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Zannoni GF, Bragantini E, Castiglione F, Fassan M, Troncone G, Inzani F, Pesci A, Santoro A, Fraggetta F. Current Prognostic and Predictive Biomarkers for Endometrial Cancer in Clinical Practice: Recommendations/Proposal from the Italian Study Group. Front Oncol 2022; 12:805613. [PMID: 35463299 PMCID: PMC9024340 DOI: 10.3389/fonc.2022.805613] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 03/11/2022] [Indexed: 12/12/2022] Open
Abstract
Endometrial carcinoma (EC) is the most common gynecological malignant disease in high-income countries, such as European countries and the USA. The 2020 edition of the World Health Organization (WHO) Classification of Tumors of the Female Genital Tract underlines the important clinical implications of the proposed new histomolecular classification system for ECs. In view of the substantial genetic and morphological heterogeneity in ECs, both classical pthological parameters and molecular classifiers have to be integrated in the pathology report. This review will focus on the most commonly adopted immunohistochemical and molecular biomarkers in daily clinical characterization of EC, referring to the most recent published recommendations, guidelines, and expert opinions.
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Affiliation(s)
- Gian Franco Zannoni
- Unità di Ginecopatologia e Patologia Mammaria, Dipartimento Scienze della Salute della Donna, del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Istituto di Anatomia Patologica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Emma Bragantini
- Department of Surgical Pathology, Ospedale S. Chiara, Trento, Italy
| | - Francesca Castiglione
- Histopathology and Molecular Diagnostics, Careggi University Hospital, Florence, Italy
| | - Matteo Fassan
- Department of Medicine - DIMED, University of Padova, Padova, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Frediano Inzani
- Unità di Ginecopatologia e Patologia Mammaria, Dipartimento Scienze della Salute della Donna, del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Anna Pesci
- Department of Pathology, Sacred Heart Hospital Don Calabria Negrar, Verona, Italy
| | - Angela Santoro
- Unità di Ginecopatologia e Patologia Mammaria, Dipartimento Scienze della Salute della Donna, del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Filippo Fraggetta
- Pathology Unit, “Cannizzaro” Hospital, Catania, Italy
- Pathology Unit, “Gravina” Hospital, Caltagirone, Italy
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152
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Park KH, Choi JY, Lim AR, Kim JW, Choi YJ, Lee S, Sung JS, Chung HJ, Jang B, Yoon D, Kim S, Sa JK, Kim YH. Genomic Landscape and Clinical Utility in Korean Advanced Pan-Cancer Patients from Prospective Clinical Sequencing: K-MASTER Program. Cancer Discov 2022; 12:938-948. [PMID: 34862196 PMCID: PMC9387587 DOI: 10.1158/2159-8290.cd-21-1064] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/13/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023]
Abstract
The fundamental principle of precision oncology is centralized on the identification of therapeutically exploitable targets that provides individual patients with cancer an opportunity to make informed decisions on a personalized level. To facilitate and adopt such concepts within clinical practice, we have initiated a nationwide, multi-institutional precision oncology screening program to examine and enroll patients into the most appropriate clinical trial based on their tumor's unique molecular properties. To determine the prevalence of essential major driver mutations and to explore their dynamic associations at both molecular and pathway levels, we present a comprehensive overview on the genomic properties of East Asian patients with cancer. We further delineate the extent of genomic diversity as well as clinical actionability in patients from Western and Eastern cultures at the pan-cancer and single-tumor entity levels. To support fellow oncology communities in future investigations involving large-scale analysis, all data have been made accessible to the public (https://kmportal.or.kr). SIGNIFICANCE We present a comprehensive overview of molecular properties of East Asian pan-cancer patients and demonstrate significant diversity in terms of genomic characteristics as well as clinical utility compared with patients with European ancestry. The results of this study will lay the groundwork for designing personalized treatments in the clinical setting. See related commentary by Moyers and Subbiah, p. 886. This article is highlighted in the In This Issue feature, p. 873.
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Affiliation(s)
- Kyong Hwa Park
- Division of Medical Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
- K-MASTER Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jung Yoon Choi
- Division of Medical Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
- K-MASTER Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ah-Reum Lim
- Division of Medical Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
- K-MASTER Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ju Won Kim
- Division of Medical Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
- K-MASTER Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Yoon Ji Choi
- Division of Medical Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
- K-MASTER Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soohyeon Lee
- Division of Medical Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
- K-MASTER Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jae Sook Sung
- K-MASTER Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hee-Joon Chung
- K-MASTER Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Byunghyun Jang
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Dayoung Yoon
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea
| | - Sukwon Kim
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jason K. Sa
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
- Corresponding Authors: Jason K. Sa, Korea University College of Medicine, 73 Goryeodae-ro, Seongbuk-gu, Seoul, Republic of Korea. Phone: 822-2286-1468; E-mail: ; and Yeul Hong Kim,
| | - Yeul Hong Kim
- Division of Medical Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
- K-MASTER Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
- Corresponding Authors: Jason K. Sa, Korea University College of Medicine, 73 Goryeodae-ro, Seongbuk-gu, Seoul, Republic of Korea. Phone: 822-2286-1468; E-mail: ; and Yeul Hong Kim,
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153
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Lee D, Wang D, Yang XR, Shi J, Landi MT, Zhu B. SUITOR: Selecting the number of mutational signatures through cross-validation. PLoS Comput Biol 2022; 18:e1009309. [PMID: 35377867 PMCID: PMC9009674 DOI: 10.1371/journal.pcbi.1009309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 04/14/2022] [Accepted: 03/09/2022] [Indexed: 11/19/2022] Open
Abstract
For de novo mutational signature analysis, the critical first step is to decide how many signatures should be expected in a cancer genomics study. An incorrect number could mislead downstream analyses. Here we present SUITOR (Selecting the nUmber of mutatIonal signaTures thrOugh cRoss-validation), an unsupervised cross-validation method that requires little assumptions and no numerical approximations to select the optimal number of signatures without overfitting the data. In vitro studies and in silico simulations demonstrated that SUITOR can correctly identify signatures, some of which were missed by other widely used methods. Applied to 2,540 whole-genome sequenced tumors across 22 cancer types, SUITOR selected signatures with the smallest prediction errors and almost all signatures of breast cancer selected by SUITOR were validated in an independent breast cancer study. SUITOR is a powerful tool to select the optimal number of mutational signatures, facilitating downstream analyses with etiological or therapeutic importance.
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Affiliation(s)
- Donghyuk Lee
- Department of Statistics, Pusan National University, Busan, Korea
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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154
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Sasame J, Ikegaya N, Kawazu M, Natsumeda M, Hayashi T, Isoda M, Satomi K, Tomiyama A, Oshima A, Honma H, Miyake Y, Takabayashi K, Nakamura T, Ueno T, Matsushita Y, Iwashita H, Kanemaru Y, Murata H, Ryo A, Terashima K, Yamanaka S, Fujii Y, Mano H, Komori T, Ichimura K, Cahill DP, Wakimoto H, Yamamoto T, Tateishi K. HSP90 inhibition overcomes resistance to molecular targeted therapy in BRAFV600E mutant high-grade glioma. Clin Cancer Res 2022; 28:2425-2439. [PMID: 35344043 DOI: 10.1158/1078-0432.ccr-21-3622] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/07/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Molecular targeted therapy using BRAF and/or MEK inhibitors has been applied to BRAFV600E mutant high-grade gliomas (HGGs); however, the therapeutic effect is limited by the emergence of drug resistance. EXPERIMENTAL DESIGN We established multiple paired BRAFV600E mutant HGG patient-derived xenograft (PDX) models based on tissues collected prior to and at relapse after molecular targeted therapy. Using these models, we dissected treatment resistant mechanisms for molecular targeted therapy and explored therapeutic targets to overcome resistance in BRAFV600E HGG models in vitro and in vivo. RESULTS We found that, despite causing no major genetic and epigenetic changes, BRAF and/or MEK inhibitor treatment deregulated multiple negative feedback mechanisms, which led to the re-activation of the MAPK pathway through c-Raf and AKT signaling. This altered oncogenic signaling primarily mediated resistance to molecular targeted therapy in BRAFV600E mutant HGG. To overcome this resistance mechanism, we performed a high-throughput drug screening to identify therapeutic agents that potently induce additive cytotoxicity with BRAF and MEK inhibitors. We discovered that HSP90 inhibition combined with BRAF/MEK inhibition coordinately deactivated the MAPK and AKT/mTOR pathways, and subsequently induced apoptosis via dephosphorylation of GSK3β (Ser9) and inhibition of Bcl-2 family proteins. This mediated potent cytotoxicity in vitro and in vivo in refractory models with acquired resistance to molecular-targeted therapy. CONCLUSIONS The combination of an HSP90 inhibitor with BRAF or MEK inhibitors can overcome the limitations of the current therapeutic strategies for BRAFV600E mutant HGG.
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Affiliation(s)
- Jo Sasame
- Yokohama City University, Yokohama, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | - Toshihide Ueno
- National Cancer Center Research Institute, Tokyo, Tokyo, Japan
| | | | | | | | | | | | - Keita Terashima
- National Center For Child Health and Development, Tokyo, Japan
| | | | - Yukihiko Fujii
- Brain Research Institute, Niigata University, Niigata, Niigata, Japan
| | | | | | | | - Daniel P Cahill
- Massachusetts General Hospital / Harvard Medical School, Boston, MA, United States
| | - Hiroaki Wakimoto
- Massachusetts General Hospital, Harvard Medical School, Boston, United States
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155
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Lee JW, Park YS, Choi JY, Chang WJ, Lee S, Sung JS, Kim B, Lee SB, Lee SY, Choi J, Kim YH. Genetic Characteristics Associated With Drug Resistance in Lung Cancer and Colorectal Cancer Using Whole Exome Sequencing of Cell-Free DNA. Front Oncol 2022; 12:843561. [PMID: 35402275 PMCID: PMC8987589 DOI: 10.3389/fonc.2022.843561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 03/01/2022] [Indexed: 12/12/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) can be used to characterize tumor genomes through next-generation sequencing (NGS)-based approaches. We aim to identify novel genetic alterations associated with drug resistance in lung cancer and colorectal cancer patients who were treated with EGFR-targeted therapy and cytotoxic chemotherapy through whole exome sequencing (WES) of cfDNA. A cohort of 18 lung cancer patients was treated with EGFR TKI or cytotoxic chemotherapy, and a cohort of 37 colorectal cancer patients was treated with EGFR monoclonal antibody or cytotoxic chemotherapy alone. Serum samples were drawn before and after development of drug resistance, and the genetic mutational profile was analyzed with WES data. For 110 paired cfDNA and matched germline DNA WES samples, mean coverage of 138x (range, 52–208.4x) and 47x (range, 30.5–125.1x) was achieved, respectively. After excluding synonymous variants, mutants identified in more than two patients at the time of acquired resistance were selected. Seven genes in lung cancer and 16 genes in colorectal cancer were found, namely, APC, TP53, KRAS, SMAD4, and EGFR. In addition, the GPR155 I357S mutation in lung cancer and ADAMTS20 S1597P and TTN R7415H mutations in colorectal cancer were frequently detected at the time of acquired resistance, indicating that these mutations have an important function in acquired resistance to chemotherapy. Our data suggest that novel genetic variants associated with drug resistance can be identified using cfDNA WES. Further validation is necessary, but these candidate genes are promising therapeutic targets for overcoming drug resistance in lung cancer and colorectal cancer.
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Affiliation(s)
- Jong Won Lee
- Cancer Research Institute, Korea University College of Medicine, Seoul, South Korea
- Brain Korea 21 Plus Project for Biomedical Science, Korea University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Young Soo Park
- Cancer Research Institute, Korea University College of Medicine, Seoul, South Korea
| | - Jung Yoon Choi
- Division of Hematology–Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, South Korea
| | - Won Jin Chang
- Division of Hematology–Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, South Korea
| | - Soohyeon Lee
- Division of Hematology–Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, South Korea
| | - Jae Sook Sung
- Cancer Research Institute, Korea University College of Medicine, Seoul, South Korea
| | - Boyeon Kim
- Cancer Research Institute, Korea University College of Medicine, Seoul, South Korea
- Brain Korea 21 Plus Project for Biomedical Science, Korea University College of Medicine, Seoul, South Korea
| | - Saet Byeol Lee
- Cancer Research Institute, Korea University College of Medicine, Seoul, South Korea
- Brain Korea 21 Plus Project for Biomedical Science, Korea University College of Medicine, Seoul, South Korea
| | - Sung Yong Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Korea University Medical Center, Korea University College of Medicine, Seoul, South Korea
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Yeul Hong Kim
- Cancer Research Institute, Korea University College of Medicine, Seoul, South Korea
- Brain Korea 21 Plus Project for Biomedical Science, Korea University College of Medicine, Seoul, South Korea
- Division of Hematology–Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, South Korea
- *Correspondence: Yeul Hong Kim,
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156
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Guan Z, Liu S, Luo L, Wu Z, Lu S, Guan Z, Tao K. Identification of Ferroptosis-Related Genes as Biomarkers for Sarcoma. Front Cell Dev Biol 2022; 10:847513. [PMID: 35309947 PMCID: PMC8929291 DOI: 10.3389/fcell.2022.847513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 01/31/2022] [Indexed: 12/25/2022] Open
Abstract
Sarcomas are seen as mixed-up nature with genetic and transcriptional heterogeneity and poor prognosis. Although the genes involved in ferroptosis are still unclear, iron loss is considered to be the core of glioblastoma, tumor progression, and tumor microenvironment. Here, we developed and tested the prognosis of SARC, which is a genetic marker associated with iron residues. The ferroptosis-related gene expression, one-way Cox analysis, and least-selection absolute regression algorithm (LASSO) are used to track prognostic-related genes and create risk assessment models. Finally, immune system infiltration and immune control point analysis are used to study the characteristics of the tumor microenvironment related to risk assessment. Moreover, LncRNA–miRNA–mRNA network was contributed in our studies. We determined the biomarker characteristics associated with iron degradation in gene 32 and developed a risk assessment model. ROC analysis showed that its model was accurately predicted, with 1, 2, 3, 4, and 5 years of overall survival in TCGA cohort of SARC patients. A comparative analysis of settings found that overall survival (OS) was lower in the high-risk than that in the low-risk group. The nomogram survival prediction model also helped to predict the OS of SARC patients. The nomogram survival prediction model has strong predictive power for the overall survival of SARC patients in TCGA dataset. GSEA analysis shows that high-risk groups are rich in inflammation, cancer-related symptoms, and pathological processes. High risk is related to immune cell infiltration and immune checkpoint. Our prediction model is based on SARC ferritin-related genes, which may support SARC prediction and provide potential attack points.
