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Torous VF, Jitpasutham T, Baloch Z, Cantley RL, Kerr DA, Liu X, Maleki Z, Merkin R, Nosé V, Pantanowitz L, Resta IT, Rossi ED, Faquin WC. Cytologic features of differentiated high-grade thyroid carcinoma: A multi-institutional study of 40 cases. Cancer Cytopathol 2024. [PMID: 38873907 DOI: 10.1002/cncy.22874] [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: 02/04/2024] [Revised: 04/04/2024] [Accepted: 04/29/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Differentiated high-grade thyroid carcinoma (DHGTC) is recently recognized by the World Health Organization (WHO) as a subgroup of thyroid carcinomas with high-grade features while retaining the architectural and/or cytologic features of well-differentiated follicular-cell-derived tumors. The cytomorphology of DHGTC is not well documented despite potential implications for patient triage and management. METHODS The pathology archives of six institutions were searched for cases diagnosed on resection as "high-grade thyroid carcinoma" using WHO criteria. The fine-needle aspiration (FNA) cohort represents a 10-year period (2013-2023); all were reviewed to confirm DHGTC classification. The corresponding FNAs were assessed for 32 cytomorphologic features. RESULTS Forty cases of DHGTC with prior FNA were identified. The mean patient age was 64.2 years. The average lesion size was 4.9 cm, and the majority demonstrated a TI-RADS score of 4 or 5 (95.2%). Three main high-grade subsets of DHGTC based on corresponding histology included papillary thyroid carcinoma (65%), follicular carcinoma (22.5%), and oncocytic carcinoma (12.5%). Over 97% of FNA cases were classified as Bethesda category IV or above. Approximately 25% of DHGTC showed cytologic features that included marked cytologic atypia, increased anisonucleosis, large oval nuclei, mitotic activity, or necrosis (p < .05); 68% of DHGTC cases were associated with high-risk molecular alterations. TERT mutations occurred in 41%, of which 89% of these were associated with a second mutation, usually RAS or BRAF p.V600E. CONCLUSIONS Cytology has a low sensitivity for DHGTC, although a subset of DHGTCs have cytologic features raising the possibility of a high-grade thyroid carcinoma. Other findings include high-risk molecular changes and clinicopathologic features such as older patient age and larger lesion size.
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Affiliation(s)
- Vanda F Torous
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Tikamporn Jitpasutham
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pathology, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Zubair Baloch
- Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Richard L Cantley
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Darcy A Kerr
- Department of Pathology and Laboratory Medicine, Dartmouth Health and Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Xiaoying Liu
- Department of Pathology and Laboratory Medicine, Dartmouth Health and Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Zahra Maleki
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ross Merkin
- Department of Medicine, Division of Hematology and Oncology, Mass General Cancer Center, Massachusetts General Hospital and Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Vania Nosé
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Liron Pantanowitz
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Isabella Tondi Resta
- Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Esther D Rossi
- Division of Anatomic Pathology and Histology, Catholic University of Sacred Heart, "Agostino Gemelli" School of Medicine, Rome, Italy
| | - William C Faquin
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
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Cheong TC, Jang A, Wang Q, Leonardi GC, Ricciuti B, Alessi JV, Di Federico A, Awad MM, Lehtinen MK, Harris MH, Chiarle R. Mechanistic patterns and clinical implications of oncogenic tyrosine kinase fusions in human cancers. Nat Commun 2024; 15:5110. [PMID: 38877018 PMCID: PMC11178778 DOI: 10.1038/s41467-024-49499-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
Tyrosine kinase (TK) fusions are frequently found in cancers, either as initiating events or as a mechanism of resistance to targeted therapy. Partner genes and exons in most TK fusions are followed typical recurrent patterns, but the underlying mechanisms and clinical implications of these patterns are poorly understood. By developing Functionally Active Chromosomal Translocation Sequencing (FACTS), we discover that typical TK fusions involving ALK, ROS1, RET and NTRK1 are selected from pools of chromosomal rearrangements by two major determinants: active transcription of the fusion partner genes and protein stability. In contrast, atypical TK fusions that are rarely seen in patients showed reduced protein stability, decreased downstream oncogenic signaling, and were less responsive to inhibition. Consistently, patients with atypical TK fusions were associated with a reduced response to TKI therapies. Our findings highlight the principles of oncogenic TK fusion formation and selection in cancers, with clinical implications for guiding targeted therapy.
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Affiliation(s)
- Taek-Chin Cheong
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Ahram Jang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Qi Wang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Giulia C Leonardi
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123, Catania, Italy
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Joao V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | | | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Maria K Lehtinen
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
- Division of Hematopathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy.
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Jitpasutham T, Andrianus S, Gubbiotti M, Nosé V, Baloch ZW, Madrigal E, Faquin WC. Thyroid nodules with DICER1 mutation or PTEN alteration: A comparative cytologic, clinical, and molecular study of 117 FNA cases. Cancer Cytopathol 2024; 132:370-385. [PMID: 38558329 DOI: 10.1002/cncy.22811] [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: 10/29/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND DICER1 mutations and PTEN alterations are increasingly detected by thyroid fine-needle aspiration (FNA). Both are associated with nodular thyroid disease and cancer. The authors analyzed a large comparative thyroid FNA cohort with DICER1 mutation or PTEN alteration. METHODS A total of 117 thyroid FNAs with DICER1 or PTEN alterations were retrieved from the databases of two academic medical institutions. Demographic, clinical, and radiologic data were collected; FNA slides were analyzed for 29 cytomorphologic features. RESULTS Of 117 thyroid FNAs, 36 (30.8%) had DICER1 mutation and 81 (69.2%) showed PTEN alteration. The DICER1 cohort had 33 (91.7%) females and three (8.3%) males (mean, 40.9 years); 61.8% had multinodular disease. FNAs were classified as atypia of undetermined significance (AUS), 23 (63.9%); follicular neoplasm (FN), 12 (33.3%); and malignant, 1 (2.8%). The PTEN subgroup had 66 (81.5%) females and 15 (18.5%) males (mean, 55.2 years) with increased multinodular disease (93.8%, p = .0016). PTEN FNAs had greater cytologic diversity: non-diagnostic, 2 (2.5%); benign, 5 (6.2%); AUS, 44 (54.3%); FN, 24 (29.6%); and malignant, 6 (7.4%). Both DICER1 and PTEN cases showed a range of resected tumor subtypes. The DICER1 cohort included thyroblastoma, and the PTEN group included anaplastic carcinoma. The cytomorphology of DICER1 and PTEN cases showed overlapping features, especially microfollicular patterns. Minor cytomorphologic differences included papillary patterns in DICER1 (p = .039), and oncocytic changes (p < .0001) in PTEN. CONCLUSIONS DICER1 and PTEN FNAs reveal many cytologic similarities. DICER1 patients are younger, and PTEN patients had multinodular disease. Awareness of these genetic cohorts can identify patients at risk for thyroid cancer.
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Affiliation(s)
- Tikamporn Jitpasutham
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Faculty of Medicine, Department of Pathology, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Stefen Andrianus
- Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maria Gubbiotti
- Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Vania Nosé
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Zubair W Baloch
- Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emilio Madrigal
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - William C Faquin
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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Miyashita Y, Hirotsu Y, Nagakubo Y, Kobayashi H, Kawaguchi M, Hata K, Saito R, Kakizaki Y, Tsutsui T, Oyama T, Omata M. Brief Report: Tepotinib as a Treatment Option in MET Exon 14 Skipping-Positive Lung Cancers-Investigating Discordance Between ArcherMET and the Oncomine Dx Target Test. JTO Clin Res Rep 2024; 5:100679. [PMID: 38841537 PMCID: PMC11150947 DOI: 10.1016/j.jtocrr.2024.100679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 06/07/2024] Open
Abstract
Introduction NSCLC is a leading cause of cancer-related mortality worldwide. Specific genetic alterations, such as MET exon 14 (METex14) skipping, have been identified in NSCLC, allowing targeted therapy. Tepotinib, a highly selective MET inhibitor, has displayed promise in patients with advanced NSCLC. Nevertheless, challenges arise when identifying treatment strategies for patients with discordant results regarding METex14 skipping detection between diagnostic tests. Methods We investigated patients with NSCLC and discordant results for METex14 skipping between the Oncomine Dx Target Test (ODxTT) and ArcherMET. Clinical response, adverse events, and the duration of tepotinib treatment were assessed, and statistical analysis was performed. Results Among the 19 patients deemed METex14 skipping positive by ODxTT, only 10 had concordant results with ArcherMET. The number of METex14 skipping reads detected by ODxTT was significantly lower in discordant cases. Of the 19 patients, 14 received tepotinib, and comparable response and disease control rates were observed in both concordant and discordant cases. The duration of treatment did not significantly differ between the two groups. Conclusions Our findings suggest that tepotinib has comparable therapeutic effects in patients with METex14 skipping-positive NSCLC irrespective of the concordance of results between ODxTT and ArcherMET. Tepotinib is a possible treatment option for patients with METex14 skipping, even in patients with discordant test results.
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Affiliation(s)
- Yoshihiro Miyashita
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yuki Nagakubo
- Division of Genetics and Clinical Laboratory, Yamanashi Central Hospital, Yamanashi, Japan
| | - Hiroaki Kobayashi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Makoto Kawaguchi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Koki Hata
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Ryota Saito
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yumiko Kakizaki
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Toshiharu Tsutsui
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Toshio Oyama
- Pathology Division, Laboratory Department, Yamanashi Central Hospital, Yamanashi, Japan
| | - Masao Omata
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
- The University of Tokyo, Tokyo, Japan
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5
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Dong F. Pan-Cancer Molecular Biomarkers: A Paradigm Shift in Diagnostic Pathology. Clin Lab Med 2024; 44:325-337. [PMID: 38821647 DOI: 10.1016/j.cll.2023.08.013] [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] [Indexed: 06/02/2024]
Abstract
The rapid adoption of next-generation sequencing in clinical oncology has enabled the detection of molecular biomarkers shared between multiple tumor types. These pan-cancer biomarkers include sequence-altering mutations, copy number changes, gene rearrangements, and mutational signatures and have been demonstrated to predict response to targeted therapy. This article reviews issues surrounding current and emerging pan-cancer molecular biomarkers in clinical oncology: technological advances that enable the broad detection of cancer mutations across hundreds of genes, the spectrum of driver and passenger mutations derived from human cancer genomes, and implications for patient care now and in the near future.
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Affiliation(s)
- Fei Dong
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Ave, Palo Alto, CA 94304, USA.
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6
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Devins KM, Baranov E, Hung YP, Dickson BC, Oliva E, Deshpande V. Large and Extensive Multilocular Peritoneal Inclusion Cysts Lack Genomic Alterations and Follow an Indolent Clinical Course Despite Rare Recurrences. Am J Surg Pathol 2024:00000478-990000000-00362. [PMID: 38813820 DOI: 10.1097/pas.0000000000002249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Peritoneal inclusion cysts (PICs) are unilocular or multilocular cystic lesions lined by bland mesothelial cells. While most are small and localized, rare examples may be large or multifocal with diffuse peritoneal involvement, causing clinical and even pathologic concern for malignancy. We examined 20 PIC, including 8 large solitary and 12 multifocal lesions. Solitary PIC were found in 7 female and 1 male patients ranging from 19 to 55 (median: 37) years. Expanded collagenous (n=2) or edematous (n=1) areas were occasionally seen in the septae, and 1 had microscopic foci of myxoid stroma. Four had hobnail cells, and 1 had minor areas of papillary mesothelial hyperplasia. Multifocal PICs occurred in 9 female and 3 male patients ranging from 26 to 80 (median: 53) years. Three showed extensive associated fibrosis with entrapment of preexisting adipose tissue, 2 had areas resembling granulation tissue, and 3 had scattered foci of myxoid stroma. Hobnail cells were present in 9, papillary mesothelial hyperplasia in 2, entrapped single cells in 1, and 2 had areas resembling adenomatoid tumors. Two of the multifocal PICs had limited local recurrences at 18 and 21 months. No patients died of disease. Clonal alterations were not identified in any of the tested PICs (mutational and fusion analysis in 5, chromosomal microarray in 1). Despite limited local recurrences, we demonstrate that even large and multifocal PICs may lack identifiable genomic alterations and are associated with benign outcomes.
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Affiliation(s)
- Kyle M Devins
- James Homer Wright Pathology Laboratories, Massachusetts General Hospital
| | - Esther Baranov
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Yin P Hung
- James Homer Wright Pathology Laboratories, Massachusetts General Hospital
| | - Brendan C Dickson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital
- Department of Laboratory Medicine and Pathobiology, University of Toronto; Toronto, Ontario, Canada
| | - Esther Oliva
- James Homer Wright Pathology Laboratories, Massachusetts General Hospital
| | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
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7
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Cornejo KM, Goyal A, Valencia Guerrero A, Astudillo M, Dias-Santagata D, Johnson MM, Feldman AS, Hoang MP. Clinicopathological and Molecular Features of Penile Melanoma With a Proposed Staging System. Am J Surg Pathol 2024:00000478-990000000-00361. [PMID: 38808927 DOI: 10.1097/pas.0000000000002247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Penile melanomas (PM) are an exceedingly rare subtype of mucosal melanoma (MM), and we reviewed the clinicopathologic features and molecular profile in 8 PMs. The patient ages ranged from 46 to 78 (mean: 62.8) years with involvement on the glans (n=5; 62.5%), penile urethra (n=2; 25%), and foreskin (n=1, 12.5%). Tumor depth ranged from 1.6 to 10.0 (mean: 5.25) mm. Most of the patients underwent partial penectomy (n=6; 75%) and sentinel lymph node (LN) biopsy N=7; 87.5%). Seven patients had metastatic disease at diagnosis, 6 involving LNs and 1 the adrenal gland, and 4 died of disease with a mean follow-up period of 40.5 (2 to 95) months. Five of 7 (71%) cases identified 15 molecular alterations within KIT, CDKN2A, NF1, PTEN, and APC (n=2 each), and NRAS, MAP3K1, CDH1, MSH6, and TERT (n=1 each). Two cases were not found to harbor genetic aberrations, and 1 case failed testing. In addition, we reviewed the English literature and included 93 cases with a reported depth of invasion and follow-up. A total of 101 PMs were analyzed for prognostic parameters, and the overall survival was significantly worse in patients with LN metastasis (P=0.0008), distant metastasis (P=0.0016), and greater depth of invasion (P=0.0222) based upon T-stage. While T4 conferred substantially worse survival, the delineation of the survival curves between T2 and T3 was less clear, and combining T2+T3 disease had a strong prognostic impact (P=0.0024). Prognostic parameters used in the staging of cutaneous melanomas may also be used in PMs. An alternative staging system expanding the inclusion criteria for T2 might provide a more accurate prognostic stratification.
