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Chabane K, Charlot C, Gugenheim D, Simonet T, Armisen D, Viailly PJ, Codet de Boisse G, Huet S, Hayette S, Alcazer V, Sujobert P. Real life evaluation of AlphaMissense predictions in hematological malignancies. Leukemia 2024; 38:420-423. [PMID: 38135759 DOI: 10.1038/s41375-023-02116-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023]
Abstract
High-throughput sequencing plays a pivotal role in hematological malignancy diagnostics, but interpreting missense mutations remains challenging. In this study, we used the newly available AlphaMissense database to assess the efficacy of machine learning to predict missense mutation effects and its impact to improve our ability to interpret them. Based on the analysis of 2073 variants from 686 patients analyzed for clinical purpose, we confirmed the very high accuracy of AlphaMissense predictions in a large real-life data set of missense mutations (AUC of ROC curve 0.95), and provided a comprehensive analysis of the discrepancies between AlphaMissense predictions and state of the art clinical interpretation.
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Affiliation(s)
- Kaddour Chabane
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d'hématologie biologique, Pierre Bénite, France
| | - Carole Charlot
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d'hématologie biologique, Pierre Bénite, France
| | | | - Thomas Simonet
- Hospices Civils de Lyon, Plateforme de séquençage NGS, cellule bioinformatique, Bron, France
| | - David Armisen
- Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Université Lyon 1, Equipe Lymphoma Immunobiology, Pierre Bénite, France
| | | | | | - Sarah Huet
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d'hématologie biologique, Pierre Bénite, France
- Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Université Lyon 1, Equipe Lymphoma Immunobiology, Pierre Bénite, France
| | - Sandrine Hayette
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d'hématologie biologique, Pierre Bénite, France
| | - Vincent Alcazer
- Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Université Lyon 1, Equipe Lymphoma Immunobiology, Pierre Bénite, France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d'hématologie clinique, Pierre Bénite, France
| | - Pierre Sujobert
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d'hématologie biologique, Pierre Bénite, France.
- Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Université Lyon 1, Equipe Lymphoma Immunobiology, Pierre Bénite, France.
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2
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Menon V, Brash DE. Next-generation sequencing methodologies to detect low-frequency mutations: "Catch me if you can". MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108471. [PMID: 37716438 PMCID: PMC10843083 DOI: 10.1016/j.mrrev.2023.108471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023]
Abstract
Mutations, the irreversible changes in an organism's DNA sequence, are present in tissues at a variant allele frequency (VAF) ranging from ∼10-8 per bp for a founder mutation to ∼10-3 for a histologically normal tissue sample containing several independent clones - compared to 1%- 50% for a heterozygous tumor mutation or a polymorphism. The rarity of these events poses a challenge for accurate clinical diagnosis and prognosis, toxicology, and discovering new disease etiologies. Standard Next-Generation Sequencing (NGS) technologies report VAFs as low as 0.5% per nt, but reliably observing rarer precursor events requires additional sophistication to measure ultralow-frequency mutations. We detail the challenge; define terms used to characterize the results, which vary between laboratories and sometimes conflict between biologists and bioinformaticists; and describe recent innovations to improve standard NGS methodologies including: single-strand consensus sequence methods such as Safe-SeqS and SiMSen-Seq; tandem-strand consensus sequence methods such as o2n-Seq and SMM-Seq; and ultrasensitive parent-strand consensus sequence methods such as DuplexSeq, PacBio HiFi, SinoDuplex, OPUSeq, EcoSeq, BotSeqS, Hawk-Seq, NanoSeq, SaferSeq, and CODEC. Practical applications are also noted. Several methods quantify VAF down to 10-5 at a nt and mutation frequency (MF) in a target region down to 10-7 per nt. By expanding to > 1 Mb of sites never observed twice, thus forgoing VAF, other methods quantify MF < 10-9 per nt or < 15 errors per haploid genome. Clonal expansion cannot be directly distinguished from independent mutations by sequencing, so it is essential for a paper to report whether its MF counted only different mutations - the minimum independent-mutation frequency MFminI - or all mutations observed including recurrences - the larger maximum independent-mutation frequency MFmaxI which may reflect clonal expansion. Ultrasensitive methods reveal that, without their use, even mutations with VAF 0.5-1% are usually spurious.
