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Yun J, Lee DS, Lee S, Yun H. Multiple Primary Cancers With Hematologic Malignancies and Germline Predisposition: A Case Series. Ann Lab Med 2024; 44:446-449. [PMID: 38449380 PMCID: PMC11169767 DOI: 10.3343/alm.2023.0444] [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: 11/09/2023] [Revised: 12/15/2023] [Accepted: 02/12/2024] [Indexed: 03/08/2024] Open
Abstract
The term "multiple primary (MP) cancers" refers to the existence of more than one cancer in the same patient. The combination of MP cancers with hematological malignancies is relatively uncommon. In this study, we present five patients diagnosed with MP cancers concomitant with hematological malignancies. We comprehensively analyzed their clinical characteristics, cytogenetic profiles, and germline and somatic variants. As first primaries, two patients had solid cancer not followed by cytotoxic therapy and three had hematologic cancer, followed by cytotoxic therapy. The second primaries were all hematologic malignancies that did not meet the criteria for therapy-related myeloid neoplasm. Notably, two (40%) out of the five patients harbored pathogenic potential/presumed germline variants in cancer predisposition genes. Therefore, germline variant testing should be considered when MP cancers with hematological malignancies require consideration for related donor stem cell transplantation.
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Affiliation(s)
- Jiwon Yun
- Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
| | - Dong Soon Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sungyoung Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
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2
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González-Avendaño M, López J, Vergara-Jaque A, Cerda O. The power of computational proteomics platforms to decipher protein-protein interactions. Curr Opin Struct Biol 2024; 88:102882. [PMID: 39003917 DOI: 10.1016/j.sbi.2024.102882] [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: 03/28/2024] [Revised: 05/31/2024] [Accepted: 06/19/2024] [Indexed: 07/16/2024]
Abstract
Adopting computational tools for analyzing extensive biological datasets has profoundly transformed our understanding and interpretation of biological phenomena. Innovative platforms have emerged, providing automated analysis to unravel essential insights about proteins and the complexities of their interactions. These computational advancements align with traditional studies, which employ experimental techniques to discern and quantify physical and functional protein-protein interactions (PPIs). Among these techniques, tandem mass spectrometry is notably recognized for its precision and sensitivity in identifying PPIs. These approaches might serve as important information enabling the identification of PPIs with potential pharmacological significance. This review aims to convey our experience using computational tools for detecting PPI networks and offer an analysis of platforms that facilitate predictions derived from experimental data.
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Affiliation(s)
- Mariela González-Avendaño
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Universidad de Talca, Talca, Chile; Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Santiago, Chile
| | - Joaquín López
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Ariela Vergara-Jaque
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Universidad de Talca, Talca, Chile; Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Santiago, Chile.
| | - Oscar Cerda
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, Universidad de Chile, Santiago, Chile.
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3
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Pavlick DC, Frampton GM, Ross JR. Understanding variants of unknown significance and classification of genomic alterations. Oncologist 2024:oyae149. [PMID: 38982622 DOI: 10.1093/oncolo/oyae149] [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: 11/01/2023] [Accepted: 04/16/2024] [Indexed: 07/11/2024] Open
Abstract
Despite recent efforts to issue clinical guidelines outlining strategies to define the pathogenicity of genomic variants, there is currently no standardized framework for which to make these assertions. This review does not present a step-by-step methodology, but rather takes a holistic approach to discuss many aspects which should be taken into consideration when determining variant pathogenicity. Categorization should be curated to reflect relevant findings within the scope of the specific medical context. Functional characterization should evaluate all available information, including results from literature reviews, different classes of genomic data repositories, and applicable computational predictive algorithms. This article further proposes a multidimensional view to infer pathogenic status from many genomic measurements across multiple axes. Notably, tumor suppressors and oncogenes exhibit fundamentally different biology which helps refine the importance of effects on splicing, mutation interactions, copy number thresholds, rearrangement annotations, germline status, and genome-wide signatures. Understanding these relevant datapoints with thoughtful perspective could aid in the reclassification of variants of unknown significance (VUS), which are ambiguously understood and currently have uncertain clinical implications. Ongoing assessments of VUS examining these relevant biological axes could lead to more accurate classification of variant pathogenicity interpretation in diagnostic oncology.
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Affiliation(s)
- Dean C Pavlick
- Department of Computational Discovery, Foundation Medicine, Inc., Boston, MA, United States
| | - Garrett M Frampton
- Department of Computational Discovery, Foundation Medicine, Inc., Boston, MA, United States
| | - Jeffrey R Ross
- Department of Pathology, Foundation Medicine, Inc., Boston, MA, United States, and
- Departments of Pathology, Medicine (Oncology), and Urology, Upstate Medical University, Syracuse, NY, United States
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4
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Shah PS, Hughes EG, Sukhadia SS, Green DC, Houde BE, Tsongalis GJ, Tafe LJ. Validation and Implementation of a Somatic-Only Tumor Exome for Routine Clinical Application. J Mol Diagn 2024:S1525-1578(24)00151-X. [PMID: 38972591 DOI: 10.1016/j.jmoldx.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 05/13/2024] [Accepted: 05/30/2024] [Indexed: 07/09/2024] Open
Abstract
Next-generation sequencing-based genomic testing is standard of care for tumor workflows. However, its application across different institutions continues to be challenging given the diversity of needs and resource availability among different institutions globally. Moreover, the use of a variety of different panels, including those from a few individual genes to those involving hundreds of genes, results in a relatively skewed distribution of care for patients. It is imperative to obtain a higher level of standardization without having to be restricted to specific kits or requiring repeated validations, which are generally expensive. We show the validation and clinical implementation of the DH-CancerSeq assay, a tumor-only whole-exome-based sequencing assay with integrated informatics, while providing similar input requirements, sensitivity, and specificity to a previously validated targeted gene panel and maintaining similar turnaround times for patient care.
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Affiliation(s)
- Parth S Shah
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire; Genome Informatics, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire; Dartmouth Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Edward G Hughes
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Shrey S Sukhadia
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire; Genome Informatics, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Donald C Green
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Brianna E Houde
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Gregory J Tsongalis
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire; Dartmouth Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Laura J Tafe
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire; Dartmouth Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire.
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5
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Luo Y, Xia Y, Liu D, Li X, Li H, Liu J, Zhou D, Dong Y, Li X, Qian Y, Xu C, Tao K, Li G, Pan W, Zhong Q, Liu X, Xu S, Wang Z, Liu R, Zhang W, Shan W, Fang T, Wang S, Peng Z, Jin P, Jin N, Shi S, Chen Y, Wang M, Jiao X, Luo M, Gong W, Wang Y, Yao Y, Zhao Y, Huang X, Ji X, He Z, Zhao G, Liu R, Wu M, Chen G, Hong L, Ma D, Fang Y, Liang H, Gao Q. Neoadjuvant PARPi or chemotherapy in ovarian cancer informs targeting effector Treg cells for homologous-recombination-deficient tumors. Cell 2024:S0092-8674(24)00653-6. [PMID: 38971151 DOI: 10.1016/j.cell.2024.06.013] [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: 01/18/2023] [Revised: 02/12/2024] [Accepted: 06/10/2024] [Indexed: 07/08/2024]
Abstract
Homologous recombination deficiency (HRD) is prevalent in cancer, sensitizing tumor cells to poly (ADP-ribose) polymerase (PARP) inhibition. However, the impact of HRD and related therapies on the tumor microenvironment (TME) remains elusive. Our study generates single-cell gene expression and T cell receptor profiles, along with validatory multimodal datasets from >100 high-grade serous ovarian cancer (HGSOC) samples, primarily from a phase II clinical trial (NCT04507841). Neoadjuvant monotherapy with the PARP inhibitor (PARPi) niraparib achieves impressive 62.5% and 73.6% response rates per RECIST v.1.1 and GCIG CA125, respectively. We identify effector regulatory T cells (eTregs) as key responders to HRD and neoadjuvant therapies, co-occurring with other tumor-reactive T cells, particularly terminally exhausted CD8+ T cells (Tex). TME-wide interferon signaling correlates with cancer cells upregulating MHC class II and co-inhibitory ligands, potentially driving Treg and Tex fates. Depleting eTregs in HRD mouse models, with or without PARP inhibition, significantly suppresses tumor growth without observable toxicities, underscoring the potential of eTreg-focused therapeutics for HGSOC and other HRD-related tumors.
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Affiliation(s)
- Yikai Luo
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yu Xia
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Dan Liu
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiong Li
- Department of Gynecology & Obstetrics, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Huayi Li
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jiahao Liu
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Dongchen Zhou
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yu Dong
- Precision Scientific (Beijing) Co., Ltd., Beijing 100085, China
| | - Xin Li
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yiyu Qian
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Cheng Xu
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kangjia Tao
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Guannan Li
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wen Pan
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qing Zhong
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xingzhe Liu
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Sen Xu
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhi Wang
- Department of Gynecology & Obstetrics, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Ronghua Liu
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Zhang
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wanying Shan
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tian Fang
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Siyuan Wang
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zikun Peng
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ping Jin
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ning Jin
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shennan Shi
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuxin Chen
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mengjie Wang
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaofei Jiao
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mengshi Luo
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wenjian Gong
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ya Wang
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yue Yao
- Precision Scientific (Beijing) Co., Ltd., Beijing 100085, China
| | - Yi Zhao
- Precision Scientific (Beijing) Co., Ltd., Beijing 100085, China
| | - Xinlin Huang
- Precision Scientific (Beijing) Co., Ltd., Beijing 100085, China
| | - Xuwo Ji
- Precision Scientific (Beijing) Co., Ltd., Beijing 100085, China
| | - Zhaoren He
- BioMap (Beijing) Intelligence Technology Limited, Beijing 100089, China
| | - Guangnian Zhao
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Rong Liu
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mingfu Wu
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Gang Chen
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Li Hong
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ding Ma
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Yong Fang
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Qinglei Gao
- National Clinical Research Center for Obstetrics and Gynecology, Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education, Hubei Provincial Key Laboratory of Tumor Invasion and Metastasis), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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6
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Karchin R, Radivojac P, O'Donnell-Luria A, Greenblatt MS, Tolstorukov MY, Sonkin D. Improving transparency of computational tools for variant effect prediction. Nat Genet 2024:10.1038/s41588-024-01821-8. [PMID: 38956207 DOI: 10.1038/s41588-024-01821-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Affiliation(s)
- Rachel Karchin
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD, USA.
- Departments of Biomedical Engineering, Oncology, and Computer Science, The Johns Hopkins University, Baltimore, MD, USA.
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Marc S Greenblatt
- Department of Medicine and University of Vermont Cancer Center, University of Vermont, Larner College of Medicine, Burlington, VT, USA
| | - Michael Y Tolstorukov
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dmitriy Sonkin
- National Cancer Institute, Division of Cancer Treatment and Diagnosis, Rockville, MD, USA.
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7
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Cioppi F, Cantini G, Ercolino T, Chetta M, Zanatta L, Nesi G, Mannelli M, Maggi M, Canu L, Luconi M. Targeted Next Generation Sequencing molecular profiling and its clinical application in adrenocortical cancer. Eur J Endocrinol 2024; 191:17-30. [PMID: 38917236 DOI: 10.1093/ejendo/lvae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 05/07/2024] [Accepted: 06/20/2024] [Indexed: 06/27/2024]
Abstract
OBJECTIVE Adrenal cortical carcinoma (ACC) is a rare malignancy with a generally poor but heterogeneous prognosis, especially depending on the tumour stage at diagnosis. Identification of somatic gene alterations combined with clinical/histopathological evaluation of the tumour can help improve prognostication. We applied a simplified targeted-Next-Generation Sequencing (NGS) panel to characterise the mutational profiles of ACCs, providing potentially relevant information for better patient management. DESIGN AND METHODS Thirty frozen tumour specimens from a local ACC series were retrospectively analysed by a custom-NGS panel (CDKN2A, CTNNB1, DAXX, MED12, NF1, PRKAR1A, RB1, TERT, TP53, ZNRF3) to detect somatic prioritised single-nucleotide variants. This cohort was integrated with 86 patients from the ACC-TCGA series bearing point-mutations in the same genes and their combinations identified by our panel. Primary endpoints of the analysis on the total cohort (113 patients) were overall survival (OS) and progression-free survival (PFS), and hazard ratio (HR) for the different alterations grouped by the signalling pathways/combinations affected. RESULTS Different PFS, OS, and HR were associated to the different pathways/combinations, being NF1 + TP53 and Wnt/β-catenin + Rb/p53 combined mutations the most deleterious, with a statistical significance for progression HR which is retained only in low-(I/II) stages-NF1 + TP53 combination: HR = 2.96[1.01-8.69] and HR = 13.23[3.15-55.61], all and low stages, respectively; Wnt/β-catenin + Rb/p53 combined pathways: HR = 6.47[2.54-16.49] and HR = 16.24[3.87-68.00], all and low-stages, respectively. CONCLUSIONS A simplified targeted-NGS approach seems the best routinely applicable first step towards somatic genetic characterisation of ACC for prognostic assessment. This approach proved to be particularly promising in low-stage cases, suggesting the need for more stringent surveillance and personalised treatment.
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Affiliation(s)
- Francesca Cioppi
- Department of Experimental and Clinical Medicine, University of Florence, 50139 Florence, Italy
- European Network for the Study of Adrenal Tumours (ENSAT) Centre of Excellence, University of Florence, 50139 Florence, Italy
| | - Giulia Cantini
- European Network for the Study of Adrenal Tumours (ENSAT) Centre of Excellence, University of Florence, 50139 Florence, Italy
- Department of Experimental and Clinical Biomedical Sciences, Endocrinology Section, University of Florence, 50139 Florence, Italy
- Centro di Ricerca e Innovazione sulle Patologie Surrenaliche, AOU Careggi, 50139 Florence, Italy
| | - Tonino Ercolino
- Azienda Ospedaliero-Universitaria Careggi, (AOUC), 50139 Florence, Italy
| | - Massimiliano Chetta
- Medical Genetics, Azienda Ospedaliera di Rilievo Nazionale (A.O.R.N.) Cardarelli, Padiglione, 80131 Naples, Italy
| | - Lorenzo Zanatta
- European Network for the Study of Adrenal Tumours (ENSAT) Centre of Excellence, University of Florence, 50139 Florence, Italy
- Department of Experimental and Clinical Biomedical Sciences, Endocrinology Section, University of Florence, 50139 Florence, Italy
- Azienda Ospedaliero-Universitaria Careggi, (AOUC), 50139 Florence, Italy
| | - Gabriella Nesi
- Department of Health Sciences, University of Florence, 50139 Florence, Italy
| | - Massimo Mannelli
- European Network for the Study of Adrenal Tumours (ENSAT) Centre of Excellence, University of Florence, 50139 Florence, Italy
- Department of Experimental and Clinical Biomedical Sciences, Endocrinology Section, University of Florence, 50139 Florence, Italy
- Centro di Ricerca e Innovazione sulle Patologie Surrenaliche, AOU Careggi, 50139 Florence, Italy
| | - Mario Maggi
- European Network for the Study of Adrenal Tumours (ENSAT) Centre of Excellence, University of Florence, 50139 Florence, Italy
- Department of Experimental and Clinical Biomedical Sciences, Endocrinology Section, University of Florence, 50139 Florence, Italy
- Centro di Ricerca e Innovazione sulle Patologie Surrenaliche, AOU Careggi, 50139 Florence, Italy
- Azienda Ospedaliero-Universitaria Careggi, (AOUC), 50139 Florence, Italy
| | - Letizia Canu
- European Network for the Study of Adrenal Tumours (ENSAT) Centre of Excellence, University of Florence, 50139 Florence, Italy
- Department of Experimental and Clinical Biomedical Sciences, Endocrinology Section, University of Florence, 50139 Florence, Italy
- Centro di Ricerca e Innovazione sulle Patologie Surrenaliche, AOU Careggi, 50139 Florence, Italy
- Azienda Ospedaliero-Universitaria Careggi, (AOUC), 50139 Florence, Italy
| | - Michaela Luconi
- European Network for the Study of Adrenal Tumours (ENSAT) Centre of Excellence, University of Florence, 50139 Florence, Italy
- Department of Experimental and Clinical Biomedical Sciences, Endocrinology Section, University of Florence, 50139 Florence, Italy
- Centro di Ricerca e Innovazione sulle Patologie Surrenaliche, AOU Careggi, 50139 Florence, Italy
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8
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Poonsombudlert K, Mott S, Miller B, Dhakal P, Snow A, Hornberg S, Yodsuwan R, Strouse C, Shaikh H, Magalhaes-Silverman M, Sutamtewagul G. Transplant versus no transplant in myelodysplastic syndrome and acute myeloid leukemia with TP53 mutation; a referral center experience. Eur J Haematol 2024; 113:16-23. [PMID: 38511425 DOI: 10.1111/ejh.14199] [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: 01/03/2024] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
A remarkably high rate of post-transplant relapse in patients with TP53-mutated myelodysplastic syndrome/acute myeloid leukemia (MDS/AML) calls to question the utility of allogeneic stem cell transplant (HSCT). We, therefore, performed a retrospective analysis to compare the outcomes between HSCT (N = 38) versus non-HSCT (N = 45) approaches. Patients in the HSCT cohort were younger (median age 63 vs. 72) while patients in the non-HSCT cohort more commonly had complex karyotype with chromosome 17 aberrancy and 5q deletion (p < .01). A total of 69 TP53 variants including 64 pathogenic variants, and 5 variants of undetermined significance were detected. Nine patients (4 in HSCT and 5 in non-HSCT) had multi-hit TP53 variants. After induction: 57.9% versus 56.6% in the HSCT versus non-HSCT cohort achieved morphologic complete remission. Median time to HSCT was 6 months and median follow-up was 15.1 months for HSCT and 5.7 months for non-HSCT. Median disease-free survival (DFS) and overall survival (OS) were 11.7 and 15.9 months for HSCT, and 4.1 and 5.7 months for non-HSCT cohorts, respectively. Non-relapse mortality at 12 months was 22% versus 44% for HSCT versus non-HSCT. In the HSCT cohort, the rate of grade II-IV acute and chronic graft-versus-host disease (GVHD) was 55% and 18%, respectively. None of the patients from the non-HSCT cohort were alive while four patients from the HSCT cohort were alive, in remission, and without GVHD (GRFS) at the time of abstraction. Better treatment strategies for patients with TP53-mutated MDS/AML remain an area of unmet clinical need.
