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Cattaneo G, Ventin M, Arya S, Kontos F, Michelakos T, Sekigami Y, Cai L, Villani V, Sabbatino F, Chen F, Sadagopan A, Deshpande V, Moore PA, Ting DT, Bardeesy N, Wang X, Ferrone S, Ferrone CR. Interplay between B7-H3 and HLA class I in the clinical course of pancreatic ductal adenocarcinoma. Cancer Lett 2024; 587:216713. [PMID: 38364961 DOI: 10.1016/j.canlet.2024.216713] [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: 10/17/2023] [Revised: 01/16/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024]
Abstract
Human leukocyte antigen (HLA) class I defects are associated with cancer progression. However, their prognostic significance is controversial and may be modulated by immune checkpoints. Here, we investigated whether the checkpoint B7-H3 modulates the relationship between HLA class I and pancreatic ductal adenocarcinoma (PDAC) prognosis. PDAC tumors were analyzed for the expression of B7-H3, HLA class I, HLA class II molecules, and for the presence of tumor-infiltrating immune cells. We observed defective HLA class I and HLA class II expressions in 75% and 59% of PDAC samples, respectively. HLA class I and B7-H3 expression were positively related at mRNA and protein level, potentially because of shared regulation by RELA, a sub-unit of NF-kB. High B7-H3 expression and low CD8+ T cell density were indicators of poor survival, while HLA class I was not. Defective HLA class I expression was associated with unfavorable survival only in patients with low B7-H3 expression. Favorable survival was observed only when HLA class I expression was high and B7-H3 expression low. Our results provide the rationale for targeting B7-H3 in patients with PDAC tumors displaying high HLA class I levels.
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Affiliation(s)
- Giulia Cattaneo
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States. https://twitter.com/GCattaneoPhD
| | - Marco Ventin
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Shahrzad Arya
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Filippos Kontos
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Theodoros Michelakos
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Yurie Sekigami
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Lei Cai
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Vincenzo Villani
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Francesco Sabbatino
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | | | - Ananthan Sadagopan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | | | - David T Ting
- MassGeneral Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Nabeel Bardeesy
- MassGeneral Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Xinhui Wang
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Soldano Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Cristina R Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States; Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, United States.
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2
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Misra S, Hakim A, Smith MP, Deshpande V, Wolf JL, Carroll BJ. Images in Vascular Medicine: Enterocolic lymphocytic phlebitis as a rare vascular cause of colitis. Vasc Med 2024:1358863X241236774. [PMID: 38557390 DOI: 10.1177/1358863x241236774] [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: 04/04/2024]
Affiliation(s)
- Shantum Misra
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Aaron Hakim
- Beth Israel Deaconess Medical Center, Boston, MA, USA
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Bal M, Deshpande V. Advancements in diagnosing IgG4-related disease of the head and neck: Navigating diagnostic pitfalls. Semin Diagn Pathol 2024; 41:54-65. [PMID: 38185595 DOI: 10.1053/j.semdp.2023.12.003] [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: 12/25/2023] [Accepted: 12/26/2023] [Indexed: 01/09/2024]
Abstract
IgG4-related disease (IgG4-RD) is an immune-mediated condition affecting nearly any organ. This review focuses on the nuances of diagnosing IgG4-RD affecting the head and neck. Salivary gland involvement, especially of the submandibular glands, often permits a definitive diagnosis on biopsy. However, elevated IgG4+ plasma cells are nonspecific and can be seen in chronic sialadenitis, lymphoma, and other mimics. Careful correlation of clinical and pathological findings is essential. Given the significant overlap with chronic sinusitis, IgG4-RD of the sinonasal region is difficult to diagnose histologically. Laryngeal and pharyngeal involvement appears rare as an isolated finding of IgG4-RD. Mastoid disease is uncommon and remains a diagnosis of exclusion. Thyroid manifestations pose challenges given unclear diagnostic criteria - Riedel's thyroiditis likely represents IgG4-RD, but the fibrosing variant of Hashimoto's thyroiditis as a form of the so-called 'IgG4-related thyroiditis' requires better characterisation. Eosinophilic angiocentric fibrosis, despite histologic similarities, only partially overlaps with IgG4-RD. This review aims to guide diagnosing IgG4-RD in the head and neck through a systematic, organ-focused discussion of the clinical context, the utility of immunostaining, histological mimics, and controversial issues that pose diagnostic pitfalls. Increased awareness of the nuances and difficulties diagnosing IgG4-RD affecting the head and neck will improve recognition of this protean disease.
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Affiliation(s)
- Munita Bal
- Department of Pathology, Tata Memorial Center, Homi Bhabha National Institute, Mumbai, Maharastra, India
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Goto N, Westcott PMK, Goto S, Imada S, Taylor MS, Eng G, Braverman J, Deshpande V, Jacks T, Agudo J, Yilmaz ÖH. SOX17 enables immune evasion of early colorectal adenomas and cancers. Nature 2024; 627:636-645. [PMID: 38418875 DOI: 10.1038/s41586-024-07135-3] [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: 03/23/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
A hallmark of cancer is the avoidance of immune destruction. This process has been primarily investigated in locally advanced or metastatic cancer1-3; however, much less is known about how pre-malignant or early invasive tumours evade immune detection. Here, to understand this process in early colorectal cancers (CRCs), we investigated how naive colon cancer organoids that were engineered in vitro to harbour Apc-null, KrasG12D and Trp53-null (AKP) mutations adapted to the in vivo native colonic environment. Comprehensive transcriptomic and chromatin analyses revealed that the endoderm-specifying transcription factor SOX17 became strongly upregulated in vivo. Notably, whereas SOX17 loss did not affect AKP organoid propagation in vitro, its loss markedly reduced the ability of AKP tumours to persist in vivo. The small fraction of SOX17-null tumours that grew displayed notable interferon-γ (IFNγ)-producing effector-like CD8+ T cell infiltrates in contrast to the immune-suppressive microenvironment in wild-type counterparts. Mechanistically, in both endogenous Apc-null pre-malignant adenomas and transplanted organoid-derived AKP CRCs, SOX17 suppresses the ability of tumour cells to sense and respond to IFNγ, preventing anti-tumour T cell responses. Finally, SOX17 engages a fetal intestinal programme that drives differentiation away from LGR5+ tumour cells to produce immune-evasive LGR5- tumour cells with lower expression of major histocompatibility complex class I (MHC-I). We propose that SOX17 is a transcription factor that is engaged during the early steps of colon cancer to orchestrate an immune-evasive programme that permits CRC initiation and progression.
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Affiliation(s)
- Norihiro Goto
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter M K Westcott
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Saori Goto
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shinya Imada
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - George Eng
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jonathan Braverman
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Hospital and Harvard Medical School, Boston, MA, USA
| | - Tyler Jacks
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Judith Agudo
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Immunology, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Boston, MA, USA.
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA, USA.
- New York Stem Cell Foundation-Robertson Investigator, New York, NY, USA.
| | - Ömer H Yilmaz
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Beth Israel Deaconess Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Deshpande V. Unraveling the complexities of IgG4-related disease: Musings from a histopathologist. Semin Diagn Pathol 2024; 41:43-44. [PMID: 38238220 DOI: 10.1053/j.semdp.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 03/24/2024]
Affiliation(s)
- Vikram Deshpande
- Beth Israel Deaconess Medical Center, Harvard Medical School, USA.
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Huang Q, Lew E, Cheng Y, Shinagare S, Deshpande V, Gold JS, Wiener D, Weber HC. Esophageal adenocarcinoma heterogeneity in clinicopathology and prognosis: A single center longitudinal study of 146 cases over a 20-year period. Ann Diagn Pathol 2024; 70:152285. [PMID: 38518703 DOI: 10.1016/j.anndiagpath.2024.152285] [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: 12/26/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/24/2024]
Abstract
Recent genomic studies suggest that esophageal adenocarcinoma (EAC) is not homogeneous and can be divided into true (tEAC) and probable (pEAC) groups. We compared clinicopathologic and prognostic features between the two groups of EAC. Based on endoscopic, radiologic, surgical, and pathologic reports, tumors with epicenters beyond 2 cm of the gastroesophageal junction (GEJ) were assigned to the tEAC group (N = 63), while epicenters within 2 cm of, but not crossing the GEJ, were allocated to the pEAC group (N = 83). All 146 consecutive patients were male (age: median 70 years, range: 51-88) and White-predominant (98.6 %). There was no significant difference in gastroesophageal reflux disease, obesity, comorbidity, and the prevalence of Barrett's esophagus, and cases diagnosed during endoscopic surveillance. However, compared to the pEAC group, the tEAC group had significantly more cases with hiatal hernia (P = 0.003); their tumors were significantly smaller in size (P = 0.007), more frequently with tubular/papillary adenocarcinoma (P = 0.001), had fewer cases with poorly cohesive carcinoma (P = 0.018), and demonstrated better prognosis in stage I disease (P = 0.012); 5-year overall survival (34.9 months) was significantly longer (versus 16.8 months in pEACs) (P = 0.043). Compared to the patients without resection, the patients treated with endoscopic or surgical resection showed significantly better outcomes, irrespective of stages. We concluded that EACs were heterogeneous with two distinct tEAC and pEAC groups in clinicopathology and prognosis; resection remained the better option for improved outcomes. CONDENSED ABSTRACT: Esophageal adenocarcinoma can be divided into true or probable groups with distinct clinicopathology and better prognosis in the former than in the latter. we showed that resection remained the better option for improved outcomes.
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Affiliation(s)
- Qin Huang
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
| | - Edward Lew
- Department of Gastroenterology, Veterans Affairs Boston Healthcare System and Harvard Medical School, West Roxbury, MA, USA
| | - Yuqing Cheng
- Department of Pathology, Changzhou Second People's Hospital and Nanjing Medical University, Changzhou, China
| | - Shweta Shinagare
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Jason S Gold
- Department of Surgery, Veterans Affairs Boston Healthcare System and Harvard Medical School, West Roxbury, MA, USA
| | - Daniel Wiener
- Department of Surgery, Veterans Affairs Boston Healthcare System and Harvard Medical School, West Roxbury, MA, USA
| | - H Christian Weber
- Department of Gastroenterology, Veterans Affairs Boston Healthcare System and Boston University Medical School, West Roxbury, MA, USA
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Yilmaz O, Westerhoff M, Panarelli N, Hart J, Groisman G, Ruz-Caracuel I, Loughrey M, Matsukuma K, Lee SH, Yilmaz O, Gonzalez RS, Deshpande V. Lymphoglandular Complex-Like Colorectal Carcinoma-A Series of 20 Colorectal Cases, Including Newly Reported Features of Malignant Behavior. Am J Surg Pathol 2024; 48:70-79. [PMID: 38054635 DOI: 10.1097/pas.0000000000002141] [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] [Indexed: 12/07/2023]
Abstract
Distinguishing colon carcinoma that is surrounded by well-circumscribed lymphoid tissue from adenomas involving lymphoglandular complexes can be difficult. We assessed a multi-institutional international cohort of 20 colorectal carcinomas with associated prominent lymphoid infiltrates, which we referred to as lymphoglandular complex-like carcinoma (LGCC). We collected clinical and endoscopic features, including lesion size, endoscopic appearance, location, procedure, follow-up, AJCC stage, and mismatch repair status. We recorded the presence of the following histologic features: haphazard gland distribution, gland angulation, gland fusion, solid nest formation, single-cell formation, stromal desmoplasia, presence of lymphovascular invasion and perineural invasion, presence of lamina propria, cytologic atypia as low- or high-grade, presence of goblet cells in the invasive component, and the presence of a surface lesion. Most cases (9 of 13) were described endoscopically as sessile polyps with an average size of 1.56 cm. Most cases (90%) were associated with a surface lesion, of which the majority were tubular adenomas, though a subset was associated with sessile serrated lesions with dysplasia (3 of 18). All cases of LGCC demonstrated haphazard gland distribution and either gland angulation, fusion, or solid nest formation. A portion of cases demonstrated single-cell infiltration (35%) and desmoplasia (50%), and rarely lymphovascular invasion was present (5%). A subset (10%) of cases invaded beyond the submucosa. Deficient mismatch repair was present in 22% (2 of 9) of cases for which it was performed. In cases of colectomy or completion colectomy, nodal metastasis was present in 38% (3 of 8). No cases demonstrated disease recurrence or disease-specific mortality. Overall, LGCC represents an enigmatic subset of carcinomas that is important to distinguish from adenomas involving lymphoglandular complexes due to its varying prognostic outcomes.
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Affiliation(s)
- Osman Yilmaz
- Department of Pathology, Beth Israel Deaconess Medical Center
- Harvard Medical School, Boston, MA
| | | | - Nicole Panarelli
- Department of Pathology, Montefiore Albert Einstein College of Medicine, New York, NY
| | - John Hart
- Department of Pathology, University of Chicago, Chicago, IL
| | - Gabriel Groisman
- Department of Pathology, Hillel Yaffe Medical Center, Hadera, Israel
| | - Ignacio Ruz-Caracuel
- Department of Pathology, Hospital Universitario Ramon y Cajal, IRYCIS, CIBERONC, Madrid, Spain
| | - Maurice Loughrey
- Department of Pathology, Royal Victoria Hospital Belfast Trust, Belfast, N. Ireland
| | - Karen Matsukuma
- Department of Pathology, University of California Davis, Sacramento, CA
| | - Soo Hyun Lee
- Department of Pathology, Boston University Medical Center
| | - Omer Yilmaz
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | | | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center
- Harvard Medical School, Boston, MA
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Larque AB, Lozano-Calderon S, Cote GM, Chen YL, Hung YP, Deshpande V, Nielsen GP, Chebib I. Multivariate evaluation of prognostic markers in synovial sarcoma. J Clin Pathol 2023; 77:16-21. [PMID: 36288948 DOI: 10.1136/jcp-2022-208518] [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: 07/29/2022] [Accepted: 10/05/2022] [Indexed: 11/04/2022]
Abstract
AIMS Synovial sarcoma (SS) is an aggressive neoplasm but with varied clinical outcomes despite standard treatment protocols. Several clinicopathological features and immunohistochemical stains have been proposed as prognostic markers in SS. The aim of this study was to evaluate SS from a single institution for prognostically relevant clinicopathological and immunohistochemical factors. METHODS We identified a single-institution cohort of SS with follow-up. Clinical and pathological factors examined included age, sex, tumour location, AJCC (American Joint Committee on Cancer) stage, tumour size, grade and status of surgical margins. Immunohistochemical staining for p16, p53, RB1, MYC, PTEN (phosphatase and tensin homologue), β-catenin, MDM2 and Ki67 proliferative index was performed on tissue microarray. Cox proportional hazard model was used for multivariate assessment of overall survival (OS) and disease-free survival (DFS). RESULTS 133 patients with SS met the inclusion criteria for our cohort, with 100 having complete dataset for all study covariates. On Cox regression multivariate analysis, location (axial vs extremity, p<0.001), AJCC stage (p<0.001), p16 expression (≥75%, p=0.021) were significantly associated with worse OS, whereas PTEN intensity (score 2, p<0.001) and p53 expression (null/≥75%, p=0.013) were correlated with improved OS. For DFS analysis, location (axial vs extremity, p=0.030), tumour size (≥5 cm, p=0.009) and MYC expression (≥33%, p=0.013) were associated with inferior outcome. Only PTEN intensity (score 2, p<0.001) correlated with improved DFS. CONCLUSIONS In reviewing numerous clinicopathological and immunohistochemical markers, this study shows that location, AJCC stage, p16, p53 and PTEN expression were prognostically significant in multivariate analysis for OS in a uniformly treated SS cohort. Location, tumour size, MYC and PTEN expression were significantly associated with DFS.
