College of American Pathologists, American Society for Clinical Pathology, and the American Society of Clinical Oncology. J Clin Oncol 2017; 35:446-464. [PMID: 28129524 DOI: 10.1200/jco.2016.69.4836] [Citation(s) in RCA: 232] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Context ERBB2 (erb-b2 receptor tyrosine kinase 2 or HER2) is currently the only biomarker established for selection of a specific therapy for patients with advanced gastroesophageal adenocarcinoma (GEA). However, there are no comprehensive guidelines for the assessment of HER2 in patients with GEA. Objectives To establish an evidence-based guideline for HER2 testing in patients with GEA, formalize the algorithms for methods to improve the accuracy of HER2 testing while addressing which patients and tumor specimens are appropriate, and to provide guidance on clinical decision making. Design The College of American Pathologists (CAP), American Society for Clinical Pathology (ASCP), and the American Society of Clinical Oncology (ASCO) convened an Expert Panel to conduct a systematic review of the literature to develop an evidence-based guideline with recommendations for optimal HER2 testing in patients with GEA. Results The Panel is proposing 11 recommendations with strong agreement from the open comment participants. Recommendations The Panel recommends that tumor specimen(s) from all patients with advanced GEA, who are candidates for HER2-targeted therapy, should be assessed for HER2 status before the initiation of HER2-targeted therapy. Clinicians should offer combination chemotherapy and an HER2-targeted agent as initial therapy for all patients with HER2-positive advanced GEA. For pathologists, guidance is provided for morphologic selection of neoplastic tissue, testing algorithms, scoring methods, interpretation and reporting of results, and laboratory quality assurance. Conclusion This guideline provides specific recommendations for assessment of HER2 in patients with advanced GEA while addressing pertinent technical issues and clinical implications of the results.
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Affiliation(s)
- Angela N Bartley
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Mary Kay Washington
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Carol Colasacco
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Christina B Ventura
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nofisat Ismaila
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Al B Benson
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alfredo Carrato
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Margaret L Gulley
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Dhanpat Jain
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sanjay Kakar
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Helen J Mackay
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Catherine Streutker
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Laura Tang
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Megan Troxell
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jaffer A Ajani
- Angela N. Bartley, St Joseph Mercy Hospital, Ann Arbor, MI; Mary Kay Washington, Vanderbilt University Medical Center, Nashville, TN; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield; Al B. Benson III, Northwestern University, Chicago, IL; Nofisat Ismaila, American Society of Clinical Oncology, Alexandria, VA; Alfredo Carrato, Ramón y Cajal University Hospital, Madrid, Spain; Margaret L. Gulley, University of North Carolina, Chapel Hill, NC; Dhanpat Jain, Yale University School of Medicine, New Haven, CT; Sanjay Kakar, University of California, San Francisco, CA; Helen J. Mackay, Princess Margaret Cancer Centre; Catherine Streutker, St Michael's Hospital, University of Toronto, Toronto, Canada; Laura Tang, Memorial Sloan Kettering Cancer Center, New York, NY; Megan Troxell, Stanford University Medical Center, Stanford, CA; and Jaffer A. Ajani, The University of Texas MD Anderson Cancer Center, Houston, TX
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Bartley AN, Washington MK, Ventura CB, Ismaila N, Colasacco C, Benson AB, Carrato A, Gulley ML, Jain D, Kakar S, Mackay HJ, Streutker C, Tang L, Troxell M, Ajani JA. HER2 Testing and Clinical Decision Making in Gastroesophageal Adenocarcinoma: Guideline From the College of American Pathologists, American Society for Clinical Pathology, and American Society of Clinical Oncology. Arch Pathol Lab Med 2016; 140:1345-1363. [PMID: 27841667 DOI: 10.5858/arpa.2016-0331-cp] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - ERBB2 (erb-b2 receptor tyrosine kinase 2 or HER2) is currently the only biomarker established for selection of a specific therapy for patients with advanced gastroesophageal adenocarcinoma (GEA). However, there are no comprehensive guidelines for the assessment of HER2 in patients with GEA. OBJECTIVES - To establish an evidence-based guideline for HER2 testing in patients with GEA, to formalize the algorithms for methods to improve the accuracy of HER2 testing while addressing which patients and tumor specimens are appropriate, and to provide guidance on clinical decision making. DESIGN - The College of American Pathologists, American Society for Clinical Pathology, and American Society of Clinical Oncology convened an expert panel to conduct a systematic review of the literature to develop an evidence-based guideline with recommendations for optimal HER2 testing in patients with GEA. RESULTS - The panel is proposing 11 recommendations with strong agreement from the open-comment participants. RECOMMENDATIONS - The panel recommends that tumor specimen(s) from all patients with advanced GEA, who are candidates for HER2-targeted therapy, should be assessed for HER2 status before the initiation of HER2-targeted therapy. Clinicians should offer combination chemotherapy and a HER2-targeted agent as initial therapy for all patients with HER2-positive advanced GEA. For pathologists, guidance is provided for morphologic selection of neoplastic tissue, testing algorithms, scoring methods, interpretation and reporting of results, and laboratory quality assurance. CONCLUSIONS - This guideline provides specific recommendations for assessment of HER2 in patients with advanced GEA while addressing pertinent technical issues and clinical implications of the results.
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Affiliation(s)
- Angela N Bartley
- From the Department of Pathology, St. Joseph Mercy Hospital, Ann Arbor, Michigan (Dr Bartley); the Department of Pathology, Vanderbilt University Medical Center, Nashville, Tennessee (Dr Washington); Surveys (Ms Ventura) and Governance (Ms Colasacco), College of American Pathologists, Northfield, Illinois; Quality and Guidelines Department, American Society of Clinical Oncology, Alexandria, Virginia (Dr Ismaila); the Division of Hematology/Oncology, Northwestern University, Chicago, Illinois (Dr Benson); Medical Oncology Department, Ramon y Cajal University Hospital, Madrid, Spain (Dr Carrato); the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Gulley); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Jain); the Department of Pathology and Laboratory Medicine, UCSF, San Francisco, California (Dr Kakar); the Division of Medical Oncology and Hematology, University of Toronto/Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada (Dr Mackay); the Department of Laboratory Medicine, St. Michael's Hospital, Toronto, Ontario, Canada (Dr Streutker); the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York (Dr Tang); the Department of Pathology, Stanford University Medical Center, Stanford, California (Dr Troxell); and the Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston (Dr Ajani)
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Bartley AN, Washington MK, Ventura CB, Ismaila N, Colasacco C, Benson AB, Carrato A, Gulley ML, Jain D, Kakar S, Mackay HJ, Streutker C, Tang L, Troxell M, Ajani JA. HER2 Testing and Clinical Decision Making in Gastroesophageal Adenocarcinoma: Guideline From the College of American Pathologists, American Society for Clinical Pathology, and American Society of Clinical Oncology. Am J Clin Pathol 2016; 146:647-669. [PMID: 28077399 PMCID: PMC6272805 DOI: 10.1093/ajcp/aqw206] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
CONTEXT ERBB2 (erb-b2 receptor tyrosine kinase 2 or HER2) is currently the only biomarker established for selection of a specific therapy for patients with advanced gastroesophageal adenocarcinoma (GEA). However, there are no comprehensive guidelines for the assessment of HER2 in patients with GEA. OBJECTIVES To establish an evidence-based guideline for HER2 testing in patients with GEA, to formalize the algorithms for methods to improve the accuracy of HER2 testing while addressing which patients and tumor specimens are appropriate, and to provide guidance on clinical decision making. DESIGN The College of American Pathologists, American Society for Clinical Pathology, and American Society of Clinical Oncology convened an expert panel to conduct a systematic review of the literature to develop an evidence-based guideline with recommendations for optimal HER2 testing in patients with GEA. RESULTS The panel is proposing 11 recommendations with strong agreement from the open-comment participants. RECOMMENDATIONS The panel recommends that tumor specimen(s) from all patients with advanced GEA, who are candidates for HER2-targeted therapy, should be assessed for HER2 status before the initiation of HER2-targeted therapy. Clinicians should offer combination chemotherapy and a HER2-targeted agent as initial therapy for all patients with HER2-positive advanced GEA. For pathologists, guidance is provided for morphologic selection of neoplastic tissue, testing algorithms, scoring methods, interpretation and reporting of results, and laboratory quality assurance. CONCLUSIONS This guideline provides specific recommendations for assessment of HER2 in patients with advanced GEA while addressing pertinent technical issues and clinical implications of the results.
