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Stolnicu S, Praiss AM, Allison D, Tessier-Cloutier B, Flynn J, Iasonos A, Hoang L, Terinte C, Pesci A, Mateoiu C, Lastra RR, Kiyokawa T, Ali-Fehmi R, Kheil M, Oliva E, Devins K, Abu-Rustum N, Soslow RA. Proposal of Novel Binary Grading Systems for Cervical Squamous Cell Carcinoma. Int J Gynecol Pathol 2024; 43:203-214. [PMID: 38085957 PMCID: PMC11031322 DOI: 10.1097/pgp.0000000000000979] [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] [Indexed: 04/20/2024]
Abstract
We compared grading systems and examined associations with tumor stroma and survival in patients with cervical squamous cell carcinoma. Available tumor slides were collected from 10 international institutions. Broders tumor grade, Jesinghaus grade (informed by the pattern of tumor invasion), Silva pattern, and tumor stroma were retrospectively analyzed; associations with overall survival (OS), progression-free survival (PFS), and presence of lymph node metastases were examined. Binary grading systems incorporating tumor stromal changes into Broders and Jesinghaus grading systems were developed. Of 670 cases, 586 were reviewed for original Broders tumor grade, 587 for consensus Broders grade, 587 for Jesinghaus grade, 584 for Silva pattern, and 556 for tumor stroma. Reproducibility among grading systems was poor (κ = 0.365, original Broders/consensus Broders; κ = 0.215, consensus Broders/Jesinghaus). Median follow-up was 5.7 years (range, 0-27.8). PFS rates were 93%, 79%, and 71%, and OS rates were 98%, 86%, and 79% at 1, 5, and 10 years, respectively. On univariable analysis, original Broders ( P < 0.001), consensus Broders ( P < 0.034), and Jesinghaus ( P < 0.013) grades were significant for OS; original Broders grade was significant for PFS ( P = 0.038). Predictive accuracy for OS and PFS were 0.559 and 0.542 (original Broders), 0.542 and 0.525 (consensus Broders), 0.554 and 0.541 (Jesinghaus grade), and 0.512 and 0.515 (Silva pattern), respectively. Broders and Jesinghaus binary tumor grades were significant on univariable analysis for OS and PFS, and predictive value was improved. Jesinghaus tumor grade ( P < 0.001) and both binary systems (Broders, P = 0.007; Jesinghaus, P < 0.001) were associated with the presence of lymph node metastases. Histologic grade has poor reproducibility and limited predictive accuracy for squamous cell carcinoma. The proposed binary grading system offers improved predictive accuracy for survival and the presence of lymph none metastases.
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Affiliation(s)
- Simona Stolnicu
- Department of Pathology, University of Medicine, Pharmacy, Sciences and Technology “George E Palade” of Targu Mures, Targu Mures, Romania
| | - Aaron M. Praiss
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas Allison
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Jessica Flynn
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexia Iasonos
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lien Hoang
- Vancouver General Hospital, Vancouver, BC, Canada
| | | | - Anna Pesci
- IRCSS Ospedale Sacro Cuore Don Calabria, Negrar, Italy
| | - Claudia Mateoiu
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | | | - Rouba Ali-Fehmi
- Department of Pathology, Wayne State University, Detroit, MI, USA
| | - Mira Kheil
- Department of Pathology, Wayne State University, Detroit, MI, USA
| | | | - Kyle Devins
- Massachusetts General Hospital, Boston, MA, USA
| | - Nadeem Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Robert A. Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Chiang S, Tessier-Cloutier B, Klein E, Ardon O, Mueller JJ, Leitao MM, Abu-Rustum NR, Ellenson LH. Establishing guidelines for sentinel lymph node ultrastaging in endometrial cancer. Int J Gynecol Cancer 2024:ijgc-2023-005157. [PMID: 38388180 DOI: 10.1136/ijgc-2023-005157] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Many sentinel lymph node (SLN) ultrastaging protocols for endometrial cancer exist, but there is no consensus method. OBJECTIVE This study aims to develop guidelines for size criteria in SLN evaluation for endometrial cancer, to determine whether a single cytokeratin AE1:AE3 immunohistochemical slide provides sufficient data for diagnosis, and to compare cost efficiency between current and limited ultrastaging protocols at a large tertiary care institution. METHODS Our current SLN ultrastaging protocol consists of cutting two adjacent paraffin block sections at two levels (L1 and L2), 50 μm apart, with two slides at each level stained with hematoxylin and eosin and cytokeratin AE1:AE3 immunohistochemistry. We retrospectively reviewed digitized L1 and L2 slides of all positive ultrastaged SLNs from patients treated for endometrial cancer between January 2013 and January 2020. SLN diagnosis was defined by measuring the largest cluster of contiguous tumor cells in a single cross section: macrometastasis (>2.0 mm), micrometastasis (>0.2 to ≤2.0 mm or >200 cells), or isolated tumor cells (≤0.2 mm or ≤200 cells). Concordance between L1 and L2 results was evaluated. Cost efficiency between current (two immunohistochemical slides per block) and proposed limited (one immunohistochemical slide per block) protocols was compared. RESULTS Digitized slides of 147 positive SLNs from 109 patients were reviewed; 4.1% of SLNs were reclassified based on refined size criteria. Complete concordance between L1 and L2 interpretations was seen in 91.8% of SLNs. A false-negative rate of 0%-0.9% in detecting micrometastasis and macrometastasis using a limited protocol was observed. Estimated charge-level savings of a limited protocol were 50% per patient. CONCLUSION High diagnostic accuracy in SLN interpretation may be achieved using a limited ultrastaging protocol of one immunohistochemical slide per block and linear measurement of the largest cluster of contiguous tumor cells. Implementation of the proposed limited ultrastaging protocol may result in laboratory cost savings with minimal impact on health outcomes.
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Affiliation(s)
- Sarah Chiang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Eric Klein
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Orly Ardon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jennifer J Mueller
- Department of Surgery, Gynecology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mario M Leitao
- Department of Surgery, Gynecology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem R Abu-Rustum
- Department of Surgery, Gynecology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lora H Ellenson
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Huber R, Lee J, Borretta L, Tessier-Cloutier B, Lum A, Yip S, Horst BA. TERT promoter mutations in atypical melanocytic lesions: A series of seven cases with adverse melanoma-specific outcome. Hum Pathol 2024; 144:34-39. [PMID: 38224873 DOI: 10.1016/j.humpath.2024.01.003] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
Abstract
The majority of melanocytic proliferations can be readily categorized as benign or malignant based on histologic assessment under the microscope by a trained dermatopathologist. However, a subset of lesions, termed Atypical Melanocytic Proliferations (AMPs), are histologically ambiguous, leading to possible diagnostic error and suboptimal treatment. Mutations in the promoter region of the catalytic subunit of telomerase, telomerase reverse transcriptase (TERT), are commonly found in melanomas but are rare in melanocytic nevi. In this study, we aimed to determine the prevalence of hot spot TERT promoter (TERT-p) mutations in AMPs with adverse melanoma-specific outcome. Studies were approved by respective institutional review boards. Using a multi-center database, we identified seven cases of melanocytic proliferations with a clinical follow-up period of at least 4 years, which were initially diagnosed as AMPs, and which recurred either as melanoma at site of prior biopsy or as metastatic melanoma. Sequencing of the TERT-p region showed hotspot mutations in three cases (43 %), suggesting that TERT-p mutations are enriched and could aid in the identification of AMPs with adverse outcome. In comparison with existing ancillary techniques for prognostication of AMPs, TERT-p mutation analysis may have advantages in terms of cost effectiveness and turnaround time, and is a promising diagnostic parameter with potential widespread utility.
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Affiliation(s)
- Reed Huber
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada
| | - Jonathan Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada
| | - Lisa Borretta
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | | | - Amy Lum
- Molecular Oncology, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada
| | - Basil A Horst
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada.
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Kommoss FK, Lee CH, Tessier-Cloutier B, Gilks CB, Stewart CJ, von Deimling A, Köbel M. Mesonephric-like adenocarcinoma harbours characteristic copy number variations and a distinct DNA methylation signature closely related to mesonephric adenocarcinoma of the cervix. J Pathol 2024; 262:4-9. [PMID: 37850576 DOI: 10.1002/path.6217] [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: 06/22/2023] [Revised: 08/09/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023]
Abstract
Mesonephric-like adenocarcinoma (MLA) of the female genital tract is an uncommon histotype that can arise in both the endometrium and the ovary. The exact cell of origin and histogenesis currently remain unknown. Here, we investigated whole genome DNA methylation patterns and copy number variations (CNVs) in a series of MLAs in the context of a large cohort of various gynaecological carcinoma types. CNV analysis of 19 MLAs uncovered gains of chromosomes 1q (18/19, 95%), 10 (15/19, 79%), 12 (14/19, 74%), and 2 (10/19, 53%), as well as loss of chromosome 1p (7/19, 37%). Gains of chromosomes 1q, 10, and 12 were also identified in the majority of mesonephric adenocarcinomas of the uterine cervix (MAs) as well as subsets of endometrioid carcinomas (ECs) and low-grade serous carcinomas of the ovary (LGSCs) but only in a minority of serous carcinomas of the uterine corpus (USCs), clear cell carcinomas (CCCs), and tubo-ovarian high-grade serous carcinomas (HGSCs). While losses of chromosome 1p together with gains of chromosome 1q were also identified in both MA and LGSC, gains of chromosome 2 were almost exclusively identified in MLA and MA. Unsupervised hierarchical clustering and t-SNE analysis of DNA methylation data (Illumina EPIC array) identified a co-clustering for MLAs and MAs, which was distinct from clusters of ECs, USCs, CCCs, LGSCs, and HGSCs. Group-wise comparisons confirmed a close epigenetic relationship between MLA and MA. These findings, in conjunction with the established histological and immunophenotypical overlap, suggest bona fide mesonephric differentiation, and support a more precise terminology of mesonephric-type adenocarcinoma instead of MLA in these tumours. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Felix Kf Kommoss
- Department of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Cheng-Han Lee
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | | | - C Blake Gilks
- Department of Laboratory Medicine and Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Colin Jr Stewart
- Department of Anatomical Pathology, King Edward Memorial Hospital, Subiaco, WA, Australia
- School for Women's and Infants' Health, University of Western Australia, Perth, WA, Australia
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital and CCU Neuropathology DKFZ, Heidelberg, Germany
| | - Martin Köbel
- Department of Laboratory Medicine and Pathology, University of Calgary, Calgary, AB, Canada
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5
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Tessier-Cloutier B, Kommoss FKF, Kolin DL, Němejcová K, Smith D, Pors J, Stewart CJR, McCluggage WG, Foulkes WD, von Deimling A, Köbel M, Lee CH. Dedifferentiated and Undifferentiated Ovarian Carcinoma: An Aggressive and Molecularly Distinct Ovarian Tumor Characterized by Frequent SWI/SNF Complex Inactivation. Mod Pathol 2024; 37:100374. [PMID: 37925057 DOI: 10.1016/j.modpat.2023.100374] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/17/2023] [Accepted: 10/28/2023] [Indexed: 11/06/2023]
Abstract
Dedifferentiated and undifferentiated ovarian carcinomas (DDOC/UDOC) are rare neoplasms defined by the presence of an undifferentiated carcinoma. In this study, we detailed the clinical, pathological, immunohistochemical, and molecular features of a series of DDOC/UDOC. We collected a multi-institutional cohort of 23 DDOC/UDOC and performed immunohistochemistry for core switch/sucrose nonfermentable (SWI/SNF) complex proteins (ARID1A, ARID1B, SMARCA4, and SMARCB1), mismatch repair (MMR) proteins, and p53. Array-based genome-wide DNA methylation and copy number variation analyses were performed on a subset of cases with comparison made to a previously reported cohort of undifferentiated endometrial carcinoma (UDEC), small cell carcinoma of the ovary, hypercalcemic type (SCCOHT), and tubo-ovarian high-grade serous carcinoma (HGSC). The age of all 23 patients with DDOC/UDOC ranged between 22 and 71 years (with an average age of 50 years), and a majority of them presented with extraovarian disease (16/23). Clinical follow-up was available for 19 patients. Except for 2 patients, the remaining 17 patients died from disease, with rapid disease progression resulting in mortality within a year in stage II-IV settings (median disease-specific survival of 3 months). Eighteen of 22 cases with interpretable immunohistochemistry results showed loss of expression of core SWI/SNF protein(s) that are expected to result in SWI/SNF complex inactivation as 10 exhibited coloss of ARID1A and ARID1B, 7 loss of SMARCA4, and 1 loss of SMARCB1. Six of 23 cases were MMR-deficient. Two of 20 cases exhibited mutation-type p53 immunoreactivity. Methylation profiles showed coclustering of DDOC/UDOC with UDEC, which collectively were distinct from SCCOHT and HGSC. However, DDOC/UDOC showed an intermediate degree of copy number variation, which was slightly greater, compared with SCCOHT but much less compared with HGSC. Overall, DDOC/UDOC, like its endometrial counterpart, is highly aggressive and is characterized by frequent inactivation of core SWI/SNF complex proteins and MMR deficiency. Its molecular profile overlaps with UDEC while being distinct from SCCOHT and HGSC.
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Affiliation(s)
- Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | - Felix K F Kommoss
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - David L Kolin
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Kristýna Němejcová
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - DuPreez Smith
- Department of Obstetrics and Gynecology, University of Alberta, Edmonton, Alberta, Canada
| | - Jennifer Pors
- Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, British Columbia, Canada
| | - Colin J R Stewart
- Department of Pathology, King Edward Memorial Hospital, Perth, Australia
| | - W Glenn McCluggage
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - William D Foulkes
- Departments of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany; CCU Neuropathology, German Cancer Center (DKFZ), Heidelberg, Germany
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Cheng-Han Lee
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.
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Stolnicu S, Allison D, Praiss AM, Tessier-Cloutier B, Momeni Boroujeni A, Flynn J, Iasonos A, Serrette R, Hoang L, Patrichi A, Terinte C, Pesci A, Mateoiu C, Lastra RR, Kiyokawa T, Ali-Fehmi R, Kheil M, Oliva E, Devins KM, Abu-Rustum NR, Soslow RA. Incidence and Clinicopathologic Characteristics of Human Papillomavirus-independent Invasive Squamous Cell Carcinomas of the Cervix: A Morphologic, Immunohistochemical, and Human Papilloma-Virologic Study of 670 Cases. Am J Surg Pathol 2023; 47:1376-1389. [PMID: 37702216 PMCID: PMC10840845 DOI: 10.1097/pas.0000000000002122] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
We aimed to determine the frequency of human papillomavirus-independent (HPVI) cervical squamous cell carcinoma (SCC) and to describe clinicopathologic characteristics. Among 670 patients with surgically treated SCCs in an established multi-institutional cohort, 447 had available tissue. Tissue microarrays were constructed and studied by in situ hybridization (ISH) for high-risk and low-risk human papillomavirus (HPV) mRNA and immunohistochemistry for p16 and p53. Tumors were HPVI if negative by HPV ISH and they failed to show diffuse p16 positivity by immunohistochemistry, and human papillomavirus-associated (HPVA) if positive by HPV ISH. Ten HPVI SCCs and 435 HPVA SCCs were identified; 2 cases were equivocal and excluded from analysis. The overall rate of HPVI SCC was low (2%) but was higher among older patients (7% in patients above 60 y of age and 17% in patients above 70 y of age). Compared with HPVA, patients with HPVI SCC were significantly older (median age, 72 vs. 49, P <0.001) and diagnosed at a higher stage (40% vs. 18% with stage III/IV disease, P =0.055). p53 expression was varied; 2 cases (20%) had null expression and 8 (80%) had wild-type expression. HPVI SCCs were heterogenous, with keratinizing, nonkeratinizing, and warty morphologies observed. Several cases had a precursor lesion reminiscent of differentiated vulvar intraepithelial neoplasia, with prominent basal atypia and hypereosinophilia or a basaloid-like morphology. Two patients (20%) had distant recurrences within 12 months, and 3 (30%) died of disease during follow-up. HPVI SCCs are rare tumors that are more common among older patients with higher stage disease and have important clinical and histologic differences from HPVA SCCs.
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Affiliation(s)
- Simona Stolnicu
- Department of Pathology, University of Medicine, Pharmacy, Science and Technology "George E Palade" of Targu Mures, Targu Mures
| | | | | | | | | | - Jessica Flynn
- Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center
| | - Alexia Iasonos
- Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center
| | | | - Lien Hoang
- Department of Pathology, Vancouver General Hospital, Vancouver, BC, Canada
| | - Andrei Patrichi
- Department of Pathology, University of Medicine, Pharmacy, Science and Technology "George E Palade" of Targu Mures, Targu Mures
| | | | - Anna Pesci
- Hospital "Sacro Cuore Don Calabria", Negrar, Italy
| | - Claudia Mateoiu
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Takako Kiyokawa
- Department of Pathology, The Jikei University School of Medicine, Tokyo, Japan
| | - Rouba Ali-Fehmi
- Department of Pathology, Wayne State University, Detroit, MI
| | - Mira Kheil
- Department of Pathology, Wayne State University, Detroit, MI
| | | | | | - Nadeem R Abu-Rustum
- Surgery
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY
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7
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Kertowidjojo EC, Tessier-Cloutier B, Veronica WP, Chui H. Low-grade serous ovarian carcinoma: a brief overview of the histopathologic features and differential diagnosis. Int J Gynecol Cancer 2023:ijgc-2023-004774. [PMID: 37923319 DOI: 10.1136/ijgc-2023-004774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Affiliation(s)
| | | | | | - Herman Chui
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Shen S, Ma W, Brown D, Da Cruz Paula A, Zhou Q, Iaosonos A, Tessier-Cloutier B, Ross DS, Troso-Sandoval T, Reis-Filho JS, Abu-Rustum N, Zhang Y, Ellenson LH, Weigelt B, Makker V, Chui MH. HER2 Genetic Intratumor Heterogeneity Is Associated With Resistance to Trastuzumab and Trastuzumab Emtansine Therapy in Recurrent High-Grade Endometrial Cancer. Mod Pathol 2023; 36:100299. [PMID: 37558129 PMCID: PMC10841308 DOI: 10.1016/j.modpat.2023.100299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/17/2023] [Revised: 07/11/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023]
Abstract
Anti-HER2 targeted therapies have recently demonstrated clinical activity in the treatment of high-grade endometrial carcinomas (ECs), particularly serous carcinomas with HER2 amplification and/or overexpression. Intratumor heterogeneity of HER2 amplification or HER2 genetic intratumor heterogeneity (G-ITH) has been associated with resistance to anti-HER2 therapies in breast and gastroesophageal cancers; however, its clinical relevance in EC is unknown. To characterize HER2 G-ITH in EC, archival specimens from a clinically annotated cohort of 57 ECs treated with trastuzumab or trasutuzmab emtansine in the recurrent (n = 38) or adjuvant (n = 19) setting were subjected to central pathology review, HER2 assessment by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), and next-generation sequencing. HER2 G-ITH, defined as HER2 amplification in 5% to 50% of tumor cells examined by FISH, was identified in 36% (19/53) of ECs and was associated with lower HER2 copy number and levels of protein expression. HER2 IHC revealed spatially distinct areas of strong expression juxtaposed with areas of low/absent expression in tumors with the "cluster" pattern of G-ITH, whereas the "mosaic" pattern was typically associated with a diffuse admixture of cells with variable levels of HER2 expression. HER2 G-ITH was frequently observed in cases with IHC/FISH or FISH/next-generation sequencing discrepancies and/or with an equivocal/negative FISH result (9/13, 69%). Although the objective response rate to anti-HER2 therapy in recurrent ECs was 52% (13/25) for tumors lacking HER2 G-ITH, none (0%, 0/10) of the patients with HER2 G-ITH achieved a complete or partial response (P = .005). HER2 G-ITH was significantly associated with worse progression-free survival (hazard ratio, 2.88; 95% CI, 1.33-6.27; P = .005) but not overall survival. HER2 IHC score, HER2/CEP17 ratio, HER2 copy number, histologic subtype, and other genetic alterations, including PIK3CA hotspot mutations, were not significantly associated with therapeutic response or survival outcomes. Treatment responses were not restricted to serous carcinomas, supporting consideration of anti-HER2 therapy in patients with HER2-positive high-grade ECs of non-serous histology. Our results demonstrate that HER2 G-ITH is an important determinant of response to trastuzumab and trastuzumab emtansine in EC, providing a rationale for the development of novel therapeutic strategies to target HER2-nonamplified resistant tumor subpopulations, such as HER2 antibody-drug conjugates with bystander effects.