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Affiliation(s)
- Ana-Belen Larque
- Department of Pathology, University of Barcelona, Barcelona, Spain
| | - Santiago Lozano-Calderon
- Department of Orthopaedic Surgery, Massachuestts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Gregory M Cote
- Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Yen-Lin Chen
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Yin P Hung
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - G Petur Nielsen
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ivan Chebib
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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Taylor MS, Wu C, Fridy PC, Zhang SJ, Senussi Y, Wolters JC, Cajuso T, Cheng WC, Heaps JD, Miller BD, Mori K, Cohen L, Jiang H, Molloy KR, Chait BT, Goggins MG, Bhan I, Franses JW, Yang X, Taplin ME, Wang X, Christiani DC, Johnson BE, Meyerson M, Uppaluri R, Egloff AM, Denault EN, Spring LM, Wang TL, Shih IM, Fairman JE, Jung E, Arora KS, Yilmaz OH, Cohen S, Sharova T, Chi G, Norden BL, Song Y, Nieman LT, Pappas L, Parikh AR, Strickland MR, Corcoran RB, Mustelin T, Eng G, Yilmaz ÖH, Matulonis UA, Chan AT, Skates SJ, Rueda BR, Drapkin R, Klempner SJ, Deshpande V, Ting DT, Rout MP, LaCava J, Walt DR, Burns KH. Ultrasensitive Detection of Circulating LINE-1 ORF1p as a Specific Multicancer Biomarker. Cancer Discov 2023; 13:2532-2547. [PMID: 37698949 PMCID: PMC10773488 DOI: 10.1158/2159-8290.cd-23-0313] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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] [Received: 03/24/2023] [Revised: 08/09/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023]
Abstract
Improved biomarkers are needed for early cancer detection, risk stratification, treatment selection, and monitoring treatment response. Although proteins can be useful blood-based biomarkers, many have limited sensitivity or specificity for these applications. Long INterspersed Element-1 (LINE-1) open reading frame 1 protein (ORF1p) is a transposable element protein overexpressed in carcinomas and high-risk precursors during carcinogenesis with negligible expression in normal tissues, suggesting ORF1p could be a highly specific cancer biomarker. To explore ORF1p as a blood-based biomarker, we engineered ultrasensitive digital immunoassays that detect mid-attomolar (10-17 mol/L) ORF1p concentrations in plasma across multiple cancers with high specificity. Plasma ORF1p shows promise for early detection of ovarian cancer, improves diagnostic performance in a multianalyte panel, provides early therapeutic response monitoring in gastroesophageal cancers, and is prognostic for overall survival in gastroesophageal and colorectal cancers. Together, these observations nominate ORF1p as a multicancer biomarker with potential utility for disease detection and monitoring. SIGNIFICANCE The LINE-1 ORF1p transposon protein is pervasively expressed in many cancers and is a highly specific biomarker of multiple common, lethal carcinomas and their high-risk precursors in tissue and blood. Ultrasensitive ORF1p assays from as little as 25 μL plasma are novel, rapid, cost-effective tools in cancer detection and monitoring. See related commentary by Doucet and Cristofari, p. 2502. This article is featured in Selected Articles from This Issue, p. 2489.
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Affiliation(s)
- Martin S. Taylor
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
| | - Connie Wu
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Peter C. Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York
| | - Stephanie J. Zhang
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Yasmeen Senussi
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Justina C. Wolters
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tatiana Cajuso
- Department of Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Wen-Chih Cheng
- Department of Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - John D. Heaps
- Department of Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Bryant D. Miller
- Department of Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Kei Mori
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- Healthcare Optics Research Laboratory, Canon U.S.A., Inc., Cambridge, Massachusetts
| | - Limor Cohen
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York
| | | | - Irun Bhan
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Joseph W. Franses
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Xiaoyu Yang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Xinan Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - David C. Christiani
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Bruce E. Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Ravindra Uppaluri
- Department of Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ann Marie Egloff
- Department of Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Elyssa N. Denault
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Laura M. Spring
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Tian-Li Wang
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ie-Ming Shih
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Euihye Jung
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kshitij S. Arora
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
| | - Osman H. Yilmaz
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Sonia Cohen
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Tatyana Sharova
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Gary Chi
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Bryanna L. Norden
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Yuhui Song
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Linda T. Nieman
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Leontios Pappas
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Aparna R. Parikh
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Matthew R. Strickland
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ryan B. Corcoran
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - George Eng
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Ömer H. Yilmaz
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Ursula A. Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit and Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Steven J. Skates
- MGH Biostatistics, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Bo R. Rueda
- Department of Obstetrics and Gynecology, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Ronny Drapkin
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Samuel J. Klempner
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Vikram Deshpande
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
| | - David T. Ting
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, the Netherlands
| | - David R. Walt
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Kathleen H. Burns
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
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10
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Coley AK, Lu C, Pankaj A, Emmett MJ, Lang ER, Song Y, Xu KH, Xu N, Patel BK, Chougule A, Nieman LT, Aryee MJ, Ferrone CR, Deshpande V, Franses JW, Ting DT. Dysregulated Repeat Element Viral-like Immune Response in Hepatocellular Carcinoma. bioRxiv 2023:2023.12.04.570014. [PMID: 38105940 PMCID: PMC10723373 DOI: 10.1101/2023.12.04.570014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Purpose Dysregulation of viral-like repeat RNAs are a common feature across many malignancies that are linked with immunological response, but the characterization of these in hepatocellular carcinoma (HCC) is understudied. In this study, we performed RNA in situ hybridization (RNA-ISH) of different repeat RNAs, immunohistochemistry (IHC) for immune cell subpopulations, and spatial transcriptomics to understand the relationship of HCC repeat expression, immune response, and clinical outcomes. Experimental Design RNA-ISH for LINE1, HERV-K, HERV-H, and HSATII repeats and IHC for T-cell, Treg, B-cell, macrophage, and immune checkpoint markers were performed on 43 resected HCC specimens. Spatial transcriptomics on tumor and vessel regions of interest was performed on 28 specimens from the same cohort. Results High HERV-K and high LINE1 expression were both associated with worse overall survival. There was a positive correlation between LINE1 expression and FOXP3 T-regulatory cells (r = 0.51 p < 0.001) as well as expression of the TIM3 immune checkpoint (r = 0.34, p = 0.03). Spatial transcriptomic profiling of HERV-K high and LINE-1 high tumors identified elevated expression of multiple genes previously associated with epithelial mesenchymal transition, cellular proliferation, and worse overall prognosis in HCC including SSX1, MAGEC2, and SPINK1. Conclusion Repeat RNAs may serve as useful prognostic biomarkers in HCC and may also serve as novel therapeutic targets. Additional study is needed to understand the mechanisms by which repeat RNAs impact HCC tumorigenesis.
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Affiliation(s)
- Avril K. Coley
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Surgery, Massachusetts General Hospital Harvard Medical School; Boston, MA, USA
| | - Chenyue Lu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Health Sciences and Technology Program; Cambridge, MA, USA
| | - Amaya Pankaj
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Matthew J. Emmett
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Evan R. Lang
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Yuhui Song
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Katherine H. Xu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Nova Xu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Bidish K. Patel
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Abhijit Chougule
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Linda T. Nieman
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Martin J. Aryee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health; Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA, USA
- Broad Institute of Harvard and MIT; Cambridge, MA, USA
| | | | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School; Boston, MA, USA
| | - Joseph W. Franses
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
- Health Sciences and Technology Program; Cambridge, MA, USA
- Section of Hematology-Oncology, Department of Medicine, University of Chicago; Chicago, IL, USA
| | - David T. Ting
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
- Health Sciences and Technology Program; Cambridge, MA, USA
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11
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Tzouanas CN, Sherman MS, Shay JE, Rubin AJ, Mead BE, Dao TT, Butzlaff T, Mana MD, Kolb KE, Walesky C, Pepe-Mooney BJ, Smith CJ, Prakadan SM, Ramseier ML, Tong EY, Joung J, Chi F, McMahon-Skates T, Winston CL, Jeong WJ, Aney KJ, Chen E, Nissim S, Zhang F, Deshpande V, Lauer GM, Yilmaz ÖH, Goessling W, Shalek AK. Chronic metabolic stress drives developmental programs and loss of tissue functions in non-transformed liver that mirror tumor states and stratify survival. bioRxiv 2023:2023.11.30.569407. [PMID: 38077056 PMCID: PMC10705501 DOI: 10.1101/2023.11.30.569407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Under chronic stress, cells must balance competing demands between cellular survival and tissue function. In metabolic dysfunction-associated steatotic liver disease (MASLD, formerly NAFLD/NASH), hepatocytes cooperate with structural and immune cells to perform crucial metabolic, synthetic, and detoxification functions despite nutrient imbalances. While prior work has emphasized stress-induced drivers of cell death, the dynamic adaptations of surviving cells and their functional repercussions remain unclear. Namely, we do not know which pathways and programs define cellular responses, what regulatory factors mediate (mal)adaptations, and how this aberrant activity connects to tissue-scale dysfunction and long-term disease outcomes. Here, by applying longitudinal single-cell multi -omics to a mouse model of chronic metabolic stress and extending to human cohorts, we show that stress drives survival-linked tradeoffs and metabolic rewiring, manifesting as shifts towards development-associated states in non-transformed hepatocytes with accompanying decreases in their professional functionality. Diet-induced adaptations occur significantly prior to tumorigenesis but parallel tumorigenesis-induced phenotypes and predict worsened human cancer survival. Through the development of a multi -omic computational gene regulatory inference framework and human in vitro and mouse in vivo genetic perturbations, we validate transcriptional (RELB, SOX4) and metabolic (HMGCS2) mediators that co-regulate and couple the balance between developmental state and hepatocyte functional identity programming. Our work defines cellular features of liver adaptation to chronic stress as well as their links to long-term disease outcomes and cancer hallmarks, unifying diverse axes of cellular dysfunction around core causal mechanisms.
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Affiliation(s)
- Constantine N. Tzouanas
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- These authors contributed equally
| | - Marc S. Sherman
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
- These authors contributed equally
| | - Jessica E.S. Shay
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Alcohol Liver Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- These authors contributed equally
| | - Adam J. Rubin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benjamin E. Mead
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyler T. Dao
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Titus Butzlaff
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Miyeko D. Mana
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Kellie E. Kolb
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chad Walesky
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian J. Pepe-Mooney
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Colton J. Smith
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sanjay M. Prakadan
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michelle L. Ramseier
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Evelyn Y. Tong
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Julia Joung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Science, MA, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Fangtao Chi
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Thomas McMahon-Skates
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Carolyn L. Winston
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Woo-Jeong Jeong
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Katherine J. Aney
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ethan Chen
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sahar Nissim
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Gastroenterology Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Science, MA, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Georg M. Lauer
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ömer H. Yilmaz
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
- These senior authors contributed equally
| | - Wolfram Goessling
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA, USA
- These senior authors contributed equally
| | - Alex K. Shalek
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- These senior authors contributed equally
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12
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Umetsu SE, Joseph NM, Cho SJ, Morotti R, Deshpande V, Jain D, Kakar S. Focal nodular hyperplasia-like nodules arising in the setting of hepatic vascular disorders with portosystemic shunting show β-catenin activation. Hum Pathol 2023; 142:20-26. [PMID: 37806391 DOI: 10.1016/j.humpath.2023.09.010] [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: 06/14/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/10/2023]
Abstract
Hepatocellular nodules can develop in the setting of chronic hepatic vascular disorders including those characterized by portosystemic shunts such as Abernethy malformation and post-Fontan procedure. The nodules can range from benign lesions such as regenerative nodules, focal nodular hyperplasia (FNH), and hepatocellular adenoma (HCA) to malignant neoplasms such as hepatocellular carcinoma (HCC). In many instances, these nodules are difficult to place into well-defined categories based on radiologic or histologic features. Nodular lesions that resemble FNH are common in this context and have been described as FNH-like nodules, the nature of which is not well-established. This study examines 6 liver resections from patients with vascular disease characterized by portosystemic shunts. A wide range of nodules were present in these cases, including regenerative nodules (n = 2), FNH and FNH-like (n = 30), HCA (n = 10), HCA-like (n = 13), and HCC (n = 2). Six nodules from 3 patients were categorized as FNH-like due to one or more features such as nodular architecture, fibrous septa, and ductular reaction, but lack of typical map-like glutamine synthetase (GS) staining. Further characterization of these 6 FNH-like nodules showed diffuse GS staining in all nodules (3 diffuse homogeneous, 3 diffuse heterogeneous). Targeted next-generation sequencing identified CTNNB1 alterations in all tested FNH-like nodules (n = 4). These results indicate that FNH-like nodules in the setting of chronic hepatic vascular disorders can be neoplastic. Since the presence of β-catenin activation portends a potential risk for malignant progression, GS and β-catenin immunohistochemistry should be obtained in all cases showing FNH-like morphology, with molecular analysis performed in cases with indeterminate staining pattern.
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Affiliation(s)
- Sarah E Umetsu
- Department of Pathology, University of California, San Francisco, San Francisco, CA, 94143, USA.
| | - Nancy M Joseph
- Department of Pathology, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Soo-Jin Cho
- Department of Pathology, University of California, San Francisco, San Francisco, CA, 94143, USA
| | | | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Dhanpat Jain
- Department of Pathology, Yale University, New Haven, CT, 06520, USA
| | - Sanjay Kakar
- Department of Pathology, University of California, San Francisco, San Francisco, CA, 94143, USA
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13
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Patel BK, Raabe MJ, Lang ER, Song Y, Lu C, Deshpande V, Nieman LT, Aryee MJ, Chen YB, Ting DT, DeFilipp Z. Spatial transcriptomics reveals distinct tissue niches linked with steroid responsiveness in acute gastrointestinal GVHD. Blood 2023; 142:1831-1844. [PMID: 37699201 PMCID: PMC10731919 DOI: 10.1182/blood.2023020644] [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] [Received: 04/05/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023] Open
Abstract
Severe acute graft-versus-host disease (aGVHD) is associated with significant mortality and morbidity, especially in steroid-resistant (SR) cases. Spatial transcriptomic technology can elucidate tissue-based interactions in vivo and possibly identify predictors of treatment response. Tissue sections from 32 treatment-naïve patients with biopsy-confirmed lower gastrointestinal (GI) aGVHD were obtained. The GeoMx digital spatial profiler was used to capture transcriptome profiles of >18 000 genes from different foci of immune infiltrates, colonic epithelium, and vascular endothelium. Each tissue compartment sampled showed 2 distinct clusters that were analyzed for differential expression and spatially resolved correlation of gene signatures. Classic cell-mediated immunity signatures, normal differentiated epithelial cells, and inflamed vasculature dominated foci sampled from steroid-sensitive cases. In contrast, a neutrophil predominant noncanonical inflammation with regenerative epithelial cells and some indication of angiogenic endothelial response was overrepresented in areas from SR cases. Evaluation of potential prognostic biomarkers identified ubiquitin specific peptidase 17-like (USP17L) family of genes as being differentially expressed in immune cells from patients with worsened survival. In summary, we demonstrate distinct tissue niches with unique gene expression signatures within lower GI tissue from patients with aGVHD and provide evidence of a potential prognostic biomarker.
