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Dehner CA, Johnson EF, Wieland CN, Camilleri MJ, Kajdacsy-Balla A, Oliveira AM, Halling KC, Gupta S, Guo R. Fusion-driven cutaneous and superficial mesenchymal and adnexal tumors-A clinicopathologic and molecular study of 15 cases, including a novel case of ACTB::ZMIZ2-rearranged adnexal carcinoma. J Cutan Pathol 2024; 51:538-548. [PMID: 38556256 DOI: 10.1111/cup.14610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/22/2024] [Accepted: 03/13/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND While the list of fusion-driven soft tissue neoplasms is expanding rapidly, their importance among cutaneous and superficial mesenchymal and adnexal neoplasms remains poorly understood. This challenge is especially evident in cases with ambiguous histopathology that are difficult to classify based on morphology. AIMS Our goal was to investigate the benefits of next-generation sequencing in diagnosing complex cutaneous neoplasms. MATERIALS & METHODS Departmental archives were searched for fusion-driven cutaneous neoplasms. Slides were retrieved and clinical information including follow-up was obtained. RESULTS Fifteen cases occurred in eight female and seven male patients, with a median age of 26 years (range: 1-83) at diagnosis. Tumors involved the extremities (9), scalp (5), and head and neck (1). Predominant features included myoepithelial (5), nested spindled with clear cytoplasm (2), atypical adnexal/squamoid (2), small round blue cell (2), cellular spindled (3), and fibrohistiocytic morphology (1). Most frequently encountered fusions involved EWSR1 (6) fused to ERG (1), FLI1 (1), CREB1 (2), CREM (1), PBX3 (1), followed by PLAG1 (4) with LIFR (2), TRPS1 (1) and CHCHD7. Additional fusions encountered were YAP1::NUTM1, EML4::ALK, SS18::SSX1 (2), and a novel fusion: ACTB::ZMIZ2. Integration of histologic features and molecular findings led to final diagnoses of primary cutaneous Ewing sarcoma (2), soft tissue myoepithelioma (4), cutaneous syncytial myoepithelioma (1), cutaneous adnexal carcinoma (1), porocarcinoma (1), inflammatory myofibroblastic tumor (1), synovial sarcoma (2), clear cell sarcoma (2), and angiomatoid fibrous histiocytoma (1). DISCUSSION AND CONCLUSION Our results show that fusion testing can be a helpful diagnostic tool, especially in cases with unusual or uncommon morphology in superficial sites. Furthermore, it can allow for the identification of potential therapeutic targets in some instances.
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Affiliation(s)
- Carina A Dehner
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Anatomic Pathology and Laboratory Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Emma F Johnson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Dermatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Carrie N Wieland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Dermatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael J Camilleri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Dermatology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Andre M Oliveira
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ruifeng Guo
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, Florida, USA
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2
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Warmke LM, Collier CD, Niziolek PJ, Davis JL, Zou YS, Michal M, Bell RC, Policarpio-Nicolas MLC, Cheng YW, Duckworth L, Dermawan JK, Fritchie KJ, Dehner CA. Novel CRTC1::MRTFB(MKL2) Gene Fusion Detected in Myxoid Mesenchymal Neoplasms With Myogenic Differentiation Involving Bone and Soft Tissues. Mod Pathol 2024; 37:100518. [PMID: 38763420 DOI: 10.1016/j.modpat.2024.100518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/23/2024] [Accepted: 05/11/2024] [Indexed: 05/21/2024]
Abstract
Appropriate classification of fusion-driven bone and soft tissue neoplasms continues to evolve, often relying on the careful integration of morphologic findings with immunohistochemical, molecular, and clinical data. Herein, we present 3 cases of a morphologically distinct myxoid mesenchymal neoplasm with myogenic differentiation and novel CRTC1::MRTFB (formerly MKL2) gene fusion. Three tumors occurred in 1 male and 2 female patients with a median age of 72 years (range: 28-78). Tumors involved the left iliac bone, the right thigh, and the left perianal region with a median size of 4.0 cm (4.0-7.6 cm). Although 1 tumor presented as an incidental finding, the other 2 tumors were noted, given their persistent growth. At the time of the last follow-up, 1 patient was alive with unresected disease at 6 months, 1 patient was alive without evidence of disease at 12 months after surgery, and 1 patient died of disease 24 months after diagnosis. On histologic sections, the tumors showed multinodular growth and were composed of variably cellular spindle to round-shaped cells with distinct brightly eosinophilic cytoplasm embedded within a myxoid stroma. One tumor showed overt smooth muscle differentiation. Cytologic atypia and mitotic activity ranged from minimal (2 cases) to high (1 case). By immunohistochemistry, the neoplastic cells expressed focal smooth muscle actin, h-caldesmon, and desmin in all tested cases. Skeletal muscle markers were negative. Next-generation sequencing detected nearly identical CRTC1::MRTFB gene fusions in all cases. We suggest that myxoid mesenchymal tumors with myogenic differentiation harboring a CRTC1::MRTFB fusion may represent a previously unrecognized, distinctive entity that involves soft tissue and bone. Continued identification of these novel myxoid neoplasms with myogenic differentiation will be important in determining appropriate classification, understanding biologic potential, and creating treatment paradigms.