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MESH Headings
- Humans
- Myelodysplastic Syndromes/therapy
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/mortality
- Myelodysplastic Syndromes/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/diagnosis
- Male
- Middle Aged
- Female
- Mutation
- Hematopoietic Stem Cell Transplantation
- Tumor Suppressor Protein p53/genetics
- Aged
- Retrospective Studies
- Adult
- Transplantation, Homologous
- Treatment Outcome
- Graft vs Host Disease/etiology
- Prognosis
- Aged, 80 and over
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Affiliation(s)
- Kittika Poonsombudlert
- Holden Comprehensive Cancer Center, University of Iowa Hospital and Clinics, Iowa City, Iowa, USA
| | - Sarah Mott
- Holden Comprehensive Cancer Center, University of Iowa Hospital and Clinics, Iowa City, Iowa, USA
| | - Benda Miller
- Holden Comprehensive Cancer Center, University of Iowa Hospital and Clinics, Iowa City, Iowa, USA
| | - Prajwal Dhakal
- Holden Comprehensive Cancer Center, University of Iowa Hospital and Clinics, Iowa City, Iowa, USA
| | - Anthony Snow
- Holden Comprehensive Cancer Center, University of Iowa Hospital and Clinics, Iowa City, Iowa, USA
| | - Sarah Hornberg
- Holden Comprehensive Cancer Center, University of Iowa Hospital and Clinics, Iowa City, Iowa, USA
| | - Ratdanai Yodsuwan
- Holden Comprehensive Cancer Center, University of Iowa Hospital and Clinics, Iowa City, Iowa, USA
| | - Christopher Strouse
- Holden Comprehensive Cancer Center, University of Iowa Hospital and Clinics, Iowa City, Iowa, USA
| | - Hira Shaikh
- Holden Comprehensive Cancer Center, University of Iowa Hospital and Clinics, Iowa City, Iowa, USA
| | | | - Grerk Sutamtewagul
- Holden Comprehensive Cancer Center, University of Iowa Hospital and Clinics, Iowa City, Iowa, USA
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9
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Palathingal Bava E, Sanfrancesco JM, Alkashash A, Favazza L, Aldilami A, Williamson SR, Cheng L, Idrees MT, Al-Obaidy KI. Acquired cystic disease associated renal cell carcinoma: A clinicopathologic and molecular study of 31 tumors. Hum Pathol 2024; 149:48-54. [PMID: 38862094 DOI: 10.1016/j.humpath.2024.06.002] [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: 04/02/2024] [Revised: 05/31/2024] [Accepted: 06/08/2024] [Indexed: 06/13/2024]
Abstract
Acquired cystic disease associated renal cell carcinomas (ACD-RCC) are rare and their molecular and histopathological characteristics are still being explored. We therefore investigated the clinicopathologic and molecular characteristics of 31 tumors. The patients were predominantly male (n = 30), with tumors mainly left-sided (n = 17), unifocal (n = 19), and unilateral (n = 29) and a mean tumor size of 25 mm (range, 3-65 mm). Microscopically, several histologic patterns were present, including pure classic sieve-like (n = 4), and varied proportions of mixed classic sieve-like with papillary (n = 23), tubulocystic (n = 9), compact tubular (n = 4) and solid (n = 1) patterns. Calcium-oxalate crystals were seen in all tumors. Molecular analysis of 9 tumors using next generation sequencing showed alterations in SMARCB1 in 3 tumors (1 with frameshift deletion and 2 with copy number loss in chromosome 22 involving SMARCB1 region), however, INI1 stain was retained in all. Nonrecurrent genetic alterations in SETD2, NF1, NOTCH4, BRCA2 and CANT1 genes were also seen. Additionally, MTOR p.Pro351Ser was identified in one tumor. Copy number analysis showed gains in chromosome 16 (n = 5), 17 (n = 2) and 8 (n = 2) as well as loss in chromosome 22 (n = 2). In summary, ACD-RCC is a recognized subtype of kidney tumors, with several histological architectural patterns. Our molecular data identifies genetic alterations in chromatin modifying genes (SMARCB1 and SETD2), which may suggest a role of such genes in ACD-RCC development.
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Affiliation(s)
- Ejas Palathingal Bava
- Department of Pathology and Laboratory Medicine, Henry Ford Health, Detroit, MI, USA.
| | | | - Ahmed Alkashash
- Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN, USA.
| | - Laura Favazza
- Department of Pathology and Laboratory Medicine, Henry Ford Health, Detroit, MI, USA.
| | - Akram Aldilami
- Department of Neurology, Henry Ford Health, Detroit, MI, USA.
| | - Sean R Williamson
- Pathology and Laboratory Medicine Institute, The Cleveland Clinic, Cleveland, OH, USA.
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI, USA.
| | - Mohammed T Idrees
- Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN, USA.
| | - Khaleel I Al-Obaidy
- Department of Pathology and Laboratory Medicine, Henry Ford Health, Detroit, MI, USA; Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, MI, USA.
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10
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Park JH, Seo AN, Kim M. Diagnostic Usefulness of p53 Immunostaining in Gastric Cancer and Dysplasia: A Real-world Clinical Experience. In Vivo 2024; 38:1865-1874. [PMID: 38936896 PMCID: PMC11215596 DOI: 10.21873/invivo.13641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND/AIM Gastric cancer and its precancerous lesions represent a significant public health concern. A subset of gastric cancers exhibits mutations in the TP53 gene, often accompanying distinctive morphologic alterations. This study aimed to assess the diagnostic efficacy of p53 immunostaining in real-world clinical settings. PATIENTS AND METHODS A retrospective analysis was conducted on 50 cases of gastric tumors and tumor-like lesions, wherein p53 immunostaining played a pivotal diagnostic role. The staining pattern of p53 was examined in conjunction with clinicopathologic parameters. RESULTS Mutant p53 staining pattern demonstrated a significant association with high-grade nuclear atypia (p<0.001), high-grade dysplasia, and tubular adenocarcinoma (p<0.001), as well as microsatellite instability status (p=0.034). Furthermore, the diagnostic utility of p53 immunostaining was evident in scenarios where: 1) biopsy specimens contained few tumor cells, 2) pathologic evaluation of resection margins was limited by cauterization artifacts, and 3) distinction between low-grade and high-grade gastric dysplasia was challenging. CONCLUSION P53 immunostaining can be helpful for the diagnosis of gastric tumor and tumor-like lesions, and accurate pathologic margin evaluation, particularly in lesions demonstrating intestinal-type differentiation and some degree of nuclear atypia.
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Affiliation(s)
- Ji Hyun Park
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - An Na Seo
- Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Moonsik Kim
- Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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11
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Xia W, Zhang S, Ye Y, Xiao H, Zhang Y, Ning G, Zhang Y, Wang W, Fei GH. Clinicopathological and molecular characterization of resected lung adenocarcinoma: Correlations with histopathological grading systems in Chinese patients. Pathol Res Pract 2024; 259:155359. [PMID: 38810376 DOI: 10.1016/j.prp.2024.155359] [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: 02/07/2024] [Revised: 05/04/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
PURPOSE Driver mutations inform lung adenocarcinoma (LUAD) targeted therapy. Association of histopathological attributes and molecular profiles facilitates clinically viable testing platforms. We assessed correlations between LUAD clinicopathological features, mutational landscapes, and two grading systems among Chinese cases. METHODS 79 Chinese LUAD patients undergoing resection were subjected to targeted sequencing. 68 were invasive nonmucinous adenocarcinoma (INMA), graded via: predominant histologic pattern-based grading system (P-GS) or novel IASLC grading system (I-GS). Driver mutation distributions were appraised and correlated with clinical and pathological data. RESULTS Compared to INMA, non-INMA exhibited smaller, well-differentiated tumors with higher mucin content. INMA grade correlated with size, lymph invasion (P-GS), and driver/EGFR mutations. Mutational spectra varied markedly between grades, with EGFR p.L858R and exon 19 deletion mutations predominating in lower grades; while high-grade P-GS tumors often harbored EGFR copy number variants and complex alterations alongside wild-type cases. I-GS upgrade of P-GS grade 2 to grade 3 was underpinned by ≥20 % high-grade regions bearing p.L858R or ALK fusions. Both systems defined tumors of distinctive phenotypic attributes and molecular genotypes. CONCLUSIONS INMA represent larger, mucin-poor, molecularly heterogeneous LUAD with divergent grade-specific mutation profiles. Stronger predictor of clinicopathological attributes and driver mutations, P-GS stratification offers greater accuracy for molecular testing. A small panel encompassing EGFR and ALK captures the majority of P-GS grade 1/2 mutations whereas expanded panels are optimal for grade 3.
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Affiliation(s)
- Wanli Xia
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Siyuan Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Yuanzi Ye
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China.
| | - Han Xiao
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Ying Zhang
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Guangyao Ning
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Yanbei Zhang
- Department of Geriatric Respiratory and Critical Care, Anhui Geriatric Institute, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Wei Wang
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China; Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China.
| | - Guang-He Fei
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China; Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, PR China.
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12
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Malcikova J, Pavlova S, Baliakas P, Chatzikonstantinou T, Tausch E, Catherwood M, Rossi D, Soussi T, Tichy B, Kater AP, Niemann CU, Davi F, Gaidano G, Stilgenbauer S, Rosenquist R, Stamatopoulos K, Ghia P, Pospisilova S. ERIC recommendations for TP53 mutation analysis in chronic lymphocytic leukemia-2024 update. Leukemia 2024; 38:1455-1468. [PMID: 38755420 PMCID: PMC11217004 DOI: 10.1038/s41375-024-02267-x] [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: 01/04/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024]
Abstract
In chronic lymphocytic leukemia (CLL), analysis of TP53 aberrations (deletion and/or mutation) is a crucial part of treatment decision-making algorithms. Technological and treatment advances have resulted in the need for an update of the last recommendations for TP53 analysis in CLL, published by ERIC, the European Research Initiative on CLL, in 2018. Based on the current knowledge of the relevance of low-burden TP53-mutated clones, a specific variant allele frequency (VAF) cut-off for reporting TP53 mutations is no longer recommended, but instead, the need for thorough method validation by the reporting laboratory is emphasized. The result of TP53 analyses should always be interpreted within the context of available laboratory and clinical information, treatment indication, and therapeutic options. Methodological aspects of introducing next-generation sequencing (NGS) in routine practice are discussed with a focus on reliable detection of low-burden clones. Furthermore, potential interpretation challenges are presented, and a simplified algorithm for the classification of TP53 variants in CLL is provided, representing a consensus based on previously published guidelines. Finally, the reporting requirements are highlighted, including a template for clinical reports of TP53 aberrations. These recommendations are intended to assist diagnosticians in the correct assessment of TP53 mutation status, but also physicians in the appropriate understanding of the lab reports, thus decreasing the risk of misinterpretation and incorrect management of patients in routine practice whilst also leading to improved stratification of patients with CLL in clinical trials.
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Affiliation(s)
- Jitka Malcikova
- Department of Internal Medicine, Hematology and Oncology, and Institute of Medical Genetics and Genomics, University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine, Hematology and Oncology, and Institute of Medical Genetics and Genomics, University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Eugen Tausch
- Division of CLL, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Mark Catherwood
- Haematology Department, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Davide Rossi
- Hematology, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Thierry Soussi
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Hematopoietic and Leukemic Development, UMRS_938, Sorbonne University, Paris, France
| | - Boris Tichy
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Arnon P Kater
- Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | | | - Frederic Davi
- Sorbonne Université, Paris, France
- Department of Hematology, Hôpital Pitié-Salpêtière, AP-HP, Paris, France
| | - Gianluca Gaidano
- Division of Haematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Stephan Stilgenbauer
- Division of CLL, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Paolo Ghia
- Università Vita-Salute San Raffaele, Milan, Italy.
- Strategic Research Program on CLL, Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy.
| | - Sarka Pospisilova
- Department of Internal Medicine, Hematology and Oncology, and Institute of Medical Genetics and Genomics, University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic.
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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13
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Choi YJ, Min YK, Lee ST, Choi JR, Shin S. NUP214 Rearrangements in Leukemia Patients: A Case Series From a Single Institution. Ann Lab Med 2024; 44:335-342. [PMID: 38145892 PMCID: PMC10961622 DOI: 10.3343/alm.2023.0301] [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: 07/29/2023] [Revised: 10/16/2023] [Accepted: 12/08/2023] [Indexed: 12/27/2023] Open
Abstract
Background The three best-known NUP214 rearrangements found in leukemia (SET:: NUP214, NUP214::ABL1, and DEK::NUP214) are associated with treatment resistance and poor prognosis. Mouse experiments have shown that NUP214 rearrangements alone are insufficient for leukemogenesis; therefore, the identification of concurrent mutations is important for accurate assessment and tailored patient management. Here, we characterized the demographic characteristics and concurrent mutations in patients harboring NUP214 rearrangements. Methods To identify patients with NUP214 rearrangements, RNA-sequencing results of diagnostic bone marrow aspirates were retrospectively studied. Concurrent targeted next-generation sequencing results, patient demographics, karyotypes, and flow cytometry information were also reviewed. Results In total, 11 patients harboring NUP214 rearrangements were identified, among whom four had SET::NUP214, three had DEK::NUP214, and four had NUP214::ABL1. All DEK::NUP214-positive patients were diagnosed as having AML. In patients carrying SET::NUP214 and NUP214::ABL1, T-lymphoblastic leukemia was the most common diagnosis (50%, 4/8). Concurrent gene mutations were found in all cases. PFH6 mutations were the most common (45.5%, 5/11), followed by WT1 (27.3%, 3/11), NOTCH1 (27.3%, 3/11), FLT3-internal tandem duplication (27.3%, 3/11), NRAS (18.2%, 2/11), and EZH2 (18.2%, 2/11) mutations. Two patients represented the second and third reported cases of NUP214::ABL1-positive AML. Conclusions We examined the characteristics and concurrent test results, including gene mutations, of 11 leukemia patients with NUP214 rearrangement. We hope that the elucidation of the context in which they occurred will aid future research on tailored monitoring and treatment.