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Affiliation(s)
- Sherry Shen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Weining Ma
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David Brown
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Qin Zhou
- Department of Biostatistics and Epidemiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexia Iaosonos
- Department of Biostatistics and Epidemiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dara S Ross
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nadeem Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yanming Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lora H Ellenson
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vicky Makker
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - M Herman Chui
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
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9
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Praiss AM, Allison D, Tessier-Cloutier B, Flynn J, Iasonos A, Hoang L, Patrichi A, Terinte C, Pesci A, Mateoiu C, Lastra RR, Puscasiu L, Kiyokawa T, Ali-Fehmi R, Kheil M, Oliva E, Devins KM, Abu-Rustum NR, Soslow RA, Stolnicu S. Extensive versus focal lymphovascular invasion in squamous cell carcinoma of the cervix: A comprehensive international, multicenter, retrospective clinicopathologic study. Gynecol Oncol 2023; 176:147-154. [PMID: 37541128 PMCID: PMC10809424 DOI: 10.1016/j.ygyno.2023.07.011] [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: 02/01/2023] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 08/06/2023]
Abstract
OBJECTIVE We evaluated clinicopathologic parameters of patients with cervical squamous cell carcinoma (SCC) who were treated with initial surgical management and assessed their relation to survival outcomes. Specifically, we evaluated the relation between extent of lymphovascular invasion (LVI) and survival outcomes. METHODS All available tumor slides from patients with initially surgically treated cervical SCC were collected from 10 institutions and retrospectively analyzed. Standard clinicopathological parameters, tumor stroma, and extent of LVI were assessed (focal: <5 spaces, extensive: ≥5 spaces). PFS and OS were evaluated using Kaplan-Meier methodology. Univariable and multivariable Cox proportional hazards models were created to determine prognostic survival-related risk factors. RESULTS A total of 670 tumor samples were included in the analysis. Median age at diagnosis was 47 years (IQR: 38-60), 457 patients (72%) had a 2018 International Federation of Gynecology and Obstetrics (FIGO) stage I tumor, and 155 tumors (28%) were flat and/or ulcerated. There were 303 nonkeratinizing tumors (51%), 237 keratinizing tumors (40%), and 356 histologic grade 2 tumors (61%). Quantifiable LVI was present in 321 cases (51%; 23% focal and 33% extensive). On multivariable analysis for PFS, extensive and focal LVI had worse outcomes compared to negative LVI (HR: 2.38 [95% CI: 1.26-4.47] and HR: 1.54 [95% CI: 0.76-3.11], respectively; P = 0.02). The difference did not reach statistical significance for OS. CONCLUSION Presence of LVI is a prognostic marker for patients with cervical SCC. Quantification (extensive vs. focal vs. negative) of LVI may be an important biomarker for oncologic outcome.
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Affiliation(s)
- Aaron M Praiss
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas Allison
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Jessica Flynn
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexia Iasonos
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lien Hoang
- Department of Pathology, Vancouver General Hospital, Vancouver, BC, Canada
| | - Andrei Patrichi
- Department of Pathology, University of Medicine, Pharmacy, Science and Technology "George E Palade" of Targu Mures, Targu Mures, Romania
| | | | - Anna Pesci
- Ospedale Sacro Cuore Don Calabria, Negrar, Italy
| | - Claudia Mateoiu
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Ricardo R Lastra
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Lucian Puscasiu
- Department of Gynecology, University of Medicine, Pharmacy, Sciences and Technology "George E Palade" of Targu Mures, Romania
| | | | - Rouba Ali-Fehmi
- Department of Pathology, Wayne State University, Detroit, MI, USA
| | - Mira Kheil
- Department of Pathology, Wayne State University, Detroit, MI, USA
| | | | | | - Nadeem R Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Robert A Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA..
| | - Simona Stolnicu
- Department of Pathology, University of Medicine, Pharmacy, Science and Technology "George E Palade" of Targu Mures, Targu Mures, Romania
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10
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Tessier-Cloutier B. ARID1B Immunohistochemistry Is an Important Test for the Diagnosis of Dedifferentiated and Undifferentiated Gynecologic Malignancies. Cancers (Basel) 2023; 15:4229. [PMID: 37686505 PMCID: PMC10486746 DOI: 10.3390/cancers15174229] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023] Open
Abstract
Dedifferentiated and undifferentiated endometrial and ovarian carcinomas (DDC/UDC) are aggressive malignancies defined by morphologic and molecular undifferentiation, and associated with core SWI/SNF deficiency. Their main differential diagnoses include high-grade endometrial and ovarian carcinomas that often show overlapping morphologic and molecular profiles. Loss of cell lineage markers expression by immunohistochemistry (IHC) is commonly used to assist diagnosis, but it has poor specificity, while core SWI/SNF deficiency is much more specific. Approximately half of SWI/SNF-deficient DDC/UDC are associated with loss of ARID1B expression, yet, unlike the other core SWI/SNF proteins (SMARCA4 and SMARCB1), this test is rarely available, even in tertiary centers. Mutational testing for ARID1B is increasingly common among targeted DNA sequencing panels, but it is difficult to interpret in the absence of IHC results. Overall, the importance of including ARID1B IHC as part of the routine panel for undifferentiated gynecologic malignancies should be emphasized, especially as SWI/SNF inactivation is becoming a necessary biomarker for diagnostics, clinical management, and clinical trial enrollment.
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Affiliation(s)
- Basile Tessier-Cloutier
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; ; Tel.: +1-(514)-934-1934
- Division of Pathology, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
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11
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Yang H, Almadani N, Thompson EF, Tessier-Cloutier B, Chen J, Ho J, Senz J, McConechy MK, Chow C, Ta M, Cheng A, Karnezis A, Huvila J, McAlpine JN, Gilks B, Jamieson A, Hoang LN. Classification of Vulvar Squamous Cell Carcinoma and Precursor Lesions by p16 and p53 Immunohistochemistry: Considerations, Caveats, and an Algorithmic Approach. Mod Pathol 2023; 36:100145. [PMID: 36828360 DOI: 10.1016/j.modpat.2023.100145] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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] [Received: 01/11/2023] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
There is emerging evidence that vulvar squamous cell carcinoma (VSCC) can be prognostically subclassified into 3 groups based on human papillomavirus (HPV) and p53 status: HPV-associated (HPV+), HPV-independent/p53 wild-type (HPV-/p53wt), or HPV-independent/p53 abnormal (HPV-/p53abn). Our goal was to assess the feasibility of separating VSCC and its precursors into these 3 groups using p16 and p53 immunohistochemistry (IHC). A tissue microarray containing 225 VSCC, 43 usual vulvar intraepithelial neoplasia (uVIN/HSIL), 10 verruciform acanthotic vulvar intraepithelial neoplasia (vaVIN), and 34 differentiated VIN (dVIN), was stained for p16 and p53. Noncomplementary p16 and p53 patterns were resolved by repeating p53 IHC and HPV RNA in situ hybridization (ISH) on whole sections, and sequencing for TP53. Of 82 p16-positive VSCC, 73 (89%) had complementary p16 and p53 patterns and were classified into the HPV+ group, 4 (4.9%) had wild-type p53 staining, positive HPV ISH and were classified into the HPV+ group, whereas 5 (6.1%) had p53 abnormal IHC patterns (1 null, 4 overexpression), negativity for HPV ISH, and harbored TP53 mutations (1 splice site, 4 missense); they were classified as HPV-/p53abn. Of 143 p16-negative VSCC, 142 (99.3%) had complementary p53 and p16 patterns: 115 (80.4%) HPV-/p53abn and 27 (18.9%) HPV-/p53wt. One had a basal-sparing p53 pattern, positivity for HPV ISH and was negative for TP53 mutations-HPV+ category. The use of IHC also led to revised diagnoses-HSIL to dVIN (3/43), dVIN to vaVIN (8/34), and dVIN to HSIL (3/34). Overall, 215/225 VSCC (95.6%) could be easily classifiable into 3 groups with p16 and p53 IHC. We identified several caveats, with the major caveat being that "double-positive" p16/p53 should be classified as HPV-/p53abn. We propose an algorithm that will facilitate the application of p16 and p53 IHC to classify VSCC in pathology practice.
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Affiliation(s)
- Hang Yang
- Pathology and Laboratory Medicine, University of British Columbia and Vancouver General Hospital, British Columbia, Canada
| | - Noorah Almadani
- Department of Pathology, Ministry of the National Guard - Health Affairs, and King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Emily F Thompson
- Pathology and Laboratory Medicine, University of British Columbia and Vancouver General Hospital, British Columbia, Canada
| | | | - Julia Chen
- Medical Undergraduate Program, University of British Columbia, British Columbia, Canada
| | - Julie Ho
- Pathology and Laboratory Medicine, University of British Columbia and Vancouver General Hospital, British Columbia, Canada; Genetic Pathology Evaluation Center (GPEC) and Molecular and Advanced Pathology Core (MAPcore), British Columbia, Canada
| | - Janine Senz
- Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | | | - Christine Chow
- Genetic Pathology Evaluation Center (GPEC) and Molecular and Advanced Pathology Core (MAPcore), British Columbia, Canada
| | - Monica Ta
- Genetic Pathology Evaluation Center (GPEC) and Molecular and Advanced Pathology Core (MAPcore), British Columbia, Canada
| | - Angela Cheng
- Genetic Pathology Evaluation Center (GPEC) and Molecular and Advanced Pathology Core (MAPcore), British Columbia, Canada
| | - Anthony Karnezis
- Pathology and Laboratory Medicine, UC Davis Medical Center, California
| | - Jutta Huvila
- Department of Pathology, University of Turku, Turku University Hospital, Turku, Finland
| | - Jessica N McAlpine
- Gynecologic Oncology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blake Gilks
- Pathology and Laboratory Medicine, University of British Columbia and Vancouver General Hospital, British Columbia, Canada; Genetic Pathology Evaluation Center (GPEC) and Molecular and Advanced Pathology Core (MAPcore), British Columbia, Canada
| | - Amy Jamieson
- Gynecologic Oncology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lynn N Hoang
- Pathology and Laboratory Medicine, University of British Columbia and Vancouver General Hospital, British Columbia, Canada; Genetic Pathology Evaluation Center (GPEC) and Molecular and Advanced Pathology Core (MAPcore), British Columbia, Canada.
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12
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Wang XQ, Tessier-Cloutier B, Saunders J, Harvey M, Armstrong L, Ng T, Dunham C, Bush JW. Characterization of Switch/Sucrose Nonfermenting Complex Proteins and Nestin Expression in a Cohort of Pediatric Central Nervous System Tumors. Appl Immunohistochem Mol Morphol 2023; 31:304-310. [PMID: 37036408 DOI: 10.1097/pai.0000000000001122] [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] [Received: 12/23/2021] [Accepted: 03/09/2023] [Indexed: 04/11/2023]
Abstract
Tumors of the central nervous system (CNS) in pediatric patients have undergone significant diagnostic refinement through the use of immunohistochemistry (IHC) and molecular techniques. The utility of these novel IHC antibodies has been demonstrated with the inactivation of the switch/sucrose nonfermenting (SWI/SNF) chromatin-remodeling complex in the diagnosis of atypical teratoid/rhabdoid tumors, predominantly through the loss of integrase interactor 1 (INI1; SMARCB1 ). Alternatively, these tumors may have inactivation of brahma-related gene 1 (BRG1; SMARCA4 ) in a subset of cases. The role of other SWI/SNF component proteins and their expression in pediatric brain tumors is not well established. Nestin, an intermediate filament, has been shown to be present in some pediatric CNS tumors, but of uncertain diagnostic and prognostic significance. We sought to explore the immunohistochemical expression profile for common SWI/SNF subunits and nestin in a pediatric CNS tumor cohort. Using a 118-sample tissue microarray, we performed IHC for INI1, BRG1, brahma (BRM), ARID1A, ARID1B, polybromo 1, and nestin. In 19 cases, INI1 was lost and BRG1 was lost in 2 cases. Interestingly, 6 cases originally diagnosed as primitive neuroectodermal tumors showed isolated loss of BRM. Other SWI/SNF proteins did not provide further diagnostic resolution. Nestin was positive in 76.2% of INI1/BRG1-deficient tumors, compared with 29.1% in INI1/BRG1-intact tumors yielding a sensitivity of 76.2%, specificity of 68.0%, and a P value of <0.001, but nestin positivity did not correlate specifically with poor outcomes. In conclusion, we confirm the utility of BRG1 IHC in the workup of pediatric CNS tumors, which may facilitate a difficult diagnosis when conventional markers are inconclusive, or as a first-line marker in cases where intraoperative smears are suggestive of atypical teratoid/rhabdoid tumor. Although nestin expression was associated with SWI/SNF inactivation, it did not yield statistically significant diagnostic or prognostic information in our study. Interestingly, we identified 6 tumors with isolated BRM IHC loss, the significance of which is uncertain but warrants further investigation.
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Affiliation(s)
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital
| | - Jessica Saunders
- Department of Pathology and Laboratory Medicine
- Division of Anatomical Pathology, British Columbia Children's Hospital and Women's Health Center, Vancouver, BC, Canada
| | - Melissa Harvey
- Division of Pediatric Hematology/Oncology/BMT, British Columbia Children's Hospital, and Department of Pediatrics
| | - Linlea Armstrong
- Provincial Medical Genetics Program, British Columbia Children's Hospital and Women's Health Center, and Department of Medical Genetics, University of British Columbia
| | - Tony Ng
- Department of Pathology and Laboratory Medicine
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital
| | - Christopher Dunham
- Department of Pathology and Laboratory Medicine
- Division of Anatomical Pathology, British Columbia Children's Hospital and Women's Health Center, Vancouver, BC, Canada
| | - Jonathan W Bush
- Department of Pathology and Laboratory Medicine
- Division of Anatomical Pathology, British Columbia Children's Hospital and Women's Health Center, Vancouver, BC, Canada
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13
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Kommoss FKF, Schmidt D, Kommoss F, Tessier-Cloutier B. Small-cell carcinoma of the ovary hypercalcaemic type shows a wild-type immunohistochemical staining pattern of p53. Histopathology 2023. [PMID: 37067676 DOI: 10.1111/his.14926] [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] [Received: 03/15/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/18/2023]
Affiliation(s)
| | - Dietmar Schmidt
- Wissenschaftspark Trier, MVZ für Histologie, Zytologie und molekulare Diagnostik GmbH, Trier
| | - Friedrich Kommoss
- Medizin Campus Bodensee, Institute of Pathology, Friedrichshafen, Germany
| | - Basile Tessier-Cloutier
- Department of Pathology, McGill University, Montreal, QC
- Division of Pathology, McGill University Health Centre, Montreal, QC, Canada
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14
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Tsang ES, Csizmok V, Williamson LM, Pleasance E, Topham JT, Karasinska JM, Titmuss E, Schrader I, Yip S, Tessier-Cloutier B, Mungall K, Ng T, Sun S, Lim HJ, Loree JM, Laskin J, Marra MA, Jones SJM, Schaeffer DF, Renouf DJ. Homologous recombination deficiency signatures in gastrointestinal and thoracic cancers correlate with platinum therapy duration. NPJ Precis Oncol 2023; 7:31. [PMID: 36964191 PMCID: PMC10039042 DOI: 10.1038/s41698-023-00368-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 03/08/2023] [Indexed: 03/26/2023] Open
Abstract
There is emerging evidence about the predictive role of homologous recombination deficiency (HRD), but this is less defined in gastrointestinal (GI) and thoracic malignancies. We reviewed whole genome (WGS) and transcriptomic (RNA-Seq) data from advanced GI and thoracic cancers in the Personalized OncoGenomics trial (NCT02155621) to evaluate HRD scores and single base substitution (SBS)3, which is associated with BRCA1/2 mutations and potentially predictive of defective HRD. HRD scores were calculated by sum of loss of heterozygosity, telomeric allelic imbalance, and large-scale state transitions scores. Regression analyses examined the association between HRD and time to progression on platinum (TTPp). We included 223 patients with GI (n = 154) or thoracic (n = 69) malignancies. TTPp was associated with SBS3 (p < 0.01) but not HRD score in patients with GI malignancies, whereas neither was associated with TTPp in thoracic malignancies. Tumors with gBRCA1/2 mutations and a somatic second alteration exhibited high SBS3 and HRD scores, but these signatures were also present in several tumors with germline but no somatic second alterations, suggesting silencing of the wild-type allele or BRCA1/2 haploinsufficiency. Biallelic inactivation of an HR gene, including loss of XRCC2 and BARD1, was identified in BRCA1/2 wild-type HRD tumors and these patients had prolonged response to platinum. Thoracic cases with high HRD score were associated with high RECQL5 expression (p ≤ 0.025), indicating another potential mechanism of HRD. SBS3 was more strongly associated with TTPp in patients with GI malignancies and may be complementary to using HRD and BRCA status in identifying patients who benefit from platinum therapy.
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Affiliation(s)
- Erica S Tsang
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
- Pancreas Centre BC, Vancouver, BC, Canada
| | - Veronika Csizmok
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | | | | | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Intan Schrader
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Tony Ng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sophie Sun
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Howard J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Jonathan M Loree
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada.
- Pancreas Centre BC, Vancouver, BC, Canada.
