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Cornejo KM, Hutchinson L, O'Donnell P, Meng X, Tomaszewicz K, Shalin SC, Cassarino DS, Chan MP, Quinn TR, Googe PB, Nazarian RM. Molecular Profiling of Syringocystadenocarcinoma Papilliferum Reveals RAS-Activating Mutations. Arch Pathol Lab Med 2024; 148:215-222. [PMID: 37074845 DOI: 10.5858/arpa.2022-0474-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2023] [Indexed: 04/20/2023]
Abstract
CONTEXT.— Syringocystadenocarcinoma papilliferum (SCACP) is a rare adnexal carcinoma and the malignant counterpart of syringocystadenoma papilliferum (SCAP), which is commonly located on the head and neck and may arise in association with a nevus sebaceus. RAS mutations have been identified in both SCAP and nevus sebaceus. OBJECTIVE.— To evaluate the clinicopathologic and molecular features of SCACPs, which have not been previously explored. DESIGN.— We obtained 11 SCACPs from 6 institutions and reviewed the clinicopathologic features. We also performed molecular profiling using next-generation sequencing. RESULTS.— The cohort comprised 6 women and 5 men with ages ranging from 29 to 96 years (mean, 73.6 years). The neoplasms occurred on the head and neck (n = 8; 73%) and extremities (n = 3; 27%). Three tumors possibly arose in a nevus sebaceus. A total of 4 cases showed at least carcinoma in situ (adenocarcinoma, n = 3; squamous cell carcinoma [SCC], n = 1), and 7 cases were invasive (SCC, n = 5; mixed adenocarcinoma + SCC, n = 2). A total of 8 of 11 cases (73%) had hot spot mutations consisting of HRAS (n = 4), KRAS (n = 1), BRAF (n = 1), TP53 (n = 4), ATM (n = 2), FLT3 (n = 1), CDKN2A (n = 1), and PTEN (n = 1). All 4 cases with HRAS mutations occurred on the head and neck, whereas the KRAS mutation occurred on the extremity. CONCLUSIONS.— RAS-activating mutations were detected in 50% of the cases, of which most (80%) involved HRAS and occurred on the head and neck, which shows overlapping features with SCAP, supporting that a subset may arise as a result of malignant transformation and likely an early oncogenic event.
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Affiliation(s)
- Kristine M Cornejo
- From the Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts (Cornejo, Nazarian)
| | - Lloyd Hutchinson
- Department of Pathology, University of Massachusetts Memorial Medical Center, Worcester, Massachusetts (Hutchinson, O'Donnell, Meng, Tomaszewicz)
| | - Patrick O'Donnell
- Department of Pathology, University of Massachusetts Memorial Medical Center, Worcester, Massachusetts (Hutchinson, O'Donnell, Meng, Tomaszewicz)
| | - Xiuling Meng
- Department of Pathology, University of Massachusetts Memorial Medical Center, Worcester, Massachusetts (Hutchinson, O'Donnell, Meng, Tomaszewicz)
| | - Keith Tomaszewicz
- Department of Pathology, University of Massachusetts Memorial Medical Center, Worcester, Massachusetts (Hutchinson, O'Donnell, Meng, Tomaszewicz)
| | - Sara C Shalin
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas (Shalin)
| | - David S Cassarino
- Southern California Permanente Medical Group, Sunset Medical Center, Department of Pathology, Los Angeles, California (Cassarino)
| | - May P Chan
- Department of Pathology, University of Michigan Health System, Ann Arbor, Michigan (Chan)
| | - Timothy R Quinn
- Massachusetts General Physicians Organization Dermatopathology Associates, Newton, Massachusetts (Quinn)
| | - Paul B Googe
- the Department of Dermatology, University of North Carolina School of Medicine, Chapel Hill, North Carolina (Googe)
| | - Rosalynn M Nazarian
- From the Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts (Cornejo, Nazarian)
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2
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Covington JD, Zong Y, Talat A, Strock C, Tomaszewicz K, Zivny J, Yang MX. Mass-Forming Gastric Heterotopia of the Rectum: A Series of 3 Cases from a Single Tertiary Health Center. Am J Case Rep 2022; 23:e936631. [PMID: 35881563 PMCID: PMC9339256 DOI: 10.12659/ajcr.936631] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Case series
Patient: Male, 25-year-old • Female, 58-year-old • Male, 33-year-old