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Affiliation(s)
- Angela N Bartley
- From the Department of Pathology, St Joseph Mercy Hospital, Ann Arbor, MI
| | - Mary Kay Washington
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN
| | | | - Nofisat Ismaila
- Quality and Guidelines Department, American Society of Clinical Oncology, Alexandria, VA
| | - Carol Colasacco
- Surveys and Governance, College of American Pathologists, Northfield, IL
| | - Al B Benson
- Division of Hematology/Oncology, Northwestern University, Chicago, IL
| | - Alfredo Carrato
- Medical Oncology Department, Ramon y Cajal University Hospital, Madrid, Spain
| | - Margaret L Gulley
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill
| | - Dhanpat Jain
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | - Sanjay Kakar
- Department of Pathology and Laboratory Medicine, UCSF, San Francisco, CA
| | - Helen J Mackay
- Division of Medical Oncology and Hematology, University of Toronto/Sunnybrook Odette Cancer Centre, Toronto, Canada
| | | | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Megan Troxell
- Department of Pathology, Stanford University Medical Center, Stanford, CA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
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Affiliation(s)
- Brandi N Reeves
- Division of Hematology/Oncology, University of North Carolina, Chapel Hill
| | - Margaret L Gulley
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill
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Montgomery ND, Coward WB, Johnson S, Yuan J, Gulley ML, Mathews SP, Kaiser-Rogers K, Rao KW, Sanger WG, Sanmann JN, Fedoriw Y. Karyotypic abnormalities associated with Epstein–Barr virus status in classical Hodgkin lymphoma. Cancer Genet 2016; 209:408-416. [DOI: 10.1016/j.cancergen.2016.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 12/31/2022]
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Abstract
We report a case of a lymphoepitheliomalike carcinoma arising in the gallbladder of a 60-year-old woman. The gallbladder wall was completely replaced with a tumor that extended into the adjacent liver parenchyma.The tumor was histologically and immunophenotypically indistinguishable from lymphoepithelioma of the nasopharynx, which is an undifferentiated malignant epithelial neoplasm that is histologically distinctive owing to a prominent reactive lymphoid infiltrate. It is believed that the Epstein-Barr virus may play a role in the pathogenesis of nasopharyngeal lymphoepitheliomas; however, our case in the gallbladder was not associated with of Epstein-Barr virus DNA. To the best of our knowledge, this is the first published case of a lymphoepitheliomalike carcinoma of the gallbladder. Int J Surg Pathol 4(3):00-00, 1997
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Affiliation(s)
- David L. Todd
- Departments of Pathology, The University of Texas M. D. Anderson Cancer Center, Houston
| | - Jae Y. Ro
- Departments of Pathology, The University of Texas M. D. Anderson Cancer Center, Houston
| | - Margaret L. Gulley
- the University of Texas Health Science Center at San Antonio and Audie Murphy Memorial Veteran's Hospital, San Antonio, Texas
| | - Alberto G. Ayala
- Departments of Pathology, The University of Texas M. D. Anderson Cancer Center, Houston
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Treece AL, Duncan DL, Tang W, Elmore S, Morgan DR, Meyers MO, Dominguez RL, Speck O, Gulley ML. Gastric adenocarcinoma microRNA profiles in fixed tissue and in plasma reveal cancer-associated and Epstein-Barr virus-related expression patterns. J Transl Med 2016; 96:661-71. [PMID: 26950485 PMCID: PMC5767475 DOI: 10.1038/labinvest.2016.33] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 12/09/2015] [Accepted: 01/12/2016] [Indexed: 12/27/2022] Open
Abstract
MicroRNA expression in formalin-fixed paraffin-embedded tissue (FFPE) or plasma may add value for cancer management. The GastroGenus miR Panel was developed to measure 55 cancer-specific human microRNAs, Epstein-Barr virus (EBV)-encoded microRNAs, and controls. This Q-rtPCR panel was applied to 100 FFPEs enriched for adenocarcinoma or adjacent non-malignant mucosa, and to plasma of 31 patients. In FFPE, microRNAs upregulated in malignant versus adjacent benign gastric mucosa were hsa-miR-21, -155, -196a, -196b, -185, and -let-7i. Hsa-miR-18a, 34a, 187, -200a, -423-3p, -484, and -744 were downregulated. Plasma of cancer versus non-cancer controls had upregulated hsa-miR-23a, -103, and -221 and downregulated hsa-miR-378, -346, -486-5p, -200b, -196a, -141, and -484. EBV-infected versus uninfected cancers expressed multiple EBV-encoded microRNAs, and concomitant dysregulation of four human microRNAs suggests that viral infection may alter cellular biochemical pathways. Human microRNAs were dysregulated between malignant and benign gastric mucosa and between plasma of cancer patients and non-cancer controls. Strong association of EBV microRNA expression with known EBV status underscores the ability of microRNA technology to reflect disease biology. Expression of viral microRNAs in concert with unique human microRNAs provides novel insights into viral oncogenesis and reinforces the potential for microRNA profiles to aid in classifying gastric cancer subtypes. Pilot studies of plasma suggest the potential for a noninvasive addition to cancer diagnostics.
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Affiliation(s)
- Amanda L Treece
- Pathology and Laboratory Medicine,University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Daniel L Duncan
- Pathology and Laboratory Medicine,University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Weihua Tang
- Pathology and Laboratory Medicine,University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sandra Elmore
- Pathology and Laboratory Medicine,University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Douglas R Morgan
- Lineberger Comprehensive Cancer Center,Gastroenterology,Vanderbilt University, Nashville, TN,University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Michael O Meyers
- Lineberger Comprehensive Cancer Center,Surgical Oncology,University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Olga Speck
- Pathology and Laboratory Medicine,University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Margaret L Gulley
- Pathology and Laboratory Medicine,Lineberger Comprehensive Cancer Center,University of North Carolina at Chapel Hill, Chapel Hill, NC
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22
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Treece AL, Montgomery ND, Patel NM, Civalier CJ, Dodd LG, Gulley ML, Booker JK, Weck KE. FNA smears as a potential source of DNA for targeted next-generation sequencing of lung adenocarcinomas. Cancer Cytopathol 2016; 124:406-14. [PMID: 26882436 DOI: 10.1002/cncy.21699] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/04/2016] [Accepted: 01/04/2016] [Indexed: 11/12/2022]
Abstract
BACKGROUND Diff-Quik-stained fine-needle aspiration (FNA) smears and touch preparations from biopsies represent alternative specimens for molecular testing when cell block or biopsy material is insufficient. This study describes the use of these samples for targeted next-generation sequencing (NGS) of primary and metastatic lung adenocarcinoma and reports the DNA quality and success rates of FNA smears versus other specimens from 1 year of clinical use. METHODS A validation set of 10 slides from 9 patients with prior clinical epidermal growth factor receptor (EGFR) Sanger sequencing and KRAS pyrosequencing (5 KRAS-positive/EGFR-negative and 4 KRAS-negative/EGFR-negative) underwent DNA extraction, quality assessment, and targeted NGS. Subsequently, lung adenocarcinoma specimens submitted for NGS solid tumor mutation panel testing in 1 calendar year (60 biopsies, 57 resections, 33 FNA cell blocks, 12 FNA smears, and 10 body fluid cell blocks) were reviewed for specimen adequacy, sequencing success, and DNA quality. RESULTS All 10 validation samples met the DNA quality threshold (delta Ct threshold < 8; range, -2.2 to 4.9) and yielded 0.5 to 22 μg of DNA. The KRAS and EGFR mutation status from FNA smears according to NGS was concordant with previous clinical testing for all 10 samples. In the 1-year review, FNA smears were 100% successful, and this suggested a performance equivalent to or better than the performance of established specimen types, including FNA cell blocks. DNA quality according to ΔCt was significantly better with FNA smears versus biopsies, resections, and FNA cell blocks. CONCLUSIONS FNA smears of lung adenocarcinomas are high-quality alternative specimens for a targeted NGS panel with a high success rate in clinical practice. Cancer Cytopathol 2016;124:406-14. © 2016 American Cancer Society.
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Affiliation(s)
- Amanda L Treece
- Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, Colorado
| | - Nathan D Montgomery
- Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Nirali M Patel
- Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Chris J Civalier
- Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Leslie G Dodd
- Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Margaret L Gulley
- Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jessica K Booker
- Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Karen E Weck
- Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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Camargo MC, Bowlby R, Chu A, Pedamallu CS, Thorsson V, Elmore S, Mungall A, Bass A, Gulley ML, Rabkin CS. Abstract 4621: Validation and calibration of next-generation sequencing to identify Epstein-Barr Virus-positive gastric cancer. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-4621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Gastric adenocarcinoma was recently classified by a large genomic study into four molecular subtypes, including one defined by Epstein-Barr virus (EBV)-positivity. EBV infection in tumors is conventionally assessed by in situ hybridization (ISH), but detection of viral nucleic acids by next-generation sequencing represents a potential alternative.
Methods: Normalized EBV read counts were determined by whole genome, whole exome, mRNA and miRNA sequencing for 295 fresh-frozen gastric tumor samples. Formalin-fixed, paraffin-embedded tissue sections were retrieved for ISH confirmation of 13 high-EBV and 11 low-EBV cases selected at random.
Results: By each sequencing method, numbers of EBV reads were bimodally distributed across tumors, with a minority having much higher counts. In pairwise comparisons, individual samples were either consistently high or consistently low by all genomic methods for which data were available. Empiric cut-offs based on molecular data of 1000 normalized reads for whole genome, 100 for exome, 4 for mRNA and 5000 for miRNA had perfect concordance identifying 26 (9%) tumors as EBV-positive. One sample tested by ISH lacked tumor cells. For the 23 tumors with EBV status determined by both approaches, EBV-positivity or -negativity by molecular testing was confirmed by EBER-ISH in all but one case (kappa = 0.91). The exception was a microsatellite instability-type cancer EBV-negative by both mRNA and miRNA sequencing, with equivocally positive ISH interpretation.
Conclusions: EBV-positive gastric tumors may be accurately identified by quantifying viral sequences in genomic data. Simultaneous analyses of human and viral DNA, mRNA and miRNA could streamline tumor profiling for clinical care and research.