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Affiliation(s)
- Yu Jeong Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Young Kyu Min
- Department of Laboratory Medicine, Severance Hospital, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
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14
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Zhang Z, Fu C, Sun Y, Liu Y, Wang Q, Yan W, Wu C, Wang Q, Zeng Z, Wen L, Shen H, Yao L, Liu D, Chen S, Pan J. High hyperdiploid karyotype with ≥ 49 chromosomes represents a heterogeneous subgroup of acute myeloid leukemia with differential TP53 mutation status and prognosis: a single-center study from China. Ann Hematol 2024; 103:2337-2346. [PMID: 38849603 DOI: 10.1007/s00277-024-05834-5] [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: 02/21/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
High hyperdiploid karyotype with ≥ 49 chromosomes (which will be referred to as HHK) is rare in acute myeloid leukemia (AML). The European leukemia network (ELN) excluded those harboring only numerical changes (with ≥ 3 chromosome gains) from CK and listed them in the intermediate risk group, while the UK National Cancer Research Institute Adult Leukaemia Working Group classification defined ≥ 4 unrelated chromosome abnormalities as the cutoff for a poorer prognosis. Controversies occurred among studies on the clinical outcome of HHK AML, and their molecular characteristics remained unstudied. We identified 1.31% (133/10,131) HHK cases within our center, among which 48 cases only had numerical changes (NUM), 42 had ELN defined adverse abnormalities (ADV) and 43 had other structural abnormalities (STR). Our study demonstrated that: (1) No statistical significance for overall survival (OS) was observed among three cytogenetic subgroups (NUM, STR and ADV) and HHK AML should be assigned to the adverse cytogenetic risk group. (2) The OS was significantly worse in HHK AML with ≥ 51 chromosomes compared with those with 49-50 chromosomes. (3) The clinical characteristics were similar between NUM and STR group compared to ADV group. The former two groups had higher white blood cell counts and blasts, lower platelet counts, and mutations associated with signaling, while the ADV group exhibited older age, higher chromosome counts, higher percentage of myelodysplastic syndrome (MDS) history, and a dominant TP53 mutation.
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Affiliation(s)
- Zhiyu Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Chunmei Fu
- Department of Hematology, Xuzhou Central Hospital, 199 Quanshan District, Xuzhou, China
| | - Yingxin Sun
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Department of Hematology, Affiliated hospital of Nantong University, Nantong University, Nantong, China
| | - Yizi Liu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Qian Wang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Wanhui Yan
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Chunxiao Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Qingrong Wang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Zhao Zeng
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Lijun Wen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Hongjie Shen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Li Yao
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Dandan Liu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Suning Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
| | - Jinlan Pan
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
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15
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Stigliani A, Ialchina R, Yao J, Czaplinska D, Dai Y, Andersen HB, Rennie S, Andersson R, Pedersen SF, Sandelin A. Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance. Cell Rep 2024; 43:114409. [PMID: 38944837 DOI: 10.1016/j.celrep.2024.114409] [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: 02/13/2023] [Revised: 12/11/2023] [Accepted: 06/12/2024] [Indexed: 07/02/2024] Open
Abstract
Harsh environments in poorly perfused tumor regions may select for traits driving cancer aggressiveness. Here, we investigated whether tumor acidosis interacts with driver mutations to exacerbate cancer hallmarks. We adapted mouse organoids from normal pancreatic duct (mN10) and early pancreatic cancer (mP4, KRAS-G12D mutation, ± p53 knockout) from extracellular pH 7.4 to 6.7, representing acidic niches. Viability was increased by acid adaptation, a pattern most apparent in wild-type (WT) p53 organoids, and exacerbated upon return to pH 7.4. This led to increased survival of acid-adapted organoids treated with gemcitabine and/or erlotinib, and, in WT p53 organoids, acid-induced attenuation of drug effects. New genetic variants became dominant during adaptation, yet they were unlikely to be its main drivers. Transcriptional changes induced by acid and drug adaptation differed overall, but acid adaptation increased the expression of gemcitabine resistance genes. Thus, adaptation to acidosis increases cancer cell viability after chemotherapy.
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Affiliation(s)
- Arnaud Stigliani
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark
| | - Renata Ialchina
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, DK2100 Copenhagen Ø, Denmark
| | - Jiayi Yao
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark
| | - Dominika Czaplinska
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, DK2100 Copenhagen Ø, Denmark
| | - Yifan Dai
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark
| | - Henriette Berg Andersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, DK2100 Copenhagen Ø, Denmark
| | - Sarah Rennie
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark
| | - Robin Andersson
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark
| | - Stine Falsig Pedersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, DK2100 Copenhagen Ø, Denmark.
| | - Albin Sandelin
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark.
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16
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Werner R, Crosbie R, Dorney M, Connolly A, Collins D, Hand CK, Burke L. Implementation of an ISO 15189 accredited next generation sequencing service for cell-free total nucleic acid (cfTNA) analysis to facilitate driver mutation reporting in blood: the experience of a clinical diagnostic laboratory. J Clin Pathol 2024:jcp-2024-209514. [PMID: 38914446 DOI: 10.1136/jcp-2024-209514] [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: 03/04/2024] [Accepted: 06/11/2024] [Indexed: 06/26/2024]
Abstract
AIMS Next generation sequencing (NGS) on tumour tissue is integral to the delivery of personalised medicine and targeted therapy. NGS on liquid biopsy, a much less invasive technology, is an emerging clinical tool that has rapidly expanded clinical utility. Gene mutations in cell-free total nucleic acids (cfTNA) circulating in the blood are representative of whole tumour biology and can reveal different mutations from different tumour sites, thus addressing tumour heterogeneity challenges. METHODS The novel Ion Torrent Genexus NGS system with automated sample preparation, onboard library preparation, templating, sequencing, data analysis and Oncomine Reporter software was used. cfTNA extracted from plasma was verified with the targeted pan-cancer (~50 genes) Oncomine Precision Assay (OPA). Assessment criteria included analytical sensitivity, specificity, limits of detection (LOD), accuracy, repeatability, reproducibility and the establishment of performance metrics. RESULTS An ISO 15189 accredited, minimally invasive cfTNA NGS diagnostic service has been implemented. High sensitivity (>83%) and specificity between plasma and tissue were observed. A sequencing LOD of 1.2% was achieved when the depth of coverage was >22 000×. A reduction (>68%) in turnaround time (TAT) of liquid biopsy results was achieved: 5 days TAT for in-house analysis from sample receipt to a final report issued to oncologists as compared with >15 days from reference laboratories. CONCLUSION Tumour-derived somatic variants can now be reliably assessed from plasma to provide minimally invasive tumour profiling. Successful implementation of this accredited service resulted in:Appropriate molecular profiling of patients where tumour tissue is unavailable or inaccessible.Rapid TAT of plasma NGS results.
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Affiliation(s)
- Reiltin Werner
- Pathology Department, Cork University Hospital, Cork, Ireland
- Department of Pathology, School of Medicine, University College Cork College of Medicine and Health, Cork, Ireland
| | - Ruth Crosbie
- Pathology Department, Cork University Hospital, Cork, Ireland
| | - Mairead Dorney
- Pathology Department, Cork University Hospital, Cork, Ireland
| | - Amy Connolly
- Pathology Department, Cork University Hospital, Cork, Ireland
| | | | - Collette K Hand
- Department of Pathology, School of Medicine, University College Cork College of Medicine and Health, Cork, Ireland
| | - Louise Burke
- Pathology Department, Cork University Hospital, Cork, Ireland
- Department of Pathology, School of Medicine, University College Cork College of Medicine and Health, Cork, Ireland
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17
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Guerini-Rocco E, Venetis K, Cursano G, Mane E, Frascarelli C, Pepe F, Negrelli M, Olmeda E, Vacirca D, Ranghiero A, Trapani D, Criscitiello C, Curigliano G, Rolfo C, Malapelle U, Fusco N. Standardized molecular pathology workflow for ctDNA-based ESR1 testing in HR+/HER2- metastatic breast cancer. Crit Rev Oncol Hematol 2024; 201:104427. [PMID: 38917944 DOI: 10.1016/j.critrevonc.2024.104427] [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: 04/23/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024] Open
Abstract
Mutations in the estrogen receptor alpha gene (ESR1) can lead to resistance to endocrine therapy (ET) in hormone receptor-positive (HR+)/ HER2- metastatic breast cancer (MBC). ESR1 mutations can be detected in up to 40 % of patients pretreated with ET in circulating tumor DNA (ctDNA). Data from prospective randomized trials highlight those patients with HR+/HER2- MBC with detectable ESR1 mutations experience better outcomes when receiving novel selective estrogen receptor degraders (SERDs). There is a high need for optimizing ESR1 testing strategies on liquid biopsy samples in HR+/HER2- MBC, including a hugh quality workflow implementation and molecular pathology reporting standardization. Our manuscript aims to elucidate the clinical and biological rationale for ESR1 testing in MBC, while critically examining the currently available guidelines and recommendations for this specific type of molecular testing on ctDNA. The objective will extend to the critical aspects of harmonization and standardization, specifically focusing on the pathology laboratory workflow. Finally, we propose a clear and comprehensive model for reporting ESR1 testing results on ctDNA in HR+/HER2- MBC.
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Affiliation(s)
- Elena Guerini-Rocco
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | | - Giulia Cursano
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy
| | - Eltjona Mane
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy
| | - Chiara Frascarelli
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Francesco Pepe
- Department of Public Health, Federico II University of Naples, Naples, Italy
| | - Mariachiara Negrelli
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy; School of Pathology, University of Milan, Milan, Italy
| | - Edoardo Olmeda
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy; School of Pathology, University of Milan, Milan, Italy
| | - Davide Vacirca
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy
| | - Alberto Ranghiero
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy
| | - Dario Trapani
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy
| | - Carmen Criscitiello
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy
| | - Giuseppe Curigliano
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Umberto Malapelle
- Department of Public Health, Federico II University of Naples, Naples, Italy
| | - Nicola Fusco
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.
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18
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Moore ME, Williams E, Pelkey L, Courville EL. A comparison of WHO-5 and ICC classifications in a series of myeloid neoplasms, considerations for hematopathologists and molecular pathologists. Cancer Genet 2024; 286-287:25-28. [PMID: 38964162 DOI: 10.1016/j.cancergen.2024.06.003] [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: 03/10/2024] [Revised: 05/19/2024] [Accepted: 06/15/2024] [Indexed: 07/06/2024]
Abstract
OBJECTIVES The International Consensus Classification (ICC) and 5th Edition of the World Health Organization Classification (WHO-5) made substantive updates to the classification of myeloid neoplasms. This study compares the systems in a series of myeloid neoplasms with increased blasts, analyzing implications for diagnostic workflow and reporting. METHODS Bone marrow biopsies categorized as myelodysplastic syndrome with excess blasts (MDS-EB) or acute myeloid leukemia (AML) by WHO-R4 were identified. Results of morphology review, karyotype, fluorescence in situ hybridization, and next-generation sequencing were compiled. Cases were retrospectively re-classified by WHO-5 and ICC. RESULTS 46 cases were reviewed. 28 cases (61 %) had ≥20 % blasts, with the remaining cases having 5-19.5 % blasts. The most common differences in classification were 1) the designation of MDS versus MDS/AML (10/46, 22 %) for cases with 10-19 % blasts and 2) the ICC's designation of TP53 variants as a separate classifier for AML (8/46, 17 %). Bi-allelic/multi-hit TP53 alterations were identified in 15 cases (33 %). Variants of potential germline significance were identified in 29 (63 %) cases. CONCLUSIONS While terminology differences between WHO-5 and ICC exist, both systems invoke similar opportunities for improved reporting: standardized classification of pathogenic variants (notably TP53), streamlined systems to evaluate for potential germline variants, and integrated reporting of morphologic and genetic data.
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Affiliation(s)
- Margaret E Moore
- University of Virginia, Department of Pathology and Laboratory Medicine, United States.
| | - Eli Williams
- University of Virginia, Department of Pathology and Laboratory Medicine, United States
| | - Lauren Pelkey
- University of Virginia, Department of Pathology and Laboratory Medicine, United States
| | - Elizabeth L Courville
- University of Virginia, Department of Pathology and Laboratory Medicine, United States
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19
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Wallen ZD, Ko H, Nesline MK, Hastings SB, Strickland KC, Previs RA, Zhang S, Pabla S, Conroy J, Jackson JB, Saini KS, Jensen TJ, Eisenberg M, Caveney B, Sathyan P, Severson EA, Ramkissoon SH. Real-world comprehensive genomic and immune profiling reveals distinct age- and sex-based genomic and immune landscapes in tumors of patients with non-small cell lung cancer. Front Immunol 2024; 15:1413956. [PMID: 38975340 PMCID: PMC11224431 DOI: 10.3389/fimmu.2024.1413956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/07/2024] [Indexed: 07/09/2024] Open
Abstract
Introduction Younger patients with non-small cell lung cancer (NSCLC) (<50 years) represent a significant patient population with distinct clinicopathological features and enriched targetable genomic alterations compared to older patients. However, previous studies of younger NSCLC suffer from inconsistent findings, few studies have incorporated sex into their analyses, and studies targeting age-related differences in the tumor immune microenvironment are lacking. Methods We performed a retrospective analysis of 8,230 patients with NSCLC, comparing genomic alterations and immunogenic markers of younger and older patients while also considering differences between male and female patients. We defined older patients as those ≥65 years and used a 5-year sliding threshold from <45 to <65 years to define various groups of younger patients. Additionally, in an independent cohort of patients with NSCLC, we use our observations to inform testing of the combinatorial effect of age and sex on survival of patients given immunotherapy with or without chemotherapy. Results We observed distinct genomic and immune microenvironment profiles for tumors of younger patients compared to tumors of older patients. Younger patient tumors were enriched in clinically relevant genomic alterations and had gene expression patterns indicative of reduced immune system activation, which was most evident when analyzing male patients. Further, we found younger male patients treated with immunotherapy alone had significantly worse survival compared to male patients ≥65 years, while the addition of chemotherapy reduced this disparity. Contrarily, we found younger female patients had significantly better survival compared to female patients ≥65 years when treated with immunotherapy plus chemotherapy, while treatment with immunotherapy alone resulted in similar outcomes. Discussion These results show the value of comprehensive genomic and immune profiling (CGIP) for informing clinical treatment of younger patients with NSCLC and provides support for broader coverage of CGIP for younger patients with advanced NSCLC.
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Affiliation(s)
| | - Heidi Ko
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
| | - Mary K. Nesline
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
| | | | - Kyle C. Strickland
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
- Duke University Medical Center, Duke Cancer Institute, Department of Pathology, Durham, NC, United States
| | - Rebecca A. Previs
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
- Duke University Medical Center, Duke Cancer Institute, Department of Obstetrics and Gynecology, Durham, NC, United States
| | - Shengle Zhang
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
| | - Sarabjot Pabla
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
| | - Jeffrey Conroy
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
| | | | - Kamal S. Saini
- Fortrea Inc, Medical Oncology, Durham, NC, United States
| | | | - Marcia Eisenberg
- Labcorp, Early Development Laboratories, Burlington, NC, United States
| | - Brian Caveney
- Labcorp, Early Development Laboratories, Burlington, NC, United States
| | | | | | - Shakti H. Ramkissoon
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
- Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Department of Pathology, Winston-Salem, NC, United States
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20
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Weller J, Potthoff AL, Zeyen T, Schaub C, Duffy C, Schneider M, Herrlinger U. Current status of precision oncology in adult glioblastoma. Mol Oncol 2024. [PMID: 38899374 DOI: 10.1002/1878-0261.13678] [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: 11/16/2023] [Revised: 04/05/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
The concept of precision oncology, the application of targeted drugs based on comprehensive molecular profiling, has revolutionized treatment strategies in oncology. This review summarizes the current status of precision oncology in glioblastoma (GBM), the most common and aggressive primary brain tumor in adults with a median survival below 2 years. Targeted treatments without prior target verification have consistently failed. Patients with BRAF V600E-mutated GBM benefit from BRAF/MEK-inhibition, whereas targeting EGFR alterations was unsuccessful due to poor tumor penetration, tumor cell heterogeneity, and pathway redundancies. Systematic screening for actionable molecular alterations resulted in low rates (< 10%) of targeted treatments. Efficacy was observed in one-third and currently appears to be limited to BRAF-, VEGFR-, and mTOR-directed treatments. Advancing precision oncology for GBM requires consideration of pathways instead of single alterations, new trial concepts enabling rapid and adaptive drug evaluation, a focus on drugs with sufficient bioavailability in the CNS, and the extension of target discovery and validation to the tumor microenvironment, tumor cell networks, and their interaction with immune cells and neurons.