Final Diagnosis: Rectal gastric heterotopia
Symptoms: Anal pain • hematochezia
Medication: —
Clinical Procedure: Endoscopic mucosal resection
Specialty: Gastroenterology and Hepatology
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Affiliation(s)
- Jeffrey D. Covington
- Department of Pathology, University of Massachusetts Medical School, Worcester, USA, MA
| | - Yang Zong
- Department of Pathology, University of Massachusetts Medical School, Worcester, USA, MA
| | - Arslan Talat
- Department of Gastroenterology, University of Massachusetts Medical School, Worcester, USA, MA
| | - Cara Strock
- Department of Pathology, University of Massachusetts Medical School, Worcester, USA, MA
| | - Keith Tomaszewicz
- Department of Pathology, University of Massachusetts Medical School, Worcester, USA, MA
| | - Jaroslav Zivny
- Department of Gastroenterology, University of Massachusetts Medical School, Worcester, USA, MA
| | - Michelle X. Yang
- Department of Pathology, University of Massachusetts Medical School, Worcester, USA, MA
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3
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Selove W, Hutchinson L, Makarenko V, Meng X, Tomaszewicz K, Ramanathan M, Cerny J, Nath R, Chen B, Woda B, Bledsoe JR. Impact of pretransplant mutation status on survival after allogeneic stem cell transplant for acute myeloid leukemia. eJHaem 2021; 2:514-519. [PMID: 35844698 PMCID: PMC9175694 DOI: 10.1002/jha2.260] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 11/24/2022]
Affiliation(s)
- William Selove
- Department of Pathology UMass Memorial Medical Center University of Massachusetts Worcester Massachusetts USA
| | - Lloyd Hutchinson
- Department of Pathology UMass Memorial Medical Center University of Massachusetts Worcester Massachusetts USA
| | - Vladislav Makarenko
- Department of Pathology UMass Memorial Medical Center University of Massachusetts Worcester Massachusetts USA
| | - Xiuling Meng
- Department of Pathology UMass Memorial Medical Center University of Massachusetts Worcester Massachusetts USA
| | - Keith Tomaszewicz
- Department of Pathology UMass Memorial Medical Center University of Massachusetts Worcester Massachusetts USA
| | - Muthalagu Ramanathan
- Department of Hematology‐Oncology UMass Memorial Medical Center University of Massachusetts Worcester Massachusetts USA
| | - Jan Cerny
- Department of Hematology‐Oncology UMass Memorial Medical Center University of Massachusetts Worcester Massachusetts USA
| | - Rajneesh Nath
- Department of Hematology Medical Oncology Banner MD Anderson Cancer Center Clinic Gilbert Arizona USA
| | - Benjamin Chen
- Bristol Myers Squibb Company Cambridge Massachusetts USA
| | - Bruce Woda
- Department of Pathology UMass Memorial Medical Center University of Massachusetts Worcester Massachusetts USA
| | - Jacob R. Bledsoe
- Department of Pathology UMass Memorial Medical Center University of Massachusetts Worcester Massachusetts USA
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4
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Sun T, Hutchinson L, Tomaszewicz K, Caporelli ML, Meng X, McCauley K, Fischer AH, Cosar EF, Cornejo KM. Diagnostic value of a comprehensive, urothelial carcinoma-specific next-generation sequencing panel in urine cytology and bladder tumor specimens. Cancer Cytopathol 2021; 129:537-547. [PMID: 33539671 DOI: 10.1002/cncy.22410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/02/2020] [Revised: 11/06/2020] [Accepted: 01/04/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Urine cytology can reliably diagnose high-grade urothelial carcinoma (HGUC) but not low-grade urothelial carcinoma (LGUC), and a more sensitive test is needed. Previously, a pilot study highlighted the possible diagnostic utility of next-generation sequencing (NGS) in identifying both LGUC and HGUC in urine cytology specimens. METHODS Twenty-eight urine ThinPrep cytology specimens and preceding or subsequent bladder tumor biopsy/resection specimens obtained within 3 months were included in the study (LGUC, n = 15; HGUC, n = 13). A customized, bladder-specific NGS panel was performed; it covered 69 