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Affiliation(s)
- Laura M Warmke
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Christopher D Collier
- Department of Orthopedic Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Paul J Niziolek
- Department of Radiology and Imaging Sciences, Musculoskeletal Imaging, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jessica L Davis
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ying S Zou
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland
| | | | - Robert C Bell
- Department of Pathology, Michigan University, Ann Arbor, Michigan
| | | | - Yu-Wei Cheng
- Department of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Lauren Duckworth
- Department of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Josephine K Dermawan
- Department of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Karen J Fritchie
- Department of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Carina A Dehner
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana.
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3
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Michal M, Agaimy A, Croce S, Mechtersheimer G, Gross JM, Xing D, Bell DA, Gupta S, Mosaieby E, Martínek P, Klubíčková N, Michalová K, Bouda J, Fínek J, Hernandez T, Michal M, Schoolmeester JK, Ondič O. PLAG1-Rearranged Uterine Sarcomas: A Study of 11 Cases Showing a Wide Phenotypical Spectrum Not Limited to Myxoid Leiomyosarcoma-like Morphology. Mod Pathol 2024; 37:100552. [PMID: 38942115 DOI: 10.1016/j.modpat.2024.100552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 06/07/2024] [Accepted: 06/20/2024] [Indexed: 06/30/2024]
Abstract
PLAG1 gene fusions were recently identified in a subset of uterine myxoid leiomyosarcomas (M-LMS). However, we have encountered cases of PLAG1-rearranged uterine sarcomas lacking M-LMS-like morphology and/or any expression of smooth muscle markers. To better characterize their clinicopathologic features, we performed a multiinstitutional search that yielded 11 cases. The patients ranged in age from 34 to 72 years (mean, 57 years). All tumors arose in the uterine corpus, ranging in size from 6.5 to 32 cm (mean, 15 cm). The most common stage at presentation was pT1b (n = 6), and 3 cases had stage pT1 (unspecified), and 1 case each presented in stages pT2a and pT3b. Most were treated only with hysterectomy and adnexectomy. The follow-up (range, 7-71 months; median, 39 months) was available for 7 patients. Three cases (7-21 months of follow-up) had no evidence of disease. Three of the 4 remaining patients died of disease within 55 to 71 months, while peritoneal spread developed in the last patient, and the patient was transferred for palliative care at 39 months. Morphologically, the tumors showed a high intertumoral and intratumoral heterogeneity. M-LMS-like and epithelioid leiomyosarcoma-like morphology were present in 3 and 5 primary tumors, respectively, the remaining mostly presented as nondescript ovoid or spindle cell sarcomas. Unusual morphologic findings included prominently hyalinized stroma (n = 3), adipocytic differentiation with areas mimicking myxoid liposarcoma (n = 2), osteosarcomatous differentiation (n = 1), and undifferentiated pleomorphic sarcoma-like areas (n = 1). The mitotic activity ranged from 3 to 24 mitoses per 10 high-power fields (mean, 9); 3 of 10 cases showed necrosis. In 3 of 11 cases, no expression of smooth muscle actin, h-caldesmon, or desmin was noted, whereas 5 of 5 cases expressed PLAG1. By RNA sequencing, the following fusion partners were identified: PUM1, CHCHD7 (each n = 2), C15orf29, CD44, MYOCD, FRMD6, PTK2, and TRPS1 (each n = 1). One case only showed PLAG1 gene break by fluorescence in situ hybridization. Our study documents a much broader morphologic spectrum of PLAG1-rearranged uterine sarcomas than previously reported, encompassing but not limited to M-LMS-like morphology with occasional heterologous (particularly adipocytic) differentiation. As it is currently difficult to precisely define their line of differentiation, for the time being, we suggest using a descriptive name "PLAG1-rearranged uterine sarcoma."
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Affiliation(s)
- Michael Michal
- Bioptical Laboratory, Ltd, Pilsen, Czech Republic; Department of Pathology, Charles University, Faculty of Medicine in Pilsen, Pilsen, Czech Republic.