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15
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Thompson EF, Wong RWC, Trevisan G, Tessier-Cloutier B, Almadani N, Chen J, Cheng A, Karnezis A, McConechy MK, Lum A, Senz J, McAlpine JN, Huntsman DG, Gilks B, Jamieson A, Hoang LN. p53-Abnormal "Fields of Dysplasia" in Human Papillomavirus-Independent Vulvar Squamous Cell Carcinoma Impacts Margins and Recurrence Risk. Mod Pathol 2023; 36:100010. [PMID: 36853783 DOI: 10.1016/j.modpat.2022.100010] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/22/2022] [Accepted: 09/16/2022] [Indexed: 01/11/2023]
Abstract
Abnormal p53 (p53abn) immunohistochemical (IHC) staining patterns can be found in vulvar squamous cell carcinoma (VSCC) and differentiated vulvar intraepithelial neoplasia (dVIN). They can also be found in the adjacent skin that shows morphology that falls short of the traditional diagnostic threshold for dVIN. Vulvectomy specimens containing human papillomavirus-independent p53abn VSCC with margins originally reported as negative for invasive and in situ disease were identified. Sections showing the closest approach by invasive or in situ neoplasia to margins were stained with p53 IHC stains. We evaluated the following: (1) detection of morphologically occult p53abn in situ neoplasia, (2) rates of margin status change after p53 IHC staining, and (3) effect of p53abn IHC staining at margins on the 2-year local recurrence rates. Seventy-three human papillomavirus-independent p53abn VSCCs were included. Half (35/73, 48%) had documented an in situ lesion in the original report. The use of p53 IHC staining identified 21 additional cases (29%) with the p53abn in situ lesions that were originally unrecognized. The histology of in situ lesions in the p53abn "field" varied and became more subtle (morphologically occult) farther away from the VSCC. Fifteen (21%) cases had a morphologically occult and previously unrecognized p53abn in situ lesion present at a resection margin, which conferred an increased risk of local recurrence (5/7 [71.4%] vs 6/22 [27.3%], P = .036). The p53abn in situ lesions at a margin were confirmed to have TP53 mutations by sequencing. p53 IHC staining identified morphologically occult p53abn in situ lesions surrounding human papillomavirus-independent VSCC. p53abn IHC staining at a margin was associated with a 3-fold increased risk of local recurrence.
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Affiliation(s)
- Emily F Thompson
- Pathology and Laboratory Medicine, University of British Columbia and Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Richard W C Wong
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, China
| | - Giorgia Trevisan
- Cellular Pathology, Barts Health NHS Trust, London, United Kingdom
| | - Basile Tessier-Cloutier
- Pathology and Laboratory Medicine, University of British Columbia and Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Noorah Almadani
- Department of Pathology, Ministry of the National Guard - Health Affairs, and King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Julia Chen
- Medical Undergraduate Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Angela Cheng
- Genetic Pathology Evaluation Center, Vancouver, British Columbia, Canada
| | - Anthony Karnezis
- Pathology and Laboratory Medicine, UC Davis Medical Center, Sacramento, California
| | | | - Amy Lum
- Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Janine Senz
- Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jessica N McAlpine
- Gynecologic Oncology, University of British Columbia, Vancouver, British Columbia, Canada
| | - David G Huntsman
- Genetic Pathology Evaluation Center, Vancouver, British Columbia, Canada; Canexia Health, Vancouver, British Columbia, Canada; Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Blake Gilks
- Pathology and Laboratory Medicine, University of British Columbia and Vancouver General Hospital, Vancouver, British Columbia, Canada; Genetic Pathology Evaluation Center, Vancouver, British Columbia, Canada
| | - Amy Jamieson
- Gynecologic Oncology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lynn N Hoang
- Pathology and Laboratory Medicine, University of British Columbia and Vancouver General Hospital, Vancouver, British Columbia, Canada; Genetic Pathology Evaluation Center, Vancouver, British Columbia, Canada.
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16
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Ji JX, Cochrane DR, Negri GL, Colborne S, Spencer Miko SE, Hoang LN, Farnell D, Tessier-Cloutier B, Huvila J, Thompson E, Leung S, Chiu D, Chow C, Ta M, Köbel M, Feil L, Anglesio M, Goode EL, Bolton K, Morin GB, Huntsman DG. The proteome of clear cell ovarian carcinoma. J Pathol 2022; 258:325-338. [PMID: 36031730 PMCID: PMC9649886 DOI: 10.1002/path.6006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 05/29/2022] [Revised: 08/05/2022] [Accepted: 08/26/2022] [Indexed: 01/19/2023]
Abstract
Clear cell ovarian carcinoma (CCOC) is the second most common subtype of epithelial ovarian carcinoma. Late-stage CCOC is not responsive to gold-standard chemotherapy and results in suboptimal outcomes for patients. In-depth molecular insight is urgently needed to stratify the disease and drive therapeutic development. We conducted global proteomics for 192 cases of CCOC and compared these with other epithelial ovarian carcinoma subtypes. Our results showed distinct proteomic differences in CCOC compared with other epithelial ovarian cancer subtypes including alterations in lipid and purine metabolism pathways. Furthermore, we report potential clinically significant proteomic subgroups within CCOC, suggesting the biologic plausibility of stratified treatment for this cancer. Taken together, our results provide a comprehensive understanding of the CCOC proteomic landscape to facilitate future understanding and research of this disease. © 2022 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Jennifer X Ji
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Dawn R Cochrane
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Shane Colborne
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Sandra E Spencer Miko
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Lynn N Hoang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - David Farnell
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jutta Huvila
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
- Department of Biomedicine, University of Turku, Turku, Finland
| | - Emily Thompson
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Samuel Leung
- Genetic Pathology Evaluation Center, Vancouver, BC, Canada
| | - Derek Chiu
- Genetic Pathology Evaluation Center, Vancouver, BC, Canada
| | - Christine Chow
- Genetic Pathology Evaluation Center, Vancouver, BC, Canada
| | - Monica Ta
- Genetic Pathology Evaluation Center, Vancouver, BC, Canada
| | - Martin Köbel
- Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Lucas Feil
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Michael Anglesio
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Ellen L Goode
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Kelly Bolton
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
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17
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Praetorius TH, Leonova A, Lac V, Senz J, Tessier-Cloutier B, Nazeran TM, Köbel M, Grube M, Kraemer B, Yong PJ, Kommoss S, Anglesio MS. Molecular analysis suggests oligoclonality and metastasis of endometriosis lesions across anatomically defined subtypes. Fertil Steril 2022; 118:524-534. [PMID: 35715244 DOI: 10.1016/j.fertnstert.2022.05.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 11/16/2021] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 01/13/2023]
Abstract
OBJECTIVE To investigate the heterogeneity of somatic cancer-driver mutations within patients and across endometriosis types. DESIGN A single-center cohort, retrospective study. SETTING Tertiary specialist-care center at a university hospital. PATIENT(S) Patients with surgically and histologically confirmed endometriosis of at least 2 anatomically distinct types (ovarian, deep infiltrating, and superficial). INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Specimens were analyzed for the presence or absence of somatic cancer-driver mutations using targeted panel sequencing with orthogonal validation using droplet digital polymerase chain reaction and mutation-surrogate immunohistochemistry. RESULT(S) It was found that 13 of 27 patients had informative somatic driver mutations in endometriosis lesions; of these 13 patients, 9 had identical mutations across distinct lesions. Endometriomas showed a higher mutational complexity, with functionally redundant driver mutations in the same gene and within the same lesions. CONCLUSION(S) Our data are consistent with clonality across endometriosis lesions, regardless of subtype. Further, the finding of redundancy in mutations within the same gene and lesions is consistent with endometriosis representing an oligoclonal disease with dissemination likely to consist of multiple epithelial clones traveling together. This suggests that the current anatomically defined classification of endometriosis does not fully recognize the etiology of the disease. A novel classification should consider genomic and other molecular features to promote personalized endometriosis diagnosis and care.
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Affiliation(s)
- Teresa H Praetorius
- Department of Women's Health, Tübingen University Hospital, Tübingen, Germany; British Columbia's Gynecological Cancer Research Program (OVCARE), University of British Columbia, Vancouver General Hospital, and BC Cancer, Vancouver, Canada
| | - Anna Leonova
- British Columbia's Gynecological Cancer Research Program (OVCARE), University of British Columbia, Vancouver General Hospital, and BC Cancer, Vancouver, Canada; Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, Canada
| | - Vivian Lac
- British Columbia's Gynecological Cancer Research Program (OVCARE), University of British Columbia, Vancouver General Hospital, and BC Cancer, Vancouver, Canada
| | - Janine Senz
- British Columbia's Gynecological Cancer Research Program (OVCARE), University of British Columbia, Vancouver General Hospital, and BC Cancer, Vancouver, Canada
| | - Basile Tessier-Cloutier
- British Columbia's Gynecological Cancer Research Program (OVCARE), University of British Columbia, Vancouver General Hospital, and BC Cancer, Vancouver, Canada; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tayyebeh M Nazeran
- British Columbia's Gynecological Cancer Research Program (OVCARE), University of British Columbia, Vancouver General Hospital, and BC Cancer, Vancouver, Canada
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
| | - Marcel Grube
- Department of Women's Health, Tübingen University Hospital, Tübingen, Germany
| | - Bernhard Kraemer
- Department of Women's Health, Tübingen University Hospital, Tübingen, Germany
| | - Paul J Yong
- British Columbia's Gynecological Cancer Research Program (OVCARE), University of British Columbia, Vancouver General Hospital, and BC Cancer, Vancouver, Canada; Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, Canada; BC Women's Centre for Pelvic Pain & Endometriosis, BC Women's Hospital and Health Centre, Vancouver, Canada
| | - Stefan Kommoss
- Department of Women's Health, Tübingen University Hospital, Tübingen, Germany
| | - Michael S Anglesio
- British Columbia's Gynecological Cancer Research Program (OVCARE), University of British Columbia, Vancouver General Hospital, and BC Cancer, Vancouver, Canada; Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, Canada.
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18
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Tessier-Cloutier B, Grewal JK, Jones MR, Pleasance E, Shen Y, Cai E, Dunham C, Hoang L, Horst B, Huntsman DG, Ionescu D, Karnezis AN, Lee AF, Lee CH, Lee TH, Twa DD, Mungall AJ, Mungall K, Naso JR, Ng T, Schaeffer DF, Sheffield BS, Skinnider B, Smith T, Williamson L, Zhong E, Regier DA, Laskin J, Marra MA, Gilks CB, Jones SJ, Yip S. The impact of whole genome and transcriptome analysis (WGTA) on predictive biomarker discovery and diagnostic accuracy of advanced malignancies. J Pathol Clin Res 2022; 8:395-407. [PMID: 35257510 PMCID: PMC9161328 DOI: 10.1002/cjp2.265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 07/07/2021] [Revised: 01/15/2022] [Accepted: 02/04/2022] [Indexed: 12/13/2022]
Abstract
In this study, we evaluate the impact of whole genome and transcriptome analysis (WGTA) on predictive molecular profiling and histologic diagnosis in a cohort of advanced malignancies. WGTA was used to generate reports including molecular alterations and site/tissue of origin prediction. Two reviewers analyzed genomic reports, clinical history, and tumor pathology. We used National Comprehensive Cancer Network (NCCN) consensus guidelines, Food and Drug Administration (FDA) approvals, and provincially reimbursed treatments to define genomic biomarkers associated with approved targeted therapeutic options (TTOs). Tumor tissue/site of origin was reassessed for most cases using genomic analysis, including a machine learning algorithm (Supervised Cancer Origin Prediction Using Expression [SCOPE]) trained on The Cancer Genome Atlas data. WGTA was performed on 652 cases, including a range of primary tumor types/tumor sites and 15 malignant tumors of uncertain histogenesis (MTUH). At the time WGTA was performed, alterations associated with an approved TTO were identified in 39 (6%) cases; 3 of these were not identified through routine pathology workup. In seven (1%) cases, the pathology workup either failed, was not performed, or gave a different result from the WGTA. Approved TTOs identified by WGTA increased to 103 (16%) when applying 2021 guidelines. The histopathologic diagnosis was reviewed in 389 cases and agreed with the diagnostic consensus after WGTA in 94% of non‐MTUH cases (n = 374). The remainder included situations where the morphologic diagnosis was changed based on WGTA and clinical data (0.5%), or where the WGTA was non‐contributory (5%). The 15 MTUH were all diagnosed as specific tumor types by WGTA. Tumor board reviews including WGTA agreed with almost all initial predictive molecular profile and histopathologic diagnoses. WGTA was a powerful tool to assign site/tissue of origin in MTUH. Current efforts focus on improving therapeutic predictive power and decreasing cost to enhance use of WGTA data as a routine clinical test.
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Affiliation(s)
- Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jasleen K Grewal
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Martin R Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Ellen Cai
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chris Dunham
- Department of Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada
| | - Lynn Hoang
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Basil Horst
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Diana Ionescu
- Department of Anatomical Pathology, BC Cancer, Vancouver, BC, Canada
| | - Anthony N Karnezis
- Department of Pathology and Laboratory Medicine, UC Davis, Sacramento, CA, USA
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada
| | - Cheng Han Lee
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Tae Hoon Lee
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - David Dw Twa
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Julia R Naso
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tony Ng
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Brandon S Sheffield
- Department of Pathology and Laboratory Medicine, William Osler Health System, Brampton, ON, Canada
| | - Brian Skinnider
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Tyler Smith
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Laura Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Ellia Zhong
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Dean A Regier
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - Janessa Laskin
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Steven Jm Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada.,Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
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19
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Praiss A, Navitski A, Cohen S, Tessier-Cloutier B, Broach V, O'Cearbhaill RE. Immunotherapy for recurrent or metastatic vulvar carcinoma: A case report and review of current guidelines. Gynecol Oncol Rep 2022; 41:100982. [PMID: 35496740 PMCID: PMC9048086 DOI: 10.1016/j.gore.2022.100982] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 01/16/2023] Open
Abstract
There are limited treatment options for patients with advanced vulvar cancer. However, several immune checkpoint inhibitors (ICIs) are FDA-approved or NCCN-Compendia-listed for qualified patients with advanced disease. In this case report, we present a patient with metastatic vulvar squamous cell carcinoma who was treated with pembrolizumab in the setting of disease progression following prior treatment with radiation and chemotherapy. Best response to immunotherapy was an unconfirmed partial response. We summarize the current role of ICIs in treating advanced vulvar cancer, which is largely extrapolated from the squamous cell skin cancer and cervical cancer guidelines. Additionally, we emphasize the need for more inclusive clinical trials and a better understanding of vulvar cancer molecular biology, as well as the identification of biomarkers to predict response to targeted therapy in patients with advanced vulvar cancer.
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Affiliation(s)
- Aaron Praiss
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anastasia Navitski
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Seth Cohen
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Vance Broach
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Roisin E O'Cearbhaill
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
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20
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Tessier-Cloutier B, Kang EY, Alex D, Stewart CJR, McCluggage WG, Köbel M, Lee CH. Endometrial neuroendocrine carcinoma and undifferentiated carcinoma are distinct entities with overlap in neuroendocrine marker expression. Histopathology 2022; 81:44-54. [PMID: 35394077 DOI: 10.1111/his.14639] [Citation(s) in RCA: 2] [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: 01/07/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 11/30/2022]
Abstract
AIMS Dedifferentiated/undifferentiated endometrial carcinomas (DDEC/UDEC) frequently harbor genomic activation of SWItch/Sucrose Non-Fermentable (SWI/SNF) complex proteins, and can show histologic overlap with neuroendocrine carcinoma (NEC). This study compares the expression of neuroendocrine markers, SWI/SNF proteins and mismatch repair (MMR) proteins in DDEC/UDEC and NEC. METHODS AND RESULTS The expressions of synaptophysin, chromogranin, CD56, ARID1A, ARID1B, SMARCA4, SMARCB1 and MMR proteins were evaluated by immunohistochemistry on 44 SWI/SNF-deficient DDEC/UDEC and 15 NEC. 33 of 44 (75%) DDEC/UDEC showed expression of at least one neuroendocrine marker with 18 of 44 (41%) expressing 2 or more neuroendocrine markers, whereas all 15 NEC showed expression of at least one neuroendocrine marker with 14 of 15 (93%) expressing 2 or more neuroendocrine markers. Neuroendocrine marker expression in DDEC/UDEC was typically focal when present, with an average extent of 17%, 4% and 8% for synaptophysin, chromogranin and CD56 in the positive cases respectively, in contrast to 73%, 40% and 62% in the positive NEC cases respectively. All 15 NEC showed intact expression of SWI/SNF proteins except for 1 that showed isolated loss of ARID1A. 38 of 44 DDEC/UDEC were MMR-abnormal (34 with loss of MLH1 and PMS2, 4 with loss of PMS2 alone) whereas all NEC retained MMR protein expression. CONCLUSIONS Our study demonstrates frequent but typically focal neuroendocrine marker expression in SWI/SNF-deficient DDEC/UDEC, while NECs typically express 2 or more neuroendocrine markers with diffuse expression in at least one marker. ARID1B, SMARCA4 and SMARCB1 immunohistochemistry can be used to aid differentiation between DDEC/UDEC and NEC.