Citation Format: M. Constanza Camargo, Reanne Bowlby, Andy Chu, Chandra S. Pedamallu, Vesteinn Thorsson, Sandra Elmore, Andrew Mungall, Adam Bass, Margaret L. Gulley, Charles S. Rabkin. Validation and calibration of next-generation sequencing to identify Epstein-Barr Virus-positive gastric cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4621. doi:10.1158/1538-7445.AM2015-4621
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Affiliation(s)
| | - Reanne Bowlby
- 2BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andy Chu
- 2BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | | | | | - Adam Bass
- 6Dana-Farber Cancer Inst., Boston, MA
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Ma SD, Xu X, Plowshay J, Ranheim EA, Burlingham WJ, Jensen JL, Asimakopoulos F, Tang W, Gulley ML, Cesarman E, Gumperz JE, Kenney SC. LMP1-deficient Epstein-Barr virus mutant requires T cells for lymphomagenesis. J Clin Invest 2014; 125:304-15. [PMID: 25485679 DOI: 10.1172/jci76357] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 10/31/2014] [Indexed: 12/15/2022] Open
Abstract
Epstein-Barr virus (EBV) infection transforms B cells in vitro and is associated with human B cell lymphomas. The major EBV oncoprotein, latent membrane protein 1 (LMP1), mimics constitutively active CD40 and is essential for outgrowth of EBV-transformed B cells in vitro; however, EBV-positive diffuse large B cell lymphomas and Burkitt lymphomas often express little or no LMP1. Thus, EBV may contribute to the development and maintenance of human lymphomas even in the absence of LMP1. Here, we found that i.p. injection of human cord blood mononuclear cells infected with a LMP1-deficient EBV into immunodeficient mice induces B cell lymphomas. In this model, lymphoma development required the presence of CD4+ T cells in cord blood and was inhibited by CD40-blocking Abs. In contrast, LMP1-deficient EBV established persistent latency but did not induce lymphomas when directly injected into mice engrafted with human fetal CD34+ cells and human thymus. WT EBV induced lymphomas in both mouse models and did not require coinjected T cells in the cord blood model. Together, these results demonstrate that LMP1 is not essential for EBV-induced lymphomas in vivo and suggest that T cells supply signals that substitute for LMP1 in EBV-positive B cell lymphomagenesis.
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Prat A, Lluch A, Albanell J, Barry WT, Fan C, Chacón JI, Parker JS, Calvo L, Plazaola A, Arcusa A, Seguí-Palmer MA, Burgues O, Ribelles N, Rodriguez-Lescure A, Guerrero A, Ruiz-Borrego M, Munarriz B, López JA, Adamo B, Cheang MCU, Li Y, Hu Z, Gulley ML, Vidal MJ, Pitcher BN, Liu MC, Citron ML, Ellis MJ, Mardis E, Vickery T, Hudis CA, Winer EP, Carey LA, Caballero R, Carrasco E, Martín M, Perou CM, Alba E. Predicting response and survival in chemotherapy-treated triple-negative breast cancer. Br J Cancer 2014; 111:1532-41. [PMID: 25101563 PMCID: PMC4200088 DOI: 10.1038/bjc.2014.444] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 06/26/2014] [Accepted: 07/13/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In this study, we evaluated the ability of gene expression profiles to predict chemotherapy response and survival in triple-negative breast cancer (TNBC). METHODS Gene expression and clinical-pathological data were evaluated in five independent cohorts, including three randomised clinical trials for a total of 1055 patients with TNBC, basal-like disease (BLBC) or both. Previously defined intrinsic molecular subtype and a proliferation signature were determined and tested. Each signature was tested using multivariable logistic regression models (for pCR (pathological complete response)) and Cox models (for survival). Within TNBC, interactions between each signature and the basal-like subtype (vs other subtypes) for predicting either pCR or survival were investigated. RESULTS Within TNBC, all intrinsic subtypes were identified but BLBC predominated (55-81%). Significant associations between genomic signatures and response and survival after chemotherapy were only identified within BLBC and not within TNBC as a whole. In particular, high expression of a previously identified proliferation signature, or low expression of the luminal A signature, was found independently associated with pCR and improved survival following chemotherapy across different cohorts. Significant interaction tests were only obtained between each signature and the BLBC subtype for prediction of chemotherapy response or survival. CONCLUSIONS The proliferation signature predicts response and improved survival after chemotherapy, but only within BLBC. This highlights the clinical implications of TNBC heterogeneity, and suggests that future clinical trials focused on this phenotypic subtype should consider stratifying patients as having BLBC or not.
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Affiliation(s)
- A Prat
- Translational Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Pg Vall d'Hebron, 119-129, 08035 Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - A Lluch
- Department of Medical Oncology and Department of Pathology, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
| | - J Albanell
- Department of Medical Oncology, Hospital del Mar, IMIM, 08003 Barcelona, Spain
- Department of Medical Oncology, Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - W T Barry
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - C Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27519, USA
| | - J I Chacón
- Department of Medical Oncology, Hospital Virgen de la Salud, 45004 Toledo, Spain
| | - J S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27519, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27519, USA
| | - L Calvo
- Department of Medical Oncology, Complexo Hospitalario Universitario de A Coruña, 15002 A Coruña, Spain
| | - A Plazaola
- Department of Medical Oncology, Onkologikoa, 20014 San Sebastián, Spain
| | - A Arcusa
- Department of Medical Oncology, Consorci Sanitari de Terrassa, 08225 Barcelona, Spain
| | - M A Seguí-Palmer
- Department of Medical Oncology, Corporació Sanitària Parc Taulí, 08208 Sabadell, Spain
| | - O Burgues
- Department of Medical Oncology and Department of Pathology, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
| | - N Ribelles
- Department of Medical Oncology and Department of Pathology, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - A Rodriguez-Lescure
- Department of Medical Oncology, Hospital General de Elche, 03203 Alicante, Spain
| | - A Guerrero
- Department of Medical Oncology, Instituto Valenciano de Oncología (IVO), 46009 Valencia, Spain
| | - M Ruiz-Borrego
- Department of Medical Oncology, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - B Munarriz
- Department of Medical Oncology, Hospital Universitario La Fe, 46026 Valencia, Spain
| | - J A López
- Department of Medical Oncology, Hospital San Camilo, 28006 Madrid, Spain
| | - B Adamo
- Translational Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Pg Vall d'Hebron, 119-129, 08035 Barcelona, Spain
| | - M C U Cheang
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27519, USA
| | - Y Li
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27519, USA
| | - Z Hu
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27519, USA
| | - M L Gulley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27519, USA
| | - M J Vidal
- Translational Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Pg Vall d'Hebron, 119-129, 08035 Barcelona, Spain
| | - B N Pitcher
- Alliance Statistical and Data Center, Duke University, Durham, NC 27708, USA
| | - M C Liu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - M L Citron
- ProHEALTH Care Associates, LLP, Lake Success, NY 11803, USA
| | - M J Ellis
- Department of Oncology, Washington University, St. Louis, MO 63130, USA
| | - E Mardis
- Department of Oncology, Washington University, St. Louis, MO 63130, USA
| | - T Vickery
- Department of Oncology, Washington University, St. Louis, MO 63130, USA
| | - C A Hudis
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - E P Winer
- Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - L A Carey
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27519, USA
| | - R Caballero
- GEICAM (Spanish Breast Cancer Research Group), 28700 Madrid, Spain
| | - E Carrasco
- GEICAM (Spanish Breast Cancer Research Group), 28700 Madrid, Spain
| | - M Martín
- GEICAM (Spanish Breast Cancer Research Group), 28700 Madrid, Spain
- Department of Medical Oncology, Instituto de Investigación Sanitaria Hospital Universitario Gregorio Marañón, Facultad de Medicina, Universidad Complutense, 28007 Madrid, Spain
| | - C M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27519, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27519, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27519, USA
| | - E Alba
- Department of Medical Oncology and Department of Pathology, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
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Gulley ML, Morgan DR. Molecular oncology testing in resource-limited settings. J Mol Diagn 2014; 16:601-11. [PMID: 25242061 DOI: 10.1016/j.jmoldx.2014.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/15/2014] [Accepted: 07/22/2014] [Indexed: 12/14/2022] Open
Abstract
Cancer prevalence and mortality are high in developing nations, where resources for cancer control are inadequate. Nearly one-quarter of cancers in resource-limited nations are infection related, and molecular assays can capitalize on this relationship by detecting pertinent pathogen genomes and human gene variants to identify those at highest risk for progression to cancer, to classify lesions, to predict effective therapy, and to monitor tumor burden over time. Prime examples are human papillomavirus in cervical neoplasia, Helicobacter pylori and Epstein-Barr virus in gastric adenocarcinoma and lymphoma, and hepatitis B or C virus in hepatocellular cancer. Research is underway to engineer devices that overcome social, economic, and technical barriers limiting effective laboratory support. Additional challenges include an educated workforce, infrastructure for quality metrics and record keeping, and funds to sustain molecular test services. The combination of well-designed interfaces, novel and robust electrochemical technology, and telemedicine tools will promote adoption by frontline providers. Fast turnaround is crucial for surmounting loss to follow-up, although increased use of cell phones, even in rural areas, enhances options for patient education and engagement. Links to a broadband network facilitate consultation and centralized storage of medical data. Molecular technology shows promise to address gaps in health care through rapid, user-friendly, and cost-effective devices reflecting clinical priorities in resource-poor areas.