frequently mutated or altered genes in urothelial carcinoma (UC) that were reported by The Cancer Genome Atlas and the Catalogue of Somatic Mutations in Cancer. RESULTS The sequencing results were compared between the urine cytology specimens and the corresponding bladder tumor biopsies/resections. TP53 was the most frequently identified mutation in HGUC cases (11 of 13 [85%]). PIK3CA and KDM6A were the most frequently identified mutations in LGUC: they occurred in 7 of 15 cases (47%) and in 6 of 15 cases (40%), respectively. Additional frequent mutations identified in the panel included ARID1A (n = 5), EP300 (n = 4), LRP1B (n = 3), ERBB2 (n = 2), STAG2 (n = 2), FGFR3 (n = 3), MLL (n = 2), MLL3 (n = 2), CREBBP1 (n = 1), RB1 (n = 1), and FAT4 (n = 1). Overall, the concordance between the cytology and surgical specimens was 75%. The sensitivity and specificity for identifying mutations in urine cytology specimens were 84% and 100%, respectively. CONCLUSIONS A bladder-specific NGS panel increases the sensitivity and specificity of urine cytology's diagnostic utility in both low- and high-grade tumors and may serve as a noninvasive surveillance method in the follow-up of patients with UC harboring known mutations.
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Affiliation(s)
- Tong Sun
- Department of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Lloyd Hutchinson
- Department of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Keith Tomaszewicz
- Department of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Mandi-Lee Caporelli
- Department of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Xiuling Meng
- Department of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Kathleen McCauley
- Department of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Andrew H Fischer
- Department of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Ediz F Cosar
- Department of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Kristine M Cornejo
- Department of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, Massachusetts.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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5
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Cornejo KM, Cosar EF, Paner GP, Yang P, Tomaszewicz K, Meng X, Mehta V, Sirintrapun SJ, Barkan GA, Hutchinson L. Mutational Profile Using Next-Generation Sequencing May Aid in the Diagnosis and Treatment of Urachal Adenocarcinoma. Int J Surg Pathol 2019; 28:51-59. [PMID: 31496327 DOI: 10.1177/1066896919872535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Objectives. The rare urachal adenocarcinoma (UAC) of the bladder has striking morphologic and immunohistochemical overlap with colorectal adenocarcinoma (CAC) and bladder adenocarcinoma (BAC). To date, the mutational status in UAC and BAC has not been well investigated. Methods. We retrospectively evaluated 34 UACs (mucinous, n = 9; intestinal, n = 3; signet ring cell, n = 1; not otherwise specified, n = 21) and 4 BACs (n = 4). Next-generation sequencing analysis of 50 cancer "hotspot" gene mutations using the Ampliseq Cancer Hotspot Panel v2 was performed. Two UAC cases did not have adequate DNA quality with poor sequencing coverage and were excluded from the study. Results. RAS mutations were identified in 16 of 32 (50%) UACs (15 KRAS; 1 NRAS) and none of the BACs (0%). TP53 mutations were found in both UACs (18/32; 56%) and BACs (4/4; 100%). GNAS (n = 4), SMAD4 (n = 3), and BRAF (n = 1) mutations were only found in UACs. In contrast, APC (n = 2) mutations were only found in BACs. The mucinous subtype of UAC contained a SMAD4 mutation in 33% of cases (3/9), which was not identified in any other subtype (0/23; 0%) (P = .0169). The only BRAF mutation was identified in the single signet ring cell subtype of UAC. There were no other differences in the mutation profile when comparing histologic subtypes of UAC. Conclusions. In summary, UAC and BAC have overlapping but distinct mutation profiles and these differences may aid in separating these 2 entities. Next-generation sequencing to identify therapeutic targets or resistance markers may aid treatment decisions.