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Affiliation(s)
- Zhiyuan Guan
- Department of Orthopedics, The Shanghai tenth People's Hospital of Tongji University, Shanghai, China
| | | | - Liying Luo
- Department of Nursing, Xuzhou Municipal Hospital Affiliated with Xuzhou Medical University, Jiangsu, China
| | - Zhong Wu
- Department of Orthopedics, The Shanghai tenth People's Hospital of Tongji University, Shanghai, China
| | - Shan Lu
- Department of Nursing, Xuzhou Municipal Hospital Affiliated with Xuzhou Medical University, Jiangsu, China
| | - Zhiqiang Guan
- Department of Dermatology, Xuzhou Municipal Hospital Affiliated with Xuzhou Medical University, Xuzhou, China
| | - Kun Tao
- Nanjing Medical University, Nanjing, China
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157
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Liu T, Zhang J, Lin C, Liu G, Xie G, Dai Z, Yu P, Wang J, Guo L. Molecular Characterization Clinical and Immunotherapeutic Characteristics of m5C Regulator NOP2 Across 33 Cancer Types. Front Cell Dev Biol 2022; 10:839136. [PMID: 35372330 PMCID: PMC8966037 DOI: 10.3389/fcell.2022.839136] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/21/2022] [Indexed: 01/10/2023] Open
Abstract
Background: Recent studies have identified that RNA 5-methylcytosine (m5C) is a wide-spread epigenetic modification in tumorigenesis. However, the clinical and immunotherapeutic values of m5C regulator NOP2 in 33 cancers remain unclear.Methods: The mRNA expression data and clinical data of 33 cancers were downloaded from The Cancer Genome Atlas (TCGA) database. The immunotherapy data including GSE67501, GSE78220, GSE35640, and IMvigor210 were downloaded from the Gene Expression Omnibus (GEO) database and the website based on the Creative Commons 3.0 license (http://research-pub.Gene.com/imvigor210corebiologies). The expression, survival, clinical parameters, tumor mutation burden (TMB), microsatellite instability (MSI), and tumor microenvironment (TME) were evaluated. Finally, the relationship between NOP2 and immunotherapy response was further explored.Results: NOP2 was significantly upregulated in most cancers, and high NOP2 expression was associated with poor prognosis. TMB, MSI, and NOP2 activities were involved in the dysregulation of NOP2. NOP2 was closely associated with immune cell infiltration, immune modulators, and immunotherapeutic inactivation.Conclusions: We comprehensively explored the clinical and immunotherapeutic values of NOP2 in cancers, providing evidence regarding the function of NOP2 and its role in clinical treatment.
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Affiliation(s)
- Taisheng Liu
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- Guangzhou Medical University, Guangzhou, China
| | - Chunxuan Lin
- Department of Pneumology, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan, China
| | - Guihong Liu
- Department of Radiation Oncology, DongGuan Tungwah Hospital, Dongguan, China
| | - Guofeng Xie
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Zili Dai
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Peng Yu
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jian Wang
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Jian Wang, ; Liyi Guo,
| | - Liyi Guo
- Department of Oncology and Hematology, The Sixth People’s Hospital of Huizhou City, Huiyang Hospital Affiliated to Southern Medical University, Huizhou, China
- *Correspondence: Jian Wang, ; Liyi Guo,
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158
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Bellone S, Roque DM, Siegel ER, Buza N, Hui P, Bonazzoli E, Guglielmi A, Zammataro L, Nagarkatti N, Zaidi S, Lee J, Silasi DA, Huang GS, Andikyan V, Damast S, Clark M, Azodi M, Schwartz PE, Tymon-Rosario JR, Harold JA, Mauricio D, Zeybek B, Menderes G, Altwerger G, Ratner E, Alexandrov LB, Iwasaki A, Kong Y, Song E, Dong W, Elvin JA, Choi J, Santin AD. A phase 2 evaluation of pembrolizumab for recurrent Lynch-like versus sporadic endometrial cancers with microsatellite instability. Cancer 2022; 128:1206-1218. [PMID: 34875107 PMCID: PMC9465822 DOI: 10.1002/cncr.34025] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/19/2021] [Accepted: 08/10/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Microsatellite instability-high (MSI-H)/mismatch repair deficiency (dMMR) is a biomarker for responses to immune checkpoint inhibitors (ICIs). Whether mechanisms underlying microsatellite instability alter responses to ICIs is unclear. This article reports data from a prospective phase 2 pilot study of pembrolizumab in patients with recurrent MSI-H endometrial cancer (EC) analyzed by whole exome sequencing (WES) and potential mechanisms of primary/secondary ICI resistance (NCT02899793). METHODS Patients with measurable MSI-H/dMMR EC confirmed by polymerase chain reaction/immunohistochemistry were evaluated by WES and received 200 mg of pembrolizumab every 3 weeks for ≤2 years. The primary end point was the objective response rate (ORR). Secondary end points included progression-free survival (PFS) and overall survival (OS). RESULTS Twenty-five patients (24 evaluable) were treated. Six patients (25%) harbored Lynch/Lynch-like tumors, whereas 18 (75%) had sporadic EC. The tumor mutation burden was higher in Lynch-like tumors (median, 2939 mutations/megabase [Mut/Mb]; interquartile range [IQR], 867-5108 Mut/Mb) than sporadic tumors (median, 604 Mut/Mb; IQR, 411-798 Mut/Mb; P = .0076). The ORR was 100% in Lynch/Lynch-like patients but only 44% in sporadic patients (P = .024). The 3-year PFS and OS proportions were 100% versus 30% (P = .017) and 100% versus 43% (P = .043), respectively. CONCLUSIONS This study suggests prognostic significance of Lynch-like cancers versus sporadic MSI-H/dMMR ECs for ORR, PFS, and OS when patients are treated with pembrolizumab. Larger confirmatory studies in ECs and other MSI-H/dMMR tumors are necessary. Defective antigen processing/presentation and deranged induction in interferon responses serve as mechanisms of resistance in sporadic MSI-H ECs. Oligoprogression in MSI-H/dMMR patients appears salvageable with surgical resection and/or local treatment and the continuation of pembrolizumab off study. Clinical studies evaluating separate MSI-H/dMMR EC subtypes treated with ICIs are warranted.
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Affiliation(s)
- Stefania Bellone
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Dana M Roque
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Eric R Siegel
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Natalia Buza
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Pei Hui
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Elena Bonazzoli
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Adele Guglielmi
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Luca Zammataro
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Nupur Nagarkatti
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Samir Zaidi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jungsoo Lee
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Dan-Arin Silasi
- Division of Gynecologic Oncology, Mercy Clinic, St. Louis, Missouri
| | - Gloria S Huang
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Vaagn Andikyan
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Shari Damast
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Mitchell Clark
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Masoud Azodi
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Peter E Schwartz
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Joan R Tymon-Rosario
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Justin A Harold
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Dennis Mauricio
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Burak Zeybek
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Gulden Menderes
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Gary Altwerger
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Elena Ratner
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California
| | - Akiko Iwasaki
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Yong Kong
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Eric Song
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Weilai Dong
- Laboratory of Human Genetics and Genomics, Rockefeller University, New York, New York
| | - Julia A Elvin
- Cancer Genomics Research, Foundation Medicine, Cambridge, Massachusetts
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Alessandro D Santin
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
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159
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Durando ML, Menghani SV, Baumann JL, Robles DG, Day TA, Vaziri C, Scott AJ. Four-Year Disease-Free Remission in a Patient With POLE Mutation-Associated Colorectal Cancer Treated Using Anti-PD-1 Therapy. J Natl Compr Canc Netw 2022; 20:218-223. [PMID: 35276675 DOI: 10.6004/jnccn.2021.7115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/18/2021] [Indexed: 11/17/2022]
Abstract
The stability of the human genome depends upon a delicate balance between replication by high- and low-fidelity DNA polymerases. Aberrant replication by error-prone polymerases or loss of function of high-fidelity polymerases predisposes to genetic instability and, in turn, cancer. DNA polymerase epsilon (Pol ε) is a high-fidelity, processive polymerase that is responsible for the majority of leading strand synthesis, and mutations in Pol ε have been increasingly associated with various human malignancies. The clinical significance of Pol ε mutations, including how and whether they should influence management decisions, remains poorly understood. In this report, we describe a 24-year-old man with an aggressive stage IV high-grade, poorly differentiated colon carcinoma who experienced a dramatic response to single-agent checkpoint inhibitor immunotherapy after rapidly progressing on standard chemotherapy. His response was complete and durable and has been maintained for more than 48 months. Genetic testing revealed a P286R mutation in the endonuclease domain of POLE and an elevated tumor mutational burden of 126 mutations per megabase, both of which have been previously associated with response to immunotherapy. Interestingly, tumor staining for PD-L1 was negative. This case study highlights the importance of genetic profiling of both early and late-stage cancers, the clinical significance of POLE mutations, and how the interplay between genetic instability and immune-checkpoint blockade can impact clinical decision-making.
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Affiliation(s)
- Michael L Durando
- 1Banner-University Medical Center Tucson, Tucson, Arizona.,2Division of Hematology and Oncology, Department of Medicine.,3University of Arizona Cancer Center
| | | | - Jessica L Baumann
- 5Department of Pathology, University of Arizona College of Medicine-Tucson, Tucson, Arizona.,6Now with Roche Tissue Diagnostics, Tucson, Arizona
| | - Danny G Robles
- 1Banner-University Medical Center Tucson, Tucson, Arizona.,7Department of Surgery, University of Arizona College of Medicine-Tucson, Tucson, Arizona
| | - Tovah A Day
- 8Department of Biology, Northeastern University, Boston, Massachusetts; and
| | - Cyrus Vaziri
- 9Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Aaron J Scott
- 1Banner-University Medical Center Tucson, Tucson, Arizona.,2Division of Hematology and Oncology, Department of Medicine.,3University of Arizona Cancer Center
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160
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Park VS, Sun MJS, Frey WD, Williams LG, Hodel KP, Strauss JD, Wellens SJ, Jackson JG, Pursell ZF. Mouse model and human patient data reveal critical roles for Pten and p53 in suppressing POLE mutant tumor development. NAR Cancer 2022; 4:zcac004. [PMID: 35252866 PMCID: PMC8892059 DOI: 10.1093/narcan/zcac004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/17/2022] [Accepted: 02/17/2022] [Indexed: 12/24/2022] Open
Abstract
Mutations in the exonuclease domain of POLE are associated with tumors harboring very high mutation burdens. The mechanisms linking this significant mutation accumulation and tumor development remain poorly understood. Pole+/P286R;Trp53+/– mice showed accelerated cancer mortality compared to Pole+/P286R;Trp53+/+ mice. Cells from Pole+/P286R mice showed increased p53 activation, and subsequent loss of p53 permitted rapid growth, implicating canonical p53 loss of heterozygosity in POLE mutant tumor growth. However, p53 status had no effect on tumor mutation burden or single base substitution signatures in POLE mutant tumors from mice or humans. Pten has important roles in maintaining genome stability. We find that PTEN mutations are highly enriched in human POLE mutant tumors, including many in POLE signature contexts. One such signature mutation, PTEN-F341V, was previously shown in a mouse model to specifically decrease nuclear Pten and lead to increased DNA damage. We found tumors in Pole+/P286R mice that spontaneously acquired PtenF341V mutations and were associated with significantly reduced nuclear Pten and elevated DNA damage. Re-analysis of human TCGA (The Cancer Genome Atlas) data showed that all PTEN-F341V mutations occurred in tumors with mutations in POLE. Taken together with recent published work, our results support the idea that development of POLE mutant tumors may involve disabling surveillance of nuclear DNA damage in addition to POLE-mediated hypermutagenesis.