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Affiliation(s)
- Bidish K. Patel
- Center for Cancer Research, Mass General Cancer Center, Boston, MA
| | - Michael J. Raabe
- Center for Cancer Research, Mass General Cancer Center, Boston, MA
| | - Evan R. Lang
- Center for Cancer Research, Mass General Cancer Center, Boston, MA
| | - Yuhui Song
- Center for Cancer Research, Mass General Cancer Center, Boston, MA
| | - Chenyue Lu
- Center for Cancer Research, Mass General Cancer Center, Boston, MA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Linda T. Nieman
- Center for Cancer Research, Mass General Cancer Center, Boston, MA
| | - Martin J. Aryee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA
| | - Yi-Bin Chen
- Hematopoietic Cell Transplant and Cellular Therapy Program, Massachusetts General Hospital, Boston, MA
| | - David T. Ting
- Center for Cancer Research, Mass General Cancer Center, Boston, MA
- Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Zachariah DeFilipp
- Hematopoietic Cell Transplant and Cellular Therapy Program, Massachusetts General Hospital, Boston, MA
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14
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Arya S, Ventin M, Nebbia M, Fernandez-Del Castillo C, Lionetto G, Qadan M, Lillemoe KD, Deshpande V, Catalano OA, Thiele EA, Ferrone CR. Long-Term Outcomes of Tuberous Sclerosis Complex-Associated Non-functional Pancreatic Neuroendocrine Tumors: Should We Be More Conservative? Ann Surg Oncol 2023; 30:7748-7755. [PMID: 37648887 PMCID: PMC10562497 DOI: 10.1245/s10434-023-14157-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 07/30/2023] [Indexed: 09/01/2023]
Abstract
BACKGROUND Hereditary syndromes such as tuberous sclerosis complex (TSC) account for 10% of pancreatic neuroendocrine tumors (PNETs). Surgical intervention is the current standard of care for sporadic PNETs (spPNETs) that are >2 cm in size. We compared the long-term outcomes of resected TSC-PNETs with patients with spPNETs. METHODS We conducted a retrospective review of perioperative data and outcomes of TSC-PNETs compared with spPNETs. Inclusion criteria involved selecting patients whose tumors were no larger than 5.1 cm, the maximum size observed in the TSC-PNET group. RESULTS Of the 347 patients resected for PNETs, 14 were TSC-PNETs and 241 were non-functional spPNETs. The median age for the whole cohort was 56 years (interquartile range [IQR] 21.0) and 47% were female. The median follow-up was 103.8 months (95% confidence interval [CI] 89.2-118.6). Specifically, 14 patients with TSC-PNETs and 194 patients with spPNETs were included. Compared with spPNETs, patients with TSC-PNETs were operated on at a younger age (24.0 vs. 57.5 years; p < 0.001), were more frequently multifocal (28.5% vs. 0.0%; p < 0.001), were more likely to undergo minimally invasive operations (78.6% vs. 24.3%; p < 0.001), and had more R1 resections (28.6% vs. 5.7%; p = 0.006). Local and distant tumor recurrence was only observed in the spPNET group. The 5-year mortality rates for the spPNET and TSC-PNET groups were 6.2% and 0.0%, respectively. No PNET-related deaths were observed among TSC-PNETs. CONCLUSION None of the TSC-PNET patients recurred after a median follow-up of 78.0 months. The risk-benefit of aggressive pancreatic operations in TSC-PNET patients is still unclear and our findings suggest a conservative approach should be considered.
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Affiliation(s)
- Shahrzad Arya
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marco Ventin
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Martina Nebbia
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Gabriella Lionetto
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Motaz Qadan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Keith D Lillemoe
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Onofrio A Catalano
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth A Thiele
- Herscot Center for Tuberous Sclerosis Complex, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cristina R Ferrone
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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15
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Neyaz A, Crotty R, Rickelt S, Pankaj A, Stojanova M, Michelakos TP, Sekigami Y, Kontos F, Parrack PH, Patil DT, Heaphy CM, Ferrone CR, Deshpande V. Predicting recurrence in pancreatic neuroendocrine tumours: role of ARX and alternative lengthening of telomeres (ALT). Histopathology 2023; 83:546-558. [PMID: 37455385 DOI: 10.1111/his.14996] [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: 12/09/2022] [Revised: 05/11/2023] [Accepted: 06/04/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND While many pancreatic neuroendocrine tumours (PanNET) show indolent behaviour, predicting the biological behaviour of small nonfunctional PanNETs remains a challenge. Nonfunctional PanNETs with an epigenome and transcriptome that resemble islet alpha cells (ARX-positive) are more aggressive than neoplasms that resemble islet beta cells (PDX1-positive). In this study, we explore the ability of immunohistochemistry for ARX and PDX1 and telomere-specific fluorescence in situ hybridisation (FISH) for alternative lengthening of telomeres (ALT) to predict recurrence. METHODS Two hundred fifty-six patients with PanNETs were identified, and immunohistochemistry for ARX and PDX1 was performed. Positive staining was defined as strong nuclear staining in >5% of tumour cells. FISH for ALT was performed in a subset of cases. RESULTS ARX reactivity correlated with worse disease-free survival (DFS) (P = 0.011), while there was no correlation between PDX1 reactivity and DFS (P = 0.52). ALT-positive tumours (n = 63, 31.8%) showed a significantly lower DFS (P < 0.0001) than ALT-negative tumours (n = 135, 68.2%). ARX reactivity correlated with ALT positivity (P < 0.0001). Among nonfunctional tumours, recurrence was noted in 18.5% (30/162) of ARX-positive tumours and 7.5% (5/67) of ARX-negative tumours. Among WHO grade 1 and 2 PanNETs with ≤2 cm tumour size, 14% (6/43) of ARX-positive tumours recurred compared to 0 of 33 ARX-negative tumours and 33.3% (3/9) ALT-positive tumours showed recurrence versus 4.4% (2/45) ALT-negative tumours. CONCLUSION Immunohistochemistry for ARX and ALT FISH status may aid in distinguishing biologically indolent cases from aggressive small low-grade PanNETs, and help to identify patients who may preferentially benefit from surgical intervention.
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Affiliation(s)
- Azfar Neyaz
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Rory Crotty
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Steffen Rickelt
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Boston, MA, USA
| | - Amaya Pankaj
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | | | - Yurie Sekigami
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Filippos Kontos
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Paige H Parrack
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Deepa T Patil
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Christopher M Heaphy
- Department of Medicine, Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
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16
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Rowell MC, Deschênes-Simard X, Lopes-Paciencia S, Le Calvé B, Kalegari P, Mignacca L, Fernandez-Ruiz A, Guillon J, Lessard F, Bourdeau V, Igelmann S, Duman AM, Stanom Y, Kottakis F, Deshpande V, Krizhanovsky V, Bardeesy N, Ferbeyre G. Targeting ribosome biogenesis reinforces ERK-dependent senescence in pancreatic cancer. Cell Cycle 2023; 22:2172-2193. [PMID: 37942963 PMCID: PMC10732607 DOI: 10.1080/15384101.2023.2278945] [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: 08/29/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
Pancreatic adenocarcinomas (PDAC) often possess mutations in K-Ras that stimulate the ERK pathway. Aberrantly high ERK activation triggers oncogene-induced senescence, which halts tumor progression. Here we report that low-grade pancreatic intraepithelial neoplasia displays very high levels of phospho-ERK consistent with a senescence response. However, advanced lesions that have circumvented the senescence barrier exhibit lower phospho-ERK levels. Restoring ERK hyperactivation in PDAC using activated RAF leads to ERK-dependent growth arrest with senescence biomarkers. ERK-dependent senescence in PDAC was characterized by a nucleolar stress response including a selective depletion of nucleolar phosphoproteins and intranucleolar foci containing RNA polymerase I designated as senescence-associated nucleolar foci (SANF). Accordingly, combining ribosome biogenesis inhibitors with ERK hyperactivation reinforced the senescence response in PDAC cells. Notably, comparable mechanisms were observed upon treatment with the platinum-based chemotherapy regimen FOLFIRINOX, currently a first-line treatment option for PDAC. We thus suggest that drugs targeting ribosome biogenesis can improve the senescence anticancer response in pancreatic cancer.
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Affiliation(s)
- MC. Rowell
- Département de Biochimie et Médecine Moléculaire, Centre de recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - X. Deschênes-Simard
- Département de Biochimie et Médecine Moléculaire, Maisonneuve-Rosemont Hospital, Université de Montréal, Montreal, QC, Canada
| | - S. Lopes-Paciencia
- Département de Biochimie et Médecine Moléculaire, Centre de recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - B. Le Calvé
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, QC, Canada
| | - P. Kalegari
- Département de Biochimie et Médecine Moléculaire, Centre de recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - L. Mignacca
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, QC, Canada
| | - A. Fernandez-Ruiz
- Département de Biochimie et Médecine Moléculaire, Centre de recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - J. Guillon
- Département de Biochimie et Médecine Moléculaire, Centre de recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - F. Lessard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, QC, Canada
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Research Centre, Canada, Present
| | - V. Bourdeau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, QC, Canada
| | - S Igelmann
- Département de Biochimie et Médecine Moléculaire, Centre de recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, QC, Canada
| | - AM. Duman
- Département de Biochimie et Médecine Moléculaire, Centre de recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Y. Stanom
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, QC, Canada
| | - F. Kottakis
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - V. Deshpande
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - V. Krizhanovsky
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - N. Bardeesy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - G. Ferbeyre
- Département de Biochimie et Médecine Moléculaire, Centre de recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, QC, Canada
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17
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Lee SH, Pankaj A, Neyaz A, Ono Y, Rickelt S, Ferrone C, Ting D, Patil DT, Yilmaz O, Berger D, Deshpande V, Yılmaz O. Immune microenvironment and lymph node yield in colorectal cancer. Br J Cancer 2023; 129:917-924. [PMID: 37507544 PMCID: PMC10491581 DOI: 10.1038/s41416-023-02372-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 03/08/2023] [Revised: 07/05/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Lymph node (LN) harvesting is associated with outcomes in colonic cancer. We sought to interrogate whether a distinctive immune milieu of the primary tumour is associated with LN yield. METHODS A total of 926 treatment-naive patients with colorectal adenocarcinoma with more than 12 LNs (LN-high) were compared with patients with 12 or fewer LNs (LN-low). We performed immunohistochemistry and quantification on tissue microarrays for HLA class I/II proteins, beta-2-microglobulin (B2MG), CD8, CD163, LAG3, PD-L1, FoxP3, and BRAF V600E. RESULTS The LN-high group was comprised of younger patients, longer resections, larger tumours, right-sided location, and tumours with deficient mismatch repair (dMMR). The tumour microenvironment showed higher CD8+ cells infiltration and B2MG expression on tumour cells in the LN-high group compared to the LN-low group. The estimated mean disease-specific survival was higher in the LN-high group than LN-low group. On multivariate analysis for prognosis, LN yield, CD8+ cells, extramural venous invasion, perineural invasion, and AJCC stage were independent prognostic factors. CONCLUSION Our findings corroborate that higher LN yield is associated with a survival benefit. LN yield is associated with an immune high microenvironment, suggesting that tumour immune milieu influences the LN yield.
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Affiliation(s)
- Soo Hyun Lee
- Department of Pathology, Boston Medical Center, Boston, MA, USA
| | - Amaya Pankaj
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Azfar Neyaz
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Yuho Ono
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Steffen Rickelt
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cristina Ferrone
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - David Ting
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Deepa T Patil
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Omer Yilmaz
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - David Berger
- Harvard Medical School, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Osman Yılmaz
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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18
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Ha CS, Yao D, Xu Z, Liu C, Liu H, Elkins D, Kile M, Deshpande V, Kong Z, Bauchy M, Zheng XR. Rapid inverse design of metamaterials based on prescribed mechanical behavior through machine learning. Nat Commun 2023; 14:5765. [PMID: 37718343 PMCID: PMC10505607 DOI: 10.1038/s41467-023-40854-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 08/11/2023] [Indexed: 09/19/2023] Open
Abstract
Designing and printing metamaterials with customizable architectures enables the realization of unprecedented mechanical behaviors that transcend those of their constituent materials. These behaviors are recorded in the form of response curves, with stress-strain curves describing their quasi-static footprint. However, existing inverse design approaches are yet matured to capture the full desired behaviors due to challenges stemmed from multiple design objectives, nonlinear behavior, and process-dependent manufacturing errors. Here, we report a rapid inverse design methodology, leveraging generative machine learning and desktop additive manufacturing, which enables the creation of nearly all possible uniaxial compressive stress‒strain curve cases while accounting for process-dependent errors from printing. Results show that mechanical behavior with full tailorability can be achieved with nearly 90% fidelity between target and experimentally measured results. Our approach represents a starting point to inverse design materials that meet prescribed yet complex behaviors and potentially bypasses iterative design-manufacturing cycles.
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Affiliation(s)
- Chan Soo Ha
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Desheng Yao
- Department of Material Science and Engineering, University of California, Berkeley, CA, USA
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, USA
| | - Zhenpeng Xu
- Department of Material Science and Engineering, University of California, Berkeley, CA, USA
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, USA
| | - Chenang Liu
- Industrial Engineering and Management, Oklahoma State University, Stillwater, OK, USA
| | - Han Liu
- Department of Computer Science and Technology, Sichuan University, Chengdu, China
| | - Daniel Elkins
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, USA
- Grado Department of Industrial and Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Matthew Kile
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Vikram Deshpande
- Department of Engineering, University of Cambridge, Cambridge, UK.
| | - Zhenyu Kong
- Grado Department of Industrial and Systems Engineering, Virginia Tech, Blacksburg, VA, USA.
| | - Mathieu Bauchy
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, USA.
| | - Xiaoyu Rayne Zheng
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, USA.
- Department of Material Science and Engineering, University of California, Berkeley, CA, USA.
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, USA.
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19
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Neyaz A, Rickelt S, Yilmaz OH, Parrack PH, Lu C, Yilmaz O, Wu EY, Choi WT, Gala M, Ting DT, Odze RD, Patil DT, Deshpande V. Quantitative p53 immunostaining aids in the detection of prevalent dysplasia. J Clin Pathol 2023; 76:582-590. [PMID: 36823143 DOI: 10.1136/jcp-2022-208721] [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: 12/06/2022] [Accepted: 02/02/2023] [Indexed: 02/25/2023]
Abstract
AIMS The lack of accepted scoring criteria has precluded the use of p53 in routine practice. We evaluate the utility of automated quantitative p53 analysis in risk stratifying Barrett's oesophagus (BE) patients using non-dysplastic BE (NDBE) biopsies in a multicentric cohort of BE progressor (P) and non-progressor (NP) patients. METHODS NDBE biopsies prior to the diagnosis of advanced neoplasia from 75 BE-P, and index and last surveillance biopsies from 148 BE-NP were stained for p53, and scored digitally as 1+, 2+ and 3+. A secondary cohort of 30 BE-P was evaluated. RESULTS Compared with BE-NP, BE-P was predominantly men (p=0.001), ≥55 years of age (p=0.008), with longer BE segments (71% vs 33%; p<0.001). The mean number of 3+p53 positive cells and 3+ positive glands were significantly more in BE-P versus BE-NP NDBE biopsies (175 vs 9.7, p<0.001; 9.8 vs 0.1; p<0.001, respectively). At a cut-off of ≥10 p53 (3+) positive cells, the sensitivity and specificity of the assay to identify BE-P were 39% and 93%. On multivariate analysis, scoring p53 in NDBE biopsies, age, gender and length of BE were significantly associated with neoplastic progression. 54% of patients classified as prevalent dysplasia showed an abnormal p53 immunohistochemical stain. These findings were validated in the secondary cohort. CONCLUSIONS Automated p53 analysis in NDBE biopsies serves as a promising tool for assessing BE neoplastic progression and risk stratification. Our study highlights the practical applicability of p53 assay to routine surveillance practice and its ability to detect prevalent dysplasia.