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Affiliation(s)
- Kristine M Cornejo
- University of Massachusetts Medical School, UMass Memorial Medical Center, Worcester, MA, USA
| | - Ediz F Cosar
- University of Massachusetts Medical School, UMass Memorial Medical Center, Worcester, MA, USA
| | | | - Ping Yang
- Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Keith Tomaszewicz
- University of Massachusetts Medical School, UMass Memorial Medical Center, Worcester, MA, USA
| | - Xiuling Meng
- University of Massachusetts Medical School, UMass Memorial Medical Center, Worcester, MA, USA
| | - Vikas Mehta
- Mount Sinai Hospital Medical Center, Chicago, IL, USA
| | | | | | - Lloyd Hutchinson
- University of Massachusetts Medical School, UMass Memorial Medical Center, Worcester, MA, USA
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6
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Sakhdari A, Moghaddam PA, Ok CY, Walter O, Tomaszewicz K, Caporelli ML, Meng X, LaFemina J, Whalen G, Belkin E, Zivny J, Wassef W, Woda BA, Hutchinson LM, Cosar EF. Somatic molecular analysis augments cytologic evaluation of pancreatic cyst fluids as a diagnostic tool. Oncotarget 2019; 10:4026-4037. [PMID: 31258847 PMCID: PMC6592293 DOI: 10.18632/oncotarget.26999] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 02/08/2019] [Accepted: 05/20/2019] [Indexed: 12/16/2022] Open
Abstract
Objective: Better tools are needed for early diagnosis and classification of pancreatic cystic lesions (PCL) to trigger intervention before neoplastic precursor lesions progress to adenocarcinoma. We evaluated the capacity of molecular analysis to improve the accuracy of cytologic diagnosis for PCL with an emphasis on non-diagnostic/negative specimens. Design: In a span of 7 years, at a tertiary care hospital, 318 PCL endoscopic ultrasound-guided fine needle aspirations (EUS-FNA) were evaluated by cytologic examination and molecular analysis. Mucinous PCL were identified based on a clinical algorithm and 46 surgical resections were used to verify this approach. The mutation allele frequency (MAF) of commonly altered genes (BRAF, CDKN2A, CTNNB1, GNAS, RAS, PIK3CA, PTEN, SMAD4, TP53 and VHL) was evaluated for their ability to identify and grade mucinous PCL. Results: Cytology showed a diagnostic sensitivity of 43.5% for mucinous PCL due in part to the impact of non-diagnostic (28.8%) and negative (50.5%) specimens. Incorporating an algorithmic approach or molecular analysis markedly increased the accuracy of cytologic evaluation. Detection of mucinous PCL by molecular analysis was 93.3% based on the detection of KRAS and/or GNAS gene mutations (p = 0.0001). Additional genes provided a marginal improvement in sensitivity but were associated with cyst type (e.g. VHL) and grade (e.g. SMAD4). In the surgical cohort, molecular analysis and the proposed algorithm showed comparable sensitivity (88.9% vs. 100%). Conclusions: Incorporating somatic molecular analysis in the cytologic evaluation of EUS-FNA increases diagnostic accuracy for detection, classification and grading of PCL. This approach has the potential to improve patient management.
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Affiliation(s)
- Ali Sakhdari
- University of Massachusetts Medical School, Department of Pathology, Worcester, MA, USA
- MD Anderson Cancer Center, Department of Hematopathology, Houston, TX, USA
| | - Parnian Ahmadi Moghaddam
- University of Massachusetts Medical School, Department of Pathology, Worcester, MA, USA
- Massachusetts General Hospital, Department of Pathology, Boston, MA, USA
- University of Texas, Health Science Center, Department of Pathology, Houston, TX, USA
| | - Chi Young Ok
- University of Massachusetts Medical School, Department of Pathology, Worcester, MA, USA
- MD Anderson Cancer Center, Department of Hematopathology, Houston, TX, USA
| | - Otto Walter
- University of Massachusetts Medical School, Department of Pathology, Worcester, MA, USA
| | - Keith Tomaszewicz
- University of Massachusetts Medical School, Department of Pathology, Worcester, MA, USA
| | - Mandi-Lee Caporelli
- University of Massachusetts Medical School, Department of Pathology, Worcester, MA, USA
| | - Xiuling Meng
- University of Massachusetts Medical School, Department of Pathology, Worcester, MA, USA
| | - Jennifer LaFemina
- University of Massachusetts Medical School, Department of Surgery, Worcester, MA, USA
| | - Giles Whalen
- University of Massachusetts Medical School, Department of Surgery, Worcester, MA, USA
| | - Edward Belkin
- University of Massachusetts Medical School, Department of Medicine, Worcester, MA, USA
| | - Jaroslav Zivny
- University of Massachusetts Medical School, Department of Medicine, Worcester, MA, USA
| | - Wahid Wassef
- University of Massachusetts Medical School, Department of Medicine, Worcester, MA, USA