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Affiliation(s)
- Margaret L Gulley
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.
| | - Douglas R Morgan
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University, Nashville, Tennessee
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Pearlstein MV, Zedek DC, Ollila DW, Treece A, Gulley ML, Groben PA, Thomas NE. Validation of the VE1 immunostain for the BRAF V600E mutation in melanoma. J Cutan Pathol 2014; 41:724-32. [PMID: 24917033 DOI: 10.1111/cup.12364] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 06/02/2014] [Accepted: 06/07/2014] [Indexed: 01/07/2023]
Abstract
BACKGROUND BRAF mutation status, and therefore eligibility for BRAF inhibitors, is currently determined by sequencing methods. We assessed the validity of VE1, a monoclonal antibody against the BRAF V600E mutant protein, in the detection of mutant BRAF V600E melanomas as classified by DNA pyrosequencing. METHODS The cases were 76 metastatic melanoma patients with only one known primary melanoma who had had BRAF codon 600 pyrosequencing of either their primary (n = 19), metastatic (n = 57) melanoma, or both (n = 17). All melanomas (n = 93) were immunostained with the BRAF VE1 antibody using a red detection system. The staining intensity of these specimens was scored from 0 to 3+ by a dermatopathologist. Scores of 0 and 1+ were considered as negative staining while scores of 2+ and 3+ were considered positive. RESULTS The VE1 antibody showed a sensitivity of 85% and a specificity of 100% as compared to DNA pyrosequencing results. There was 100% concordance between VE1 immunostaining of primary and metastatic melanomas from the same patient. V600K, V600Q, and V600R BRAF melanomas did not positively stain with VE1. CONCLUSIONS This hospital-based study finds high sensitivity and specificity for the BRAF VE1 immunostain in comparison to pyrosequencing in detection of BRAF V600E in melanomas.
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Camargo MC, Koriyama C, Matsuo K, Kim WH, Herrera-Goepfert R, Liao LM, Yu J, Carrasquilla G, Sung JJ, Alvarado-Cabrero I, Lissowska J, Meneses-Gonzalez F, Yatabe Y, Ding T, Hu N, Taylor PR, Morgan DR, Gulley ML, Torres J, Akiba S, Rabkin CS. Case-case comparison of smoking and alcohol risk associations with Epstein-Barr virus-positive gastric cancer. Int J Cancer 2014; 134:948-53. [PMID: 23904115 PMCID: PMC3961829 DOI: 10.1002/ijc.28402] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/05/2013] [Accepted: 07/12/2013] [Indexed: 12/13/2022]
Abstract
Helicobacter pylori is the primary cause of gastric cancer. However, monoclonal Epstein-Barr virus (EBV) nucleic acid is also present in up to 10% of these tumors worldwide. EBV prevalence is increased with male sex, nonantral localization and surgically disrupted anatomy. To further examine associations between EBV and gastric cancer, we organized an international consortium of 11 studies with tumor EBV status assessed by in situ hybridization. We pooled individual-level data on 2,648 gastric cancer patients, including 184 (7%) with EBV-positive cancers; all studies had information on cigarette use (64% smokers) and nine had data on alcohol (57% drinkers). We compared patients with EBV-positive and EBV-negative tumors to evaluate smoking and alcohol interactions with EBV status. To account for within-population clustering, multilevel logistic regression models were used to estimate interaction odds ratios (OR) adjusted for distributions of sex (72% male), age (mean 59 years), tumor histology (56% Lauren intestinal-type), anatomic subsite (61% noncardia) and year of diagnosis (1983-2012). In unadjusted analyses, the OR of EBV positivity with smoking was 2.2 [95% confidence interval (CI) 1.6-3.2]. The OR was attenuated to 1.5 (95% CI 1.01-2.3) by adjustment for the possible confounders. There was no significant interaction of EBV status with alcohol drinking (crude OR 1.4; adjusted OR 1.0). Our data indicate the smoking association with gastric cancer is stronger for EBV-positive than EBV-negative tumors. Conversely, the null association with alcohol does not vary by EBV status. Distinct epidemiologic characteristics of EBV-positive cancer further implicate the virus as a cofactor in gastric carcinogenesis.
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Affiliation(s)
- M. Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Chihaya Koriyama
- Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Keitaro Matsuo
- Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka, Japan
| | - Woo-Ho Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | | | - Linda M. Liao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | | | - Jun Yu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Gabriel Carrasquilla
- Centro de Estudios e Investigación en Salud, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Joseph J.Y. Sung
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Isabel Alvarado-Cabrero
- Servicio de Patología, UMAE Oncología, CMN SXXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Jolanta Lissowska
- Division of Cancer Epidemiology and Prevention, M Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland
| | - Fernando Meneses-Gonzalez
- Programa de Residencia en Epidemiología, Dirección General Adjunta de Epidemiología, Secretaría de Salud, Mexico City, Mexico
| | - Yashushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Ti Ding
- Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Philip R. Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Douglas R. Morgan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
- Division of Gastroenterology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Margaret L. Gulley
- Department of Pathology and Laboratory Medicine and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, CMN SXXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Suminori Akiba
- Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Charles S. Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
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Camargo MC, Kim WH, Chiaravalli AM, Kim KM, Corvalan AH, Matsuo K, Yu J, Sung JJY, Herrera-Goepfert R, Meneses-Gonzalez F, Kijima Y, Natsugoe S, Liao LM, Lissowska J, Kim S, Hu N, Gonzalez CA, Yatabe Y, Koriyama C, Hewitt SM, Akiba S, Gulley ML, Taylor PR, Rabkin CS. Improved survival of gastric cancer with tumour Epstein-Barr virus positivity: an international pooled analysis. Gut 2014; 63:236-43. [PMID: 23580779 PMCID: PMC4384434 DOI: 10.1136/gutjnl-2013-304531] [Citation(s) in RCA: 271] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND OBJECTIVE About 9% of gastric carcinomas have Epstein-Barr virus (EBV) in the tumour cells, but it is unclear whether viral presence influences clinical progression. We therefore examined a large multicentre case series for the association of tumour EBV status with survival after gastric cancer diagnosis, accounting for surgical stage and other prognostic factors. METHODS We combined individual-level data on 4599 gastric cancer patients diagnosed between 1976 and 2010 from 13 studies in Asia (n=8), Europe (n=3), and Latin America (n=2). EBV positivity of tumours was assessed by in situ hybridisation. Mortality HRs for EBV positivity were estimated by Cox regression models stratified by study, adjusted for distributions of sex (71% male), age (mean 58 years), stage (52% tumour-node-metastasis stages III or IV), tumour histology (49% poorly differentiated, 57% Lauren intestinal-type), anatomic subsite (70% non-cardia) and year of diagnosis. Variations by study and continent were assessed using study-specific HRs for EBV positivity. RESULTS During median 3.0 years follow-up, 49% of patients died. Stage was strongly predictive of mortality, with unadjusted HRs (vs stage I) of 3.1 for stage II, 8.1 for stage III and 13.2 for stage IV. Tumour EBV positivity was 8.2% overall and inversely associated with stage (adjusted OR: 0.79 per unit change). Adjusted for stage and other confounders, EBV positivity was associated with lower mortality (HR, 0.72; 95% CI 0.61 to 0.86), with low heterogeneity among the study populations (p=0.2). The association did not significantly vary across patient or tumour characteristics. There was no significant variation among the three continent-specific HRs (p=0.4). CONCLUSIONS Our findings suggest that tumour EBV positivity is an additional prognostic indicator in gastric cancer. Further studies are warranted to identify the mechanisms underlying this protective association.
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Affiliation(s)
- M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Woo-Ho Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | | | - Kyoung-Mee Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Alejandro H Corvalan
- Department of Hematology and Oncology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Keitaro Matsuo
- Division of Molecular Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Jun Yu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph J Y Sung
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Fernando Meneses-Gonzalez
- Programa de Residencia en Epidemiología, Dirección General Adjunta de Epidemiología, Secretaría de Salud, México City, México
| | - Yuko Kijima
- Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Shoji Natsugoe
- Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Linda M Liao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Jolanta Lissowska
- Division of Cancer Epidemiology and Prevention, M Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland
| | - Sung Kim
- Division of Cancer Epidemiology and Prevention, M Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Carlos A Gonzalez
- Unit of Nutrition, Environment and Cancer, Epidemiology Research Program, Catalan Institute of Oncology, Barcelona, Spain; on behalf of the Euro-gast EPIC study
| | - Yashushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Chihaya Koriyama
- Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Stephen M Hewitt
- Tissue Array Research Program and Applied Molecular Pathology Laboratory, Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland, USA
| | - Suminori Akiba
- Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Margaret L Gulley
- Department of Pathology and Laboratory Medicine, The Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Philip R Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
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Robb JA, Gulley ML, Fitzgibbons PL, Kennedy MF, Cosentino LM, Washington K, Dash RC, Branton PA, Jewell SD, Lapham RL. A call to standardize preanalytic data elements for biospecimens. Arch Pathol Lab Med 2013; 138:526-37. [PMID: 23937609 DOI: 10.5858/arpa.2013-0250-cp] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Biospecimens must have appropriate clinical annotation (data) to ensure optimal quality for both patient care and research. Clinical preanalytic variables are the focus of this study. OBJECTIVE To define the essential preanalytic variables (data fields) that should be attached to every collected biospecimen and to provide a complete list of such variables, along with their relative importance, which can vary, depending on downstream use, institutional needs, and information technology capabilities. DESIGN The College of American Pathologists Diagnostic Intelligence and Health Information Technology Committee sponsored a Biorepository Working Group to develop a ranked list of the preanalytic variables for annotating biospecimens. Members of the working group were experts in anatomic, clinical, and molecular pathology; biobanking; medical informatics; and accreditation. Several members had experience with federal government programs, such as the National Cancer Institute's Biospecimens and Biorepository Branch and the National Cancer Institute's Community Cancer Center Program. Potential preanalytic variables were identified and ranked along with available supporting evidence, definitions, and potential negative effects if the variable was not attached to the biospecimen. Additional national and international stakeholders reviewed the draft manuscript. RESULTS The ranked listing of 170 preanalytic variables produced can be used as a guide for site-specific implementation into patient care and/or research biorepository processes. Conclusions.-In our collective experience, it is often difficult to choose which of the many preanalytic variables to attach to any specific set of biospecimens used for patient care and/or research. The provided ranked list should aid in the selection of preanalytic variables for a given biospecimen collection.