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Affiliation(s)
- Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Meijuan J S Sun
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Wesley D Frey
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Leonard G Williams
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Karl P Hodel
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Juliet D Strauss
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Sydney J Wellens
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - James G Jackson
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
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161
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Morano F, Raimondi A, Pagani F, Lonardi S, Salvatore L, Cremolini C, Murgioni S, Randon G, Palermo F, Antonuzzo L, Pella N, Racca P, Prisciandaro M, Niger M, Corti F, Bergamo F, Zaniboni A, Ratti M, Palazzo M, Cagnazzo C, Calegari MA, Marmorino F, Capone I, Conca E, Busico A, Brich S, Tamborini E, Perrone F, Di Maio M, Milione M, Di Bartolomeo M, de Braud F, Pietrantonio F. Temozolomide Followed by Combination With Low-Dose Ipilimumab and Nivolumab in Patients With Microsatellite-Stable, O 6-Methylguanine-DNA Methyltransferase-Silenced Metastatic Colorectal Cancer: The MAYA Trial. J Clin Oncol 2022; 40:1562-1573. [PMID: 35258987 PMCID: PMC9084437 DOI: 10.1200/jco.21.02583] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This is a multicenter, single-arm phase II trial evaluating the efficacy and safety of an immune-sensitizing strategy with temozolomide priming followed by a combination of low-dose ipilimumab and nivolumab in patients with microsatellite-stable (MSS) and O6-methylguanine–DNA methyltransferase (MGMT)–silenced metastatic colorectal cancer (mCRC). MAYA shows that temozolomide priming followed by Ipi/Nivo combo induces durable benefit in MSS/MGMT-silenced mCRC.![]()
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Affiliation(s)
- Federica Morano
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Alessandra Raimondi
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Filippo Pagani
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Lonardi
- Medical Oncology 3, Istituto Oncologico Veneto IOV-IRCSS, Padua, Italy
| | - Lisa Salvatore
- Comprehensive Cancer Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.,Università Cattolica del Sacro Cuore, Rome, Italy
| | - Chiara Cremolini
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy.,Department of Translational Research and New Technology in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Sabina Murgioni
- Medical Oncology 1, Istituto Oncologico Veneto IOV-IRCSS, Padua, Italy
| | - Giovanni Randon
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Federica Palermo
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Lorenzo Antonuzzo
- Clinical Oncology Unit, Careggi University Hospital, Florence, Italy.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Nicoletta Pella
- Department of Oncology, ASUFC University Hospital of Udine, Udine, Italy
| | - Patrizia Racca
- ColoRectal Cancer Unit, Department of Oncology, AOU Città della Salute e della Scienza di Torino, Turin, Italy
| | - Michele Prisciandaro
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monica Niger
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesca Corti
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesca Bergamo
- Medical Oncology 1, Istituto Oncologico Veneto IOV-IRCSS, Padua, Italy
| | | | - Margherita Ratti
- Department of Medical Oncology, Azienda Socio Sanitaria Territoriale of Cremona, Cremona, Italy
| | - Michele Palazzo
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Celeste Cagnazzo
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Maria Alessandra Calegari
- Comprehensive Cancer Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Federica Marmorino
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy.,Department of Translational Research and New Technology in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Iolanda Capone
- Department of the Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Elena Conca
- Department of the Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Adele Busico
- Department of the Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Silvia Brich
- Department of the Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Elena Tamborini
- Department of the Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Federica Perrone
- Department of the Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Massimo Di Maio
- Department of Oncology, University of Turin, Division of Medical Oncology, Ordine Mauriziano Hospital, Turin, Italy
| | - Massimo Milione
- Department of the Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Maria Di Bartolomeo
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Filippo de Braud
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Filippo Pietrantonio
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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Natesan D, Zhang L, Martell HJ, Jindal T, Devine P, Stohr B, Espinosa-Mendez C, Grenert J, Van Ziffle J, Joseph N, Umetsu S, Onodera C, Turski M, Chan E, Desai A, Aggarwal R, Wong A, Porten S, Chou J, Friedlander T, Fong L, Small EJ, Sweet-Cordero A, Koshkin VS. APOBEC Mutational Signature and Tumor Mutational Burden as Predictors of Clinical Outcomes and Treatment Response in Patients With Advanced Urothelial Cancer. Front Oncol 2022; 12:816706. [PMID: 35321431 PMCID: PMC8935010 DOI: 10.3389/fonc.2022.816706] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/10/2022] [Indexed: 12/21/2022] Open
Abstract
Introduction Tumor mutational burden (TMB) and APOBEC mutational signatures are potential prognostic markers in patients with advanced urothelial carcinoma (aUC). Their utility in predicting outcomes to specific therapies in aUC warrants additional study. Methods We retrospectively reviewed consecutive UC cases assessed with UCSF500, an institutional assay that uses hybrid capture enrichment of target DNA to interrogate 479 common cancer genes. Hypermutated tumors (HM), defined as having TMB ≥10 mutations/Mb, were also assessed for APOBEC mutational signatures, while non-HM (NHM) tumors were not assessed due to low TMB. The logrank test was used to determine if there were differences in overall survival (OS) and progression-free survival (PFS) among patient groups of interest. Results Among 75 aUC patients who had UCSF500 testing, 46 patients were evaluable for TMB, of which 19 patients (41%) had HM tumors and the rest had NHM tumors (27 patients). An additional 29 patients had unknown TMB status. Among 19 HM patients, all 16 patients who were evaluable for analysis had APOBEC signatures. HM patients (N=19) were compared with NHM patients (N=27) and had improved OS from diagnosis (125.3 months vs 35.7 months, p=0.06) but inferior OS for patients treated with chemotherapy (7.0 months vs 13.1 months, p=0.04). Patients with APOBEC (N=16) were compared with remaining 56 patients, comprised of 27 NHM patients and 29 patients with unknown TMB, showing APOBEC patients to have improved OS from diagnosis (125.3 months vs 44.5 months, p=0.05) but inferior OS for patients treated with chemotherapy (7.0 months vs 13.1 months, p=0.05). Neither APOBEC nor HM status were associated with response to immunotherapy. Conclusions In a large, single-institution aUC cohort assessed with UCSF500, an institutional NGS panel, HM tumors were common and all such tumors that were evaluated for mutational signature analysis had APOBEC signatures. APOBEC signatures and high TMB were prognostic of improved OS from diagnosis and both analyses also predicted inferior outcomes with chemotherapy treatment.
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Affiliation(s)
- Divya Natesan
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Li Zhang
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Henry J. Martell
- Department of Pediatrics, Benioff Children’s Hospital, University of California, San Francisco, San Francisco, CA, United States
| | - Tanya Jindal
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Patrick Devine
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Bradley Stohr
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Carlos Espinosa-Mendez
- Department of Pediatrics, Benioff Children’s Hospital, University of California, San Francisco, San Francisco, CA, United States
| | - James Grenert
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Jessica Van Ziffle
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Nancy Joseph
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Sarah Umetsu
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Courtney Onodera
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Michelle Turski
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Emily Chan
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Arpita Desai
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Rahul Aggarwal
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Anthony Wong
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Sima Porten
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Jonathan Chou
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Terence Friedlander
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Lawrence Fong
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Eric J. Small
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Alejandro Sweet-Cordero
- Department of Pediatrics, Benioff Children’s Hospital, University of California, San Francisco, San Francisco, CA, United States
| | - Vadim S. Koshkin
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
- *Correspondence: Vadim S. Koshkin,
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163
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Henderson JJ, Das A, Morgenstern DA, Sudhaman S, Bianchi V, Chung J, Negm L, Edwards M, Kram DE, Osborn M, Hawkins C, Bouffet E, Cho YJ, Tabori U. Immune Checkpoint Inhibition as Single Therapy for Synchronous Cancers Exhibiting Hypermutation: An IRRDC Study. JCO Precis Oncol 2022; 6:e2100286. [PMID: 35235414 PMCID: PMC8906457 DOI: 10.1200/po.21.00286] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Two targets with one arrow: #Immunotherapy as single treatment for synchronous RRD #glioblastoma and #metastatic cancers.![]()
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Affiliation(s)
- Jacob J Henderson
- Mary Bridge Children's Hospital, Division of Pediatric Hematology/Oncology, Tacoma, WA.,Papé Pediatric Research Institute, Division of Pediatric Neurology, Department of Pediatrics, Oregon Health and Sciences University, Portland, OR
| | - Anirban Das
- Hospital for Sick Children and University of Toronto, Toronto, CA
| | | | - Sumedha Sudhaman
- Hospital for Sick Children and University of Toronto, Toronto, CA
| | - Vanessa Bianchi
- Hospital for Sick Children and University of Toronto, Toronto, CA
| | - Jill Chung
- Hospital for Sick Children and University of Toronto, Toronto, CA
| | - Logine Negm
- Hospital for Sick Children and University of Toronto, Toronto, CA
| | - Melissa Edwards
- Hospital for Sick Children and University of Toronto, Toronto, CA
| | - David E Kram
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, Wake Forest School of Medicine, Winston Salem, NC
| | - Michael Osborn
- Royal Adelaide Hospital, Adelaide, Australia.,Women's and Children's Hospital, North Adelaide, Australia
| | - Cynthia Hawkins
- Hospital for Sick Children and University of Toronto, Toronto, CA
| | - Eric Bouffet
- Hospital for Sick Children and University of Toronto, Toronto, CA
| | - Yoon-Jae Cho
- Papé Pediatric Research Institute, Division of Pediatric Neurology, Department of Pediatrics, Oregon Health and Sciences University, Portland, OR
| | - Uri Tabori
- Hospital for Sick Children and University of Toronto, Toronto, CA
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164
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Jongmans MCJ, Zhang J, Hoogerbrugge N, Ligtenberg MJL, De Voer RM. Genetic Cancer Susceptibility in Adolescents and Adults 25 Years or Younger With Colorectal Cancer. Gastroenterology 2022; 162:969-974.e6. [PMID: 34767783 DOI: 10.1053/j.gastro.2021.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 12/22/2022]
Affiliation(s)
- Marjolijn C J Jongmans
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Junxiao Zhang
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | -
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Department of Pathology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Richarda M De Voer
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.
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165
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Shah SM, Demidova EV, Lesh RW, Hall MJ, Daly MB, Meyer JE, Edelman MJ, Arora S. Therapeutic implications of germline vulnerabilities in DNA repair for precision oncology. Cancer Treat Rev 2022; 104:102337. [PMID: 35051883 PMCID: PMC9016579 DOI: 10.1016/j.ctrv.2021.102337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 12/12/2022]
Abstract
DNA repair vulnerabilities are present in a significant proportion of cancers. Specifically, germline alterations in DNA repair not only increase cancer risk but are associated with treatment response and clinical outcomes. The therapeutic landscape of cancer has rapidly evolved with the FDA approval of therapies that specifically target DNA repair vulnerabilities. The clinical success of synthetic lethality between BRCA deficiency and poly(ADP-ribose) polymerase (PARP) inhibition has been truly revolutionary. Defective mismatch repair has been validated as a predictor of response to immune checkpoint blockade associated with durable responses and long-term benefit in many cancer patients. Advances in next generation sequencing technologies and their decreasing cost have supported increased genetic profiling of tumors coupled with germline testing of cancer risk genes in patients. The clinical adoption of panel testing for germline assessment in high-risk individuals has generated a plethora of genetic data, particularly on DNA repair genes. Here, we highlight the therapeutic relevance of germline aberrations in DNA repair to identify patients eligible for precision treatments such as PARP inhibitors (PARPis), immune checkpoint blockade, chemotherapy, radiation therapy and combined treatment. We also discuss emerging mechanisms that regulate DNA repair.
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Affiliation(s)
- Shreya M Shah
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Science Scholars Program, Temple University, Philadelphia, PA, United States
| | - Elena V Demidova
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Kazan Federal University, Kazan, Russian Federation
| | - Randy W Lesh
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Geisinger Commonwealth School of Medicine, Scranton, PA, United States
| | - Michael J Hall
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Mary B Daly
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Joshua E Meyer
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States; Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Martin J Edelman
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States.
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States.
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166
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Abstract
DNA repair and DNA damage signaling pathways are critical for the maintenance of genomic stability. Defects of DNA repair and damage signaling contribute to tumorigenesis, but also render cancer cells vulnerable to DNA damage and reliant on remaining repair and signaling activities. Here, we review the major classes of DNA repair and damage signaling defects in cancer, the genomic instability that they give rise to, and therapeutic strategies to exploit the resulting vulnerabilities. Furthermore, we discuss the impacts of DNA repair defects on both targeted therapy and immunotherapy, and highlight emerging principles for targeting DNA repair defects in cancer therapy.
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Affiliation(s)
- Jessica L Hopkins
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
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167
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Pan-Cancer Analysis of Microfibrillar-Associated Protein 2 (MFAP2) Based on Bioinformatics and qPCR Verification. JOURNAL OF ONCOLOGY 2022; 2022:8423173. [PMID: 35211173 PMCID: PMC8863482 DOI: 10.1155/2022/8423173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 11/18/2022]
Abstract
MFAP2 has been reported to play an oncogenic role in several types of human cancers. However, the expression profile of MFAP2 in various cancers and its impact on prognosis and immune infiltration remain unclear. In this study, the mRNA expression and protein expression of MFAP2 in normal tissues, tumor cell lines, and 33 malignant tumor tissues were analyzed comprehensively using Genotype-Tissue Expression (GTEx), Cancer Cell Line Encyclopedia (CCLE), and The Cancer Genome Atlas (TCGA), Oncomine and UALCAN databases, and the expression of MFAP2 in different grades and stages of cancers was assessed using Gene Expression Profiling Interactive Analysis 2 (GEPIA2) and Tumor and Immune System Interaction Database (TISIDB). In general, MFAP2 showed distinct expression in most tumor and normal tissues, closely associated with higher tumor grade, higher tumor stage, and poor survival in multiple cancers. A search of the UALCAN database and the cBioPortal database revealed that this difference in mRNA level expression could be partly attributed to abnormal DNA methylation and mutations at the genomic level. In addition, MFAP2 expression was also associated with tumor mutation burden, microsatellite instability, and neoantigens in different cancer types. More importantly, the TIMER and TISIDB databases also showed that MFAP2 levels were significantly correlated with immune infiltration abundance and immune-related gene markers, as well as ESTIMATE scores. By qPCR, MFAP2 expression was validated in four kinds of tumor tissue samples. The present study combined several databases and performed a pan-cancer analysis of the expression profile, methylation, and mutation for MFAP2 and its implications for prognosis and immune infiltration, suggesting that MFAP2 could contribute to malignant properties of many tumors. MFAP2 may be an important biomarker with prognostic value and has the potential to be a target for tumor immunotherapy.
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168
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Guan Y, Xu B, Sui Y, Chen Z, Luan Y, Jiang Y, Wei L, Long W, Zhao S, Han L, Xu D, Lin L, Guan Q. Pan-Cancer Analysis and Validation Reveals that D-Dimer-Related Genes are Prognostic and Downregulate CD8+ T Cells via TGF-Beta Signaling in Gastric Cancer. Front Mol Biosci 2022; 9:790706. [PMID: 35274004 PMCID: PMC8902139 DOI: 10.3389/fmolb.2022.790706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/25/2022] [Indexed: 01/16/2023] Open
Abstract
Background: Cancer is considered one of the most lethal diseases worldwide. Venous thromboembolism (VTE) is the second leading cause of death in cancer patients. As one of the most reproducible predictors of thromboembolism, the D-dimer level is commonly considered by oncologists. Previous studies have demonstrated that the most correlated genes at the D-dimer level are F3, F5 and FGA. Methods: Using data from TCGA and multiple webtools, including GEPIA2, UALCAN, TIMER2.0, Kaplan-Meier Plotter and CIBERSORTx, we analyzed the tumor mutation burden (TMB), microsatellite instability (MSI) and functions of D-dimer-related genes in cancer. Validation was conducted via quantitative real-time polymerase chain reaction (qRT-PCR) and independent GEO + GTEx cohort. All statistical analyses were performed in R software and GraphPad Prism 9. Results: F3, F5 and FGA were expressed differently in multiple cancer types. TMB, MSI and anti-PD1/PDL1 therapy responses were correlated with D-dimer-related gene expression. D-Dimer-related genes expression affect the survival of cancer patients. F3 and F5 functioned in TGF-beta signaling. F3 and F5 were related to immunity and affected the fraction of CD8+ T cells by upregulating the TGF-beta signaling pathway, forming an F3, F5/TGF-beta signaling/CD8+ T cell axis. Conclusion: F3, F5 and FGA serve as satisfactory GC multibiomarkers and potentially influence the immune microenvironment and survival of cancer patients by influencing TGF-beta signaling.