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Affiliation(s)
- Vijay Menon
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520-8040, USA.
| | - Douglas E Brash
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520-8040, USA; Department of Dermatology, Yale School of Medicine, New Haven, CT 06520-8059, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520-8028, USA.
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3
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Sargas C, Ayala R, Larráyoz MJ, Chillón MC, Carrillo-Cruz E, Bilbao-Sieyro C, Prados de la Torre E, Martínez-Cuadrón D, Rodríguez-Veiga R, Boluda B, Gil C, Bernal T, Bergua JM, Algarra L, Tormo M, Martínez-Sánchez P, Soria E, Serrano J, Alonso-Domínguez JM, García-Boyero R, Amigo ML, Herrera-Puente P, Sayas MJ, Lavilla-Rubira E, Martínez-López J, Calasanz MJ, García-Sanz R, Pérez-Simón JA, Gómez-Casares MT, Sánchez-García J, Barragán E, Montesinos P. Molecular Landscape and Validation of New Genomic Classification in 2668 Adult AML Patients: Real Life Data from the PETHEMA Registry. Cancers (Basel) 2023; 15:cancers15020438. [PMID: 36672386 PMCID: PMC9856266 DOI: 10.3390/cancers15020438] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/30/2022] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Next-Generation Sequencing (NGS) implementation to perform accurate diagnosis in acute myeloid leukemia (AML) represents a major challenge for molecular laboratories in terms of specialization, standardization, costs and logistical support. In this context, the PETHEMA cooperative group has established the first nationwide diagnostic network of seven reference laboratories to provide standardized NGS studies for AML patients. Cross-validation (CV) rounds are regularly performed to ensure the quality of NGS studies and to keep updated clinically relevant genes recommended for NGS study. The molecular characterization of 2856 samples (1631 derived from the NGS-AML project; NCT03311815) with standardized NGS of consensus genes (ABL1, ASXL1, BRAF, CALR, CBL, CEBPA, CSF3R, DNMT3A, ETV6, EZH2, FLT3, GATA2, HRAS, IDH1, IDH2, JAK2, KIT, KRAS, MPL, NPM1, NRAS, PTPN11, RUNX1, SETBP1, SF3B1, SRSF2, TET2, TP53, U2AF1 and WT1) showed 97% of patients having at least one mutation. The mutational profile was highly variable according to moment of disease, age and sex, and several co-occurring and exclusion relations were detected. Molecular testing based on NGS allowed accurate diagnosis and reliable prognosis stratification of 954 AML patients according to new genomic classification proposed by Tazi et al. Novel molecular subgroups, such as mutated WT1 and mutations in at least two myelodysplasia-related genes, have been associated with an adverse prognosis in our cohort. In this way, the PETHEMA cooperative group efficiently provides an extensive molecular characterization for AML diagnosis and risk stratification, ensuring technical quality and equity in access to NGS studies.