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Affiliation(s)
- Azfar Neyaz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Steffen Rickelt
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Omer H Yilmaz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Paige H Parrack
- Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Chenyue Lu
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
| | - Osman Yilmaz
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Elizabeth Y Wu
- Pathology, Brown University Warren Alpert Medical School, Providence, Rhode Island, USA
| | - Won-Tak Choi
- Pathology, University of California, San Francisco, California, USA
| | - Manish Gala
- Department of Medicine, Gastrointestinal Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
| | - Robert D Odze
- Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Deepa T Patil
- Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
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20
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Deichmann S, Schindel L, Braun R, Bolm L, Taylor M, Deshpande V, Schilling O, Bronsert P, Keck T, Ferrone C, Wellner U, Honselmann K. Overexpression of integrin alpha 2 (ITGA2) correlates with poor survival in patients with pancreatic ductal adenocarcinoma. J Clin Pathol 2023; 76:541-547. [PMID: 35396216 DOI: 10.1136/jclinpath-2022-208176] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/07/2022] [Indexed: 01/11/2023]
Abstract
AIMS Due to the known malignant potential and the poor overall prognosis of pancreatic ductal adenocarcinoma (PDAC), the identification of new biomarkers is of utmost importance. It has been reported that integrin alpha 2 (ITGA2), plakophilin 3 (PKP3) and adenylate kinase 4 (AK4) are associated with poor survival and more aggressive malignant behaviour in multiple cancers; however, their role in PDAC is still unknown. Therefore, the aim of this study was to investigate the correlation of ITGA2, PKP3 and AK4 expression with PDAC tumour characteristics and patient survival. METHODS Of 105 patients undergoing oncological pancreatic resection between 2012 and 2018, tissue microarrays were prepared from formalin-fixed, paraffin-embedded PDAC tissues and immunohistochemically stained with PKP3, AK4 and ITGA2. Clinical and pathological patient data were retrieved from the electronic patient charts and correlated with biomarker staining scores. RESULTS ITGA2 expression was high in 43% of patients with PDAC, whereas AK4 and PKP3 expressions were high in 28% and 57%, respectively. Overall survival was negatively associated with high ITGA2 expression in comparison with low expression (13 months (95% CI 10 to 18 months) vs 25 months (95% CI 20 to 30 months), p<0.001). Expression of AK4 and PKP3 did not correlate with overall survival. Multivariate Cox regression identified ITGA2 as an independent predictor of shorter overall survival in PDAC of different lymph node status and high tumour grade (G3/G4). CONCLUSIONS ITGA2 is an independent prognostic parameter for survival in patients with resected PDAC. PKP3 and AK4 do not appear to have prognostic value for survival in PDAC.
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Affiliation(s)
- Steffen Deichmann
- Department of Surgery, University Medical Center Schleswig Holstein Lübeck Campus, Lubeck, Germany
| | - Leif Schindel
- Department of Surgery, University Medical Center Schleswig Holstein Lübeck Campus, Lubeck, Germany
| | - Rüdiger Braun
- Department of Surgery, University Medical Center Schleswig Holstein Lübeck Campus, Lubeck, Germany
| | - Louisa Bolm
- Department of Surgery, University Medical Center Schleswig Holstein Lübeck Campus, Lubeck, Germany
| | - Martin Taylor
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Oliver Schilling
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany
| | - Peter Bronsert
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany
- Tumorbank Comprehensive Cancer Center Freiburg, Core Facility for Histopathology and Digital Pathology, Medical Center University of Freiburg and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tobias Keck
- Department of Surgery, University Medical Center Schleswig Holstein Lübeck Campus, Lubeck, Germany
| | - Cristina Ferrone
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ulrich Wellner
- Department of Surgery, University Medical Center Schleswig Holstein Lübeck Campus, Lubeck, Germany
| | - Kim Honselmann
- Department of Surgery, University Medical Center Schleswig Holstein Lübeck Campus, Lubeck, Germany
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21
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Devins KM, Samore W, Nielsen GP, Deshpande V, Oliva E. Leiomyoma-like Morphology in Metastatic Uterine Inflammatory Myofibroblastic Tumors. Mod Pathol 2023; 36:100143. [PMID: 36806735 DOI: 10.1016/j.modpat.2023.100143] [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: 11/14/2022] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023]
Abstract
Uterine inflammatory myofibroblastic tumors (IMTs) are rare mesenchymal neoplasms that frequently harbor ALK gene rearrangements and have a low risk of metastasis. We reported 3 of these tumors mimicking the appearance of leiomyoma in their recurrence. These patients were 34, 43, and 45 years old. Two uterine tumors demonstrated classic morphology, with combined myxoid, compact fascicular, and hyalinized patterns and spindled cells with bipolar cytoplasmic processes, moderate atypia, and lymphoplasmacytic inflammatory infiltrates. The third had a "leiomyoma-like" appearance, with fascicles of plump spindled cells and a sparse lymphoplasmacytic infiltrate. ALK immunohistochemistry was positive in all the tumors, and all demonstrated ALK rearrangements using fluorescence in situ hybridization (n = 2) and/or RNA sequencing (n = 2). Two classic IMTs recurred at 3 and 50 months in the lung and abdomen, respectively, and recurrent tumors had a "leiomyoma-like" appearance, with 0 and 1 mitosis per 10 high-power fields, no inflammation in 1, and a sparse lymphocytic infiltrate in the other. ALK was positive in both tumors; 1 with available tissue showed an IGFBP5::ALK fusion using RNA sequencing. The third patient, who had a "leiomyoma-like" uterine tumor, experienced multiple recurrences, first in the abdomen at 100 months showing a similar appearance. Subsequent recurrence at 105 months showed transmural invasion of the sigmoid colon and a similar microscopic appearance but with the addition of infiltrative borders, moderate cellularity, mild-to-moderate atypia, and 10 mitoses per 10 high-power fields. Both recurrences were positive for ALK, and RNA sequencing revealed the same ACTG2::ALK fusion transcript identified in the primary tumor. The patient was treated with crizotinib, resulting in prolonged clinical remission, with no evidence of disease at 168 months from the initial surgery. Although "leiomyoma-like" uterine IMTs have been recently described, to our knowledge, this is the first report of recurrence of these tumors and the first report of a "leiomyoma-like" appearance in the recurrences of conventional uterine IMTs. A low threshold for performing ALK immunohistochemistry on recurrent uterine tumors can identify patients who may benefit from tyrosine kinase inhibitors.
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Affiliation(s)
- Kyle M Devins
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Wesley Samore
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - G Petur Nielsen
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Esther Oliva
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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22
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Javed AA, Pulvirenti A, Razi S, Zheng J, Michelakos T, Sekigami Y, Thompson E, Klimstra DS, Deshpande V, Singhi AD, Weiss MJ, Wolfgang CL, Cameron JL, Wei AC, Zureikat AH, Ferrone CR, He J. Grading Pancreatic Neuroendocrine Tumors Via Endoscopic Ultrasound-guided Fine Needle Aspiration: A Multi-institutional Study. Ann Surg 2023; 277:e1284-e1290. [PMID: 35081574 PMCID: PMC9364076 DOI: 10.1097/sla.0000000000005390] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 11/26/2022]
Abstract
OBJECTIVES To identify factors associated with concordance between World Health Organization (WHO) grade on cytological analysis (c-grade) and histopathological analysis (h-grade) of surgical specimen in patients with PanNETs and examine trends in utilization and accuracy of EUS-FNA in preoperatively predicting grade. BACKGROUND WHO grading system is prognostic in pancreatic neuroendo-crine tumors (PanNETs). The concordance between c-grade and h-grade is reported to be between 50% and 92%. METHODS A multicenter retrospective study was performed on patients undergoing resection for PanNETs at four high-volume centers between 2010 and 2019. Patients with functional or syndrome-associated tumors, and those receiving neoadjuvant therapy were excluded. Factors associated with concordance between c-grade and h-grade and trends of utilization of EUS-FNA were assessed. RESULTS Of 869 patients included, 517 (59.5%) underwent EUS-FNA; 452 (87.4%) were diagnostic of PanNETs and WHO-grade was reported for 270 (59.7%) patients. The concordance between c-grade and h-grade was 80.4% with moderate concordance ( Kc = 0.52, 95% CI: 0.41-0.63). Significantly higher rates of concordance were observed in patients with smaller tumors (<2 vs. ≥2cm, 81.1% vs. 60.4%, P = 0.005). Highest concordance (98.1%) was observed in patients with small tumors undergoing assessment between 2015-2019 with a near-perfect concordance ( Kc = 0.88, 95% CI: 0.61-1.00). An increase in the utilization of EUS-FNA (56.1% to 64.1%) was observed over the last 2 decades ( P = 0.017) and WHO-grade was more frequently reported (44.2% vs. 77.6%, P < 0.001). However, concordance between c-grade and h-grade did not change significantly (P = 0.118). CONCLUSION Recently, a trend towards increasing utilization and improved diagnostic accuracy of EUS-FNA has been observed in PanNETs. Concordance between c-grade and h-grade is associated with tumor size with near-perfect agreement when assessing PanNETs <2cm in size.
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Affiliation(s)
- Ammar A. Javed
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Surgery, NYU Grossman School of Medicine, New York, NY, USA
| | - Alessandra Pulvirenti
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Samrah Razi
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jian Zheng
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Yurie Sekigami
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth Thompson
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David S. Klimstra
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Vikram Deshpande
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Aatur D. Singhi
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | | | - John L. Cameron
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alice C. Wei
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Amer H. Zureikat
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Jin He
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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23
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Deshpande V, Lee SH, Crabbe A, Pankaj A, Neyaz A, Ono Y, Rickelt S, Sonal S, Ferrone CR, Ting DT, Patil D, Yilmaz O, Berger D, Yilmaz O. Clinical, pathological, genetics and intratumoural immune milieu of micropapillary carcinoma of the colon. J Clin Pathol 2023:jcp-2023-208895. [PMID: 37258254 DOI: 10.1136/jcp-2023-208895] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/14/2023] [Indexed: 06/02/2023]
Abstract
AIM Micropapillary carcinoma (MPC) is a recognised WHO variant of colonic carcinoma (CC), although little is known about its prognosis, immune microenvironment and molecular alterations. We investigated its clinical, pathological and immunological characteristics. METHODS We assessed 903 consecutive CCs and used the WHO definition to identify MPC. We recorded serrated and mucinous differentiation and mismatch repair (MMR) status. We performed immunohistochemistry and quantification on tissue microarrays for HLA class I/II proteins, beta-2-microglobulin (B2MG), CD8, CD163, LAG3, PD-L1, FoxP3, PD-L1and BRAF V600E. RESULTS We classified 8.6% (N=78) of CC as MPC. Relative to non-MPC, MPC was more often high grade (p=0.03) and showed serrated morphology (p<0.01); however, we found no association with extramural venous invasion (p=0.41) and American Joint Committee on Cancer stage (p=0.95). MPCs showed lower numbers of CD8 positive lymphocytes (p<0.01), lower tumour cell B2MG expression (p=0.04) and lower tumour cell PD-L1 expression (p<0.01). There was no difference in HLA class I/II, LAG3, FOXP3, CD163 and PD-L1 positive histiocytes. There was no association with MMR status or BRAF V600E relative to non-MPC. MPC was not associated with decreased disease-specific survival (p=0.36). CONCLUSION MPCs are associated with high-grade differentiation and a less active immune microenvironment than non-MPC. MPC is not associated with inferior disease-specific survival.
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Affiliation(s)
- Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Soo Hyun Lee
- Department of Pathology, Boston Medical Center, Boston, Massachusetts, USA
| | - Andrew Crabbe
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Amaya Pankaj
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Azfar Neyaz
- Department of Pathology, UPMC, Pittsburgh, Pennsylvania, USA
| | - Yuho Ono
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Steffen Rickelt
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Swati Sonal
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Cristina R Ferrone
- Depatment of General and Gastrointestinal Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - David T Ting
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
| | - Deepa Patil
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Omer Yilmaz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - David Berger
- Depatment of General and Gastrointestinal Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
- Massachusetts Gen Hosp, Boston, Massachusetts, USA
| | - Osman Yilmaz
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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24
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Taylor MS, Connie W, Fridy PC, Zhang SJ, Senussi Y, Wolters JC, Cheng WC, Heaps J, Miller BD, Mori K, Cohen L, Jiang H, Molloy KR, Norden BL, Chait BT, Goggins M, Bhan I, Franses JW, Yang X, Taplin ME, Wang X, Christiani DC, Johnson BE, Meyerson M, Uppaluri R, Egloff AM, Denault EN, Spring LM, Wang TL, Shih IM, Jung E, Arora KS, Zukerberg LR, Yilmaz OH, Chi G, Matulonis UA, Song Y, Nieman L, Parikh AR, Strickland M, Corcoran RB, Mustelin T, Eng G, Yilmaz ÃMH, Skates SJ, Rueda BR, Drapkin R, Klempner SJ, Deshpande V, Ting DT, Rout MP, LaCava J, Walt DR, Burns KH. Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker. bioRxiv 2023:2023.01.25.525462. [PMID: 36747644 PMCID: PMC9900799 DOI: 10.1101/2023.01.25.525462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Improved biomarkers are needed for early cancer detection, risk stratification, treatment selection, and monitoring treatment response. While proteins can be useful blood-based biomarkers, many have limited sensitivity or specificity for these applications. Long INterspersed Element-1 (LINE-1, L1) open reading frame 1 protein (ORF1p) is a transposable element protein overexpressed in carcinomas and high-risk precursors during carcinogenesis with negligible detectable expression in corresponding normal tissues, suggesting ORF1p could be a highly specific cancer biomarker. To explore the potential of ORF1p as a blood-based biomarker, we engineered ultrasensitive digital immunoassays that detect mid-attomolar (10-17 M) ORF1p concentrations in patient plasma samples across multiple cancers with high specificity. Plasma ORF1p shows promise for early detection of ovarian cancer, improves diagnostic performance in a multi-analyte panel, and provides early therapeutic response monitoring in gastric and esophageal cancers. Together, these observations nominate ORF1p as a multi-cancer biomarker with potential utility for disease detection and monitoring.
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25
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Menon AA, Deshpande V, Suster D. MDM2 for the practicing pathologist: a primer. J Clin Pathol 2023; 76:285-290. [PMID: 36898827 DOI: 10.1136/jcp-2022-208687] [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] [Accepted: 02/22/2023] [Indexed: 03/12/2023]
Abstract
The mouse double minute 2 (MDM2) gene is located on the long arm of chromosome 12 and is the primary negative regulator of p53. The MDM2 gene encodes an E3 ubiquitin-protein ligase that mediates the ubiquitination of p53, leading to its degradation. MDM2 enhances tumour formation by inactivating the p53 tumour suppressor protein. The MDM2 gene also has many p53-independent functions. Alterations of MDM2 may occur through various mechanisms and contribute to the pathogenesis of many human tumours and some non-neoplastic diseases. Detection of MDM2 amplification is used in the clinical practice setting to help diagnose multiple tumour types, including lipomatous neoplasms, low-grade osteosarcomas and intimal sarcoma, among others. It is generally a marker of adverse prognosis, and MDM2-targeted therapies are currently in clinical trials. This article provides a concise overview of the MDM2 gene and discusses practical diagnostic applications pertaining to human tumour biology.