| | - Bruce A. Woda
- University of Massachusetts Medical School, Department of Pathology, Worcester, MA, USA
| | - Lloyd M. Hutchinson
- University of Massachusetts Medical School, Department of Pathology, Worcester, MA, USA
| | - Ediz F. Cosar
- University of Massachusetts Medical School, Department of Pathology, Worcester, MA, USA
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7
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Zhu X, Salhab M, Tomaszewicz K, Meng X, Mathew C, Bathini V, Switzer B, Walter O, Cosar EF, Wang X, Lambert LA, Hutchinson LM. Heterogeneous mutational profile and prognosis conferred by TP53 mutations in appendiceal mucinous neoplasms. Hum Pathol 2019; 85:260-269. [DOI: 10.1016/j.humpath.2018.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 10/27/2022]
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8
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Gultawatvichai P, Puthawala I, Tomaszewicz K, Bathini V, Hutchinson L. Prevalence of KRAS mutation subtypes and MSI status in pancreatic cancer. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy304.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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9
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Zhu S, Ward BM, Yu J, Matthew-Onabanjo AN, Janusis J, Hsieh CC, Tomaszewicz K, Hutchinson L, Zhu LJ, Kandil D, Shaw LM. IRS2 mutations linked to invasion in pleomorphic invasive lobular carcinoma. JCI Insight 2018; 3:97398. [PMID: 29669935 DOI: 10.1172/jci.insight.97398] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 09/12/2017] [Accepted: 03/14/2018] [Indexed: 12/30/2022] Open
Abstract
Pleomorphic invasive lobular carcinoma (PILC) is an aggressive variant of invasive lobular breast cancer that is associated with poor clinical outcomes. Limited molecular data are available to explain the mechanistic basis for PILC behavior. To address this issue, targeted sequencing was performed to identify molecular alterations that define PILC. This sequencing analysis identified genes that distinguish PILC from classic ILC and invasive ductal carcinoma by the incidence of their genomic changes. In particular, insulin receptor substrate 2 (IRS2) is recurrently mutated in PILC, and pathway analysis reveals a role for the insulin receptor (IR)/insulin-like growth factor-1 receptor (IGF1R)/IRS2 signaling pathway in PILC. IRS2 mutations identified in PILC enhance invasion, revealing a role for this signaling adaptor in the aggressive nature of PILC.
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Affiliation(s)
- Sha Zhu
- Department of Molecular, Cell and Cancer Biology
| | | | - Jun Yu
- Department of Molecular, Cell and Cancer Biology
| | | | | | | | | | | | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology.,Department of Molecular Medicine, and.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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10
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Liu Q, Cornejo KM, Cheng L, Hutchinson L, Wang M, Zhang S, Tomaszewicz K, Cosar EF, Woda BA, Jiang Z. Next-Generation Sequencing to Detect Deletion of RB1 and ERBB4 Genes in Chromophobe Renal Cell Carcinoma: A Potential Role in Distinguishing Chromophobe Renal Cell Carcinoma from Renal Oncocytoma. Am J Pathol 2018; 188:846-852. [PMID: 29353061 DOI: 10.1016/j.ajpath.2017.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/24/2017] [Accepted: 12/05/2017] [Indexed: 11/30/2022]
Abstract
Overlapping morphologic, immunohistochemical, and ultrastructural features make it difficult to diagnose chromophobe renal cell carcinoma (ChRCC) and renal oncocytoma (RO). Because ChRCC is a malignant tumor, whereas RO is a tumor with benign behavior, it is important to distinguish these two entities. We aimed to identify genetic markers that distinguish ChRCC from RO by using next-generation sequencing (NGS). NGS for hotspot mutations or gene copy number changes was performed on 12 renal neoplasms, including seven ChRCC and five RO cases. Matched normal tissues from the same patients were used to exclude germline variants. Rare hotspot mutations were found in cancer-critical genes (TP53 and PIK3CA) in ChRCC but not RO. The NGS gene copy number analysis revealed multiple abnormalities. The two most common deletions were tumor-suppressor genes RB1 and ERBB4 in ChRCC but not RO. Fluorescence in situ hybridization was performed on 65 cases (ChRCC, n = 33; RO, n = 32) to verify hemizygous deletion of RB1 (17/33, 52%) or ERBB4 (11/33, 33%) in ChRCC, but not in RO (0/32, 0%). In total, ChRCCs (23/33, 70%) carry either a hemizygous deletion of RB1 or ERBB4. The combined use of RB1 and ERBB4 fluorescence in situ hybridization to detect deletion of these genes may offer a highly sensitive and specific assay to distinguish ChRCC from RO.