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Affiliation(s)
- Kristine M Cornejo
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Amrita Goyal
- Department of Dermatology, University of Minnesota, Minneapolis, MN
| | | | | | - Dora Dias-Santagata
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | | | - Adam S Feldman
- Department of Urology, Massachusetts General Hospital, Boston, MA
| | - Mai P Hoang
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
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8
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Blommel JH, Roforth MM, Jerde CR, Karsten CA, Bridgeman AR, Voss JS, Boccuto L, Ivankovic DS, Sarasua SM, Kipp BR, Murphy SJ. Evaluating User Experience and DNA Yield from Self-Collection Devices. J Appl Lab Med 2024:jfae030. [PMID: 38767175 DOI: 10.1093/jalm/jfae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/01/2024] [Indexed: 05/22/2024]
Abstract
BACKGROUND The COVID-19 pandemic emphasized an urgent need for devices used in the self-collection of biospecimens in an evolving patient care system. The mailing of biospecimen self-collection kits to patients, with samples returned via mail, provides a more convenient testing regimen, but could also impart patient sampling variabilities. User compliance with device directions is central to downstream testing of collected biospecimens and clear instructions are central to this goal. METHODS Here, we performed an evaluation of 10 oral DNA collection devices involving either swab or saliva self-collection and analyzed ease of use and comfort level with a device, as well as DNA recovery quantity/quality and sample stability. RESULTS We show that while these DNA quality/quantity metrics are comparable between devices, users prefer direct saliva collection over swab-based devices. CONCLUSIONS This information is useful in guiding future experiments including their use in human RNA, microbial, or viral sample collection/recovery and their use in clinical testing.
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Affiliation(s)
- Joseph H Blommel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC, United States
| | - Matthew M Roforth
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Calvin R Jerde
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Carley A Karsten
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Amber R Bridgeman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Jesse S Voss
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Luigi Boccuto
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC, United States
| | - Diana S Ivankovic
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC, United States
| | - Sara M Sarasua
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC, United States
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Stephen J Murphy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
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Schmitt AD, Sikkink K, Ahmed AA, Melnyk S, Reid D, Van Meter L, Guest EM, Lansdon LA, Pastinen T, Pushel I, Yoo B, Farooqi MS. Evaluation of Hi-C sequencing for the detection of gene fusions in hematologic and solid pediatric cancer samples. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.10.24306838. [PMID: 38765974 PMCID: PMC11100933 DOI: 10.1101/2024.05.10.24306838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome and has shown promise in detecting genomic rearrangements in translational research studies. To evaluate HiC as a potential clinical diagnostic platform, analytical concordance with routine laboratory testing was assessed using primary pediatric leukemia and sarcoma specimens previously positive for clinically significant genomic rearrangements. Archived specimen types tested included viable and nonviable frozen leukemic cells, as well as formalin-fixed paraffin-embedded (FFPE) tumor tissues. Initially, pediatric acute myeloid leukemia (AML) and alveolar rhabdomyosarcoma (A-RMS) specimens with known genomic rearrangements were subjected to HiC analysis to assess analytical concordance. Subsequently, a discovery cohort consisting of AML and acute lymphoblastic leukemia (ALL) cases with no known genomic rearrangements based on prior clinical diagnostic testing were evaluated to determine whether HiC could detect rearrangements. Using a standard sequencing depth of 50 million raw read-pairs per sample, or approximately 5X raw genomic coverage, 100% concordance was observed between HiC and previous clinical cytogenetic and molecular testing. In the discovery cohort, a clinically relevant gene fusion was detected in 45% of leukemia cases (5/11). This study demonstrates the value of HiC sequencing to medical diagnostic testing as it identified several clinically significant rearrangements, including those that might have been missed by current clinical testing workflows. Key points HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome, facilitating detection of genomic rearrangements.HiC was 100% concordant with clinical diagnostic testing workflows for detecting clinically significant genomic rearrangements in pediatric leukemia and rhabdomyosarcoma specimens.HiC detected clinically significant genomic rearrangements not previously detected by prior clinical cytogenetic and molecular testing.HiC performed well with archived non-viable and viable frozen leukemic cell samples, as well as archived formalin-fixed paraffin-embedded tumor tissue specimens.
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10
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Tsai HK, Sabbagh MF, Montesion M, Williams EA, Arbini A, Boué DR, Harris EM, Wachter F, Grimmett L, Place AE, Lucas F, Nardi V, Kim AS, Brugnara C, Degar B, Pollard J, Harris MH, Bledsoe JR. Acute Promyelocytic Leukemia With Torque Teno Mini Virus::RARA Fusion: An Approach to Screening and Diagnosis. Mod Pathol 2024; 37:100509. [PMID: 38704030 DOI: 10.1016/j.modpat.2024.100509] [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: 03/22/2024] [Accepted: 04/20/2024] [Indexed: 05/06/2024]
Abstract
Acute promyelocytic leukemia (APL) with variant RARA translocation is linked to over 15 partner genes. Recent publications encompassing 6 cases have expanded the spectrum of RARA partners to torque teno mini virus (TTMV). This entity is likely underrecognized due to the lack of clinician and pathologist familiarity, inability to detect the fusion using routine testing modalities, and informatic challenges in its recognition within next-generation sequencing (NGS) data. We describe a clinicopathologic approach and provide the necessary tools to screen and diagnose APL with TTMV::RARA using existing clinical DNA- or RNA-based NGS assays, which led to the identification of 4 cases, all without other known cytogenetic/molecular drivers. One was identified prospectively and 3 retrospectively, including 2 from custom automated screening of multiple data sets (50,257 cases of hematopoietic malignancy, including 4809 acute myeloid leukemia/myeloid sarcoma/APL cases). Two cases presented as myeloid sarcoma, including 1 with multiple relapses after acute myeloid leukemia-type chemotherapy and hematopoietic stem cell transplant. Two cases presented as leukemia, had a poor response to induction chemotherapy, but achieved remission upon reinduction (including all-trans retinoic acid in 1 case) and subsequent hematopoietic stem cell transplant. Neoplastic cells demonstrated features of APL including frequent azurophilic granules and dim/absent CD34 and HLA-DR expression. RARA rearrangement was not detected by karyotype or fluorescent in situ hybridization. Custom analysis of NGS fusion panel data identified TTMV::RARA rearrangements and, in the prospectively identified case, facilitated monitoring in sequential bone marrow samples. APL with TTMV::RARA is a rare leukemia with a high rate of treatment failure in described cases. The diagnosis should be considered in leukemias with features of APL that lack detectable RARA fusions and other drivers, and may be confirmed by appropriate NGS tests with custom informatics. Incorporation of all-trans retinoic acid may have a role in treatment but requires accurate recognition of the fusion for appropriate classification as APL.
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Affiliation(s)
- Harrison K Tsai
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mark F Sabbagh
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Erik A Williams
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center, and Jackson Memorial Hospitals, Miami, Florida; Foundation Medicine Inc, Boston, Massachusetts
| | - Arnaldo Arbini
- Department of Pathology, NYU Grossman School of Medicine, New York City, New York
| | - Daniel R Boué
- Department of Pathology & Laboratory Medicine, Nationwide Children's Hospital and The Ohio State University, Columbus, Ohio
| | - Emily M Harris
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Franziska Wachter
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Leslie Grimmett
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andrew E Place
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Fabienne Lucas
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Annette S Kim
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Barbara Degar
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Jessica Pollard
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jacob R Bledsoe
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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11
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Zhang ML, Kwan MC, Pitman MB. Grading Cytologic Epithelial Atypia in Pancreatic Mucinous Cysts Predicts Patient Survival: Correlation With Histologic, Molecular, and Clinical Follow-Up. Mod Pathol 2024; 37:100510. [PMID: 38705280 DOI: 10.1016/j.modpat.2024.100510] [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: 11/22/2023] [Revised: 04/08/2024] [Accepted: 04/26/2024] [Indexed: 05/07/2024]
Abstract
Cytologic examination of epithelial cells in cyst fluids from pancreatic mucinous cysts is the optimal method for identifying high-grade atypia (HGA), which may represent histologic high-grade dysplasia (HGD) or invasive carcinoma and thereby classify the cyst as high risk, warranting surgical resection. Cytologic features of HGA were previously described at our institution in 2013 and implemented thereafter, but performance of grading with these criteria has not yet been reported. In total, 1322 pancreatic cyst fluid specimens (2014-2021) were identified; all pathology reports and relevant clinical data were reviewed in detail; and 230 unique cysts (217 patients) contained neoplastic mucinous epithelium. Of the 230 cysts, 178 had low-grade atypia (LGA), and 52 had HGA. Ninety-seven cysts had histologic follow-up: 77 (79%) were resections and 20 (21%) were diagnostic surgical biopsies only. Moreover, 92 (95%) were confirmed neoplastic mucinous cysts, 3 were adenocarcinomas, and 2 were benign entities. Among histologically confirmed neoplastic mucinous cysts, 58 had low-grade dysplasia (LGD); 34 had HGD, of which 14 also had invasive carcinoma. A significantly higher proportion of cysts with HGA (63%) demonstrated at least HGD on follow-up compared to those with LGA (26%, P < .001). The sensitivity and specificity of HGA for accurately classifying a high-risk cyst were 54% and 81%, respectively. Of the 230 cysts, 146 (64%) cysts had corresponding next-generation sequencing results; 31% of HGA cysts harbored a high-risk mutation (TP53, CDKN2A, and/or SMAD4) vs 7% of LGA cysts (P < .001). Among cysts without histologic confirmation, 25% of HGA cysts had high-risk mutation vs 7% of LGA cysts. The grade of cytologic atypia was predictive of overall survival and recurrence-free survival (P < .001 and P = .020, respectively). Implementation of cytologic criteria for HGA in pancreatic mucinous cysts has relatively low sensitivity but modest specificity for classifying a high-risk cyst. Although high-risk mutations were more commonly found in cysts with HGA, their frequency is overall low. Thus, evaluating the degree of cytologic atypia, which is predictive of patient survival, provides significant value and informs patient outcomes.
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Affiliation(s)
- M Lisa Zhang
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Melanie C Kwan
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Martha B Pitman
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
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12
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Zago Baltazar R, Claerhout S, Vander Borght S, Spans L, Sciot R, Schöffski P, Hompes D, Sinnaeve F, Wafa H, Renard M, van den Hout MFCM, Vernemmen A, Libbrecht L, De Roo A, Mazzeo F, van Marcke C, Deraedt K, Bourgain C, Vanden Bempt I. Recurrent and novel fusions detected by targeted RNA sequencing as part of the diagnostic workflow of soft tissue and bone tumours. J Pathol Clin Res 2024; 10:e12376. [PMID: 38738521 PMCID: PMC11089496 DOI: 10.1002/2056-4538.12376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/16/2024] [Accepted: 04/15/2024] [Indexed: 05/14/2024]
Abstract
The identification of gene fusions has become an integral part of soft tissue and bone tumour diagnosis. We investigated the added value of targeted RNA-based sequencing (targeted RNA-seq, Archer FusionPlex) to our current molecular diagnostic workflow of these tumours, which is based on fluorescence in situ hybridisation (FISH) for the detection of gene fusions using 25 probes. In a series of 131 diagnostic samples targeted RNA-seq identified a gene fusion, BCOR internal tandem duplication or ALK deletion in 47 cases (35.9%). For 74 cases, encompassing 137 FISH analyses, concordance between FISH and targeted RNA-seq was evaluated. A positive or negative FISH result was confirmed by targeted RNA-seq in 27 out of 49 (55.1%) and 81 out of 88 (92.0%) analyses, respectively. While negative concordance was high, targeted RNA-seq identified a canonical gene fusion in seven cases despite a negative FISH result. The 22 discordant FISH-positive analyses showed a lower percentage of rearrangement-positive nuclei (range 15-41%) compared to the concordant FISH-positive analyses (>41% of nuclei in 88.9% of cases). Six FISH analyses (in four cases) were finally considered false positive based on histological and targeted RNA-seq findings. For the EWSR1 FISH probe, we observed a gene-dependent disparity (p = 0.0020), with 8 out of 35 cases showing a discordance between FISH and targeted RNA-seq (22.9%). This study demonstrates an added value of targeted RNA-seq to our current diagnostic workflow of soft tissue and bone tumours in 19 out of 131 cases (14.5%), which we categorised as altered diagnosis (3 cases), added precision (6 cases), or augmented spectrum (10 cases). In the latter subgroup, four novel fusion transcripts were found for which the clinical relevance remains unclear: NAB2::NCOA2, YAP1::NUTM2B, HSPA8::BRAF, and PDE2A::PLAG1. Overall, targeted RNA-seq has proven extremely valuable in the diagnostic workflow of soft tissue and bone tumours.
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Affiliation(s)
| | - Sofie Claerhout
- Department of Human GeneticsUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Sara Vander Borght
- Department of Human GeneticsUniversity Hospitals KU LeuvenLeuvenBelgium
- Department of PathologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Lien Spans
- Department of Human GeneticsUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Raphael Sciot
- Department of PathologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Patrick Schöffski
- Department of General Medical OncologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Daphne Hompes
- Department of Surgical OncologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Friedl Sinnaeve
- Department of Orthopaedic SurgeryUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Hazem Wafa
- Department of Orthopaedic SurgeryUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Marleen Renard
- Department of Paediatric Hemato‐OncologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Mari FCM van den Hout
- Department of PathologyMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Astrid Vernemmen
- Department of PathologyMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Louis Libbrecht
- Department of PathologyCliniques Universitaires Saint‐LucBrusselsBelgium
- Department of PathologyAZ GroeningeKortrijkBelgium
| | - An‐Katrien De Roo
- Department of PathologyCliniques Universitaires Saint‐LucBrusselsBelgium
- Institute of Experimental and Clinical ResearchUCLouvainBrusselsBelgium
| | - Filomena Mazzeo
- Institute of Experimental and Clinical ResearchUCLouvainBrusselsBelgium
- Breast ClinicKing Albert II Cancer Institute, Cliniques Universitaires Saint‐LucBrusselsBelgium
- Department of Medical OncologyKing Albert II Cancer Institute, Cliniques Universitaires Saint‐LucBrusselsBelgium
| | - Cédric van Marcke
- Institute of Experimental and Clinical ResearchUCLouvainBrusselsBelgium
- Breast ClinicKing Albert II Cancer Institute, Cliniques Universitaires Saint‐LucBrusselsBelgium
- Department of Medical OncologyKing Albert II Cancer Institute, Cliniques Universitaires Saint‐LucBrusselsBelgium
| | - Karen Deraedt
- Department of PathologyZiekenhuis Oost‐LimburgGenkBelgium
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13
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Lemmens M, Dorsheimer L, Zeller A, Dietz-Baum Y. Non-clinical safety assessment of novel drug modalities: Genome safety perspectives on viral-, nuclease- and nucleotide-based gene therapies. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 896:503767. [PMID: 38821669 DOI: 10.1016/j.mrgentox.2024.503767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/08/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
Gene therapies have emerged as promising treatments for various conditions including inherited diseases as well as cancer. Ensuring their safe clinical application requires the development of appropriate safety testing strategies. Several guidelines have been provided by health authorities to address these concerns. These guidelines state that non-clinical testing should be carried out on a case-by-case basis depending on the modality. This review focuses on the genome safety assessment of frequently used gene therapy modalities, namely Adeno Associated Viruses (AAVs), Lentiviruses, designer nucleases and mRNAs. Important safety considerations for these modalities, amongst others, are vector integrations into the patient genome (insertional mutagenesis) and off-target editing. Taking into account the constraints of in vivo studies, health authorities endorse the development of novel approach methodologies (NAMs), which are innovative in vitro strategies for genotoxicity testing. This review provides an overview of NAMs applied to viral and CRISPR/Cas9 safety, including next generation sequencing-based methods for integration site analysis and off-target editing. Additionally, NAMs to evaluate the oncogenicity risk arising from unwanted genomic modifications are discussed. Thus, a range of promising techniques are available to support the safe development of gene therapies. Thorough validation, comparisons and correlations with clinical outcomes are essential to identify the most reliable safety testing strategies. By providing a comprehensive overview of these NAMs, this review aims to contribute to a better understanding of the genome safety perspectives of gene therapies.