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Affiliation(s)
- Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eun-Young Kang
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Deepu Alex
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, British Columbia, Canada
| | - Colin J R Stewart
- Department of Histopathology, King Edward Memorial Hospital and School for Women's and Infants' Health, University of Western Australia, Perth, Western Australia, Australia
| | - W Glenn McCluggage
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Cheng-Han Lee
- Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, British Columbia, Canada.,Department of Laboratory Medicine and Pathology, Royal Alexandra Hospital, Edmonton, Canada.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
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21
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Kommoss FK, Tessier-Cloutier B, Witkowski L, Forgo E, Koelsche C, Köbel M, Foulkes WD, Lee CH, Kolin DL, von Deimling A, Howitt BE. Cellular context determines DNA methylation profiles in SWI/SNF-deficient cancers of the gynecologic tract. J Pathol 2022; 257:140-145. [PMID: 35218556 DOI: 10.1002/path.5889] [Citation(s) in RCA: 2] [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: 12/11/2021] [Revised: 01/23/2022] [Accepted: 02/24/2022] [Indexed: 11/06/2022]
Abstract
SWI/SNF (SWItch/Sucrose Non-Fermentable) complex deficiency has been reported in a wide variety of cancers and is often associated with an undifferentiated phenotype. In the gynecologic tract SWI/SNF deficient cancers are diagnostically challenging and little is known about their cellular origins. Here we show that undifferentiated endometrial carcinoma (UDEC), SMARCA4-deficient uterine sarcoma (SDUS) and ovarian small cell carcinoma, hypercalcemic type (SCCOHT) harbor distinct DNA methylation signatures despite shared morphology and SWI/SNF inactivation. Our results indicate that cellular context is an important determinant of the epigenetic landscape, even in the setting of core SWI/SNF deficiency, and therefore methylation profiling may represent a useful diagnostic tool in undifferentiated, SWI/SNF-deficient cancers. Furthermore, applying copy number analyses and group-wise differential methylation analyses including endometrioid endometrial carcinomas and extracranial malignant rhabdoid tumors, we uncover analogous molecular features in SDUS and SCCOHT in contrast to UDEC. These results suggest SDUS and SCCOHT to represent chromosomally stable SWI/SNF deficient cancers of the gynecologic tract, which are within the broader spectrum of malignant rhabdoid tumors. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Felix Kf Kommoss
- Department of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Leora Witkowski
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada.,Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Erna Forgo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christian Koelsche
- Department of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Köbel
- Department of Laboratory Medicine and Pathology, University of Calgary, Calgary, AB, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada.,Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Cheng-Han Lee
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - David L Kolin
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital and CCU Neuropathology DKFZ, Heidelberg, Germany
| | - Brooke E Howitt
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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22
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Naso JR, Tessier-Cloutier B, Senz J, Huntsman DG, Churg A. Significance of p53 immunostaining in mesothelial proliferations and correlation with TP53 mutation status. Mod Pathol 2022; 35:77-81. [PMID: 34497363 DOI: 10.1038/s41379-021-00920-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/24/2021] [Accepted: 08/30/2021] [Indexed: 11/09/2022]
Abstract
p53 immunohistochemistry has long been proposed for the separation of benign from malignant mesothelial proliferations, with the older literature suggesting that any degree of positivity supported a diagnosis of mesothelioma. However, using modern immunohistochemistry platforms in other organ systems, notably gynecologic tumors, it has become clear that p53 staining can represent wild-type protein, and only specific staining patterns (absent, overexpression, or cytoplasmic expression) are indicative of a TP53 mutation. We applied these principles to two tissue microarrays containing 94 mesotheliomas and 66 reactive mesothelial proliferations. Seven/65 (11%) epithelioid mesotheliomas showed aberrant staining (four absent and three overexpression patterns) as did 5/29 (17%) of sarcomatoid mesotheliomas (all overexpression patterns). We sequenced the TP53 gene (exons 2-11) in five of the epithelioid and three of the sarcomatoid cases with aberrant staining as well as 12 epithelioid and eight sarcomatoid mesotheliomas with wild-type staining. All three sarcomatoid cases with aberrant staining showed mutated TP53, as did three of the epithelioid cases; in two of the epithelioid cases no mutation was detected, most likely because of large deletions not detected by this assay. In contrast, none of the 20 mesotheliomas with wild-type staining contained mutated TP53. We conclude that absent or overexpression p53 staining patterns can be used as a marker of a malignant vs. a benign mesothelial proliferation. The sensitivity of p53 staining by itself is low, but here addition of p53 to BAP1/MTAP staining increased sensitivity from 72 to 81% for epithelioid and 38 to 50% for sarcomatoid mesotheliomas.
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Affiliation(s)
- Julia R Naso
- Department of Pathology, Vancouver General Hospital, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology, Vancouver General Hospital, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Janine Senz
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Andrew Churg
- Department of Pathology, Vancouver General Hospital, Vancouver, BC, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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23
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Pors J, Tessier-Cloutier B, Thompson E, Almadani N, Ho J, Gilks B, Huntsman D, Hoang L. Targeted Molecular Sequencing of Recurrent and Multifocal Non-HPV-associated Squamous Cell Carcinoma of the Vulva. Int J Gynecol Pathol 2021; 40:391-399. [PMID: 33323855 DOI: 10.1097/pgp.0000000000000742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recurrent vulvar squamous cell carcinomas (SCCs) are a poorly understood and aggressive group of treatment-resistant neoplasms. Currently, it remains unclear whether these are in fact recurrences of the same primary tumor, or the development of entirely new tumors. Here, to address this question, we examined the mutational profile of a series of patients with recurrent or multifocal non-human papilloma virus (HPV)-associated vulvar SCC. We performed a targeted 33-gene next-generation sequencing panel on a series of 14 patients with recurrent or multifocal non-HPV-associated vulvar SCC and precursor neoplasms. This amounted to 54 cases (33 SCC, 1 verrucous carcinoma, 13 differentiated vulvar intraepithelial neoplasia, and 7 differentiated exophytic vulvar intraepithelial lesion), with 79 mutations detected altogether. TP53 [51/79 (65%)] was the most frequently mutated gene. Mutations in PIK3CA [16/79 (20%)), HRAS [6/79 (8%)], PTEN [4/79 (5%)], EGFR [1/79 (1%)], and GNAS [1/79 (1%)] were occasionally seen. Most patients with SCC [5/9 (56%)] recurrent, 4/5 (80%) multifocal] demonstrated a clonal relationship, and harbored the same mutations in the same genes in metachronous or synchronous tumors. A subset of the recurrent tumors [2/5 (40%)] recurred with additional mutations. These clonal relationships were shared between SCC and differentiated vulvar intraepithelial neoplasia in each case. By contrast, a small number of recurrent tumors [3/9 (33%)] demonstrated novel mutations, entirely different from the primary tumor. Thus, our findings suggest that recurrent non-HPV-associated vulvar SCC can arise from 2 mechanisms.
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24
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Kang EY, Tessier-Cloutier B, Duggan MA, Stewart CJR, Lee CH, Köbel M. Loss of ARID1B and SMARCB1 expression are specific for the diagnosis of dedifferentiated/undifferentiated carcinoma in tumours of the upper gynaecological tract and cervix. Histopathology 2021; 79:160-167. [PMID: 33432679 DOI: 10.1111/his.14333] [Citation(s) in RCA: 7] [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: 11/16/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 11/27/2022]
Abstract
AIMS Genomic inactivation of ARID1B in ARID1A-inactivated tumour and genomic inactivation of SMARCB1 represent two recurrent mechanisms, core SWItch/sucrose non-fermentable (SWI/SNF) complex inactivation, that are associated with de-differentiation in endometrial carcinoma. Approximately one-third of dedifferentiated/undifferentiated endometrial carcinomas (DDEC/UEC) show loss of ARID1B expression with a minor subset showing loss of SMARCB1 expression, but little is known regarding the specificity of ARID1B or SMARCB1 loss in gynaecological tract tumours in general. The aim of this study was to examine the frequency of ARID1B and SMARCB1 loss by immunohistochemistry in a series of gynaecological tract epithelial/mesenchymal neoplasms. METHODS AND RESULTS We evaluated 1849 tumours that included 748 endometrial carcinomas, 101 uterine carcinosarcomas/adenosarcomas, 64 uterine sarcomas, 221 cervical carcinomas and 715 ovarian carcinomas/borderline tumours by tissue microarrays (TMA). We observed ARID1B loss in 35 of 86 (41%) and SMARCB1 loss in three of 86 (3%) DDEC/UEC, but not in any other uterine tumour types examined. ARID1B-deficient DDEC/UEC also showed concurrent loss of ARID1A expression. All SMARCB1-deficient tumours showed loss of MLH1 and PMS2, while 29 of 35 ARID1B-deficient tumours showed loss of MLH1 and PMS2 or loss of MSH6. All ovarian carcinomas/borderline tumours and cervical carcinomas showed intact expression of ARID1B and SMARCB1. CONCLUSION Our findings indicate that the loss of expression of ARID1B or SMARCB1 by immunohistochemistry is highly specific for undifferentiated carcinoma among tumours of the upper gynaecological tract and cervix, and therefore can be used to identify these highly aggressive malignant tumours.
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Affiliation(s)
- Eun-Young Kang
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Máire A Duggan
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Colin J R Stewart
- Department of Histopathology, King Edward Memorial Hospital and School for Women's and Infants' Health, University of Western Australia, Perth, Western Australia, Australia
| | - Cheng-Han Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, British Columbia, Canada
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
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25
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Keung MS, Streijger F, Herrity A, Ethridge J, Dougherty SM, Aslan S, Webster M, Fisk S, Deegan EG, Tessier-Cloutier B, Chen KYN, Morrison C, Okon EB, Tigchelaar S, Manouchehri N, Kim KT, Shortt K, So K, Damaser MS, Sherwood LC, Howland DR, Boakye M, Hubscher C, Stothers L, Kavanagh A, Kwon BK. Characterization of Lower Urinary Tract Dysfunction after Thoracic Spinal Cord Injury in Yucatan Minipigs. J Neurotrauma 2021; 38:1306-1326. [PMID: 33499736 DOI: 10.1089/neu.2020.7404] [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] [Indexed: 01/23/2023] Open
Abstract
There is an increasing need to develop approaches that will not only improve the clinical management of neurogenic lower urinary tract dysfunction (NLUTD) after spinal cord injury (SCI), but also advance therapeutic interventions aimed at recovering bladder function. Although pre-clinical research frequently employs rodent SCI models, large animals such as the pig may play an important translational role in facilitating the development of devices or treatments. Therefore, the objective of this study was to develop a urodynamics protocol to characterize NLUTD in a porcine model of SCI. An iterative process to develop the protocol to perform urodynamics in female Yucatan minipigs began with a group of spinally intact, anesthetized pigs. Subsequently, urodynamic studies were performed in a group of awake, lightly restrained pigs, before and after a contusion-compression SCI at the T2 or T9-T11 spinal cord level. Bladder tissue was obtained for histological analysis at the end of the study. All anesthetized pigs had bladders that were acontractile, which resulted in overflow incontinence once capacity was reached. Uninjured, conscious pigs demonstrated appropriate relaxation and contraction of the external urethral sphincter during the voiding phase. SCI pigs demonstrated neurogenic detrusor overactivity and a significantly elevated post-void residual volume. Relative to the control, SCI bladders were heavier and thicker. The developed urodynamics protocol allows for repetitive evaluation of lower urinary tract function in pigs at different time points post-SCI. This technique manifests the potential for using the pig as an intermediary, large animal model for translational studies in NLUTD.
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Affiliation(s)
- Martin S Keung
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Neuroscience, Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Femke Streijger
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - April Herrity
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA.,Department of Neurosurgery, University of Louisville, Louisville, Kentucky, USA
| | - Jay Ethridge
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA.,Department of Neurosurgery, University of Louisville, Louisville, Kentucky, USA
| | - Susan M Dougherty
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA.,Department of Neurosurgery, University of Louisville, Louisville, Kentucky, USA
| | - Sevda Aslan
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA.,Department of Neurosurgery, University of Louisville, Louisville, Kentucky, USA
| | - Megan Webster
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shera Fisk
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Emily G Deegan
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Basile Tessier-Cloutier
- Pathology and Laboratory Medicine, and Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kuan-Yin N Chen
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charlotte Morrison
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elena B Okon
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Seth Tigchelaar
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Neda Manouchehri
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kyoung-Tae Kim
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Neurosurgery, School of Medicine, Kyungpook National University, National University Hospital, Daegu, South Korea
| | - Katelyn Shortt
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kitty So
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Margot S Damaser
- Biomedical Engineering Department, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Advanced Platform Technology Center, Louis Stokes Cleveland U.S. Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Leslie C Sherwood
- Comparative Medicine Research Unit, and University of Louisville, Louisville, Kentucky, USA
| | - Dena R Howland
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA.,Department of Neurosurgery, University of Louisville, Louisville, Kentucky, USA.,Research Service, Robley Rex U.S. Department of Veterans Affairs Medical Center, Louisville, Kentucky, USA
| | - Max Boakye
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA.,Department of Neurosurgery, University of Louisville, Louisville, Kentucky, USA
| | - Charles Hubscher
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA.,Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, Kentucky, USA
| | - Lynn Stothers
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Urologic Sciences, and Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alex Kavanagh
- Urologic Sciences, and Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Brian K Kwon
- International Collaboration on Repair Discoveries (ICORD), Departments of Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Vancouver Spine Surgery Institute, Department of Orthopaedics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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26
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Lebovitz C, Wretham N, Osooly M, Milne K, Dash T, Thornton S, Tessier-Cloutier B, Sathiyaseelan P, Bortnik S, Go NE, Halvorsen E, Cederberg RA, Chow N, Dos Santos N, Bennewith KL, Nelson BH, Bally MB, Lam WL, Gorski SM. Loss of Parkinson's susceptibility gene LRRK2 promotes carcinogen-induced lung tumorigenesis. Sci Rep 2021; 11:2097. [PMID: 33483550 PMCID: PMC7822882 DOI: 10.1038/s41598-021-81639-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 07/18/2020] [Accepted: 01/07/2021] [Indexed: 12/13/2022] Open
Abstract
Pathological links between neurodegenerative disease and cancer are emerging. LRRK2 overactivity contributes to Parkinson’s disease, whereas our previous analyses of public cancer patient data revealed that decreased LRRK2 expression is associated with lung adenocarcinoma (LUAD). The clinical and functional relevance of LRRK2 repression in LUAD is unknown. Here, we investigated associations between LRRK2 expression and clinicopathological variables in LUAD patient data and asked whether LRRK2 knockout promotes murine lung tumorigenesis. In patients, reduced LRRK2 was significantly associated with ongoing smoking and worse survival, as well as signatures of less differentiated LUAD, altered surfactant metabolism and immunosuppression. We identified shared transcriptional signals between LRRK2-low LUAD and postnatal alveolarization in mice, suggesting aberrant activation of a developmental program of alveolar growth and differentiation in these tumors. In a carcinogen-induced murine lung cancer model, multiplex IHC confirmed that LRRK2 was expressed in alveolar type II (AT2) cells, a main LUAD cell-of-origin, while its loss perturbed AT2 cell morphology. LRRK2 knockout in this model significantly increased tumor initiation and size, demonstrating that loss of LRRK2, a key Parkinson’s gene, promotes lung tumorigenesis.
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Affiliation(s)
- Chandra Lebovitz
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Nicole Wretham
- Department of Experimental Therapeutics, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Maryam Osooly
- Department of Experimental Therapeutics, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Katy Milne
- Deeley Research Centre, BC Cancer, Victoria, BC, V8R 6V5, Canada
| | - Tia Dash
- Deeley Research Centre, BC Cancer, Victoria, BC, V8R 6V5, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8P 5C2, Canada
| | - Shelby Thornton
- Deeley Research Centre, BC Cancer, Victoria, BC, V8R 6V5, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8P 5C2, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Paalini Sathiyaseelan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Svetlana Bortnik
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Nancy Erro Go
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Elizabeth Halvorsen
- Department of Integrative Oncology, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Rachel A Cederberg
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Integrative Oncology, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Norman Chow
- Department of Experimental Therapeutics, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Nancy Dos Santos
- Department of Experimental Therapeutics, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Kevin L Bennewith
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Integrative Oncology, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Brad H Nelson
- Deeley Research Centre, BC Cancer, Victoria, BC, V8R 6V5, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8P 5C2, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Marcel B Bally
- Department of Experimental Therapeutics, BC Cancer, Vancouver, BC, V5Z 1L3, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Wan L Lam
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Integrative Oncology, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Sharon M Gorski
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada. .,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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27
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Tsang ES, Csizmok V, Williamson L, Pleasance ED, Topham JT, Karasinska J, Titmuss E, Schrader KA, Cafferty F, Yip S, Tessier-Cloutier B, Mungall K, Sun S, Lim HJ, Loree JM, Laskin JJ, Marra MA, Jones SJM, Schaeffer DF, Renouf DJ. Beyond BRCA? clinical utility of homologous recombination deficiency in gastrointestinal cancers. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.3_suppl.472] [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: 11/20/2022] Open
Abstract
472 Background: There is emerging evidence about the predictive role of homologous recombination deficiency (HRD) in multiple cancers. The clinical utility of HRD is less well defined in gastrointestinal (GI) malignancies. Methods: We reviewed the whole genome (WGS) and transcriptomic (RNA-Seq) data of patients with advanced GI cancers between 2012-2018 in the Personalized Oncogenomics trial (NCT02155621). Scores were calculated as the sum of loss of heterozygosity, telomeric allelic imbalance, and large-scale state transitions scores. HRD was defined as a score ≥34. Mutational analysis was performed to determine the presence of mutational signature 3, which is usually strongly associated with BRCA status. Retrospective chart review was conducted to extract treatment and survival outcomes. Overall survival (OS) from initiation of first-line systemic therapy and time to progression on platinum therapy (TTPp) were calculated. Linear and multivariable regression analyses were conducted. Results: Of 154 patients with GI primaries, 56% were male and 105 (68%) were exposed to a platinum agent in the metastatic setting. Primary sites included upper GI (N=20, 9%), pancreas (N=35, 16%), colorectal (N=74, 33%), and other GI primary (N=25, 11%). Ten patients (6%) had a BRCA1/2 mutation, 20 (13%) had a high HRD score, and 11 (7%) had a high signature 3 score (>0.05). Six patients had both high HRD and high signature 3 scores (Table). On linear regression, high HRD scores and mutational signature 3 were independently associated with longer TTPp (β=4.17, 95% CI 0.15-8.19, p=0.04; β=8.03, 95% CI 2.87-13.18, p<0.05, respectively). On multivariable linear regression, after adjusting for HRD score, BRCA1/2 status, and tumor site, only cases with a mutational signature 3 retained significance ( p<0.05). HRD status was not prognostic for OS (HR 1.02, 95% CI 0.65-1.62, p=0.92). Conclusions: Within a cohort of patients with GI malignancies characterized by WGS and RNA-Seq, mutational signature 3 was more strongly associated with TTPp compared to HRD score. These data highlight potential predictive implications of Signature 3 to complement HRD and BRCA status in identifying patients who may benefit from exposure to platinum therapy. [Table: see text]
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Affiliation(s)
| | - Veronika Csizmok
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Laura Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Erin D. Pleasance
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | | | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | | | | | | | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - Howard John Lim
- British Columbia Cancer Vancouver, and CCTG Co-Chair, Vancouver, BC, Canada
| | | | | | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - David F. Schaeffer
- Department of Pathology & Laboratory Medicine Vancouver General Hospital, Vancouver, BC, Canada
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28
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Orlando KA, Douglas AK, Abudu A, Wang Y, Tessier-Cloutier B, Su W, Peters A, Sherman LS, Moore R, Nguyen V, Negri GL, Colborne S, Morin GB, Kommoss F, Lang JD, Hendricks WP, Raupach EA, Pirrotte P, Huntsman DG, Trent JM, Parker JS, Raab JR, Weissman BE. Re-expression of SMARCA4/BRG1 in small cell carcinoma of ovary, hypercalcemic type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism. eLife 2020; 9:59073. [PMID: 33355532 PMCID: PMC7813545 DOI: 10.7554/elife.59073] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 05/19/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer. SCCOHT tumors have inactivating mutations in SMARCA4 (BRG1), one of the two mutually exclusive ATPases of the SWI/SNF chromatin remodeling complex. To address the role that BRG1 loss plays in SCCOHT tumorigenesis, we performed integrative multi-omic analyses in SCCOHT cell lines +/- BRG1 reexpression. BRG1 reexpression induced a gene and protein signature similar to an epithelial cell and gained chromatin accessibility sites correlated with other epithelial originating TCGA tumors. Gained chromatin accessibility and BRG1 recruited sites were strongly enriched for transcription-factor-binding motifs of AP-1 family members. Furthermore, AP-1 motifs were enriched at the promoters of highly upregulated epithelial genes. Using a dominant-negative AP-1 cell line, we found that both AP-1 DNA-binding activity and BRG1 reexpression are necessary for the gene and protein expression of epithelial genes. Our study demonstrates that BRG1 reexpression drives an epithelial-like gene and protein signature in SCCOHT cells that depends upon by AP-1 activity.