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Affiliation(s)
- Qingqing Liu
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kristine M Cornejo
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Liang Cheng
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Lloyd Hutchinson
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Mingsheng Wang
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Shaobo Zhang
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Keith Tomaszewicz
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Ediz F Cosar
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Bruce A Woda
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Zhong Jiang
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts.
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11
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Magotra M, Sakhdari A, Lee PJ, Tomaszewicz K, Dresser K, Hutchinson LM, Woda BA, Chen BJ. Immunohistochemical loss of 5-hydroxymethylcytosine expression in acute myeloid leukaemia: relationship to somatic gene mutations affecting epigenetic pathways. Histopathology 2016; 69:1055-1065. [PMID: 27458708 DOI: 10.1111/his.13046] [Citation(s) in RCA: 8] [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] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/22/2016] [Indexed: 12/17/2022]
Abstract
AIMS Genes affecting epigenetic pathways are frequently mutated in myeloid malignancies, including acute myeloid leukaemia (AML). The genes encoding TET2, IDH1 and IDH2 are among the most commonly mutated genes, and cause defective conversion of 5-methylcytosine into 5-hydroxymethylcytosine (5hmC), impairing demethylation of DNA, and presumably serving as driver mutations in leukaemogenesis. The aim of this study was to correlate 5hmC immunohistochemical loss with the mutation status of genes involved in epigenetic pathways in AML. METHODS AND RESULTS Immunohistochemical staining with an anti-5hmC antibody was performed on 41 decalcified, formalin-fixed paraffin-embedded (FFPE) bone marrow biopsies from patients with AML. Archived DNA was subjected to next-generation sequencing for analysis of a panel of genes, including TET2, IDH1, IDH2, WT1 and DNMT3A. TET2, IDH1, IDH2, WT1 and DNMT3A mutations were found in 46% (19/41) of the cases. Ten of 15 cases (67%) with TET2, IDH1, IDH2 or WT1 mutations showed deficient 5hmC staining, whereas nine of 26 cases (35%) without a mutation in these genes showed loss of 5hmC. It is of note that all four cases with TET2 mutations showed deficient 5hmC staining. CONCLUSIONS Overall, somatic mutations in TET2, IDH1, IDH2, WT1 and DNMT3A were common in our cohort of AML cases. Immunohistochemical staining for 5hmC was lost in the majority of cases harbouring mutations in these genes, reflecting the proposed relationship between dysfunctional epigenetic pathways and leukaemogenesis.