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Affiliation(s)
- James A Robb
- From the Department of Pathology, University of North Carolina, Chapel Hill (Dr Gulley); the Department of Pathology, St Jude Medical Center, Fullerton, California (Dr Fitzgibbons); the College of American Pathologists, Northfield, Illinois (Ms Kennedy); the Department of Translational Medicine, Biogen Idec, Cambridge, Massachusetts (Dr Cosentino); the Department of Pathology, Vanderbilt Medical Center, Nashville, Tennessee (Dr Washington); the Department of Pathology, Duke Medical Center, Durham, North Carolina (Dr Dash); the Biorepositories and Biospecimens Research Branch, National Cancer Institute, National Institutes of Health, Rockville, Maryland (Dr Branton); the Department of Biospecimen Science, Van Andel Institute, Grand Rapids, Michigan (Dr Jewell); and the Department of Pathology, Spartanburg Regional Medical Center, Spartanburg, South Carolina (Dr Lapham)
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Olson D, Gulley ML, Tang W, Wokocha C, Mechanic O, Hosseinipour M, Gold SH, Nguluwe N, Mwansambo C, Shores C. Phase I clinical trial of valacyclovir and standard of care cyclophosphamide in children with endemic Burkitt lymphoma in Malawi. Clin Lymphoma Myeloma Leuk 2012; 13:112-8. [PMID: 23260601 DOI: 10.1016/j.clml.2012.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 10/12/2012] [Accepted: 11/13/2012] [Indexed: 12/12/2022]
Abstract
UNLABELLED Treatment options for Epstein-Barr virus (EBV)-associated Burkitt lymphoma in Africa are limited because of chemotherapy-associated toxicity. Since other EBV-associated diseases respond to antiviral agents, we investigated adding an antiviral agent, valacyclovir, to the current chemotherapy regimen in Malawi. In this phase I safety study, we showed that cyclophosphamide combined with valacyclovir was safe. Phase II efficacy trials should now be undertaken. BACKGROUND Nucleoside analogues, including acyclovir, ganciclovir, and their precursors, have shown some efficacy against several Epstein-Barr virus (EBV)-associated diseases, including active EBV infection and posttransplantation lymphoproliferative disorder (PTLD). They have also been proposed as a possible treatment for EBV-associated malignancies, including endemic Burkitt lymphoma. The safety of nucleoside analogues in combination with chemotherapy in the developing world has not been studied and is necessary before any large scale efficacy trials are conducted. PATIENTS AND METHODS Children 3-15 years old meeting inclusion criteria were assigned to a 3+3 dose escalation trial of combination valacyclovir (15 and 30 mg/kg, 3 times daily for 40 days) and cyclophosphamide (CPM) (40 mg/kg day 1, 60 mg/kg on days 8, 18, and 28) or CPM monotherapy. Subjects were monitored for clinical and laboratory toxicity and had EBV levels measured regularly. Dose-limiting toxicity (DLT) was our primary outcome. RESULTS We found that the combination of valacyclovir and CPM was safe and did not lead to any DLT compared with CPM monotherapy. The most common side effects were vomiting, abdominal pain, and tumor site pain, which were similar in both arms. Patients with measurable serum EBV showed decreased loads over their treatment course. CONCLUSIONS We recommend a phase II valacyclovir dose of 30 mg/kg 3 times daily for 40 days. We also observed that 6 of our 12 patients with presumed Burkitt lymphoma had measurable EBV viral loads that decreased over the course of their treatment, suggesting that phase II studies should investigate this correlation further. This study paves the way for a phase II efficacy trial of combined valacyclovir and CPM in the treatment of endemic Burkitt lymphoma.
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Affiliation(s)
- Daniel Olson
- University of North Carolina Project, Lilongwe, Malawi.
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Tang W, Morgan DR, Meyers MO, Dominguez RL, Martinez E, Kakudo K, Kuan PF, Banet N, Muallem H, Woodward K, Speck O, Gulley ML. Epstein-barr virus infected gastric adenocarcinoma expresses latent and lytic viral transcripts and has a distinct human gene expression profile. Infect Agent Cancer 2012; 7:21. [PMID: 22929309 PMCID: PMC3598565 DOI: 10.1186/1750-9378-7-21] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Accepted: 08/22/2012] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND EBV DNA is found within the malignant cells of 10% of gastric cancers. Modern molecular technology facilitates identification of virus-related biochemical effects that could assist in early diagnosis and disease management. METHODS In this study, RNA expression profiling was performed on 326 macrodissected paraffin-embedded tissues including 204 cancers and, when available, adjacent non-malignant mucosa. Nanostring nCounter probes targeted 96 RNAs (20 viral, 73 human, and 3 spiked RNAs). RESULTS In 182 tissues with adequate housekeeper RNAs, distinct profiles were found in infected versus uninfected cancers, and in malignant versus adjacent benign mucosa. EBV-infected gastric cancers expressed nearly all of the 18 latent and lytic EBV RNAs in the test panel. Levels of EBER1 and EBER2 RNA were highest and were proportional to the quantity of EBV genomes as measured by Q-PCR. Among protein coding EBV RNAs, EBNA1 from the Q promoter and BRLF1 were highly expressed while EBNA2 levels were low positive in only 6/14 infected cancers. Concomitant upregulation of cellular factors implies that virus is not an innocent bystander but rather is linked to NFKB signaling (FCER2, TRAF1) and immune response (TNFSF9, CXCL11, IFITM1, FCRL3, MS4A1 and PLUNC), with PPARG expression implicating altered cellular metabolism. Compared to adjacent non-malignant mucosa, gastric cancers consistently expressed INHBA, SPP1, THY1, SERPINH1, CXCL1, FSCN1, PTGS2 (COX2), BBC3, ICAM1, TNFSF9, SULF1, SLC2A1, TYMS, three collagens, the cell proliferation markers MYC and PCNA, and EBV BLLF1 while they lacked CDH1 (E-cadherin), CLDN18, PTEN, SDC1 (CD138), GAST (gastrin) and its downstream effector CHGA (chromogranin). Compared to lymphoepithelioma-like carcinoma of the uterine cervix, gastric cancers expressed CLDN18, EPCAM, REG4, BBC3, OLFM4, PPARG, and CDH17 while they had diminished levels of IFITM1 and HIF1A. The druggable targets ERBB2 (Her2), MET, and the HIF pathway, as well as several other potential pharmacogenetic indicators (including EBV infection itself, as well as SPARC, TYMS, FCGR2B and REG4) were identified in some tumor specimens. CONCLUSION This study shows how modern molecular technology applied to archival fixed tissues yields novel insights into viral oncogenesis that could be useful in managing affected patients.
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Affiliation(s)
- Weihua Tang
- Department of Pathology & Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, 913 Brinkhous-Bullitt Building, Chapel Hill, NC, 27599-7525, USA.
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Ryan JL, Shen YJ, Morgan DR, Thorne LB, Kenney SC, Dominguez RL, Gulley ML. Epstein-Barr virus infection is common in inflamed gastrointestinal mucosa. Dig Dis Sci 2012; 57:1887-98. [PMID: 22410851 PMCID: PMC3535492 DOI: 10.1007/s10620-012-2116-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 02/22/2012] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Epstein-Barr virus (EBV) is present in the malignant epithelial cells of 10% of all gastric adenocarcinomas; however, localization of the virus in normal gastrointestinal mucosa is largely unexplored. In the present study, we measured EBV DNA and localized viral gene products in gastritis specimens (n = 89), normal gastric and colonic mucosa (n = 14), Crohn's disease (n = 9), and ulcerative colitis (n = 11) tissues. METHODS A battery of sensitive and specific quantitative polymerase chain reactions targeted six disparate regions of the EBV genome: BamH1 W, EBNA1, LMP1, LMP2, BZLF1, and EBER1. EBV infection was localized by EBV-encoded RNA (EBER) in situ hybridization and by immunohistochemical stains for viral latent proteins LMP1 and LMP2 and for viral lytic proteins BMRF1 and BZLF1. B lymphocytes were identified using CD20 immunostains. RESULTS EBV DNA was essentially undetectable in normal gastric mucosa but was present in 46% of gastritis lesions, 44% of normal colonic mucosa, 55% of Crohn's disease, and 64% of ulcerative colitis samples. Levels of EBV DNA exceeded what would be expected based on the numbers of B lymphocytes in inflamed tissues, suggesting that EBV is preferentially localized to inflammatory gastrointestinal lesions. Histochemical staining revealed EBER expression in lymphoid cells of some PCR-positive lesions. The viral lytic viral proteins, BMRF1 and BZLF1, were expressed in lymphoid cells of two ulcerative colitis tissues, both of which had relatively high viral loads by quantitative PCR. CONCLUSION EBV-infected lymphocytes are frequently present in inflamed gastric and colonic mucosa. Active viral replication in some lesions raises the possibility of virus-related perpetuation of gastrointestinal inflammation.