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Affiliation(s)
- Claudia Sargas
- Grupo Acreditado de Investigación en Hematología, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain
| | - Rosa Ayala
- Hospital Universitario 12 de Octubre, National Cancer Research Center, Complutense University, 28041 Madrid, Spain
| | - María José Larráyoz
- CIMA LAB Diagnostics, Departamento de Bioquímica y Genética, Universidad de Navarra, 31008 Pamplona, Spain
| | - María Carmen Chillón
- Servicio de Hematología, Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC, Centro de Investigación del Cáncer–IBMCC (USAL–CSIC), 37007 Salamanca, Spain
| | - Estrella Carrillo-Cruz
- Hospital Universitario Virgen del Rocío, Instituto de Biomedicina (IBIS/CSIC/CIBERONC), Universidad de Sevilla, 41013 Sevilla, Spain
| | - Cristina Bilbao-Sieyro
- Hospital Universitario de Gran Canaria Dr. Negrín, 35010 Las Palmas de Gran Canaria, Spain
| | - Esther Prados de la Torre
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), 14004 Córdoba, Spain
| | - David Martínez-Cuadrón
- Servicio de Hematología, Grupo Acreditado de Investigación en Hematología, Hospital Universitario y Politécnico La Fe, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain
| | - Rebeca Rodríguez-Veiga
- Servicio de Hematología, Grupo Acreditado de Investigación en Hematología, Hospital Universitario y Politécnico La Fe, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain
| | - Blanca Boluda
- Servicio de Hematología, Grupo Acreditado de Investigación en Hematología, Hospital Universitario y Politécnico La Fe, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain
| | - Cristina Gil
- Hospital General Universitario de Alicante, 03010 Alicante, Spain
| | - Teresa Bernal
- Hospital Universitario Central de Asturias, Instituto Universitario (IUOPA), Instituto de Investigación del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | | | - Lorenzo Algarra
- Hospital Universitario General de Albacete, 02006 Albacete, Spain
| | - Mar Tormo
- Hospital Clínico Universitario–INCLIVA, 46010 Valencia, Spain
| | - Pilar Martínez-Sánchez
- Hospital Universitario 12 de Octubre, National Cancer Research Center, Complutense University, 28041 Madrid, Spain
| | - Elena Soria
- Hospital Universitario Virgen del Rocío, Instituto de Biomedicina (IBIS/CSIC/CIBERONC), Universidad de Sevilla, 41013 Sevilla, Spain
| | - Josefina Serrano
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), 14004 Córdoba, Spain
| | | | | | - María Luz Amigo
- Hospital Universitario Morales Messeguer, 30008 Murcia, Spain
| | | | | | | | - Joaquín Martínez-López
- Hospital Universitario 12 de Octubre, National Cancer Research Center, Complutense University, 28041 Madrid, Spain
| | - María José Calasanz
- CIMA LAB Diagnostics, Departamento de Bioquímica y Genética, Universidad de Navarra, 31008 Pamplona, Spain
| | - Ramón García-Sanz
- Servicio de Hematología, Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC, Centro de Investigación del Cáncer–IBMCC (USAL–CSIC), 37007 Salamanca, Spain
| | - José Antonio Pérez-Simón
- Hospital Universitario Virgen del Rocío, Instituto de Biomedicina (IBIS/CSIC/CIBERONC), Universidad de Sevilla, 41013 Sevilla, Spain
| | | | - Joaquín Sánchez-García
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), 14004 Córdoba, Spain
| | - Eva Barragán
- Hospital General Universitario de Alicante, 03010 Alicante, Spain
- Servicio Análisis Clínicos, Grupo Acreditado de Investigación en Hematología, Hospital Universitario y Politécnico La Fe, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain
- Correspondence: ; Tel.: +34-961-244589
| | - Pau Montesinos
- Servicio de Hematología, Grupo Acreditado de Investigación en Hematología, Hospital Universitario y Politécnico La Fe, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain
- Hospital General Universitario de Alicante, 03010 Alicante, Spain
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Lobl MB, Clarey DD, Higgins S, Sutton A, Wysong A. Sequencing of cutaneous squamous cell carcinoma primary tumors and patient-matched metastases reveals ALK as a potential driver in metastases and low mutational concordance in immunocompromised patients. JID INNOVATIONS 2022; 2:100122. [PMID: 35620707 PMCID: PMC9127419 DOI: 10.1016/j.xjidi.2022.100122] [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: 09/20/2021] [Revised: 02/11/2022] [Accepted: 02/28/2022] [Indexed: 11/23/2022] Open
Abstract
Cutaneous squamous cell carcinoma is a common skin cancer that is responsible for 1,000,000 cases and up to 9,000 deaths annually in the United States. Metastases occur in 2–5% of patients and are responsible for significant morbidity and mortality. The objective of this study is to perform targeted next-generation sequencing on a cohort of squamous cell carcinoma primary tumors and patient-matched lymph node metastases. An oncology 76-gene panel was run from formalin-fixed paraffin-embedded samples of patient-matched primary squamous cell carcinomas (10) and resultant metastases (10). ALK was discovered to be a driver mutation in metastases using two different algorithms, oncoCLUSTand dNdScv. Mutational concordance between primary tumors and metastases was notably lower in immunosuppressed patients, especially among pathogenic mutations (41.7% vs. 83.3%, P = 0.01). Sequencing of matched squamous cell carcinoma primary tumors and lymph node metastases identified genes and pathways that may have clinical importance, most notably ALK as a potential driver mutation of metastasis. Sequencing of both primary tumors and metastases may improve the efficacy of targeted therapies.