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Affiliation(s)
- Minoti Magotra
- Department of Pathology, University of Massachusetts Memorial Medical Center and University of Massachusetts Medical School, Worcester, MA, USA
| | - Ali Sakhdari
- Department of Pathology, University of Massachusetts Memorial Medical Center and University of Massachusetts Medical School, Worcester, MA, USA
| | - Paul J Lee
- Department of Pathology, University of Massachusetts Memorial Medical Center and University of Massachusetts Medical School, Worcester, MA, USA
| | - Keith Tomaszewicz
- Department of Pathology, University of Massachusetts Memorial Medical Center and University of Massachusetts Medical School, Worcester, MA, USA
| | - Karen Dresser
- Department of Pathology, University of Massachusetts Memorial Medical Center and University of Massachusetts Medical School, Worcester, MA, USA
| | - Lloyd M Hutchinson
- Department of Pathology, University of Massachusetts Memorial Medical Center and University of Massachusetts Medical School, Worcester, MA, USA
| | - Bruce A Woda
- Department of Pathology, University of Massachusetts Memorial Medical Center and University of Massachusetts Medical School, Worcester, MA, USA
| | - Benjamin J Chen
- Department of Pathology, University of Massachusetts Memorial Medical Center and University of Massachusetts Medical School, Worcester, MA, USA
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12
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Kamionek M, Ahmadi Moghaddam P, Sakhdari A, Kovach AE, Welch M, Meng X, Dresser K, Tomaszewicz K, Cosar EF, Mark EJ, Fraire AE, Hutchinson L. Mutually exclusive extracellular signal-regulated kinase pathway mutations are present in different stages of multi-focal pulmonary Langerhans cell histiocytosis supporting clonal nature of the disease. Histopathology 2016; 69:499-509. [DOI: 10.1111/his.12955] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/21/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Michal Kamionek
- Department of Pathology; Massachusetts General Hospital; Boston MA USA
| | | | - Ali Sakhdari
- Department of Pathology; University of Massachusetts Medical School; Worcester MA USA
| | | | - Matthew Welch
- Department of Pathology; University of Massachusetts Medical School; Worcester MA USA
| | - Xiuling Meng
- Department of Pathology; University of Massachusetts Medical School; Worcester MA USA
| | - Karen Dresser
- Department of Pathology; University of Massachusetts Medical School; Worcester MA USA
| | - Keith Tomaszewicz
- Department of Pathology; University of Massachusetts Medical School; Worcester MA USA
| | - Ediz F Cosar
- Department of Pathology; University of Massachusetts Medical School; Worcester MA USA
| | - Eugene J Mark
- Department of Pathology; Massachusetts General Hospital; Boston MA USA
| | - Armando E Fraire
- Department of Pathology; University of Massachusetts Medical School; Worcester MA USA
| | - Lloyd Hutchinson
- Department of Pathology; University of Massachusetts Medical School; Worcester MA USA
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Cornejo KM, Hutchinson L, Cosar EF, Smith T, Tomaszewicz K, Dresser K, Deng A. Is it a primary or metastatic melanocytic neoplasm of the central nervous system?: A molecular based approach. Pathol Int 2014; 63:559-64. [PMID: 24274719 DOI: 10.1111/pin.12107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 04/12/2013] [Accepted: 10/03/2013] [Indexed: 12/11/2022]
Abstract
Primary melanocytic neoplasms of the central nervous system (CNS) are uncommon and must be distinguished from metastatic lesions as patients with metastatic disease carry a worse prognosis. Therefore, tools to aid in the diagnosis of a primary CNS melanocytic neoplasm would be of clinical utility. Primary CNS melanocytic neoplasms, including uveal melanomas have frequent mutations in GNAQ and GNA11, but are rare in cutaneous and mucosal melanomas. Additionally, primary uveal melanomas often exhibit monosomy 3 conferring an elevated risk of metastasis. We present a 63 year-old male with a melanocytic neoplasm in the thoracic spinal cord. Molecular studies revealed the tumor contained a GNAQ mutation and four-color fluorescent in situ hybridization (FISH) composed of chromosome enumeration probes for 3, 7, 17 and a locus specific probe for 9p21/CDKN2A yielded a normal result (i.e. two copies per cell), favoring a primary versus metastatic melanocytic neoplasm of the CNS. We report a case in which the combination of mutational analysis and FISH aided in identifying the origin of the neoplasm.