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Affiliation(s)
- Johannes Weller
- Department of Neurooncology, Center for Neurology, University Hospital Bonn, Germany
| | | | - Thomas Zeyen
- Department of Neurooncology, Center for Neurology, University Hospital Bonn, Germany
| | - Christina Schaub
- Department of Neurooncology, Center for Neurology, University Hospital Bonn, Germany
| | - Cathrina Duffy
- Department of Neurooncology, Center for Neurology, University Hospital Bonn, Germany
| | | | - Ulrich Herrlinger
- Department of Neurooncology, Center for Neurology, University Hospital Bonn, Germany
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21
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Sonkin D, Thomas A, Teicher BA. Cancer treatments: Past, present, and future. Cancer Genet 2024; 286-287:18-24. [PMID: 38909530 DOI: 10.1016/j.cancergen.2024.06.002] [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: 03/25/2024] [Revised: 05/21/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
There is a rich history of cancer treatments which provides a number of important lessons for present and future cancer therapies. We outline this history by looking in the past, reviewing the current landscape of cancer treatments, and by glancing at the potential future cancer therapies.
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Affiliation(s)
- Dmitriy Sonkin
- National Cancer Institute, Division of Cancer Treatment and Diagnosis, Rockville, MD 20850, USA.
| | - Anish Thomas
- National Cancer Institute, Center for Cancer Research, Bethesda, MD 20892, USA
| | - Beverly A Teicher
- National Cancer Institute, Division of Cancer Treatment and Diagnosis, Rockville, MD 20850, USA
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22
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Condello V, Poma AM, Macerola E, Vignali P, Paulsson JO, Zedenius J, Basolo F, Juhlin CC. Prevalence, Molecular Landscape, and Clinical Impact of DICER1 and DGCR8 Mutated Follicular-Patterned Thyroid Nodules. J Clin Endocrinol Metab 2024; 109:1733-1744. [PMID: 38252873 PMCID: PMC11180504 DOI: 10.1210/clinem/dgae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/07/2023] [Accepted: 01/18/2024] [Indexed: 01/24/2024]
Abstract
BACKGROUND Mutations in micro-RNA (miRNA) regulators DICER1 and DGCR8 have recently been uncovered, revealing a potential novel mechanism driving thyroid tumor development. However, the true frequency of these hotspot mutations in follicular-patterned thyroid tumors (FTs) and their relation to established driver gene events remain elusive. METHODS A total of 440 FTs from 2 institutions were interrogated for DICER1, DGCR8, and RAS family hotspot mutations using Sanger sequencing. Whole-exome sequencing was also performed to identify additional driver gene aberrations in DICER1/DGCR8-mutant cases. Subsets of cases were further analyzed using miRNA expression profiling, and key dysregulated miRNAs were validated as markers of DICER1 mutations using quantitative RT-PCR analysis. The Cancer Genome Atlas (TCGA) database was also probed for DICER1/DGCR8 mutations and miRNA dysregulation. RESULTS Fourteen (3.2%) and 4 (1%) FTs harbored DICER1 and DGCR8 hotspot mutations, respectively, in the combined cohort, and no cases with normal tissue available were found to exhibit a constitutional variant. Two DGCR8-mutant cases also harbored oncogenic RAS mutations. Whole-exome sequencing analysis did not identify additional driver gene events in DICER1/DGCR8-positive cases. Comprehensive miRNA expression profiling revealed a unique pattern of dysregulated miRNAs in DICER1/DGCR8-mutant cases compared with wild-type lesions. Moreover, DICER1-mutant cases showed a remarkable reduction of 5' arm miRNAs, findings corroborated in the TCGA cohort. CONCLUSION DICER1 and DGCR8 hotspot mutations are rare in unselected cohorts of FTs, and mutated cases exhibit a specific miRNA profile. Although DGCR8 mutations may coexist with established RAS gene alterations, FTs with DICER1 variants were devoid of other driver gene events.
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Affiliation(s)
- Vincenzo Condello
- Department of Oncology-Pathology, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Anello M Poma
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, 56126 Pisa, Italy
| | - Elisabetta Macerola
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, 56126 Pisa, Italy
| | - Paola Vignali
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, 56126 Pisa, Italy
| | - Johan O Paulsson
- Department of Oncology-Pathology, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Jan Zedenius
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 64 Stockholm, Sweden
- Department of Breast, Endocrine Tumors, and Sarcoma, Karolinska University Hospital, 171 64 Stockholm, Sweden
| | - Fulvio Basolo
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, 56126 Pisa, Italy
| | - C Christofer Juhlin
- Department of Oncology-Pathology, Karolinska Institutet, 171 64 Stockholm, Sweden
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, 171 64 Stockholm, Sweden
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23
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Öfverholm I, Wallander K, Haglund C, Chellappa V, Wejde J, Gellerbring A, Wirta V, Renevey A, Caceres E, Tsagkozis P, Mayrhofer M, Papakonstantinou A, Linder-Stragliotto C, Bränström R, Larsson O, Lindberg J, Lin Y, Haglund de Flon F. Comprehensive Genomic Profiling Alters Clinical Diagnoses in a Significant Fraction of Tumors Suspicious of Sarcoma. Clin Cancer Res 2024; 30:2647-2658. [PMID: 38573684 DOI: 10.1158/1078-0432.ccr-24-0384] [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] [Received: 02/02/2024] [Revised: 03/13/2024] [Accepted: 04/01/2024] [Indexed: 04/05/2024]
Abstract
PURPOSE Tumor classification is a key component in personalized cancer care. For soft-tissue and bone tumors, this classification is currently based primarily on morphology assessment and IHC staining. However, these standard-of-care methods can pose challenges for pathologists. We therefore assessed how whole-genome and whole-transcriptome sequencing (WGTS) impacted tumor classification and clinical management when interpreted together with histomorphology. EXPERIMENTAL DESIGN We prospectively evaluated WGTS in routine diagnostics of 200 soft-tissue and bone tumors suspicious for malignancy, including DNA and RNA isolation from the tumor, and DNA isolation from a peripheral blood sample or any non-tumor tissue. RESULTS On the basis of specific genomic alterations or absence of presumed findings, WGTS resulted in reclassification of 7% (13/197) of the histopathologic diagnoses. Four cases were downgraded from low-grade sarcomas to benign lesions, and two cases were reclassified as metastatic malignant melanomas. Fusion genes associated with specific tumor entities were found in 30 samples. For malignant soft-tissue and bone tumors, we identified treatment relevant variants in 15% of cases. Germline pathogenic variants associated with a hereditary cancer syndrome were found in 22 participants (11%). CONCLUSIONS WGTS provides an important dimension of data that aids in the classification of soft-tissue and bone tumors, correcting a significant fraction of clinical diagnoses, and identifies molecular targets relevant for precision medicine. However, genetic findings need to be evaluated in their morphopathologic context, just as germline findings need to be evaluated in the context of patient phenotype and family history.
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Affiliation(s)
- Ingegerd Öfverholm
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Wallander
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilia Haglund
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Venkatesh Chellappa
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Wejde
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Gellerbring
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Annick Renevey
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Eva Caceres
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Panagiotis Tsagkozis
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Markus Mayrhofer
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Andri Papakonstantinou
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Breast Cancer, Endocrine Tumors and Sarcoma, Karolinska University Hospital, Stockholm, Sweden
| | | | - Robert Bränström
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Breast Cancer, Endocrine Tumors and Sarcoma, Karolinska University Hospital, Stockholm, Sweden
| | - Olle Larsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yingbo Lin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Felix Haglund de Flon
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
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24
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Choi Y, Choi SA, Koh EJ, Yun I, Park S, Jeon S, Kim Y, Park S, Woo D, Phi JH, Park SH, Kim DS, Kim SH, Choi JW, Lee JW, Jung TY, Bhak J, Lee S, Kim SK. Comprehensive multiomics analysis reveals distinct differences between pediatric choroid plexus papilloma and carcinoma. Acta Neuropathol Commun 2024; 12:93. [PMID: 38867333 PMCID: PMC11167863 DOI: 10.1186/s40478-024-01814-y] [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: 02/08/2024] [Accepted: 06/02/2024] [Indexed: 06/14/2024] Open
Abstract
Choroid plexus tumors (CPTs) are intraventricular tumors derived from the choroid plexus epithelium and occur frequently in children. The aim of this study was to investigate the genomic and epigenomic characteristics of CPT and identify the differences between choroid plexus papilloma (CPP) and choroid plexus carcinoma (CPC). We conducted multiomics analyses of 20 CPT patients including CPP and CPC. Multiomics analysis included whole-genome sequencing, whole-transcriptome sequencing, and methylation sequencing. Mutually exclusive TP53 and EPHA7 point mutations, coupled with the amplification of chromosome 1, were exclusively identified in CPC. In contrast, amplification of chromosome 9 was specific to CPP. Differential gene expression analysis uncovered a significant overexpression of genes related to cell cycle regulation and epithelial-mesenchymal transition pathways in CPC compared to CPP. Overexpression of genes associated with tumor metastasis and progression was observed in the CPC subgroup with leptomeningeal dissemination. Furthermore, methylation profiling unveiled hypomethylation in major repeat regions, including long interspersed nuclear elements, short interspersed nuclear elements, long terminal repeats, and retrotransposons in CPC compared to CPP, implying that the loss of epigenetic silencing of transposable elements may play a role in tumorigenesis of CPC. Finally, the differential expression of AK1, regulated by both genomic and epigenomic factors, emerged as a potential contributing factor to the histological difference of CPP against CPC. Our results suggest pronounced genomic and epigenomic disparities between CPP and CPC, providing insights into the pathogenesis of CPT at the molecular level.
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Affiliation(s)
- Yeonsong Choi
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | - Seung Ah Choi
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Eun Jung Koh
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ilsun Yun
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | - Suhyun Park
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | | | | | - Sangbeen Park
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Donggeon Woo
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Ji Hoon Phi
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Neuroscience Research Institute, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Seok Kim
- Department of Pediatric Neurosurgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Se Hoon Kim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Won Choi
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ji Won Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Tae-Young Jung
- Department of Neurosurgery, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea
| | - Jong Bhak
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
- Clinomics Inc., Ulsan, Republic of Korea
| | - Semin Lee
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea.
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea.
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
- Neuroscience Research Institute, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea.
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25
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Goldsmith SR, Shouse G, Wong FL, Bosworth A, Iukuridze A, Chen S, Rhee JW, Mei M, Htut M, Janakiram M, Forman SJ, Pillai R, Budde LE, Armenian SH. Clonal Hematopoiesis is Associated With Severe Cytokine Release Syndrome in Patients Treated With Chimeric Antigen Receptor T-Cell (CART) Therapy. Transplant Cell Ther 2024:S2666-6367(24)00465-2. [PMID: 38871057 DOI: 10.1016/j.jtct.2024.06.008] [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: 04/10/2024] [Revised: 05/24/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024]
Abstract
Among patients receiving CD19 or B-cell maturation antigen (BCMA) CAR T therapy, inflammation pre- and post-CAR T infusion is implicated in the development of toxicities including cytokine release syndrome (CRS), immune effector cell-associated neurotoxicity syndrome (ICANS), and likely contributes to prolonged cytopenias. Clonal hematopoiesis (CH), the clonal expansion of hematopoietic stem cells harboring somatic mutations, has been associated with inflammasome upregulation. Herein, we examined the prevalence of pre-CAR T CH in a predominantly transplant-naïve cohort of recipients with non-Hodgkin lymphoma (NHL) or multiple myeloma (MM), and assessed the relationship between the presence of CH mutations and CAR T-related outcomes including CRS, ICANS, prolonged cytopenia, progression-free survival (PFS), and overall survival (OS). This study included 62 patients with NHL or MM who underwent CD19 or BCMA CAR T therapy from 2017 to 2022 at City of Hope and had available pre-CAR T cryopreserved peripheral blood mononuclear cells (PBMCs). DNA was isolated with QIAamp DNA Mini Kit (Qiagen) from PBMC samples (94% collected <30d of CART infusion), on which we performed targeted exome sequencing (108 pre-defined gene panel with 1000x sequencing depth) to determine the presence of CH (variant allele frequency [VAF] ≥2%). Multivariable logistic regression was used to examine the association between CH and absolute neutrophil count (ANC) recovery at day +30 and +60, maximum grade CRS and ICANS, grade <2 versus 2+, and OS and PFS at 1y. Covariates considered were age at CART, baseline ANC, sex, race, CAR-HEMATOTOX, LDH, bridging therapy (Y/N), and number of prior lines of therapy. Fifteen (24%) patients had at least one pathogenic CH mutation; 2 (13%) had ≥2 CH mutations concurrently. DMT3A mutations were the most common; 29% of mutations had VAFs >10%. Patients with CH were significantly more likely to develop grade ≥2 CRS (60% versus 28%, p = .03) compared to those without CH (odds ratio [OR] 3.9, 95% CI 1.2-13.2; p = .027). Accounting for baseline ANC (which was higher among the CH cohort and associated with delayed ANC recovery, p = .02) patients with CH did not have a significantly different rate of delayed ANC recovery compared to those without CH (adjusted OR 0.37, 95% CI 0.09-1.5; p = .17). There was no association between CH and ICANS, nor with 1y PFS or OS. CH was frequent (24%) in this cohort of CAR T recipients and was associated with a higher risk of development of grade ≥2 CRS after CAR T. Additional validation studies are currently underway, which may set the stage for consideration of pre-CAR T CH as a biomarker for risk stratification towards more proactive CRS prophylaxis. Translational studies could aim to prove a direct relationship between CH-mutated myeloid cells and CRS.
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Affiliation(s)
- Scott R Goldsmith
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope.
| | - Geoffrey Shouse
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope
| | - F Lennie Wong
- Department of Population Sciences Program, City of Hope
| | | | | | - Sitong Chen
- Department of Population Sciences Program, City of Hope
| | - June-Wha Rhee
- Department of Population Sciences Program, City of Hope; Department of Medicine, City of Hope
| | - Matthew Mei
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope
| | - Myo Htut
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope
| | - Murali Janakiram
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope
| | - Stephen J Forman
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope
| | | | - L Elizabeth Budde
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope
| | - Saro H Armenian
- Department of Population Sciences Program, City of Hope; Department of Pediatrics, City of Hope
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26
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Nguyen T, Ordulu Z, Shrestha S, Patel U, Crispen PL, Brown L, Falzarano SM, Ghayee HK, Perdomo Rodriguez JP. Case report: A novel somatic SDHB variant in a patient with bladder paraganglioma. Front Endocrinol (Lausanne) 2024; 15:1386285. [PMID: 38911036 PMCID: PMC11190172 DOI: 10.3389/fendo.2024.1386285] [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: 02/14/2024] [Accepted: 05/22/2024] [Indexed: 06/25/2024] Open
Abstract
Background Paragangliomas (PGL) are rare neuroendocrine tumors derived from the autonomic nervous system paraganglia. Urinary bladder paragangliomas (UBPGL) originate from the sympathetic neurons of the urinary bladder wall and represent 0.7% of all paragangliomas and <0.05% of all bladder tumors. PGL and UBPGL can be associated with SDHB, SDHD, NF1, and VHL gene variants, with the most common germline alterations found in SDHB and VHL. Case report We report a case of a 42-year-old woman who presented with menorrhagia/hematuria, uterine leiomyomas, as well as cardiac and bladder masses. The cardiac mass was favored to be a myxoma based on clinical findings, while the bladder mass was diagnosed as UBPGL. A novel SDHB mutation (c.642G>A, p Q214Q), detected in the UBPGL, was proven to be somatic. Although this variant was seemingly synonymous, it was predicted to have a loss of function due to the splice site effect, which was further supported by the immunohistochemical loss of SDHB. Conclusion This case highlights the challenges of diagnosing an extremely rare entity, bladder paraganglioma, with an emphasis on the multidisciplinary approach to navigate various clinical and imaging findings that may initially be misleading. In addition, a novel loss of function SDHB variant that could have been overlooked as a synonymous variant is herein reported, while also illustrating the importance of both germline and somatic mutation testing.