| | - Abbas Agaimy
- Institute of Pathology, Friedrich Alexander University Erlangen-Nürnberg, University Hospital, Erlangen, Germany
| | - Sabrina Croce
- Department of BioPathology, Anticancer Center, Institut Bergonié, Bordeaux, France
| | | | - John M Gross
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Deyin Xing
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Debra A Bell
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Elaheh Mosaieby
- Bioptical Laboratory, Ltd, Pilsen, Czech Republic; Department of Pathology, Charles University, Faculty of Medicine in Pilsen, Pilsen, Czech Republic
| | | | - Natálie Klubíčková
- Bioptical Laboratory, Ltd, Pilsen, Czech Republic; Department of Pathology, Charles University, Faculty of Medicine in Pilsen, Pilsen, Czech Republic
| | - Květoslava Michalová
- Bioptical Laboratory, Ltd, Pilsen, Czech Republic; Department of Pathology, Charles University, Faculty of Medicine in Pilsen, Pilsen, Czech Republic
| | - Jiří Bouda
- Department of Gynecology and Obstetrics, Charles University, Faculty of Medicine in Pilsen and Charles University Hospital Pilsen, Pilsen, Czech Republic
| | - Jindřich Fínek
- Department of Oncology and Radiotherapeutics, Charles University, Faculty of Medicine in Pilsen, Pilsen, Czech Republic
| | - Tahyna Hernandez
- Department of Pathology and Laboratory Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York
| | - Michal Michal
- Bioptical Laboratory, Ltd, Pilsen, Czech Republic; Department of Pathology, Charles University, Faculty of Medicine in Pilsen, Pilsen, Czech Republic
| | | | - Ondrej Ondič
- Bioptical Laboratory, Ltd, Pilsen, Czech Republic; Department of Pathology, Charles University, Faculty of Medicine in Pilsen, Pilsen, Czech Republic
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4
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Koshyk O, Dehner CA, van den Hout MFCM, Bempt IV, Sciot R, Huang HY, Agaimy A, Din NU, Klubíčková N, Mosaieby E, Skálová A, Michalová K, Schöffski P, Oliveira AM, Halling KC, Gupta S, Gross JM, Nin JWM, Michal M, Folpe AL, Kosemehmetoglu K, Torres-Mora J, Michal M. EWSR1::POU2AF3(COLCA2) Sarcoma: An Aggressive, Polyphenotypic Sarcoma With a Head and Neck Predilection. Mod Pathol 2023; 36:100337. [PMID: 37742928 DOI: 10.1016/j.modpat.2023.100337] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/25/2023] [Accepted: 09/15/2023] [Indexed: 09/26/2023]
Abstract
EWSR1::POU2AF3 (COLCA2) sarcomas are a recently identified group of undifferentiated round/spindle cell neoplasms with a predilection for the head and neck region. Herein, we report our experience with 8 cases, occurring in 5 men and 3 women (age range, 37-74 years; median, 60 years). Tumors involved the head/neck (4 cases), and one each the thigh, thoracic wall, fibula, and lung. Seven patients received multimodal therapy; 1 patient was treated only with surgery. Clinical follow-up (8 patients; range, 4-122 months; median, 32 months) showed 5 patients with metastases (often multifocal, with a latency ranging from 7 to 119 months), and 3 of them also with local recurrence. The median local recurrence-free and metastasis-free survival rates were 24 months and 29 months, respectively. Of the 8 patients, 1 died of an unknown cause, 4 were alive with metastatic disease, 1 was alive with unresectable local disease, and 2 were without disease. The tumors were composed of 2 morphologic subgroups: (1) relatively bland tumors consisting of spindled to stellate cells with varying cellularity and fibromyxoid stroma (2 cases) and (2) overtly malignant tumors composed of nests of "neuroendocrine-appearing" round cells surrounded by spindled cells (6 cases). Individual cases in the second group showed glandular, osteogenic, or rhabdomyoblastic differentiation. Immunohistochemical results included CD56 (4/4 cases), GFAP (5/8), SATB2 (4/6), keratin (AE1/AE3) (5/8), and S100 protein (4/7). RNA sequencing identified EWSR1::POU2AF3 gene fusion in all cases. EWSR1 gene rearrangement was confirmed by fluorescence in situ hybridization in 5 cases. Our findings confirm the head/neck predilection and aggressive clinical behavior of EWSR1::POU2AF3 sarcomas and widen the morphologic spectrum of these rare lesions to include relatively bland spindle cell tumors and tumors with divergent differentiation.
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Affiliation(s)
- Olena Koshyk
- Department of Pathology, Charles University, Faculty of Medicine in Plzeň, Czech Republic; Medical Laboratory CSD, Ltd, Kyiv, Ukraine
| | - Carina A Dehner
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Mari F C M van den Hout
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Isabelle Vanden Bempt
- Department for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Raf Sciot
- Department of Pathology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Hsuan-Ying Huang
- Department of Anatomical Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung City, Taiwan
| | - Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander University Erlangen-Nürnberg, University Hospital, Erlangen, Germany
| | - Nasir Ud Din
- Section of Histopathology, Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Natálie Klubíčková
- Department of Pathology, Charles University, Faculty of Medicine in Plzeň, Czech Republic; Bioptical Laboratory, Ltd, Plzeň, Czech Republic
| | - Elaheh Mosaieby
- Department of Pathology, Charles University, Faculty of Medicine in Plzeň, Czech Republic; Bioptical Laboratory, Ltd, Plzeň, Czech Republic
| | - Alena Skálová
- Department of Pathology, Charles University, Faculty of Medicine in Plzeň, Czech Republic; Bioptical Laboratory, Ltd, Plzeň, Czech Republic
| | - Květoslava Michalová
- Department of Pathology, Charles University, Faculty of Medicine in Plzeň, Czech Republic; Bioptical Laboratory, Ltd, Plzeň, Czech Republic
| | - Patrick Schöffski
- Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium; Department of Oncology, KU Leuven, Laboratory of Experimental Oncology, Leuven, Belgium
| | - Andre M Oliveira
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - John M Gross
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Johanna W M Nin
- Department of Internal Medicine, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Michal Michal
- Department of Pathology, Charles University, Faculty of Medicine in Plzeň, Czech Republic; Bioptical Laboratory, Ltd, Plzeň, Czech Republic
| | - Andrew L Folpe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Jorge Torres-Mora
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Michael Michal
- Department of Pathology, Charles University, Faculty of Medicine in Plzeň, Czech Republic; Bioptical Laboratory, Ltd, Plzeň, Czech Republic.