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5
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Lima A, Sousa H, Nobre A, Faria AL, Machado M. The Impact of COVID-19 Pandemic in Portuguese Cancer Patients: A Retrospective Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:8552. [PMID: 34444302 PMCID: PMC8391914 DOI: 10.3390/ijerph18168552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/19/2021] [Accepted: 08/09/2021] [Indexed: 01/08/2023]
Abstract
Literature reports that SARS-CoV-2 infection in cancer patients may be associated with higher severity and mortality, nevertheless the knowledge is limited. We aimed to describe patients' demographic characteristics and COVID-19 disease outcomes in Portuguese cancer patients. We conducted a retrospective study in a cohort of cancer patients diagnosed with COVID-19. A total of 127 individuals were included: 46.5% males and 53.5% females, with a median age of 72 years. Clinicopathological characteristics were used in univariate and multivariable logistic regression analyses to estimate odds ratios for each variable with outcomes adjusting for potential confounders. Our cohort revealed that 84.3% of patients had more than one risk factor for severe disease rather than cancer. In total, 36.2% of patients were admitted to the Department of Internal Medicine, 14.2% developed severe disease, 1.6% required Intensive Care Unit, and mortality was observed in 11.8%. Severe COVID-19 disease was associated with unfit (ECOG PS > 2) patients (p = 0.009; OR = 6.39; 95% CI: 1.60-25.59), chronic kidney disease (p = 0.004; OR = 20.7; 95% CI: 2.64-162.8), immunosuppression (p < 0.001; OR = 10.3; 95% CI: 2.58-41.2), and presence of respiratory symptoms at diagnosis (p = 0.033; OR = 5.05; 95% CI: 1.14-22.4). Increased risk for mortality was associated with unfit patients (p = 0.036; OR = 4.22; 95% CI: 1.10-16.3), cardiac disease (p = 0.003; OR = 8.26; 95% CI: 2.03-33.6) and immunosuppression (p = 0.022; OR = 5.06; 95% CI: 1.27-20.18). Our results demonstrated that unfit and immunosuppressed patients, with chronic kidney disease and cardiac disease, have, respectively, an increased risk for severe disease and mortality related to COVID-19. Hence, this study provides important information on risk factors for severe COVID-19 disease and associated mortality in a Portuguese cancer population.
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Affiliation(s)
- Aurea Lima
- Centro Hospitalar de Entre o Douro e Vouga EPE, Medical Oncology Department, Unit of Santa Maria da Feira, Rua Dr. Cândido Pinho 5, 4520-211 Santa Maria da Feira, Portugal; (A.N.); (A.L.F.); (M.M.)
- Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Porto Comprehensive Cancer Center (Porto.CCC), Molecular Oncology and Viral Pathology Group, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal;
- Cooperativa de Ensino Superior Politécnico e Universitário (CESPU), Department of Pharmaceutical Sciences, Institute of Research and Advanced Training in Health Sciences and Technologies, Rua Central de Gandra 1317, 4585-116 Gandra, Portugal
| | - Hugo Sousa
- Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Porto Comprehensive Cancer Center (Porto.CCC), Molecular Oncology and Viral Pathology Group, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal;
- Virology Service, Portuguese Institute of Oncology of Porto (IPO-Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Amanda Nobre
- Centro Hospitalar de Entre o Douro e Vouga EPE, Medical Oncology Department, Unit of Santa Maria da Feira, Rua Dr. Cândido Pinho 5, 4520-211 Santa Maria da Feira, Portugal; (A.N.); (A.L.F.); (M.M.)
| | - Ana Luisa Faria
- Centro Hospitalar de Entre o Douro e Vouga EPE, Medical Oncology Department, Unit of Santa Maria da Feira, Rua Dr. Cândido Pinho 5, 4520-211 Santa Maria da Feira, Portugal; (A.N.); (A.L.F.); (M.M.)
| | - Manuela Machado
- Centro Hospitalar de Entre o Douro e Vouga EPE, Medical Oncology Department, Unit of Santa Maria da Feira, Rua Dr. Cândido Pinho 5, 4520-211 Santa Maria da Feira, Portugal; (A.N.); (A.L.F.); (M.M.)