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Affiliation(s)
- Julie L. Ryan
- Department of Dermatology & Radiation Oncology, University of Rochester Medical Center, Rochester, NY
| | - You-Jun Shen
- Virginia Beach General Hospital, Virginia Beach, VA
| | - Douglas R. Morgan
- Gastroenterology and Hepatology Division, Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Leigh B. Thorne
- Department of Pathology and Laboratory Medicine and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Shannon C. Kenney
- Departments of Medicine and Oncology, University of Wisconsin, Madison, WI
| | - Ricardo L. Dominguez
- Department of Gastroenterology, Western Regional Hospital, Santa Rosa de Copan, Honduras
| | - Margaret L. Gulley
- Department of Pathology and Laboratory Medicine and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
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Tang W, Hu Z, Muallem H, Gulley ML. Quality assurance of RNA expression profiling in clinical laboratories. J Mol Diagn 2012; 14:1-11. [PMID: 22020152 PMCID: PMC3338342 DOI: 10.1016/j.jmoldx.2011.09.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/09/2011] [Accepted: 09/14/2011] [Indexed: 12/12/2022] Open
Abstract
RNA expression profiles are increasingly used to diagnose and classify disease, based on expression patterns of as many as several thousand RNAs. To ensure quality of expression profiling services in clinical settings, a standard operating procedure incorporates multiple quality indicators and controls, beginning with preanalytic specimen preparation and proceeding thorough analysis, interpretation, and reporting. Before testing, histopathological examination of each cellular specimen, along with optional cell enrichment procedures, ensures adequacy of the input tissue. Other tactics include endogenous controls to evaluate adequacy of RNA and exogenous or spiked controls to evaluate run- and patient-specific performance of the test system, respectively. Unique aspects of quality assurance for array-based tests include controls for the pertinent outcome signatures that often supersede controls for each individual analyte, built-in redundancy for critical analytes or biochemical pathways, and software-supported scrutiny of abundant data by a laboratory physician who interprets the findings in a manner facilitating appropriate medical intervention. Access to high-quality reagents, instruments, and software from commercial sources promotes standardization and adoption in clinical settings, once an assay is vetted in validation studies as being analytically sound and clinically useful. Careful attention to the well-honed principles of laboratory medicine, along with guidance from government and professional groups on strategies to preserve RNA and manage large data sets, promotes clinical-grade assay performance.
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Affiliation(s)
- Weihua Tang
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Zhiyuan Hu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Hind Muallem
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Margaret L. Gulley
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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Tang W, Hu Z, Muallem H, Gulley ML. Clinical implementation of RNA signatures for pharmacogenomic decision-making. Pharmgenomics Pers Med 2011; 4:95-107. [PMID: 23226056 PMCID: PMC3513222 DOI: 10.2147/pgpm.s14888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Indexed: 12/14/2022]
Abstract
RNA profiling is increasingly used to predict drug response, dose, or toxicity based on analysis of drug pharmacokinetic or pharmacodynamic pathways. Before implementing multiplexed RNA arrays in clinical practice, validation studies are carried out to demonstrate sufficient evidence of analytic and clinical performance, and to establish an assay protocol with quality assurance measures. Pathologists assure quality by selecting input tissue and by interpreting results in the context of the input tissue as well as the technologies that were used and the clinical setting in which the test was ordered. A strength of RNA profiling is the array-based measurement of tens to thousands of RNAs at once, including redundant tests for critical analytes or pathways to promote confidence in test results. Instrument and reagent manufacturers are crucial for supplying reliable components of the test system. Strategies for quality assurance include careful attention to RNA preservation and quality checks at pertinent steps in the assay protocol, beginning with specimen collection and proceeding through the various phases of transport, processing, storage, analysis, interpretation, and reporting. Specimen quality is checked by probing housekeeping transcripts, while spiked and exogenous controls serve as a check on analytic performance of the test system. Software is required to manipulate abundant array data and present it for interpretation by a laboratory physician who reports results in a manner facilitating therapeutic decision-making. Maintenance of the assay requires periodic documentation of personnel competency and laboratory proficiency. These strategies are shepherding genomic arrays into clinical settings to provide added value to patients and to the larger health care system.
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Affiliation(s)
- Weihua Tang
- Department of Pathology and Laboratory Medicine
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Elloumi F, Hu Z, Li Y, Parker JS, Gulley ML, Amos KD, Troester MA. Systematic bias in genomic classification due to contaminating non-neoplastic tissue in breast tumor samples. BMC Med Genomics 2011; 4:54. [PMID: 21718502 PMCID: PMC3151208 DOI: 10.1186/1755-8794-4-54] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 06/30/2011] [Indexed: 12/15/2022] Open
Abstract
Background Genomic tests are available to predict breast cancer recurrence and to guide clinical decision making. These predictors provide recurrence risk scores along with a measure of uncertainty, usually a confidence interval. The confidence interval conveys random error and not systematic bias. Standard tumor sampling methods make this problematic, as it is common to have a substantial proportion (typically 30-50%) of a tumor sample comprised of histologically benign tissue. This "normal" tissue could represent a source of non-random error or systematic bias in genomic classification. Methods To assess the performance characteristics of genomic classification to systematic error from normal contamination, we collected 55 tumor samples and paired tumor-adjacent normal tissue. Using genomic signatures from the tumor and paired normal, we evaluated how increasing normal contamination altered recurrence risk scores for various genomic predictors. Results Simulations of normal tissue contamination caused misclassification of tumors in all predictors evaluated, but different breast cancer predictors showed different types of vulnerability to normal tissue bias. While two predictors had unpredictable direction of bias (either higher or lower risk of relapse resulted from normal contamination), one signature showed predictable direction of normal tissue effects. Due to this predictable direction of effect, this signature (the PAM50) was adjusted for normal tissue contamination and these corrections improved sensitivity and negative predictive value. For all three assays quality control standards and/or appropriate bias adjustment strategies can be used to improve assay reliability. Conclusions Normal tissue sampled concurrently with tumor is an important source of bias in breast genomic predictors. All genomic predictors show some sensitivity to normal tissue contamination and ideal strategies for mitigating this bias vary depending upon the particular genes and computational methods used in the predictor.
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Affiliation(s)
- Fathi Elloumi
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Tang W, Banet N, Muallem H, Sailey CJ, Hu Z, Ma S, Kenney S, Raab‐Traub N, Gulley ML. Validation of Array‐based RNA Expression Profiles in Paraffin‐embedded Samples of Epstein‐Barr Virus‐related Malignancy. FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.lb313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | - Zhiyuan Hu
- Lineberger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillNC
| | - Shidong Ma
- Department of OncologyMcArdle LaboratoryUniversity of WisconsinMadisonWI
| | - Shannon Kenney
- Department of OncologyMcArdle LaboratoryUniversity of WisconsinMadisonWI
| | - Nancy Raab‐Traub
- Lineberger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillNC
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Ryan JL, Jones RJ, Kenney SC, Rivenbark AG, Tang W, Knight ER, Coleman WB, Gulley ML. Epstein-Barr virus-specific methylation of human genes in gastric cancer cells. Infect Agent Cancer 2010; 5:27. [PMID: 21194482 PMCID: PMC3023757 DOI: 10.1186/1750-9378-5-27] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 12/31/2010] [Indexed: 12/13/2022] Open
Abstract
Background Epstein-Barr Virus (EBV) is found in 10% of all gastric adenocarcinomas but its role in tumor development and maintenance remains unclear. The objective of this study was to examine EBV-mediated dysregulation of cellular factors implicated in gastric carcinogenesis. Methods Gene expression patterns were examined in EBV-negative and EBV-positive AGS gastric epithelial cells using a low density microarray, reverse transcription PCR, histochemical stains, and methylation-specific DNA sequencing. Expression of PTGS2 (COX2) was measured in AGS cells and in primary gastric adenocarcinoma tissues. Results In array studies, nearly half of the 96 human genes tested, representing 15 different cancer-related signal transduction pathways, were dysregulated after EBV infection. Reverse transcription PCR confirmed significant impact on factors having diverse functions such as cell cycle regulation (IGFBP3, CDKN2A, CCND1, HSP70, ID2, ID4), DNA repair (BRCA1, TFF1), cell adhesion (ICAM1), inflammation (COX2), and angiogenesis (HIF1A). Demethylation using 5-aza-2'-deoxycytidine reversed the EBV-mediated dysregulation for all 11 genes listed here. For some promoter sequences, CpG island methylation and demethylation occurred in an EBV-specific pattern as shown by bisulfite DNA sequencing. Immunohistochemistry was less sensitive than was western blot for detecting downregulation of COX2 upon EBV infection. Virus-related dysregulation of COX2 levels in vitro was not recapitulated in vivo among naturally infected gastric cancer tissues. Conclusions EBV alters human gene expression in ways that could contribute to the unique pathobiology of virus-associated cancer. Furthermore, the frequency and reversability of methylation-related transcriptional alterations suggest that demethylating agents have therapeutic potential for managing EBV-related carcinoma.
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Affiliation(s)
- Julie L Ryan
- Department of Pathology and Laboratory Medicine and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7525, USA.
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Abstract
Colorectal cancer is the second most common cause of cancer death in the United States. Understanding the biochemical pathways underlying carcinogenesis has paved the way for more effective treatments and better outcomes. BRAF mutation testing has a role in (1) differentiating sporadic colorectal cancer from Lynch syndrome, (2) identifying cancers lacking BRAF mutation that are more likely to respond to epidermal growth factor receptor inhibitor therapy, and (3) conferring worse prognosis in colorectal cancer that is microsatellite stable. Several analytic methods are available to reliably detect BRAF mutations. Real-time polymerase chain reaction identifies the most common BRAF mutation, V600E, in frozen or paraffin-embedded colorectal cancer tissue. Traditional DNA sequencing and the somewhat more-sensitive pyrosequencing method can detect multiple alternative BRAF mutations that are predicted to constitutively activate signaling through the MAPK pathway, promoting tumor growth and survival. Pathologists play an important role in assay validation as well as in consulting with clinicians about indications for testing, ensuring quality of testing, and interpreting results in conjunction with other clinicopathologic factors important in the management of affected patients.