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Affiliation(s)
- Krystal Ann Orlando
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Amber K Douglas
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Aierken Abudu
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Weiping Su
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States
| | - Alec Peters
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States
| | - Larry S Sherman
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States.,Department Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, United States
| | - Rayvon Moore
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Vinh Nguyen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Gian Luca Negri
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Shane Colborne
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Gregg B Morin
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | | | - Jessica D Lang
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - William Pd Hendricks
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Elizabeth A Raupach
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, Canada
| | - Jeffrey M Trent
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Jesse R Raab
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Bernard E Weissman
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
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29
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Coope RJ, Schlosser C, Corbett RD, Pleasance S, Tessier-Cloutier B, Pandoh P, Kirk H, Haile S, Zhao Y, Mungall AJ, Marra MA. Whole-slide laser microdissection for tumour enrichment. J Pathol 2020; 253:225-233. [PMID: 33135777 DOI: 10.1002/path.5575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 02/07/2020] [Revised: 10/24/2020] [Accepted: 10/26/2020] [Indexed: 12/30/2022]
Abstract
The practical application of genome-scale technologies to precision oncology research requires flexible tissue processing strategies that can be used to differentially select both tumour and normal cell populations from formalin-fixed, paraffin-embedded tissues. As tumour sequencing scales towards clinical implementation, practical difficulties in scheduling and obtaining fresh tissue biopsies at scale, including blood samples as surrogates for matched 'normal' DNA, have focused attention on the use of formalin-preserved clinical samples collected routinely for diagnostic purposes. In practice, such samples often contain both tumour and normal cells which, if correctly partitioned, could be used to profile both tumour and normal genomes, thus identifying somatic alterations. Here we report a semi-automated method for laser microdissecting entire slide-mounted tissue sections to enrich for cells of interest with sufficient yield for whole genome and transcriptome sequencing. Using this method, we demonstrated enrichment of tumour material from mixed tumour-normal samples by up to 67%. Leveraging new methods that allow for the extraction of high-quality nucleic acids from small amounts of formalin-fixed tissues, we further showed that the method was successful in yielding sequence data of sufficient quality for use in BC Cancer's Personalized OncoGenomics (POG) program. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Robin Jn Coope
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Colin Schlosser
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Richard D Corbett
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Stephen Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Heather Kirk
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Simon Haile
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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30
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Fernandes S, Safavi A, Tessier-Cloutier B, Lee A, Baird R. Heterotopic gastric mucosa in the rectum. Journal of Pediatric Surgery Case Reports 2020. [DOI: 10.1016/j.epsc.2020.101673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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31
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Tsang ES, Grisdale CJ, Pleasance E, Topham JT, Mungall K, Reisle C, Choo C, Carreira M, Bowlby R, Karasinska JM, MacMillan D, Williamson LM, Chuah E, Moore RA, Mungall AJ, Zhao Y, Tessier-Cloutier B, Ng T, Sun S, Lim HJ, Schaeffer DF, Renouf DJ, Yip S, Laskin J, Marra MA, Jones SJM, Loree JM. Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers. Clin Cancer Res 2020; 27:522-531. [PMID: 33148671 DOI: 10.1158/1078-0432.ccr-20-1900] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/11/2020] [Accepted: 10/29/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Gene fusions are important oncogenic drivers and many are actionable. Whole-genome and transcriptome (WGS and RNA-seq, respectively) sequencing can discover novel clinically relevant fusions. EXPERIMENTAL DESIGN Using WGS and RNA-seq, we reviewed the prevalence of fusions in a cohort of 570 patients with cancer, and compared prevalence to that predicted with commercially available panels. Fusions were annotated using a consensus variant calling pipeline (MAVIS) and required that a contig of the breakpoint could be constructed and supported from ≥2 structural variant detection approaches. RESULTS In 570 patients with advanced cancer, MAVIS identified 81 recurrent fusions by WGS and 111 by RNA-seq, of which 18 fusions by WGS and 19 by RNA-seq were noted in at least 3 separate patients. The most common fusions were EML4-ALK in thoracic malignancies (9/69, 13%), and CMTM8-CMTM7 in colorectal cancer (4/73, 5.5%). Combined genomic and transcriptomic analysis identified novel fusion partners for clinically relevant genes, such as NTRK2 (novel partners: SHC3, DAPK1), and NTRK3 (novel partners: POLG, PIBF1). CONCLUSIONS Utilizing WGS/RNA-seq facilitates identification of novel fusions in clinically relevant genes, and detected a greater proportion than commercially available panels are expected to find. A significant benefit of WGS and RNA-seq is the innate ability to retrospectively identify variants that becomes clinically relevant over time, without the need for additional testing, which is not possible with panel-based approaches.
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Affiliation(s)
- Erica S Tsang
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - Cameron J Grisdale
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | | | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Caralyn Reisle
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Caleb Choo
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Marcus Carreira
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | | | - Daniel MacMillan
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | | | - Tony Ng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Sophie Sun
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - Howard J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, Canada.,Pancreas Centre BC, Vancouver, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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Tessier-Cloutier B, Coatham M, Carey M, Nelson GS, Hamilton S, Lum A, Soslow RA, Stewart CJ, Postovit LM, Köbel M, Lee CH. SWI/SNF-deficiency defines highly aggressive undifferentiated endometrial carcinoma. J Pathol Clin Res 2020; 7:144-153. [PMID: 33125840 PMCID: PMC7869930 DOI: 10.1002/cjp2.188] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 08/30/2020] [Revised: 09/26/2020] [Accepted: 10/03/2020] [Indexed: 01/02/2023]
Abstract
Dedifferentiated/undifferentiated endometrial carcinoma (DDEC/UEC) is an endometrial cancer characterized by the presence of histologically undifferentiated carcinoma. Genomic inactivation of core switch/sucrose nonfermentable (SWI/SNF) complex proteins was recently identified in approximately two-thirds of DDEC/UEC. The aim of this study was to delineate the clinical behavior of SWI/SNF-deficient DDEC/UEC in comparison to SWI/SNF-intact DDEC/UEC. The study cohort consisted of 56 SWI/SNF-deficient DDEC/UEC (2 POLE-mutated), which showed either SMARCA4 (BRG1) loss, ARID1A/1B co-loss, or SMARCB1 (INI1) loss in the undifferentiated tumor, and 26 SWI/SNF-intact DDEC/UEC (4 POLE-mutated). The average age at diagnosis was 61 years for patients with SWI/SNF-deficient tumors and 64 years for SWI/SNF-intact tumors. Mismatch repair (MMR) protein deficiency was seen in 66% of SWI/SNF-deficient and 50% of SWI/SNF-intact tumors. At initial presentation, 55% of patients with SWI/SNF-deficient tumors had extrauterine disease spread in contrast to 38% of patients with SWI/SNF-intact tumors. The 2-year disease specific survival (DSS) for stages I and II disease was 65% for SWI/SNF deficient tumors relative to 100% for SWI/SNF-intact tumors (p = 0.042). For patients with stages III and IV disease, the median survival was 4 months for SWI/SNF-deficient tumors compared to 36 months for SWI/SNF-intact tumors (p = 0.0003). All six patients with POLE-mutated tumors, including one with stage IV SWI/SNF-deficient tumor were alive with no evidence of disease. Among the patients with advanced stage SWI/SNF-deficient tumors, 68% (21 of 31) received adjuvant or neoadjuvant chemotherapy (platinum/taxane-based) and all except the patient with a POLE-mutated tumor (20 of 21) experienced disease progression either during chemotherapy or within 4 months after its completion. These findings show that core SWI/SNF-deficiency defines a highly aggressive group of undifferentiated cancer characterized by rapid disease progression that is refractory to conventional platinum/taxane-based chemotherapy. This underscores the importance of accurate clinical recognition of this aggressive tumor and the need to consider alternative systemic therapy for these tumors.
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Affiliation(s)
- Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | | | - Mark Carey
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, Canada
| | - Gregg S Nelson
- Department of Gynecologic Oncology, Tom Baker Cancer Centre and University of Calgary, Calgary, Canada
| | - Sarah Hamilton
- Department of Radiation Oncology, BC Cancer, Vancouver, Canada
| | - Amy Lum
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Robert A Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Colin Jr Stewart
- Department of Histopathology, King Edward Memorial Hospital and School for Women's and Infants' Health, University of Western Australia, Perth, Australia
| | | | - Martin Köbel
- Department of Pathology and Laboratory Medicine, Calgary Laboratory Services and University of Calgary, Calgary, Canada
| | - Cheng-Han Lee
- Department of Laboratory Medicine and Pathology, Royal Alexandra Hospital and University of Alberta, Edmonton, Canada.,Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, Canada
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33
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Gibbard E, Cochrane DR, Pors J, Negri GL, Colborne S, Cheng AS, Chow C, Farnell D, Tessier-Cloutier B, McAlpine JN, Morin GB, Schmidt D, Kommoss S, Kommoss F, Keul J, Gilks B, Huntsman DG, Hoang L. Whole-proteome analysis of mesonephric-derived cancers describes new potential biomarkers. Hum Pathol 2020; 108:1-11. [PMID: 33121982 DOI: 10.1016/j.humpath.2020.10.005] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/21/2020] [Indexed: 01/09/2023]
Abstract
Mesonephric carcinomas (MEs) and female adnexal tumors of probable Wolffian origin (FATWO) are derived from embryologic remnants of Wolffian/mesonephric ducts. Mesonephric-like carcinomas (MLCs) show identical morphology to ME of the cervix but occur in the uterus and ovary without convincing mesonephric remnants. ME, MLC, and FATWO are challenging to diagnose due to their morphologic similarities to Müllerian/paramesonephric tumors, contributing to a lack of evidence-based and tumor-specific treatments. We performed whole-proteomic analysis on 9 ME/MLC and 56 endometrial carcinomas (ECs) to identify potential diagnostic biomarkers. Although there were no convincing differences between ME and MLC, 543 proteins showed increased expression in ME/MLC relative to EC. From these proteins, euchromatic histone lysine methyltransferase 2 (EHMT2), glutathione S-transferase Mu 3 (GSTM3), eukaryotic translation elongation factor 1 alpha 2 (EEF1A2), and glycogen synthase kinase 3 beta were identified as putative biomarkers. Immunohistochemistry was performed on these candidates and GATA3 in 14 ME/MLC, 8 FATWO, 155 EC, and normal tissues. Of the candidates, only GATA3 and EHMT2 were highly expressed in mesonephric remnants and mesonephric-derived male tissues. GATA3 had the highest sensitivity and specificity for ME/MLC versus EC (93% and 99%) but was absent in FATWO. EHMT2 was 100% sensitive for ME/MLC & FATWO but was not specific (65%). Similarly, EEF1A2 was reasonably sensitive to ME/MLC (92%) and FATWO (88%) but was the least specific (38%). GSTM3 performed intermediately (sensitivity for ME/MLC and FATWO: 83% and 38%, respectively; specificity 67%). Although GATA3 remained the best diagnostic biomarker for ME/MLC, we have identified EHMT2, EEF1A2, and GSTM3 as proteins of interest in these cancers. FATWO's cell of origin is uncertain and remains an area for future research.
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Affiliation(s)
- Evan Gibbard
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, V6H 3N1, Canada; Molecular Oncology, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Dawn R Cochrane
- Molecular Oncology, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Jennifer Pors
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Gian Luca Negri
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Shane Colborne
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Angela S Cheng
- Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC, V6H 3Z6, Canada
| | - Christine Chow
- Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC, V6H 3Z6, Canada
| | - David Farnell
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Jessica N McAlpine
- Department of Gynecology and Obstetrics, Division of Gynecologic Oncology, The University of British Columbia, Vancouver, BC, V6Z 2K8, Canada
| | - Gregg B Morin
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, V6H 3N1, Canada; Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Dietmar Schmidt
- MVZ of Histology, Cytology and Molecular Diagnostics, Trier, 54296, Germany
| | - Stefan Kommoss
- Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, 72076, Germany
| | - Friedrich Kommoss
- Institute of Pathology, Medizin Campus Bodensee, Friedrichshafen, 88048, Germany
| | - Jacqueline Keul
- Department of Women's Health, Tübingen University Hospital, Tübingen, 72076, Germany
| | - Blake Gilks
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC, V6H 3Z6, Canada; Department of Anatomical Pathology, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada
| | - David G Huntsman
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, V6H 3N1, Canada; Molecular Oncology, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC, V6H 3Z6, Canada
| | - Lynn Hoang
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC, V6H 3Z6, Canada; Department of Anatomical Pathology, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada.
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34
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Praetorius T, Lac V, Tessier-Cloutier B, Nazeran T, Koebel M, Mason M, Senz J, Grube M, Krämer B, Brucker S, Staebler A, Yong P, Anglesio M, Kommoss S. Is endometriosis metastasizing? Shared somatic alterations suggest common origins across endometriotic lesions. Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1718045] [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: 10/23/2022] Open
Affiliation(s)
- T.H. Praetorius
- Universitätsfrauenklinik Tübingen
- Department of Obstetrics and Gynecology, University of British Columbia
| | - V. Lac
- Department of Molecular Oncology, British Columbia Cancer Agency
- Department of Pathology and Laboratory Medicine, University of British Columbia
| | - B. Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia
- Department of Anatomical Pathology, Vancouver General Hospital
| | - T.M. Nazeran
- Department of Molecular Oncology, British Columbia Cancer Agency
- Department of Pathology and Laboratory Medicine, University of British Columbia
| | - M. Koebel
- Department of Pathology and Laboratory Medicine, University of Calgary
| | - M.C Mason
- Department of Obstetrics and Gynecology, University of British Columbia
| | - J. Senz
- Department of Molecular Oncology, British Columbia Cancer Agency
| | - M. Grube
- Universitätsfrauenklinik Tübingen
| | | | | | - A. Staebler
- Institut für Pathologie, Universitätsklinikum Tübingen
| | - P.J. Yong
- Department of Obstetrics and Gynecology, University of British Columbia
- BC Women’s Hospital and Health Centre, BC Women’s Centre for Pelvic Pain & Endometriosis
| | - M.S. Anglesio
- Department of Obstetrics and Gynecology, University of British Columbia
- Department of Pathology and Laboratory Medicine, University of British Columbia
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35
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Levine AB, Peng J, Farnell D, Nursey M, Wang Y, Naso JR, Ren H, Farahani H, Chen C, Chiu D, Talhouk A, Sheffield B, Riazy M, Ip PP, Parra-Herran C, Mills A, Singh N, Tessier-Cloutier B, Salisbury T, Lee J, Salcudean T, Jones SJ, Huntsman DG, Gilks CB, Yip S, Bashashati A. Synthesis of diagnostic quality cancer pathology images by generative adversarial networks. J Pathol 2020; 252:178-188. [PMID: 32686118 DOI: 10.1002/path.5509] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 04/13/2020] [Revised: 07/02/2020] [Accepted: 07/10/2020] [Indexed: 12/16/2022]
Abstract
Deep learning-based computer vision methods have recently made remarkable breakthroughs in the analysis and classification of cancer pathology images. However, there has been relatively little investigation of the utility of deep neural networks to synthesize medical images. In this study, we evaluated the efficacy of generative adversarial networks to synthesize high-resolution pathology images of 10 histological types of cancer, including five cancer types from The Cancer Genome Atlas and the five major histological subtypes of ovarian carcinoma. The quality of these images was assessed using a comprehensive survey of board-certified pathologists (n = 9) and pathology trainees (n = 6). Our results show that the real and synthetic images are classified by histotype with comparable accuracies and the synthetic images are visually indistinguishable from real images. Furthermore, we trained deep convolutional neural networks to diagnose the different cancer types and determined that the synthetic images perform as well as additional real images when used to supplement a small training set. These findings have important applications in proficiency testing of medical practitioners and quality assurance in clinical laboratories. Furthermore, training of computer-aided diagnostic systems can benefit from synthetic images where labeled datasets are limited (e.g. rare cancers). We have created a publicly available website where clinicians and researchers can attempt questions from the image survey (http://gan.aimlab.ca/). © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Adrian B Levine
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jason Peng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
| | - David Farnell
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mitchell Nursey
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
| | - Yiping Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
| | - Julia R Naso
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Hezhen Ren
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Hossein Farahani
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
| | - Colin Chen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
| | - Derek Chiu
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Aline Talhouk
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, Canada
| | - Brandon Sheffield
- Department of Pathology, William Osler Health Centre-Brampton Civic Hospital, Brampton, Canada
| | - Maziar Riazy
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Philip P Ip
- Department of Pathology, University of Hong Kong, Hong Kong SAR, PR China
| | - Carlos Parra-Herran
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Anne Mills
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Naveena Singh
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Taylor Salisbury
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jonathan Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Tim Salcudean
- Electrical & Computer Engineering, University of British Columbia, Vancouver, Canada
| | - Steven Jm Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Ali Bashashati
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, Canada.,Electrical & Computer Engineering, University of British Columbia, Vancouver, Canada
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36
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Tessier-Cloutier B, Kortekaas KE, Thompson E, Pors J, Chen J, Ho J, Prentice LM, McConechy MK, Chow C, Proctor L, McAlpine JN, Huntsman DG, Gilks CB, Bosse T, Hoang LN. Major p53 immunohistochemical patterns in in situ and invasive squamous cell carcinomas of the vulva and correlation with TP53 mutation status. Mod Pathol 2020; 33:1595-1605. [PMID: 32203095 DOI: 10.1038/s41379-020-0524-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/08/2020] [Accepted: 03/08/2020] [Indexed: 01/12/2023]
Abstract
The recent literature has shown that vulvar squamous cell carcinoma (VSCC) can be stratified into two prognostically relevant groups based on human papillomavirus (HPV) status. The prognostic value of p53 for further sub-stratification, particularly in the HPV-independent group, has not been agreed upon. This disagreement is likely due to tremendous variations in p53 immunohistochemical (IHC) interpretation. To address this problem, we sought to compare p53 IHC patterns with TP53 mutation status. We studied 61 VSCC (48 conventional VSCC, 2 VSCC with sarcomatoid features, and 11 verrucous carcinomas) and 42 in situ lesions (30 differentiated vulvar intraepithelial neoplasia [dVIN], 9 differentiated exophytic vulvar intraepithelial lesions [deVIL], and 3 high-grade squamous intraepithelial lesions or usual vulvar intraepithelial neoplasia [HSIL/uVIN]). IHC for p16 and p53, and sequencing of TP53 exons 4-9 were performed. HPV in situ hybridization (ISH) was performed in selected cases. We identified six major p53 IHC patterns, two wild-type patterns: (1) scattered, (2) mid-epithelial expression (with basal sparing), and four mutant patterns: (3) basal overexpression, (4) parabasal/diffuse overexpression, (5) absent, and (6) cytoplasmic expression. These IHC patterns were consistent with TP53 mutation status in 58/61 (95%) VSCC and 39/42 (93%) in situ lesions. Cases that exhibited strong scattered staining and those with a weak basal overexpression pattern could be easily confused. The mid-epithelial pattern was exclusively observed in p16-positive lesions; the basal and parabasal layers that had absent p53 staining, appeared to correlate with the cells that were positive for HPV-ISH. This study describes a pattern-based p53 IHC interpretation framework, which can be utilized as a surrogate marker for TP53 mutational status in both VSCC and vulvar in situ lesions.