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6
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Dai M, Liu D, Liu M, Zhou F, Li G, Chen Z, Zhang Z, You H, Wu M, Zheng Q, Xiong Y, Xiong H, Wang C, Chen C, Xiong F, Zhang Y, Peng Y, Ge S, Zhen B, Yu T, Wang L, Wang H, Liu Y, Chen Y, Mei J, Gao X, Li Z, Gan L, He C, Li Z, Shi Y, Qi Y, Yang J, Tenen DG, Chai L, Mucci LA, Santillana M, Cai H. Patients with Cancer Appear More Vulnerable to SARS-CoV-2: A Multicenter Study during the COVID-19 Outbreak. Cancer Discov 2020; 10:783-791. [PMID: 32345594 PMCID: PMC7309152 DOI: 10.1158/2159-8290.cd-20-0422] [Citation(s) in RCA: 906] [Impact Index Per Article: 226.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/16/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023]
Abstract
The novel COVID-19 outbreak has affected more than 200 countries and territories as of March 2020. Given that patients with cancer are generally more vulnerable to infections, systematic analysis of diverse cohorts of patients with cancer affected by COVID-19 is needed. We performed a multicenter study including 105 patients with cancer and 536 age-matched noncancer patients confirmed with COVID-19. Our results showed COVID-19 patients with cancer had higher risks in all severe outcomes. Patients with hematologic cancer, lung cancer, or with metastatic cancer (stage IV) had the highest frequency of severe events. Patients with nonmetastatic cancer experienced similar frequencies of severe conditions to those observed in patients without cancer. Patients who received surgery had higher risks of having severe events, whereas patients who underwent only radiotherapy did not demonstrate significant differences in severe events when compared with patients without cancer. These findings indicate that patients with cancer appear more vulnerable to SARS-CoV-2 outbreak. SIGNIFICANCE: Because this is the first large cohort study on this topic, our report will provide much-needed information that will benefit patients with cancer globally. As such, we believe it is extremely important that our study be disseminated widely to alert clinicians and patients.This article is highlighted in the In This Issue feature, p. 747.
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Affiliation(s)
- Mengyuan Dai
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| | - Dianbo Liu
- Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Miao Liu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Fuxiang Zhou
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
- Department of Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Guiling Li
- Cancer Center, Union Hospital affiliated to Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhen Chen
- Department of Emergency, The Central Hospital of Wuhan affiliated to Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhian Zhang
- Department of Gynecology, The Central Hospital of Huanggang, Huanggang, Hubei, China
| | - Hua You
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Meng Wu
- Department of Ultrasound, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qichao Zheng
- Department of Ultrasound, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yong Xiong
- Department of Infectious Disease, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Huihua Xiong
- Cancer Center, Tongji Hospital affiliated to Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chun Wang
- Department of Oncology, The Central Hospital of Wuhan affiliated to Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Changchun Chen
- Department of Radiology, Hubei Cancer Hospital, Wuhan, Hubei, China
| | - Fei Xiong
- Department of Thoracic Surgery, Hubei Cancer Hospital, Wuhan, Hubei, China
| | - Yan Zhang
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yaqin Peng
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Siping Ge
- Department of Oncology, Wuhan Puren Hospital, Wuhan, Hubei, China
| | - Bo Zhen
- Department of Obstetrics and Gynecology, The Central Hospital of Xianning, Xianning, Hubei, China
| | - Tingting Yu
- Department of Oncology, The Central Hospital of Xiaogan, Xiaogan, China
| | - Ling Wang
- Department of Obstetrics and Gynecology, The People's Hospital of Huangmei, Huangmei, Hubei, China
| | - Hua Wang
- Department of Obstetrics and Gynecology, Xiangyang First People's Hospital affiliated to Hubei University of Medicine, Xiangyang, Hubei, China
| | - Yu Liu
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
- Department of Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yeshan Chen
- Cancer Center, Union Hospital affiliated to Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Junhua Mei
- Department of Gynecology, The Central Hospital of Huanggang, Huanggang, Hubei, China
| | - Xiaojia Gao
- Department of Oncology, The Central Hospital of Wuhan affiliated to Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhuyan Li
- Department of Obstetrics and Gynecology, The People's Hospital of Shiyan, Shiyan, Hubei, China
| | - Lijuan Gan
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| | - Can He
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| | - Zhen Li
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| | - Yuying Shi
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| | - Yuwen Qi
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| | - Jing Yang
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| | - Daniel G Tenen
- Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Li Chai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lorelei A Mucci
- Harvard T.H. Chan School of Public Health, Dana-Farber, Harvard Cancer Center, Boston, Massachusetts
| | - Mauricio Santillana
- Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts.