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Affiliation(s)
| | - Lena Dorsheimer
- Research and Development, Preclinical Safety, Sanofi, Industriepark Hoechst, Frankfurt am Main 65926, Germany.
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel 4070, Switzerland
| | - Yasmin Dietz-Baum
- Research and Development, Preclinical Safety, Sanofi, Industriepark Hoechst, Frankfurt am Main 65926, Germany
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14
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Hoskins I, Rao S, Tante C, Cenik C. Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression. Mol Syst Biol 2024; 20:481-505. [PMID: 38355921 PMCID: PMC11066095 DOI: 10.1038/s44320-024-00018-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Multiplexed assays of variant effect are powerful methods to profile the consequences of rare variants on gene expression and organismal fitness. Yet, few studies have integrated several multiplexed assays to map variant effects on gene expression in coding sequences. Here, we pioneered a multiplexed assay based on polysome profiling to measure variant effects on translation at scale, uncovering single-nucleotide variants that increase or decrease ribosome load. By combining high-throughput ribosome load data with multiplexed mRNA and protein abundance readouts, we mapped the cis-regulatory landscape of thousands of catechol-O-methyltransferase (COMT) variants from RNA to protein and found numerous coding variants that alter COMT expression. Finally, we trained machine learning models to map signatures of variant effects on COMT gene expression and uncovered both directional and divergent impacts across expression layers. Our analyses reveal expression phenotypes for thousands of variants in COMT and highlight variant effects on both single and multiple layers of expression. Our findings prompt future studies that integrate several multiplexed assays for the readout of gene expression.
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Affiliation(s)
- Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Charisma Tante
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
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15
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Wu Y, Guo J, Li W, Xiu X, Thirunavukarasu D, Wang Y, Wang K, Chen W, Yu Zhang D, Yang X, Fan C, Song P. Enhanced Detection of Novel Low-Frequency Gene Fusions via High-Yield Ligation and Multiplexed Enrichment Sequencing. Angew Chem Int Ed Engl 2024; 63:e202316484. [PMID: 38494435 DOI: 10.1002/anie.202316484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Panel-based methods are commonly employed for the analysis of novel gene fusions in precision diagnostics and new drug development in cancer. However, these methods are constrained by limitations in ligation yield and the enrichment of novel gene fusions with low variant allele frequencies. In this study, we conducted a pioneering investigation into the stability of double-stranded adapter DNA, resulting in improved ligation yield and enhanced conversion efficiency. Additionally, we implemented blocker displacement amplification, achieving a remarkable 7-fold enrichment of novel gene fusions. Leveraging the pre-enrichment achieved with this approach, we successfully applied it to Nanopore sequencing, enabling ultra-fast analysis of novel gene fusions within one hour with high sensitivity. This method offers a robust and remarkably sensitive mean of analyzing novel gene fusions, promising the discovery of pivotal biomarkers that can significantly improve cancer diagnostics and the development of new therapeutic strategies.
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Affiliation(s)
- Yi Wu
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinxiao Guo
- Shanghai Sixth People's Hospital Affiliated to, Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Wenjun Li
- NuProbe USA, Inc., 2575 West Bellfort Avenue, Ste. 200 Houston, TX 77054, USA
| | - Xuehao Xiu
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | | | - Yudong Wang
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Kai Wang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 322000, China
| | - Weiyu Chen
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 322000, China
| | - David Yu Zhang
- NuProbe USA, Inc., 2575 West Bellfort Avenue, Ste. 200 Houston, TX 77054, USA
| | - Xiurong Yang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ping Song
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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16
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Gremke N, Rodepeter FR, Teply-Szymanski J, Griewing S, Boekhoff J, Stroh A, Tarawneh TS, Riera-Knorrenschild J, Balser C, Hattesohl A, Middeke M, Ross P, Litmeyer AS, Romey M, Stiewe T, Wündisch T, Neubauer A, Denkert C, Wagner U, Mack EKM. NGS-Guided Precision Oncology in Breast Cancer and Gynecological Tumors-A Retrospective Molecular Tumor Board Analysis. Cancers (Basel) 2024; 16:1561. [PMID: 38672643 PMCID: PMC11048446 DOI: 10.3390/cancers16081561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Background: Precision oncology treatments are being applied more commonly in breast and gynecological oncology through the implementation of Molecular Tumor Boards (MTBs), but real-world clinical outcome data remain limited. Methods: A retrospective analysis was conducted in patients with breast cancer (BC) and gynecological malignancies referred to our center's MTB from 2018 to 2023. The analysis covered patient characteristics, next-generation sequencing (NGS) results, MTB recommendations, therapy received, and clinical outcomes. Results: Sixty-three patients (77.8%) had metastatic disease, and forty-four patients (54.3%) had previously undergone three or more lines of systemic treatment. Personalized treatment recommendations were provided to 50 patients (63.3%), while 29 (36.7%) had no actionable target. Ultimately, 23 patients (29.1%) underwent molecular-matched treatment (MMT). Commonly altered genes in patients with pan-gyn tumors (BC and gynecological malignancies) included TP53 (n = 42/81, 51.9%), PIK3CA (n = 18/81, 22.2%), BRCA1/2 (n = 10/81, 12.3%), and ARID1A (n = 9/81, 11.1%). Patients treated with MMT showed significantly prolonged progression-free survival (median PFS 5.5 vs. 3.5 months, p = 0.0014). Of all patients who underwent molecular profiling, 13.6% experienced a major clinical benefit (PFSr ≥ 1.3 and PR/SD ≥ 6 months) through precision oncology. Conclusions: NGS-guided precision oncology demonstrated improved clinical outcomes in a subgroup of patients with gynecological and breast cancers.
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Affiliation(s)
- Niklas Gremke
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
- Institute of Molecular Oncology, Philipps-University, 35043 Marburg, Germany;
| | - Fiona R. Rodepeter
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Julia Teply-Szymanski
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Sebastian Griewing
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
| | - Jelena Boekhoff
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
| | - Alina Stroh
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
- Institute of Molecular Oncology, Philipps-University, 35043 Marburg, Germany;
| | - Thomas S. Tarawneh
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
| | - Jorge Riera-Knorrenschild
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
| | - Christina Balser
- Practice for Internal Medicine, Hematology and Internal Oncology, 35043 Marburg, Germany;
| | - Akira Hattesohl
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Martin Middeke
- Comprehensive Cancer Center Marburg, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (M.M.); (T.W.)
| | - Petra Ross
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
| | - Anne-Sophie Litmeyer
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Marcel Romey
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Philipps-University, 35043 Marburg, Germany;
| | - Thomas Wündisch
- Comprehensive Cancer Center Marburg, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (M.M.); (T.W.)
| | - Andreas Neubauer
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
| | - Carsten Denkert
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Uwe Wagner
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
| | - Elisabeth K. M. Mack
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
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17
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Shen Y, Thng DKH, Wong ALA, Toh TB. Mechanistic insights and the clinical prospects of targeted therapies for glioblastoma: a comprehensive review. Exp Hematol Oncol 2024; 13:40. [PMID: 38615034 PMCID: PMC11015656 DOI: 10.1186/s40164-024-00512-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/08/2024] [Indexed: 04/15/2024] Open
Abstract
Glioblastoma (GBM) is a fatal brain tumour that is traditionally diagnosed based on histological features. Recent molecular profiling studies have reshaped the World Health Organization approach in the classification of central nervous system tumours to include more pathogenetic hallmarks. These studies have revealed that multiple oncogenic pathways are dysregulated, which contributes to the aggressiveness and resistance of GBM. Such findings have shed light on the molecular vulnerability of GBM and have shifted the disease management paradigm from chemotherapy to targeted therapies. Targeted drugs have been developed to inhibit oncogenic targets in GBM, including receptors involved in the angiogenic axis, the signal transducer and activator of transcription 3 (STAT3), the PI3K/AKT/mTOR signalling pathway, the ubiquitination-proteasome pathway, as well as IDH1/2 pathway. While certain targeted drugs showed promising results in vivo, the translatability of such preclinical achievements in GBM remains a barrier. We also discuss the recent developments and clinical assessments of targeted drugs, as well as the prospects of cell-based therapies and combinatorial therapy as novel ways to target GBM. Targeted treatments have demonstrated preclinical efficacy over chemotherapy as an alternative or adjuvant to the current standard of care for GBM, but their clinical efficacy remains hindered by challenges such as blood-brain barrier penetrance of the drugs. The development of combinatorial targeted therapies is expected to improve therapeutic efficacy and overcome drug resistance.
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Affiliation(s)
- Yating Shen
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Dexter Kai Hao Thng
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Andrea Li Ann Wong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Haematology-Oncology, National University Hospital, Singapore, Singapore
| | - Tan Boon Toh
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore, Singapore.
- The Institute for Digital Medicine (WisDM), National University of Singapore, Singapore, Singapore.
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18
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Friedman JS, Durham BH, Reiner AS, Yabe M, Petrova-Drus K, Dogan A, Pulitzer M, Busam KJ, Francis JH, Rampal RK, Ulaner GA, Reddy R, Yeh R, Hatzoglou V, Lacouture ME, Rotemberg V, Mazor RD, Hershkovitz-Rokah O, Shpilberg O, Goyal G, Go RS, Abeykoon JP, Rech K, Morlote D, Fidai S, Gannamani V, Zia M, Abdel-Wahab O, Panageas KS, Rosenblum MK, Diamond EL. Mixed histiocytic neoplasms: A multicentre series revealing diverse somatic mutations and responses to targeted therapy. Br J Haematol 2024. [PMID: 38613141 DOI: 10.1111/bjh.19462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/14/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024]
Abstract
Histiocytic neoplasms are diverse clonal haematopoietic disorders, and clinical disease is mediated by tumorous infiltration as well as uncontrolled systemic inflammation. Individual subtypes include Langerhans cell histiocytosis (LCH), Rosai-Dorfman-Destombes disease (RDD) and Erdheim-Chester disease (ECD), and these have been characterized with respect to clinical phenotypes, driver mutations and treatment paradigms. Less is known about patients with mixed histiocytic neoplasms (MXH), that is two or more coexisting disorders. This international collaboration examined patients with biopsy-proven MXH with respect to component disease subtypes, oncogenic driver mutations and responses to conventional (chemotherapeutic or immunosuppressive) versus targeted (BRAF or MEK inhibitor) therapies. Twenty-seven patients were studied with ECD/LCH (19/27), ECD/RDD (6/27), RDD/LCH (1/27) and ECD/RDD/LCH (1/27). Mutations previously undescribed in MXH were identified, including KRAS, MAP2K2, MAPK3, non-V600-BRAF, RAF1 and a BICD2-BRAF fusion. A repeated-measure generalized estimating equation demonstrated that targeted treatment was statistically significantly (1) more likely to result in a complete response (CR), partial response (PR) or stable disease (SD) (odds ratio [OR]: 17.34, 95% CI: 2.19-137.00, p = 0.007), and (2) less likely to result in progression (OR: 0.08, 95% CI: 0.03-0.23, p < 0.0001). Histiocytic neoplasms represent an entity with underappreciated clinical and molecular diversity, poor responsiveness to conventional therapy and exquisite sensitivity to targeted therapy.
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Affiliation(s)
- Joshua S Friedman
- Departments of Neurology, Neurosurgery, and Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benjamin H Durham
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Molecular Pharmacology, Sloan Kettering Institute, New York, New York, USA
| | - Anne S Reiner
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mariko Yabe
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kseniya Petrova-Drus
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ahmet Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Melissa Pulitzer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Klaus J Busam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jasmine H Francis
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Raajit K Rampal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gary A Ulaner
- Molecular Imaging and Therapy, Hoag Family Cancer Institute, Newport Beach, California, USA
- Molecular Imaging and Therapy, University of Southern California, Los Angeles, California, USA
| | - Ryan Reddy
- Molecular Imaging and Therapy, Hoag Family Cancer Institute, Newport Beach, California, USA
- Molecular Imaging and Therapy, University of Southern California, Los Angeles, California, USA
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Randy Yeh
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Vaios Hatzoglou
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mario E Lacouture
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Veronica Rotemberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Roei D Mazor
- Clinic of Histiocytic Neoplasms, Institute of Hematology, Assuta Medical Center, Tel-Aviv, Israel
| | - Oshrat Hershkovitz-Rokah
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel, Israel
- Translational Research Lab, Assuta Medical Centers, Tel-Aviv, Israel
| | - Ofer Shpilberg
- Clinic of Histiocytic Neoplasms, Institute of Hematology, Assuta Medical Center, Tel-Aviv, Israel
- Adelson School of Medicine, Ariel University, Ariel, Israel
| | - Gaurav Goyal
- Department of Hematology Oncology, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Rare Histiocytic Disorders Steering Committee of the Histiocyte Society
| | - Ronald S Go
- Rare Histiocytic Disorders Steering Committee of the Histiocyte Society
- Division of Hematology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Karen Rech
- Department of Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Rare Histiocytic Disorders Steering Committee of the Histiocyte Society
| | - Diana Morlote
- Department of Hematology Oncology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Shiraz Fidai
- Department of Pathology, John H. Stroger Hospital of Cook County, Chicago, Illinois, USA
| | - Vedavyas Gannamani
- Department of Pathology, John H. Stroger Hospital of Cook County, Chicago, Illinois, USA
| | - Maryam Zia
- Department of Pathology, John H. Stroger Hospital of Cook County, Chicago, Illinois, USA
| | - Omar Abdel-Wahab
- Department of Molecular Pharmacology, Sloan Kettering Institute, New York, New York, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Katherine S Panageas
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marc K Rosenblum
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Eli L Diamond
- Rare Histiocytic Disorders Steering Committee of the Histiocyte Society
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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19
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Dashti NK, Perret R, Balzer B, Naous R, Michal M, Dermawan JK, Antonescu CR. Vascular Neoplasms With NFATC1/C2 Gene Alterations : Expanding the Clinicopathologic and Molecular Characteristics of a Distinct Entity. Am J Surg Pathol 2024; 48:487-496. [PMID: 38189436 DOI: 10.1097/pas.0000000000002175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Despite significant advances in their molecular pathogenesis, skeletal vascular tumors remain diagnostically challenging due to their aggressive radiologic appearance and significant morphologic overlap. Within the epithelioid category and at the benign end of the spectrum, recurrent FOS/FOSB fusions have defined most epithelioid hemangiomas, distinguishing them from epithelioid hemangioendothelioma and angiosarcoma. More recently, the presence of EWSR1/FUS :: NFATC1/2 fusions emerged as the genetic hallmark of a novel group of unusual vascular proliferations, often displaying epithelioid morphology, with alternating vasoformative and solid growth, variable atypia, reminiscent of composite hemangioendothelioma. In this study, we further our understanding and morphologic spectrum of NFATC -fusion positive vascular neoplasms by describing 9 new cases, including soft tissue locations and novel fusion partners. Combining with the initial cohort of 5 cases, a total of 14 patients were analyzed, showing slight female predilection and an age range of 10 to 66 (mean 42 y). Twelve patients had solitary lesions, while 2 had multifocal polyostotic (pelvic bones) disease. Overall, 12 lesions were intra-osseous and 2 in soft tissue. By targeted RNA Fusion panels or FISH, there were 6 cases of EWSR1::NFATC1 , 4 EWSR1::NFATC2 , 2 FUS::NFATC2 , 1 EWSR1 rearrangement, and 1 with a novel FABP4::NFATC2 fusion. Follow-up was available in 4 patients. One patient experienced 2 local recurrences, 11 and 15 years postdiagnosis, and one patient experienced progressive disease despite multimodality treatment (curettings, embolization, radiation) over 3 years. In summary, our extended investigation confirms that NFATC -related fusions define a distinct group of vascular neoplasms with variable architecture, epithelioid phenotype, and cytologic atypia, commonly located in the bone, occasionally multifocal and with potential for local recurrence and aggressive behavior but no metastatic potential. Molecular analysis is recommended in diagnostically challenging cases with atypical histology to exclude malignancy.