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Affiliation(s)
- Basile Tessier-Cloutier
- Department of Anatomical Pathology, Vancouver General Hospital, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kim E Kortekaas
- Department of Obstetrics and Gynecology, Leiden University Medical Center, Leiden, The Netherlands
| | - Emily Thompson
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jennifer Pors
- Department of Anatomical Pathology, Vancouver General Hospital, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Julia Chen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Julie Ho
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | | | - Christine Chow
- Genetic Pathology Evaluation Center (GPEC), Vancouver, BC, Canada
| | - Lily Proctor
- Department of Gynecology and Obstetrics, Division of Gynecologic Oncology, University of British Columbia, Vancouver, BC, Canada
| | - Jessica N McAlpine
- Department of Gynecology and Obstetrics, Division of Gynecologic Oncology, University of British Columbia, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Genetic Pathology Evaluation Center (GPEC), Vancouver, BC, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - C Blake Gilks
- Department of Anatomical Pathology, Vancouver General Hospital, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Genetic Pathology Evaluation Center (GPEC), Vancouver, BC, Canada
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Lynn N Hoang
- Department of Anatomical Pathology, Vancouver General Hospital, Vancouver, BC, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada. .,Genetic Pathology Evaluation Center (GPEC), Vancouver, BC, Canada.
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37
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Tessier-Cloutier B, Cochrane DR, Karnezis AN, Colborne S, Magrill J, Talhouk A, Zhang J, Leung S, Hughes CS, Piskorz A, Cheng AS, Greening K, du Bois A, Pfisterer J, Soslow RA, Kommoss S, Brenton JD, Morin GB, Gilks CB, Huntsman DG, Kommoss F. Proteomic analysis of transitional cell carcinoma-like variant of tubo-ovarian high-grade serous carcinoma. Hum Pathol 2020; 101:40-52. [PMID: 32360491 PMCID: PMC8204941 DOI: 10.1016/j.humpath.2020.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 11/28/2019] [Revised: 02/18/2020] [Accepted: 02/23/2020] [Indexed: 02/06/2023]
Abstract
The current World Health Organization classification does not distinguish transitional cell carcinoma of the ovary (TCC) from conventional tubo-ovarian high-grade serous carcinoma (HGSC), despite evidence suggesting improved prognosis for patients with TCC; instead, it is considered a morphologic variant of HGSC. The immunohistochemical (IHC) markers applied to date do not distinguish between TCC and HGSC. Therefore, we sought to compare the proteomic profiles of TCC and conventional HGSC to identify proteins enriched in TCC. Prognostic biomarkers in HGSC have proven to be elusive, and our aim was to identify biomarkers of TCC as a way of reliably and reproducibly identifying patients with a favorable prognosis and better response to chemotherapy compared with those with conventional HGSC. Quantitative global proteome analysis was performed on archival material of 12 cases of TCC and 16 cases of HGSC using SP3 (single-pot, solid phase-enhanced, sample preparation)-Clinical Tissue Proteomics, a recently described protocol for full-proteome analysis from formalin-fixed paraffin-embedded tissues. We identified 430 proteins that were significantly enriched in TCC over HGSC. Unsupervised co-clustering perfectly distinguished TCC from HGSC based on protein expression. Pathway analysis showed that proteins associated with cell death, necrosis, and apoptosis were highly expressed in TCCs, whereas proteins associated with DNA homologous recombination, cell mitosis, proliferation and survival, and cell cycle progression pathways had reduced expression. From the proteomic analysis, three potential biomarkers for TCC were identified, claudin-4 (CLDN4), ubiquitin carboxyl-terminal esterase L1 (UCHL1), and minichromosome maintenance protein 7 (MCM7), and tested by IHC analysis on tissue microarrays. In agreement with the proteomic analysis, IHC expression of those proteins was stronger in TCC than in HGSC (p < 0.0001). Using global proteomic analysis, we are able to distinguish TCC from conventional HGSC. Follow-up studies will be necessary to confirm that these molecular and morphologic differences are clinically significant.
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Affiliation(s)
- Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Dawn R Cochrane
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Anthony N Karnezis
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, UC Davis Medical Center, Sacramento, CA, United States
| | - Shane Colborne
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Jamie Magrill
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Aline Talhouk
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Jonathan Zhang
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Samuel Leung
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | | | - Anna Piskorz
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Angela S Cheng
- Genetic Pathology Evaluation Centre, The University of British Columbia, Vancouver, Canada
| | - Kendall Greening
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | | | | | - Robert A Soslow
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Stefan Kommoss
- Department of Obstetrics and Gynecology, Tübingen University Hospital, Tübingen, Germany
| | - James D Brenton
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Gregg B Morin
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Friedrich Kommoss
- Institute of Pathology, Medizin Campus Bodensee, Friedrichshafen, Germany.
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38
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Tessier-Cloutier B, Schaeffer DF, Bacani J, Marginean CE, Kalloger S, Köbel M, Lee CH. Loss of switch/sucrose non-fermenting complex protein expression in undifferentiated gastrointestinal and pancreatic carcinomas. Histopathology 2020; 77:46-54. [PMID: 32413172 DOI: 10.1111/his.14096] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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] [Received: 11/27/2019] [Revised: 02/10/2020] [Accepted: 02/15/2020] [Indexed: 12/23/2022]
Abstract
AIMS Undifferentiated carcinoma refers to an epithelial malignancy that lacks morphological evidence of differentiation. Recent studies have implicated the loss of constitutively expressed switch/sucrose non-fermenting (SWI/SNF) complex subunits in undifferentiated carcinomas of the gastrointestinal tract and other sites. In this study we examine the expression of SWI/SNF and mismatch repair (MMR) proteins in a series of undifferentiated carcinomas from the gastrointestinal tract and the pancreas. METHODS AND RESULTS We searched pathology databases from four Canadian health centres for primary undifferentiated carcinoma from gastrointestinal and pancreatic resection specimens. Upon review of 31 cases, 19 were confirmed to be undifferentiated carcinomas (eight colonic, six gastric, three pancreatic, one appendiceal and one duodenal). Immunohistochemical analysis of SMARCA4, SMARCA2, SMARCB1, ARID1A, ARID1B, MSH2, MSH6, MLH1 and PMS2 was performed on whole sections. Five of 19 (26%) showed loss of core SWI/SNF proteins (two loss of SMARCA4, one loss of SMARCB1 and two concurrent loss of ARID1A and ARID1B). SMARCA4, SMARCB1, or ARID1A/ARID1B-deficient undifferentiated carcinoma consistently exhibited sheet-like growth pattern, with cellular discohesion and rhabdoid morphology. Nine of 17 undifferentiated carcinomas tested were MMR-deficient by immunohistochemistry. In comparison, none of the 12 poorly differentiated carcinomas that were originally diagnosed as undifferentiated carcinomas showed loss of SMARCA4, SMARCA2, SMARCB1 or ARID1B. CONCLUSIONS Undifferentiated gastrointestinal/pancreatic carcinomas show frequent loss of expression of SWI/SNF complex proteins. The loss of these core components of SWI/SNF complex may contribute to the arrest of cellular differentiation, resulting in the undifferentiated histology and aggressive clinical behaviour.
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Affiliation(s)
- Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, Canada
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, Canada
| | - Julinor Bacani
- Department of Laboratory Medicine and Pathology, Division of Anatomical Pathology, University of Alberta, Edmonton, Canada
| | - Celia E Marginean
- Department of Anatomical Pathology, Providence Portland Medical Center, Portland, OR, USA
| | - Steve Kalloger
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
| | - Cheng-Han Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, Canada
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Kortekaas KE, Solleveld-Westerink N, Tessier-Cloutier B, Rutten TA, Poelgeest MIE, Gilks CB, Hoang LN, Bosse T. Performance of the pattern-based interpretation of p53 immunohistochemistry as a surrogate for TP53 mutations in vulvar squamous cell carcinoma. Histopathology 2020; 77:92-99. [PMID: 32236967 PMCID: PMC7383647 DOI: 10.1111/his.14109] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [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: 02/14/2020] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 01/26/2023]
Abstract
Aims The most commonly mutated gene in vulvar squamous cell carcinoma (VSCC) is TP53 and its prognostic value, particularly in HPV‐independent VSCC, is uncertain. In other tumours, p53 immunohistochemistry (IHC) is an excellent surrogate marker for TP53 mutations. In order to study this in VSCC, we assigned six p53 IHC patterns into two final classes: ‘wild‐type’ or ‘mutant’. We determined the performance and interobserver variability of this pattern‐based p53 IHC approach. Methods and results Two experienced gynaecological pathologists scored the predefined p53 IHC patterns of 59 VSCC, independently and blinded for molecular data. Agreement was calculated by Cohen's kappa. All disagreements regarding p53 IHC patterns were resolved by a consensus meeting. After DNA isolation, the presence of pathogenic TP53 variants was determined by next‐generation sequencing (NGS). Sensitivity, specificity and accuracy of p53 IHC as a surrogate marker for TP53 mutation status were calculated. Initial p53 IHC pattern interpretation showed substantial agreement between both observers (k = 0.71, P < 0.001). After consensus, 18 cases (30.5%) were assigned a final p53 IHC class as TP53 wild‐type and 41 cases (69.5%) as mutant. The accuracy between the p53 IHC class and TP53 mutation status, after the consensus meeting, was 96.6%. Moreover, the sensitivity and specificity were high 95.3% [95% confidence interval (CI) = 82.9–99.1% and 100% (95% CI = 75.9–100%)]. Conclusions Pattern‐based p53 IHC classification is highly reproducible among experienced gynaecological pathologists and accurately reflects TP53 mutations in VSCC. This approach to p53 IHC interpretation offers guidance and provides necessary clarity for resolving the proposed prognostic relevance of final p53 IHC class within HPV‐independent VSCC.
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Affiliation(s)
- Kim E Kortekaas
- Department of Obstetrics & Gynecology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Tessa A Rutten
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Mariëtte I E Poelgeest
- Department of Obstetrics & Gynecology, Leiden University Medical Center, Leiden, the Netherlands
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Lien N Hoang
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
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40
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Ji JX, Cochrane DR, Tessier-Cloutier B, Chen SY, Ho G, Pathak KV, Alcazar IN, Farnell D, Leung S, Cheng A, Chow C, Colborne S, Negri GL, Kommoss F, Karnezis A, Morin GB, McAlpine JN, Gilks CB, Weissman BE, Trent JM, Hoang L, Pirrotte P, Wang Y, Huntsman DG. Arginine Depletion Therapy with ADI-PEG20 Limits Tumor Growth in Argininosuccinate Synthase-Deficient Ovarian Cancer, Including Small-Cell Carcinoma of the Ovary, Hypercalcemic Type. Clin Cancer Res 2020; 26:4402-4413. [PMID: 32409304 DOI: 10.1158/1078-0432.ccr-19-1905] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 01/02/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
PURPOSE Many rare ovarian cancer subtypes, such as small-cell carcinoma of the ovary, hypercalcemic type (SCCOHT), have poor prognosis due to their aggressive nature and resistance to standard platinum- and taxane-based chemotherapy. The development of effective therapeutics has been hindered by the rarity of such tumors. We sought to identify targetable vulnerabilities in rare ovarian cancer subtypes. EXPERIMENTAL DESIGN We compared the global proteomic landscape of six cases each of endometrioid ovarian cancer (ENOC), clear cell ovarian cancer (CCOC), and SCCOHT to the most common subtype, high-grade serous ovarian cancer (HGSC), to identify potential therapeutic targets. IHC of tissue microarrays was used as validation of arginosuccinate synthase (ASS1) deficiency. The efficacy of arginine-depriving therapeutic ADI-PEG20 was assessed in vitro using cell lines and patient-derived xenograft mouse models representing SCCOHT. RESULTS Global proteomic analysis identified low ASS1 expression in ENOC, CCOC, and SCCOHT compared with HGSC. Low ASS1 levels were validated through IHC in large patient cohorts. The lowest levels of ASS1 were observed in SCCOHT, where ASS1 was absent in 12 of 31 cases, and expressed in less than 5% of the tumor cells in 9 of 31 cases. ASS1-deficient ovarian cancer cells were sensitive to ADI-PEG20 treatment regardless of subtype in vitro. Furthermore, in two cell line mouse xenograft models and one patient-derived mouse xenograft model of SCCOHT, once-a-week treatment with ADI-PEG20 (30 mg/kg and 15 mg/kg) inhibited tumor growth in vivo. CONCLUSIONS Preclinical in vitro and in vivo studies identified ADI-PEG20 as a potential therapy for patients with rare ovarian cancers, including SCCOHT.
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Affiliation(s)
- Jennifer X Ji
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Dawn R Cochrane
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Shary Yutin Chen
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada
| | - Germain Ho
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada
| | - Khyatiben V Pathak
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Isabel N Alcazar
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona
| | - David Farnell
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Samuel Leung
- Genetic Pathology Evaluation Center, Vancouver, Canada
| | - Angela Cheng
- Genetic Pathology Evaluation Center, Vancouver, Canada
| | | | - Shane Colborne
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Gian Luca Negri
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Friedrich Kommoss
- Institute of Pathology, Medizin Campus Bodensee, Friedrichshafen, Germany
| | - Anthony Karnezis
- Department of Pathology and Laboratory Medicine, University of California, Davis, California
| | - Gregg B Morin
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jessica N McAlpine
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Bernard E Weissman
- Department of Pathology and Laboratory Medicine, UNC-Chapel Hill, Chapel Hill, North Carolina
| | - Jeffrey M Trent
- Integrated Cancer Genomics, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Lynn Hoang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Yemin Wang
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada. .,Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada.,Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, Canada
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41
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Magrill J, Karnezis AN, Tessier-Cloutier B, Talhouk A, Kommoss S, Cochrane D, Chow C, Cheng A, Soslow R, Hauptmann S, du Bois A, Pfisterer J, Gilks CB, Huntsman DG, Kommoss F. Tubo-Ovarian Transitional Cell Carcinoma and High-grade Serous Carcinoma Show Subtly Different Immunohistochemistry Profiles. Int J Gynecol Pathol 2020; 38:552-561. [PMID: 30059451 DOI: 10.1097/pgp.0000000000000538] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Tubo-ovarian transitional cell carcinoma (TCC) is grouped with high-grade serous carcinoma (HGSC) in the current World Health Organization classification. TCC is associated with BRCA mutations and a better prognosis compared with HGSC. Previous papers examining the immunohistochemical features of TCC have studied limited numbers of samples. No marker reflecting the biological difference between TCC and HGSC is known. We collected a large cohort of TCC to determine whether TCC and HGSC could be distinguished by immunohistochemistry. A tissue microarray was built from 89 TCC and a control cohort of 232 conventional HGSC. Immunohistochemistry was performed, scored, and statistically analyzed for routine markers of HGSC and urothelial tumors: PAX8, WT1, p53, p16, ER, p63, and GATA3. Using scoring cutoffs commonly employed in clinical practice, the immunohistochemical profile of TCC was indistinguishable from HGSC for all markers. However, more detailed scoring criteria revealed statistically significant differences between the 2 groups of tumors with respect to ER, PAX8, and WT1. HGSC showed more diffuse and intense staining for PAX8 (P=0.004 and 0.001, respectively) and WT1 (P=0.002 and 0.002, respectively); conversely, TCC showed more intense staining for ER (P=0.007). TCC and HGSC therefore show subtle differences in their immunohistochemical profiles which might reflect underlying (epi)genetic differences. Further studies using proteomic analysis will focus on the identification of differentially expressed proteins that might serve as markers of TCC-like differentiation, which could help explain biologic differences between TCC and HGSC and might identify other cases of HGSC with a better prognosis.
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Affiliation(s)
- Jamie Magrill
- British Columbia Cancer Agency (J.M., A.N.K., A.T., D.C., D.G.H.) Department of Pathology, University of British Columbia (A.N.K., B.T.-C., C.C., A.C., C.B.G., D.G.H.), Vancouver, British Columbia, Canada Memorial Sloan Kettering Cancer Center, New York, New York (R.S.) Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands (S.H.) Department of Women's Health, Tübingen University Hospital, Tübingen (S.K.) Department of Gynecologic Oncology, Kliniken Essen Mitte, Essen (A.D.B.) Gynecologic Oncology Center, Kiel (J.P.) Institute of Pathology, Friedrichshafen (F.K.), Germany
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42
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Kommoss FKF, Stichel D, Schrimpf D, Kriegsmann M, Tessier-Cloutier B, Talhouk A, McAlpine JN, Chang KTE, Sturm D, Pfister SM, Romero-Pérez L, Kirchner T, Grünewald TGP, Buslei R, Sinn HP, Mechtersheimer G, Schirmacher P, Schmidt D, Lehr HA, Sahm F, Huntsman DG, Gilks CB, Kommoss F, von Deimling A, Koelsche C. DNA methylation-based profiling of uterine neoplasms: a novel tool to improve gynecologic cancer diagnostics. J Cancer Res Clin Oncol 2019; 146:97-104. [PMID: 31768620 DOI: 10.1007/s00432-019-03093-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 11/07/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023]
Abstract
PURPOSE Uterine neoplasms comprise a broad spectrum of lesions, some of which may pose a diagnostic challenge even to experienced pathologists. Recently, genome-wide DNA methylation-based classification of central nervous system tumors has been shown to increase diagnostic precision in clinical practice when combined with standard histopathology. In this study, we describe DNA methylation patterns of a diverse set of uterine neoplasms and test the applicability of array-based DNA methylation profiling. METHODS A multicenter cohort including prototypical epithelial and mesenchymal uterine neoplasms was collected. Tumors were subject to pathology review and array-based DNA methylation profiling (Illumina Infinium HumanMethylation450 or EPIC [850k] BeadChip). Methylation data were analyzed by unsupervised hierarchical clustering and t-SNE analysis. RESULTS After sample retrieval and pathology review the study cohort consisted of 49 endometrial carcinomas (EC), 5 carcinosarcomas (MMMT), 8 uterine leiomyomas (ULMO), 7 uterine leiomyosarcomas (ULMS), 15 uterine tumor resembling ovarian sex cord tumors (UTROSCT), 17 low-grade endometrial stromal sarcomas (LGESS) and 9 high-grade endometrial stromal sarcomas (HGESS). Analysis of methylation data identified distinct methylation clusters, which correlated with established diagnostic categories of uterine neoplasms. MMMT clustered together with EC, while ULMO, ULMS and UTROSCT each formed distinct clusters. The LGESS cluster differed from that of HGESS, and within the branch of HGESS, we observed a notable subgrouping of YWHAE- and BCOR-rearranged tumors. CONCLUSION Herein, we describe distinct DNA methylation signatures in uterine neoplasms and show that array-based DNA methylation analysis holds promise as an ancillary tool to further characterize uterine neoplasms, especially in cases which are diagnostically challenging by conventional techniques.