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Affiliation(s)
- Shree G Sharma
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, USA
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Abstract
Colorectal cancer is the second most common cause of cancer death in the United States. Understanding the biochemical pathways underlying carcinogenesis has paved the way for more effective treatments and better outcomes. BRAF mutation testing has a role in (1) differentiating sporadic colorectal cancer from Lynch syndrome, (2) identifying cancers lacking BRAF mutation that are more likely to respond to epidermal growth factor receptor inhibitor therapy, and (3) conferring worse prognosis in colorectal cancer that is microsatellite stable. Several analytic methods are available to reliably detect BRAF mutations. Real-time polymerase chain reaction identifies the most common BRAF mutation, V600E, in frozen or paraffin-embedded colorectal cancer tissue. Traditional DNA sequencing and the somewhat more-sensitive pyrosequencing method can detect multiple alternative BRAF mutations that are predicted to constitutively activate signaling through the MAPK pathway, promoting tumor growth and survival. Pathologists play an important role in assay validation as well as in consulting with clinicians about indications for testing, ensuring quality of testing, and interpreting results in conjunction with other clinicopathologic factors important in the management of affected patients.
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Affiliation(s)
- Shree G Sharma
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, USA
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Neuhauser TS, Lancaster K, Haws R, Drehner D, Gulley ML, Lichy JH, Taubenberger JK. Rapidly Progressive T Cell Lymphoma Presenting as Acute Renal Failure: Case Report and Review of the Literature. ACTA ACUST UNITED AC 2010. [DOI: 10.1080/15513819709168586] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Tang W, Harmon P, Gulley ML, Mwansambo C, Kazembe PN, Martinson F, Wokocha C, Kenney SC, Hoffman I, Sigel C, Maygarden S, Hoffman M, Shores C. Viral response to chemotherapy in endemic burkitt lymphoma. Clin Cancer Res 2010; 16:2055-64. [PMID: 20233888 DOI: 10.1158/1078-0432.ccr-09-2424] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE Some EBV-directed therapies are predicted to be effective only when lytic viral replication occurs. We studied whether cyclophosphamide chemotherapy induces EBV to switch from latent to lytic phases of infection in a series of EBV-associated Burkitt lymphomas. EXPERIMENTAL DESIGN Children with first presentation of an expanding, solid maxillary or mandibular mass consistent with Burkitt lymphoma underwent fine-needle aspiration just prior to the initiation of cyclophosphamide therapy and again 1 to 5 days later. Aspirated cells were examined for latent and lytic EBV infection using in situ hybridization to EBV-encoded RNA (EBER), immunohistochemical analysis of the lytic EBV proteins BZLF1 and BMRF1, reverse transcription PCR targeting BZLF1 transcripts, and EBV viral load measurement by quantitative PCR. RESULTS Among 21 lymphomas expressing EBER prior to chemotherapy, 9 of 10 still expressed EBER on day 1 after therapy whereas only 2 of 11 (18%) specimens still expressed EBER at days 3 to 5, implying that chemotherapy was fairly effective at eliminating latently infected cells. Neither of the lytic products, BZLF1 or BMRF1, were significantly upregulated at the posttherapy time points examined. However, EBV genomic copy number increased in 5 of 10 samples 1 day after treatment began, suggesting that viral replication occurs within the first 24 hours. CONCLUSION Cyclophosphamide may induce the lytic phase of EBV infection and is fairly effective in diminishing EBER-expressing tumor cells within 5 days. These findings provide the rationale for a trial testing synergistic tumor cell killing using cyclophosphamide with a drug like ganciclovir targeting lytically infected cells.
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Affiliation(s)
- Weihua Tang
- Departments of Pathology and Laboratory Medicine, Otolaryngology/Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7525, USA
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Abstract
Management of patients with acute myeloid leukemia relies on genetic tests that inform diagnosis and prognosis, predict response to therapy, and measure minimal residual disease. The value of genetics is reinforced in the revised 2008 World Health Organization acute myeloid leukemia classification scheme. The various analytic procedures-karyotype, fluorescence in situ hybridization, reverse transcription polymerase chain reaction, DNA sequencing, and microarray technology-each have advantages in certain clinical settings, and understanding their relative merits assists in specimen allocation and in effective utilization of health care resources. Karyotype and array technology represent genome-wide screens, whereas the other methods target specific prognostic features such as t(15;17) PML-RARA, t(8;21) RUNX1-RUNX1T1, inv(16) CBFB-MYH11, 11q23 MLL rearrangement, FLT3 internal tandem duplication, or NPM1 mutation. New biomarkers and pharmacogenetic tests are emerging. The pathologist's expertise is critical in 1) consulting with clinicians about test selection as well as specimen collection and handling; 2) allocating tissue for immediate testing and preserving the remaining specimen for any downstream testing that is indicated once morphology and other pertinent test results are known; 3) performing tests that maximize outcome based on the strengths and limitations of each assay in each available specimen type; and 4) interpreting and conveying results to the rest of the health care team in a format that facilitates clinical management. Acute myeloid leukemia leads the way for modern molecular medicine.
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Affiliation(s)
- Margaret L Gulley
- Department of Pathology and Laboratory Medicine, 913 Brinkhous-Bullitt Building, University of North Carolina, Chapel Hill, NC 27599-7525, USA.
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Benders AA, Tang W, Middeldorp JM, Greijer AE, Thorne LB, Funkhouser WK, Kimryn Rathmell W, Gulley ML. Epstein-Barr virus latent membrane protein 1 is not associated with vessel density nor with hypoxia inducible factor 1 alpha expression in nasopharyngeal carcinoma tissue. Head Neck Pathol 2009; 3:276-82. [PMID: 20596845 PMCID: PMC2811562 DOI: 10.1007/s12105-009-0148-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 10/28/2009] [Indexed: 12/12/2022]
Abstract
Hypoxia-inducible factor-1alpha (HIF-1alpha) and the neo-angiogenic factors induced as a result of hypoxia-inducible factor transcriptional activation may contribute to tumorigenesis by inducing vessel formation that in turn provides oxygen and nutrients promoting tumor expansion. In vitro studies of nasopharyngeal carcinoma (NPC), an aggressive malignancy that is nearly always infected by Epstein-Barr virus, show HIF-1alpha is upregulated by viral latent membrane protein 1 (LMP1). The current study used immunohistochemistry to examine the extent to which HIF-1alpha and LMP1 are co-expressed in naturally infected NPC tissues. Analytic procedures were optimized for sensitive localization of HIF-1alpha and LMP1 in fixed tissue sections using immunohistochemistry with sensitive fluorescent and signal amplification technologies. Vessel density was quantified by CD31 immunohistochemistry. LMP1 was expressed focally in all 18 NPCs examined, including 7/8 in situ lesions. There was no consistent co-localization with HIF-1alpha which was usually only weakly expressed in a subset of neoplastic cells. Neither LMP1 nor HIF-1alpha expression correlated with vessel density, and degree of vascularization varied widely among cases. Advanced immunohistochemical technologies reveal that LMP1 is expressed more commonly than previously reported in NPC. There is no consistent relationship between LMP1 and either HIF-1alpha expression or degree of microvasculature. The biologic basis for the wide variation in vessel density deserves further investigation.
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Affiliation(s)
- Alexander A. Benders
- Department of Pathology and Laboratory Medicine, The Lineberger Comprehensive Cancer Center, University of North Carolina, 101 Manning Dr, 913 Brinkhous-Bullitt Building, Chapel Hill, NC 27599-7525 USA
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Weihua Tang
- Department of Pathology and Laboratory Medicine, The Lineberger Comprehensive Cancer Center, University of North Carolina, 101 Manning Dr, 913 Brinkhous-Bullitt Building, Chapel Hill, NC 27599-7525 USA
| | - Jaap M. Middeldorp
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Astrid E. Greijer
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Leigh B. Thorne
- Department of Pathology and Laboratory Medicine, The Lineberger Comprehensive Cancer Center, University of North Carolina, 101 Manning Dr, 913 Brinkhous-Bullitt Building, Chapel Hill, NC 27599-7525 USA
| | - William K. Funkhouser
- Department of Pathology and Laboratory Medicine, The Lineberger Comprehensive Cancer Center, University of North Carolina, 101 Manning Dr, 913 Brinkhous-Bullitt Building, Chapel Hill, NC 27599-7525 USA
| | - W. Kimryn Rathmell
- Departments of Medicine and Genetics, The Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC USA
| | - Margaret L. Gulley
- Department of Pathology and Laboratory Medicine, The Lineberger Comprehensive Cancer Center, University of North Carolina, 101 Manning Dr, 913 Brinkhous-Bullitt Building, Chapel Hill, NC 27599-7525 USA
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Sepulveda AR, Jones D, Ogino S, Samowitz W, Gulley ML, Edwards R, Levenson V, Pratt VM, Yang B, Nafa K, Yan L, Vitazka P. CpG methylation analysis--current status of clinical assays and potential applications in molecular diagnostics: a report of the Association for Molecular Pathology. J Mol Diagn 2009; 11:266-78. [PMID: 19541921 DOI: 10.2353/jmoldx.2009.080125] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Methylation of CpG islands in gene promoter regions is a major molecular mechanism of gene silencing and underlies both cancer development and progression. In molecular oncology, testing for the CpG methylation of tissue DNA has emerged as a clinically useful tool for tumor detection, outcome prediction, and treatment selection, as well as for assessing the efficacy of treatment with the use of demethylating agents and monitoring for tumor recurrence. In addition, because CpG methylation occurs early in pre-neoplastic tissues, methylation tests may be useful as markers of cancer risk in patients with either infectious or inflammatory conditions. The Methylation Working Group of the Clinical Practice Committee of the Association of Molecular Pathology has reviewed the current state of clinical testing in this area. We report here our summary of both the advantages and disadvantages of various methods, as well as the needs for standardization and reporting. We then conclude by summarizing the most promising areas for future clinical testing in cancer molecular diagnostics.