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Affiliation(s)
- Thao Nguyen
- Department of Medicine, University of Florida, Gainesville, FL, United States
| | - Zehra Ordulu
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - Sunaina Shrestha
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - Urja Patel
- Division of Endocrinology, University of Florida, Gainesville, FL, United States
| | - Paul L. Crispen
- Department of Urology, University of Florida, Gainesville, FL, United States
| | - Lisa Brown
- Department of Genetics, University of Florida, Gainesville, FL, United States
| | - Sara M. Falzarano
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, United States
- Department of Urology, University of Florida, Gainesville, FL, United States
- Health Cancer Center, University of Florida, Gainesville, FL, United States
| | - Hans K. Ghayee
- Division of Endocrinology, University of Florida, Gainesville, FL, United States
- Division of Endocrinology, Malcom Randall Veterans Affairs (VA) Medical Center, Gainesville, FL, United States
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27
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Kartal-Kaess M, Karow A, Bacher U, Pabst T, Joncourt R, Zweier C, Kuehni CE, Porret NA, Roessler J. Clonal hematopoiesis of indeterminate potential is rare in pediatric patients undergoing autologous stem cell transplantation. Pediatr Hematol Oncol 2024:1-10. [PMID: 38840569 DOI: 10.1080/08880018.2024.2362885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/28/2024] [Indexed: 06/07/2024]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) describes recurrent somatic gene mutations in the blood of healthy individuals, associated with higher risk for hematological malignancies and higher all-cause mortality by cardiovascular disease. CHIP increases with age and is more common in adult patients after chemotherapy or radiation for cancer. Furthermore, in some adult patients undergoing autologous stem cell transplantation (ASCT) or thereafter, CHIP has been identified. In children and adolescents, it remains unclear how cellular stressors such as cytotoxic therapy influence the incidence and expansion of CHIP. We conducted a retrospective study on 33 pediatric patients mostly with solid tumors undergoing ASCT for presence of CHIP. We analyzed CD34+ selected peripheral blood stem cell grafts after several cycles of chemotherapy, prior to cell infusion, by next-generation sequencing including 18 "CHIP-genes". Apart from a somatic variant in TP53 in one patient no other variants indicative of CHIP were identified. As a CHIP-unrelated finding, germline variants in CHEK2 and in ATM were identified in two and four patients, respectively. In conclusion, we could not detect "typical" CHIP variants in our cohort of pediatric cancer patients undergoing ASCT. However, more studies with larger patient numbers are necessary to assess if chemotherapy in the pediatric setting contributes to an increased CHIP incidence and at what time point.
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Affiliation(s)
- Mutlu Kartal-Kaess
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Inselspital, University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Axel Karow
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Inselspital, University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Ulrike Bacher
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Thomas Pabst
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Medical Oncology, Inselspital, Bern University Hospital, Bern, University of Bern, Bern, Switzerland
| | - Raphael Joncourt
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Claudia E Kuehni
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Inselspital, University Hospital, University of Bern, Bern, Switzerland
- Childhood Cancer Research Group, Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Naomi Azur Porret
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jochen Roessler
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Inselspital, University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
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28
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Furtado LV, Bifulco C, Dolderer D, Hsiao SJ, Kipp BR, Lindeman NI, Ritterhouse LL, Temple-Smolkin RL, Zehir A, Nowak JA. Recommendations for Tumor Mutational Burden Assay Validation and Reporting: A Joint Consensus Recommendation of the Association for Molecular Pathology, College of American Pathologists, and Society for Immunotherapy of Cancer. J Mol Diagn 2024:S1525-1578(24)00115-6. [PMID: 38851389 DOI: 10.1016/j.jmoldx.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/05/2024] [Accepted: 05/07/2024] [Indexed: 06/10/2024] Open
Abstract
Tumor mutational burden (TMB) has been recognized as a predictive biomarker for immunotherapy response in several tumor types. Several laboratories offer TMB testing, but there is significant variation in how TMB is calculated, reported, and interpreted among laboratories. TMB standardization efforts are underway, but no published guidance for TMB validation and reporting is currently available. Recognizing the current challenges of clinical TMB testing, the Association for Molecular Pathology convened a multidisciplinary collaborative working group with representation from the American Society of Clinical Oncology, the College of American Pathologists, and the Society for the Immunotherapy of Cancer to review the laboratory practices surrounding TMB and develop recommendations for the analytical validation and reporting of TMB testing based on survey data, literature review, and expert consensus. These recommendations encompass pre-analytical, analytical, and postanalytical factors of TMB analysis, and they emphasize the relevance of comprehensive methodological descriptions to allow comparability between assays.
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Affiliation(s)
- Larissa V Furtado
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Carlo Bifulco
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Providence Portland Medical Center, Portland, Oregon
| | - Daniel Dolderer
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Jupiter Medical Center, Jupiter, Florida
| | - Susan J Hsiao
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Benjamin R Kipp
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Neal I Lindeman
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Weill Cornell Medicine, New York, New York
| | - Lauren L Ritterhouse
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Ahmet Zehir
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jonathan A Nowak
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
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29
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Li JJ, Wu XJ, Farzin M, Bray V, Williamson J, Pal A, Yip PY, Hagelamin A, Ding P, Nindra U, Vinod S, French B, Chua W, Gupta R, Cooper WA, Wang B, Lee CS. The histopathological spectrum and molecular changes associated with KRAS G12C mutation in non-small cell lung carcinoma. Pathology 2024:S0031-3025(24)00139-9. [PMID: 38918148 DOI: 10.1016/j.pathol.2024.04.002] [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: 10/24/2023] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 06/27/2024]
Abstract
KRAS G12C is the most common KRAS mutation in non-small cell lung carcinoma (NSCLC), for which targeted therapy has recently been developed. From the 732 cases of NSCLC that underwent next-generation sequencing at the Department of Anatomical Pathology, Liverpool Hospital, between July 2021 and May 2023, we retrieved 83 (11%) consecutive cases of KRAS G12C mutated NSCLC, and analysed their clinical, pathological, and molecular features. Of the 83 cases of KRAS G12C mutated NSCLC, there were 46 (55%) men and 37 (45%) women, with mean age of 72 years. Of the 49 cases with known clinical information, 94% were current or ex-smokers, and 49% were stage IV at diagnosis with median survival of 12 months. Sixty-three percent were histology cases and the remainder were cytology cases. Eighty-two percent were non-mucinous adenocarcinomas, with conventional histology including lepidic, acinar, solid, single cells and micropapillary patterns, and 62% were poorly differentiated. There were five (6%) cases of mucinous adenocarcinoma, one case of pleomorphic carcinoma and one case of high-grade fetal adenocarcinoma. TTF1 was positive in the majority (89%) of cases. Nineteen (23%) cases had TP53 co-mutation, and these cases had trends towards higher PD-L1 expression, poor differentiation, and presentation as stage IV disease, but the differences were not statistically significant. KRAS G12C mutated NSCLCs almost exclusively occurred in smokers and were mostly non-mucinous adenocarcinomas with conventional histological patterns which ranged from well to poorly differentiated. Around a quarter had TP53 co-mutation, the histological impacts and immune profile of which need to be assessed in a larger study.
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Affiliation(s)
- Jing Jing Li
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW, Australia; Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia.
| | - Xiao Juan Wu
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW, Australia
| | - Mahtab Farzin
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW, Australia
| | - Victoria Bray
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW, Australia
| | - Jonathan Williamson
- Department of Respiratory Medicine, Liverpool Hospital, Liverpool, NSW, Australia
| | - Abhijit Pal
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia; Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW, Australia; Department of Medical Oncology, Bankstown-Lidcombe Hospital, Lidcombe, NSW, Australia
| | - Po Yee Yip
- Department of Medical Oncology, Campbelltown Hospital, Campbelltown, NSW, Australia
| | - Abeer Hagelamin
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW, Australia
| | - Pei Ding
- Department of Medical Oncology, Nepean Hospital, Kingswood, NSW, Australia; Crown Princess Mary Cancer Centre, Westmead Hospital, NSW, Australia
| | - Udit Nindra
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW, Australia
| | - Shalini Vinod
- Department of Radiation Oncology, Liverpool Hospital, NSW, Australia
| | - Bruce French
- Department of Cardiothoracic Surgery, Liverpool Hospital, NSW, Australia
| | - Wei Chua
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW, Australia; School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Ruta Gupta
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Wendy A Cooper
- School of Medicine, Western Sydney University, Sydney, NSW, Australia; Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Bin Wang
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW, Australia
| | - C Soon Lee
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW, Australia; School of Medicine, Western Sydney University, Sydney, NSW, Australia; Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia; South Western Sydney Clinical School, University of New South Wales, Liverpool, NSW, Australia.
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30
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Gould C, McBean M, Thompson E, Lickiss J, Tiong IS, Westerman D, Blombery P. Observations from a national sample exchange program for molecular haematology testing. Pathology 2024; 56:540-547. [PMID: 38413254 DOI: 10.1016/j.pathol.2023.12.413] [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: 07/25/2023] [Revised: 11/27/2023] [Accepted: 12/07/2023] [Indexed: 02/29/2024]
Abstract
External quality assessment programs (EQAP) for molecular haematology generally only assess the analytical phase of laboratory testing or provide limited evaluation of post-analytical components. We incorporated comprehensive post-analytical evaluation into an existing national inter-laboratory sample exchange program for molecular haematology due to the increasing complexity of diagnostic molecular testing and interpretation. We report key findings from four years of longitudinal data using this approach. Eighteen participating laboratories enrolled in an annual reciprocal sample exchange program from 2019-2022, which covered conventional and next-generation sequencing (NGS) assays. Participants submitted results on their laboratory information system-generated reports which then underwent central review. Reports were assessed according to consensus values and relevant national and international reporting standards and guidelines. A total of 680 reports were received. Laboratories had high concordance in the analytical phase of testing, with incorrect variant detection observed in a total of six of 680 (0.9%) reports. In contrast, post-analytical concordance was much lower, with at least one discordance observed in 28.9-57.6% of all conventional reports and 33.3-100% NGS reports. The most frequent post-analytical discordances were: (1) not including key technical information on reports (total 41.9% conventional, 47.2% NGS); (2) not using standard gene and variant nomenclature (total 28.2% conventional, 25.6% NGS). NGS reports also demonstrated discrepancies in variant classification (total 20.4%) and interpretation (total 10.2%). The rate of discrepancies generally improved year-on-year. Inter-laboratory concordance for molecular haematology testing is high in the analytical phase, however opportunities exist for improvement in the post-analytical phase. Given that result interpretation is crucial for clinical decision-making and that molecular testing is a complex and evolving field, we suggest that EQAPs should comprehensively evaluate both analytical and post-analytical components of laboratory performance in order to harmonise reporting and to support the accurate interpretation of molecular haematology tests.
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Affiliation(s)
- Clare Gould
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.
| | - Michelle McBean
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Ella Thompson
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Jennifer Lickiss
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Ing Soo Tiong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - David Westerman
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia
| | - Piers Blombery
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia
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Slack JC, Church AJ. Molecular Alterations in Pediatric Solid Tumors. Clin Lab Med 2024; 44:277-304. [PMID: 38821645 DOI: 10.1016/j.cll.2023.08.012] [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
Pediatric tumors can be divided into hematologic malignancies, central nervous system tumors, and extracranial solid tumors of bone, soft tissue, or other organ systems. Molecular alterations that impact diagnosis, prognosis, treatment, and familial cancer risk have been described in many pediatric solid tumors. In addition to providing a concise summary of clinically relevant molecular alterations in extracranial pediatric solid tumors, this review discusses conventional and next-generation sequencing-based molecular techniques, relevant tumor predisposition syndromes, and the increasing integration of molecular data into the practice of diagnostic pathology for children with solid tumors.
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Affiliation(s)
- Jonathan C Slack
- Pathology & Laboratory Medicine Institute (Robert J. Tomsich), Cleveland Clinic, Cleveland, OH, USA
| | - Alanna J Church
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
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Thiery J, Fahrner M. Integration of proteomics in the molecular tumor board. Proteomics 2024; 24:e2300002. [PMID: 38143279 DOI: 10.1002/pmic.202300002] [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: 07/24/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023]
Abstract
Cancer remains one of the most complex and challenging diseases in mankind. To address the need for a personalized treatment approach for particularly complex tumor cases, molecular tumor boards (MTBs) have been initiated. MTBs are interdisciplinary teams that perform in-depth molecular diagnostics to cooperatively and interdisciplinarily advise on the best therapeutic strategy. Current molecular diagnostics are routinely performed on the transcriptomic and genomic levels, aiming to identify tumor-driving mutations. However, these approaches can only partially capture the actual phenotype and the molecular key players of tumor growth and progression. Thus, direct investigation of the expressed proteins and activated signaling pathways provide valuable complementary information on the tumor-driving molecular characteristics of the tissue. Technological advancements in mass spectrometry-based proteomics enable the robust, rapid, and sensitive detection of thousands of proteins in minimal sample amounts, paving the way for clinical proteomics and the probing of oncogenic signaling activity. Therefore, proteomics is currently being integrated into molecular diagnostics within MTBs and holds promising potential in aiding tumor classification and identifying personalized treatment strategies. This review introduces MTBs and describes current clinical proteomics, its potential in precision oncology, and highlights the benefits of multi-omic data integration.
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Affiliation(s)
- Johanna Thiery
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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O'Neill AF, Church AJ, Feraco A, Spidle J, Wall CB, Kim HB, Elisofon S, Vakili K, Pimkin M, Dharia NV, Shelman NR, Perez-Atayde AR, Rodriguez-Galindo C. Clinical and immunophenotype correlating with response to immunotherapy in paediatric patients with primary liver carcinoma. A case series. EBioMedicine 2024; 104:105147. [PMID: 38749302 PMCID: PMC11108818 DOI: 10.1016/j.ebiom.2024.105147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Paediatric hepatocellular carcinomas (HCC) traditionally arise in the context of a normal structural and functional liver and carry a dismal prognosis. While chemotherapy is the frontline standard, there is emerging interest in the study of immunotherapies for paediatric patients with relapsed/refractory disease. There is limited data to support whether immunotherapies will be of utility in this patient population. METHODS Six paediatric patients (median age:16 years, range: 12-17 at the time of treatment) with advanced hepatocellular neosplams, either conventional hepatocellular or fibrolamellar carcinoma, were treated with immunotherapy. Patients were consented to institutional genomic profiling and biobanking protocols. Baseline samples and serial tissue samples, when available, were evaluated for somatic mutation rate, actionable gene mutations, and pan-immune bulk RNA expression profiling. Results were correlated with clinical course. FINDINGS Three patients responded to checkpoint inhibition: one achieved a complete, durable response and the other two, prolonged stable disease. Three additional patients progressed. Diagnostic tissue from the complete responder demonstrated a higher relative mutational burden and robust immune infiltrate. Pre-treatment samples from the three responders demonstrated decreased expression of genes associated with T-cell dysfunction. INTERPRETATION A subset of patients with primary paediatric hepatocellular tumours will respond to immunotherapy. Immunotherapies are currently under prospective study for relapsed/refractory liver tumours in paediatric patients. Results from this report support the prospective collection of serial serum and tissue samples which may further identify genomic and immunophenotypic patterns predictive of response. FUNDING This work was supported by Philanthropic funds (Pan Mass Challenge, Team Angus and Team Perspective).