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5
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Dehner CA, Broski SM, Meis JM, Murugan P, Chrisinger JSA, Sosa C, Petersen M, Halling KC, Gupta S, Folpe AL. Fusion-driven Spindle Cell Rhabdomyosarcomas of Bone and Soft Tissue: A Clinicopathologic and Molecular Genetic Study of 25 Cases. Mod Pathol 2023; 36:100271. [PMID: 37422156 DOI: 10.1016/j.modpat.2023.100271] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/10/2023]
Abstract
The evolving classification of rhabdomyosarcoma (RMS) now includes spindle cell RMS (SRMS). Bone/soft tissue SRMS often harbor TFCP2, or less often MEIS1 rearrangements. We studied 25 fusion-driven SRMS involving bone (n = 19) and soft tissue (n = 6). Osseous SRMS occurred in 13 women and 6 men (median age: 41 years) and involved the pelvis (5), sacrum (2), spine (4), maxilla (4), mandible (1), skull (1), and femur (2). Follow-up (median: 5 months) demonstrated local recurrence in 2/16 and distant metastases in 8/17 patients (median time to metastasis: 1 month). Eight patients died of disease; 9 were alive with disease. Soft tissue SRMS occurred in 4 men and 2 women (median: 50 years). Follow-up (median: 10 months) revealed distant metastasis at diagnosis (1), alive with unresected tumor (1), and no evidence of disease (4). Next-generation sequencing demonstrated FUS::TFCP2 (12), EWSR1::TFCP2 (3) and MEIS1::NCOA2 (2); FISH identified EWSR1 (2) rearrangements. Most TFCP2-rearranged SRMS (13/17) showed spindled/epithelioid morphology, rarely with rhabdomyoblasts. The bone tumors were diffusely desmin and MyoD1 positive with limited myogenin; 10/13 were ALK -positive and 6/15 were keratin positive. Soft tissue SRMS harbored EWSR1::TFCP2, MEIS1::NCOA2, ZFP64::NCOA2, MEIS1::FOXO1, TCF12::VGLL3 and DCTN1::ALK, and displayed spindled/epithelioid, leiomyomatous, and myxofibrosarcoma-like morphologies. Immunohistochemistry (IHC) was positive for MyoD1 (6/6), focal desmin (5/6), myogenin (3/6), and keratin (1/6). We conclude that TFCP2-rearranged SRMS of bone and soft tissue show consistent morphologic and IHC features, likely representing a distinct subset of RMS. Non-TFCP2 fusion-positive SRMS could represent a single RMS subset, multiple subtypes of RMS, or "fusion-defined" sarcomas with rhabdomyoblastic differentiation.
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Affiliation(s)
- Carina A Dehner
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Jeanne M Meis
- Department of Pathology and Laboratory Medicine, The University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Paari Murugan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - John S A Chrisinger
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Carlos Sosa
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew Petersen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Andrew L Folpe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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6
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Mistretta B, Rankothgedera S, Castillo M, Rao M, Holloway K, Bhardwaj A, El Noafal M, Albarracin C, El-Zein R, Rezaei H, Su X, Akbani R, Shao XM, Czerniecki BJ, Karchin R, Bedrosian I, Gunaratne PH. Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer. Front Immunol 2023; 14:1188831. [PMID: 37744342 PMCID: PMC10512078 DOI: 10.3389/fimmu.2023.1188831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/27/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction We present here a strategy to identify immunogenic neoantigen candidates from unique amino acid sequences at the junctions of fusion proteins which can serve as targets in the development of tumor vaccines for the treatment of breastcancer. Method We mined the sequence reads of breast tumor tissue that are usually discarded as discordant paired-end reads and discovered cancer specific fusion transcripts using tissue from cancer free controls as reference. Binding affinity predictions of novel peptide sequences crossing the fusion junction were analyzed by the MHC Class I binding predictor, MHCnuggets. CD8+ T cell responses against the 15 peptides were assessed through in vitro Enzyme Linked Immunospot (ELISpot). Results We uncovered 20 novel fusion transcripts from 75 breast tumors of 3 subtypes: TNBC, HER2+, and HR+. Of these, the NSFP1-LRRC37A2 fusion transcript was selected for further study. The 3833 bp chimeric RNA predicted by the consensus fusion junction sequence is consistent with a read-through transcription of the 5'-gene NSFP1-Pseudo gene NSFP1 (NSFtruncation at exon 12/13) followed by trans-splicing to connect withLRRC37A2 located immediately 3' through exon 1/2. A total of 15 different 8-mer neoantigen peptides discovered from the NSFP1 and LRRC37A2 truncations were predicted to bind to a total of 35 unique MHC class I alleles with a binding affinity of IC50<500nM.); 1 of which elicited a robust immune response. Conclusion Our data provides a framework to identify immunogenic neoantigen candidates from fusion transcripts and suggests a potential vaccine strategy to target the immunogenic neopeptides in patients with tumors carrying the NSFP1-LRRC37A2 fusion.