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Affiliation(s)
- Felix K F Kommoss
- Department of Pathology, Institute of Pathology, Heidelberg University Hospital, INF 224, 69120, Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mark Kriegsmann
- Department of Pathology, Institute of Pathology, Heidelberg University Hospital, INF 224, 69120, Heidelberg, Germany
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia and BC Cancer Agency, Vancouver, BC, Canada
| | - Aline Talhouk
- Department of Pathology and Laboratory Medicine, University of British Columbia and BC Cancer Agency, Vancouver, BC, Canada
| | - Jessica N McAlpine
- Division of Gynecologic Oncology, Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, BC, Canada
| | - Kenneth T E Chang
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Dominik Sturm
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Rolf Buslei
- Institute of Pathology, Sozialstiftung Bamberg, Bamberg, Germany
| | - Hans-Peter Sinn
- Department of Pathology, Institute of Pathology, Heidelberg University Hospital, INF 224, 69120, Heidelberg, Germany
| | - Gunhild Mechtersheimer
- Department of Pathology, Institute of Pathology, Heidelberg University Hospital, INF 224, 69120, Heidelberg, Germany
| | - Peter Schirmacher
- Department of Pathology, Institute of Pathology, Heidelberg University Hospital, INF 224, 69120, Heidelberg, Germany
| | | | - Hans-Anton Lehr
- Institute of Pathology, Medizin Campus Bodensee, Friedrichshafen, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia and BC Cancer Agency, Vancouver, BC, Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, University of British Columbia and BC Cancer Agency, Vancouver, BC, Canada
| | - Friedrich Kommoss
- Institute of Pathology, Medizin Campus Bodensee, Friedrichshafen, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Koelsche
- Department of Pathology, Institute of Pathology, Heidelberg University Hospital, INF 224, 69120, Heidelberg, Germany.
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Ho GC, Cochrane DR, Gibbard EW, Campbell K, Tessier-Cloutier B, Greening K, Kalantari F, Trigo-Gonzalez G, Wang Y, McAlpine JN, Shah SP, Huntsman DG. Abstract GMM-030: MODELS AND ANALYTIC TECHNIQUES OF MULLERIAN TISSUE-DERIVED ORGANOIDS. Clin Cancer Res 2019. [DOI: 10.1158/1557-3265.ovcasymp18-gmm-030] [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
INTRODUCTION: Ovarian cancer is the 5th deadliest cancer found in women and is the deadliest involving the gynecological tract. Most epithelial ovarian cancers have extra-ovarian origins and can be stratified into various histotypes: high and low-grade serous (HGS and LGS), endometrioid (ENOC), clear cell (CCOC), and mucinous – each of which are proposed to have distinct precursor lesions. We present organoids as a useful model to study precursor lesions and the process of tumorigenesis in epithelial ovarian carcinomas. Organoids recapitulate the in vivo growth microenvironment and are useful to study the mechanisms of tumorigenesis from healthy cells. We have previously proposed that ENOC arise from the secretory cell lineage, while CCOC originate from the ciliated cell lineage, and organoids are an ideal model to examine in greater depth the impact of mutation on specific cell populations, such as ciliated cells.
METHODS: Surgical fallopian tube and endometrial tissues, removed for non-cancer reasons, were cultured in 2D followed by plating into Matrigel. Matrigel cultures were supplemented with media containing stem/progenitor differentiation factors promoting organoid growth. To study the effect of mutations often found in ovarian cancers on organoid growth and development, gene knockouts were produced using CRISPR lentiviruses on cells prior to Matrigel culture. Lentiviral transductions were optimized for organoid formation and for minimizing invasiveness accrued on cells. CRISPR gRNA constructs were validated by Western Blot and qPCR. Organoids containing knockouts of p53, BRCA1 and BRCA2 were used to model precursor lesions of HGS, whereas ARID1A knockouts and an inducible PIK3CA activating mutations were used to model CCOC.
To gain further insight into ciliated cells of the endometrium, organoids were treated with the notch inhibitor-DBZ to drive differentiation of cells towards a ciliated cell lineage. We analyzed organoids by single-cell RNA sequencing (scRNA-seq), immunohistochemistry (IHC), and immunofluorescence staining (IF). Single cells were derived by purifying the organoids from Matrigel followed by a chemical and physical digestion. scRNA-seq was performed utilizing the 10X Genomics Platform and analyzed by in-house bioinformaticians. Bioinformatic analyses included stringent QC to remove low-quality and dead cells, before applying unsupervised learning algorithms like PCA and Gaussian mixture modeling as well as differential expression analysis to understand both how samples relate to each other and cell types discovered within each sample.
RESULTS: We successfully recapitulated the histology observed in tissues by growing endometrial and fallopian tube organoids. The notch inhibitor, DBZ forced ciliated cell differentiation, as observed by IHC, IF and scRNA-seq. scRNA-seq clustering of DBZ-treated organoid cultures revealed a possible intermediary state between progenitor and ciliated cells. Initial IHC and IF analyses of CRISPR-mediated organoids reveal successful gene manipulation.
CONCLUSIONS: Organoid cultures present as a powerful method for modelling precursor lesions; they can be readily manipulated genetically and with rapid turnaround compared to conventional mouse models. Organoids are also amenable to sequencing at single-cell resolution. The ability to model ovarian cancers with permanent knockouts in human tissue serves as a necessary link between animal models and human therapy.
Citation Format: Germain C. Ho, Dawn R. Cochrane, Evan W. Gibbard, Kieran Campbell, Basile Tessier-Cloutier, Kendall Greening, Forouh Kalantari, Genny Trigo-Gonzalez, Yemin Wang, Jessica N. McAlpine, Sohrab P. Shah, David G. Huntsman. MODELS AND ANALYTIC TECHNIQUES OF MULLERIAN TISSUE-DERIVED ORGANOIDS [abstract]. In: Proceedings of the 12th Biennial Ovarian Cancer Research Symposium; Sep 13-15, 2018; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2019;25(22 Suppl):Abstract nr GMM-030.
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Affiliation(s)
- Germain C. Ho
- 1Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada,
- 2Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada,
| | - Dawn R. Cochrane
- 1Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada,
| | - Evan W. Gibbard
- 1Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada,
| | - Kieran Campbell
- 1Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada,
- 3Department of Statistics, University of British Columbia, Vancouver, BC, Canada,
- 4UBC Data Science Institute, University of British Columbia, Vancouver, BC, Canada,
| | - Basile Tessier-Cloutier
- 2Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada,
| | - Kendall Greening
- 2Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada,
| | - Forouh Kalantari
- 1Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada,
| | - Genny Trigo-Gonzalez
- 2Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada,
| | - Yemin Wang
- 1Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada,
- 2Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada,
| | - Jessica N. McAlpine
- 5Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, BC, Canada,
| | - Sohrab P. Shah
- 1Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada,
- 2Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada,
- 6Memorial Sloan Kettering Cancer Centre, New York City, NY
| | - David G. Huntsman
- 1Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada,
- 2Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada,
- 5Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, BC, Canada,
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Cochrane DR, Tessier-Cloutier B, Ho G, Campbell K, Gibbard E, Lawrence KM, Nazeran T, Karnezis AN, Salamanca C, Cheng AS, McAlpine JN, Shah S, Hoang LN, Gilks CB, Huntsman DG. Abstract GMM-020: CELL OF ORIGIN, MUTATION AND MICROENVIRONMENT: MODELING EARLY EVENTS OF ENDOMETRIOSIS ASSOCIATED CANCERS. Clin Cancer Res 2019. [DOI: 10.1158/1557-3265.ovcasymp18-gmm-020] [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
Both clear cell ovarian carcinoma (CCOC) and endometrioid ovarian carcinoma (ENOC) are associated with ovarian endometriotic cysts, which is believed to be their precursor lesion. However, genomic evidence is lacking which could explain how these two clinically distinct histotypes of ovarian cancer arise from the same precursor lesion. We therefore hypothesized that these cancers arise from distinct cells of origin within endometrial tissue. Global proteomic analysis of ovarian cancer histotypes identified CTH as a marker for CCOC. We further found that CTH is highly expressed in the ciliated cells of endometrium (both ectopic endometrium and endometriosis), and of the fallopian tube, with little expression in the secretory cells. We also find that other ciliated cell markers are expressed in CCOC, whereas endometrial secretory cell markers are expressed in ENOC. We propose a new model of CCOC and ENOC histogenesis wherein ENOC is derived from cells of secretory cell lineage whereas CCOC is derived from cells of ciliated cell lineage. However, it remains unclear how external factors in the endometriotic cyst cooperate with cell of origin and mutation to promote cancer formation. To study normal tissue biology, we are using organoid cultures of normal endometrium. As ciliated cells of the endometrium are rare, and we have a particular interest in determining whether they have other features that may link them to CCOC, we used a Notch inhibitor, DBZ, to force ciliated cell differentiation in the organoids. We observed a dramatic shift in the cellular content with DBZ treamtment towards ciliated cells. We performed single cell RNA sequencing (scRNAseq) on these endometrial organoids. In the normal endometrial organoids, cells were predominantly a secretory phenotype, characterized by high ESR1 expression, with a minor ciliated cell population. The ciliated cell population expressed several known ciliated markers (FOXJ1 and DNAH12). Upon treatment with DBZ, the number of secretory cells decreases dramatically and two populations of cells emerge which have ciliated cell markers. The larger ciliated cell population is similar to the ciliated cells in the untreated organoids. The smaller ciliated cell population in the DBZ treated organoids express some ciliated cell markers, but clusters separately from normal ciliated cells. We believe this population may reprepsent an intermediary population, which has not fully differentiated. Interestingly, this population expresses the cytokine IL6, while the normal ciliated cell population does not. This is of note because CCOCs express more IL6 compared to the other histotypes. Therefore, we can speculate that this intermediary ciliated cell population may represent cells from which CCOC arise, however more testing is needed. In the future, the scRNAseq data from organoids will be compared to CCOC and ENOC tumors to determine whether the tumors resemble more closely one population of normal cells. We will use viral transduction to introduce mutations into the organoid cultures to determine whether specific mutation leads to transformation towards a CCOC or ENOC-like phenotype. These studies will enable us to tease apart the relative contribution of mutation, microenvironment and the cell of origin to promote tumor formation.
Citation Format: Dawn R Cochrane, Basile Tessier-Cloutier, Germain Ho, Kieran Campbell, Evan Gibbard, Katherine M Lawrence, Tayyebeh Nazeran, Anthony N. Karnezis, Clara Salamanca, Angela S Cheng, Jessica N McAlpine, Sohrab Shah, Lien N Hoang, C Blake Gilks and David G Huntsman. CELL OF ORIGIN, MUTATION AND MICROENVIRONMENT: MODELING EARLY EVENTS OF ENDOMETRIOSIS ASSOCIATED CANCERS [abstract]. In: Proceedings of the 12th Biennial Ovarian Cancer Research Symposium; Sep 13-15, 2018; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2019;25(22 Suppl):Abstract nr GMM-020.
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Affiliation(s)
- Dawn R Cochrane
- 1Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada,
| | - Basile Tessier-Cloutier
- 2Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada,
| | - Germain Ho
- 2Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada,
| | - Kieran Campbell
- 1Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada,
| | - Evan Gibbard
- 1Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada,
| | | | - Tayyebeh Nazeran
- 2Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada,
| | - Anthony N. Karnezis
- 2Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada,
| | - Clara Salamanca
- 1Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada,
| | - Angela S Cheng
- 1Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada,
| | - Jessica N McAlpine
- 3Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, BC, Canada,
| | - Sohrab Shah
- 4Memorial Sloan Kettering Cancer Centre, New York City, NY
| | - Lien N Hoang
- 2Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada,
| | - C Blake Gilks
- 2Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada,
| | - David G Huntsman
- 1Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada,
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Chun HJE, Johann PD, Milne K, Zapatka M, Buellesbach A, Ishaque N, Iskar M, Erkek S, Wei L, Tessier-Cloutier B, Lever J, Titmuss E, Topham JT, Bowlby R, Chuah E, Mungall KL, Ma Y, Mungall AJ, Moore RA, Taylor MD, Gerhard DS, Jones SJM, Korshunov A, Gessler M, Kerl K, Hasselblatt M, Frühwald MC, Perlman EJ, Nelson BH, Pfister SM, Marra MA, Kool M. Identification and Analyses of Extra-Cranial and Cranial Rhabdoid Tumor Molecular Subgroups Reveal Tumors with Cytotoxic T Cell Infiltration. Cell Rep 2019; 29:2338-2354.e7. [PMID: 31708418 PMCID: PMC6905433 DOI: 10.1016/j.celrep.2019.10.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [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: 01/18/2019] [Revised: 08/20/2019] [Accepted: 10/02/2019] [Indexed: 11/23/2022] Open
Abstract
Extra-cranial malignant rhabdoid tumors (MRTs) and cranial atypical teratoid RTs (ATRTs) are heterogeneous pediatric cancers driven primarily by SMARCB1 loss. To understand the genome-wide molecular relationships between MRTs and ATRTs, we analyze multi-omics data from 140 MRTs and 161 ATRTs. We detect similarities between the MYC subgroup of ATRTs (ATRT-MYC) and extra-cranial MRTs, including global DNA hypomethylation and overexpression of HOX genes and genes involved in mesenchymal development, distinguishing them from other ATRT subgroups that express neural-like features. We identify five DNA methylation subgroups associated with anatomical sites and SMARCB1 mutation patterns. Groups 1, 3, and 4 exhibit cytotoxic T cell infiltration and expression of immune checkpoint regulators, consistent with a potential role for immunotherapy in rhabdoid tumor patients. Chun et al. report similarities between the MYC subgroup of cranial and extracranial rhabdoid tumors (RTs) at genetic, gene-expression, and epigenetic levels. They identify five DNA methylation subgroups of RTs across multiple organ sites, and some subgroups exhibit increased levels of immune cell infiltration and immune checkpoint expression.
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Affiliation(s)
- Hye-Jung E Chun
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Pascal D Johann
- Hopp Children's Cancer Center, Heidelberg 69120, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg 69120, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Katy Milne
- Deeley Research Centre, BC Cancer, Victoria, BC V8R 6V5, Canada
| | - Marc Zapatka
- Department of Molecular Genetics, DKFZ, Heidelberg 69120, Germany
| | - Annette Buellesbach
- Hopp Children's Cancer Center, Heidelberg 69120, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg 69120, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Naveed Ishaque
- Center for Digital Health, Berlin Institute of Health and Charité-Universitätsmedizin Berlin, Berlin 10117, Germany; Heidelberg Center for Personalized Oncology, DKFZ, Heidelberg 69120, Germany
| | - Murat Iskar
- Department of Molecular Genetics, DKFZ, Heidelberg 69120, Germany
| | - Serap Erkek
- Hopp Children's Cancer Center, Heidelberg 69120, Germany
| | - Lisa Wei
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Jake Lever
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - James T Topham
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Michael D Taylor
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | | | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry; and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Muenster, Muenster 48149, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Muenster, Muenster 48149, Germany
| | - Michael C Frühwald
- University Children's Hospital Augsburg, Swabian Children's Cancer Center, Augsburg 86156, Germany
| | - Elizabeth J Perlman
- Department of Pathology and Laboratory Medicine, Lurie Children's Hospital, Northwestern University's Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, IL 60611, USA
| | - Brad H Nelson
- Deeley Research Centre, BC Cancer, Victoria, BC V8R 6V5, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3E6, Canada
| | - Stefan M Pfister
- Hopp Children's Cancer Center, Heidelberg 69120, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg 69120, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.
| | - Marcel Kool
- Hopp Children's Cancer Center, Heidelberg 69120, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg 69120, Germany.
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Lac V, Verhoef L, Aguirre-Hernandez R, Nazeran TM, Tessier-Cloutier B, Praetorius T, Orr NL, Noga H, Lum A, Khattra J, Prentice LM, Co D, Köbel M, Mijatovic V, Lee AF, Pasternak J, Bleeker MC, Krämer B, Brucker SY, Kommoss F, Kommoss S, Horlings HM, Yong PJ, Huntsman DG, Anglesio MS. Iatrogenic endometriosis harbors somatic cancer-driver mutations. Hum Reprod 2019; 34:69-78. [PMID: 30428062 DOI: 10.1093/humrep/dey332] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/01/2018] [Indexed: 12/17/2022] Open
Abstract
STUDY QUESTION Does incisional endometriosis (IE) harbor somatic cancer-driver mutations? SUMMARY ANSWER We found that approximately one-quarter of IE cases harbor somatic-cancer mutations, which commonly affect components of the MAPK/RAS or PI3K-Akt-mTor signaling pathways. WHAT IS KNOWN ALREADY Despite the classification of endometriosis as a benign gynecological disease, it shares key features with cancers such as resistance to apoptosis and stimulation of angiogenesis and is well-established as the precursor of clear cell and endometrioid ovarian carcinomas. Our group has recently shown that deep infiltrating endometriosis (DE), a form of endometriosis that rarely undergoes malignant transformation, harbors recurrent somatic mutations. STUDY DESIGN, SIZE, DURATION In a retrospective study comparing iatrogenically induced and endogenously occurring forms of endometriosis unlikely to progress to cancer, we examined endometriosis specimens from 40 women with IE and 36 women with DE. Specimens were collected between 2004 and 2017 from five hospital sites in either Canada, Germany or the Netherlands. IE and DE cohorts were age-matched and all women presented with histologically typical endometriosis without known history of malignancy. PARTICIPANTS/MATERIALS, SETTING, METHODS Archival tissue specimens containing endometriotic lesions were macrodissected and/or laser-capture microdissected to enrich endometriotic stroma and epithelium and a hypersensitive cancer hotspot sequencing panel was used to assess for presence of somatic mutations. Mutations were subsequently validated using droplet digital PCR. PTEN and ARID1A immunohistochemistry (IHC) were performed as surrogates for somatic events resulting in functional loss of respective proteins. MAIN RESULTS AND THE ROLE OF CHANCE Overall, we detected somatic cancer-driver events in 11 of 40 (27.5%) IE cases and 13 of 36 (36.1%) DE cases, including hotspot mutations in KRAS, ERBB2, PIK3CA and CTNNB1. Heterogeneous PTEN loss occurred at similar rates in IE and DE (7/40 vs 5/36, respectively), whereas ARID1A loss only occurred in a single case of DE. While rates of detectable somatic cancer-driver events between IE and DE are not statistically significant (P > 0.05), KRAS activating mutations were more prevalent in DE. LIMITATIONS, REASONS FOR CAUTION Detection of somatic cancer-driver events were limited to hotspots analyzed in our panel-based sequencing assay and loss of protein expression by IHC from archival tissue. Whole genome or exome sequencing, or epigenetic analysis may uncover additional somatic alterations. Moreover, because of the descriptive nature of this study, the functional roles of identified mutations within the context of endometriosis remain unclear and causality cannot be established. WIDER IMPLICATIONS OF THE FINDINGS The alterations we report may be important in driving the growth and survival of endometriosis in ectopic regions of the body. Given the frequency of mutation in surgically displaced endometrium (IE), examination of similar somatic events in eutopic endometrium, as well as clinically annotated cases of other forms of endometriosis, in particular endometriomas that are most commonly linked to malignancy, is warranted. STUDY FUNDING/COMPETING INTEREST(S) This study was funded by a Canadian Cancer Society Impact Grant [701603, PI Huntsman], Canadian Institutes of Health Research Transitional Open Operating Grant [MOP-142273, PI Yong], the Canadian Institutes of Health Research Foundation Grant [FDN-154290, PI Huntsman], the Canadian Institutes of Health Research Project Grant [PJT-156084, PIs Yong and Anglesio], and the Janet D. Cottrelle Foundation through the BC Cancer Foundation [PI Huntsman]. D.G. Huntsman is a co-founder and shareholder of Contextual Genomics Inc., a for profit company that provides clinical reporting to assist in cancer patient treatment. R. Aguirre-Hernandez, J. Khattra and L.M. Prentice have a patent MOLECULAR QUALITY ASSURANCE METHODS FOR USE IN SEQUENCING pending and are current (or former) employees of Contextual Genomics Inc. The remaining authors have no competing interests to declare. TRIAL REGISTRATION NUMBER Not applicable.