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Affiliation(s)
- Allison F O'Neill
- Dana-Farber Cancer Institute/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Department of Pediatric Oncology, Boston, MA, USA.
| | - Alanna J Church
- Boston Children's Hospital and Harvard Medical School, Department of Pathology, Boston, MA, USA
| | - Angela Feraco
- Dana-Farber Cancer Institute/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Department of Pediatric Oncology, Boston, MA, USA
| | - Jennifer Spidle
- Dana-Farber Cancer Institute/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Department of Pediatric Oncology, Boston, MA, USA
| | - Catherine B Wall
- Dana-Farber Cancer Institute/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Department of Pediatric Oncology, Boston, MA, USA
| | - Heung Bae Kim
- Boston Children's Hospital and Harvard Medical School, Department of Surgery, Boston, MA, USA
| | - Scott Elisofon
- Boston Children's Hospital and Harvard Medical School, Department of Hepatology, Boston, MA, USA
| | - Khashayar Vakili
- Boston Children's Hospital and Harvard Medical School, Department of Surgery, Boston, MA, USA
| | - Max Pimkin
- Dana-Farber Cancer Institute/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Department of Pediatric Oncology, Boston, MA, USA
| | | | - Nathan R Shelman
- University of Kentucky, Department of Pathology, Lexington, KY, USA
| | - Antonio R Perez-Atayde
- Boston Children's Hospital and Harvard Medical School, Department of Pathology, Boston, MA, USA
| | - Carlos Rodriguez-Galindo
- St. Jude Children's Research Hospital, Departments of Global Pediatric Medicine and Oncology, Memphis, TN, USA
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Garza D, Hildebrand MS, Penington AJ, Brown N, de Silva MG. Australian healthcare professionals' perspectives on genetic counseling and genetic diagnosis in vascular anomalies. J Genet Couns 2024; 33:677-688. [PMID: 37632295 DOI: 10.1002/jgc4.1776] [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: 04/19/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
Genomic technologies are now utilized for the genetic diagnosis of vascular anomalies. This provides the opportunity for genetic counselors to make a significant contribution to patient care for this complex disease. The aim of this study was to explore Australian healthcare professionals' perspectives on the relatively recent integration of molecular diagnostic testing for vascular anomalies, with or without genetic counseling support. Nine semi-structured interviews were conducted with Australian healthcare professionals involved in the provision of care for individuals with vascular anomalies. Thematic analysis identified six themes: (1) Molecular diagnosis is beneficial; (2) psychosocial needs can motivate families to pursue a molecular diagnosis; (3) molecular genetic testing for vascular anomalies is complex; (4) genetic service provision is not a one size fits all; (5) a client-centered approach for genetic service provision can go a long way; and (6) the value of genetic counselors. Based on our findings, implementation of a vascular anomalies genetic diagnostic program inclusive of genetic counseling may be challenging, yet such programs are likely to benefit both patients and their families, as well as healthcare professionals. As this paradigm shift unfolds, genetic counselors have an opportunity to contribute to the vascular anomaly field by educating healthcare professionals and patients, by participating in multidisciplinary clinics to support complex cases and by raising awareness regarding their practice and potential contributions.
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Affiliation(s)
- Denisse Garza
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Tasmanian Clinical Genetics Service, Hobart, Tasmania, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Michael S Hildebrand
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Epilepsy Research Centre, Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, Victoria, Australia
| | - Anthony J Penington
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Natasha Brown
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Michelle G de Silva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
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Krishnamurthy K, Chai J, Liu X, Wang Y, Naeem R, Goldstein DY. Clinical validation of the Ion Torrent Oncomine Myeloid Assay GX v2 on the Genexus Integrated Sequencer as a stand-alone assay for single-nucleotide variants, insertions/deletions, and fusion genes: Challenges, performance, and perspectives. Am J Clin Pathol 2024:aqae063. [PMID: 38823030 DOI: 10.1093/ajcp/aqae063] [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: 03/03/2024] [Accepted: 04/26/2024] [Indexed: 06/03/2024] Open
Abstract
OBJECTIVES Myeloid neoplasms require comprehensive characterization of genetic abnormalities, including single-nucleotide variants, small insertions and deletions, and fusions and translocations for management. The Oncomine Myeloid Assay GX v2 (Thermo Fisher Scientific) analyzes 17 full genes, 28 hotspot genes, 30 fusion driver genes, and 5 expression genes. METHODS The validation set included 192 DNA samples, 28 RNA samples, and 9 cell lines and contrived controls. The DNA and RNA were extracted from both peripheral blood and bone marrow. Library preparation, templating, and sequencing was performed on the fully automated Genexus Integrated Sequencer (Thermo Fisher Scientific). The sequencing data were analyzed by manual curation, default Oncomine filters and the Oncomine Reporter (Thermo Fisher Scientific). RESULTS Of the 600 reference pathogenic DNA variants targeted by the assay, concordance was seen in 98.3% of unfiltered variant call format files. Precision and reproducibility were 100%, and the lower limit of detection was 2% variant allele frequency for DNA. Inability to detect variants in long homopolymer regions intrinsic to the Ion Torrent chemistry led to 7 missed variants; 100% concordance was seen with reference RNA samples. CONCLUSIONS This extensive clinical validation of the Oncomine Myeloid Assay GX v2 on the Genexus Integrated Sequencer with its built-in bioinformatics pipeline and Ion Torrent Oncomine Reporter shows robust performance in terms of variant calling accuracy, precision, and reproducibility, with the advantage of a rapid turnaround time of 2 days. The greatest limitation is the inability to detect variants in long homopolymer regions.
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Affiliation(s)
| | - Jiani Chai
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
| | - Xiaowei Liu
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
| | - Yanhua Wang
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
- Albert Einstein College of Medicine, Bronx, New York, US
| | - Rizwan Naeem
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
- Albert Einstein College of Medicine, Bronx, New York, US
| | - D Yitzchak Goldstein
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
- Albert Einstein College of Medicine, Bronx, New York, US
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Della Porta MG, Martinelli G, Rambaldi A, Santoro A, Voso MT. A practical algorithm for acute myeloid leukaemia diagnosis following the updated 2022 classifications. Crit Rev Oncol Hematol 2024; 198:104358. [PMID: 38615870 DOI: 10.1016/j.critrevonc.2024.104358] [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: 11/02/2023] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024] Open
Abstract
Disease classification of complex and heterogenous diseases, such as acute myeloid leukaemia (AML), is continuously updated to define diagnoses, appropriate treatments, and assist research and education. Recent availability of molecular profiling techniques further benefits the classification of AML. The World Health Organization (WHO) classification of haematolymphoid tumours and the International Consensus Classification of myeloid neoplasms and acute leukaemia from 2022 are two updated versions of the WHO 2016 classification. As a consequence, the European LeukemiaNet 2022 recommendations on the diagnosis and management of AML in adults have been also updated. The current review provides a practical interpretation of these guidelines to facilitate the diagnosis of AML and discusses genetic testing, disease genetic heterogeneity, and FLT3 mutations. We propose a practical algorithm for the speedy diagnosis of AML. Future classifications may need to incorporate gene mutation combinations to enable personalised treatment regimens in the management of patients with AML.
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Affiliation(s)
- Matteo Giovanni Della Porta
- Cancer Center, IRCCS Humanitas Research Hospital, Milan, Italy; Department of Biomedical Sciences, Humanitas University, Milan, Italy.
| | - Giovanni Martinelli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori "Dino Armadori", Meldola, Italy; University of Bologna, Bologna, Italy
| | - Alessandro Rambaldi
- Department of Oncology and Hematology, University of Milan, Milan, Italy and Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Alessandra Santoro
- UOSD Laboratory of Oncohematology, Cellular Manipulation and Cytogenetics, Department of Genetic, Oncohematology a Rare Disease, AOR "Villa Sofia-Cervello", Palermo, Italy
| | - Maria Teresa Voso
- UOSD Diagnostica Avanzata Oncoematologia, Policlinico Tor Vergata, and Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
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Prendeville S, Kaur H, Ansari S, Al Qa'qa' S, Stockley TL, Lajkosz K, van der Kwast T, Cheung CC, Selvarajah S. Somatic Tumor Testing in Prostate Cancer: Experience of a Tertiary Care Center Including Pathologist-Driven Reflex Testing of Localized Tumors at Diagnosis. Mod Pathol 2024; 37:100489. [PMID: 38588883 DOI: 10.1016/j.modpat.2024.100489] [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: 11/19/2023] [Revised: 02/17/2024] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
Somatic tumor testing in prostate cancer (PCa) can guide treatment options by identifying clinically actionable variants in DNA damage repair genes, including acquired variants not detected using germline testing alone. Guidelines currently recommend performing somatic tumor testing in metastatic PCa, whereas there is no consensus on the role of testing in regional disease, and the optimal testing strategy is only evolving. This study evaluates the frequency, distribution, and pathologic correlates of somatic DNA damage repair mutations in metastatic and localized PCa following the implementation of pathologist-driven reflex testing at diagnosis. A cohort of 516 PCa samples were sequenced using a custom next-generation sequencing panel including homologous recombination repair and mismatch repair genes. Variants were classified based on the Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists guidelines. In total, 183 (35.5%) patients had at least one variant, which is as follows: 72 of 516 (13.9%) patients had at least 1 tier I or tier II variant, whereas 111 of 516 (21.5%) patients had a tier III variant. Tier I/II variant(s) were identified in 27% (12/44) of metastatic biopsy samples and 13% (61/472) of primary samples. Overall, 12% (62/516) of patients had at least 1 tier I/II variant in a homologous recombination repair gene, whereas 2.9% (10/516) had at least 1 tier I/II variant in a mismatch repair gene. The presence of a tier I/II variant was not significantly associated with the grade group (GG) or presence of intraductal/cribriform carcinoma in the primary tumor. Among the 309 reflex-tested hormone-naive primary tumors, tier I/II variants were identified in 10% (31/309) of cases, which is as follows: 9.2% (9/98) GG2; 9% (9/100) GG3; 9.1% (4/44) GG4; and 13.4% (9/67) GG5 cases. Our findings confirm the use of somatic tumor testing in detecting variants of clinical significance in PCa and provide insights that can inform the design of testing strategies. Pathologist-initiated reflex testing streamlines the availability of the results for clinical decision-making; however, pathologic parameters such as GG and the presence of intraductal/cribriform carcinoma may not be reliable to guide patient selection.
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Affiliation(s)
- Susan Prendeville
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Harpreet Kaur
- Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Shervin Ansari
- Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Shifaa' Al Qa'qa'
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Pathology and Forensic Medicine, Faculty of Medicine, Al-Balqa Applied University, Al-Salt, Jordan
| | - Tracy L Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Katherine Lajkosz
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Theodorus van der Kwast
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Carol C Cheung
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shamini Selvarajah
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
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Kusne Y, Lasho T, Finke C, Elsabbagh Z, McCue S, Hobday T, Starr J, Bekaii-Saab T, Halfdanarson TR, Patnaik MM, Ou FS, Sonbol MB. Clonal Hematopoiesis in Patients With Neuroendocrine Tumor Treated With Lutetium-177 and the Risk of Thrombocytopenia: A Prospective Study. JCO Precis Oncol 2024; 8:e2400143. [PMID: 38976813 DOI: 10.1200/po.24.00143] [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: 03/05/2024] [Revised: 04/29/2024] [Accepted: 05/16/2024] [Indexed: 07/10/2024] Open
Abstract
PURPOSE Thrombocytopenia is a relatively common dose-limiting toxicity during peptide receptor radionuclide therapy (PRRT) in patients with NET. Although uncommon, some patients develop persistent cytopenia and eventually therapy-related myeloid neoplasm (t-MN), which has a dismal prognosis. As the indications for PRRT are expanding, it is important to investigate factors that may predict cytopenias during/after PRRT. We prospectively evaluated the prevalence of clonal hematopoiesis (CH) and cytopenia in patients with NET undergoing PRRT. MATERIALS AND METHODS Patients with metastatic NET with plan to receive four cycles of lutetium-177 were enrolled. CH was evaluated before PRRT using a panel of 220 genes with a targeted depth of ≥1,000×. Patients were followed during PRRT and every 3 months thereafter. RESULTS Of 37 patients enrolled, the median age was 68 years and 51.4% were male. Previous treatment exposures included alkylating agents in 30%, platinum agents in 8%, and external radiation in 13%. CH was detected in 35.1% using a variant allele frequency (VAF) cutoff of ≥2% and 45.9% with a VAF of ≥1%. The most common mutations were in age-related genes (DNMT3A, TET2). CH was not associated with anemia or neutropenia; however, it was associated with lower platelet count at baseline and more time spent in a thrombocytopenic state during/after PRRT. Five patients had bone marrow biopsies (BMBs) because of sustained hematologic dysfunction post-PRRT, and of those, diagnoses included clonal cytopenia of undetermined significance (CCUS) in three and idiopathic cytopenia of undetermined significance (ICUS) in two. CONCLUSION CH is present in 35.1% of patients with NET and is associated with thrombocytopenia risk during PRRT. Future studies with long-term follow-up will delineate whether CH might be a predictor for higher risk of t-MN after PRRT.
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Affiliation(s)
- Yael Kusne
- Division of Hematology/Oncology, Mayo Clinic, Phoenix, AZ
| | - Terra Lasho
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Christy Finke
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Zaid Elsabbagh
- Division of Hematology/Oncology, Mayo Clinic, Phoenix, AZ
| | - Shaylene McCue
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN
| | - Timothy Hobday
- Division of Medical Oncology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Jason Starr
- Division of Hematology/Oncology, Mayo Clinic, Jacksonville, FL
| | | | | | - Mrinal M Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Fang-Shu Ou
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN
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Østergaard S, Schejbel L, Breinholt MF, Pedersen MØ, Hammer T, Munksgaard L, Nørgaard P, Høgdall E, Gjerdrum LMR, Nielsen TH. Mutational landscape in Waldenström macroglobulinemia evaluated using a next-generation sequencing lymphoma panel in routine clinical practice. Leuk Lymphoma 2024; 65:758-767. [PMID: 38340359 DOI: 10.1080/10428194.2024.2313623] [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: 06/26/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
Abstract
Next-generation sequencing (NGS) affords comprehensive insights into the genomic landscape of lymphomas. We examined the mutational pattern in patients with Waldenström macroglobulinemia (WM) or lymphoplasmacytic lymphoma (LPL) as well as the diagnostic and clinical utility of a tailored NGS lymphoma panel. A consecutive series of 45 patients was reviewed and NGS analysis was performed as part of a routine diagnostic setup. The custom designed NGS panel assayed all coding sequences of 59 genes of known clinical significance in lymphoid neoplasms. The most frequently mutated genes were MYD88, CXCR4, BIRC3, CD79B, and ARID1A. Additional somatic mutations were detected in 17 genes with four mutations categorized as pathogenic or likely pathogenic. BIRC3 and TP53 mutations were associated with adverse clinical phenotypes. NGS performance for the MYD88L265P variant was 96% when compared to qPCR. In conclusion, targeted NGS provided important diagnostic and prognostic information in a routine clinical setting.
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Affiliation(s)
- Simon Østergaard
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Lone Schejbel
- Department of Pathology, Copenhagen University Hospital, Herlev, Denmark
| | | | - Mette Ølgod Pedersen
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Troels Hammer
- Department of Hematology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Lars Munksgaard
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
| | - Peter Nørgaard
- Department of Pathology, Copenhagen University Hospital, Herlev, Denmark
- Department of Pathology, Hvidovre Hospital, Hvidovre, Denmark
| | - Estrid Høgdall
- Department of Pathology, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Lise Mette Rahbek Gjerdrum
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Torsten Holm Nielsen
- Department of Hematology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
- Danish Medicines Agency, Copenhagen, Denmark
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Al-Shinnag M, Cheong PL, Goodwin A, Trent R, Yu B. Germline potential should not be overlooked for cancer variants identified in tumour-only somatic mutation testing. Pathology 2024; 56:468-472. [PMID: 38627125 DOI: 10.1016/j.pathol.2024.03.001] [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: 11/09/2023] [Revised: 03/04/2024] [Accepted: 03/19/2024] [Indexed: 05/13/2024]
Abstract
DNA sequencing of tumour tissue has become the standard care for many solid cancers because of the option to detect somatic variants that have significant therapeutic, diagnostic and prognostic implications. Variants found within the tumour may be either somatic or germline in origin. Somatic cancer gene panels are developed to detect acquired (somatic) variants that are relevant for therapeutic or molecular characterisation of the tumour, expanding gene panels now include genes which may also inform patient management such as cancer predisposition syndromes (CPS) genes. Identifying germline cancer predisposition variants can alter cancer management, the risk of developing new primary cancers and risk for cancer in at-risk family members. This paper discusses the clinical, technical and ethical challenges related to identifying and reporting potential germline pathogenic variants that are detected on tumour sequencing. It also highlights the existence of the eviQ national guidelines for CPS with advice on germline confirmation of somatic findings to pathology laboratories in Australia.