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Affiliation(s)
- Brandon Mistretta
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Sakuni Rankothgedera
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Micah Castillo
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Mitchell Rao
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Kimberly Holloway
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Anjana Bhardwaj
- Department of Breast Surgical Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Maha El Noafal
- Department of Medicine, Houston Methodist Research Institute, Houston, TX, United States
| | - Constance Albarracin
- Department of Pathology, The UT MD Anderson Cancer Center, Houston, TX, United States
| | - Randa El-Zein
- Department of Medicine, Houston Methodist Research Institute, Houston, TX, United States
| | - Hengameh Rezaei
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Xiaoping Su
- Department of Bioinformatics & Computational Biology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Rehan Akbani
- Department of Bioinformatics & Computational Biology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Xiaoshan M. Shao
- Biomedical Engineering Department, Institute for Computational Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Brian J. Czerniecki
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Rachel Karchin
- Biomedical Engineering Department, Institute for Computational Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Isabelle Bedrosian
- Department of Breast Surgical Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Preethi H. Gunaratne
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
- Department of Breast Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, United States
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7
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Hiemenz MC, Kaur J, Kuang Z, Huang RSP, Harries L, Metzger D, Schiavone K, Millis SZ, Lin DI, Lechpammer M, Decker B, Mata DA, Reddy A, Parke M, Lee EY, Cui X, Iwenofu OH, Buehler D, Henderson L, Baldwin EM, Boikos SA, Ramkissoon SH, Smith SC. POU2AF3-rearranged sarcomas: A novel tumor defined by fusions of EWSR1 or FUS to a gene formerly designated COLCA2. Genes Chromosomes Cancer 2023; 62:460-470. [PMID: 36862145 DOI: 10.1002/gcc.23136] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/30/2023] [Accepted: 02/25/2023] [Indexed: 03/03/2023] Open
Abstract
Gene fusions involving EWSR1 or FUS as the 5' partner have been reported in a diverse array of sarcomas. Here, we characterize the histopathology and genomics of six tumors harboring a gene fusion between EWSR1 or FUS and POU2AF3, an understudied, putative colorectal cancer predisposition gene. Striking morphologic features reminiscent of synovial sarcoma were observed including a biphasic appearance with variable fusiform to epithelioid cytomorphology and staghorn-type vasculature. RNA sequencing demonstrated variable breakpoints in EWSR1/FUS along with similar breakpoints in POU2AF3 that encompassed a 3' portion of this gene. For cases in which additional information was available, the behavior of these neoplasms was aggressive with local spread and/or distant metastases. Although further studies are needed to confirm the functional significance of our findings, POU2AF3 fusions to EWSR1 or FUS may define a novel type of POU2AF3-rearranged sarcomas with aggressive, malignant behavior.
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Affiliation(s)
| | | | - Zheng Kuang
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | | | - Dana Metzger
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | | | | | | | | | | | | | - Matthew Parke
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Eun Y Lee
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Xiaoyan Cui
- Department of Pathology and Laboratory Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - O Hans Iwenofu
- Department of Pathology and Laboratory Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Darya Buehler
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Les Henderson
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Erin M Baldwin
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sosipatros A Boikos
- Department of Hematology and Oncology, Georgetown Lombardi Comprehensive Cancer Center, Washington DC, USA
| | - Shakti H Ramkissoon
- Foundation Medicine, Cambridge, Massachusetts, USA
- Department of Pathology, Wake Forest School of Medicine and Wake Forest Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
| | - Steven C Smith
- Departments of Pathology and Surgery and Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
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8
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Ulici V, Hornick JL, Davis JL, Mehrotra S, Meis JM, Halling KC, Fletcher CD, Kao E, Folpe AL. "E-MGNET": Extra-Enteric Malignant Gastrointestinal Neuroectodermal Tumor- A Clinicopathological and Molecular Genetic Study of 11 Cases. Mod Pathol 2023; 36:100160. [PMID: 36934861 DOI: 10.1016/j.modpat.2023.100160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/28/2023] [Accepted: 03/12/2023] [Indexed: 03/19/2023]
Abstract