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Affiliation(s)
- Nooshin K Dashti
- Department of Pathology and Laboratory Medicine Dartmouth Health
- Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Raul Perret
- Department of Biopathology, Institut Bergonié, Comprehensive Cancer Center
- Bordeaux Institute of Oncology, BRIC, INSERM, Bordeaux University, Bergonié Institute, Bordeaux, France
| | | | - Rana Naous
- University of Pittsburgh Medical Center, Shadyside, Pittsburgh, PA
| | - Michael Michal
- Biopticka Laboratory, Pilsen, Czech Republic
- Department of Pathology, Charles University, Faculty of Medicine in Plzen, Czech Republic
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - Cristina R Antonescu
- Department of Pathology and Lab Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY
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20
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Pelster MS, Silverman IM, Schonhoft JD, Johnson A, Selenica P, Ulanet D, Rimkunas V, Reis-Filho JS. Post-therapy emergence of an NBN reversion mutation in a patient with pancreatic acinar cell carcinoma. NPJ Precis Oncol 2024; 8:82. [PMID: 38561473 PMCID: PMC10985087 DOI: 10.1038/s41698-024-00497-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 12/21/2023] [Indexed: 04/04/2024] Open
Abstract
Pancreatic acinar cell carcinoma (PACC) is a rare form of pancreatic cancer that commonly harbors targetable alterations, including activating fusions in the MAPK pathway and loss-of-function (LOF) alterations in DNA damage response/homologous recombination DNA repair-related genes. Here, we describe a patient with PACC harboring both somatic biallelic LOF of NBN and an activating NTRK1 fusion. Upon disease progression following 13 months of treatment with folinic acid, fluorouracil, irinotecan, and oxaliplatin (FOLFIRINOX), genomic analysis of a metastatic liver biopsy revealed the emergence of a novel reversion mutation restoring the reading frame of NBN. To our knowledge, genomic reversion of NBN has not been previously reported as a resistance mechanism in any tumor type. The patient was treated with, but did not respond to, targeted treatment with a selective NTRK inhibitor. This case highlights the complex but highly actionable genomic landscape of PACC and underlines the value of genomic profiling of rare tumor types such as PACC.
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Affiliation(s)
| | | | | | | | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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21
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Kumbrink J, Demes MC, Jeroch J, Bräuninger A, Hartung K, Gerstenmaier U, Marienfeld R, Hillmer A, Bohn N, Lehning C, Ferch F, Wild P, Gattenlöhner S, Möller P, Klauschen F, Jung A. Development, testing and validation of a targeted NGS-panel for the detection of actionable mutations in lung cancer (NSCLC) using anchored multiplex PCR technology in a multicentric setting. Pathol Oncol Res 2024; 30:1611590. [PMID: 38605929 PMCID: PMC11006983 DOI: 10.3389/pore.2024.1611590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/15/2024] [Indexed: 04/13/2024]
Abstract
Lung cancer is a paradigm for a genetically driven tumor. A variety of drugs were developed targeting specific biomarkers requiring testing for tumor genetic alterations in relevant biomarkers. Different next-generation sequencing technologies are available for library generation: 1) anchored multiplex-, 2) amplicon based- and 3) hybrid capture-based-PCR. Anchored multiplex PCR-based sequencing was investigated for routine molecular testing within the national Network Genomic Medicine Lung Cancer (nNGM). Four centers applied the anchored multiplex ArcherDX-Variantplex nNGMv2 panel to re-analyze samples pre-tested during routine diagnostics. Data analyses were performed by each center and compiled centrally according to study design. Pre-defined standards were utilized, and panel sensitivity was determined by dilution experiments. nNGMv2 panel sequencing was successful in 98.9% of the samples (N = 90). With default filter settings, all but two potential MET exon 14 skipping variants were identified at similar allele frequencies. Both MET variants were found with an adapted calling filter. Three additional variants (KEAP1, STK11, TP53) were called that were not identified in pre-testing analyses. Only total DNA amount but not a qPCR-based DNA quality score correlated with average coverage. Analysis was successful with a DNA input as low as 6.25 ng. Anchored multiplex PCR-based sequencing (nNGMv2) and a sophisticated user-friendly Archer-Analysis pipeline is a robust and specific technology to detect tumor genetic mutations for precision medicine of lung cancer patients.
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Affiliation(s)
- Jörg Kumbrink
- Institute of Pathology, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Melanie-Christin Demes
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany
| | - Jan Jeroch
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany
| | - Andreas Bräuninger
- Institute of Pathology, Justus Liebig University Giessen, Giessen, Germany
| | - Kristin Hartung
- Institute of Pathology, Justus Liebig University Giessen, Giessen, Germany
| | | | | | - Axel Hillmer
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | | | | | - Peter Wild
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany
| | | | - Peter Möller
- Institute of Pathology, University Ulm, Ulm, Germany
| | - Frederick Klauschen
- Institute of Pathology, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Andreas Jung
- Institute of Pathology, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
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22
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Kwan MC, Pitman MB, Fernandez-Del Castillo C, Zhang ML. Revisiting the performance of cyst fluid carcinoembryonic antigen as a diagnostic marker for pancreatic mucinous cysts: a comprehensive 20-year institutional review. Gut 2024; 73:629-638. [PMID: 38195219 DOI: 10.1136/gutjnl-2023-331138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
OBJECTIVE Elevated pancreatic cyst fluid carcinoembryonic antigen (CEA) has been routinely used to classify mucinous cysts. This study incorporates original data that established the CEA ≥192 ng/mL threshold with over 20 years of additional data and reassesses the diagnostic performance of CEA for differentiating mucinous from non-mucinous cysts. DESIGN 1169 pancreatic cysts (1999-2021) with CEA results were identified. 394 cases had histological confirmation as the diagnostic standard. Additionally, 237 cysts without histological confirmation demonstrated KRAS, GNAS, or RNF43 mutations by molecular testing and were combined with the histologically confirmed cysts for separate analysis on a total cohort of 631 cysts. RESULTS Median CEA was significantly higher in mucinous cysts (323.9 ng/mL, n=314) versus non-mucinous cysts (204.6 ng/mL, n=80) (p<0.001). Receiver operating characteristic curve analysis demonstrated an optimal CEA cut-off of 20 ng/mL (area under the curve: 80%), though the specificity was lower than desired (sensitivity 89%, specificity 64%). At the previously established threshold of 192 ng/mL, sensitivity and specificity were 56% and 78%, respectively. To achieve a specificity of 85% as originally reported, a CEA threshold of 250 ng/mL was needed; the 13 false positive cases at this threshold included 4 benign simple cysts, 2 squamoid cysts, 1 serous cystadenoma, 1 lymphoepithelial cyst and 5 more uncommon entities. All results remained similar within the total cohort after including additional cases with KRAS/GNAS/RNF43 mutations only. CONCLUSION Cyst fluid CEA continues to be a useful test in the diagnosis of mucinous pancreatic cysts but does not appear as specific as previously reported. Raising the CEA threshold to 250 ng/mL to maintain specificity for differentiating mucinous from non-mucinous cysts may be considered.
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Affiliation(s)
- Melanie C Kwan
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Martha Bishop Pitman
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Carlos Fernandez-Del Castillo
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - M Lisa Zhang
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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23
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Yeung MC, Dermawan JK, Liu AP, Lam AY, Antonescu CR, Shek TW. Spindle cell neoplasms with novel LTK fusion - Expanding the spectrum of kinase fusion-positive soft tissue tumors. Genes Chromosomes Cancer 2024; 63:e23227. [PMID: 38517106 PMCID: PMC10963038 DOI: 10.1002/gcc.23227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/09/2024] [Accepted: 01/24/2024] [Indexed: 03/23/2024] Open
Abstract
AIMS Kinase fusion-positive soft tissue tumors represent an emerging, molecularly defined group of mesenchymal tumors with a wide morphologic spectrum and diverse activating kinases. Here, we present two cases of soft tissue tumors with novel LTK fusions. METHODS AND RESULTS Both cases presented as acral skin nodules (big toe and middle finger) in pediatric patients (17-year-old girl and 2-year-old boy). The tumors measured 2 and 3 cm in greatest dimension. Histologically, both cases exhibited bland-looking spindle cells infiltrating adipose tissue and accompanied by collagenous stroma. One case additionally displayed perivascular hyalinization and band-like stromal collagen. Both cases exhibited focal S100 staining, and one case had patchy coexpression of CD34. Targeted RNA-seq revealed the presence of novel in-frame MYH9::LTK and MYH10::LTK fusions, resulting in upregulation of LTK expression. Of interest, DNA methylation-based unsupervised clustering analysis in one case showed that the tumor clustered with dermatofibrosarcoma protuberans (DFSP). One tumor was excised with amputation with no local recurrence or distant metastasis at 18-month follow-up. The other case was initially marginally excised with local recurrence after one year, followed by wide local excision, with no evidence of disease at 10 years of follow-up. CONCLUSIONS This is the first reported case series of soft tissue tumors harboring LTK fusion, expanding the molecular landscape of soft tissue tumors driven by activating kinase fusions. Furthermore, studies involving a larger number of cases and integrated genomic analyses will be warranted to fully elucidate the pathogenesis and classification of these tumors.
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Affiliation(s)
- Maximus C.F. Yeung
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Anthony P.Y. Liu
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children’s Hospital, Hong Kong
| | - Albert Y.L. Lam
- Division of General Orthopaedics and Oncology, Department of Orthopedics and Traumatology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tony W.H. Shek
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
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24
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Patton A, Dermawan JK. Current updates in sarcoma biomarker discovery: emphasis on next-generation sequencing-based methods. Pathology 2024; 56:274-282. [PMID: 38185613 DOI: 10.1016/j.pathol.2023.10.015] [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: 10/02/2023] [Revised: 10/25/2023] [Accepted: 10/29/2023] [Indexed: 01/09/2024]
Abstract
Soft tissue sarcomas comprise a heterogeneous group of neoplasms. Although soft tissue malignancies make up only 2% of adult cancers, classification based on histomorphology presents a diagnostic challenge. Characterisation of soft tissue sarcomas by molecular analysis is rapidly evolving to improve diagnostic accuracy and develop targeted therapies. This review highlights the advances in molecular techniques, including current next-generation sequencing-based assays (fusion detection by RNA sequencing, targeted/whole exome sequencing, microRNA profiling), as well as emerging methods (liquid biopsies, DNA methylation profiling, single-cell molecular profiling and next-generation immunohistochemistry) for future clinical applications.
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Affiliation(s)
- Ashley Patton
- Department of Pathology & Laboratory Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
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25
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Rahman MM, Wang L, Rahman MM, Chen Y, Zhang W, Wang J, Lee LP, Wan Y. Rapid in situ mutation detection in extracellular vesicle-DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582068. [PMID: 38464277 PMCID: PMC10925088 DOI: 10.1101/2024.02.26.582068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
A PCR- and sequencing-free mutation detection assay facilitates cancer diagnosis and reduces over-reliance on specialized equipment. This benefit was highlighted during the pandemic when high demand for viral nucleic acid testing often sidelined mutation analysis. This shift led to substantial challenges for patients on targeted therapy in tracking mutations. Here, we report a 30-minute DNA mutation detection technique using Cas12a-loaded liposomes in a microplate reader, a fundamental laboratory tool. CRISPR-Cas12a complex and fluorescence-quenching (FQ) probes are introduced into tumor-derived extracellular vesicles (EV) through membrane fusion. When CRISPR-RNA hybridizes with the DNA target, activated Cas12a can trans-cleave FQ probes, resulting in fluorescence signals for the quantification of DNA mutation. Future advancements in multiplex and high-throughput mutation detection using this assay will streamline self-diagnosis and treatment monitoring at home.
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Affiliation(s)
- Md Mofizur Rahman
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA
- Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Lixue Wang
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA
- Department of Radiotherapy, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Md Motiar Rahman
- Department of Chemistry, Binghamton University, Binghamton, NY, USA
| | - Yundi Chen
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA
| | - Wenlong Zhang
- Twist Bioscience Corporation, San Francisco, CA, USA
| | - Jing Wang
- Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
- Department of Oncology and Hematology, Yizheng Hospital of Nanjing Drum Tower Hospital Group, Yizheng, Jiangsu, China
| | - Luke P Lee
- Harvard Medical School, Harvard University; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, Korea
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, Korea
| | - Yuan Wan
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA
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26
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Wang X, Sun Y, Zhao JY, Guan XW, Wang YY, Hong DY, Zhang ZL, Li YH, Yang PY, Jiang T, Xu ZF. Utility, benefits, and risks of newborn genetic screening carrier reports for families. J Glob Health 2024; 14:04044. [PMID: 38389402 PMCID: PMC10884785 DOI: 10.7189/jogh.14.04044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
Background Newborn genetic screening (NBGS) based on next-generation sequencing offers enhanced disease detection and better detection rates than traditional newborn screening. However, challenges remain, especially around reporting the NBGS carrier results. Therefore, we aimed to investigate the NBGS carrier parents' views on NBGS and NBGS reports in China. Methods We distributed a survey querying demographic information, knowledge and perceptions of NBGS, the impact of NBGS on a total of 2930 parents, and their decision-making to parents of newborns reported as carriers in NBGS in Nanjing, China in 2022. Results The average age of the survey respondents was 30.7 years (standard deviation = 3.6). Most (68.38%) felt informed about NBGS, especially women, the highly educated, and high earners. Nearly all (98.74%) saw NBGS as crucial for early disease detection, with 73.18% believing it positively impacts their future. However, 19.16% felt it might cause anxiety, especially among the less educated. Concerns included potential discrimination due to exposed genetic data and strained family ties. Many suggested NBGS coverage by medical insurance to ease financial burdens. Conclusions Through our study, we gained insights into parents' perspectives and concerns regarding the NBGS carrier result reporting, thus providing relevant information for further refinement and clinical promotion of the NBGS project.