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Affiliation(s)
- Mohammad Al-Shinnag
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown NSW, Australia; Institute of Precision Medicine and Bioinformatics, Sydney Local Health District, Camperdown, NSW, Australia; New South Wales Health Pathology (East), NSW, Australia; Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
| | - Pak Leng Cheong
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown NSW, Australia; Institute of Precision Medicine and Bioinformatics, Sydney Local Health District, Camperdown, NSW, Australia; New South Wales Health Pathology (East), NSW, Australia; Central Clinical School, Faculty of Medicine and Health, the University of Sydney, NSW, Australia
| | - Annabel Goodwin
- Central Clinical School, Faculty of Medicine and Health, the University of Sydney, NSW, Australia; Department of Cancer Genetics, Royal Prince Alfred Hospital, Camperdown, NSW, Australia; Medical Oncology, Concord Repatriation General Hospital, Concord, NSW, Australia
| | - Ronald Trent
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown NSW, Australia; Institute of Precision Medicine and Bioinformatics, Sydney Local Health District, Camperdown, NSW, Australia; New South Wales Health Pathology (East), NSW, Australia; Central Clinical School, Faculty of Medicine and Health, the University of Sydney, NSW, Australia
| | - Bing Yu
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown NSW, Australia; Institute of Precision Medicine and Bioinformatics, Sydney Local Health District, Camperdown, NSW, Australia; New South Wales Health Pathology (East), NSW, Australia; Central Clinical School, Faculty of Medicine and Health, the University of Sydney, NSW, Australia.
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Yamaguchi T, Ikegami M, Aruga T, Kanemasa Y, Horiguchi SI, Kawai K, Takao M, Yamada T, Ishida H. Genomic landscape of comprehensive genomic profiling in patients with malignant solid tumors in Japan. Int J Clin Oncol 2024:10.1007/s10147-024-02554-8. [PMID: 38795236 DOI: 10.1007/s10147-024-02554-8] [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: 01/11/2024] [Accepted: 05/14/2024] [Indexed: 05/27/2024]
Abstract
BACKGROUND Comprehensive genomic profiling (CGP) can aid the discovery of clinically useful, candidate antitumor agents; however, the variant annotations sometimes differ among the various types of CGP tests as well as the public database. The aim of this study is to clarify the genomic landscape of evaluating detected variants in patients with a malignant solid tumor. METHODS The present, cross-sectional study used data from 57,084 patients with a malignant solid tumor who underwent CGP at the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) between June 1, 2019 and August 18, 2023. The pathogenicity of the variants was annotated using public databases. RESULTS As a result of re-annotation of the detected variants, 20.1% were pathogenic and 1.4% were benign. The mean number of pathogenic variants was 4.30 (95% confidence interval: 4.27-4.32) per patient. Of the entire cohort, 5.7% had no pathogenic variant. The co-occurrence of the genes depended on the tumor type. Germline findings were detected in 6.2%, 8.8%, and 15.8% of the patients using a tumor/normal panel, tumor-only panel, and liquid panel, respectively, with the most common gene being BRCA2 followed by TP53 and BRCA1. CONCLUSIONS The detected variants should be re-annotated because several benign variants or variants of unknown significance were included in the CGP, and the genomic landscape derived from these results will help researchers and physicians interpret the results of CGP tests. The method of extracting presumptive, germline, pathogenic variants from patients using a tumor-only panel or circulating tumor DNA panel requires improvement.
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Affiliation(s)
- Tatsuro Yamaguchi
- Department of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan.
| | - Masachika Ikegami
- Department of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
- Department of Musculoskeletal Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, 3-18-22 Honkomagome, Bunkyo-Ku, Tokyo, 113-8677, Japan
| | - Tomoyuki Aruga
- Department of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Yusuke Kanemasa
- Department of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
- Department of Medical Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Shin-Ichiro Horiguchi
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Kazushige Kawai
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Misato Takao
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Takeshi Yamada
- Department of Surgery, Nihon Medical University, Tokyo, Japan
| | - Hideyuki Ishida
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Kawagoe, Japan
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Revencu N, Eijkelenboom A, Bracquemart C, Alhopuro P, Armstrong J, Baselga E, Cesario C, Dentici ML, Eyries M, Frisk S, Karstensen HG, Gene-Olaciregui N, Kivirikko S, Lavarino C, Mero IL, Michiels R, Pisaneschi E, Schönewolf-Greulich B, Wieland I, Zenker M, Vikkula M. Assessment of gene-disease associations and recommendations for genetic testing for somatic variants in vascular anomalies by VASCERN-VASCA. Orphanet J Rare Dis 2024; 19:213. [PMID: 38778413 PMCID: PMC11110196 DOI: 10.1186/s13023-024-03196-9] [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: 12/12/2023] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Vascular anomalies caused by somatic (postzygotic) variants are clinically and genetically heterogeneous diseases with overlapping or distinct entities. The genetic knowledge in this field is rapidly growing, and genetic testing is now part of the diagnostic workup alongside the clinical, radiological and histopathological data. Nonetheless, access to genetic testing is still limited, and there is significant heterogeneity across the approaches used by the diagnostic laboratories, with direct consequences on test sensitivity and accuracy. The clinical utility of genetic testing is expected to increase progressively with improved theragnostics, which will be based on information about the efficacy and safety of the emerging drugs and future molecules. The aim of this study was to make recommendations for optimising and guiding the diagnostic genetic testing for somatic variants in patients with vascular malformations. RESULTS Physicians and lab specialists from 11 multidisciplinary European centres for vascular anomalies reviewed the genes identified to date as being involved in non-hereditary vascular malformations, evaluated gene-disease associations, and made recommendations about the technical aspects for identification of low-level mosaicism and variant interpretation. A core list of 24 genes were selected based on the current practices in the participating laboratories, the ISSVA classification and the literature. In total 45 gene-phenotype associations were evaluated: 16 were considered definitive, 16 strong, 3 moderate, 7 limited and 3 with no evidence. CONCLUSIONS This work provides a detailed evidence-based view of the gene-disease associations in the field of vascular malformations caused by somatic variants. Knowing both the gene-phenotype relationships and the strength of the associations greatly help laboratories in data interpretation and eventually in the clinical diagnosis. This study reflects the state of knowledge as of mid-2023 and will be regularly updated on the VASCERN-VASCA website (VASCERN-VASCA, https://vascern.eu/groupe/vascular-anomalies/ ).
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Affiliation(s)
- Nicole Revencu
- Center for Human Genetics, Cliniques universitaires Saint-Luc, University of Louvain, VASCERN VASCA European Reference Centre, Brussels, Belgium
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud University Medical Center, VASCERN VASCA European Reference Centre, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Claire Bracquemart
- Normandie Univ, UNICAEN, Service de Génétique, CHU Caen Normandie, BIOTARGEN EA 7450, VASCERN VASCA European Reference Centre, Caen, 14000, France
| | - Pia Alhopuro
- HUS Diagnostic Center, Laboratory of Genetics, University of Helsinki and Helsinki University Hospital, VASCERN VASCA European Reference Centre, Helsinki, Finland
| | - Judith Armstrong
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, CIBER-ER (Biomedical Network Research Center for Rare Diseases), Instituto de Salud Carlos III (ISCIII), Madrid, and Genomic Unit, Molecular and Genetic Medicine Section, Hospital Sant Joan de Déu, VASCERN VASCA European Reference Centre, Barcelona, Spain
| | - Eulalia Baselga
- Department of Dermatology, Hospital Sant Joan de Deu, VASCERN VASCA European Reference Centre, Barcelona, Spain
| | - Claudia Cesario
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital and Research Institute, IRCCS, VASCERN VASCA European Reference Centre, Rome, Italy
| | - Maria Lisa Dentici
- Medical Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, VASCERN VASCA European Reference Centre, 00165, Rome, Italy
| | - Melanie Eyries
- Sorbonne Université, Département de Génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, VASCERN VASCA European Reference Centre, Paris, France
| | - Sofia Frisk
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Clinical Genetics, Karolinska University Hospital, VASCERN VASCA European Reference Centre, Stockholm, Sweden
| | - Helena Gásdal Karstensen
- Department of Genetics, Center of Diagnostics, Copenhagen University Hospital - Rigshospitalet, VASCERN VASCA European Reference Centre, Copenhagen, Denmark
| | - Nagore Gene-Olaciregui
- Laboratory of Molecular Oncology, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, VASCERN VASCA European Reference Centre, Barcelona, Spain
| | - Sirpa Kivirikko
- Department of Clinical Genetics, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, VASCERN VASCA European Reference Centre, Helsinki, Finland
| | - Cinzia Lavarino
- Laboratory of Molecular Oncology, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, VASCERN VASCA European Reference Centre, Barcelona, Spain
| | - Inger-Lise Mero
- Department of Medical Genetics, Oslo University Hospital, VASCERN VASCA European Reference Centre, Oslo, Norway
| | - Rodolphe Michiels
- Center for Human Genetics, Cliniques universitaires Saint-Luc, University of Louvain, VASCERN VASCA European Reference Centre, Brussels, Belgium
| | - Elisa Pisaneschi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital and Research Institute, IRCCS, VASCERN VASCA European Reference Centre, Rome, Italy
| | - Bitten Schönewolf-Greulich
- Department of Genetics, Center of Diagnostics, Copenhagen University Hospital - Rigshospitalet, VASCERN VASCA European Reference Centre, Copenhagen, Denmark
| | - Ilse Wieland
- Institute of Human Genetics, University Hospital Otto-Von-Guericke-University, Magdeburg, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Otto-Von-Guericke-University, Magdeburg, Germany
| | - Miikka Vikkula
- Center for Vascular Anomalies, Cliniques Universitaires Saint-Luc, Brussels, Belgium.
- Human Molecular Genetics , de Duve Institute, University of Louvain, VASCERN VASCA European Reference Centre, Brussels, Belgium.
- WELBIO Department, WEL Research Institute, Avenue Pasteur, 6, 1300, Wavre, Belgium.
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Kim N, Hahn S, Choi YJ, Cho H, Chung H, Jang JE, Lyu CJ, Lee ST, Choi JR, Cheong JW, Shin S. Comprehensive insights into AML relapse: genetic mutations, clonal evolution, and clinical outcomes. Cancer Cell Int 2024; 24:174. [PMID: 38764048 PMCID: PMC11103850 DOI: 10.1186/s12935-024-03368-4] [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: 10/16/2023] [Accepted: 05/10/2024] [Indexed: 05/21/2024] Open
Abstract
INTRODUCTION Acute myeloid leukemia (AML) is a complex hematologic malignancy characterized by uncontrolled proliferation of myeloid precursor cells within bone marrow. Despite advances in understanding of its molecular underpinnings, AML remains a therapeutic challenge due to its high relapse rate and clonal evolution. METHODS In this retrospective study, we analyzed data from 24 AML patients diagnosed at a single institution between January 2017 and August 2023. Comprehensive genetic analyses, including chromosomal karyotyping, next-generation sequencing, and gene fusion assays, were performed on bone marrow samples obtained at initial diagnosis and relapse. Clinical data, treatment regimens, and patient outcomes were also documented. RESULTS Mutations in core genes of FLT3, NPM1, DNMT3A, and IDH2 were frequently discovered in diagnostic sample and remained in relapse sample. FLT3-ITD, TP53, KIT, RUNX1, and WT1 mutation were acquired at relapse in one patient each. Gene fusion assays revealed stable patterns, while chromosomal karyotype analyses indicated a greater diversity of mutations in relapsed patients. Clonal evolution patterns varied, with some cases showing linear or branching evolution and others exhibiting no substantial change in core mutations between diagnosis and relapse. CONCLUSIONS Our study integrates karyotype, gene rearrangements, and gene mutation results to provide a further understanding of AML heterogeneity and evolution. We demonstrate the clinical relevance of specific mutations and clonal evolution patterns, emphasizing the need for personalized therapies and measurable residual disease monitoring in AML management. By bridging the gap between genetics and clinical outcome, we move closer to tailored AML therapies and improved patient prognoses.
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Affiliation(s)
- Namsoo Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Seungmin Hahn
- Department of Pediatric Hematology-Oncology, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Yu Jeong Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Hyunsoo Cho
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Haerim Chung
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Ji Eun Jang
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Chuhl Joo Lyu
- Department of Pediatric Hematology-Oncology, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
- Dxome Co. Ltd, Seongnam-si, Gyeonggi-do, Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
- Dxome Co. Ltd, Seongnam-si, Gyeonggi-do, Korea
| | - June-Won Cheong
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
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Mehdi M, Szabo A, Shreenivas A, Thomas JP, Tsai S, Christians KK, Evans DB, Clarke CN, Hall WA, Erickson B, Ahmed G, Thapa B, McFall T, George B, Kurzrock R, Kamgar M. Chemotherapy-free treatment targeting fusions and driver mutations in KRAS wild-type pancreatic ductal adenocarcinoma, a case series. Ther Adv Med Oncol 2024; 16:17588359241253113. [PMID: 38770091 PMCID: PMC11104030 DOI: 10.1177/17588359241253113] [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: 12/04/2023] [Accepted: 04/18/2024] [Indexed: 05/22/2024] Open
Abstract
Background KRAS wild-type (WT) pancreatic ductal adenocarcinoma (PDAC) represents a distinct entity with unique biology. The therapeutic impact of matched targeted therapy in these patients in a real-world setting, to date, is less established. Objectives The aim of our study was to review our institutional database to identify the prevalence of actionable genomic alterations in patients with KRAS-WT tumors and to evaluate the therapeutic impact of matched targeted therapy in these patients. Design We reviewed electronic medical records of patients with KRAS-WT PDAC and advanced disease (n = 14) who underwent clinical-grade tissue ± liquid next-generation sequencing (315-648 genes for tissue) between years 2015 and 2021. Methods Demographic and disease characteristics were summarized using descriptive parameters. Progression-free survival (PFS) and overall survival (OS) were estimated using the Kaplan-Meier method. Results Of 236 PDAC patients, 14 had advanced/metastatic disease with KRAS-WT tumors. Median age at diagnosis was 66 years. There was a high frequency of potentially actionable genomic alterations, including three (21%) with BRAF alterations, two (14%) with fusions [RET-PCM1 and FGFR2-POC1B (N = 1 each)]; and one with a druggable EGFR (EGFR E746_A755delISERD) variant; two other patients had an STK11 and a MUTYH alteration. Five patients were treated with matched targeted therapy, with three having durable benefit: (i) erlotinib for EGFR-altered tumor, followed by osimertinib/capmatinib when MET amplification emerged (first-line therapy); (ii) pralsetinib for RET fusion (fifth line); and (iii) dabrafenib/trametinib for BRAF N486_P490del (third line). Duration of time on chemotherapy-free matched targeted therapy for these patients was 17+, 11, and 18+ months, respectively. Conclusion Sustained therapeutic benefit can be achieved in a real-world setting in a subset of patients with advanced/metastatic KRAS-WT PDAC treated with chemotherapy-free matched targeted agents. Prospective studies are warranted.
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Affiliation(s)
- Maahum Mehdi
- Department of Medicine, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - Aniko Szabo
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - Aditya Shreenivas
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - James P. Thomas
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - Susan Tsai
- Department of Surgery, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - Kathleen K. Christians
- Department of Surgery, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - Douglas B. Evans
- Department of Surgery, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - Callisia N. Clarke
- Department of Surgery, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - William A. Hall
- Department of Radiation Oncology, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - Beth Erickson
- Department of Radiation Oncology, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - Gulrayz Ahmed
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - Bicky Thapa
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - Thomas McFall
- Department of Biochemistry, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - Ben George
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - Razelle Kurzrock
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, Milwaukee, WI, USA
| | - Mandana Kamgar
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin and the LaBahn Pancreatic Cancer Program, 9200 West Wisconsin Avenue, Milwaukee, WI 53226, USA
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Connell E, Gerard É, Oules B, Brunet-Possenti F, Lamoureux A, Bonnefille H, Mary-Prey S, Carrasquilla A, Mouret S, Kramkimel N, Lesage C, Stoebner PE, Bartoli A, Monestier S, Correard F, Gros A, Jeanson A, Ouafik L, Gaudy-Marqueste C, Tomasini P, Charles J, Amini-Adle M, Malissen N. Molecularly matched targeted therapy: a promising approach for refractory metastatic melanoma. Oncologist 2024:oyae085. [PMID: 38761384 DOI: 10.1093/oncolo/oyae085] [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: 09/20/2023] [Accepted: 03/26/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND Only a fraction of patients with metastatic melanoma derive durable benefit from approved treatments. The clinical impact of personalized medicine strategies for melanoma, apart from BRAF, NRAS, or CKIT targeting, has rarely been reported. MATERIALS AND METHODS By means of the Group of Cutaneous Oncology of the French Society of Dermatology, we retrospectively included all patients with advanced melanoma aged 18 years and older for whom molecular testing identified one or more actionable molecular alterations and who accordingly received molecularly matched therapy. We excluded patients with only BRAF, NRAS, or CKIT alterations and patients who received molecularly matched therapy for less than 15 days. RESULTS We included 26 patients with a median follow-up of 8 months (1-54), a median age of 63 years (24-89), and a sex ratio of 2.7. These patients had been heavily pretreated, and 64% had elevated LDH levels. The disease control rate was 38%, with 4 cases of partial response (overall response rate: 15%) and 6 of stable disease for at least 6 months. The median duration of treatment was 3.1 months (0.9-13.5). Among patients with disease control, the median duration of control was 6.6 months (2.6-13.5) and 3 cases were ongoing at the end of the study. Patients with controlled disease had GNA11, MAP2K1, FYCO1-RAF1, HRAS, ATM, CCND1, MDM2/CDK4, and CDKN2A/NRAS alterations. CONCLUSIONS High-throughput sequencing followed by matched targeted therapy is a promising approach for patients with advanced melanoma refractory to approved treatments.