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Affiliation(s)
- Aswathy Ashok Menon
- Department of Pathology, Neuberg Anand Reference Laboratory, Bengaluru, Karnataka, India
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - David Suster
- Department of Pathology, Rutgers University New Jersey Medical School, Newark, New Jersey, USA
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26
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Tomaszewski KJ, Neyaz A, Sauder K, Rickelt S, Zhang ML, Yilmaz O, Crotty R, Shroff S, Odze R, Mattia A, Patil DT, Deshpande V. Defining an abnormal p53 immunohistochemical stain in Barrett's oesophagus-related dysplasia: a single-positive crypt is a sensitive and specific marker of dysplasia. Histopathology 2023; 82:555-566. [PMID: 36458877 DOI: 10.1111/his.14848] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 10/20/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022]
Abstract
AIMS p53 is an independent risk stratification marker in Barrett's oesophagus (BE), but no universally accepted definition exists for abnormal p53 staining. Herein, we assess p53 stains in two cohorts to: (1) define abnormal p53 staining in BE-related dysplasia (BERD) and (2) assess the specificity and sensitivity of this cut-point for the diagnosis of dysplasia. METHODS Cohort 1 (n = 313) included (1) dysplastic BE biopsies, (2) prior non-dysplastic BE (NDBE) biopsies from the same patients and (3) NDBE biopsies from patients who never progressed to dysplasia. Cohort 2 (n = 191) consisted of BE biopsies in which p53 staining aided in diagnosing dysplasia. Automated p53 staining quantification was performed on cohort 1. A semiquantitative p53 analysis, performed on both cohorts, included: (1) number of strongly positive glands, (2) strong glandular surface staining, (3) percentage of strongly positive glands and (4) null phenotype. RESULTS NDBE biopsies from cohort 1 patients who progressed to dysplasia were more likely to show p53 positivity than non-progressors (16.9 versus 0.6%) (P = 0.0001). The optimal quantitative cut-point for distinguishing dysplastic from never-dysplasia biopsies was 10 strongly positive cells. By semiquantitative analysis, a single strongly p53-positive gland distinguished dysplastic from never-dysplasia BE (sensitivity 98.6%, specificity 99.4%). The semiquantitative and quantitative analyses correlated (P = 0.0001). In cohort 2, the sensitivity and specificity for BERD of ≥ 1 strongly positive p53 gland were 86.0 and 88.6%. CONCLUSIONS A single strongly positive p53 gland is sensitive and specific for BERD. Automated p53 analysis may reduce subjectivity associated with the diagnosis of BERD.
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Affiliation(s)
| | - Azfar Neyaz
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Kenan Sauder
- Department of Pathology, Newton-Wellesley Hospital, Newton, MA, USA
| | - Steffen Rickelt
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - M Lisa Zhang
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Omer Yilmaz
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Rory Crotty
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Stuti Shroff
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Robert Odze
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Anthony Mattia
- Department of Pathology, Newton-Wellesley Hospital, Newton, MA, USA
| | - Deepa T Patil
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Vikram Deshpande
- Beth Israel Deaconess Medical Center, Brigham and Women's Hospital, Boston, MA, USA
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27
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Yilmaz O, Pinto K, Deshpande V. Navigating the Challenges Associated With a Diagnosis of Autoimmune Pancreatitis and IgG4-Related Sclerosing Cholangitis. Arch Pathol Lab Med 2023; 147:283-293. [PMID: 36136300 DOI: 10.5858/arpa.2021-0549-ra] [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] [Accepted: 04/26/2022] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The pancreatobiliary tract exhibits a spectrum of heterogeneous fibroinflammatory conditions that may be the result of a primary immune-mediated mechanism, or a reaction to neoplasm. This often results in significant overlap regarding clinical presentation, symptoms, radiographic findings, serology, and histopathology between inflammatory and neoplastic lesions of the pancreas, which can lead to inadvertent surgical intervention. Among the multitude of primary fibroinflammatory pancreatic diseases, autoimmune pancreatitis, including type 1 and type 2 autoimmune pancreatitis, and immunoglobulin G4-related sclerosing cholangitis (IgG4-RSC) are particularly challenging and require a multidisciplinary perspective to reliably make a diagnosis. This is of particular significance because these diseases typically have a favorable prognosis and readily respond to steroid therapy. OBJECTIVE.— To present a multimodal approach to highlight distinctive and overlapping qualities that will aid in the diagnosis of these entities. DATA SOURCES.— The review and analysis of literature describing autoimmune pancreatitis types 1 and 2 and IgG4-RSC. CONCLUSIONS.— Diagnosis of autoimmune pancreatitis types 1 and 2 and IgG4-RSC requires a multimodal approach that relies on clinical, radiographic, serologic, histopathologic, and immunohistochemical correlation.
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Affiliation(s)
- Osman Yilmaz
- From the Department of Pathology, Boston University Medical Center, Boston, Massachusetts (Yilmaz)
| | - Karen Pinto
- The Department of Pathology, Kuwait Cancer Control, Al-Farwaniya, Kuwait (Pinto)
| | - Vikram Deshpande
- The Department of Pathology, Massachusetts General Hospital, Boston (Deshpande)
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28
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Shi L, Shen W, Davis MI, Kong K, Vu P, Saha SK, Adil R, Kreuzer J, Egan R, Lee TD, Greninger P, Shrimp JH, Zhao W, Wei TY, Zhou M, Eccleston J, Sussman J, Manocha U, Weerasekara V, Kondo H, Vijay V, Wu MJ, Kearney SE, Ho J, McClanaghan J, Murchie E, Crowther GS, Patnaik S, Boxer MB, Shen M, Ting DT, Kim WY, Stanger BZ, Deshpande V, Ferrone CR, Benes CH, Haas W, Hall MD, Bardeesy N. SULT1A1-dependent sulfonation of alkylators is a lineage-dependent vulnerability of liver cancers. Nat Cancer 2023; 4:365-381. [PMID: 36914816 DOI: 10.1038/s43018-023-00523-0] [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] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 02/03/2023] [Indexed: 03/14/2023]
Abstract
Adult liver malignancies, including intrahepatic cholangiocarcinoma and hepatocellular carcinoma, are the second leading cause of cancer-related deaths worldwide. Most individuals are treated with either combination chemotherapy or immunotherapy, respectively, without specific biomarkers for selection. Here using high-throughput screens, proteomics and in vitro resistance models, we identify the small molecule YC-1 as selectively active against a defined subset of cell lines derived from both liver cancer types. We demonstrate that selectivity is determined by expression of the liver-resident cytosolic sulfotransferase enzyme SULT1A1, which sulfonates YC-1. Sulfonation stimulates covalent binding of YC-1 to lysine residues in protein targets, enriching for RNA-binding factors. Computational analysis defined a wider group of structurally related SULT1A1-activated small molecules with distinct target profiles, which together constitute an untapped small-molecule class. These studies provide a foundation for preclinical development of these agents and point to the broader potential of exploiting SULT1A1 activity for selective targeting strategies.
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Affiliation(s)
- Lei Shi
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Cancer Program, Broad Institute, Cambridge, MA, USA
| | - William Shen
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Mindy I Davis
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Ke Kong
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Phuong Vu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Supriya K Saha
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Ramzi Adil
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Johannes Kreuzer
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Regina Egan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Tobie D Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Patricia Greninger
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Jonathan H Shrimp
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Wei Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Ting-Yu Wei
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Mi Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason Eccleston
- Division of Gastroenterology, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan Sussman
- Division of Gastroenterology, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ujjawal Manocha
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vajira Weerasekara
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Cancer Program, Broad Institute, Cambridge, MA, USA
| | - Hiroshi Kondo
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Cancer Program, Broad Institute, Cambridge, MA, USA
| | - Vindhya Vijay
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Cancer Program, Broad Institute, Cambridge, MA, USA
| | - Meng-Ju Wu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Cancer Program, Broad Institute, Cambridge, MA, USA
| | - Sara E Kearney
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jeffrey Ho
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Joseph McClanaghan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Ellen Murchie
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Giovanna S Crowther
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Samarjit Patnaik
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Matthew B Boxer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ben Z Stanger
- Division of Gastroenterology, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vikram Deshpande
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Cristina R Ferrone
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
| | - Nabeel Bardeesy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
- The Cancer Program, Broad Institute, Cambridge, MA, USA.
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29
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Hung YP, Chebib I, Bredella MA, Berner EA, Taylor-Black Q, Choy E, Cote GM, Chen YL, MacDonald SM, Schwab JH, Raskin KA, Newman ET, Selig MK, Deshpande V, Hornick JL, Lozano-Calderón SA, Nielsen GP. Prognostic Significance of Percentage and Size of Dedifferentiation in Dedifferentiated Chondrosarcoma. Mod Pathol 2023; 36:100069. [PMID: 36788104 DOI: 10.1016/j.modpat.2022.100069] [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: 07/08/2022] [Revised: 11/17/2022] [Accepted: 12/11/2022] [Indexed: 01/11/2023]
Abstract
Dedifferentiated chondrosarcoma is rare, aggressive, and microscopically bimorphic. How pathologic features such as the amounts of dedifferentiation affect prognosis remains unclear. We evaluated the percentages and sizes of dedifferentiation in a consecutive institutional series of dedifferentiated chondrosarcomas from 1999 to 2021. The statistical analysis included cox proportional hazard models and log-rank tests. Of the 67 patients (26 women, 41 men; age, 39 to >89 [median 61] years; 2 with Ollier disease), 58 presented de novo; 9 were identified with conventional chondrosarcomas 0.6-13.2 years (median, 5.5 years) prior. Pathologic fracture and distant metastases were noted in 27 and 7 patients at presentation. The tumors involved the femur (n = 27), pelvis (n = 22), humerus (n = 7), tibia (n = 4), scapula/ribs (n = 4), spine (n = 2), and clivus (n = 1). In the 56 resections, the tumors ranged in size from 3.5 to 46.0 cm (median, 11.5 cm) and contained 1%-99.5% (median, 70%) dedifferentiated components that ranged in size from 0.6 to 24.0 cm (median, 7.3 cm). No correlation was noted between total size and percentage of dedifferentiation. The dedifferentiated components were typically fibrosarcomatous or osteosarcomatous, whereas the associated cartilaginous components were predominantly grade 1-2, rarely enchondromas or grade 3. The entire cohort's median overall survival and progression-free survival were 11.8 and 5.4 months, respectively. In the resected cohort, although the total size was not prognostic, the percentage of dedifferentiation ≥20% and size of dedifferentiation >3.0 cm each predicted worse overall survival (9.9 vs 72.5 months; HR, 3.76; 95% CI, 1.27-11.14; P = .02; 8.7 vs 58.9 months; HR, 3.03; 95% CI, 1.21-7.57; P = .02, respectively) and progression-free survival (5.3 vs 62.1 months; HR, 3.05; 95% CI, 1.13-8.28; P = .03; 5.3 vs 56.6 months; HR, 2.50; 95% CI, 1.06-5.88; P = .04, respectively). In conclusion, both the percentages and sizes of dedifferentiation were better prognostic predictors than total tumor sizes in dedifferentiated chondrosarcomas, highlighting the utility of their pathologic evaluations.
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Affiliation(s)
- Yin P Hung
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts.
| | - Ivan Chebib
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Miriam A Bredella
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Emily A Berner
- Department of Orthopedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Quinn Taylor-Black
- Department of Orthopedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Edwin Choy
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Division of Hematology Oncology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Gregory M Cote
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Division of Hematology Oncology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Yen-Lin Chen
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Shannon M MacDonald
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Joseph H Schwab
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Orthopedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kevin A Raskin
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Orthopedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Erik T Newman
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Orthopedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Martin K Selig
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Santiago A Lozano-Calderón
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Orthopedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - G Petur Nielsen
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
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30
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Varma M, Delahunt B, Cheng L, Chetty R, Compérat E, Deshpande V, Egevad L, van der Kwast TH, Lopez-Beltran A, McCluggage WG. Tumour grading: communication is the key. J Clin Pathol 2023; 76:291-292. [PMID: 36813559 DOI: 10.1136/jcp-2023-208824] [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] [Received: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/24/2023]
Affiliation(s)
- Murali Varma
- Department of Cellular Pathology, University Hospital of Wales, Cardiff, UK
| | - Brett Delahunt
- Malaghan Institute of Medical Research, Newtown, New Zealand
| | - Liang Cheng
- Pathology and Laboratory Medicine, Brown University Warren Alpert Medical School and Lifespan Academic Medical Center, Providence, Rhode Island, USA
| | | | - Eva Compérat
- Department of Pathology, Medical University Vienna, Vienna, Austria
| | - Vikram Deshpande
- Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Lars Egevad
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Theodorus H van der Kwast
- Pathology, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Antonio Lopez-Beltran
- Pathology and Surgery, Universidad de Cordoba Facultad de Medicina y Enfermeria, Cordoba, Spain
| | - W Glenn McCluggage
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, UK
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Lozano-Calderón SA, Albergo JI, Groot OQ, Merchan NA, El Abiad JM, Salinas V, Gomez Mier LC, Montoya CS, Ferrone ML, Ready JE, Linares FJ, Levin AS, Peleteiro Pensado M, Pozo Kreilinger JJ, Ruiz IB, Ortiz-Cruz EJ, Gebhardt MC, Cote GM, Choy E, Spentzos D, Hung YP, Deshpande V, Chebib IA, McCulloch RA, Farfalli G, Aponte Tinao L, Morris CD, Petur Nielsen G, Anderson ME, Jeys LM. Complete tumor necrosis after neoadjuvant chemotherapy defines good responders in patients with Ewing sarcoma. Cancer 2023; 129:60-70. [PMID: 36305090 DOI: 10.1002/cncr.34506] [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: 12/13/2021] [Revised: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Survival in patients who have Ewing sarcoma is correlated with postchemotherapy response (tumor necrosis). This treatment response has been categorized as the response rate, similar to what has been used in osteosarcoma. There is controversy regarding whether this is appropriate or whether it should be a dichotomy of complete versus incomplete response, given how important a complete response is for in overall survival of patients with Ewing sarcoma. The purpose of this study was to evaluate the impact that the amount of chemotherapy-induced necrosis has on (1) overall survival, (2) local recurrence-free survival, (3) metastasis-free survival, and (4) event-free survival in patients with Ewing sarcoma. METHODS In total, 427 patients who had Ewing sarcoma or tumors in the Ewing sarcoma family and received treatment with preoperative chemotherapy and surgery at 10 international institutions were included. Multivariate Cox proportional-hazards analyses were used to assess the associations between tumor necrosis and all four outcomes while controlling for clinical factors identified in bivariate analysis, including age, tumor volume, location, surgical margins, metastatic disease at presentation, and preoperative radiotherapy. RESULTS Patients who had a complete (100%) tumor response to chemotherapy had increased overall survival (hazard ratio [HR], 0.26; 95% CI, 0.14-0.48; p < .01), recurrence-free survival (HR, 0.40; 95% CI, 0.20-0.82; p = .01), metastasis-free survival (HR, 0.27; 95% CI, 0.15-0.46; p ≤ .01), and event-free survival (HR, 0.26; 95% CI, 0.16-0.41; p ≤ .01) compared with patients who had a partial (0%-99%) response. CONCLUSIONS Complete tumor necrosis should be the index parameter to grade response to treatment as satisfactory in patients with Ewing sarcoma. Any viable tumor in these patients after neoadjuvant treatment should be of oncologic concern. These findings can affect the design of new clinical trials and the risk-stratified application of conventional or novel treatments.