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Hongbing Cai
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
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7
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Foussier L, Vitellius G, Bouligand J, Amazit L, Bouvattier C, Young J, Trabado S, Lombès M. Functional Characterization of Glucocorticoid Receptor Variants Is Required to Avoid Misinterpretation of NGS Data. J Endocr Soc 2019; 3:865-881. [PMID: 31008420 PMCID: PMC6467410 DOI: 10.1210/js.2019-00028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 02/28/2019] [Indexed: 01/23/2023] Open
Abstract
Recent advances in genetic analysis technologies such as next-generation sequencing (NGS) have considerably increased the incidental discovery of genetic abnormalities. Six heterozygous missense mutations of the human glucocorticoid receptor (GR; encoded by the NR3C1 gene) have been identified in the context of genetic screening of endocrine pathologies. GR, a nuclear receptor, hormone-induced transcription factor, is involved in many physiological processes. Nevertheless, the pathogenic significance of incidentally discovered mutations remains obscure. The aim of this work was to characterize these variants by evaluating their functional impact on GR signaling. Six original GR variants, located in exon 2, led to amino acid substitutions of the N-terminal domain of GR (F65V, M86V, A229T, A304E, N374S, and R386Q), excluding mainly the activation function tau core 1 domain, the potential site of functional interaction with transcriptional coregulators. Transient cotransfection in HEK293T cells of mutated GR-expressing vectors and a luciferase reporter established dose-response curves for dexamethasone. This excluded any major transactivation abnormality of the mutated GRs (ligand concentration leading to 50% maximal transactivation capacity ≈ 0.2 nM), with maximal transactivation capacity identical to that of the wild-type (WT) GR and without modification of the potentiation of transcriptional coactivator steroid receptor coactivator 2 except in N374S. Moreover, protein expression of mutated GRs and their cytonuclear translocation studied by immunocytochemistry were almost unchanged compared with WT GR. These results underline the silent nature of these missense GR variants and call for cautious interpretation of the discovery of genetic incidentalomas by NGS in the absence of detailed characterization in order to appropriately assess their functional impact on a particular signaling pathway.