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Affiliation(s)
- Yiming Guan
- Department of Laboratory Medicine, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bing Xu
- Department of Neurology, Shenyang First People's Hospital (Shenyang Brain Hospital), Shenyang Medical College, Shenyang, China
| | - Yi Sui
- Department of Neurology, Shenyang First People's Hospital (Shenyang Brain Hospital), Shenyang Medical College, Shenyang, China
| | - Zhezhou Chen
- Department of Laboratory Medicine, Shenyang First People's Hospital (Shenyang Brain Hospital), Shenyang Medical College, Shenyang, China
| | - Yu Luan
- Department of Laboratory Medicine, Shenyang First People's Hospital (Shenyang Brain Hospital), Shenyang Medical College, Shenyang, China
| | - Yan Jiang
- Department of Laboratory Medicine, Shenyang First People's Hospital (Shenyang Brain Hospital), Shenyang Medical College, Shenyang, China
| | - Lijuan Wei
- Department of Laboratory Medicine, Shenyang First People's Hospital (Shenyang Brain Hospital), Shenyang Medical College, Shenyang, China
| | - Wenjing Long
- Department of Laboratory Medicine, Shenyang First People's Hospital (Shenyang Brain Hospital), Shenyang Medical College, Shenyang, China
| | - Sansan Zhao
- Department of Laboratory Medicine, Shenyang First People's Hospital (Shenyang Brain Hospital), Shenyang Medical College, Shenyang, China
| | - Lei Han
- Centre for Cancer Molecular Diagnosis, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Dakang Xu
- Department of Laboratory Medicine, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lin Lin
- Department of Laboratory Medicine, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Qi Guan, ; Lin Lin,
| | - Qi Guan
- Department of Laboratory Medicine, Shenyang First People's Hospital (Shenyang Brain Hospital), Shenyang Medical College, Shenyang, China
- *Correspondence: Qi Guan, ; Lin Lin,
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169
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Qureshi S, Chan N, George M, Ganesan S, Toppmeyer D, Omene C. Immune Checkpoint Inhibitors in Triple Negative Breast Cancer: The Search for the Optimal Biomarker. Biomark Insights 2022; 17:11772719221078774. [PMID: 35221668 PMCID: PMC8874164 DOI: 10.1177/11772719221078774] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/04/2022] [Indexed: 12/14/2022] Open
Abstract
Triple negative breast cancer (TNBC) is a high-risk and aggressive malignancy characterized by the absence of estrogen receptors (ER) and progesterone receptors (PR) on the surface of malignant cells, and by the lack of overexpression of human epidermal growth factor 2 (HER2). It has limited therapeutic options compared to other subtypes of breast cancer. There is now a growing body of evidence on the role of immunotherapy in TNBC, however much of the data from clinical trials is conflicting and thus, challenging for clinicians to integrate the data into clinical practice. Landmark phase III trials using immunotherapy in the early-stage neoadjuvant setting concluded that the addition of immunotherapy to chemotherapy improved the pathologic complete response (pCR) rate compared to chemotherapy with placebo while others found no significant improvement in pCR. Phase III trials have investigated the utility of immunotherapy in previously untreated metastatic TNBC, and these studies have similarly arrived at inconsistent conclusions. Some studies showed no benefit while others demonstrated a clinically significant improvement in overall survival in the PD-L1 positive population. It is not yet clear which biomarkers are most useful, and assays for these biomarkers have not been standardized. Given the often serious and severe side effects of immunotherapy, it is important and necessary to identify predictive biomarkers of response and resistance in order to enhance patient selection. In this review, we will discuss both the challenges of traditional biomarkers and the opportunities of emerging biomarkers for patient selection.
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Affiliation(s)
- Sadaf Qureshi
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Nancy Chan
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Mridula George
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Shridar Ganesan
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Deborah Toppmeyer
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Coral Omene
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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170
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Pandey P, Arora S, Rosen GL. MetaMutationalSigs: comparison of mutational signature refitting results made easy. Bioinformatics 2022; 38:2344-2347. [PMID: 35157026 PMCID: PMC9004636 DOI: 10.1093/bioinformatics/btac091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 12/07/2021] [Accepted: 02/09/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION The analysis of mutational signatures is becoming increasingly common in cancer genetics, with emerging implications in cancer evolution, classification, treatment decision and prognosis. Recently, several packages have been developed for mutational signature analysis, with each using different methodology and yielding significantly different results. Because of the non-trivial differences in tools' refitting results, researchers may desire to survey and compare the available tools, in order to objectively evaluate the results for their specific research question, such as which mutational signatures are prevalent in different cancer types. RESULTS Due to the need for effective comparison of refitting mutational signatures, we introduce a user-friendly software that can aggregate and visually present results from different refitting packages. AVAILABILITY AND IMPLEMENTATION MetaMutationalSigs is implemented using R and python and is available for installation using Docker and available at: https://github.com/EESI/MetaMutationalSigs.
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Affiliation(s)
- Palash Pandey
- Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical and Computer Engineering, College of Engineering, Drexel University, Philadelphia, PA 19104, USA,Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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171
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Liu Y, Gusev A, Heng YJ, Alexandrov LB, Kraft P. Somatic mutational profiles and germline polygenic risk scores in human cancer. Genome Med 2022; 14:14. [PMID: 35144655 PMCID: PMC8832866 DOI: 10.1186/s13073-022-01016-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 01/24/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The mutational profile of cancer reflects the activity of the mutagenic processes which have been operative throughout the lineage of the cancer cell. These processes leave characteristic profiles of somatic mutations called mutational signatures. Mutational signatures, including single-base substitution (SBS) signatures, may reflect the effects of exogenous or endogenous exposures. METHODS We used polygenic risk scores (PRS) to summarize common germline variation associated with cancer risk and other cancer-related traits and examined the association between somatic mutational profiles and germline PRS in 12 cancer types from The Cancer Genome Atlas. Somatic mutational profiles were constructed from whole-exome sequencing data of primary tumors. PRS were calculated for the 12 selected cancer types and 9 non-cancer traits, including cancer risk determinants, hormonal factors, and immune-mediated inflammatory diseases, using germline genetic data and published summary statistics from genome-wide association studies. RESULTS We found 17 statistically significant associations between somatic mutational profiles and germline PRS after Bonferroni correction (p < 3.15 × 10-5), including positive associations between germline inflammatory bowel disease PRS and number of somatic mutations attributed to signature SBS1 in prostate cancer and APOBEC-related signatures in breast cancer. Positive associations were also found between age at menarche PRS and mutation counts of SBS1 in overall and estrogen receptor-positive breast cancer. Consistent with prior studies that found an inverse association between the pubertal development PRS and risk of prostate cancer, likely reflecting hormone-related mechanisms, we found an inverse association between age at menarche PRS and mutation counts of SBS1 in prostate cancer. Inverse associations were also found between several cancer PRS and tumor mutation counts. CONCLUSIONS Our analysis suggests that there are robust associations between tumor somatic mutational profiles and germline PRS. These may reflect the mechanisms through hormone regulation and immune responses that contribute to cancer etiology and drive cancer progression.
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Affiliation(s)
- Yuxi Liu
- grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XProgram in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115 USA
| | - Alexander Gusev
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215 USA
| | - Yujing J. Heng
- grid.38142.3c000000041936754XDepartment of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 USA
| | - Ludmil B. Alexandrov
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Peter Kraft
- grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XProgram in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
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172
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Yuan Y, Jiang X, Tang L, Wang J, Zhang D, Cho WC, Duan L. FOXM1/lncRNA TYMSOS/miR-214-3p–Mediated High Expression of NCAPG Correlates With Poor Prognosis and Cell Proliferation in Non–Small Cell Lung Carcinoma. Front Mol Biosci 2022; 8:785767. [PMID: 35211508 PMCID: PMC8862726 DOI: 10.3389/fmolb.2021.785767] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/31/2021] [Indexed: 12/25/2022] Open
Abstract
Lung cancer is the most common cancer with high mortality. Increasing evidence has demonstrated that nonstructural maintenance of chromosomes condensin I complex subunit G (NCAPG) plays a crucial role in the progression of human cancers. However, the biological function and underlying mechanism of NCAPG in non–small cell lung cancer (NSCLC) are still unclear. Here, we utilized diverse public databases to analyze the expression of NCAPG in pan-cancer. We found that NCAPG was highly expressed in various human cancers, especially in NSCLC. NCAPG expression was significantly positively correlated with poor clinical-pathological features, poor prognosis, tumor mutational burden, DNA microsatellite instability, and immune cell infiltration in NSCLC. In addition, our results showed that depletion of NCAPG significantly inhibited NSCLC cell proliferation, migration, and self-renewal abilities, yet these could be reversed by adding microRNA (miRNA)-214-3p. Knockdown of long noncoding RNA (lncRNA) thymidylate synthetase opposite strand (TYMSOS) also inhibits the NSCLC cell proliferation, migration, and self-renewal abilities. In summary, our findings demonstrated that the crucial roles of the FOXM1/lncRNA-TYMSOS/miRNA-214-3p/NCAPG axis in NSCLC may shed light on how NCAPG may act as a therapeutic target for NSCLC.
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Affiliation(s)
- Yixiao Yuan
- The Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiulin Jiang
- The Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/ Kunming Institute of Zoology, Kunming, China
| | - Lin Tang
- The Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Juan Wang
- The Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Dahang Zhang
- The Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, Hong Kong SAR, China
- *Correspondence: Lincan Duan, ; William C. Cho,
| | - Lincan Duan
- The Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
- *Correspondence: Lincan Duan, ; William C. Cho,
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173
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Díaz-Talavera A, Montero-Conde C, Leandro-García LJ, Robledo M. PrimPol: A Breakthrough among DNA Replication Enzymes and a Potential New Target for Cancer Therapy. Biomolecules 2022; 12:248. [PMID: 35204749 PMCID: PMC8961649 DOI: 10.3390/biom12020248] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 02/01/2023] Open
Abstract
DNA replication can encounter blocking obstacles, leading to replication stress and genome instability. There are several mechanisms for evading this blockade. One mechanism consists of repriming ahead of the obstacles, creating a new starting point; in humans, PrimPol is responsible for carrying out this task. PrimPol is a primase that operates in both the nucleus and mitochondria. In contrast with conventional primases, PrimPol is a DNA primase able to initiate DNA synthesis de novo using deoxynucleotides, discriminating against ribonucleotides. In vitro, PrimPol can act as a DNA primase, elongating primers that PrimPol itself sythesizes, or as translesion synthesis (TLS) DNA polymerase, elongating pre-existing primers across lesions. However, the lack of evidence for PrimPol polymerase activity in vivo suggests that PrimPol only acts as a DNA primase. Here, we provide a comprehensive review of human PrimPol covering its biochemical properties and structure, in vivo function and regulation, and the processes that take place to fill the gap-containing lesion that PrimPol leaves behind. Finally, we explore the available data on human PrimPol expression in different tissues in physiological conditions and its role in cancer.
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Affiliation(s)
- Alberto Díaz-Talavera
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (C.M.-C.); (L.J.L.-G.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Cristina Montero-Conde
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (C.M.-C.); (L.J.L.-G.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Luis Javier Leandro-García
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (C.M.-C.); (L.J.L.-G.); (M.R.)
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (C.M.-C.); (L.J.L.-G.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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174
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Garmezy B, Gheeya J, Lin HY, Huang Y, Kim T, Jiang X, Thein KZ, Pilié PG, Zeineddine F, Wang W, Shaw KR, Rodon J, Shen JP, Yuan Y, Meric-Bernstam F, Chen K, Yap TA. Clinical and Molecular Characterization of POLE Mutations as Predictive Biomarkers of Response to Immune Checkpoint Inhibitors in Advanced Cancers. JCO Precis Oncol 2022; 6:e2100267. [PMID: 35108036 PMCID: PMC8820927 DOI: 10.1200/po.21.00267] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/16/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022] Open
Abstract
PURPOSE DNA polymerase epsilon is critical to DNA proofreading and replication. Mutations in POLE have been associated with hypermutated tumors and antitumor response to immune checkpoint inhibitor (ICI) therapy. We present a clinicopathologic analysis of patients with advanced cancers harboring POLE mutations, the pattern of co-occurring mutations, and their response to ICI therapy within the context of mutation pathogenicity. METHODS We conducted a retrospective analysis of next-generation sequencing data at MD Anderson Cancer Center to identify patient tumors with POLE mutations and their co-occurring mutations. The pathogenicity of each mutation was annotated using InterVar and ClinVar. Differences in therapeutic response to ICI, survival, and co-occurring mutations were reported by POLE pathogenicity status. RESULTS Four hundred fifty-eight patient tumors with POLE mutations were identified from 14,229 next-generation sequencing reports; 15.0% of POLE mutations were pathogenic, 15.9% benign, and 69.1% variant of unknown significance. Eighty-two patients received either programmed death 1 or programmed death ligand-1 inhibitors as monotherapy or in combination with cytotoxic T-cell lymphocyte-4 inhibitors. Patients with pathogenic POLE mutations had improved clinical benefit rate (82.4% v 30.0%; P = .013), median progression-free survival (15.1 v 2.2 months; P < .001), overall survival (29.5 v 6.8 months; P < .001), and longer treatment duration (median 15.5 v 2.5 months; P < .001) compared to those with benign variants. Progression-free survival and overall survival remained superior when adjusting for number of co-occurring mutations (≥ 10 v < 10) and/or microsatellite instability status (proficient mismatch repair v deficient mismatch repair). The number of comutations was not associated with response to ICI (clinical benefit v progressive disease: median 13 v 11 comutations; P = .18). CONCLUSION Pathogenic POLE mutations were associated with clinical benefit to ICI therapy. Further studies are warranted to validate POLE mutation as a predictive biomarker of ICI therapy.