Malignant gastrointestinal neuroectodermal tumors (MGNET), also known as "gastrointestinal clear cell sarcoma-like tumor", are very rare, aggressive sarcomas characterized by enteric location, distinctive pathologic features, and EWSR1/FUS::ATF1/CREB1 fusions. Despite identical genetics, the clinicopathologic features of MGNET are otherwise quite different from clear cell sarcoma of soft parts (CCS). Only exceptional extra-enteric MGNET (E-MGNET) have been reported. We report a series of 11 E-MGNET, the largest to date. Cases diagnosed as MGNET and occurring in non-intestinal locations were retrieved. Clinical follow-up was obtained. The tumors occurred in 3 males and 8 females (14-70 years of age, median 33 years) and involved the soft tissues of the neck (3), shoulder (1), buttock (2), orbit (1), and tongue/parapharyngeal space (1), the urinary bladder (1) and the falciform ligament/liver (1). Tumors showed morphologic features of enteric MGNET (small, relatively uniform, round to ovoid cells with round, regular nuclei containing small nucleoli, growing in multinodular and vaguely lobular patterns, with solid, pseudoalveolar and pseudopapillary architecture). Immunohistochemical results were: S100 protein (11/11), SOX10 (11/11), synaptophysin (3/10), CD56 (7/9), CD117 (3/9), DOG1 (0/4), ALK (4/8), chromogranin A (0/10), HMB45 (0/11), Melan-A (0/11), tyrosinase (0/4), MiTF (0/11). NGS results were: EWSR1::ATF1 (7 cases), EWSR1::CREB1 (3 cases) and EWSR1::PBX1 (1 case). The EWSR1::PBX1-positive tumor was similar to other cases, including osteoclast-like giant cells, and negative for myoepithelial markers. Clinical follow-up (range: 10 to 70 months; median 34 months) showed 4 patients dead of disease (10.5, 12, 25 and 64 months after diagnosis), 1 patient alive with extensive metastases (43 months after diagnosis), 1 patient alive with persistent local disease (11 months after diagnosis), and 4 alive without disease (10, 47, 53 and 70 months after diagnosis). One case is too recent for follow-up. The clinicopathologic and molecular genetic features of rare E-MGNET are essentially identical to those occurring in intestinal locations. Otherwise-typical E-MGNET may harbor EWSR1::PBX1, a finding previously unreported in this tumor type. As in enteric locations, the behavior of E-MGNET is aggressive, with metastases and/or death from disease in at least 50% of patients. E-MGNET should be distinguished from CCS and other tumors with similar fusions. ALK expression appears to be a common feature of tumors harboring EWSR1/FUS::ATF1/CREB1 fusion but is unlikely to predict therapeutic response to ALK inhibition. Future advances in our understanding of these unusual tumors will hopefully lead to improved nomenclature.
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Affiliation(s)
- Veronica Ulici
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Jessica L Davis
- Department of Pathology, University of Indiana, Indianapolis, IN
| | - Swati Mehrotra
- Department of Pathology and Laboratory Medicine, Loyola University Medical Center, Maywood, IL
| | - Jeanne M Meis
- Department of Anatomical Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kevin C Halling
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN
| | | | - Erica Kao
- Department of Pathology, Brooke Army Medical Center, San Antonio, TX
| | - Andrew L Folpe
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN.
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9
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Agaimy A, Baněčková M, De Almeida J, Dickson BC, Dimmler A, Hartmann W, Laé M, Pablik J, Schubart C, Skálová A, Stoehr R, Trautmann M, Wardelmann E, Wassef M, Weinreb I. Recurrent EWSR1::COLCA2 Fusions Define a Novel Sarcoma With Spindle/Round Cell Morphology and Strong Predilection for the Sinonasal Tract. Am J Surg Pathol 2023; 47:361-369. [PMID: 36580038 DOI: 10.1097/pas.0000000000002000] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The last 2 decades have attended a dynamic evolution in the nosology of poorly differentiated sinonasal tract malignancies, with several new molecularly defined entities having been described in addition to delineation of the genetic driver/s of some established older entities. These discoveries, however, mostly concerned epithelial-derived neoplasms (carcinomas). Adamantinoma-like Ewing sarcoma and biphenotypic sinonasal sarcoma are the major representatives of the newly defined mesenchymal categories. The colorectal cancer associated 2 (COLCA2) has been discovered recently as a colorectal cancer risk gene locus, but fusions involving this gene have not been well characterized. We, herein, describe clinicopathologic and molecular features of a novel sinonasal sarcoma characterized by undifferentiated spindle/round cell morphology and defined by recurrent EWSR1::COLCA2 fusions. All patients (n=5) were adults (3 female and 2 male) with a median age of 46 years (range, 23 to 60 y). The tumors originated in different subsites of the sinonasal tract with frequent multisite involvement. Original diagnoses were undifferentiated or unclassified round cell/spindle cell neoplasm/sarcoma (n=4) and neuroendocrine carcinoma (n=1). Surgery with or without adjuvant chemoradiation was the treatment in all cases. At the last follow-up, 1 patient developed multiple local recurrences over 21 years and another developed local recurrence and distant metastasis to bone 27 months after diagnosis. A third patient developed local recurrence 11 months later. Two patients were disease-free at 23, and 24 months. Histology showed nondescript highly cellular neoplasms with an admixture of spindled and round cells disposed into solid sheets and fascicles with brisk mitotic activity. Immunohistochemistry was negative for all lineage-specific markers with only limited focal membranous CD99 (4 of 5 cases) and weak pankeratin (1 of 5 cases) expression. Targeted RNA sequencing revealed an EWSR1::COLCA2 fusion, verified by EWSR1 fluorescence in situ hybridization, in all cases. This series identifies a novel member in the undifferentiated spindle/round cell sarcoma category with strong predilection for the sinonasal tract. None of >10,000 epithelial and mesenchymal neoplasms tested at the authors' centers during the same period showed this fusion, highlighting rarity of tumors carrying this gene fusion. Accordingly, molecular testing of unclassified sinonasal malignancies/sarcomas showing round and spindle cell morphology is recommended to enhance the identification and further characterization of this entity.