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Affiliation(s)
- Loïc Foussier
- INSERM UMR_S U1185, Fac Med Paris Sud, Université Paris-Saclay, Le Kremlin Bicêtre, France
| | - Géraldine Vitellius
- INSERM UMR_S U1185, Fac Med Paris Sud, Université Paris-Saclay, Le Kremlin Bicêtre, France
| | - Jérôme Bouligand
- INSERM UMR_S U1185, Fac Med Paris Sud, Université Paris-Saclay, Le Kremlin Bicêtre, France.,Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, Hôpitaux Universitaires Paris Sud, AH-HP, CHU Bicêtre, France
| | - Larbi Amazit
- INSERM UMR_S U1185, Fac Med Paris Sud, Université Paris-Saclay, Le Kremlin Bicêtre, France.,Unité Mixte de Service 32 (UMS-32), Institut Biomédical de Bicêtre, Le Kremlin-Bicêtre, France
| | - Claire Bouvattier
- Service d'Endocrinologie Pédiatrique, Assistance publique des hôpitaux de Paris, Hôpitaux Universitaires Paris Sud, AH-HP, CHU Bicêtre, France
| | - Jacques Young
- INSERM UMR_S U1185, Fac Med Paris Sud, Université Paris-Saclay, Le Kremlin Bicêtre, France.,Service d'Endocrinologie et des Maladies de la Reproduction, Hôpitaux Universitaires Paris Sud, AH-HP, CHU Bicêtre, Le Kremlin Bicêtre, France
| | - Séverine Trabado
- INSERM UMR_S U1185, Fac Med Paris Sud, Université Paris-Saclay, Le Kremlin Bicêtre, France.,Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, Hôpitaux Universitaires Paris Sud, AH-HP, CHU Bicêtre, France
| | - Marc Lombès
- INSERM UMR_S U1185, Fac Med Paris Sud, Université Paris-Saclay, Le Kremlin Bicêtre, France.,Service d'Endocrinologie et des Maladies de la Reproduction, Hôpitaux Universitaires Paris Sud, AH-HP, CHU Bicêtre, Le Kremlin Bicêtre, France
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8
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Sujobert P, Le Bris Y, de Leval L, Gros A, Merlio JP, Pastoret C, Huet S, Sarkozy C, Davi F, Callanan M, Thieblemont C, Sibon D, Asnafi V, Preudhomme C, Gaulard P, Jardin F, Salles G, Macintyre E. The Need for a Consensus Next-generation Sequencing Panel for Mature Lymphoid Malignancies. Hemasphere 2019; 3:e169. [PMID: 31723808 PMCID: PMC6745936 DOI: 10.1097/hs9.0000000000000169] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/27/2018] [Indexed: 02/07/2023] Open
Abstract
Supplemental Digital Content is available in the text.
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Affiliation(s)
- Pierre Sujobert
- Hospices Civils de Lyon, Service d’Hématologie Biologique, Pierre Bénite, France
- INSERM1052, CNRS 5286, Université Claude Bernard, Faculté de Médecine Lyon-Sud Charles Mérieux, Université de Lyon, Pierre Bénite, France
| | - Yannick Le Bris
- Service d’Hématologie Biologique, Centre Hospitalier Universitaire de Nantes, France
- CRCINA, INSERM, CNRS, Université de Nantes, Université d’Angers, Nantes, France
| | - Laurence de Leval
- Institut de Pathologie, Hôpital Universitaire de Lausanne (CHUV), Lausanne, Suisse
| | - Audrey Gros
- CHU de Bordeaux et Université de Bordeaux, INSERM U 1053, Bordeaux, France
| | | | - Cedric Pastoret
- Laboratoire d’Hématologie, Pôle de Biologie, CHU Rennes; INSERM, UMR U1236, Université Rennes1, Rennes, France
| | - Sarah Huet
- Hospices Civils de Lyon, Service d’Hématologie Biologique, Pierre Bénite, France
- INSERM1052, CNRS 5286, Université Claude Bernard, Faculté de Médecine Lyon-Sud Charles Mérieux, Université de Lyon, Pierre Bénite, France
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie Rockefeller, 69373 Lyon Cedex, France
| | - Clémentine Sarkozy
- INSERM1052, CNRS 5286, Université Claude Bernard, Faculté de Médecine Lyon-Sud Charles Mérieux, Université de Lyon, Pierre Bénite, France
- Hospices Civils de Lyon, Service d’Hématologie Clinique, Pierre Bénite, France
| | - Frédéric Davi
- AP-HP, Hôpital Pitié-Salpêtrière, Service d’Hématologie Biologique, et Sorbonne Université, UMR-S 1138, Paris, France
| | - Mary Callanan
- INSERM 1209, CNRS UMR 5309, Universite Grenoble-Alpes, Institut Pour l’Avancee des Biosciences, Grenoble, France
- Centre d’Innovation en Genetique et Epigenetique Onco-Hematologique, Centre Hospitalier de Dijon-Bourgogne, Dijon, France