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Affiliation(s)
- Benjamin Garmezy
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jinesh Gheeya
- The University of Texas Health Science Center at Houston, Houston, TX
| | - Heather Y. Lin
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yuefan Huang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Taebeom Kim
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xianli Jiang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kyaw Z. Thein
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Patrick G. Pilié
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Fadl Zeineddine
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wanlin Wang
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kenna R. Shaw
- Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jordi Rodon
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ying Yuan
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX
- Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Timothy A. Yap
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX
- Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
- The Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX
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175
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A novel POLD1 pathogenic variant identified in two families with a cancer spectrum mimicking Lynch syndrome. Eur J Med Genet 2022; 65:104409. [DOI: 10.1016/j.ejmg.2021.104409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/22/2021] [Accepted: 12/17/2021] [Indexed: 11/22/2022]
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176
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Abstract
PURPOSE OF REVIEW Liquid biopsies have emerged as a noninvasive alternative to tissue biopsy with potential applications during all stages of pediatric oncology care. The purpose of this review is to provide a survey of pediatric cell-free DNA (cfDNA) studies, illustrate their potential applications in pediatric oncology, and to discuss technological challenges and approaches to overcome these hurdles. RECENT FINDINGS Recent literature has demonstrated liquid biopsies' ability to inform treatment selection at diagnosis, monitor clonal evolution during treatment, sensitively detect minimum residual disease following local control, and provide sensitive posttherapy surveillance. Advantages include reduced procedural anesthesia, molecular profiling unbiased by tissue heterogeneity, and ability to track clonal evolution. Challenges to wider implementation in pediatric oncology, however, include blood volume restrictions and relatively low mutational burden in childhood cancers. Multiomic approaches address challenges presented by low-mutational burden, and novel bioinformatic analyses allow a single assay to yield increasing amounts of information, reducing blood volume requirements. SUMMARY Liquid biopsies hold tremendous promise in pediatric oncology, enabling noninvasive serial surveillance with adaptive care. Already integrated into adult care, recent advances in technologies and bioinformatics have improved applicability to the pediatric cancer landscape.
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Affiliation(s)
- R Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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177
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Pfister SM, Reyes-Múgica M, Chan JKC, Hasle H, Lazar AJ, Rossi S, Ferrari A, Jarzembowski JA, Pritchard-Jones K, Hill DA, Jacques TS, Wesseling P, López Terrada DH, von Deimling A, Kratz CP, Cree IA, Alaggio R. A Summary of the Inaugural WHO Classification of Pediatric Tumors: Transitioning from the Optical into the Molecular Era. Cancer Discov 2022; 12:331-355. [PMID: 34921008 PMCID: PMC9401511 DOI: 10.1158/2159-8290.cd-21-1094] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/28/2021] [Accepted: 11/18/2021] [Indexed: 01/07/2023]
Abstract
Pediatric tumors are uncommon, yet are the leading cause of cancer-related death in childhood. Tumor types, molecular characteristics, and pathogenesis are unique, often originating from a single genetic driver event. The specific diagnostic challenges of childhood tumors led to the development of the first World Health Organization (WHO) Classification of Pediatric Tumors. The classification is rooted in a multilayered approach, incorporating morphology, IHC, and molecular characteristics. The volume is organized according to organ sites and provides a single, state-of-the-art compendium of pediatric tumor types. A special emphasis was placed on "blastomas," which variably recapitulate the morphologic maturation of organs from which they originate. SIGNIFICANCE: In this review, we briefly summarize the main features and updates of each chapter of the inaugural WHO Classification of Pediatric Tumors, including its rapid transition from a mostly microscopic into a molecularly driven classification systematically taking recent discoveries in pediatric tumor genomics into account.
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Affiliation(s)
- Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Miguel Reyes-Múgica
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Division of Pediatric Pathology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - John K C Chan
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong, SAR China
| | - Henrik Hasle
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sabrina Rossi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Ferrari
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Jason A Jarzembowski
- Department of Pathology, Children's Wisconsin and Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Kathy Pritchard-Jones
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - D Ashley Hill
- Department of Pathology, Children's National Hospital, Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Thomas S Jacques
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Pieter Wesseling
- Laboratory for Childhood Cancer Pathology, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Department of Pathology, Amsterdam University Medical Centers/VUmc, Amsterdam, the Netherlands
| | - Dolores H López Terrada
- Department of Pathology, Texas Children's Hospital and Baylor College of Medicine, Houston, Texas
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Ian A Cree
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rita Alaggio
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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178
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Zeng P, Zhang X, Xiang T, Ling Z, Lin C, Diao H. Secreted phosphoprotein 1 as a potential prognostic and immunotherapy biomarker in multiple human cancers. Bioengineered 2022; 13:3221-3239. [PMID: 35067176 PMCID: PMC8973783 DOI: 10.1080/21655979.2021.2020391] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Ping Zeng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xujun Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Tianxin Xiang
- Department of Hospital Infection Control, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zongxin Ling
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Chenhong Lin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hongyan Diao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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179
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Dahl JM, Thomas N, Tracy MA, Hearn BL, Perera L, Kennedy SR, Herr AJ, Kunkel TA. Probing the mechanisms of two exonuclease domain mutators of DNA polymerase ϵ. Nucleic Acids Res 2022; 50:962-974. [PMID: 35037018 DOI: 10.1093/nar/gkab1255] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/21/2021] [Accepted: 12/08/2021] [Indexed: 11/15/2022] Open
Abstract
We report the properties of two mutations in the exonuclease domain of the Saccharomyces cerevisiae DNA polymerase ϵ. One, pol2-Y473F, increases the mutation rate by about 20-fold, similar to the catalytically dead pol2-D290A/E290A mutant. The other, pol2-N378K, is a stronger mutator. Both retain the ability to excise a nucleotide from double-stranded DNA, but with impaired activity. pol2-Y473F degrades DNA poorly, while pol2-N378K degrades single-stranded DNA at an elevated rate relative to double-stranded DNA. These data suggest that pol2-Y473F reduces the capacity of the enzyme to perform catalysis in the exonuclease active site, while pol2-N378K impairs partitioning to the exonuclease active site. Relative to wild-type Pol ϵ, both variants decrease the dNTP concentration required to elicit a switch between proofreading and polymerization by more than an order of magnitude. While neither mutation appears to alter the sequence specificity of polymerization, the N378K mutation stimulates polymerase activity, increasing the probability of incorporation and extension of a mismatch. Considered together, these data indicate that impairing the primer strand transfer pathway required for proofreading increases the probability of common mutations by Pol ϵ, elucidating the association of homologous mutations in human DNA polymerase ϵ with cancer.
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Affiliation(s)
- Joseph M Dahl
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, DHHS, Research Triangle Park, NC 27709, USA
| | - Natalie Thomas
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, DHHS, Research Triangle Park, NC 27709, USA
| | - Maxwell A Tracy
- Department of Laboratory Medicine and Pathology, UW Medicine, Seattle, WA 98195, USA
| | - Brady L Hearn
- Department of Laboratory Medicine and Pathology, UW Medicine, Seattle, WA 98195, USA
| | - Lalith Perera
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, DHHS, Research Triangle Park, NC 27709, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, UW Medicine, Seattle, WA 98195, USA
| | - Alan J Herr
- Department of Laboratory Medicine and Pathology, UW Medicine, Seattle, WA 98195, USA
| | - Thomas A Kunkel
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, DHHS, Research Triangle Park, NC 27709, USA
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180
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Jiang L, Yu H, Ness S, Mao P, Guo F, Tang J, Guo Y. Comprehensive Analysis of Co-Mutations Identifies Cooperating Mechanisms of Tumorigenesis. Cancers (Basel) 2022; 14:415. [PMID: 35053577 PMCID: PMC8774165 DOI: 10.3390/cancers14020415] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 12/16/2022] Open
Abstract
Somatic mutations are one of the most important factors in tumorigenesis and are the focus of most cancer-sequencing efforts. The co-occurrence of multiple mutations in one tumor has gained increasing attention as a means of identifying cooperating mutations or pathways that contribute to cancer. Using multi-omics, phenotypical, and clinical data from 29,559 cancer subjects and 1747 cancer cell lines covering 78 distinct cancer types, we show that co-mutations are associated with prognosis, drug sensitivity, and disparities in sex, age, and race. Some co-mutation combinations displayed stronger effects than their corresponding single mutations. For example, co-mutation TP53:KRAS in pancreatic adenocarcinoma is significantly associated with disease specific survival (hazard ratio = 2.87, adjusted p-value = 0.0003) and its prognostic predictive power is greater than either TP53 or KRAS as individually mutated genes. Functional analyses revealed that co-mutations with higher prognostic values have higher potential impact and cause greater dysregulation of gene expression. Furthermore, many of the prognostically significant co-mutations caused gains or losses of binding sequences of RNA binding proteins or micro RNAs with known cancer associations. Thus, detailed analyses of co-mutations can identify mechanisms that cooperate in tumorigenesis.
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Affiliation(s)
- Limin Jiang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin 300350, China
| | - Hui Yu
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA; (H.Y.); (S.N.); (P.M.)
| | - Scott Ness
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA; (H.Y.); (S.N.); (P.M.)
| | - Peng Mao
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA; (H.Y.); (S.N.); (P.M.)
| | - Fei Guo
- School of Computer Science and Engineering, Central South University, Changsha 410083, China;
| | - Jijun Tang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
| | - Yan Guo
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA; (H.Y.); (S.N.); (P.M.)
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181
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Gong X, Cheng J, Zhang K, Wang Y, Li S, Luo Y. Transcriptome sequencing reveals Gastrodia elata Blume could increase the cell viability of eNPCs under hypoxic condition by improving DNA damage repair ability. JOURNAL OF ETHNOPHARMACOLOGY 2022; 282:114646. [PMID: 34530095 DOI: 10.1016/j.jep.2021.114646] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Gastrodia elata Blume (GEB), known as Tianma in China, is a traditional medicinal herb that has been reported to have various pharmacological effects and neuroprotection, has long been used for treating dizziness, epilepsy, stroke. However, explanation of its underlying mechanisms remains a great challenge. AIM OF THE STUDY The neuroprotective mechanism of GEB on hypoxia-induced neuronal injury in cultured mouse embryonic neural progenitor cells (eNPCs) was investigated, with emphasis on the eNPCs proliferation and DNA damage repair. MATERIALS AND METHODS In this study, hypoxia was focused, which may be caused by stroke or acute cerebral ischemia and is considered as one of the important factors contributing to the Central Nervous System diseases. CoCl2 was adopted to construct a hypoxic/ischemic condition in eNPCs. eNPCs proliferation analysis validated GEB neuroprotective effect under hypoxic/ischemic condition. Transcriptome and weighted gene co-expression network analysis (WGCNA) screened the special gene-network module correlated with what appeared to have significant positive correlation with GEB. Then, Gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were performed to explore the biological functions of selected genes in the modules that had high correlation with GEB. RESULTS GEB has neuroprotective effect and could rescue eNPCs proliferation under hypoxic/ischemic condition induced by CoCl2. Transcriptome and WGCNA unveil the neuroprotective mechanism of GEB on improving DNA damage repair ability by increasing the expression of genes associated with DNA repair and replication. Western blotting and qPCR showed that GEB could improve DNA damage repair ability by increasing the expression of Mcm2, Mcm6, Pold2, Pole, Pole2, Rfc1, Pole4, Dna2 and Rpa2, which were associated with DNA damage and replication. CONCLUSION Through transcriptome and WGCNA, this study unveiled Gastrodia elata Blume could increase the cell viability of eNPCs under hypoxic condition by improving DNA damage repair ability.
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Affiliation(s)
- Xi Gong
- Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 999 Xuefu Rd., Honggutan New District, Nanchang, Jiangxi, 330031, China
| | - Jing Cheng
- Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 999 Xuefu Rd., Honggutan New District, Nanchang, Jiangxi, 330031, China
| | - Kunshan Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Yanlu Wang
- Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 999 Xuefu Rd., Honggutan New District, Nanchang, Jiangxi, 330031, China
| | - Siguang Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China.
| | - Yuping Luo
- Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 999 Xuefu Rd., Honggutan New District, Nanchang, Jiangxi, 330031, China; Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China.
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182
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Marret G, Bièche I, Dupain C, Borcoman E, du Rusquec P, Ricci F, Hescot S, Sablin MP, Tresca P, Bello D, Dubot C, Loirat D, Frelaut M, Lecerf C, Le Tourneau C, Kamal M. Genomic Alterations in Head and Neck Squamous Cell Carcinoma: Level of Evidence According to ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT). JCO Precis Oncol 2022; 5:215-226. [PMID: 34994597 DOI: 10.1200/po.20.00280] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Development of high-throughput technologies helped to decipher tumor genomic landscapes revealing actionable molecular alterations. We aimed to rank the level of evidence of recurrent actionable molecular alterations in head and neck squamous cell carcinoma (HNSCC) on the basis of the European Society for Medical Oncology (ESMO) Scale for Clinical Actionability of Molecular Targets (ESCAT) to help the clinicians prioritize treatment. We identified actionable alterations in 33 genes. HRAS-activating mutations were ranked in tier IB because of the efficacy of tipifarnib (farnesyltransferase inhibitor) in HRAS-mutated patients with HNSCC (nonrandomized clinical trial). Microsatellite instability (MSI), high tumor mutational burden (TMB), and NTRK fusions were ranked in tier IC because of PD-1 and TRK tyrosine kinase inhibitors tissue-agnostic approvals. CDKN2A-inactivating alterations and EGFR amplification were ranked in tier IIA because of the efficacy of palbociclib (CDK4/6 inhibitor) and afatinib (tyrosine kinase inhibitor) in these respective molecular subgroups in retrospective analyses of clinical trials. Molecular alterations in several genes, including PIK3CA gene, were ranked in tier IIIA because of clinical benefit in other tumor types, whereas molecular alterations in IGF1R and TP53 genes were ranked in tier IVA and tier V, respectively. The most compelling actionable molecular alterations in HNSCC according to ESCAT include HRAS-activating mutations, MSI, high TMB, NTRK fusions, CDKN2A-inactivating alterations, and EGFR amplification.