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Affiliation(s)
- Abbas Agaimy
- Institute of Pathology, Erlangen University Hospital, Comprehensive Cancer Center, European Metropolitan Area Erlangen-Nuremberg (CCC ER-EMN), Friedrich Alexander University of Erlangen-Nuremberg, Erlangen
| | - Martina Baněčková
- Department of Pathology, Charles University, Faculty of Medicine in Plzen
- Bioptic Laboratory Ltd, Plzen, Czech Republic
| | - John De Almeida
- Department of Otolaryngology, Head and Neck Surgery, Princess Margaret Hospital, University of Toronto
| | - Brendan C Dickson
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital
- Department of Pathobiology and Laboratory Medicine, University of Toronto
| | - Arno Dimmler
- Institut und Gemeinschaftspraxis für Pathologie, ViDia Christliche Kliniken Karlsruhe, Karlsruhe
| | - Wolfgang Hartmann
- Gerhard-Domagk-Institute of Pathology, Münster University Hospital
- Division of Translational Pathology, Gerhard-Domagk-Institute of Pathology, Münster University Hospital, Münster
| | - Marick Laé
- Department of Pathology, Centre Henri Becquerel, INSERM U1245, Université Rouen Normandie, Rouen
| | - Jessica Pablik
- Department of Pathology, University Hospital Dresden, Dresden, Germany
| | - Christoph Schubart
- Institute of Pathology, Erlangen University Hospital, Comprehensive Cancer Center, European Metropolitan Area Erlangen-Nuremberg (CCC ER-EMN), Friedrich Alexander University of Erlangen-Nuremberg, Erlangen
| | - Alena Skálová
- Department of Pathology, Charles University, Faculty of Medicine in Plzen
- Bioptic Laboratory Ltd, Plzen, Czech Republic
| | - Robert Stoehr
- Institute of Pathology, Erlangen University Hospital, Comprehensive Cancer Center, European Metropolitan Area Erlangen-Nuremberg (CCC ER-EMN), Friedrich Alexander University of Erlangen-Nuremberg, Erlangen
| | - Marcel Trautmann
- Gerhard-Domagk-Institute of Pathology, Münster University Hospital
- Division of Translational Pathology, Gerhard-Domagk-Institute of Pathology, Münster University Hospital, Münster
| | - Eva Wardelmann
- Gerhard-Domagk-Institute of Pathology, Münster University Hospital
| | - Michel Wassef
- Department of Pathology, Hôpital Lariboisière, Paris, France
| | - Ilan Weinreb
- Laboratory Medicine Program, University Health Network, Toronto General Hospital, Toronto, ON, Canada
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10
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Duncavage EJ, Coleman JF, de Baca ME, Kadri S, Leon A, Routbort M, Roy S, Suarez CJ, Vanderbilt C, Zook JM. Recommendations for the Use of in Silico Approaches for Next-Generation Sequencing Bioinformatic Pipeline Validation: A Joint Report of the Association for Molecular Pathology, Association for Pathology Informatics, and College of American Pathologists. J Mol Diagn 2023; 25:3-16. [PMID: 36244574 DOI: 10.1016/j.jmoldx.2022.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/21/2022] Open
Abstract
In silico approaches for next-generation sequencing (NGS) data modeling have utility in the clinical laboratory as a tool for clinical assay validation. In silico NGS data can take a variety of forms, including pure simulated data or manipulated data files in which variants are inserted into existing data files. In silico data enable simulation of a range of variants that may be difficult to obtain from a single physical sample. Such data allow laboratories to more accurately test the performance of clinical bioinformatics pipelines without sequencing additional cases. For example, clinical laboratories may use in silico data to simulate low variant allele fraction variants to test the analytical sensitivity of variant calling software or simulate a range of insertion/deletion sizes to determine the performance of insertion/deletion calling software. In this article, the Working Group reviews the different types of in silico data with their strengths and limitations, methods to generate in silico data, and how data can be used in the clinical molecular diagnostic laboratory. Survey data indicate how in silico NGS data are currently being used. Finally, potential applications for which in silico data may become useful in the future are presented.