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Affiliation(s)
- Kristine M Cornejo
- Department of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, MA, USA
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14
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Cornejo KM, Hutchinson L, Deng A, Tomaszewicz K, Welch M, Lyle S, Dresser K, Cosar EF. BRAF/KRAS gene sequencing of sebaceous neoplasms after mismatch repair protein analysis. Hum Pathol 2014; 45:1213-20. [DOI: 10.1016/j.humpath.2014.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 01/28/2014] [Accepted: 02/07/2014] [Indexed: 01/29/2023]
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Shen Y, Irons M, Miller DT, Cheung SW, Lip V, Sheng X, Tomaszewicz K, Shao H, Fang H, Tang HS, Irons M, Walsh CA, Platt O, Gusella JF, Wu BL. Development of a focused oligonucleotide-array comparative genomic hybridization chip for clinical diagnosis of genomic imbalance. Clin Chem 2007; 53:2051-9. [PMID: 17901113 DOI: 10.1373/clinchem.2007.090290] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [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] [Indexed: 11/06/2022]
Abstract
BACKGROUND Submicroscopic genomic imbalance underlies well-defined microdeletion and microduplication syndromes and contributes to general developmental disorders such as mental retardation and autism. Array comparative genomic hybridization (CGH) complements routine cytogenetic methods such as karyotyping and fluorescence in situ hybridization (FISH) for the detection of genomic imbalance. Oligonucleotide arrays in particular offer advantages in ease of manufacturing, but standard arrays for single-nucleotide polymorphism genotyping or linkage analysis offer variable coverage in clinically relevant regions. We report the design and validation of a focused oligonucleotide-array CGH assay for clinical laboratory diagnosis of genomic imbalance. METHODS We selected >10 000 60-mer oligonucleotide features from Agilent's eArray probe library to interrogate all subtelomeric and pericentromeric regions and 95 additional clinically relevant regions for a total of 179 loci. Sensitivity and specificity were measured for 105 patient samples, including 51 with known genomic-imbalance events, as detected by bacterial artificial chromosome-based array CGH, FISH, or multiplex ligation-dependent probe amplification. RESULTS Focused array CGH detected all known regions of genomic imbalance in 51 validation samples with 100% concordance and an excellent signal-to-noise ratio. The mean SD among log(2) ratios of all noncontrol features without copy number alteration was 0.062 (median, 0.055). Clinical testing of another 211 samples from individuals with developmental delay, unexplained mental retardation, dysmorphic features, or multiple congenital anomalies revealed genomic imbalance in 25 samples (11.9%). CONCLUSIONS This focused oligonucleotide-array CGH assay, a flexible, robust method for clinically diagnosing genetic disorders associated with genomic imbalance, offers appreciable advantages over currently available platforms.
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Affiliation(s)
- Yiping Shen
- Department of Laboratory Medicine, Children's Hospital Boston, Boston, MA 02115, USA
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Tomaszewicz K, Kang P, Wu BL. Detection of homozygous and heterozygous SMN deletions of spinal muscular atrophy in a single assay with multiplex ligation-dependent probe amplification. Beijing Da Xue Xue Bao Yi Xue Ban 2005; 37:55-7. [PMID: 15719043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
OBJECTIVE Spinal muscular atrophy(SMA), an autosomal recessive neuromuscular degeneration of the anterior horn cells of the spinal cord and brain stem, results in one of the most common diseases with muscle fatigue and atrophy. Most SMA cases including all the types are due to the homozygous deletion of at least exon 7 within the survival motor neuron 1 (SMN-1) gene. Although a "golden standard" assay (PCR with mismatch primer followed by enzyme digestion) is very reliable for the identification of homozygous SMN-1 deletion, the carrier detection of heterozygous SMN-1 deletion remains a challenge. METHODS Some PCR-based gene dosage assays or multiplex PCR allow for the determination of the copy number of SMN-1 gene to identify heterozygous deletion, but these procedures are often time consuming and available on a limited clinical basis. Recently developed MLPA (multiplex ligation-dependent probe amplification) is an efficient procedure that can accurately analyze relative quantification to establish the copy number of the SMN gene. We performed a validation for simultaneous detection of homozygous SMN-1 deletions of SMA patients and heterozygous SMN-1 deletions of SMA carriers in a simple assay using a MLPA-SMA assay specific reagent. RESULTS Six out of 20 patients with SMA were found to have homozygous SMN-1 deletion, confirmed by the PCR/digestion assay. All 4 parents of the children with SMA had heterozygous SMN-1 deletion, confirmed by an independent relative quantitative analysis. CONCLUSION MLPA provides a simple, rapid and accurate method of simultaneously detecting homozygous deletions and heterozygous deletions in a single assay for both SMN-1 and SMN-2 genes.
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Affiliation(s)
- Keith Tomaszewicz
- Department of Laboratory Medicine, Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
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