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Affiliation(s)
| | - Ivan Bièche
- Department of Genetics, Institut Curie, Paris Descartes University, Paris, France.,INSERM U1016 Research Unit, Cochin Institute, Paris, France
| | - Célia Dupain
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Edith Borcoman
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Pauline du Rusquec
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Francesco Ricci
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Ségolène Hescot
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Marie-Paule Sablin
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Patricia Tresca
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Diana Bello
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Coraline Dubot
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Delphine Loirat
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Maxime Frelaut
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Charlotte Lecerf
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France.,INSERM U900, Institut Curie, Mines Paris Tech, Saint-Cloud, France.,Paris-Saclay University, Paris, France
| | - Maud Kamal
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
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183
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Das A, Sudhaman S, Morgenstern D, Coblentz A, Chung J, Stone SC, Alsafwani N, Liu ZA, Karsaneh OAA, Soleimani S, Ladany H, Chen D, Zatzman M, Cabric V, Nobre L, Bianchi V, Edwards M, Sambira Nahum LC, Ercan AB, Nabbi A, Constantini S, Dvir R, Yalon-Oren M, Campino GA, Caspi S, Larouche V, Reddy A, Osborn M, Mason G, Lindhorst S, Bronsema A, Magimairajan V, Opocher E, De Mola RL, Sabel M, Frojd C, Sumerauer D, Samuel D, Cole K, Chiaravalli S, Massimino M, Tomboc P, Ziegler DS, George B, Van Damme A, Hijiya N, Gass D, McGee RB, Mordechai O, Bowers DC, Laetsch TW, Lossos A, Blumenthal DT, Sarosiek T, Yen LY, Knipstein J, Bendel A, Hoffman LM, Luna-Fineman S, Zimmermann S, Scheers I, Nichols KE, Zapotocky M, Hansford JR, Maris JM, Dirks P, Taylor MD, Kulkarni AV, Shroff M, Tsang DS, Villani A, Xu W, Aronson M, Durno C, Shlien A, Malkin D, Getz G, Maruvka YE, Ohashi PS, Hawkins C, Pugh TJ, Bouffet E, Tabori U. Genomic predictors of response to PD-1 inhibition in children with germline DNA replication repair deficiency. Nat Med 2022; 28:125-135. [PMID: 34992263 PMCID: PMC8799468 DOI: 10.1038/s41591-021-01581-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 10/15/2021] [Indexed: 02/08/2023]
Abstract
Cancers arising from germline DNA mismatch repair deficiency or polymerase proofreading deficiency (MMRD and PPD) in children harbour the highest mutational and microsatellite insertion–deletion (MS-indel) burden in humans. MMRD and PPD cancers are commonly lethal due to the inherent resistance to chemo-irradiation. Although immune checkpoint inhibitors (ICIs) have failed to benefit children in previous studies, we hypothesized that hypermutation caused by MMRD and PPD will improve outcomes following ICI treatment in these patients. Using an international consortium registry study, we report on the ICI treatment of 45 progressive or recurrent tumors from 38 patients. Durable objective responses were observed in most patients, culminating in a 3 year survival of 41.4%. High mutation burden predicted response for ultra-hypermutant cancers (>100 mutations per Mb) enriched for combined MMRD + PPD, while MS-indels predicted response in MMRD tumors with lower mutation burden (10–100 mutations per Mb). Furthermore, both mechanisms were associated with increased immune infiltration even in ‘immunologically cold’ tumors such as gliomas, contributing to the favorable response. Pseudo-progression (flare) was common and was associated with immune activation in the tumor microenvironment and systemically. Furthermore, patients with flare who continued ICI treatment achieved durable responses. This study demonstrates improved survival for patients with tumors not previously known to respond to ICI treatment, including central nervous system and synchronous cancers, and identifies the dual roles of mutation burden and MS-indels in predicting sustained response to immunotherapy. Hypermutation and microsatellite burden determine responses and long-term survival following PD-1 blockade in children and young adults with refractory cancers resulting from germline DNA replication repair deficiency.
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Affiliation(s)
- Anirban Das
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatric Haematology/ Oncology, Tata Medical Centre, Kolkata, India
| | - Sumedha Sudhaman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Daniel Morgenstern
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Ailish Coblentz
- Department of Diagnostic Imaging, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jiil Chung
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Simone C Stone
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Noor Alsafwani
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Pathology, College of Medicine, Imam Abdulrahman Bin Faisal University (IAU), Dammam, Saudi Arabia
| | - Zhihui Amy Liu
- Department of Biostatistics, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Ola Abu Al Karsaneh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Shirin Soleimani
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Hagay Ladany
- Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Tel-Aviv, Israel
| | - David Chen
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Matthew Zatzman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Vanja Cabric
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Liana Nobre
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Vanessa Bianchi
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Melissa Edwards
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lauren C Sambira Nahum
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ayse B Ercan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Arash Nabbi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shlomi Constantini
- Department of Pediatric Neurosurgery, Dana Children's Hospital, Tel-Aviv, Israel
| | - Rina Dvir
- Department of Pediatric Hematology-Oncology, Tel-Aviv Sourasky Medical Centre, Tel-Aviv, Israel
| | - Michal Yalon-Oren
- Department of Pediatric Hematology-Oncology, Sheba Medical Centre, Ramat Gan, Israel
| | - Gadi Abebe Campino
- Department of Pediatric Hematology-Oncology, Sheba Medical Centre, Ramat Gan, Israel
| | - Shani Caspi
- Department of Pediatric Hematology-Oncology, Sheba Medical Centre, Ramat Gan, Israel
| | - Valerie Larouche
- Department of Paediatric Haematology/Oncology, Centre Hospitalier de Quebec-Universite Laval, Quebec City, Quebec, Canada
| | - Alyssa Reddy
- Departments of Neurology and Pediatrics, University of California, San Francisco, CA, USA
| | - Michael Osborn
- Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Gary Mason
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Scott Lindhorst
- Neuro-Oncology, Department of Neurosurgery, and Department of Medicine, Division of Hematology/Medical Oncology, Medical University of South Carolina, Charleston, SC, USA
| | - Annika Bronsema
- Department of Paediatric Haematology and Oncology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Vanan Magimairajan
- Department of Paediatric Haematology-Oncology, Cancer Care Manitoba, Research Institute in Oncology and Haematology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Enrico Opocher
- Paediatric Haematology, Oncology and Stem Cell Transplant Division, Padua University Hospital, Padua, Italy
| | - Rebecca Loret De Mola
- Pediatric Hematology-Oncology, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Magnus Sabel
- Department of Paediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden.,Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Charlotta Frojd
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - David Sumerauer
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | - David Samuel
- Department of Pediatric Oncology, Valley Children's Hospital, Madera, CA, USA
| | - Kristina Cole
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelpha, PA, USA
| | - Stefano Chiaravalli
- Paediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maura Massimino
- Paediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Patrick Tomboc
- Department of Pediatrics, J.W. Ruby Memorial Hospital - West Virginia University, Morgantown, WV, USA
| | - David S Ziegler
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Ben George
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - An Van Damme
- Department of Paediatric Haematology and Oncology, Saint Luc University Hospital, Université Catholique de Louvain, Brussels, Belgium
| | - Nobuko Hijiya
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Irving Medical Centre, New York, NY, USA
| | - David Gass
- Atrium Health Levine Children's Hospital, Charlotte, NC, USA
| | - Rose B McGee
- Cancer Predisposition Division, Oncology Department, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Oz Mordechai
- Department of Pediatric Hematology Oncology, Rambam Health Care Campus, Haifa, Israel
| | - Daniel C Bowers
- Department of Pediatrics, The University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Theodore W Laetsch
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelpha, PA, USA
| | - Alexander Lossos
- Department of Oncology, Leslie and Michael Gaffin Center for Neuro-Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Deborah T Blumenthal
- Neuro-Oncology Service, Tel-Aviv Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | | | - Lee Yi Yen
- Department of Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jeffrey Knipstein
- Division of Pediatric Hematology/ Oncology/ BMT, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Anne Bendel
- Department of Pediatric Hematology-Oncology, Children's Hospitals and Clinics of Minnesota, St Paul, MN, USA
| | | | - Sandra Luna-Fineman
- Department of Pediatrics, Anschutz Medical Campus, Children's Hospital of Colorado, Aurora, CO, USA
| | - Stefanie Zimmermann
- Paediatric Haematology and Oncology, University Hospital Frankfurt, Frankfurt, Germany
| | - Isabelle Scheers
- Paediatric Gastroenterology, Hepatology and Nutrition Unit, Cliniques Universitaires St Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Kim E Nichols
- Cancer Predisposition Division, Oncology Department, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Michal Zapotocky
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | - Jordan R Hansford
- Children's Cancer Centre, Royal Children's Hospital, Murdoch Children's Research Institute, University of Melbourne, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelpha, PA, USA
| | - Peter Dirks
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Abhaya V Kulkarni
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Child Health Evaluative Sciences, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Manohar Shroff
- Department of Diagnostic Imaging, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Derek S Tsang
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Anita Villani
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Carol Durno
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - David Malkin
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Gad Getz
- Massachusetts General Hospital Cancer Center and Department of Pathology, Charlestown, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yosef E Maruvka
- Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Tel-Aviv, Israel
| | - Pamela S Ohashi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Cynthia Hawkins
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Eric Bouffet
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Uri Tabori
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada. .,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada. .,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada. .,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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184
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Immunotherapy for Neuro-oncology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1342:233-258. [PMID: 34972967 DOI: 10.1007/978-3-030-79308-1_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Immunotherapy has changed the landscape of treatment of many solid and hematological malignancies and is at the forefront of cancer breakthroughs. Several circumstances unique to the central nervous system (CNS) such as limited space for an inflammatory response, difficulties with repeated sampling, corticosteroid use for management of cerebral edema, and immunosuppressive mechanisms within the tumor and brain parenchyma have posed challenges in clinical development of immunotherapy for intracranial tumors. Nonetheless, the success of immunotherapy in brain metastases (BMs) from solid cancers such as melanoma and non-small cell lung cancer (NSCLC) proves that the CNS is not an immune-privileged organ and is capable of initiating and regulating immune responses that lead to tumor control. However, the development of immunotherapeutics for the most malignant primary brain tumor, glioblastoma (GBM), has been challenging due to systemic and profound tumor-mediated immunosuppression unique to GBM, intratumoral and intertumoral heterogeneity, and lack of stably expressed clonal antigens. Here, we review recent advances in the field of immunotherapy for neuro-oncology with a focus on BM, GBM, and rare CNS cancers.
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185
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Suk Y, Gwynne WD, Burns I, Venugopal C, Singh SK. Childhood Medulloblastoma: An Overview. Methods Mol Biol 2022; 2423:1-12. [PMID: 34978683 DOI: 10.1007/978-1-0716-1952-0_1] [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: 06/14/2023]
Abstract
Medulloblastoma (MB) is the most common malignant pediatric brain tumor, representing 60% of childhood intracranial embryonal tumors. Despite multimodal advances in therapies over the last 20 years that have yielded a 5-year survival rate of 75%, high-risk patients (younger than 3 years, subtotal resection, metastatic lesions at diagnosis) still experience a 5-year overall survival of less than 70%. In this introductory chapter on pediatric MB, we describe the initial discrimination of MB based on histopathological examination and the more recent progress made in global gene expression profiling methods that have allowed scientists to more accurately subclassify and prognosticate on MB based on molecular characteristics. The identification of subtype-specific molecular drivers and pathways presents novel therapeutic targets that could lead to MB subtype-specific treatment modalities. Additionally, we detail how the cancer stem cell (CSC) hypothesis provides an explanation for tumor recurrence, and the potential for CSC-targeted therapies to address treatment-refractory MB. These personalized therapies can potentially increase MB survivorship and negate some of the long-term neurotoxicity associated with the current standard of care for MB patients.
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Affiliation(s)
- Yujin Suk
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | - William D Gwynne
- Department of Surgery, McMaster University, Hamilton, ON, Canada
| | - Ian Burns
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | - Chitra Venugopal
- Department of Surgery, McMaster University, Hamilton, ON, Canada
| | - Sheila K Singh
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
- Department of Surgery, McMaster University, Hamilton, ON, Canada.
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186
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Long JM, Powers JM, Katona BW. Evaluation of Classic, Attenuated, and Oligopolyposis of the Colon. Gastrointest Endosc Clin N Am 2022; 32:95-112. [PMID: 34798989 PMCID: PMC8607742 DOI: 10.1016/j.giec.2021.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The goal of this review is to provide an overview of evaluating patients with adenomatous polyposis of the colon, including elements such as generating a differential diagnosis, referral considerations for genetic testing, genetic testing options, and expected outcomes from genetic testing in these individuals. In more recent years, adenomatous colonic polyposis has evolved beyond the more robustly characterized familial adenomatous polyposis (FAP) and MUTYH-associated polyposis (MAP) now encompassing more newly described genes and associated syndromes. Technological innovation, from whole-exome sequencing to multigene panel testing, has dramatically increased the amount of genotypic and phenotypic data amassed in adenomatous polyposis cohorts, which has contributed greatly to informing diagnosis and clinical management of affected individuals and their families.
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Affiliation(s)
- Jessica M. Long
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jacquelyn M. Powers
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Bryson W. Katona
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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187
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Lang SS, Kumar NK, Madsen P, Gajjar AA, Gajjar E, Resnick AC, Storm PB. Neurotrophic Tyrosine Receptor Kinase Fusion in Pediatric Central Nervous System Tumors. Cancer Genet 2022; 262-263:64-70. [DOI: 10.1016/j.cancergen.2022.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/29/2021] [Accepted: 01/18/2022] [Indexed: 12/16/2022]
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188
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Sehested A, Meade J, Scheie D, Østrup O, Bertelsen B, Misiakou MA, Sarosiek T, Kessler E, Melchior LC, Munch-Petersen HF, Pai RK, Schmuth M, Gottschling H, Zschocke J, Gallon R, Wimmer K. Constitutional POLE variants causing a phenotype reminiscent of constitutional mismatch repair deficiency. Hum Mutat 2022; 43:85-96. [PMID: 34816535 DOI: 10.1002/humu.24299] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022]
Abstract
Heterozygous POLE or POLD1 germline pathogenic variants (PVs) cause polymerase proofreading associated polyposis (PPAP), a constitutional polymerase proofreading deficiency that typically presents with colorectal adenomas and carcinomas in adulthood. Constitutional mismatch-repair deficiency (CMMRD), caused by germline bi-allelic PVs affecting one of four MMR genes, results in a high propensity for the hematological, brain, intestinal tract, and other malignancies in childhood. Nonmalignant clinical features, such as skin pigmentation alterations, are found in nearly all CMMRD patients and are important diagnostic markers. Here, we excluded CMMRD in three cancer patients with highly suspect clinical phenotypes but identified in each a constitutional heterozygous POLE PV. These, and two additional POLE PVs identified in published CMMRD-like patients, have not previously been reported as germline PVs despite all being well-known somatic mutations in hyper-mutated tumors. Together, these five cases show that specific POLE PVs may have a stronger "mutator" effect than known PPAP-associated POLE PVs and may cause a CMMRD-like phenotype distinct from PPAP. The common underlying mechanism, that is, a constitutional replication error repair defect, and a similar tumor spectrum provide a good rationale for monitoring these patients with a severe constitutional polymerase proofreading deficiency according to protocols proposed for CMMRD.