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Affiliation(s)
- Santiago A Lozano-Calderón
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Jose Ignacio Albergo
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Hospital Italiano, Buenos Aires, Argentina
| | - Olivier Q Groot
- Department of Orthopedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nelson A Merchan
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Boston Children's Hospital, Beth Israel Deaconess Medical Center, Dana-Farber Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Jad M El Abiad
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, The Johns Hopkins Hospital, Johns Hopkins University, Baltimore, Maryland, USA
| | - Vanessa Salinas
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Luis Carlos Gomez Mier
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Camilo Soto Montoya
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Marco L Ferrone
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Brigham and Women's Hospital, Dana-Farber Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - John E Ready
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Brigham and Women's Hospital, Dana-Farber Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Francisco J Linares
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Hospital Universitario San Ignacio, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Adam S Levin
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, The Johns Hopkins Hospital, Johns Hopkins University, Baltimore, Maryland, USA
| | - Manuel Peleteiro Pensado
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Hospital Universitario La Paz, Madrid, Spain
| | - José Juan Pozo Kreilinger
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Hospital Universitario La Paz, Madrid, Spain
| | - Irene Barrientos Ruiz
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Hospital Universitario La Paz, Madrid, Spain
| | - Eduardo J Ortiz-Cruz
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Hospital Universitario La Paz, Madrid, Spain
| | - Mark C Gebhardt
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Boston Children's Hospital, Beth Israel Deaconess Medical Center, Dana-Farber Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Gregory M Cote
- Division of Sarcoma and Connective Tissue Oncology, Department of Hematology and Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Edwin Choy
- Division of Sarcoma and Connective Tissue Oncology, Department of Hematology and Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Dimitrios Spentzos
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Yin P Hung
- Division of Bone and Soft Tissue Pathology, Department of Pathology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Vikram Deshpande
- Division of Bone and Soft Tissue Pathology, Department of Pathology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Ivan A Chebib
- Division of Bone and Soft Tissue Pathology, Department of Pathology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Robert Allan McCulloch
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Royal Orthopedic Hospital National Health Service Trust, Aston University, Birmingham, UK
| | - Germán Farfalli
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Hospital Italiano, Buenos Aires, Argentina
| | - Luis Aponte Tinao
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Hospital Italiano, Buenos Aires, Argentina
| | - Carol D Morris
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, The Johns Hopkins Hospital, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gunnlaugur Petur Nielsen
- Division of Bone and Soft Tissue Pathology, Department of Pathology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Megan E Anderson
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Boston Children's Hospital, Beth Israel Deaconess Medical Center, Dana-Farber Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Lee M Jeys
- Musculoskeletal Oncology Service, Department of Orthopedic Surgery, Royal Orthopedic Hospital National Health Service Trust, Aston University, Birmingham, UK
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Deshpande V. Journal of Clinical Pathology: 75 years and counting. J Clin Pathol 2023; 76:1. [PMID: 36418114 DOI: 10.1136/jcp-2022-208605] [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] [Received: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/24/2022]
Affiliation(s)
- Vikram Deshpande
- Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Antonello D, von Mering C, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV. Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [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: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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35
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Chua M, Kim D, Choi J, Lee NG, Deshpande V, Schwab J, Lev MH, Gonzalez RG, Gee MS, Do S. Tackling prediction uncertainty in machine learning for healthcare. Nat Biomed Eng 2022:10.1038/s41551-022-00988-x. [PMID: 36581695 DOI: 10.1038/s41551-022-00988-x] [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: 04/25/2022] [Accepted: 11/17/2022] [Indexed: 12/31/2022]
Abstract
Predictive machine-learning systems often do not convey the degree of confidence in the correctness of their outputs. To prevent unsafe prediction failures from machine-learning models, the users of the systems should be aware of the general accuracy of the model and understand the degree of confidence in each individual prediction. In this Perspective, we convey the need of prediction-uncertainty metrics in healthcare applications, with a focus on radiology. We outline the sources of prediction uncertainty, discuss how to implement prediction-uncertainty metrics in applications that require zero tolerance to errors and in applications that are error-tolerant, and provide a concise framework for understanding prediction uncertainty in healthcare contexts. For machine-learning-enabled automation to substantially impact healthcare, machine-learning models with zero tolerance for false-positive or false-negative errors must be developed intentionally.
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Affiliation(s)
- Michelle Chua
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Doyun Kim
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Jongmun Choi
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Nahyoung G Lee
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Joseph Schwab
- Department of Orthopedic Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Michael H Lev
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Ramon G Gonzalez
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Michael S Gee
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Synho Do
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA. .,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
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36
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Sridharan V, Neyaz A, Chogule A, Baiev I, Reyes S, Barr Fritcher EG, Lennerz JK, Sukov W, Kipp B, Ting DT, Deshpande V, Goyal L. FGFR mRNA Expression in Cholangiocarcinoma and Its Correlation with FGFR2 Fusion Status and Immune Signatures. Clin Cancer Res 2022; 28:5431-5439. [PMID: 36190545 PMCID: PMC9751751 DOI: 10.1158/1078-0432.ccr-22-1244] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/28/2022] [Accepted: 09/28/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE Selective FGFR inhibitors are effective against cholangiocarcinomas that harbor gene alterations in FGFR2. Clinical trials suggest that expression of wild-type FGFR mRNA can predict sensitivity to FGFR inhibitors, but this biomarker has not been well characterized in cholangiocarcinoma. This study explores the prevalence of FGFR mRNA overexpression in cholangiocarcinoma, its role in predicting sensitivity to FGFR inhibitors, and its association with immune markers. EXPERIMENTAL DESIGN Tissue microarrays of intrahepatic (ICC) and extrahepatic cholangiocarcinomas (ECC) resected between 2004 and 2015 were used to evaluate FGFR1-4 mRNA expression levels by RNA in situ hybridization (ISH). Expression levels of FGFR2 mRNA were correlated with FGFR2 fusion status and with patient outcomes. Immune markers expression was assessed by IHC and CSF1 and CSF1 receptor expression were examined by RNA ISH. RESULTS Among 94 patients with resected cholangiocarcinoma, the majority had ICC (77%). FGFR2 fusions were identified in 23% of ICCs and 5% of ECCs. High levels of FGFR mRNA in FGFR2 fusion-negative ICC/ECC were seen for: FGFR1 (ICC/ECC: 15%/0%), FGFR2 (ICC/ECC: 57%/0%), FGFR3 (ICC/ECC: 53%/18%), and FGFR4 (ICC/ECC: 32%/0%). Overall, 62% of fusion-negative cholangiocarcinomas showed high levels of FGFR mRNA. In patients with advanced FGFR2 fusion-positive ICC, high levels of FGFR2 mRNA did not correlate with clinical benefit. FGFR2 fusion-positive tumors showed a paucity of PD-L1 on tumor cells. CONCLUSIONS FGFR mRNA overexpression occurs frequently in cholangiocarcinoma in the absence of genetic alterations in FGFR. This study identifies a molecular subpopulation in cholangiocarcinoma for which further investigation of FGFR inhibitors is merited outside currently approved indications.
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Affiliation(s)
- Vishwajith Sridharan
- Mass General Cancer Center, Boston, Massachusetts.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Azfar Neyaz
- Mass General Cancer Center, Boston, Massachusetts
| | | | - Islam Baiev
- Mass General Cancer Center, Boston, Massachusetts
| | - Stephanie Reyes
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | | | | | - William Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Benjamin Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - David T. Ting
- Mass General Cancer Center, Boston, Massachusetts.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Vikram Deshpande
- Mass General Cancer Center, Boston, Massachusetts.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lipika Goyal
- Mass General Cancer Center, Boston, Massachusetts.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.,Corresponding Author: Lipika Goyal, Stanford Cancer Center, 875 Blake Wilbur Drive, Palo Alto, CA 94304. Phone: 650-498-6000; E-mail:
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37
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Javed AA, Pulvirenti A, Zheng J, Michelakos T, Sekigami Y, Razi S, McIntyre CA, Thompson E, Klimstra DS, Deshpande V, Singhi AD, Weiss MJ, Wolfgang CL, Cameron JL, Wei AC, Zureikat AH, Ferrone CR, He J. A novel tool to predict nodal metastasis in small pancreatic neuroendocrine tumors: A multicenter study. Surgery 2022; 172:1800-1806. [PMID: 36192215 DOI: 10.1016/j.surg.2022.08.022] [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: 04/06/2022] [Revised: 07/25/2022] [Accepted: 08/19/2022] [Indexed: 01/06/2023]
Abstract
BACKGROUND Nonfunctional pancreatic neuroendocrine tumors display a wide range of biological behavior, and nodal disease is associated with metastatic disease and poorer survival. The aim of this study was to develop a tool to predict nodal disease in patients with small (≤2 cm) nonfunctional pancreatic neuroendocrine tumors. METHODS A multicenter retrospective study was performed on patients undergoing resection for small nonfunctional pancreatic neuroendocrine tumors. Patients with genetic syndromes, metastatic disease at diagnosis, neoadjuvant therapy, or positive resection margin were excluded. Factors associated with nodal disease were identified to develop a predictive model. Internal validation was performed using bootstrap with 1,000 resamples. RESULTS Nodal disease was observed in 39 (11.1%) of the 353 patients included. Presence of nodal disease was significantly associated with lower 5-year disease-free survival (71.6% vs 96.2%, P < .001). Two predictors were strongly associated with nodal disease: G2 grade (odds ratio: 3.51, 95% confidence interval: 1.71-7.22, P = .001) and tumor size (per mm increase, odds ratio: 1.14, 95% confidence interval: 1.03-1.25, P = .009). Adequate discrimination was observed with an area under the curve of 0.71 (95% confidence interval: 0.63-0.80). Based on risk distribution, 3 risk groups of nodal disease were identified; low (<5%), intermediate (≥5% to <20%), and high (≥20%) risk. The observed mean risk of nodal disease was 3.7% in the low-risk patients, 9.6% in the intermediate-risk patients, and 30.4% in the high-risk patients (P < .001). The 10-year disease-free survival in the low, intermediate, and high-risk groups was 100%, 88.8%, and 50.1%, respectively. CONCLUSION Our model using tumor grade and size can predict nodal disease in small nonfunctional pancreatic neuroendocrine tumors. Integration of this tool into clinical practice could help guide management of these patients.
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Affiliation(s)
- Ammar A Javed
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD. http://www.twitter.com/ammar_asrar
| | | | - Jian Zheng
- Department of Surgery, University of Pittsburgh School of Medicine, PA
| | | | - Yurie Sekigami
- Department of Surgery, Massachusetts General Hospital, Boston, MA
| | - Samrah Razi
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Caitlin A McIntyre
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth Thompson
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - David S Klimstra
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vikram Deshpande
- Department of Surgery, Massachusetts General Hospital, Boston, MA
| | - Aatur D Singhi
- Department of Surgery, University of Pittsburgh School of Medicine, PA
| | | | | | - John L Cameron
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alice C Wei
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Amer H Zureikat
- Department of Surgery, University of Pittsburgh School of Medicine, PA
| | | | - Jin He
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD.
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38
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Sonal S, Deshpande V, Ting DT, Cusack JC, Parikh AR, Neyaz A, Pankaj A, Taylor MS, Dinaux AM, Leijssen LGJ, Boudreau C, Locascio JJ, Kunitake H, Goldstone RN, Bordeianou LG, Cauley CE, Ricciardi R, Berger DL. ASO Visual Abstract: Molecular Basis of Extramural Vascular Invasion (EMVI) in Colorectal Carcinoma : Tumor Microenvironment in EMVI-Positive Colorectal Carcinoma. Ann Surg Oncol 2022; 29:7384-7385. [PMID: 36008742 DOI: 10.1245/s10434-022-12343-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Swati Sonal
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - James C Cusack
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Aparna R Parikh
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Azfar Neyaz
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Amaya Pankaj
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Anne M Dinaux
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Chirurgie, Albert Schweitzer Ziekenhuis, Dordrecht, Zuid-Holland, Netherlands
| | - Lieve G J Leijssen
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Chloe Boudreau
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Joseph J Locascio
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hiroko Kunitake
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Robert N Goldstone
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Liliana G Bordeianou
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Christy E Cauley
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Rocco Ricciardi
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David L Berger
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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39
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Chawla A, Qadan M, Castillo CFD, Wo JY, Allen JN, Clark JW, Murphy JE, Catalano OA, Ryan DP, Ting DT, Deshpande V, Weekes CD, Parikh A, Lillemoe KD, Hong TS, Ferrone CR. Prospective Phase II Trials Validate the Effect of Neoadjuvant Chemotherapy on Pattern of Recurrence in Pancreatic Adenocarcinoma. Ann Surg 2022; 276:e502-e509. [PMID: 33086310 DOI: 10.1097/sla.0000000000004585] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The objective of this study was to characterize the patterns of first recurrence after curative-intent resection for pancreatic adenocarcinoma (PDAC). SUMMARY OF BACKGROUND DATA We evaluated the first site of recurrence after neoadjuvant treatment as locoregional (LR) or distant metastasis (DM). To validate our findings, we evaluated the pattern from 2 phase II clinical trials evaluating neoadjuvant chemotherapy (NAC) in PDAC. METHODS We identified site of first recurrence from a retrospective cohort of patients from 2011 to 2017 treated with NAC followed by chemoradiation and then an operation or an operation first followed by adjuvant therapy, and 2 separate prospective cohorts of patients derived from 2 phase II clinical trials evaluating patients treated with NAC in borderline-resectable and locally advanced PDAC. RESULTS In the retrospective cohorts, 160 out of 285 patients (56.1%) recurred after a median disease-free survival (mDFS) of 17.2 months. The pattern of recurrence was DM in 81.9% of patients, versus LR in 11.1%. This pattern was consistent in patients treated with upfront resection and adjuvant chemotherapy (DM 83.0%, LR 16.9%) regardless of margin-involvement (DM 80.1%, LR 19.4%). The use of NAC did not alter pattern of recurrence; 81.7% had DM and 18.3% had LR. This pattern also remained consistent regardless of margin-involvement (DM 94.1%, LR 5.9%). In the Phase II borderline-resectable trial (NCI# 01591733) cohort of 32 patients, the mDFS was 34.2 months. Pattern of recurrence remained predominantly DM (88.9%) versus LR (11.1%). In the Phase II locally-advanced trial (NCI# 01821729) cohort of 34 patients, the mDFS was 30.7 months. Although there was a higher rate of local recurrence in this cohort, pattern of first recurrence remained predominantly DM (66.6%) versus LR (33.3%) and remained consistent independent of margin-status. CONCLUSIONS The pattern of recurrence in PDAC is predominantly DM rather than LR, and is consistent regardless of the use of NAC and margin involvement.
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Affiliation(s)
- Akhil Chawla
- Division of Surgical Oncology, Department of Surgery, Northwestern Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Motaz Qadan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Jennifer Y Wo
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jill N Allen
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jeffrey W Clark
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Janet E Murphy
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Onofrio A Catalano
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - David P Ryan
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - David T Ting
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Colin D Weekes
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Aparna Parikh
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Keith D Lillemoe
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Theodore S Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Cristina R Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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40
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Goto N, Goto S, Imada S, Hosseini S, Deshpande V, Yilmaz ÖH. Lymphatics and fibroblasts support intestinal stem cells in homeostasis and injury. Cell Stem Cell 2022; 29:1246-1261.e6. [PMID: 35931033 PMCID: PMC9720889 DOI: 10.1016/j.stem.2022.06.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 03/02/2022] [Revised: 05/20/2022] [Accepted: 06/22/2022] [Indexed: 01/19/2023]
Abstract
Lgr5+ intestinal stem cells (ISCs) depend on niche factors for their proper function. However, the source of these ISC niche factors and how they support ISCs in vivo remain controversial. Here, we report that ISCs depend on lymphatic endothelial cells (LECs) and RSPO3+GREM1+ fibroblasts (RGFs). In the intestine and colon, LECs are surrounded by RGFs and are located near ISCs at the crypt base. Both LECs and RGFs provide the critical ISC niche factor RSPO3 to support ISCs, where RSPO3 loss in both cell types drastically compromises ISC numbers, villi length, and repair after injury. In response to injury, LEC and RGF numbers expand and produce greater amounts of RSPO3 and other growth/angiocrine factors to foster intestinal repair. We propose that LECs represent a novel niche component for ISCs, which together with RGFs serve as the major in vivo RSPO3 source for ISCs in homeostasis and injury-mediated regeneration.