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Affiliation(s)
- Antonia R Sepulveda
- Methylation Working Group of the Association for Molecular Pathology Clinical Practice Committee, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
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Jennings L, Van Deerlin VM, Gulley ML. Recommended principles and practices for validating clinical molecular pathology tests. Arch Pathol Lab Med 2009; 133:743-55. [PMID: 19415949 DOI: 10.5858/133.5.743] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2008] [Indexed: 11/06/2022]
Abstract
CONTEXT The use of DNA- and RNA-based tests continues to grow for applications as varied as inherited disease, infectious disease, cancer, identity testing, human leukocyte antigen typing, and pharmacogenetics. Progress is driven in part by the huge growth in knowledge about the molecular basis of disease coupled with advancements in technologic capabilities. In addition to requirements for clinical utility, every molecular test also may have limitations that must be carefully considered before clinical implementation. Analytic and clinical performance characteristics as well as test limitations are established and documented through the process of test validation. OBJECTIVE To describe the established principles of test validation, along with relevant regulations in the United States, in order to provide a rational approach to introducing molecular tests into the clinical laboratory. DATA SOURCES PubMed review of published literature, published guidelines, and online information from national and international professional organizations. CONCLUSIONS These resources and recommendations provide a framework for validating clinical tests.
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Affiliation(s)
- Lawrence Jennings
- Department of Pathology and Laboratory Medicine, Children's Memorial Hospital, Chicago, Illinois, USA
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Ryan JL, Jones RJ, Elmore SH, Kenney SC, Miller G, Schroeder JC, Gulley ML. Epstein-Barr virus WZhet DNA can induce lytic replication in epithelial cells in vitro, although WZhet is not detectable in many human tissues in vivo. Intervirology 2009; 52:8-16. [PMID: 19349713 DOI: 10.1159/000210833] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 02/18/2009] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVE WZhet is a rearranged and partially deleted form of the Epstein-Barr virus (EBV) genome in which the BamH1W region becomes juxtaposed with and activates BZLF1, resulting in constitutive viral replication. We tested whether WZhet induces viral replication in epithelial cells, and we studied its prevalence in a wide range of lesional tissues arising in vivo. METHODS A quantitative real-time PCR assay targeting EBV WZhet DNA was developed to measure this recombinant form of the EBV genome. RESULTS WZhet DNA was undetectable in any of 324 plasma or paraffin-embedded tissue samples from patients with EBV-associated and EBV-negative disorders. These included specimens from patients with Hodgkin or non-Hodgkin lymphoma, post-transplant lymphoproliferation, nasopharyngeal or gastric adenocarcinoma, and infectious mononucleosis. However, WZhet DNA was detected in vitro in EBV-infected AGS gastric cancer cells. Additionally, transient transfection of infected AGS gastric cancer cells showed that viral replication could be induced by a WZhet plasmid. CONCLUSION This is the first evidence that WZhet induces the EBV lytic cycle in an epithelial cell line. Our negative findings in natural settings suggest that WZhet is a defective viral product that thrives in the absence of a host immune system but is rarely present in vivo.
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Affiliation(s)
- Julie L Ryan
- Department of Dermatology, University of Rochester Medical Center, Rochester, N.Y., USA
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Ryan JL, Morgan DR, Dominguez RL, Thorne LB, Elmore SH, Mino-Kenudson M, Lauwers GY, Booker JK, Gulley ML. High levels of Epstein-Barr virus DNA in latently infected gastric adenocarcinoma. J Transl Med 2009; 89:80-90. [PMID: 19002111 PMCID: PMC2612099 DOI: 10.1038/labinvest.2008.103] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Gastric adenocarcinoma is the second leading cause of cancer death worldwide. Epstein-Barr virus (EBV) is present in the malignant cells of approximately 10% of cases. It is unclear whether EBV is being missed in some gastric adenocarcinomas due to insensitive test methods or partial EBV genome loss. In this study, we screened 113 gastric adenocarcinomas from low- and high-incidence regions (United States and Central America) for the presence of EBV using a battery quantitative real-time PCR (Q-PCR) assays targeting disparate segments of the EBV genome (BamH1W, EBNA1, LMP1, LMP2, BZLF1, EBER1) and histochemical stains targeting EBV-encoded RNA (EBER), the latent proteins LMP1 and LMP2, and the lytic proteins BMRF1 and BZLF1. EBV DNA was detected by Q-PCR in 48/75 United States cancers (64%) and in 38/38 Central American cancers (100%), which was a significant difference. EBER was localized to malignant epithelial cells in 8/48 (17%) United States and 3/38 (8%) Central American cancers. Viral loads were considerably higher for EBER-positive vs EBER-negative cancers (mean 162 986 vs 62 EBV DNA copies per 100,000 cells). A viral load of 2000 copies per 100,000 cells is recommended as the threshold distinguishing EBER-positive from EBER-negative tumors. One infected cancer selectively failed to amplify the LMP2 gene because of a point mutation, whereas another cancer had an atypical pattern of Q-PCR positivity suggesting deletion of large segments of the EBV genome. Three different viral latency profiles were observed in the cancers based on constant expression of EBER and focal or variable expression of LMP1 or LMP2, without lytic protein expression. We conclude that EBV DNA levels generally reflect EBER status, and a panel of at least two Q-PCR assays is recommended for sensitive identification of infected cancers.
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Affiliation(s)
- Julie L. Ryan
- Department of Dermatology & Radiation Oncology, University of Rochester Medical Center, Rochester, NY
| | - Douglas R. Morgan
- Department of Gastroenterology, University of North Carolina, Chapel Hill, NC
,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Ricardo L. Dominguez
- Department of Medicine, Western Regional Hospital, Santa Rosa de Copan, Honduras
| | - Leigh B. Thorne
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC
,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Sandra H. Elmore
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Gregory Y. Lauwers
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Jessica K. Booker
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC
| | - Margaret L. Gulley
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC
,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
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Dittmer DP, Hilscher CJ, Gulley ML, Yang EV, Chen M, Glaser R. Multiple pathways for Epstein-Barr virus episome loss from nasopharyngeal carcinoma. Int J Cancer 2008; 123:2105-12. [PMID: 18688856 DOI: 10.1002/ijc.23685] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Epstein-Barr virus (EBV) is the prototypical example for episomal persistence of genetic information. Yet, little is known about how this viral episome is lost. Episome loss occurs naturally in nasopharyngeal carcinoma (NPC) upon explantation into culture. Using whole-genome profiling, we found evidence for 2 different pathways of episome loss: (i) rapid loss of the entire episome or (ii) successive mutation/deletion of the episome until at least 1 essential cis-element is destroyed. This second phenotype was seen in a clone of HONE-1 NPC cells that maintains the EBV episome for prolonged time in culture. The conceptual insights provided by our quantitative analysis should aid our understanding of mammalian episomes, as well as lead to designs to cure latent viral infection.
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Affiliation(s)
- Dirk P Dittmer
- Lineberger Comprehensive Cancer Center, Center for AIDS Research and Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA.
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50
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Glaser SL, Gulley ML, Clarke CA, Keegan TH, Chang ET, Shema SJ, Craig FE, Digiuseppe JA, Dorfman RF, Mann RB, Anton-Culver H, Ambinder RF. Racial/ethnic variation in EBV-positive classical Hodgkin lymphoma in California populations. Int J Cancer 2008; 123:1499-507. [PMID: 18646185 DOI: 10.1002/ijc.23741] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Epstein-Barr virus (EBV) is detected in the tumor cells of some but not all Hodgkin lymphoma (HL) patients, and evidence indicates that EBV-positive and -negative HL are distinct entities. Racial/ethnic variation in EBV-positive HL in international comparisons suggests etiologic roles for environmental and genetic factors, but these studies used clinical series and evaluated EBV presence by differing protocols. Therefore, we evaluated EBV presence in the tumors of a large (n = 1,032), racially and sociodemographically diverse series of California incident classical HL cases with uniform pathology re-review and EBV detection methods. Tumor EBV-positivity was associated with Hispanic and Asian/Pacific Islander (API) but not black race/ethnicity, irrespective of demographic and clinical factors. Complex race-specific associations were observed between EBV-positive HL and age, sex, histology, stage, neighborhood socioeconomic status (SES), and birth place. In Hispanics, EBV-positive HL was associated not only with young and older age, male sex, and mixed cellularity histology, but also with foreign birth and lower SES in females, suggesting immune function responses to correlates of early childhood experience and later environmental exposures, respectively, as well as of pregnancy. For APIs, a lack of association with birth place may reflect the higher SES of API than Hispanic immigrants. In blacks, EBV-positive HL was associated with later-stage disease, consistent with racial/ethnic variation in certain cytokine polymorphisms. The racial/ethnic variation in our findings suggests that EBV-positive HL results from an intricate interplay of early- and later-life environmental, hormonal, and genetic factors leading to depressed immune function and poorly controlled EBV infection.
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Affiliation(s)
- Sally L Glaser
- Northern California Cancer Center, Fremont, CA 94538, USA.
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