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Affiliation(s)
- Astrid Sehested
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Julia Meade
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - David Scheie
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Olga Østrup
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Birgitte Bertelsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Maria Anna Misiakou
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Elena Kessler
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Linea C Melchior
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Reetesh K Pai
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Matthias Schmuth
- Department of Dermatology, Venereology and Allergy, Medical University of Innsbruck, Innsbruck, Austria
| | - Hendrik Gottschling
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Johannes Zschocke
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Richard Gallon
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Katharina Wimmer
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
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189
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Molecular characteristics and clinical outcomes of patients with Neurofibromin 1-altered metastatic colorectal cancer. Oncogene 2022; 41:260-267. [PMID: 34728807 PMCID: PMC8738154 DOI: 10.1038/s41388-021-02074-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022]
Abstract
Loss-of-function alterations of Neurofibromin 1 (NF1) activate RAS, a driver of colorectal cancer. However, the clinical implications of NF1 alterations are largely unknown. We performed a comprehensive molecular profiling of NF1-mutant colorectal cancer using data from 8150 patients included in a dataset of commercial CLIA-certified laboratory (Caris Life Sciences). In addition, NF1 expression levels were tested for associations with clinical outcomes using data from 431 patients in the CALGB/SWOG 80405 trial. In the Caris dataset, 2.2% of patients had pathogenic or presumed pathogenic NF1 mutations. NF1-mutant tumors more frequently harbored PIK3CA (25.0% vs. 16.7%) and PTEN mutations (24.0% vs. 4.2%) than wild type tumors. Gene set enrichment analysis revealed that MAPK and PI3K pathway signatures were enriched in NF1-mutant tumors. In the CALGB/SWOG 80405 cohort, low NF1 expression was associated with poor prognosis, and high NF1 expression was associated with better efficacy of cetuximab than bevacizumab. Together, we revealed concurrent genetic alterations in the PI3K pathways in NF1-mutant tumors, suggesting the need to simultaneously block MAPK and PI3K pathways in treatment. The potential of NF1 alteration as a novel biomarker for targeted therapy was highlighted, warranting further investigations in clinical settings.
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190
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Franzese N, Fan J, Sharan R, Leiserson MD. ScalpelSig Designs Targeted Genomic Panels from Data to Detect Activity of Mutational Signatures. J Comput Biol 2022; 29:56-73. [PMID: 34986026 PMCID: PMC8812502 DOI: 10.1089/cmb.2021.0453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Over the past decade, a promising line of cancer research has utilized machine learning to mine statistical patterns of mutations in cancer genomes for information. Recent work shows that these statistical patterns, commonly referred to as "mutational signatures," have diverse therapeutic potential as biomarkers for cancer therapies. However, translating this potential into reality is hindered by limited access to sequencing in the clinic. Almost all methods for mutational signature analysis (MSA) rely on whole genome or whole exome sequencing data, while sequencing in the clinic is typically limited to small gene panels. To improve clinical access to MSA, we considered the question of whether targeted panels could be designed for the purpose of mutational signature detection. Here we present ScalpelSig, to our knowledge the first algorithm that automatically designs genomic panels optimized for detection of a given mutational signature. The algorithm learns from data to identify genome regions that are particularly indicative of signature activity. Using a cohort of breast cancer genomes as training data, we show that ScalpelSig panels substantially improve accuracy of signature detection compared to baselines. We find that some ScalpelSig panels even approach the performance of whole exome sequencing, which observes over 10 × as much genomic material. We test our algorithm under a variety of conditions, showing that its performance generalizes to another dataset of breast cancers, to smaller panel sizes, and to lesser amounts of training data.
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Affiliation(s)
- Nicholas Franzese
- Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.,Department of Computer Science, Northwestern University, Evanston, Illinois, USA.,National Institutes of Health, Bethesda, Maryland, USA
| | - Jason Fan
- Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Roded Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Mark D.M. Leiserson
- Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.,Address correspondence to: Dr. Mark D.M. Leiserson, Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
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191
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Zheng M. Tumor mutation burden for predicting immune checkpoint blockade response: the more, the better. J Immunother Cancer 2022; 10:e003087. [PMID: 35101940 PMCID: PMC8804687 DOI: 10.1136/jitc-2021-003087] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Recently, the US Food and Drug Administration (FDA) has approved immune checkpoint blockade (ICB) for treating cancer patients with tumor mutation burden (TMB) >10 mutations/megabase (mut/Mb). However, high TMB (TMB-H) defined by >10 mut/Mb fails to predict ICB response across different cancer types, which has raised serious concerns on the current FDA approval. Thus, to better implement TMB as a robust biomarker of ICB response, an optimal and generalizable TMB cut-off within and across cancer types must be addressed as soon as possible. METHODS Using Morris's and Kurzrock's cohorts (n=1662 and 102), we exhaustively tested all possible TMB cut-offs for predicting ICB treatment outcomes in 10 cancer types. The bootstrap method was applied to generate 10,000 randomly resampled cohorts using original cohorts to measure the reproducibility of TMB cut-off. ICB treatment outcomes were analyzed by overall survival, progression-free survival and objective response rate. RESULTS No universally valid TMB cut-off was available for all cancer types. Only in cancer types with higher TMB (category I), such as melanoma, colorectal cancer, bladder cancer, and non-small cell lung cancer, the associations between TMB-H and ICB treatment outcomes were less affected by TMB cut-off selection. Moreover, high TMB (category I) cancer types shared a wide range of TMB cut-offs and a universally optimal TMB cut-off of 13 mut/Mb for predicting favorable ICB outcomes. In contrast, low TMB (category II) cancer types, for which the prognostic associations were sensitive to TMB cut-off selection, showed markedly limited and distinct ranges of significantly favorable TMB cut-offs. Equivalent results were obtained in the analyses of pooled tumors. CONCLUSIONS Our finding-the correlation that TMB-H is more robustly associated with favorable ICB treatment outcomes in cancer types with higher TMBs-can be used to predict whether TMB could be a robust predictive biomarker in cancer types for which TMB data are available, but ICB treatment has not been investigated. This theory was tested in cancer of unknown primary successfully. Additionally, the universal TMB cut-off of 13 mut/Mb might reveal a general requirement to trigger the sequential cascade from somatic mutations to an effective antitumor immunity.
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Affiliation(s)
- Ming Zheng
- Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, China
- Beijing Institute of Basic Medical Sciences, Beijing, China
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192
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Seidel MG, Kashofer K, Moser T, Thueringer A, Liegl-Atzwanger B, Leithner A, Szkandera J, Benesch M, El-Heliebi A, Heitzer E. Clinical implementation of plasma cell-free circulating tumor DNA quantification by digital droplet PCR for the monitoring of Ewing sarcoma in children and adolescents. Front Pediatr 2022; 10:926405. [PMID: 36046479 PMCID: PMC9420963 DOI: 10.3389/fped.2022.926405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/15/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Treatment stratification and response assessment in pediatric sarcomas has relied on imaging studies and surgical/histopathological evidence of vital tumor cells. Such studies and evidence collection processes often involve radiation and/or general anesthesia in children. Cell-free circulating tumor DNA (ctDNA) detection in blood plasma is one available method of so-called liquid biopsies that has been shown to correlate qualitatively and quantitatively with the existence of vital tumor cells in the body. Our clinical observational study focused on the utility and feasibility of ctDNA detection in pediatric Ewing sarcoma (EWS) as a marker of minimal residual disease (MRD). PATIENTS AND METHODS We performed whole genome sequencing (WGS) to identify the exact breakpoints in tumors known to carry the EWS-FLI1 fusion gene. Patient-specific fusion breakpoints were tracked in peripheral blood plasma using digital droplet PCR (ddPCR) before, during, and after therapy in six children and young adults with EWS. Presence and levels of fusion breakpoints were correlated with clinical disease courses. RESULTS We show that the detection of ctDNA in the peripheral blood of EWS patients (i) is feasible in the clinical routine and (ii) allows for the longitudinal real-time monitoring of MRD activity in children and young adults. Although changing ctDNA levels correlated well with clinical outcome within patients, between patients, a high variability was observed (inter-individually). CONCLUSION ctDNA detection by ddPCR is a highly sensitive, specific, feasible, and highly accurate method that can be applied in EWS for follow-up assessments as an additional surrogate parameter for clinical MRD monitoring and, potentially, also for treatment stratification in the near future.
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Affiliation(s)
- Markus G Seidel
- Division for Pediatric Hematology-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Karl Kashofer
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Tina Moser
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Andrea Thueringer
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Bernadette Liegl-Atzwanger
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Andreas Leithner
- Department of Orthopedics and Trauma, Medical University of Graz, Graz, Austria
| | - Joanna Szkandera
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Martin Benesch
- Division for Pediatric Hematology-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Amin El-Heliebi
- BioTechMed-Graz, Graz, Austria.,Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria.,Center for Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Ellen Heitzer
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
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193
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Michaeli O, Ladany H, Erez A, Shachar SB, Izraeli S, Lidzbarsky G, Basel-Salmon L, Biskup S, Maruvka YE, Toledano H, Goldberg Y. Di-genic inheritance of germline POLE and PMS2 pathogenic variants causes a unique condition associated with pediatric cancer predisposition. Clin Genet 2021; 101:442-447. [PMID: 34967012 DOI: 10.1111/cge.14106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/12/2021] [Accepted: 12/25/2021] [Indexed: 11/25/2022]
Abstract
Polymerase proofreading-associated polyposis (PPAP) and Lynch syndrome, caused by mutated POLE and mismatch repair (MMR) genes, respectively, are associated with adult-onset cancer. PPAP and MMR-deficient tumors are both hypermutated, and each has a unique mutational signature. We describe a 4.5-year-old boy with multiple café au lait spots who presented with metastatic Sonic Hedgehog-activated medulloblastoma, with partial response to intensive chemotherapy and immunotherapy. Tumor showed microsatellite stability, loss of PMS2 nuclear expression, and an exceptionally high tumor mutational burden of 276 Mut/Mb. Germline molecular analysis revealed an inherited heterozygous pathogenic POLE variant and a de novo heterozygous PMS2 pathogenic variant. The tumor featured the MMR, POLE, and POLE+MMR mutational signatures. This is the first description of a di-genic condition, which we named "POL-LYNCH syndrome", manifested by an aggressive ultra-mutant pediatric medulloblastoma with a unique genomic signature. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Orli Michaeli
- Department of Pediatric Hematology and Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Hagay Ladany
- Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Ayelet Erez
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Shay Ben Shachar
- Clalit Research Institute & Department of Genetics, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Shai Izraeli
- Department of Pediatric Hematology and Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gabriel Lidzbarsky
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
| | - Lina Basel-Salmon
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
| | - Saskia Biskup
- CeGaT Center for Genomics and Transcriptomics, Tuebingen, Germany
| | - Yosef E Maruvka
- Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Helen Toledano
- Department of Pediatric Hematology and Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Goldberg
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
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194
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Barresi V, Simbolo M, Mafficini A, Martini M, Calicchia M, Piredda ML, Ciaparrone C, Bonizzato G, Ammendola S, Caffo M, Pinna G, Sala F, Lawlor RT, Ghimenton C, Scarpa A. IDH-wild type glioblastomas featuring at least 30% giant cells are characterized by frequent RB1 and NF1 alterations and hypermutation. Acta Neuropathol Commun 2021; 9:200. [PMID: 34952640 PMCID: PMC8709962 DOI: 10.1186/s40478-021-01304-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/08/2021] [Indexed: 01/07/2023] Open
Abstract
Giant cell glioblastoma (GC-GBM) is a rare variant of IDH-wt GBM histologically characterized by the presence of numerous multinucleated giant cells and molecularly considered a hybrid between IDH-wt and IDH-mutant GBM. The lack of an objective definition, specifying the percentage of giant cells required for this diagnosis, may account for the absence of a definite molecular profile of this variant. This study aimed to clarify the molecular landscape of GC-GBM, exploring the mutations and copy number variations of 458 cancer-related genes, tumor mutational burden (TMB), and microsatellite instability (MSI) in 39 GBMs dichotomized into having 30-49% (15 cases) or ≥ 50% (24 cases) GCs. The type and prevalence of the genetic alterations in this series was not associated with the GCs content (< 50% or ≥ 50%). Most cases (82% and 51.2%) had impairment in TP53/MDM2 and PTEN/PI3K pathways, but a high proportion also featured TERT promoter mutations (61.5%) and RB1 (25.6%) or NF1 (25.6%) alterations. EGFR amplification was detected in 18% cases in association with a shorter overall survival (P = 0.004). Sixteen (41%) cases had a TMB > 10 mut/Mb, including two (5%) that harbored MSI and one with a POLE mutation. The frequency of RB1 and NF1 alterations and TMB counts were significantly higher compared to 567 IDH wild type (P < 0.0001; P = 0.0003; P < 0.0001) and 26 IDH-mutant (P < 0.0001; P = 0.0227; P < 0.0001) GBMs in the TCGA PanCancer Atlas cohort. These findings demonstrate that the molecular landscape of GBMs with at least 30% giant cells is dominated by the impairment of TP53/MDM2 and PTEN/PI3K pathways, and additionally characterized by frequent RB1 alterations and hypermutation and by EGFR amplification in more aggressive cases. The high frequency of hypermutated cases suggests that GC-GBMs might be candidates for immune check-point inhibitors clinical trials.