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Affiliation(s)
- Eric J Duncavage
- In Silico Pipeline Validation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
| | - Joshua F Coleman
- In Silico Pipeline Validation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Monica E de Baca
- In Silico Pipeline Validation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Pacific Pathology Partners, Seattle, Washington
| | - Sabah Kadri
- In Silico Pipeline Validation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Anne and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Annette Leon
- In Silico Pipeline Validation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Color Health, Burlingame, California
| | - Mark Routbort
- In Silico Pipeline Validation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas
| | - Somak Roy
- In Silico Pipeline Validation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Cincinnati Children's Hospital, Cincinnati, Ohio
| | - Carlos J Suarez
- In Silico Pipeline Validation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Stanford University, Palo Alto, California
| | - Chad Vanderbilt
- In Silico Pipeline Validation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Justin M Zook
- In Silico Pipeline Validation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Biomarker and Genomic Sciences Group, National Institute of Standards and Technology, Gaithersburg, Maryland
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11
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Sources of Cancer Neoantigens beyond Single-Nucleotide Variants. Int J Mol Sci 2022; 23:ijms231710131. [PMID: 36077528 PMCID: PMC9455963 DOI: 10.3390/ijms231710131] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
The success of checkpoint blockade therapy against cancer has unequivocally shown that cancer cells can be effectively recognized by the immune system and eliminated. However, the identity of the cancer antigens that elicit protective immunity remains to be fully explored. Over the last decade, most of the focus has been on somatic mutations derived from non-synonymous single-nucleotide variants (SNVs) and small insertion/deletion mutations (indels) that accumulate during cancer progression. Mutated peptides can be presented on MHC molecules and give rise to novel antigens or neoantigens, which have been shown to induce potent anti-tumor immune responses. A limitation with SNV-neoantigens is that they are patient-specific and their accurate prediction is critical for the development of effective immunotherapies. In addition, cancer types with low mutation burden may not display sufficient high-quality [SNV/small indels] neoantigens to alone stimulate effective T cell responses. Accumulating evidence suggests the existence of alternative sources of cancer neoantigens, such as gene fusions, alternative splicing variants, post-translational modifications, and transposable elements, which may be attractive novel targets for immunotherapy. In this review, we describe the recent technological advances in the identification of these novel sources of neoantigens, the experimental evidence for their presentation on MHC molecules and their immunogenicity, as well as the current clinical development stage of immunotherapy targeting these neoantigens.
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12
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Snow JT, Georgantzoglou N, Green DC, Parra O, LeBlanc RE, Yan S, Sriharan A, Momtahen S, Winnick KN, Dimonitsas E, Stavrianos S, Lakiotaki E, Korkolopoulou P, Revelos K, Guo R, Linos K. Molecular analysis of NUT-positive poromas and porocarcinomas identifies novel break points of YAP1::NUTM1 fusions. J Cutan Pathol 2022; 49:850-858. [PMID: 35665951 DOI: 10.1111/cup.14265] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Poromas, and their malignant counterparts, porocarcinomas, harbor recurrent translocations involving YAP1-MAML2, YAP1-NUTM1, and infrequently WWTR1-NUTM1; YAP1-NUTM1 being the most common in porocarcinomas. NUT immunohistochemistry (IHC) can be used to identify NUTM1-translocated tumors. This study sought to investigate potential novel NUTM1-fusion partners among NUT IHC-positive poromas and porocarcinomas. METHODS 13 NUT IHC-positive poroid tumors (4 poromas, 9 porocarcinomas) were identified within a multi-institutional international cohort. Next Generation Sequencing (NGS) assessed for NUTM1 fusion partners. RESULTS NGS detected a NUTM1 fusion in 12/13 cases: YAP1-NUTM1 (11/12 cases) and WWTR1-NUTM1 (1/12 cases). Two of the cases (2/12) with NUTM1 fusion were not called by the NGS algorithm but had at least one read spanning YAP1-NUTM1 breakpoints upon manual review. A NUTM1 fusion was not identified in one case, however, the sample had low RNA quality. The following fusion events were identified: YAP1 exon 4 :: NUTM1 exon 3 in six cases, YAP1 exon 6 :: NUTM1 exon 2 in one case, YAP1 exon 3 :: NUTM1 exon 3 in three cases, WWTR1 exon 3 :: NUTM1 exon 3 in one case and YAP1 exon 8 :: NUTM1 exon 3 fusion in one case. CONCLUSION While no novel NUTM1 fusion partners were identified within our cohort, twelve of thirteen cases had discoverable NUTM1 fusions; YAP1-NUTM1 fusion was detected in 11 cases (92%) and WWTR1-NUTM1 in 1 case (8%). These data corroborate findings from other recent investigations and further substantiate the utility of NUT IHC in diagnosing a subset of poroid neoplasms. Additionally, two of our cases harbored fusions of YAP1 exon 6 to NUTM1 exon 3 and YAP1 exon 8 to NUTM1 exon 2, which have not been reported before in poroid neoplasms and indicate novel break points of YAP1.
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Affiliation(s)
- Justin T Snow
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH
| | - Natalia Georgantzoglou
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH
| | - Donald C Green
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH
| | - Ourania Parra
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH
| | - Robert E LeBlanc
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH.,Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Shaofeng Yan
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH.,Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Aravindhan Sriharan
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH.,Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Shabnam Momtahen
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH.,Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Kimberley N Winnick
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH
| | - Emmanouil Dimonitsas
- Department of plastic surgery, Greek Anticancer Institute, Saint Savvas Hospital, Athens, Greece
| | - Spiros Stavrianos
- Department of plastic surgery, Greek Anticancer Institute, Saint Savvas Hospital, Athens, Greece
| | - Eleftheria Lakiotaki
- First department of pathology, Medical school, National and Kapodistrian University of Athens, Athens, Greece
| | - Penelope Korkolopoulou
- First department of pathology, Medical school, National and Kapodistrian University of Athens, Athens, Greece
| | - Kyriakos Revelos
- Department of Pathology, 251 General Airforce Hospital, Athens, Greece
| | - Ruifeng Guo
- Department of Laboratory Medicine and Pathology, Department of Dermatology, Mayo Clinic, Rochester, MN
| | - Konstantinos Linos
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH.,Geisel School of Medicine at Dartmouth, Hanover, NH
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