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Affiliation(s)
- V Lac
- Department of Molecular Oncology, BC Cancer Research Centre, Room 3-218, 675 West 10th Ave, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, Rm G227, 2211 Wesbrook Mall, University of British Columbia, Vancouver, British Columbia, Canada
| | - L Verhoef
- Department of Pathology of Antoni van Leeuwenhoek, Netherlands Cancer Institute, Plesmanlaan 121, CX Amsterdam, The Netherlands
| | - R Aguirre-Hernandez
- Contextual Genomics, 2389 Health Sciences Mall #204, Vancouver, British Columbia, Canada
| | - T M Nazeran
- Department of Molecular Oncology, BC Cancer Research Centre, Room 3-218, 675 West 10th Ave, Vancouver, British Columbia, Canada.,Department of Anatomical Pathology, Vancouver General Hospital, 899 W 12th Ave, Vancouver, British Columbia, Canada
| | - B Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, Rm G227, 2211 Wesbrook Mall, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Anatomical Pathology, Vancouver General Hospital, 899 W 12th Ave, Vancouver, British Columbia, Canada
| | - T Praetorius
- Department of Molecular Oncology, BC Cancer Research Centre, Room 3-218, 675 West 10th Ave, Vancouver, British Columbia, Canada.,Department of Women's Health, Tuebingen University Hospital, Calwerstrasse 7, Tuebingen, Germany
| | - N L Orr
- Department of Obstetrics and Gynaecology, University of British Columbia, Suite 930, 1125 Howe Street, Vancouver, British Columbia, Canada.,BC Women's Centre for Pelvic Pain & Endometriosis, BC Women's Hospital and Health Centre, Women' Health Centre, F2-4500 Oak St, Vancouver, British Columbia, Canada
| | - H Noga
- Department of Obstetrics and Gynaecology, University of British Columbia, Suite 930, 1125 Howe Street, Vancouver, British Columbia, Canada.,BC Women's Centre for Pelvic Pain & Endometriosis, BC Women's Hospital and Health Centre, Women' Health Centre, F2-4500 Oak St, Vancouver, British Columbia, Canada
| | - A Lum
- Department of Molecular Oncology, BC Cancer Research Centre, Room 3-218, 675 West 10th Ave, Vancouver, British Columbia, Canada
| | - J Khattra
- Contextual Genomics, 2389 Health Sciences Mall #204, Vancouver, British Columbia, Canada
| | - L M Prentice
- Contextual Genomics, 2389 Health Sciences Mall #204, Vancouver, British Columbia, Canada
| | - D Co
- Department of Molecular Oncology, BC Cancer Research Centre, Room 3-218, 675 West 10th Ave, Vancouver, British Columbia, Canada
| | - M Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada
| | - V Mijatovic
- Academic Endometriosis Center VUmc, Department of Reproductive Medicine, VU University Medical Center, De Boelelaan 1117, HV Amsterdam, The Netherlands
| | - A F Lee
- Department of Pathology and Laboratory Medicine, Rm G227, 2211 Wesbrook Mall, University of British Columbia, Vancouver, British Columbia, Canada
| | - J Pasternak
- Department of Women's Health, Tuebingen University Hospital, Calwerstrasse 7, Tuebingen, Germany
| | - M C Bleeker
- Academic Endometriosis Center VUmc, Department of Reproductive Medicine, VU University Medical Center, De Boelelaan 1117, HV Amsterdam, The Netherlands
| | - B Krämer
- Department of Women's Health, Tuebingen University Hospital, Calwerstrasse 7, Tuebingen, Germany
| | - S Y Brucker
- Department of Women's Health, Tuebingen University Hospital, Calwerstrasse 7, Tuebingen, Germany
| | - F Kommoss
- Institute of Pathology, Medizin Campus Bodensee, Roentgenstrasse 2, Friedrichshafen, Germany
| | - S Kommoss
- Department of Women's Health, Tuebingen University Hospital, Calwerstrasse 7, Tuebingen, Germany
| | - H M Horlings
- Department of Pathology of Antoni van Leeuwenhoek, Netherlands Cancer Institute, Plesmanlaan 121, CX Amsterdam, The Netherlands
| | - P J Yong
- Department of Obstetrics and Gynaecology, University of British Columbia, Suite 930, 1125 Howe Street, Vancouver, British Columbia, Canada.,BC Women's Centre for Pelvic Pain & Endometriosis, BC Women's Hospital and Health Centre, Women' Health Centre, F2-4500 Oak St, Vancouver, British Columbia, Canada
| | - D G Huntsman
- Department of Molecular Oncology, BC Cancer Research Centre, Room 3-218, 675 West 10th Ave, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, Rm G227, 2211 Wesbrook Mall, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Anatomical Pathology, Vancouver General Hospital, 899 W 12th Ave, Vancouver, British Columbia, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Suite 930, 1125 Howe Street, Vancouver, British Columbia, Canada
| | - M S Anglesio
- Department of Molecular Oncology, BC Cancer Research Centre, Room 3-218, 675 West 10th Ave, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, Rm G227, 2211 Wesbrook Mall, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Suite 930, 1125 Howe Street, Vancouver, British Columbia, Canada
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47
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Xia Z, Cochrane DR, Tessier-Cloutier B, Leung S, Karnezis AN, Cheng AS, Farnell DA, Magrill J, Schmidt D, Kommoss S, Kommoss FKF, Kommoss F, McAlpine JN, Gilks CB, Koebel M, Rabban JT, Huntsman DG. Expression of L1 retrotransposon open reading frame protein 1 in gynecologic cancers. Hum Pathol 2019; 92:39-47. [PMID: 31220479 DOI: 10.1016/j.humpath.2019.06.001] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/24/2022]
Abstract
LINE-1 (L1) retrotransposons are mobile genetic elements capable of "copy-and-pasting" their own sequences into random genomic loci, and one of the proteins it uses to achieve mobility is LINE-1 open reading frame 1 protein (L1ORF1p). L1ORF1p expression is found across many epithelial cancers, including small cohorts of ovarian and endometrial cancers, and is highly expressed in cancers with mutant p53 expressions. Here we aimed to gain insights into L1ORF1p expression levels within specific histotypes of ovarian cancers: high-grade serous (n = 585), low-grade serous (n = 26), clear cell (n = 132), endometrioid (n = 148), and mucinous (n = 32) ovarian cancers, as well as endometrial cancers (n = 607) using tissue microarray (TMA's). We demonstrated that L1ORF1p expression is associated with advanced stage and serous histotype in gynecological cancers. Like previous studies, we found a higher proportion of L1ORF1p expression in cases with aberrant p53 expression. We evaluated the expression of L1ORF1p in serous tubal intraepithelial carcinomas (STICs) (n = 6) and p53 signature lesions (n = 2) in fallopian tubes. Three STIC cases displayed aberrant p53 overexpression with corresponding L1ORF1p expression in the same tissues, but such correlation was not seen in the two p53 signature lesions, suggesting that L1 protein may be expressed after dysplastic transformation. The remaining three STIC cases have TP53 nonsense mutations with absent p53 expression but a strong and clear L1ORF1p expression within the STIC lesions. While L1ORF1p may not be prognostic in gynecological cancers, it may be useful clinically as a diagnostic IHC marker for p53 null STIC lesions and this warrants further investigation.
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Affiliation(s)
- Zhouchunyang Xia
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
| | - Dawn R Cochrane
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z 4E6, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
| | - Samuel Leung
- Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC V6H 3Z6, Canada
| | - Anthony N Karnezis
- Department of Pathology and Laboratory Medicine, University of California, Davis, CA 95817, USA
| | - Angela S Cheng
- Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC V6H 3Z6, Canada
| | - David A Farnell
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
| | - Jamie Magrill
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z 4E6, Canada
| | | | - Stefan Kommoss
- Department of Obstetrics and Gynecology, University of Tübingen, 72076, Germany
| | - Felix K F Kommoss
- Institute of Pathology, Heidelberg University Hospital, 69120, Germany
| | - Friederich Kommoss
- Institute of Pathology, Medizin Campus Bodensee, Friedrichshafen, 88048, Germany
| | - Jessica N McAlpine
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
| | - Martin Koebel
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB T2N 2T9, Canada
| | - Joseph T Rabban
- Department of Pathology and Laboratory Medicine, University of California, San Francisco, CA 94158, USA
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1L3, Canada; Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
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Tessier-Cloutier B, Cai E, Schaeffer DF. Off-label use of common predictive biomarkers in gastrointestinal malignancies: a critical appraisal. Diagn Pathol 2019; 14:62. [PMID: 31221175 PMCID: PMC6587260 DOI: 10.1186/s13000-019-0843-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 03/28/2019] [Accepted: 06/11/2019] [Indexed: 12/13/2022] Open
Abstract
The use of immunohistochemistry (IHC) as a companion diagnostic is an increasingly important part of the case workup by pathologists and is often central to clinical decision making. New predictive molecular markers are constantly sought for to improve treatment stratification parallel to drug development. Unfortunately, official biomarker guidelines lag behind, and pathologists are often left hesitating when medical oncologists request off-labelled biomarker testing. We performed a literature review of five commonly requested off-label IHC predictive biomarkers in gastrointestinal tract (GIT) malignancies: HER2, mismatch repair (MMR), PD-L1, BRAF V600E and ROS1. We found that HER2 amplification is rare and poorly associated to IHC overexpression in extracolonic and extragastric GIT cancers; however in KRAS wild type colorectal cancers, which fail conventional treatment, HER2 IHC may be useful and should be considered. For MMR testing, more evidence is needed to recommend reflex testing in GIT cancers for treatment purposes. MMR testing should not be discouraged in patients considered for second line checkpoint inhibitor therapy. With the exception of gastric tumors, PD-L1 IHC is a weak predictor of checkpoint inhibitor response in the GIT and should be replaced by MMR in this context. BRAF inhibitors showed activity in BRAF V600E mutated cholangiocarcinomas and pancreatic carcinomas in non-first line settings. ROS1 translocation is extremely rare and poorly correlated to ROS1 IHC expression in the GIT; currently there is no role for ROS1 IHC testing in GIT cancers. Overall, the predictive biomarker literature has grown exponentially, and official guidelines need to be updated more regularly to support pathologists’ testing decisions.
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Affiliation(s)
- Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, Vancouver General Hospital, 910 West 10th Ave, Vancouver, BC, Canada
| | - Ellen Cai
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, Vancouver General Hospital, 910 West 10th Ave, Vancouver, BC, Canada
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada. .,Department of Pathology and Laboratory Medicine, Vancouver General Hospital, 910 West 10th Ave, Vancouver, BC, Canada.
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Tessier-Cloutier B, Twa DD, Baecklund E, Gascoyne R, Johnson NA, Backlin C, Kamen DL, Clarke AE, Ramsey-Goldman R, Lee JL, Farinha P, Bernatsky S. Cell of origin in diffuse large B-cell lymphoma in systemic lupus erythematosus: molecular and clinical factors associated with survival. Lupus Sci Med 2019; 6:e000324. [PMID: 31205728 PMCID: PMC6541753 DOI: 10.1136/lupus-2019-000324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 02/04/2019] [Revised: 03/25/2019] [Accepted: 04/04/2019] [Indexed: 12/29/2022]
Abstract
Background SLE is associated with increased risk of diffuse large B-cell lymphoma (DLBCL). DLBCL is routinely classified by cell of origin (COO), with germinal centre B-cell (GCB) being more common and indicating better prognosis in the general population. We studied COO subtyping in patients with SLE diagnosed with DLBCL and their survival. Patients and methods We evaluated 20 cases of SLE with DLBCL. Immunohistochemistry analysis was performed (BCL2, MYC, BCL6, CD10, CD20, FOXP1, GCET1, MUM1) in tissue microarrays. We examined associations between molecular and clinical features, including overall survival. Results Of the 20 DLBCL SLE cases, 12/20 cases (60%) were classified as non-GCB using Hans or Choi algorithms. MYC and BCL2 protein expression was positive in 6/20 (30%) and 8/20 (40%) SLE cases, respectively, with 2/20 (10%) co-expressing both markers. Seven (7/20) had only extranodal involvement at DLBCL diagnosis. As expected, non-GCB cases had worse survival. Cases presenting exclusively with extranodal disease were associated with shorter SLE duration and better survival despite higher BCL2 protein expression. Conclusions We present novel data characterising DLBCL in SLE. Sixty per cent of the DLBCL in patients with SLE were non-GCB. The nodal and extranodal distribution in SLE was similar to what is known in the general population, but extranodal disease occurred more often with short SLE duration and was associated with longer overall survival. More research on cancer in SLE is the key to further understanding the complex interplay between cancer and the immune system.
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Affiliation(s)
- Basile Tessier-Cloutier
- Anatomical Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Dw Twa
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eva Baecklund
- Department of Medical Sciences, Uppsala Universitet, Uppsala, Sweden
| | - Randy Gascoyne
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Pathology Department and Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Nathalie A Johnson
- Department of Medicine, Sir Mortimer B Davis Jewish General Hospital, Montreal, Québec, Canada
| | - Carin Backlin
- Department of Rheumatology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Diane L Kamen
- Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | | | | | - Jennifer Lf Lee
- Division of Clinical Epidemiology, McGill University Health Centre, Montreal, Québec, Canada
| | - Pedro Farinha
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Pathology Department and Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Sasha Bernatsky
- Division of Clinical Epidemiology, McGill University Health Centre, Montreal, Québec, Canada.,Department of Medicine, McGill University, Montreal, Québec, Canada
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50
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Grewal JK, Tessier-Cloutier B, Jones M, Gakkhar S, Ma Y, Moore R, Mungall AJ, Zhao Y, Taylor MD, Gelmon K, Lim H, Renouf D, Laskin J, Marra M, Yip S, Jones SJM. Application of a Neural Network Whole Transcriptome-Based Pan-Cancer Method for Diagnosis of Primary and Metastatic Cancers. JAMA Netw Open 2019; 2:e192597. [PMID: 31026023 PMCID: PMC6487574 DOI: 10.1001/jamanetworkopen.2019.2597] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
IMPORTANCE A molecular diagnostic method that incorporates information about the transcriptional status of all genes across multiple tissue types can strengthen confidence in cancer diagnosis. OBJECTIVE To determine the practical use of a whole transcriptome-based pan-cancer method in diagnosing primary and metastatic cancers and resolving complex diagnoses. DESIGN, SETTING, AND PARTICIPANTS This cross-sectional diagnostic study assessed Supervised Cancer Origin Prediction Using Expression (SCOPE), a machine learning method using whole-transcriptome RNA sequencing data. Training was performed on publicly available primary cancer data sets, including The Cancer Genome Atlas. Testing was performed retrospectively on untreated primary cancers and treated metastases from volunteer adult patients at BC Cancer in Vancouver, British Columbia, from January 1, 2013, to March 31, 2016, and testing spanned 10 822 samples and 66 output classes representing untreated primary cancers (n = 40) and adjacent normal tissues (n = 26). SCOPE's performance was demonstrated on 211 untreated primary mesothelioma cancers and 201 treatment-resistant metastatic cancers. Finally, SCOPE was used to identify the putative site of origin in 15 cases with initial presentation as cancers with unknown primary of origin. RESULTS A total of 10 688 adult patient samples representing 40 untreated primary tumor types and 26 adjacent-normal tissues were used for training. Demographic data were not available for all data sets. Among the training data set, 5157 of 10 244 (50.3%) were male and the mean (SD) age was 58.9 (14.5) years. Testing was performed on 211 patients with untreated primary mesothelioma (173 [82.0%] male; mean [SD] age, 64.5 [11.3] years); 201 patients with treatment-resistant cancers (141 [70.1%] female; mean [SD] age, 55.6 [12.9] years); and 15 patients with cancers of unknown primary of origin; among the treatment-resistant cancers, 168 were metastatic, and 33 were the primary presentation. An accuracy rate of 99% was obtained for primary epithelioid mesotheliomas tested (125 of 126). The remaining 85 mesotheliomas had a mixed etiology (sarcomatoid mesotheliomas) and were correctly identified as a mixture of their primary components, with potential implications in resolving subtypes and incidences of mixed histology. SCOPE achieved an overall mean (SD) accuracy rate of 86% (11%) and F1 score of 0.79 (0.12) on the 201 treatment-resistant cancers and matched 12 of 15 of the putative diagnoses for cancers with indeterminate diagnosis from conventional pathology. CONCLUSIONS AND RELEVANCE These results suggest that machine learning approaches incorporating multiple tumor profiles can more accurately identify the cancerous state and discriminate it from normal cells. SCOPE uses the whole transcriptomes from normal and tumor tissues, and results of this study suggest that it performs well for rare cancer types, primary cancers, treatment-resistant metastatic cancers, and cancers of unknown primary of origin. Genes most relevant in SCOPE's decision making were examined, and several are known biological markers of respective cancers. SCOPE may be applied as an orthogonal diagnostic method in cases where the site of origin of a cancer is unknown, or when standard pathology assessment is inconclusive.
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Affiliation(s)
- Jasleen K. Grewal
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin Jones
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Sitanshu Gakkhar
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Richard Moore
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Andrew J. Mungall
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yongjun Zhao
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Michael D. Taylor
- Division of Neurosurgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Karen Gelmon
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Howard Lim
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Daniel Renouf
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Marco Marra
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J. M. Jones
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
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