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Affiliation(s)
- Norihiro Goto
- Department of Biology, The David H. Koch Institute for
Integrative Cancer Research at MIT, Massachusetts Institute of Technology,
Cambridge, MA 02139, USA,Correspondence:
(N.G.), (Ö.H.Y.)
| | - Saori Goto
- Department of Biology, The David H. Koch Institute for
Integrative Cancer Research at MIT, Massachusetts Institute of Technology,
Cambridge, MA 02139, USA
| | - Shinya Imada
- Department of Biology, The David H. Koch Institute for
Integrative Cancer Research at MIT, Massachusetts Institute of Technology,
Cambridge, MA 02139, USA
| | - Sahar Hosseini
- Department of Pathology, Massachusetts General Hospital and
Harvard Medical School, Boston, MA 02114, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital and
Harvard Medical School, Boston, MA 02114, USA
| | - Ömer H. Yilmaz
- Department of Biology, The David H. Koch Institute for
Integrative Cancer Research at MIT, Massachusetts Institute of Technology,
Cambridge, MA 02139, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Pathology, Massachusetts General Hospital and
Harvard Medical School, Boston, MA 02114, USA,Lead contact,Correspondence:
(N.G.), (Ö.H.Y.)
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41
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Sonal S, Deshpande V, Ting DT, Cusack JC, Parikh AR, Neyaz A, Pankaj A, Taylor MS, Dinaux AM, Leijssen LGJ, Boudreau C, Locascio JJ, Kunitake H, Goldstone RN, Bordeianou LG, Cauley CE, Ricciardi R, Berger DL. Molecular Basis of Extramural Vascular Invasion (EMVI) in Colorectal Carcinoma. Ann Surg Oncol 2022; 29:7372-7382. [PMID: 35917013 DOI: 10.1245/s10434-022-12212-w] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/27/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND Extramural vascular invasion (EMVI) is a known poor prognostic factor in colorectal carcinoma; however, its molecular basis has not been defined. This study aimed to assess the expression of molecular markers in EMVI positive colorectal carcinoma to understand their tumor microenvironment. METHODS Immunohistochemistry was performed on tissue microarrays of surgically resected colorectal cancer specimens for immunological markers, and BRAFV600E mutation (and on the tissue blocks for mismatch repair proteins). Automated quantification was used for CD8, LAG3, FOXP3, PU1, and CD163, and manual quantification was used for PDL1, HLA I markers (beta-2 microglobulin, HC10), and HLA II. The Wilcoxon rank-sum test was used to compare EMVI positive and negative tumors. A logistic regression model was fitted to assess the predictive effect of biomarkers on EMVI. RESULTS There were 340 EMVI positive and 678 EMVI negative chemo naïve tumors. PDL1 was barely expressed on tumor cells (median 0) in the entire cohort. We found a significantly lower expression of CD8, LAG3, FOXP3, PU1 cells, PDL1 positive macrophages, and beta-2 microglobulin on tumor cells in the EMVI positive subset (p ≤ 0.001). There was no association of BRAFV600E or deficient mismatch repair proteins (dMMR) with EMVI. PU1 (OR 0.8, 0.7-0.9) and low PDL1 (OR 1.6, 1.1-2.3) independently predicted EMVI on multivariate logistic regression among all biomarkers examined. CONCLUSION There is a generalized blunting of immune response in EMVI positive colorectal carcinoma, which may contribute to a worse prognosis. Tumor-associated macrophages seem to play the most significant role in determining EMVI.
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Affiliation(s)
- Swati Sonal
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center & Harvard Medical School, Boston, MA, USA
| | - James C Cusack
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Aparna R Parikh
- Massachusetts General Hospital Cancer Center & Harvard Medical School, Boston, MA, USA
| | - Azfar Neyaz
- Department of Pathology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA.,Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Amaya Pankaj
- Massachusetts General Hospital Cancer Center & Harvard Medical School, Boston, MA, USA
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Anne M Dinaux
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA.,Chirurgie, Albert Schweitzer Ziekenhuis, Dordrecht, The Netherlands
| | - Lieve G J Leijssen
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA.,Department of Gastroenterology and Hepatology, Amsterdams University Medical Centers, Amsterdam, The Netherlands
| | - Chloe Boudreau
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Joseph J Locascio
- Department of Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Hiroko Kunitake
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Robert N Goldstone
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Liliana G Bordeianou
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Christy E Cauley
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Rocco Ricciardi
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - David L Berger
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA.
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42
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Yılmaz O, Crabbe A, Neyaz A, Pankaj A, Lee SH, Hosseini S, Rickelt S, Cerda S, Zhao G, Leijsen L, Dineaux A, Shroff SG, Crotty R, Zhang ML, Yilmaz OH, Patil DT, Berger D, Deshpande V. Clinical, Pathologic, Genetics and Intratumoral Immune Milieu of Serrated Adenocarcinoma of the Colon. Histopathology 2022; 81:380-388. [PMID: 35789111 DOI: 10.1111/his.14719] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/21/2022] [Accepted: 07/02/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Serrated adenocarcinoma (SAC), a recognized WHO variant of colonic adenocarcinoma, is the purported end-product of serrated neoplasia. Yet, the diagnosis of SAC is infrequently rendered, and little is known about its prognosis, immune microenvironment, and molecular alterations. MATERIALS AND METHODS We assessed 903 consecutive colon carcinomas and recognized tumors with ≥5% (n=77) serrated pattern, and ≥50% serrated pattern (n=13). We assessed precursor polyps and synchronous polyps. We recorded demographic/clinical parameters, histological features, and MMR status. We performed immunohistochemistry and quantification on tissue microarray for HLA class I/II proteins, beta-2-microglobulin (B2MG), CD8, CD163, LAG3, PD-L1, FoxP3, PD-L1and BRAF V600E. RESULTS We identified ≥ 5% epithelial serration prevalence in 8.5% of cases, and ≥50% epithelial serration prevalence in 1.4% of cases. Precursor lesions were present in 21.4% of cases; these were mostly tubular adenomas with two traditional serrated adenoma identified. SAC with ≥ 5% serrations exhibited lower numbers of CD8 positive lymphocytes (p=0.002) and lower B2MG expression (p=0.048), although neither value was significant at ≥50% serration threshold. There was no difference in HLA class I/II, or PD-L1 expression on tumor cells and no difference in PD-L1, LAG3, FOXP3 and CD163 expression on immune cells. There was no association with MMR status, or BRAFV600E relative to conventional adenocarcinoma. There was improved disease-specific survival on univariate (but not multivariate) analysis between carcinomas with serrated pattern and non-mucinous conventional colonic carcinomas at ≥5% epithelial serrations (p=0.04). CONCLUSION SAC category shows a limited impact on survival, and this phenotype may harbor a unique immunologic milieu.
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Affiliation(s)
- Osman Yılmaz
- Department of Pathology, Boston Medical Center, Boston
| | - Andrew Crabbe
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Azfar Neyaz
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Amaya Pankaj
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Soo Hyun Lee
- Department of Pathology, Boston Medical Center, Boston
| | - Sahar Hosseini
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Steffen Rickelt
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sandra Cerda
- Department of Pathology, Boston Medical Center, Boston
| | - Grace Zhao
- Department of Pathology, Boston Medical Center, Boston
| | - Lieve Leijsen
- Department of Surgery, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Anne Dineaux
- Department of Surgery, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Stuti G Shroff
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Rory Crotty
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - M Lisa Zhang
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Omer H Yilmaz
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Deepa T Patil
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - David Berger
- Department of Surgery, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
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43
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Porter RL, Sun S, Flores MN, Berzolla E, You E, Phillips IE, Kc N, Desai N, Tai EC, Szabolcs A, Lang ER, Pankaj A, Raabe MJ, Thapar V, Xu KH, Nieman LT, Rabe DC, Kolin DL, Stover EH, Pepin D, Stott SL, Deshpande V, Liu JF, Solovyov A, Matulonis UA, Greenbaum BD, Ting DT. Satellite repeat RNA expression in epithelial ovarian cancer associates with a tumor immunosuppressive phenotype. J Clin Invest 2022; 132:155931. [PMID: 35708912 PMCID: PMC9374379 DOI: 10.1172/jci155931] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
Aberrant expression of viral-like repeat elements is a common feature in epithelial cancers, but the significant diversity of repeat species provides a distinct view of the cancer transcriptome. Repeatome profiling across ovarian, pancreatic, and colorectal cell lines identifies distinct clustering that is independent of tissue of origin that is seen with coding gene analysis. Deeper analysis of ovarian cancer cell lines demonstrated that HSATII satellite repeat expression was highly associated with epithelial mesenchymal transition (EMT) and anti-correlated with interferon (IFN) response genes indicative of a more aggressive phenotype. This relationship of HSATII with high EMT and low IFN response genes was also found in RNA-seq of primary ovarian cancers and associated with significantly shorter survival in a second independent cohort of ovarian cancer patients. Repeat RNAs were also found enriched in tumor derived extracellular vesicles that were capable of stimulating monocyte derived macrophages demonstrating a mechanism of altering the tumor microenvironment with these viral-like sequences. Targeting of HSATII with anti-sense locked nucleic acids (LNAs) stimulated IFN response and induced MHC I expression in ovarian cancer cells lines, highlighting a potential strategy of modulating the repeatome to re-establish anti-tumor cell immune surveillance.
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Affiliation(s)
- Rebecca L Porter
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Siyu Sun
- Computational Oncology, Memorial Sloan-Kettering Cancer Center, New York, United States of America
| | - Micayla N Flores
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Emily Berzolla
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Eunae You
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Ildiko E Phillips
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Neelima Kc
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Niyati Desai
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Eric C Tai
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Annamaria Szabolcs
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Evan R Lang
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Amaya Pankaj
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Michael J Raabe
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Vishal Thapar
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Katherine H Xu
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Linda T Nieman
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Daniel C Rabe
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - David L Kolin
- Department of Pathology, Brigham & Womans Hospital, Boston, United States of America
| | - Elizabeth H Stover
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States of America
| | - David Pepin
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, United States of America
| | - Shannon L Stott
- Cancer Center, Massachusetts General Hospital, Charlestown, United States of America
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, United States of America
| | - Joyce F Liu
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States of America
| | - Alexander Solovyov
- Computational Oncology, Memorial Sloan-Kettering Cancer Center, New York, United States of America
| | - Ursula A Matulonis
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States of America
| | - Benjamin D Greenbaum
- Computational Oncology, Memorial Sloan-Kettering Cancer Center, New York, United States of America
| | - David T Ting
- Massachusetts General Hospital, Harvard Medical School, Boston, United States of America
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44
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Shih AR, Hatipoglu D, Wilechansky R, Goiffon R, Deshpande V, Misdraji J, Chung RT. Persistent Cholestatic Injury and Secondary Sclerosing Cholangitis in COVID-19 Patients. Arch Pathol Lab Med 2022; 146:1184-1193. [PMID: 35657750 DOI: 10.5858/arpa.2021-0605-sa] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2022] [Indexed: 02/06/2023]
Abstract
CONTEXT.– Coronavirus disease 2019 (COVID-19) has been associated with liver injury, and a small subset of patients recovering from severe disease have shown persistent markedly elevated liver biochemistries for months after infection. OBJECTIVE.– To characterize persistent biliary injury after COVID-19. DESIGN.– A search of the pathology archives identified 7 post-COVID-19 patients with persistent biliary injury, and the clinical, radiologic, and pathologic features were assessed. RESULTS.– All patients in this cohort presented with respiratory symptoms and had a complicated clinical course with acute elevation of liver biochemistries. Alkaline phosphatase (ALP) was markedly and persistently elevated after discharge (median peak ALP: 1498 IU/L, at a median of 84 days from diagnosis). Magnetic resonance cholangiopancreatography (MRCP) showed 3 patients with irregularity, stricturing, and dilatation of intrahepatic ducts; no radiographic abnormalities were identified in the remaining 4 patients. Liver biopsies showed mild portal changes with features of cholestatic injury in 4 patients (bile duct injury and canalicular cholestasis) and marked biliary obstruction in 2 patients (profound cholestasis, ductular reaction, and bile infarcts), but no SARS-CoV-2 ribonucleic acid (RNA) was identified on in-situ hybridization. On follow-up, most patients had minimal intervention and showed marked improvement of liver biochemistries but with mild persistent elevation of ALP. CONCLUSIONS.– A subset of critically ill COVID-19 patients demonstrates marked and persistent cholestatic injury, with radiographic and histologic evidence of secondary sclerosing cholangitis, suggesting that cholestatic liver disease and secondary sclerosing cholangitis may be long-term sequelae of COVID-19 acute illness as a longstanding manifestation of critical illness.
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Affiliation(s)
- Angela R Shih
- Department of Pathology and Laboratory Medicine (Shih, Deshpande, Misdraji), at the Massachusetts General Hospital, Boston, Massachusetts
| | - Dilara Hatipoglu
- The Department of Medicine (Hatipoglu, Wilechansky, Chung), at the Massachusetts General Hospital, Boston, Massachusetts
| | - Robert Wilechansky
- Liver Center and Gastrointestinal Division (Wilechansky, Chung) at the Massachusetts General Hospital, Boston, Massachusetts.,The Department of Medicine (Hatipoglu, Wilechansky, Chung), at the Massachusetts General Hospital, Boston, Massachusetts
| | - Reece Goiffon
- Department of Radiology (Goiffon), at the Massachusetts General Hospital, Boston, Massachusetts
| | - Vikram Deshpande
- Department of Pathology and Laboratory Medicine (Shih, Deshpande, Misdraji), at the Massachusetts General Hospital, Boston, Massachusetts
| | - Joseph Misdraji
- Department of Pathology and Laboratory Medicine (Shih, Deshpande, Misdraji), at the Massachusetts General Hospital, Boston, Massachusetts
| | - Raymond T Chung
- Liver Center and Gastrointestinal Division (Wilechansky, Chung) at the Massachusetts General Hospital, Boston, Massachusetts.,The Department of Medicine (Hatipoglu, Wilechansky, Chung), at the Massachusetts General Hospital, Boston, Massachusetts
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45
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Rajurkar M, Parikh AR, Solovyov A, You E, Kulkarni AS, Chu C, Xu KH, Jaicks C, Taylor MS, Wu C, Alexander KA, Good CR, Szabolcs A, Gerstberger S, Tran AV, Xu N, Ebright RY, Van Seventer EE, Vo KD, Tai EC, Lu C, Joseph-Chazan J, Raabe MJ, Nieman LT, Desai N, Arora KS, Ligorio M, Thapar V, Cohen L, Garden PM, Senussi Y, Zheng H, Allen JN, Blaszkowsky LS, Clark JW, Goyal L, Wo JY, Ryan DP, Corcoran RB, Deshpande V, Rivera MN, Aryee MJ, Hong TS, Berger SL, Walt DR, Burns KH, Park PJ, Greenbaum BD, Ting DT. Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer. Cancer Discov 2022; 12:1462-1481. [PMID: 35320348 PMCID: PMC9167735 DOI: 10.1158/2159-8290.cd-21-1117] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 08/17/2021] [Revised: 01/27/2022] [Accepted: 03/08/2022] [Indexed: 11/16/2022]
Abstract
Altered RNA expression of repetitive sequences and retrotransposition are frequently seen in colorectal cancer, implicating a functional importance of repeat activity in cancer progression. We show the nucleoside reverse transcriptase inhibitor 3TC targets activities of these repeat elements in colorectal cancer preclinical models with a preferential effect in p53-mutant cell lines linked with direct binding of p53 to repeat elements. We translate these findings to a human phase II trial of single-agent 3TC treatment in metastatic colorectal cancer with demonstration of clinical benefit in 9 of 32 patients. Analysis of 3TC effects on colorectal cancer tumorspheres demonstrates accumulation of immunogenic RNA:DNA hybrids linked with induction of interferon response genes and DNA damage response. Epigenetic and DNA-damaging agents induce repeat RNAs and have enhanced cytotoxicity with 3TC. These findings identify a vulnerability in colorectal cancer by targeting the viral mimicry of repeat elements. SIGNIFICANCE Colorectal cancers express abundant repeat elements that have a viral-like life cycle that can be therapeutically targeted with nucleoside reverse transcriptase inhibitors (NRTI) commonly used for viral diseases. NRTIs induce DNA damage and interferon response that provide a new anticancer therapeutic strategy. This article is highlighted in the In This Issue feature, p. 1397.