| | - Catherine Thieblemont
- AP-HP, Hôpital Saint-Louis, Hémato-Oncologie, Paris, France
- Diderot Université, Sorbonne Paris-Cité, Paris, France
- Descartes Université, Paris, France
| | - David Sibon
- Service d’Hématologie Adultes, Hôpital Necker-Enfants Malades, AP-HP, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France
| | - Vahid Asnafi
- APHP Necker Enfants Malades, Université Paris Descartes, Institut Necker-Enfants Malades (INEM) et INSERM UMR 1151, Paris, France
| | - Claude Preudhomme
- Université Lille, Inserm, CHU Lille, UMR-S 1172—JPArc—Centre de Recherche Jean-Pierre Aubert Neurosciences et Cancer, Lille, France
| | - Philippe Gaulard
- Assistance Publique-Hôpitaux de Paris, CHU Henri Mondor, Département de Pathologie, Créteil, France
- INSERM U955 Équipe 9, Université Paris Est, Créteil, France
| | - Fabrice Jardin
- Département d’Hématologie Clinique et INSERM U1245, Centre Henri Becquerel, Rouen, France
| | - Gilles Salles
- INSERM1052, CNRS 5286, Université Claude Bernard, Faculté de Médecine Lyon-Sud Charles Mérieux, Université de Lyon, Pierre Bénite, France
- Hospices Civils de Lyon, Service d’Hématologie Clinique, Pierre Bénite, France
| | - Elizabeth Macintyre
- APHP Necker Enfants Malades, Université Paris Descartes, Institut Necker-Enfants Malades (INEM) et INSERM UMR 1151, Paris, France
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9
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Yang Y, Zhao M, Liu X, Ge P, Zheng F, Chen T, Sun X. Two-way detection of image features and immunolabeling of lymphoma cells with one-step microarray analysis. BIOMICROFLUIDICS 2018; 12:064106. [PMID: 30867867 PMCID: PMC6404911 DOI: 10.1063/1.5063369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/10/2018] [Indexed: 05/04/2023]
Abstract
Detecting the number of pathological lymphoma cells and lymphocyte subtypes in blood is helpful for clinical diagnosis and typing of lymphoma. In the current study, cell type is identified by cell morphological features and immunolabeled lymphocyte subtypes. Red blood cells and leukocytes were separated using a microfluidic cell chip based on physical blood cell parameters, and leukocytes were identified using five characteristic parameters: energy variance, entropy variance, moment of inertia variance, color mean, and cell area individually. The number of red blood cells that could come into contact with the leukocyte membrane was ≤2 based on the microfluidic injection flow rate of microfluidic chips. Anti-CD3 and anti-CD19 antibodies were used for immunofluorescence staining of T-lymphocyte and B-lymphocyte surface antigens, respectively. The results suggested that the microfluidic assay could detect lymphocyte surface antigen markers and intact leukocytes. Therefore, we report a one-step microfluidic chip for classifying hematological lymphoma cells based on the physical parameters of cells, which can simultaneously measure the overall morphology of blood cells and immunolabeling of lymphocyte surface antigens in one step, solving the current problem of detecting subtypes of hematological lymphoma cells based on multiple methods and multi-step detection.
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Affiliation(s)
- Yu Yang
- School of Medical Laboratory, Tianjin Medical University, Tianjin 300203, People’s Republic of China
| | - Meng Zhao
- School of Computer Science and Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
| | - Xiaodan Liu
- School of Medical Laboratory, Tianjin Medical University, Tianjin 300203, People’s Republic of China
| | - Peng Ge
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, People’s Republic of China
| | - Fang Zheng
- School of Medical Laboratory, Tianjin Medical University, Tianjin 300203, People’s Republic of China
| | - Tao Chen
- Institute of Laser Engineering, Beijing University of Technology, Beijing 100124, People’s Republic of China
| | - Xuguo Sun
- School of Medical Laboratory, Tianjin Medical University, Tianjin 300203, People’s Republic of China
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