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Affiliation(s)
- Xin Wang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Yun Sun
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | | | - Xian-Wei Guan
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Yan-Yun Wang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Dong-Yang Hong
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Zhi-Lei Zhang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Ya-Hong Li
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Pei-Ying Yang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Tao Jiang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Zheng-Feng Xu
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
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27
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Kerr DA, Cloutier JM, Margolis M, Mata DA, Rodrigues Simoes NJ, Faquin WC, Dias-Santagata D, Chopra S, Charville GW, Wangsiricharoen S, Lazar AJ, Wang WL, Rosenberg AE, Tse JY. GLI1-Altered Mesenchymal Tumors With ACTB or PTCH1 Fusion: A Molecular and Clinicopathologic Analysis. Mod Pathol 2024; 37:100386. [PMID: 37992966 DOI: 10.1016/j.modpat.2023.100386] [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: 08/01/2023] [Revised: 10/04/2023] [Accepted: 10/31/2023] [Indexed: 11/24/2023]
Abstract
Mesenchymal tumors with GLI1 fusions or amplifications have recently emerged as a distinctive group of neoplasms. The terms GLI1-altered mesenchymal tumor or GLI1-altered soft tissue tumor serve as a nosological category, although the exact boundaries/criteria require further elucidation. We examined 16 tumors affecting predominantly adults (median age: 40 years), without sex predilection. Several patients had tumors of longstanding duration (>10 years). The most common primary site was soft tissue (n = 9); other sites included epidural tissue (n = 1), vertebra (n = 1), tongue (n = 1), hard palate (n = 1), and liver (n = 1). Histologically, the tumors demonstrated multinodular growth of cytologically uniform, ovoid-to-epithelioid, occasionally short spindled cells with delicate intratumoral vasculature and frequent myxoid stroma. Mitotic activity ranged from 0 to 8 mitoses/2 mm2 (mean 2). Lymphovascular invasion/protrusion of tumor cells into endothelial-lined vascular spaces was present or suspected in 6 cases. Necrosis, significant nuclear pleomorphism, or well-developed, fascicular spindle-cell growth were absent. Half demonstrated features of the newly proposed subset, "distinctive nested glomoid neoplasm." Tumors were consistently positive for CD56 (n = 5/5). A subset was stained with S100 protein (n = 7/13), SMA (n = 6/13), keratin (n = 2/9), EMA (n = 3/7), and CD99 (n = 2/6). Tumors harbored ACTB::GLI1 (n = 15) or PTCH1::GLI1 (n = 1) fusions. The assays used did not capture cases defined by GLI1 amplification. We also identified recurrent cytogenetic gains (1q, 5, 7, 8, 12, 12q13.2-ter, 21, and X). For patients with available clinical follow-up (n = 8), half were disease free. Half demonstrated distant metastases (lungs, bone, or soft tissue). Of cases without follow-up (n = 8), 2 were known recurrences, and 1 was presumed metastasis. Our results imply a more aggressive biological potential than currently reported. Given the possibility for metastasis and disease progression, even in cytologically bland, nested tumors, close clinical surveillance, akin to that for sarcoma management, may be indicated. The term GLI1-altered mesenchymal tumor with malignant potential is proposed.
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Affiliation(s)
- Darcy A Kerr
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire; Dartmouth Geisel School of Medicine, Hanover, New Hampshire.
| | - Jeffrey M Cloutier
- Department of Pathology, MD Anderson Cancer Center, Houston, TX; Now with Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire; Now with Dartmouth Geisel School of Medicine, Hanover, New Hampshire
| | | | | | | | - William C Faquin
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Dora Dias-Santagata
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Shefali Chopra
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Gregory W Charville
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | | | | | - Wei-Lien Wang
- Department of Pathology, MD Anderson Cancer Center, Houston, TX
| | - Andrew E Rosenberg
- Department of Pathology, University of Miami and Miller School of Medicine, Miami, Florida
| | - Julie Y Tse
- Foundation Medicine, Inc., Cambridge, Massachusetts
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Chiarle R, Cheong TC, Jang A, Wang Q, Leonardi G, Ricciuti B, Alessi J, Federico AD, Awad M, Lehtinen M, Harris M. Mechanistic patterns and clinical implications of oncogenic tyrosine kinase fusions in human cancers. RESEARCH SQUARE 2024:rs.3.rs-3782958. [PMID: 38313284 PMCID: PMC10836111 DOI: 10.21203/rs.3.rs-3782958/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Tyrosine kinase (TK) fusions are frequently found in cancers, either as initiating events or as a mechanism of resistance to targeted therapy. Partner genes and exons in most TK fusions are typical and recurrent, but the underlying mechanisms and clinical implications of these patterns are poorly understood. Here, we investigated structures of > 8,000 kinase fusions and explore their generative mechanisms by applying newly developed experimental framework integrating high-throughput genome-wide gene fusion sequencing and clonal selection called Functionally Active Chromosomal Translocation Sequencing (FACTS). We discovered that typical oncogenic TK fusions recurrently seen in patients are selected from large pools of chromosomal rearrangements spontaneously occurring in cells based on two major determinants: active transcription of the fusion partner genes and protein stability. In contrast, atypical TK fusions that are rarely seen in patients showed reduced protein stability, decreased downstream oncogenic signaling, and were less responsive to inhibition. Consistently, patients with atypical TK fusions were associated with a reduced response to TKI therapies, as well as a shorter progression-free survival (PFS) and overall survival (OS) compared to patients with typical TK fusions. These findings highlight the principles of oncogenic TK fusion formation and their selection in cancers, with clinical implications for guiding targeted therapy.
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Affiliation(s)
| | | | - Ahram Jang
- Boston Children's Hospital and Harvard Medical School
| | - Qi Wang
- Boston Children's Hospital and Harvard Medical School
| | | | | | | | | | | | | | - Marian Harris
- Boston Children's Hospital and Harvard Medical School
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Tjota MY, Segal JP, Wang P. Clinical Utility and Benefits of Comprehensive Genomic Profiling in Cancer. J Appl Lab Med 2024; 9:76-91. [PMID: 38167763 DOI: 10.1093/jalm/jfad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/28/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Comprehensive genomic profiling (CGP) with next-generation sequencing detects genetic alterations of hundreds of genes simultaneously and multiple molecular biomarkers with one test. In the personalized medicine era, CGP is increasingly used for cancer diagnosis, treatment selection, and prognosis prediction. CONTENT In this review, we summarize the benefits of CGP, clinical utility of CGP, and challenges of setting up CGP in the clinical laboratories. Besides the genetic alterations identified in the cancer-related genes, other biomarkers such as tumor mutational burden, microsatellite instability, and homologous recombination deficiency are critical for initiating targeted therapy. Compared with conventional tests, CGP uses less specimen and shortens the turnaround time if multiple biomarkers need to be tested. RNA fusion assay and liquid biopsy are helpful additions to DNA-based CGP by detecting fusions/splicing variants and complementing tissue-based CGP findings, respectively. SUMMARY Many previous hurdles for implementing CGP in the clinical laboratories have been gradually alleviated such as the decrease in sequencing cost, availability of both open-source and commercial bioinformatics tools, and improved reimbursement. These changes have helped to make CGP available to a greater population of cancer patients for improving characterization of their tumors and expanding their eligibility for clinical trials. Additionally, sequencing results of the hundreds of genes on CGP panels could be further analyzed to better understand the biology of various cancers and identify new biomarkers.
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Affiliation(s)
- Melissa Yuwono Tjota
- Department of Pathology, The University of Chicago, Chicago, IL 60637, United States
| | - Jeremy P Segal
- Department of Pathology, The University of Chicago, Chicago, IL 60637, United States
| | - Peng Wang
- Department of Pathology, The University of Chicago, Chicago, IL 60637, United States
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30
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Solomon JP. Practical Considerations for Oncogenic Fusion Detection and Reporting in Solid Tumors. J Appl Lab Med 2024; 9:116-123. [PMID: 38167769 DOI: 10.1093/jalm/jfad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/15/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Chromosomal rearrangements that result in oncogenic fusions can hold tremendous clinical significance in solid tumors, often with diagnostic or treatment implications. CONTENT Traditionally, low-throughput methods such as fluorescence in situ hybridization were used to identify fusions in the clinical laboratory. With the rise of next-generation sequencing techniques and the broad adoption of comprehensive genomic profiling, the practice of screening for fusions as part of an oncologic workup has evolved. RNA sequencing methods are increasingly used, as these comprehensive high-throughput assays have many advantages over traditional techniques. Several RNA sequencing platforms are available, each with benefits and drawbacks. Regardless of the approach, systematic evaluation of the RNA sequencing results and the fusions identified by the assay should be performed. Assessment of fusion events relies upon evaluation of quality evidence, structural evidence, and functional evidence to ensure accurate fusion reporting and interpretation. SUMMARY Given the clinical significance of gene fusions in oncology, understanding the variety of assays available for fusion detection, their benefits and drawbacks, and how they are used in the identification and interpretation of gene fusions is important for the modern precision oncology practice.
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Affiliation(s)
- James P Solomon
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States
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31
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Smith BF, Hampel KJ, Sidiropoulos N. Benefits of Implementing Reflex Genomic Analysis for Nonsmall Cell Lung Cancer. J Appl Lab Med 2024; 9:28-40. [PMID: 38167774 DOI: 10.1093/jalm/jfad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/25/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Molecular biomarker analysis is standard of care in advanced nonsmall cell lung cancer (NSCLC). Pathologist-driven reflex testing protocols are one approach to initiating this analysis. Two years after insourcing genomic analysis at our institution, a reflex testing protocol for advanced NSCLC was initiated. METHODS A retrospective review of the records of 578 NSCLC biopsies was performed to assess the impact of 3 genomic testing workflows (send-out, in-house clinician-ordered, and in-house reflex) on time to initiation of molecular testing [initiation time (IT)], reporting time (RT), proportion of test failures, and test ordering practices. The proportion of test failures by test methodology was also assessed. RESULTS IT was lowest for reflex protocol orders (mean weekdays: 30.0 send-out, 27.4 in-house clinician-ordered, 0.95 reflex). Test failure was highest for send-out testing (31.7% vs. 10% each for in-house clinician-ordered and reflex). RT remained consistent across the 3 workflows (mean weekdays: 11.1 send-out, 11.9 in-house clinician-ordered, and 11.4 reflex). Guideline-congruent molecular testing increased upon insourcing genomic analysis and again upon implementing reflex testing with a reduction in nonbiomarker informed care (58.8% send-out, 19.5% in-house clinician-ordered, 11.5% reflex). CONCLUSIONS Implementation of reflex in-house genomic analysis for advanced NSCLC ensured consistency in RT and significantly decreased IT and proportion of test failures. Insourcing genomic analysis and thoughtful care pathway design improve equitable access to molecular biomarker analysis and mitigate nonbiomarker informed cancer care in NSCLC.
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Affiliation(s)
- Benjamin F Smith
- The Robert Larner, M.D. College of Medicine at the University of Vermont, Burlington, VT, United States
| | - Ken J Hampel
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Nikoletta Sidiropoulos
- The Robert Larner, M.D. College of Medicine at the University of Vermont, Burlington, VT, United States
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
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Sadigh S, DeAngelo DJ, Garcia JS, Hasserjian RP, Hergott CB, Lane AA, Lovitch SB, Lucas F, Luskin MR, Morgan EA, Pinkus GS, Pozdnyakova O, Rodig SJ, Shanmugam V, Tsai HK, Winer ES, Zemmour D, Kim AS. Cutaneous Manifestations of Myeloid Neoplasms Exhibit Broad and Divergent Morphologic and Immunophenotypic Features but Share Ancestral Clonal Mutations With Bone Marrow. Mod Pathol 2024; 37:100352. [PMID: 37839675 DOI: 10.1016/j.modpat.2023.100352] [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: 05/10/2023] [Revised: 08/14/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
In this study, we performed a comprehensive molecular analysis of paired skin and peripheral blood/bone marrow (BM) samples from 17 patients with cutaneous myeloid or cutaneous histiocytic-dendritic neoplasms. The cutaneous manifestations included 10 patients with cutaneous acute myeloid leukemia (c-AML), 2 patients with full or partial Langerhans cell differentiation, 2 patients with blastic plasmacytoid dendritic cell neoplasms (BPDCN), 1 patient with both Langerhans cell differentiation and BPDCN, and 2 patients with full or partial indeterminate dendritic cell differentiation. Seven of the 10 c-AML patients (70%) exhibited concurrent or subsequent marrow involvement by acute myeloid leukemia, with all 7 cases (100%) demonstrating shared clonal mutations in both the skin and BM. However, clonal relatedness was documented in one additional case that never had any BM involvement. Nevertheless, NPM1 mutations were identified in 7 of the 10 (70%) of these c-AML cases while one had KMT2A rearrangement and one showed inv(16). All 3 patients (100%) with Langerhans cell neoplasms, 2 patients with BPDCN (100%), and one of the 2 patients (50%) with other cutaneous dendritic cell neoplasms also demonstrated shared mutations between the skin and concurrent or subsequent myeloid neoplasms. Both BM and c-AML shared identical founding drivers, with a predominance of NPM1, DNMT3A, and translocations associated with monocytic differentiation, with common cutaneous-only mutations involving genes in the signal transduction and epigenetic pathways. Cutaneous histiocytic-dendritic neoplasms shared founding drivers in ASXL1, TET2, and/or SRSF2. However, in the Langerhans cell histiocytosis or histiocytic sarcoma cases, there exist recurrent secondary RAS pathway hits, whereas cutaneous BPDCN cases exhibit copy number or structural variants. These results enrich and broaden our understanding of clonally related cutaneous manifestations of myeloid neoplasms and further illuminate the highly diverse spectrum of morphologic and immunophenotypic features they exhibit.
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Affiliation(s)
- Sam Sadigh
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel J DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Robert P Hasserjian
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Christopher B Hergott
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Scott B Lovitch
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Fabienne Lucas
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Marlise R Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Elizabeth A Morgan
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Geraldine S Pinkus
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Olga Pozdnyakova
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Vignesh Shanmugam
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Harrison K Tsai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eric S Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David Zemmour
- Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Now with Department of Pathology, University of Michigan, Ann Arbor, Michigan.
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Li Y, Gao J, Wang D, Liu Z, Zhang H. TRIM4 Expression Related to Malignant Progression and Cisplatin Resistance in Osteosarcoma. Appl Biochem Biotechnol 2024; 196:233-244. [PMID: 37115387 DOI: 10.1007/s12010-023-04551-5] [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] [Accepted: 04/18/2023] [Indexed: 04/29/2023]
Abstract
Osteosarcoma (OS) is a high-grade intraosseous malignancy. Twenty to thirty percent of OS patients react poorly to standard therapy with a combination of surgical resection and chemotherapy. It is necessary to find molecules that play an important role in this. This study explored the role of TRIM4 in OS chemotherapy sensitivity and malignant progression. The expression of TRIM4 in OS tissues and cells was examined by RT-qPCR, immunohistochemical staining, and western blot. Specific siRNA was transfected into U2-OS and SAOS2 cells to target TRIM4. Cell biological behavior was examined by CCK-8, Transwell, and flow cytometry experiments. Cisplatin-resistant SAOS2 (SAOS2-Cis-R) cells were established, and the effect of TRIM4 expression on the cisplatin response of SAOS2 cells was tested. Knockdown of TRIM4 significantly inhibited the proliferation, migration, and invasion of U2-OS and SAOS2 cells and induced apoptosis. TRIM4 expression was significantly higher in chemotherapy-resistant OS tissues compared to chemotherapy-sensitive OS tissues. Furthermore, the expression of TRIM4 in SAOS2-Cis-R cells was significantly increased compared to parental SAOS2 cells. Moreover, overexpression of TRIM4 enhanced cisplatin resistance in parental SAOS2 cells, while the downregulation of TRIM4 expression enhanced cisplatin sensitivity of SAOS2-Cis-R cells. High TRIM4 expression might be associated with malignant progression and poor response to chemotherapy response of OS. Targeting TRIM4 may be beneficial for OS treatment or combination therapy.