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Affiliation(s)
- Emily Connell
- Dermatology and Skin Cancer Department, Aix Marseille University, APHM, CRCM Inserm U1068, CNRS U7258, Marseille, France
- Department of Early Phase Cancer Trial Center (CEPCM) "CLIP2," Aix Marseille University, APHM, Marseille, France
| | - Émilie Gerard
- Dermatology Department, CHU de Bordeaux, Bordeaux, France
| | | | | | - Anouck Lamoureux
- Dermatology Department, Montpellier Cancer Institute, Montpellier, France
| | | | | | | | - Stéphane Mouret
- Dermatology Department, CHU Grenoble Alpes, University Grenoble Alpes, INSERM U 1209, CNRS UMR 5309, Institut for Advanced Biosciences, Grenoble, France
| | | | - Candice Lesage
- Dermatology Department, CHU de Montpellier, Montpellier, France
| | | | - Axel Bartoli
- Radiology Department, Aix Marseille University, APHM, CERIMED, Marseille, France
| | - Sandrine Monestier
- Dermatology and Skin Cancer Department, Aix Marseille University, APHM, CRCM Inserm U1068, CNRS U7258, Marseille, France
- Department of Early Phase Cancer Trial Center (CEPCM) "CLIP2," Aix Marseille University, APHM, Marseille, France
| | - Florian Correard
- Pharmacy Department, Aix Marseille University, APHM, Marseille, France
| | - Audrey Gros
- Tumor Biology and Tumor Bank Department, University Hospital of Bordeaux, Bordeaux, France
| | - Arnaud Jeanson
- Department of Early Phase Cancer Trial Center (CEPCM) "CLIP2," Aix Marseille University, APHM, Marseille, France
- Multidisciplinary Oncology and Therapeutic Innovations Department, Aix Marseille University, CNRS, INSERM, CRCM, APHM, Marseille, France
| | - L'Houcine Ouafik
- Oncobiology Department, Aix Marseille University, APHM, CNRS, INP, Inst Neurophysiopathol, Marseille, France
| | - Caroline Gaudy-Marqueste
- Dermatology and Skin Cancer Department, Aix Marseille University, APHM, CRCM Inserm U1068, CNRS U7258, Marseille, France
- Department of Early Phase Cancer Trial Center (CEPCM) "CLIP2," Aix Marseille University, APHM, Marseille, France
| | - Pascale Tomasini
- Department of Early Phase Cancer Trial Center (CEPCM) "CLIP2," Aix Marseille University, APHM, Marseille, France
- Multidisciplinary Oncology and Therapeutic Innovations Department, Aix Marseille University, CNRS, INSERM, CRCM, APHM, Marseille, France
| | - Julie Charles
- Dermatology Department, CHU Grenoble Alpes, University Grenoble Alpes, INSERM U 1209, CNRS UMR 5309, Institut for Advanced Biosciences, Grenoble, France
| | - Mona Amini-Adle
- Dermatology Department, Leon Bérard Cancer Center, Lyon, France
| | - Nausicaa Malissen
- Dermatology and Skin Cancer Department, Aix Marseille University, APHM, CRCM Inserm U1068, CNRS U7258, Marseille, France
- Department of Early Phase Cancer Trial Center (CEPCM) "CLIP2," Aix Marseille University, APHM, Marseille, France
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Vanni I, Pastorino L, Andreotti V, Comandini D, Fornarini G, Grassi M, Puccini A, Tanda ET, Pastorino A, Martelli V, Mastracci L, Grillo F, Cabiddu F, Guadagno A, Coco S, Allavena E, Barbero F, Bruno W, Dalmasso B, Bellomo SE, Marchiò C, Spagnolo F, Sciallero S, Berrino E, Ghiorzo P. Combining germline, tissue and liquid biopsy analysis by comprehensive genomic profiling to improve the yield of actionable variants in a real-world cancer cohort. J Transl Med 2024; 22:462. [PMID: 38750555 PMCID: PMC11097509 DOI: 10.1186/s12967-024-05227-2] [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: 02/23/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Comprehensive next-generation sequencing is widely used for precision oncology and precision prevention approaches. We aimed to determine the yield of actionable gene variants, the capacity to uncover hereditary predisposition and liquid biopsy appropriateness instead of, or in addition to, tumor tissue analysis, in a real-world cohort of cancer patients, who may benefit the most from comprehensive genomic profiling. METHODS Seventy-eight matched germline/tumor tissue/liquid biopsy DNA and RNA samples were profiled using the Hereditary Cancer Panel (germline) and the TruSight Oncology 500 panel (tumor tissue/cfDNA) from 23 patients consecutively enrolled at our center according to at least one of the following criteria: no available therapeutic options; long responding patients potentially fit for other therapies; rare tumor; suspected hereditary cancer; primary cancer with high metastatic potential; tumor of unknown primary origin. Variants were annotated for OncoKB and AMP/ASCO/CAP classification. RESULTS The overall yield of actionable somatic and germline variants was 57% (13/23 patients), and 43.5%, excluding variants previously identified by somatic or germline routine testing. The accuracy of tumor/cfDNA germline-focused analysis was demonstrated by overlapping results of germline testing. Five germline variants in BRCA1, VHL, CHEK1, ATM genes would have been missed without extended genomic profiling. A previously undetected BRAF p.V600E mutation was emblematic of the clinical utility of this approach in a patient with a liver undifferentiated embryonal sarcoma responsive to BRAF/MEK inhibition. CONCLUSIONS Our study confirms the clinical relevance of performing extended parallel tumor DNA and cfDNA testing to broaden therapeutic options, to longitudinally monitor cfDNA during patient treatment, and to uncover possible hereditary predisposition following tumor sequencing in patient care.
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Affiliation(s)
- I Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - L Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
| | - V Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - D Comandini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - G Fornarini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - M Grassi
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - A Puccini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - E T Tanda
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
- Medical Oncology Unit 2, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - A Pastorino
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - V Martelli
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - L Mastracci
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132, Genoa, Italy
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - F Grillo
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132, Genoa, Italy
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - F Cabiddu
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - A Guadagno
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - S Coco
- Lung Cancer Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - E Allavena
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
| | - F Barbero
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - W Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
| | - B Dalmasso
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - S E Bellomo
- Pathology Unit, Candiolo Cancer Institute, FPO - IRCCS, 10060, Candiolo, Turin, Italy
| | - C Marchiò
- Pathology Unit, Candiolo Cancer Institute, FPO - IRCCS, 10060, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Torino, 10060, Turin, Italy
| | - F Spagnolo
- Medical Oncology Unit 2, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Plastic Surgery, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132, Genoa, Italy
| | - S Sciallero
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - E Berrino
- Pathology Unit, Candiolo Cancer Institute, FPO - IRCCS, 10060, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Torino, 10060, Turin, Italy
| | - P Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy.
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy.
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Barateiro LGRP, de Oliveira Cavagna R, Dos Reis MB, de Paula FE, Teixeira GR, Moreno DA, Bonatelli M, Santana I, Saggioro FP, Neder L, Stavale JN, Malheiros SMF, Garcia-Rivello H, Christiansen S, Nunes S, da Costa MJG, Pinheiro J, Júnior CA, Mançano BM, Reis RM. Somatic mutational profiling and clinical impact of driver genes in Latin-Iberian medulloblastomas: Towards precision medicine. Neuropathology 2024. [PMID: 38736183 DOI: 10.1111/neup.12979] [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: 01/29/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/14/2024]
Abstract
Medulloblastoma (MB) is the most prevalent malignant brain tumor in children, known for its heterogeneity and treatment-associated toxicity, and there is a critical need for new therapeutic targets. We analyzed the somatic mutation profile of 15 driver genes in 69 Latin-Iberian molecularly characterized medulloblastomas using the Illumina TruSight Tumor 15 panel. We classified the variants based on their clinical impact and oncogenicity. Among the patients, 66.7% were MBSHH, 13.0% MBWNT, 7.3% MBGrp3, and 13.0% MBGrp4. Among the 63 variants found, 54% were classified as Tier I/II and 31.7% as oncogenic/likely oncogenic. We observed 33.3% of cases harboring at least one mutation. TP53 (23.2%, 16/69) was the most mutated gene, followed by PIK3CA (5.8%, 4/69), KIT (4.3%, 3/69), PDGFRA (2.9%, 2/69), EGFR (1.4%, 1/69), ERBB2 (1.4%, 1/69), and NRAS (1.4%, 1/69). Approximately 41% of MBSHH tumors exhibited mutations, TP53 (32.6%) being the most frequently mutated gene. Tier I/II and oncogenic/likely oncogenic TP53 variants were associated with relapse, progression, and lower survival rates. Potentially actionable variants in the PIK3CA and KIT genes were identified. Latin-Iberian medulloblastomas, particularly the MBSHH, exhibit higher mutation frequencies than other populations. We corroborate the TP53 mutation status as an important prognostic factor, while PIK3CA and KIT are potential therapeutic targets.
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Affiliation(s)
| | | | | | | | - Gustavo Ramos Teixeira
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil
- Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Murilo Bonatelli
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil
| | - Iara Santana
- Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Luciano Neder
- Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | | | | | | | | | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal
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48
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Lee JM, Kim HS, Yoo J, Lee J, Ahn A, Cho H, Han EH, Jung J, Yoo JW, Kim S, Lee JW, Cho B, Chung NG, Kim M, Kim Y. Genomic insights into inherited bone marrow failure syndromes in a Korean population. Br J Haematol 2024. [PMID: 38735735 DOI: 10.1111/bjh.19509] [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: 01/02/2024] [Accepted: 04/24/2024] [Indexed: 05/14/2024]
Abstract
Inherited bone marrow failure syndromes (IBMFS) pose significant diagnostic challenges due to overlapping symptoms and variable expressivity, despite evolving genomic insights. The study aimed to elucidate the genomic landscape among 130 Korean patients with IBMFS. We conducted targeted next-generation sequencing (NGS) and clinical exome sequencing (CES) across the cohort, complemented by whole genome sequencing (WGS) and chromosomal microarray (CMA) in 12 and 47 cases, respectively, with negative initial results. Notably, 50% (n = 65) of our cohort achieved a genomic diagnosis. Among these, 35 patients exhibited mutations associated with classic IBMFSs (n = 33) and the recently defined IBMFS, aplastic anaemia, mental retardation and dwarfism syndrome (AmeDS, n = 2). Classic IBMFSs were predominantly detected via targeted NGS (85%, n = 28) and CES (88%, n = 29), whereas AMeDS was exclusively identified through CES. Both CMA and WGS aided in identifying copy number variations (n = 2) and mutations in previously unexplored regions (n = 2). Additionally, 30 patients were diagnosed with other congenital diseases, encompassing 13 distinct entities including inherited thrombocytopenia (n = 12), myeloid neoplasms with germline predisposition (n = 8), congenital immune disorders (n = 7) and miscellaneous genomic conditions (n = 3). CES was particularly effective in revealing these diverse diagnoses. Our findings underscore the significance of comprehensive genomic analysis in IBMFS, highlighting the need for ongoing exploration in this complex field.
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Affiliation(s)
- Jong-Mi Lee
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hoon Seok Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jaeeun Yoo
- Department of Laboratory Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jaewoong Lee
- Department of Laboratory Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ari Ahn
- Department of Laboratory Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hanwool Cho
- Department of Laboratory Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Eun Hee Han
- Department of Laboratory Medicine, Daejeon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jin Jung
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jae Won Yoo
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seongkoo Kim
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jae Wook Lee
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Bin Cho
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Nack-Gyun Chung
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yonggoo Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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49
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Liu Z, Ding S, Xu G, Fang C. Case Report: Identification of a novel PRR12 variant in a Chinese boy with developmental delay and short stature. Front Pediatr 2024; 12:1367131. [PMID: 38798311 PMCID: PMC11119739 DOI: 10.3389/fped.2024.1367131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
Proline Rich 12 (PRR12) protein is primarily expressed in the brain and localized in the nucleus. The variants in the PRR12 gene were reported to be related to neuroocular syndrome. Patients with PRR12 gene presented with intellectual disability (ID), neuropsychiatric disorders, some congenital anomalies, and with or without eye abnormalities. Here, we report an 11-year-old boy with a novel PRR12 variant c.1549_1568del, p.(Pro517Alafs*35). He was the first PRR12 deficiency patient in China and presented with ID, short stature, and mild scoliosis. He could not concentrate on his studies and was diagnosed with attention deficit hyperactivity disorder (ADHD). The insulin-like growth factor 1 (IGH-1) was low in our patient, which may be the cause of his short stature. Patients with neuroocular syndrome are rare, and further exploration is needed to understand the reason for neurodevelopmental abnormalities caused by PRR12 variants. Our study further expands on the PRR12 variants and presents a new case involving PPR12 variants.
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Affiliation(s)
- Zhengxia Liu
- Department of Neurology, Women and Children’s Hospital Affiliated to Ningbo University, Ningbo, Zhejiang, China
| | - Shuxia Ding
- Department of Endocrinology, Women and Children’s Hospital Affiliated to Ningbo University, Ningbo, Zhejiang, China
| | - Guangwei Xu
- Department of Pediatric Orthopedic, Women and Children’s Hospital Affiliated to Ningbo University, Ningbo, Zhejiang, China
| | - Chunyan Fang
- Department of Neurology, Women and Children’s Hospital Affiliated to Ningbo University, Ningbo, Zhejiang, China
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50
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Lee J, Song SH, Lee IH, Kim DJ, Lee HJ. Primary Solid Pseudopapillary Tumor of the Ovary: A Case Report and Review of the Literature. J Clin Med 2024; 13:2791. [PMID: 38792331 PMCID: PMC11121763 DOI: 10.3390/jcm13102791] [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: 03/25/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
INTRODUCTION Solid pseudopapillary neoplasms (SPNs) are rare and mainly originate from the pancreas. SPNs originating from the ovary (SPN-O) are extremely rare, and only 13 cases have been reported in the English literature since 2010. CASE We report a 31-year-old woman with SPN-O accompanied by multiple metastases in the abdominal cavity. The patient underwent staging surgery and cytoreduction. Furthermore, the multidisciplinary board decided on adjuvant chemotherapy with an FP regimen (fluorouracil plus cisplatin) because a microscopic metastasis was discovered in the peritoneum near the appendix. Next-generation sequencing showed some pathologic mutations of oncogenes/cancer-associated genes, including CTNNB1 and TP53. This is the fourteenth case of SPN-O and the first one to demonstrate the TP53 pathogenic mutant variant in SPN-O. The patient showed 8 months of disease-free survival until February 2024. CONCLUSION The combination of R0 cytoreduction with FOLFIRI chemotherapy appears to be an effective and feasible treatment option.
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Affiliation(s)
- Juhun Lee
- Department of Obstetrics and Gynecology, School of Medicine, Kyungpook National University, Kyungpook Nation University Hospital, Daegu 41944, Republic of Korea;
| | - Seung Ho Song
- Department of Surgery, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu 41944, Republic of Korea;
| | - In Hee Lee
- Department of Hematology/Oncology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu 41404, Republic of Korea;
| | - Dong Ja Kim
- Department of Forensic Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu 41404, Republic of Korea;
| | - Hyun Jung Lee
- Department of Obstetrics and Gynecology, School of Medicine, Kyungpook National University, Kyungpook Nation University Hospital, Daegu 41944, Republic of Korea;
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