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Affiliation(s)
- Valeria Barresi
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Michele Simbolo
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Maurizio Martini
- Unit of Anatomic Pathology, Catholic University of Sacred Hearth, Rome, Italy
| | - Martina Calicchia
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Maria Liliana Piredda
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Chiara Ciaparrone
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Giada Bonizzato
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Serena Ammendola
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Maria Caffo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Section of Neurosurgery, University of Messina, Messina, Italy
| | - Giampietro Pinna
- Department of Neurosciences, Unit of Neurosurgery, Hospital Trust of Verona, Verona, Italy
| | - Francesco Sala
- Department of Neurosciences, Biomedicines and Movement Sciences, Institute of Neurosurgery, University of Verona, Verona, Italy
| | - Rita Teresa Lawlor
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Claudio Ghimenton
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
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195
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Simbolo M, Bersani S, Vicentini C, Taormina SV, Ciaparrone C, Bagante F, Rusev B, Centonze G, Montresor M, Brunelli M, Pedron S, Mafficini A, Paolino G, Mattiolo P, Conci S, Milione M, Guglielmi A, Ruzzenente A, Scarpa A, Luchini C. Molecular characterization of extrahepatic cholangiocarcinoma: perihilar and distal tumors display divergent genomic and transcriptomic profiles. Expert Opin Ther Targets 2021; 25:1095-1105. [PMID: 34873971 DOI: 10.1080/14728222.2021.2013801] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Extrahepatic cholangiocarcinoma (ECC) is classified into two subtypes based on anatomic origin: distal extrahepatic (DECC) and perihilar (PHCC) cholangiocarcinoma. This study aimed to shed light on its genomic and transcriptomic profiles. RESEARCH DESIGN AND METHODS The genomic alterations of 99 ECC (47 PHCC and 52 DECC) were investigated by next-generation sequencing of 96 genes. A subgroup of cases, representative of each subtype, was further investigated using transcriptomic analysis. Bioinformatics tools were applied for clustering and pathway analysis and defining the immune composition of the tumor microenvironment. RESULTS PHCC had more frequent KRAS mutations (p = 0.0047), whereas TP53 mutations were more common in DECC (p = 0.006). Potentially actionable alterations included high-tumor mutational burden and/or microsatellite instability (7.1%), PI3KCA mutations (8.1%), and MYC (10.1%) and ERBB2 amplification (5.1%). The transcriptomic profiles showed the presence of three distinct clusters, which followed the anatomic origin and differed in immune microenvironment. DECC appeared to contain two distinct tumor subgroups, one enriched for druggable alterations and one lacking actionable opportunities. CONCLUSIONS This study provides new insights into the molecular landscape and the actionable alterations of ECC. Our findings represent a step toward improved ECC molecular taxonomy and therapeutic strategies for precision oncology.
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Affiliation(s)
- Michele Simbolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Samantha Bersani
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Caterina Vicentini
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Sergio V Taormina
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Chiara Ciaparrone
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Fabio Bagante
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Borislav Rusev
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy.,ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Giovanni Centonze
- Pathology Unit, Foundation IRCCS, Istituto Nazionale Tumori, Milano, Italy
| | - Marina Montresor
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Matteo Brunelli
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Serena Pedron
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy.,ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Gaetano Paolino
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Simone Conci
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Massimo Milione
- Pathology Unit, Foundation IRCCS, Istituto Nazionale Tumori, Milano, Italy
| | - Alfredo Guglielmi
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Ruzzenente
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy.,ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy.,ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
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196
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Evaluation of IL-2 and Dexamethasone intracavitary injection on the management of malignant effusion in children with solid tumors or lymphoma. BMC Cancer 2021; 21:1302. [PMID: 34872514 PMCID: PMC8650392 DOI: 10.1186/s12885-021-09041-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Currently, no available coherent management protocol exists for pediatric cancers associated with pleural effusion, ascites, and pericardial effusion. This study aimed to retrospectively present our experience in treating pediatric cancer patients with pleural effusion, ascites, and pericardial effusion using interleukin-2 (IL-2) and dexamethasone (DEX) intracavitary injections. METHODS Between January 1st, 2008 and December 31st, 2020, medical reports of patients diagnosed with solid tumors or lymphoma were checked to identify patients diagnosed with > 2 cm pleural effusion, and/or more than grade 1 ascites, and/or more than small pericardial effusion. Patients diagnosed with effusions and treated with IL-2 and DEX were identified as being in the effusion group. Meanwhile, patients with the same primary tumors and effusions but did not receive interleukin 2 and DEX injection were reviewed and classified as the control group. RESULTS Forty patients with solid tumors and 66 patients with lymphoma were further diagnosed with pleural effusion, ascites, or pericardial effusion. A total of 85 patients received IL-2 and DEX injection while the remaining 21 did not. The Kaplan Meier analysis revealed a significant difference between the two groups, with p < 0.01 for event free survival (EFS) and p < 0.01 for overall survival (OS), both of which had p < 0.01. Hazard ratio was found to be 0.344 for OS and 0.352 for EFS. CONCLUSIONS This retrospective study illustrates that thoracic, intraperitoneal, or pericardial intracavitary injection of DEX plus IL-2 can be an effective and safe treatment for pediatric cancers with pleural effusion, ascites, and pericardial effusion.
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197
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Thakur S, Jain M, Zhang C, Major C, Bielamowicz KJ, Lacayo NJ, Vaske O, Lewis V, Murguia-Favela L, Narendran A. Identification and in vitro validation of neoantigens for immune activation against high-risk pediatric leukemia cells. Hum Vaccin Immunother 2021; 17:5558-5562. [PMID: 34844524 DOI: 10.1080/21645515.2021.2001243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
There is experimental and clinical data to indicate the contribution of immune-escape mechanisms in relapsed/refractory pediatric leukemia. Studies have shown the accumulation of mutations that translate to peptides containing tumor-specific epitopes (neoantigens). The effectiveness of neoantigen-based vaccines has been shown in several clinical trials in adults. Though the initial results are encouraging, this knowledge must be developed to account for the uniqueness of pediatric cancer biology. We have completed the initial proof-of-concept analysis on a high-risk pediatric leukemia specimen and identified usable neoantigen sequences. We describe this approach, including the bioinformatics method and experimental model to verify their function that can be further broadened for personalized neoantigen prediction and testing for the generation of anticancer vaccines against high-risk pediatric leukemias.
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Affiliation(s)
- Satbir Thakur
- Division of Pediatric Oncology, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Mohit Jain
- Division of Pediatric Oncology, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Chunfen Zhang
- Division of Pediatric Oncology, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Candice Major
- Division of Pediatric Oncology, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Kevin J Bielamowicz
- Division of Hematology/Oncology, Arkansas Children's Hospital, Little Rock, Arkansas
| | - Norman J Lacayo
- Department of Oncology, Stanford University School of Medicine, Stanford, California
| | - Olena Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California
| | - Victor Lewis
- Division of Pediatric Oncology, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Luis Murguia-Favela
- Section of Hematology and Immunology, Alberta Children's Hospital, University of Calgary, Calgary, Alberta, Canada
| | - Aru Narendran
- Division of Pediatric Oncology, Alberta Children's Hospital, Calgary, Alberta, Canada
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198
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Billaud A, Chevalier LM, Augereau P, Frenel JS, Passot C, Campone M, Morel A. Functional pre-therapeutic evaluation by genome editing of variants of uncertain significance of essential tumor suppressor genes. Genome Med 2021; 13:174. [PMID: 34749799 PMCID: PMC8576946 DOI: 10.1186/s13073-021-00976-x] [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: 05/20/2020] [Accepted: 09/23/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Targeted therapies in oncology are promising but variants of uncertain significance (VUS) limit their use for clinical management and necessitate functional testing in vitro. Using BRCA1 and BRCA2 variants, which have consequences on PARP inhibitor sensitivity, and POLE variants, potential biomarkers of immunotherapy response, we developed a rapid functional assay based on CRISPR-Cas9 genome editing to determine the functional consequences of these variants having potentially direct implications on patients' access to targeted therapies. METHODS We first evaluated the functional impact of 26 BRCA1 and 7 BRCA2 variants by editing and comparing NGS results between the variant of interest and a silent control variant. Ten of these variants had already been classified as benign or pathogenic and were used as controls. Finally, we extended this method to the characterization of POLE VUS. RESULTS For the 23 variants that were unclassified or for which conflicting interpretations had been reported, 15 were classified as functionally normal and 6 as functionally abnormal. Another two variants were found to have intermediate consequences, both with potential impacts on splicing. We then compared these scores to the patients' responses to PARP inhibitors when possible. Finally, to prove the application of our method to the classification of variants from other tumor suppressor genes, we exemplified with three POLE VUS. Among them, two were classified with an intermediate functional impact and one was functionally abnormal. Eventually, four POLE variants previously classified in databases were also evaluated. However, we found evidence of a discordance with the classification, variant p.Leu424Val being found here functionally normal. CONCLUSIONS Our new rapid functional assay can be used to characterize the functional implication of BRCA1 and BRCA2 variants, giving patients whose variants were evaluated as functionally abnormal access to PARP inhibitor treatment. Retrospective analysis of patients' responses to PARP inhibitors, where accessible, was consistent with our functional score evaluation and confirmed the accuracy of our protocol. This method could potentially be extended to the classification of VUS from all essential tumor suppressor genes and can be performed within a timeframe compatible with clinical applications, thereby having a direct theranostic impact.
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Affiliation(s)
- Amandine Billaud
- Université d'Angers, Inserm, CRCINA, SFR ICAT, F-49000, Angers, France
- Institut de Cancérologie de l'Ouest Nantes-Angers, F-49000, Angers, France
| | - Louise-Marie Chevalier
- Université d'Angers, Inserm, CRCINA, SFR ICAT, F-49000, Angers, France
- Institut de Cancérologie de l'Ouest Nantes-Angers, F-49000, Angers, France
| | - Paule Augereau
- Institut de Cancérologie de l'Ouest Nantes-Angers, F-49000, Angers, France
| | - Jean-Sebastien Frenel
- Institut de Cancérologie de l'Ouest Nantes-Angers, F-49000, Angers, France
- Université de Nantes, Inserm, CRCINA, F-44000, Nantes, France
| | - Christophe Passot
- Institut de Cancérologie de l'Ouest Nantes-Angers, F-49000, Angers, France
| | - Mario Campone
- Institut de Cancérologie de l'Ouest Nantes-Angers, F-49000, Angers, France
- Université de Nantes, Inserm, CRCINA, F-44000, Nantes, France
| | - Alain Morel
- Université d'Angers, Inserm, CRCINA, SFR ICAT, F-49000, Angers, France.
- Institut de Cancérologie de l'Ouest Nantes-Angers, F-49000, Angers, France.
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199
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Abstract
PURPOSE OF REVIEW Recent evidence suggests high tumor mutational burden (TMB-H) as a predictor of response to immune checkpoint blockade (ICB) in cancer. However, results in TMB-H gliomas have been inconsistent. In this article, we discuss the main pathways leading to TMB-H in glioma and how these might affect immunotherapy response. RECENT FINDINGS Recent characterization of TMB-H gliomas showed that 'post-treatment' related to mismatch repair (MMR) deficiency is the most common mechanism leading to TMB-H in gliomas. Unexpectedly, preliminary evidence suggested that benefit with ICB is rare in this population. Contrary to expectations, ICB response was reported in a subset of TMB-H gliomas associated with constitutional MMR or polymerase epsilon (POLE) defects (e.g., constitutional biallelic MMRd deficiency). In other cancers, several trials suggest increased ICB efficacy is critically associated with increased lymphocyte infiltration at baseline which is missing in most gliomas. Further characterization of the immune microenvironment of gliomas is needed to identify biomarkers to select the patients who will benefit from ICB. SUMMARY Intrinsic molecular and immunological differences between gliomas and other cancers might explain the lack of efficacy of ICB in a subset of TMB-H gliomas. Novel combinations and biomarkers are awaited to improve immunotherapy response in these cancers.
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Affiliation(s)
- Diego Prost
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin
| | - Franck Bielle
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neuropathologie Laboratoire Escourolle, Paris, France
| | - Keith L Ligon
- Broad Institute of MIT and Harvard, Cambridge
- Department of Pathology, Brigham and Women's Hospital
- Department of Oncologic Pathology, Dana-Farber Cancer Institute
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Mehdi Touat
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin
- Department of Neurology, Brigham and Women's Hospital, Boston, USA
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200
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Chen K, Shields MD, Chauhan PS, Ramirez RJ, Harris PK, Reimers MA, Zevallos JP, Davis AA, Pellini B, Chaudhuri AA. Commercial ctDNA Assays for Minimal Residual Disease Detection of Solid Tumors. Mol Diagn Ther 2021; 25:757-774. [PMID: 34725800 PMCID: PMC9016631 DOI: 10.1007/s40291-021-00559-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2021] [Indexed: 12/20/2022]
Abstract
The detection of circulating tumor DNA via liquid biopsy has become an important diagnostic test for patients with cancer. While certain commercial liquid biopsy platforms designed to detect circulating tumor DNA have been approved to guide clinical decisions in advanced solid tumors, the clinical utility of these assays for detecting minimal residual disease after curative-intent treatment of nonmetastatic disease is currently limited. Predicting disease response and relapse has considerable potential for increasing the effective implementation of neoadjuvant and adjuvant therapies. As a result, many companies are rapidly investing in the development of liquid biopsy platforms to detect circulating tumor DNA in the minimal residual disease setting. In this review, we discuss the development and clinical implementation of commercial liquid biopsy platforms for circulating tumor DNA minimal residual disease detection of solid tumors. Here, we aim to highlight the technological features that enable highly sensitive detection of tumor-derived genomic alterations, the factors that differentiate these commercial platforms, and the ongoing trials that seek to increase clinical implementation of liquid biopsies using circulating tumor DNA-based minimal residual disease detection.
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Affiliation(s)
- Kevin Chen
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park Avenue, St. Louis, MO, 63108, USA
| | - Misty D Shields
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Department of Thoracic Oncology, Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Pradeep S Chauhan
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park Avenue, St. Louis, MO, 63108, USA
| | - Ricardo J Ramirez
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA
| | - Peter K Harris
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park Avenue, St. Louis, MO, 63108, USA
| | - Melissa A Reimers
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO, 63110, USA
| | - Jose P Zevallos
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew A Davis
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA.
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO, 63110, USA.
| | - Bruna Pellini
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- Department of Thoracic Oncology, Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
| | - Aadel A Chaudhuri
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park Avenue, St. Louis, MO, 63108, USA.
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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