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Affiliation(s)
- Yan Li
- Department of Joint Surgery, Shandong Second Provincial General Hospital, No.4 Duanxing West Road, Huaiyin District, Jinan, 250022, People's Republic of China
| | - Jie Gao
- Department of Joint Surgery, Shandong Second Provincial General Hospital, No.4 Duanxing West Road, Huaiyin District, Jinan, 250022, People's Republic of China
| | - Dong Wang
- Department of Joint Surgery, Shandong Second Provincial General Hospital, No.4 Duanxing West Road, Huaiyin District, Jinan, 250022, People's Republic of China
| | - Zijin Liu
- Department of Joint Surgery, Shandong Second Provincial General Hospital, No.4 Duanxing West Road, Huaiyin District, Jinan, 250022, People's Republic of China
| | - Huawu Zhang
- Department of Joint Surgery, Shandong Second Provincial General Hospital, No.4 Duanxing West Road, Huaiyin District, Jinan, 250022, People's Republic of China.
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Fan Y, Zhang B, Du X, Wang B, Yan Q, Guo L, Yao W. Regulating Tumorigenicity and Cancer Metastasis through TRKA Signaling. Curr Cancer Drug Targets 2024; 24:271-287. [PMID: 37670705 DOI: 10.2174/1568009623666230904150957] [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: 02/14/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 09/07/2023]
Abstract
Tropomyosin receptor kinase (TRK) A, TRKA, is a specific binding receptor of nerve growth factor (NGF), which plays an essential role in the occurrence and progression of human cancers. TRKA overexpression has been proven to be a powerful carcinogenic driver and has been verified in many tumors. The TRKA receptor kinase domain is over-activated in an NGF-dependent manner, accompanied by activation of downstream signal pathways, such as RAS-MAPK, PI3K-AKT, JAK2-STAT3 pathway, PLC γ pathway, and Hippo pathway, which participate in tumor cell proliferation, invasion, epithelial-mesenchymal transition (EMT), perineural invasion (PNI), drug resistance, and cancer pain. In addition, chimeric oncogenes produced by the fusion of NTRK1 and other genes are also the direct cause of tumorigenesis and cancer development. The newly developed TRK inhibitors can improve symptoms and tumor regression in cancer patients with overexpression of TRKA or NTRK1 fusion gene. With the emergence of drug resistance, next generation of TRK inhibitors can still maintain strong clinical efficacy in the case of TRK kinase domain mutations, and these inhibitors are in clinical trials. This review summarizes the characteristics and research progress of TRKA, focusing on the regulatory role of the TRKA signal pathway in different tumors. In addition, we have summarized the clinical significance of TRKA and the TRK inhibitors. This review may provide a new reference for the study of the mechanism of TRKA in different tumors, and also provide a new perspective for the in-depth understanding of the role of TRKA as a biomarker and therapeutic target in human cancer.
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Affiliation(s)
- Yichao Fan
- Henan Cancer Hospital, Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Boya Zhang
- Henan Cancer Hospital, Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Xinhui Du
- Henan Cancer Hospital, Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Bangmin Wang
- Henan Cancer Hospital, Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Qiang Yan
- Henan Cancer Hospital, Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Liangyu Guo
- Henan Cancer Hospital, Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Weitao Yao
- Henan Cancer Hospital, Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
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Suurmeijer AJH, Xu B, Torrence D, Dickson BC, Antonescu CR. Kinase fusion positive intra-osseous spindle cell tumors: A series of eight cases with review of the literature. Genes Chromosomes Cancer 2024; 63:e23205. [PMID: 37782551 DOI: 10.1002/gcc.23205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
Mesenchymal spindle cell tumors with kinase fusions, often presenting in superficial or deep soft tissue locations, may rarely occur in bone. Herein, we describe the clinicopathologic and molecular data of eight bone tumors characterized by various kinase fusions from our files and incorporate the findings with the previously reported seven cases, mainly as single case reports. In the current series all but one of the patients were young children or teenagers, with an age range from newborn to 59 years (mean 19 years). Most tumors (n = 5) presented in the head and neck area (skull base, mastoid, maxilla, and mandible), and remaining three in the tibia, pelvic bone, and chest wall. The fusions included NTRK1 (n = 3), RET (n = 2), NTRK3 (n = 2), and BRAF (n = 1). In the combined series (n = 15), most tumors (73%) occurred in children and young adults (<30 years) and showed a predilection for jaw and skull bones (40%), followed by long and small tubular bones (33%). The fusions spanned a large spectrum of kinase genes, including in descending order NTRK3 (n = 6), NTRK1 (n = 4), RET (n = 2), BRAF (n = 2), and RAF1 (n = 1). All fusions confirmed by targeted RNA sequencing were in-frame and retained the kinase domain within the fusion oncoprotein. Similar to the soft tissue counterparts, most NTRK3-positive bone tumors in this series showed high-grade morphology (5/6), whereas the majority of NTRK1 tumors were low-grade (3/4). Notably, all four tumors presenting in the elderly were high-grade spindle cell sarcomas, with adult fibrosarcoma (FS)-like, malignant peripheral nerve sheath tumor (MPNST)-like and MPNST phenotypes. Overall, 10 tumors had high-grade morphology, ranging from infantile and adult-types FS, MPNST-like, and MPNST, whereas five showed benign/low-grade histology (MPNST-like and myxoma-like). Immunohistochemically (IHC), S100 and CD34 positivity was noted in 57% and 50%, respectively, while co-expression of S100 and CD34 in 43% of cases. One-third of tumors (4 high grade and the myxoma-like) were negative for both S100 and CD34. IHC for Pan-TRK was positive in all eight NTRK-fusion positive tumors tested and negative in two tumors with other kinase fusions. Clinical follow-up was too limited to allow general conclusions.
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Affiliation(s)
- Albert J H Suurmeijer
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Bin Xu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dianne Torrence
- Department of Pathology, Northwell Health (Long Island Jewish Medical Center), New Hyde Park, New York, USA
| | - Brendan C Dickson
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Dhoundiyal S, Alam MA. Advancements in Biotechnology and Stem Cell Therapies for Breast Cancer Patients. Curr Stem Cell Res Ther 2024; 19:1072-1083. [PMID: 37815191 DOI: 10.2174/011574888x268109230924233850] [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: 06/19/2023] [Revised: 08/09/2023] [Accepted: 08/18/2023] [Indexed: 10/11/2023]
Abstract
This comprehensive review article examines the integration of biotechnology and stem cell therapy in breast cancer diagnosis and treatment. It discusses the use of biotechnological tools such as liquid biopsies, genomic profiling, and imaging technologies for accurate diagnosis and monitoring of treatment response. Stem cell-based approaches, their role in modeling breast cancer progression, and their potential for breast reconstruction post-mastectomy are explored. The review highlights the importance of personalized treatment strategies that combine biotechnological tools and stem cell therapies. Ethical considerations, challenges in clinical translation, and regulatory frameworks are also addressed. The article concludes by emphasizing the potential of integrating biotechnology and stem cell therapy to improve breast cancer outcomes, highlighting the need for continued research and collaboration in this field.
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Affiliation(s)
- Shivang Dhoundiyal
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, Uttar Pradesh, India
| | - Md Aftab Alam
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, Uttar Pradesh, India
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37
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Suurmeijer AJH, Dickson BC, Antonescu CR. Complementary value of molecular analysis to expert review in refining classification of uncommon soft tissue tumors. Genes Chromosomes Cancer 2024; 63:e23196. [PMID: 37702439 DOI: 10.1002/gcc.23196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/06/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023] Open
Abstract
The classification of many soft tissue tumors remains subjective due their rarity, significant overlap in microscopic features and often a non-specific immunohistochemical (IHC) profile. The application of molecular genetic tools, which leverage the underlying molecular pathogenesis of these neoplasms, have considerably improved the diagnostic abilities of pathologists and refined classification based on objective molecular markers. In this study, we describe the results of an international collaboration conducted over a 3-year period, assessing the added diagnostic value of applying molecular genetics to sarcoma expert pathologic review in a selected series of 84 uncommon, mostly unclassifiable mesenchymal tumors, 74 of which originated in soft tissues and 10 in bone. The case mix (71% historical, 29% contemporary) included mostly unusual and challenging soft tissue tumors, which remained unclassified even with the benefit of expert review and routine ancillary methods, including broad IHC panels and a limited number of commercially available fluorescence in situ hybridization (FISH) probes. All cases were further tested by FISH using a wide range of custom bacterial artificial chromosome probes covering most of known fusions in sarcomas, whereas targeted RNA sequencing was performed in 13 cases negative by FISH, for potential discovery of novel fusion genes. Tumor-defining molecular alterations were found in 48/84 tumors (57%). In 27 (32%) cases the tumor diagnosis was refined or revised by the additional molecular work-up, including five cases (6%), in which the updated diagnosis had clinical implications. Sarcoma classification is rapidly evolving due to an increased molecular characterization of these neoplasms, so unsurprisingly 17% of the tumors in this series harbored abnormalities only very recently described as defining novel molecularly defined soft tissue tumor subsets.
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Affiliation(s)
- Albert J H Suurmeijer
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Brendan C Dickson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Spring LM, Mortensen L, Abraham E, Keenan J, Medford A, Ma A, Padden S, Denault E, Ryan L, Iafrate AJ, Lennerz J, Hochberg E, Wander SA, Moy B, Isakoff SJ, Juric D, Brennan KA, Smith DE, Civiello B, Mulvey T, Comander A, Ellisen LW, Schwartz JH, Bardia A. Virtual Molecular and Precision Medicine Clinic to Improve Access to Clinical Trials for Patients With Metastatic Breast Cancer: An Academic/Community Collaboration. JCO Oncol Pract 2024; 20:69-76. [PMID: 37922440 DOI: 10.1200/op.23.00193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/26/2023] [Accepted: 09/26/2023] [Indexed: 11/05/2023] Open
Abstract
PURPOSE There is a demand for improved care delivery surrounding genomic testing and clinical trial enrollment among patients with metastatic breast cancer (MBC). We sought to improve the current process via real-time informal consultation and prescreening assessment for patients with MBC treated by community and academic medical oncologists by implementing a virtual molecular and precision medicine (vMAP) clinic. METHODS The vMAP program used a virtual referral system directed to a multidisciplinary team with precision medicine expertise. Providers contacted vMAP regarding patients with MBC, and on receipt of referral, the vMAP team engaged in discussion to identify if further diagnostics were needed (including genomic testing) and to identify potential clinical trials or standard treatment options. Recommendations were then sent to the referring provider within 72 hours. Pre-/postsurveys were issued to network physicians to assess for barriers, clinical trial access, and vMAP referral experience. Program implementation was evaluated with the Squire 2.0 reporting guidelines for quality improvement in health care as a framework. RESULTS Eighty-one cases from 22 providers were referred to vMAP over a 26-month period. The average response time to the referring provider with a finalized recommendation was 1.90 ± 1.82 days. A total of 86.4% of cases had clinical trial options on vMAP prescreen, with 40.7% initiating formal screening assessments and 27 patients (33.3%) ultimately enrolling on trials. On resurvey, 92% of survey responses across community oncology referring providers said that they were very likely to use vMAP again. CONCLUSION In the initial 2-year period, vMAP demonstrated an efficient means to offer real-time interpretation of genomic testing and identification of clinical trials for patients with MBC, with effective clinical trial enrollment and high rates of referring provider satisfaction.
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Affiliation(s)
- Laura M Spring
- Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Mass General Cancer Center at Waltham, Waltham, MA
| | | | | | | | - Arielle Medford
- Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Annie Ma
- Massachusetts General Hospital, Boston, MA
| | | | | | | | - A John Iafrate
- Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Jochen Lennerz
- Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Ephraim Hochberg
- Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Seth A Wander
- Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Mass General/North Shore Cancer Center, Danvers, MA
| | - Beverly Moy
- Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Mass General Cancer Center at Waltham, Waltham, MA
| | - Steven J Isakoff
- Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Dejan Juric
- Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | | | - Deborah E Smith
- Mass General Cancer Center at Cooley Dickinson Hospital, Northampton, MA
| | - Barbara Civiello
- Mass General Cancer Center at Wentworth-Douglass Hospital, Dover, NH
| | - Therese Mulvey
- Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Amy Comander
- Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Mass General Cancer Center at Waltham, Waltham, MA
- Mass General Cancer Center at Newton Wellesley Hospital, Newton, MA
| | - Leif W Ellisen
- Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Joel H Schwartz
- Massachusetts General Hospital, Boston, MA
- Mass General/North Shore Cancer Center, Danvers, MA
- Mass General Cancer Center at Cooley Dickinson Hospital, Northampton, MA
| | - Aditya Bardia
- Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Mass General Cancer Center at Waltham, Waltham, MA
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Vos JL, Burman B, Jain S, Fitzgerald CWR, Sherman EJ, Dunn LA, Fetten JV, Michel LS, Kriplani A, Ng KK, Eng J, Tchekmedyian V, Haque S, Katabi N, Kuo F, Han CY, Nadeem Z, Yang W, Makarov V, Srivastava RM, Ostrovnaya I, Prasad M, Zuur CL, Riaz N, Pfister DG, Klebanoff CA, Chan TA, Ho AL, Morris LGT. Nivolumab plus ipilimumab in advanced salivary gland cancer: a phase 2 trial. Nat Med 2023; 29:3077-3089. [PMID: 37620627 DOI: 10.1038/s41591-023-02518-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
Salivary gland cancers (SGCs) are rare, aggressive cancers without effective treatments when metastasized. We conducted a phase 2 trial evaluating nivolumab (nivo, anti-PD-1) and ipilimumab (ipi, anti-CTLA-4) in 64 patients with metastatic SGC enrolled in two histology-based cohorts (32 patients each): adenoid cystic carcinoma (ACC; cohort 1) and other SGCs (cohort 2). The primary efficacy endpoint (≥4 objective responses) was met in cohort 2 (5/32, 16%) but not in cohort 1 (2/32, 6%). Treatment safety/tolerability and progression-free survival (PFS) were secondary endpoints. Treatment-related adverse events grade ≥3 occurred in 24 of 64 (38%) patients across both cohorts, and median PFS was 4.4 months (95% confidence interval (CI): 2.4, 8.3) and 2.2 months (95% CI: 1.8, 5.3) for cohorts 1 and 2, respectively. We present whole-exome, RNA and T cell receptor (TCR) sequencing data from pre-treatment and on-treatment tumors and immune cell flow cytometry and TCR sequencing from peripheral blood at serial timepoints. Responding tumors universally demonstrated clonal expansion of pre-existing T cells and mutational contraction. Responding ACCs harbored neoantigens, including fusion-derived neoepitopes, that induced T cell responses ex vivo. This study shows that nivo+ipi has limited efficacy in ACC, albeit with infrequent, exceptional responses, and that it could be promising for non-ACC SGCs, particularly salivary duct carcinomas. ClinicalTrials.gov identifier: NCT03172624 .