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Affiliation(s)
- Mihir Rajurkar
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Aparna R. Parikh
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Alexander Solovyov
- Computational Oncology, Department of Epidemiology and Biostatistics; Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eunae You
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | | | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
| | - Katherine H. Xu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Christopher Jaicks
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Martin S. Taylor
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Connie Wu
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School; Boston, MA, USA
| | - Katherine A. Alexander
- Epigenetics Institute, Departments of Cell and Developmental Biology, Genetics, and Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Charly R. Good
- Epigenetics Institute, Departments of Cell and Developmental Biology, Genetics, and Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Annamaria Szabolcs
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Stefanie Gerstberger
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Antuan V. Tran
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
| | - Nova Xu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Richard Y. Ebright
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | | | - Kevin D. Vo
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Eric C. Tai
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Chenyue Lu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | | | - Michael J. Raabe
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Linda T. Nieman
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Niyati Desai
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Kshitij S. Arora
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Matteo Ligorio
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Vishal Thapar
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Limor Cohen
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School; Boston, MA, USA
| | - Padric M. Garden
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School; Boston, MA, USA
| | - Yasmeen Senussi
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School; Boston, MA, USA
| | - Hui Zheng
- Biostatistics Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jill N. Allen
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Lawrence S. Blaszkowsky
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Jeffrey W. Clark
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Lipika Goyal
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Jennifer Y. Wo
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - David P. Ryan
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Ryan B. Corcoran
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Vikram Deshpande
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Miguel N. Rivera
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Martin J. Aryee
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Theodore S. Hong
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Shelley L. Berger
- Epigenetics Institute, Departments of Cell and Developmental Biology, Genetics, and Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - David R. Walt
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School; Boston, MA, USA
| | - Kathleen H. Burns
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School; Boston, MA, USA
| | - Peter J. Park
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
| | - Benjamin D. Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics; Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - David T. Ting
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
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46
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Wang H, Chetty R, Hosseini M, Allende DS, Esposito I, Matsuda Y, Deshpande V, Shi J, Dhall D, Jang KT, Kim GE, Luchini C, Graham RP, Reid MD, Basturk O, Hruban RH, Krasinskas A, Klimstra DS, Adsay V. Pathologic Examination of Pancreatic Specimens Resected for Treated Pancreatic Ductal Adenocarcinoma: Recommendations From the Pancreatobiliary Pathology Society. Am J Surg Pathol 2022; 46:754-764. [PMID: 34889852 PMCID: PMC9106848 DOI: 10.1097/pas.0000000000001853] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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] [Indexed: 11/25/2022]
Abstract
Currently, there are no internationally accepted consensus guidelines for pathologic evaluation of posttherapy pancreatectomy specimens. The Neoadjuvant Therapy Working Group of Pancreatobiliary Pathology Society was formed in 2018 to review grossing protocols, literature, and major issues and to develop recommendations for pathologic evaluation of posttherapy pancreatectomy specimens. The working group generated the following recommendations: (1) Systematic and standardized grossing and sampling protocols should be adopted for pancreatectomy specimens for treated pancreatic ductal adenocarcinoma (PDAC). (2) Consecutive mapping sections along the largest gross tumor dimension are recommended to validate tumor size by histology as required by the College of American Pathologists (CAP) cancer protocol. (3) Tumor size of treated PDACs should be measured microscopically as the largest dimension of tumor outer limits that is bound by viable tumor cells, including intervening stroma. (4) The MD Anderson grading system for tumor response has a better correlation with prognosis and better interobserver concordance among pathologists than does the CAP system. (5) A case should not be classified as a complete response unless the entire pancreas, peripancreatic tissues, ampulla of Vater, common bile duct, and duodenum adjacent to the pancreas are submitted for microscopic examination. (6) Future studies on tumor response of lymph node metastases, molecular and/or immunohistochemical markers, as well as application of artificial intelligence in grading tumor response of treated PDAC are needed. In summary, systematic, standardized pathologic evaluation, accurate tumor size measurement, and reproducible tumor response grading to neoadjuvant therapy are needed for optimal patient care. The criteria and discussions provided here may provide guidance towards these goals.
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Affiliation(s)
- Huamin Wang
- Department of Anatomical Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Runjan Chetty
- Histopathology Department, Brighton & Sussex University Hospitals, Brighton, United Kingdom
| | - Mojgan Hosseini
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | | | - Irene Esposito
- Institute of Pathology, University Hospital of Duesseldorf, Duesseldorf, Germany
| | - Yoko Matsuda
- Oncology Pathology, Department of Pathology and Host-Defense, Kagawa University, Kagawa, Japan
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jiaqi Shi
- Department of Pathology & Clinical Labs, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Deepti Dhall
- Department of Pathology, The University of Alabama at Birmingham, AL, USA
| | - Kee-Taek Jang
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Grace E. Kim
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Claudio Luchini
- Department of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Rondell P. Graham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Michelle D. Reid
- Department of Pathology, Emory University Hospital, Atlanta, GA, USA
| | - Olca Basturk
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ralph H. Hruban
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alyssa Krasinskas
- Department of Pathology, Emory University Hospital, Atlanta, GA, USA
| | - David S. Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Volkan Adsay
- Department of Pathology, Koc University Hospital and KUTTAM Research Center, Istanbul, Turkey
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47
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Falade AS, Reynolds KL, Zubiri L, Deshpande V, Fintelmann FJ, Dougan M, Mooradian MJ. Case Report: Fulminant Celiac Disease With Combination Immune Checkpoint Therapy. Front Immunol 2022; 13:871452. [PMID: 35493494 PMCID: PMC9049212 DOI: 10.3389/fimmu.2022.871452] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/07/2022] [Indexed: 12/19/2022] Open
Abstract
Since the first approval of immune checkpoint inhibitors (ICIs) in 2011, these agents have rapidly become an integral treatment option across tumor types. However, with the increased adoption of ICIs, the incidence of immune-related adverse events (irAEs) continues to rise, and rare toxicity continues to be reported. Here, we present a case of a 70-year-old male patient with widespread metastatic melanoma who developed rapid onset anasarca and transaminitis after initiation of dual anti-PD-1/CTLA-4 inhibition with nivolumab and ipilimumab. An extensive workup was performed with serologies returning positive for anti-tissue transglutaminase immunoglobulin (tTG-IgA) and endoscopy revealing duodenal mucosal atrophy with duodenal biopsies confirming celiac disease. All symptoms resolved after initiation of a gluten-free diet without the addition of immunosuppression. This case highlights the importance of considering celiac disease in patients with suspected protein-losing enteropathy on ICI, the fulminant nature this uncommon irAE can present with, and underscores the broad differential clinicians must maintain when managing presumed irAEs.
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Affiliation(s)
- Ayo S. Falade
- Department of Medicine, Salem Hospital, Salem, MA, United States
- *Correspondence: Ayo S. Falade, ; Meghan J. Mooradian,
| | - Kerry L. Reynolds
- Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Leyre Zubiri
- Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, MA, United States
| | | | - Michael Dougan
- Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Meghan J. Mooradian
- Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
- *Correspondence: Ayo S. Falade, ; Meghan J. Mooradian,
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48
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Wu Q, Zhen Y, Shi L, Vu P, Greninger P, Adil R, Merritt J, Egan R, Wu MJ, Yin X, Ferrone CR, Deshpande V, Baiev I, Pinto CJ, McLoughlin DE, Walmsley CS, Stone JR, Gordan JD, Zhu AX, Juric D, Goyal L, Benes CH, Bardeesy N. EGFR Inhibition Potentiates FGFR Inhibitor Therapy and Overcomes Resistance in FGFR2 Fusion-Positive Cholangiocarcinoma. Cancer Discov 2022; 12:1378-1395. [PMID: 35420673 PMCID: PMC9064956 DOI: 10.1158/2159-8290.cd-21-1168] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/10/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022]
Abstract
FGFR inhibitors are approved for the treatment of advanced cholangiocarcinoma harboring FGFR2 fusions. However, the response rate is moderate, and resistance emerges rapidly due to acquired secondary FGFR2 mutations or due to other less-defined mechanisms. Here, we conducted high-throughput combination drug screens, biochemical analysis, and therapeutic studies using patient-derived models of FGFR2 fusion-positive cholangiocarcinoma to gain insight into these clinical profiles and uncover improved treatment strategies. We found that feedback activation of EGFR signaling limits FGFR inhibitor efficacy, restricting cell death induction in sensitive models and causing resistance in insensitive models lacking secondary FGFR2 mutations. Inhibition of wild-type EGFR potentiated responses to FGFR inhibitors in both contexts, durably suppressing MEK/ERK and mTOR signaling, increasing apoptosis, and causing marked tumor regressions in vivo. Our findings reveal EGFR-dependent adaptive signaling as an important mechanism limiting FGFR inhibitor efficacy and driving resistance and support clinical testing of FGFR/EGFR inhibitor therapy for FGFR2 fusion-positive cholangiocarcinoma. SIGNIFICANCE We demonstrate that feedback activation of EGFR signaling limits the effectiveness of FGFR inhibitor therapy and drives adaptive resistance in patient-derived models of FGFR2 fusion-positive cholangiocarcinoma. These studies support the potential of combination treatment with FGFR and EGFR inhibitors as an improved treatment for patients with FGFR2-driven cholangiocarcinoma.
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Affiliation(s)
- Qibiao Wu
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yuanli Zhen
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lei Shi
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Phuong Vu
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Patricia Greninger
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ramzi Adil
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Joshua Merritt
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Regina Egan
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Meng-Ju Wu
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Xunqin Yin
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Cristina R Ferrone
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Vikram Deshpande
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Islam Baiev
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christopher J Pinto
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel E McLoughlin
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Charlotte S Walmsley
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - James R Stone
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - John D Gordan
- Helen Diller Family Comprehensive Cancer Center and Quantitative Biosciences Institute, University of California, San Francisco
| | - Andrew X Zhu
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.,Jiahui International Cancer Center, Jiahui Health, Shanghai, China
| | - Dejan Juric
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lipika Goyal
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Cyril H Benes
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nabeel Bardeesy
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
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49
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Fourman MS, Ramsey DC, Newman ET, Schwab JH, Chen YL, Hung YP, Chebib I, Deshpande V, Petur Nielsen G, DeLaney TF, Mullen JT, Raskin KA, Lozano-Calderon S. ASO Visual Abstract: Assessing the Safety and Utility of Wound VAC Temporization of the Sarcoma or Benign Aggressive Tumor Bed Until Final Margins are Achieved. Ann Surg Oncol 2022. [DOI: 10.1245/s10434-021-11268-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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50
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Heidsma CM, van Roessel S, van Dieren S, Engelsman AF, Strobel O, Buechler MW, Schimmack S, Perinel J, Adham M, Deshpande V, Kjaer J, Norlen O, Gill AJ, Samra JS, Mittal A, Hoogwater FJH, Primavesi F, Stättner S, Besselink MG, van Eijck CHJ, Nieveen van Dijkum EJM. International Validation of a Nomogram to Predict Recurrence after Resection of Grade 1 and 2 Nonfunctioning Pancreatic Neuroendocrine Tumors. Neuroendocrinology 2022; 112:571-579. [PMID: 34343138 DOI: 10.1159/000518757] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 06/29/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Despite the low recurrence rate of resected nonfunctional pancreatic neuroendocrine tumors (NF-pNETs), nearly all patients undergo long-term surveillance. A prediction model for recurrence may help select patients for less intensive surveillance or identify patients for adjuvant therapy. The objective of this study was to assess the external validity of a recently published model predicting recurrence within 5 years after surgery for NF-pNET in an international cohort. This prediction model includes tumor grade, lymph node status and perineural invasion as predictors. METHODS Retrospectively, data were collected from 7 international referral centers on patients who underwent resection for a grade 1-2 NF-pNET between 1992 and 2018. Model performance was evaluated by calibration statistics, Harrel's C-statistic, and area under the curve (AUC) of the receiver operating characteristic curve for 5-year recurrence-free survival (RFS). A sub-analysis was performed in pNETs >2 cm. The model was improved to stratify patients into 3 risk groups (low, medium, high) for recurrence. RESULTS Overall, 342 patients were included in the validation cohort with a 5-year RFS of 83% (95% confidence interval [CI]: 78-88%). Fifty-eight patients (17%) developed a recurrence. Calibration showed an intercept of 0 and a slope of 0.74. The C-statistic was 0.77 (95% CI: 0.70-0.83), and the AUC for the prediction of 5-year RFS was 0.74. The prediction model had a better performance in tumors >2 cm (C-statistic 0.80). CONCLUSIONS External validity of this prediction model for recurrence after curative surgery for grade 1-2 NF-pNET showed accurate overall performance using 3 easily accessible parameters. This model is available via www.pancreascalculator.com.
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Affiliation(s)
- Charlotte M Heidsma
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Stijn van Roessel
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Susan van Dieren
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Anton F Engelsman
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Oliver Strobel
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, University of Heidelberg, Heidelberg, Germany
| | - Markus W Buechler
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, University of Heidelberg, Heidelberg, Germany
| | - Simon Schimmack
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, University of Heidelberg, Heidelberg, Germany
| | - Julie Perinel
- Department of Surgery, Centre Hospitalier Universitaire de Lyon, University of Lyon, Lyon, France
| | - Mustapha Adham
- Department of Surgery, Centre Hospitalier Universitaire de Lyon, University of Lyon, Lyon, France
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Josefine Kjaer
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Olov Norlen
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group Kolling Institute of Medical Research and University of Sydney, Sydney, New South Wales, Australia
| | - Jaswinder S Samra
- Department of Surgery, Royal North Shore Hospital, St Leonards, University of Sydney, Sydney, New South Wales, Australia
| | - Anubhav Mittal
- Department of Surgery, Royal North Shore Hospital, St Leonards, University of Sydney, Sydney, New South Wales, Australia
| | - Frederik J H Hoogwater
- Department of Surgery, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Florian Primavesi
- Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefan Stättner
- Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Innsbruck, Austria
- Department of Surgery, Salzkammergut Klinikum, Standort Vocklabruck, Vocklabruck, Austria
| | - Marc G Besselink
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Casper H J van Eijck
- Department of Surgery, Erasmus Medical Center, Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - E J M Nieveen van Dijkum
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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