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Affiliation(s)
- Joris L Vos
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bharat Burman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Swati Jain
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Conall W R Fitzgerald
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric J Sherman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lara A Dunn
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James V Fetten
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Loren S Michel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anuja Kriplani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth K Ng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juliana Eng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vatche Tchekmedyian
- Department of Medicine, Maine Medical Center-Tufts University School of Medicine, Portland, ME, USA
| | - Sofia Haque
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nora Katabi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fengshen Kuo
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Catherine Y Han
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zaineb Nadeem
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Yang
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vladimir Makarov
- Center for Immunotherapy and Precision Immuno-oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Raghvendra M Srivastava
- Center for Immunotherapy and Precision Immuno-oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Manu Prasad
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte L Zuur
- Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Department of Otorhinolaryngology Head and Neck Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David G Pfister
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher A Klebanoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Center for Immunotherapy and Precision Immuno-oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Alan L Ho
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Luc G T Morris
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Chen X, Wang W, Yeh J, Wu Y, Oehler VG, Naresh KN, Liu YJ. Clinical Validation of FusionPlex RNA Sequencing and Its Utility in the Diagnosis and Classification of Hematologic Neoplasms. J Mol Diagn 2023; 25:932-944. [PMID: 37813298 DOI: 10.1016/j.jmoldx.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 08/11/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023] Open
Abstract
Recurrent gene rearrangements result in gene fusions that encode chimeric proteins, driving the pathogenesis of many hematologic neoplasms. The fifth edition World Health Organization classification and International Consensus Classification 2022 include an expanding list of entities defined by such gene rearrangements. Therefore, sensitive and rapid methods are needed to identify a broad range of gene fusions for precise diagnosis and prognostication. In this study, we validated the FusionPlex Pan-Heme panel analysis using anchored multiplex PCR/targeted RNA next-generation sequencing for routine clinical testing. Furthermore, we assessed its utility in detecting gene fusions in myeloid and lymphoid neoplasms. The validation cohort of 61 cases demonstrated good concordance between the FusionPlex Pan-Heme panel and other methods, including chromosome analysis, fluorescence in situ hybridization, RT-PCR, and Sanger sequencing, with an analytic sensitivity and specificity of 95% and 100%, respectively. In an independent cohort of 28 patients indicated for FusionPlex testing, gene fusions were detected in 21 patients. The FusionPlex Pan-Heme panel analysis reliably detected fusion partners and patient-specific fusion sequences, allowing accurate classification of hematologic neoplasms and the discovery of new fusion partners, contributing to a better understanding of the pathogenesis of the diseases.
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Affiliation(s)
- Xueyan Chen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington; Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Wenjing Wang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Jeffrey Yeh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Yu Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Vivian G Oehler
- Department of Medicine, University of Washington, Seattle, Washington
| | - Kikkeri N Naresh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington; Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Yajuan J Liu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington.
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Wang T, Askan G, Ozcan K, Rana S, Zehir A, Bhanot UK, Yantiss RK, Rao DS, Wahl SJ, Bagci P, Balci S, Balachandran V, Jarnagin WR, Adsay NV, Klimstra DS, Basturk O. Tumoral Intraductal Neoplasms of the Bile Ducts Comprise Morphologically and Genetically Distinct Entities. Arch Pathol Lab Med 2023; 147:1390-1401. [PMID: 36821179 DOI: 10.5858/arpa.2022-0343-oa] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 02/24/2023]
Abstract
CONTEXT.— Tumoral (grossly visible) intraductal neoplasms of the bile ducts are still being characterized. OBJECTIVE.— To investigate their morphologic, immunohistochemical, and molecular features. DESIGN.— Forty-one cases were classified as gastric-, intestinal-, pancreatobiliary-type intraductal papillary neoplasm (IPN), intraductal oncocytic papillary neoplasm (IOPN), or intraductal tubulopapillary neoplasm (ITPN) on the basis of histology. All neoplasms were subjected to targeted next-generation sequencing. RESULTS.— The mean age at diagnosis was 69 years (42-81 years); male to female ratio was 1.3. Most neoplasms (n = 23, 56%) were extrahepatic/large (mean size, 4.6 cm). The majority (n = 32, 78%) contained high-grade dysplasia, and 68% (n = 28) revealed invasion. All gastric-type IPNs (n = 9) and most ITPNs/IOPNs showed consistent colabeling for CK7/MUC6, which was less common among others (P = .004). Intestinal-type IPNs (n = 5) showed higher rates of CK20 expression than others (P < .001). Overall, the most commonly mutated genes included TP53 and APC, while copy number variants affected ELF3 and CDKN2A/B. All gastric-type IPNs contained an alteration affecting the Wnt signaling pathway; 7 of 9 (78%) showed aberrations in the MAPK pathway. Mutations in APC and KRAS were common in gastric-type IPNs as compared with others (P = .01 for both). SMAD4 was more frequently mutated in intestinal-type IPNs (P = .02). Pancreatobiliary-type IPNs (n = 14) exhibited frequent alterations in tumor suppressor genes including TP53, CDKN2A/B, and ARID2 (P = .04, P = .01 and P = .002, respectively). Of 6 IOPNs analyzed, 3 (50%) revealed ATP1B1-PRKACB fusion. ITPNs (n = 6) showed relatively few recurrent genetic aberrations. Follow-up information was available for 38 patients (median, 58.5 months). The ratio of disease-related deaths was higher for the cases with invasion (56% versus 10%). CONCLUSIONS.— Tumoral intraductal neoplasms of the bile ducts, similar to their counterparts in the pancreas, are morphologically and genetically heterogeneous.
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Affiliation(s)
- Tao Wang
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gokce Askan
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kerem Ozcan
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Satshil Rana
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Umeshkumar K Bhanot
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rhonda K Yantiss
- Department of Pathology, Weill Cornell Medicine, New York, New York (Yantiss)
| | - Deepthi S Rao
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samuel J Wahl
- Department of Pathology, Lenox Hill Hospital, New York, New York (Wahl)
| | - Pelin Bagci
- Department of Pathology, Marmara University Hospital, Istanbul, Turkey (Bagci)
| | - Serdar Balci
- Department of Pathology, Memorial Healthcare Group, Istanbul, Turkey (Balci)
| | - Vinod Balachandran
- The Department of Surgery (Balachandran, Jarnagin), Memorial Sloan Kettering Cancer Center, New York, New York
| | - William R Jarnagin
- The Department of Surgery (Balachandran, Jarnagin), Memorial Sloan Kettering Cancer Center, New York, New York
| | - N Volkan Adsay
- The Department of Pathology, Koç University Hospital and Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey (Adsay)
| | - David S Klimstra
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Olca Basturk
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
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Dagogo-Jack I, Kiedrowski LA, Lennerz JK. Molecular heterogeneity and co-altered genes in MET-amplified ALK-positive lung cancer: Implications for MET targeted therapy. Lung Cancer 2023; 186:107383. [PMID: 37813016 DOI: 10.1016/j.lungcan.2023.107383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023]
Abstract
OBJECTIVES MET amplification is a common mechanism of resistance to second- and third-generation anaplastic lymphoma kinase (ALK) inhibitors. In case series of MET-amplified ALK-rearranged (ALK + ) lung cancer, durability of responses to combinations targeting ALK and MET is variable, suggesting heterogeneity across tumors. However, little is known about the molecular composition of this subset of ALK-rearranged (ALK + ) NSCLC. MATERIALS AND METHODS We queried tissue and plasma databases to compile a group of > 50 specimens with ALK rearrangements and concurrent MET amplification. Fluorescence in-situ hybridization (FISH) and next-generation sequencing (NGS) were utilized to quantify the range of MET copies and describe the global molecular landscape of co-altered genes. RESULTS By FISH, high-level amplification (overall MET/centromere 7 probe ratio ≥ 5) was detected in 75 % of MET-amplified ALK + NSCLC tissue specimens. Intralesional heterogeneity of MET copies was observed, with high-level amplification identified even in cells from tumors with overall low-level MET amplification. Analysis of 48 MET-amplified ALK + NSCLC plasma specimens suggested that high-level amplification is rarely (17 %) detected in plasma. In both tissue and plasma, EML4-ALK variant 1 was the predominant variant (51 %) identified in MET-amplified specimens. ALK kinase domain mutations were only present in a minority of MET-amplified ALK + NSCLCs. MET-amplified ALK + NSCLC plasma specimens were enriched for TP53 mutations (81 % vs 45 %, p = 0.002), EGFR amplification (17 % vs 4 %, p < 0.001), and MYC amplification (21 % vs 3 %, p < 0.001) compared to ALK + NSCLC specimens lacking MET amplification. CONCLUSIONS MET-amplified, ALK + NSCLC often presents with high-level and heterogeneous amplification in tissue, seldom overlaps with ALK mutations, and frequently co-occurs with alterations associated with aggressive tumor biology.
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Affiliation(s)
- Ibiayi Dagogo-Jack
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, USA; Harvard Medical School, Center for Integrated Diagnostics, Massachusetts General Hospital, USA.
| | - Lesli A Kiedrowski
- Department of Medical Affairs, Guardant Health, Inc, Center for Integrated Diagnostics, Massachusetts General Hospital, USA
| | - Jochen K Lennerz
- Harvard Medical School, Center for Integrated Diagnostics, Massachusetts General Hospital, USA; Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital, USA
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Hoskins I, Rao S, Tante C, Cenik C. Integrated multiplexed assays of variant effect reveal cis-regulatory determinants of catechol- O-methyltransferase gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551517. [PMID: 38014045 PMCID: PMC10680568 DOI: 10.1101/2023.08.02.551517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Multiplexed assays of variant effect are powerful methods to profile the consequences of rare variants on gene expression and organismal fitness. Yet, few studies have integrated several multiplexed assays to map variant effects on gene expression in coding sequences. Here, we pioneered a multiplexed assay based on polysome profiling to measure variant effects on translation at scale, uncovering single-nucleotide variants that increase and decrease ribosome load. By combining high-throughput ribosome load data with multiplexed mRNA and protein abundance readouts, we mapped the cis-regulatory landscape of thousands of catechol-O-methyltransferase (COMT) variants from RNA to protein and found numerous coding variants that alter COMT expression. Finally, we trained machine learning models to map signatures of variant effects on COMT gene expression and uncovered both directional and divergent impacts across expression layers. Our analyses reveal expression phenotypes for thousands of variants in COMT and highlight variant effects on both single and multiple layers of expression. Our findings prompt future studies that integrate several multiplexed assays for the readout of gene expression.
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Affiliation(s)
- Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Charisma Tante
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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Singh H, Keller RB, Kapner KS, Dilly J, Raghavan S, Yuan C, Cohen EF, Tolstorukov M, Andrews E, Brais LK, Da Silva A, Perez K, Rubinson DA, Surana R, Giannakis M, Ng K, Clancy TE, Yurgelun MB, Schletchter B, Clark JW, Shapiro GI, Rosenthal MH, Hornick JL, Nardi V, Li YY, Gupta H, Cherniack AD, Meyerson M, Cleary JM, Nowak JA, Wolpin BM, Aguirre AJ. Oncogenic Drivers and Therapeutic Vulnerabilities in KRAS Wild-Type Pancreatic Cancer. Clin Cancer Res 2023; 29:4627-4643. [PMID: 37463056 PMCID: PMC10795103 DOI: 10.1158/1078-0432.ccr-22-3930] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/17/2023] [Accepted: 07/14/2023] [Indexed: 07/20/2023]
Abstract
PURPOSE Approximately 8% to 10% of pancreatic ductal adenocarcinomas (PDAC) do not harbor mutations in KRAS. Understanding the unique molecular and clinical features of this subset of pancreatic cancer is important to guide patient stratification for clinical trials of molecularly targeted agents. EXPERIMENTAL DESIGN We analyzed a single-institution cohort of 795 exocrine pancreatic cancer cases (including 785 PDAC cases) with a targeted multigene sequencing panel and identified 73 patients (9.2%) with KRAS wild-type (WT) pancreatic cancer. RESULTS Overall, 43.8% (32/73) of KRAS WT cases had evidence of an alternative driver of the MAPK pathway, including BRAF mutations and in-frame deletions and receptor tyrosine kinase fusions. Conversely, 56.2% of cases did not harbor a clear MAPK driver alteration, but 29.3% of these MAPK-negative KRAS WT cases (12/41) demonstrated activating alterations in other oncogenic drivers, such as GNAS, MYC, PIK3CA, and CTNNB1. We demonstrate potent efficacy of pan-RAF and MEK inhibition in patient-derived organoid models carrying BRAF in-frame deletions. Moreover, we demonstrate durable clinical benefit of targeted therapy in a patient harboring a KRAS WT tumor with a ROS1 fusion. Clinically, patients with KRAS WT tumors were significantly younger in age of onset (median age: 62.6 vs. 65.7 years; P = 0.037). SMAD4 mutations were associated with a particularly poor prognosis in KRAS WT cases. CONCLUSIONS This study defines the genomic underpinnings of KRAS WT pancreatic cancer and highlights potential therapeutic avenues for future investigation in molecularly directed clinical trials. See related commentary by Kato et al., p. 4527.
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Affiliation(s)
- Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Rachel B. Keller
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Kevin S. Kapner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Julien Dilly
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Biological and biomedical sciences program, Harvard Medical School, Boston, MA
- The Broad Institute of Harvard and MIT, Cambridge, MA
| | - Srivatsan Raghavan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- The Broad Institute of Harvard and MIT, Cambridge, MA
| | - Chen Yuan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Elizabeth F. Cohen
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
| | - Michael Tolstorukov
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
| | - Elizabeth Andrews
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Lauren K. Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Annacarolina Da Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Pathology, Weill Cornell Medical College, New York, NY
| | - Kimberly Perez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Douglas A. Rubinson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Rishi Surana
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Thomas E. Clancy
- Harvard Medical School, Boston, MA
- Division of Surgical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Surgery, Brigham and Women’s Hospital, Boston, MA
| | - Matthew B. Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Benjamin Schletchter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Jeffrey W. Clark
- Harvard Medical School, Boston, MA
- Massachusetts General Hospital Cancer Center, Boston, MA
| | - Geoffrey I. Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Michael H. Rosenthal
- Department of Radiology, Dana-Farber Cancer Institute, Boston, MA
- Department of Radiology, Brigham and Women’s Hospital, Boston, MA
| | - Jason L. Hornick
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Yvonne Y. Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- The Broad Institute of Harvard and MIT, Cambridge, MA
| | - Hersh Gupta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- The Broad Institute of Harvard and MIT, Cambridge, MA
| | - Andrew D. Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- The Broad Institute of Harvard and MIT, Cambridge, MA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- The Broad Institute of Harvard and MIT, Cambridge, MA
| | - James M. Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Jonathan A. Nowak
- Harvard Medical School, Boston, MA
- Department of Radiology, Brigham and Women’s Hospital, Boston, MA
| | - Brian M. Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Andrew J. Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- The Broad Institute of Harvard and MIT, Cambridge, MA
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Warmke LM, Al-Ibraheemi A, Wang L, Parham D, Rudzinski ER, Stohr BA, Miles C, Habeeb O, Davis JL. FGFR1 gene fusions in a subset of pediatric mesenchymal tumors: Expanding the genetic spectrum of tumors sharing histologic overlap with infantile fibrosarcoma and "NTRK-rearranged" spindle cell neoplasms. Genes Chromosomes Cancer 2023; 62:641-647. [PMID: 37265193 DOI: 10.1002/gcc.23179] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/01/2023] [Accepted: 05/20/2023] [Indexed: 06/03/2023] Open
Abstract
As the classification of kinase-driven spindle cell tumors continues to evolve, we describe the first series of pediatric mesenchymal tumors harboring FGFR1 gene fusions that share histologic overlap with infantile fibrosarcoma and "NTRK-rearranged" spindle cell neoplasms. Herein, we present three cases of FGFR1-rearranged pediatric mesenchymal tumors, including one case with FGFR1::PARD6B gene fusion and two cases with FGFR1::EBF2 gene fusion. The tumors involved infants ranging from 3 to 9 months in age with a male-to-female ratio of 2:1. All tumors involved the deep soft tissue of the gluteal, pelvic, or perirectal region. Histologically, the tumors comprised a cellular spindle cell neoplasm with primitive stellate cells, focal myxoid stroma, focal epithelioid features, no necrosis, and occasional mitotic figures (2-6 per 10 high-power field). By immunohistochemistry, the neoplastic cells focally expressed CD34 but lacked expression of S100 protein, SMA, desmin, myogenin, MyoD1, pan-TRK, and ALK. These three cases, including a case with long-term clinical follow-up, demonstrate that FGFR1 fusions occur in a subset of newly described pediatric kinase-driven mesenchymal tumors with locally aggressive behavior. Importantly, knowledge of these genetic alterations in this spectrum of pediatric tumors is key for diagnostic and targeted therapeutic purposes.
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Affiliation(s)
- Laura M Warmke
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Alyaa Al-Ibraheemi
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, United States
| | - Larry Wang
- Department of Pathology, Children's Hospital Los Angeles, Los Angeles, California, United States
| | - David Parham
- Department of Pathology, Children's Hospital Los Angeles, Los Angeles, California, United States
| | - Erin R Rudzinski
- Department of Laboratories, Seattle Children's Hospital, Seattle, Washington, United States
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, United States
| | - Bradley A Stohr
- Department of Pathology, University of California San Francisco, San Francisco, California, United States
| | - Carina Miles
- Department of Pathology, Middlemore Hospital, Auckland, New Zealand
| | - Omar Habeeb
- Department of Pathology, Middlemore Hospital, Auckland, New Zealand
| | - Jessica L Davis
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana, United States
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46
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Zhao J, Reuther J, Scozzaro K, Hawley M, Metzger E, Emery M, Chen I, Barbosa M, Johnson L, O'Connor A, Washburn M, Hartje L, Reckase E, Johnson V, Zhang Y, Westheimer E, O'Callaghan W, Malani N, Chesh A, Moreau M, Daber R. Personalized Cancer Monitoring Assay for the Detection of ctDNA in Patients with Solid Tumors. Mol Diagn Ther 2023; 27:753-768. [PMID: 37632661 PMCID: PMC10590345 DOI: 10.1007/s40291-023-00670-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2023] [Indexed: 08/28/2023]
Abstract
BACKGROUND Highly sensitive molecular assays have been developed to detect plasma-based circulating tumor DNA (ctDNA), and emerging evidence suggests their clinical utility for monitoring minimal residual disease and recurrent disease, providing prognostic information, and monitoring therapy responses in patients with solid tumors. The Invitae Personalized Cancer Monitoring™ assay uses a patient-specific, tumor-informed variant signature identified through whole exome sequencing to detect ctDNA in peripheral blood of patients with solid tumors. METHODS The assay's tumor whole exome sequencing and ctDNA detection components were analytically validated using 250 unique human specimens and nine commercial reference samples that generated 1349 whole exome sequencing and cell-free DNA (cfDNA)-derived libraries. A comparison of tumor and germline whole exome sequencing was used to identify patient-specific tumor variant signatures and generate patient-specific panels, followed by targeted next-generation sequencing of plasma-derived cfDNA using the patient-specific panels with anchored multiplex polymerase chain reaction chemistry leveraging unique molecular identifiers. RESULTS Whole exome sequencing resulted in overall sensitivity of 99.8% and specificity of > 99.9%. Patient-specific panels were successfully designed for all 63 samples (100%) with ≥ 20% tumor content and 24 (80%) of 30 samples with ≥ 10% tumor content. Limit of blank studies using 30 histologically normal, formalin-fixed paraffin-embedded specimens resulted in 100% expected panel design failure. The ctDNA detection component demonstrated specificity of > 99.9% and sensitivity of 96.3% for a combination of 10 ng of cfDNA input, 0.008% allele frequency, 50 variants on the patient-specific panels, and a baseline threshold. Limit of detection ranged from 0.008% allele frequency when utilizing 60 ng of cfDNA input with 18-50 variants in the patient-specific panels (> 99.9% sensitivity) with a baseline threshold, to 0.05% allele frequency when using 10 ng of cfDNA input with an 18-variant panel with a monitoring threshold (> 99.9% sensitivity). CONCLUSIONS The Invitae Personalized Cancer Monitoring assay, featuring a flexible patient-specific panel design with 18-50 variants, demonstrated high sensitivity and specificity for detecting ctDNA at variant allele frequencies as low as 0.008%. This assay may support patient prognostic stratification, provide real-time data on therapy responses, and enable early detection of residual/recurrent disease.
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Affiliation(s)
- Jianhua Zhao
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA.
| | | | - Kaylee Scozzaro
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Megan Hawley
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Emily Metzger
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Matthew Emery
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Ingrid Chen
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | | | - Laura Johnson
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Alijah O'Connor
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Mike Washburn
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Luke Hartje
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Erik Reckase
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Verity Johnson
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Yuhua Zhang
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | | | | | - Nirav Malani
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Adrian Chesh
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Michael Moreau
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Robert Daber
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
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47
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Yavas A, Tan J, Ozkan HS, Yilmaz F, Reid MD, Bagci P, Shi J, Shia J, Adsay V, Klimstra DS, Basturk O. Solitary Fibrous Tumor of the Pancreas: Analysis of 9 Cases With Literature Review. Am J Surg Pathol 2023; 47:1230-1242. [PMID: 37573546 PMCID: PMC10592360 DOI: 10.1097/pas.0000000000002108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Solitary fibrous tumor (SFT) has been increasingly reported in various anatomic sites. However, it is still extremely rare in the pancreas. Herein, we present the first series of primary pancreatic SFTs. Nine cases of primary pancreatic SFTs were analyzed. The mean age was 60 years (36 to 76 y) with no sex predilection. Six tumors were in the head, 3 were in the tail. On imaging studies, tumors were described as a hypervascular mass, 2 revealed cystic areas, and 3 were favored to be neuroendocrine tumors. On biopsy, 2 cases were diagnosed as atypical spindle cell tumor; one was misdiagnosed as suspicious for sarcoma, and another case as metastatic renal cell carcinoma. Two were diagnosed as low-grade sarcoma and low-grade stromal tumor on frozen sections. Grossly, tumors were well-demarcated with a median size of 4 cm (0.9 to 15 cm). Microscopically, they were composed of ovoid to spindle tumor cells with no significant mitotic activity and were arranged in alternating hypercellular and hypocellular areas. Staghorn-like vessels and entrapped pancreatic parenchyma were also detected within all tumors. Tumor cells revealed diffuse/strong nuclear STAT6 expression in 7 of 8, CD34 in 7 of 9, and bcl-2 in 4 of 4 tested cases. One tested tumor harbored NAB2 - STAT6 fusion. Eight patients with available follow-up data were free of disease at a mean follow-up of 76 months (3 to 189 mo). SFT should be considered in the differential diagnoses of mesenchymal neoplasms of the pancreas. Immunohistochemical nuclear STAT6 expression is a characteristic feature of SFT. Primary pancreatic SFTs seem to have favorable biological behavior in our series.
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Affiliation(s)
- Aslihan Yavas
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Hulya Sahin Ozkan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Funda Yilmaz
- Department of Pathology, Ege University, Izmir, Turkey
| | - Michelle D Reid
- Department of Pathology, Emory University Hospital, Atlanta, GA, USA
| | - Pelin Bagci
- Department of Pathology, Marmara University, Istanbul, Turkey
| | - Jiaqi Shi
- Department of Pathology and Clinical Labs, University of Michigan, Ann Arbor, MI, USA
| | - Jinru Shia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Volkan Adsay
- Department of Pathology, Koc University, Istanbul, Turkey
| | - David S. Klimstra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olca Basturk
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Mitiushkina NV, Tiurin VI, Anuskina AA, Bordovskaya NA, Shestakova AD, Martianov AS, Bubnov MG, Shishkina AS, Semina MV, Romanko AA, Kuligina ES, Imyanitov EN. Molecular Analysis of Biliary Tract Cancers with the Custom 3' RACE-Based NGS Panel. Diagnostics (Basel) 2023; 13:3168. [PMID: 37891989 PMCID: PMC10605186 DOI: 10.3390/diagnostics13203168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/05/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
The technique 3' rapid amplification of cDNA ends (3' RACE) allows for detection of translocations with unknown gene partners located at the 3' end of the chimeric transcript. We composed a 3' RACE-based RNA sequencing panel for the analysis of FGFR1-4 gene rearrangements, detection of activating mutations located within FGFR1-4, IDH1/2, ERBB2 (HER2), KRAS, NRAS, BRAF, and PIK3CA genes, and measurement of the expression of ERBB2, PD-L1, and FGFR1-4 transcripts. This NGS panel was utilized for the molecular profiling of 168 biliary tract carcinomas (BTCs), including 83 intrahepatic cholangiocarcinomas (iCCAs), 44 extrahepatic cholangiocarcinomas (eCCAs), and 41 gallbladder adenocarcinomas (GBAs). The NGS failure rate was 3/168 (1.8%). iCCAs, but not other categories of BTCs, were characterized by frequent FGFR2 alterations (17/82, 20.7%) and IDH1/2 mutations (23/82, 28%). Other potentially druggable events included ERBB2 amplifications or mutations (7/165, 4.2% of all successfully analyzed BTCs) and BRAF p.V600E mutations (3/165, 1.8%). In addition to NGS, we analyzed microsatellite instability (MSI) using the standard five markers and revealed this event in 3/158 (1.9%) BTCs. There were no instances of ALK, ROS1, RET, and NTRK1-3 gene rearrangements or MET exon 14 skipping mutations. Parallel analysis of 47 iCCA samples with the Illumina TruSight Tumor 170 kit confirmed good performance of our NGS panel. In conclusion, targeted RNA sequencing coupled with the 3' RACE technology is an efficient tool for the molecular diagnostics of BTCs.
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Affiliation(s)
- Natalia V. Mitiushkina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Vladislav I. Tiurin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Aleksandra A. Anuskina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Natalia A. Bordovskaya
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Anna D. Shestakova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Aleksandr S. Martianov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St. Petersburg, Russia
| | - Mikhail G. Bubnov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Anna S. Shishkina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Maria V. Semina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Aleksandr A. Romanko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Ekaterina S. Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St. Petersburg, Russia
| | - Evgeny N. Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St. Petersburg, Russia
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Yearley AG, Chalif EJ, Gupta S, Chalif JI, Bernstock JD, Nawabi N, Arnaout O, Smith TR, Reardon DA, Laws ER. Metastatic pituitary tumors: an institutional case series. Pituitary 2023; 26:561-572. [PMID: 37523025 DOI: 10.1007/s11102-023-01341-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
PURPOSE Pituitary carcinomas are a rare entity that respond poorly to multimodal therapy. Patients follow a variable disease course that remains ill-defined. METHODS We present an institutional case series of patients treated for pituitary carcinomas over a 30-year period from 1992 to 2022. A systematic review was conducted to identify prior case series of patients with pituitary carcinomas. RESULTS Fourteen patients with a mean age at pituitary carcinoma diagnosis of 52.5 years (standard deviation [SD] 19.4) met inclusion criteria. All 14 patients had tumor subtypes confirmed by immunohistochemistry and hormone testing, with the most common being ACTH-producing pituitary adenomas (n = 12). Patients had a median progression-free survival (PFS) of 1.4 years (range 0.7-10.0) and a median overall survival (OS) of 8.4 years (range 2.3-24.0) from pituitary adenoma diagnosis. Median PFS and OS were 0.6 years (range 0.0-2.2) and 1.5 years (range 0.1-9.6) respectively upon development of metastases. Most patients (n = 12) had locally invasive disease to the cavernous sinus, dorsum sellae dura, or sphenoid sinus prior to metastasis. Common sites of metastasis included the central nervous system, liver, lung, and bone. In a pooled analysis including additional cases from the literature, treatment of metastases with chemotherapy or a combination of radiation therapy and chemotherapy significantly prolonged PFS (p = 0.02), while failing to significantly improve OS (p = 0.14). CONCLUSION Pituitary carcinomas are highly recurrent, heterogenous tumors with variable responses to treatment. Multidisciplinary management with an experienced neuro-endocrine and neuro-oncology team is needed given the unrelenting nature of this disease.
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Affiliation(s)
- Alexander G Yearley
- Harvard Medical School, Boston, MA, 02115, USA.
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, 02115, USA.
| | - Eric J Chalif
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Saksham Gupta
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Joshua I Chalif
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Joshua D Bernstock
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Noah Nawabi
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Omar Arnaout
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Timothy R Smith
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - David A Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Edward R Laws
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, 02115, USA.
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50
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Schieffer KM, Moccia A, Bucknor BA, Stonerock E, Jayaraman V, Jenkins H, McKinney A, Koo SC, Mathew MT, Mardis ER, Lee K, Reshmi SC, Cottrell CE. Expanding the Clinical Utility of Targeted RNA Sequencing Panels beyond Gene Fusions to Complex, Intragenic Structural Rearrangements. Cancers (Basel) 2023; 15:4394. [PMID: 37686670 PMCID: PMC10486946 DOI: 10.3390/cancers15174394] [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: 07/31/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Gene fusions are a form of structural rearrangement well established as driver events in pediatric and adult cancers. The identification of such events holds clinical significance in the refinement, prognostication, and provision of treatment in cancer. Structural rearrangements also extend beyond fusions to include intragenic rearrangements, such as internal tandem duplications (ITDs) or exon-level deletions. These intragenic events have been increasingly implicated as cancer-promoting events. However, the detection of intragenic rearrangements may be challenging to resolve bioinformatically with short-read sequencing technologies and therefore may not be routinely assessed in panel-based testing. Within an academic clinical laboratory, over three years, a total of 608 disease-involved samples (522 hematologic malignancy, 86 solid tumors) underwent clinical testing using Anchored Multiplex PCR (AMP)-based RNA sequencing. Hematologic malignancies were evaluated using a custom Pan-Heme 154 gene panel, while solid tumors were assessed using a custom Pan-Solid 115 gene panel. Gene fusions, ITDs, and intragenic deletions were assessed for diagnostic, prognostic, or therapeutic significance. When considering gene fusions alone, we report an overall diagnostic yield of 36% (37% hematologic malignancy, 41% solid tumors). When including intragenic structural rearrangements, the overall diagnostic yield increased to 48% (48% hematologic malignancy, 45% solid tumor). We demonstrate the clinical utility of reporting structural rearrangements, including gene fusions and intragenic structural rearrangements, using an AMP-based RNA sequencing panel.
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Affiliation(s)
- Kathleen M. Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Amanda Moccia
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Brianna A. Bucknor
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Eileen Stonerock
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Heather Jenkins
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Aimee McKinney
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Selene C. Koo
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Mariam T. Mathew
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Elaine R. Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Shalini C. Reshmi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Catherine E. Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
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