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Li J, Wei Z, Lou F, Zhang X, Duan J, Luo C, Hu X, Tu P, Liu L, Zhong R, Chen L, Du X, Zhang H. Disrupted Microbiota of Colon Results in Worse Immunity and Metabolism in Low-Birth-Weight Jinhua Newborn Piglets. Microorganisms 2024; 12:1371. [PMID: 39065139 PMCID: PMC11278573 DOI: 10.3390/microorganisms12071371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 07/28/2024] Open
Abstract
The Jinhua pig is well known in China due to its delicious meat. However, because of large litter size, low birth weight always happens. This experiment used this breed as a model to research bacterial evidence leading to growth restriction and provide a possible solution linked to probiotics. In this experiment, the differences in organs indexes, colonic morphology, short chain fatty acid (SCFA) concentrations, microbiome, and transcriptome were detected between piglets in the standard-birth-weight group (SG) and low-birth-weight group (LG) to find potential evidence leading to low birth weight. We found that LG piglets had a lower liver index (p < 0.05), deeper colonic crypt depth (p < 0.05), fewer goblet cells (p < 0.05), and more inflammatory factor infiltration. In addition, differentially expressed genes (DEGs) were mainly enriched in B-cell immunity and glucose metabolism, and LG piglets had lower concentrations of SCFAs, especially butyrate and isobutyrate (p < 0.05). Finally, most of the significantly differentially abundant microbes were fewer in LG piglets, which affected DEG expressions and SCFA concentrations further resulting in worse energy metabolism and immunity. In conclusion, colonic disrupted microbiota may cause worse glucose metabolism, immunity, and SCFA production in LG piglets, and beneficial microbes colonized in SG piglets may benefit these harmful changes.
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Affiliation(s)
- Jiaheng Li
- Institute of Animal Husbandry and Veterinary Medicine, Jinhua Academy of Agricultural Sciences, Jinhua 321011, China; (J.L.); (F.L.); (X.Z.); (X.H.); (P.T.); (X.D.)
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.W.); (J.D.); (C.L.); (L.L.); (L.C.); (H.Z.)
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, Liège University, Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Zeou Wei
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.W.); (J.D.); (C.L.); (L.L.); (L.C.); (H.Z.)
- School of Agriculture and Food Science, University College Dublin, Belfeld, D04 V1W8 Dublin, Ireland
| | - Fangfang Lou
- Institute of Animal Husbandry and Veterinary Medicine, Jinhua Academy of Agricultural Sciences, Jinhua 321011, China; (J.L.); (F.L.); (X.Z.); (X.H.); (P.T.); (X.D.)
| | - Xiaojun Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Jinhua Academy of Agricultural Sciences, Jinhua 321011, China; (J.L.); (F.L.); (X.Z.); (X.H.); (P.T.); (X.D.)
| | - Jiujun Duan
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.W.); (J.D.); (C.L.); (L.L.); (L.C.); (H.Z.)
| | - Chengzeng Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.W.); (J.D.); (C.L.); (L.L.); (L.C.); (H.Z.)
| | - Xujin Hu
- Institute of Animal Husbandry and Veterinary Medicine, Jinhua Academy of Agricultural Sciences, Jinhua 321011, China; (J.L.); (F.L.); (X.Z.); (X.H.); (P.T.); (X.D.)
| | - Pingguang Tu
- Institute of Animal Husbandry and Veterinary Medicine, Jinhua Academy of Agricultural Sciences, Jinhua 321011, China; (J.L.); (F.L.); (X.Z.); (X.H.); (P.T.); (X.D.)
| | - Lei Liu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.W.); (J.D.); (C.L.); (L.L.); (L.C.); (H.Z.)
| | - Ruqing Zhong
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.W.); (J.D.); (C.L.); (L.L.); (L.C.); (H.Z.)
| | - Liang Chen
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.W.); (J.D.); (C.L.); (L.L.); (L.C.); (H.Z.)
| | - Xizhong Du
- Institute of Animal Husbandry and Veterinary Medicine, Jinhua Academy of Agricultural Sciences, Jinhua 321011, China; (J.L.); (F.L.); (X.Z.); (X.H.); (P.T.); (X.D.)
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.W.); (J.D.); (C.L.); (L.L.); (L.C.); (H.Z.)
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2
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Massoni-Badosa R, Aguilar-Fernández S, Nieto JC, Soler-Vila P, Elosua-Bayes M, Marchese D, Kulis M, Vilas-Zornoza A, Bühler MM, Rashmi S, Alsinet C, Caratù G, Moutinho C, Ruiz S, Lorden P, Lunazzi G, Colomer D, Frigola G, Blevins W, Romero-Rivero L, Jiménez-Martínez V, Vidal A, Mateos-Jaimez J, Maiques-Diaz A, Ovejero S, Moreaux J, Palomino S, Gomez-Cabrero D, Agirre X, Weniger MA, King HW, Garner LC, Marini F, Cervera-Paz FJ, Baptista PM, Vilaseca I, Rosales C, Ruiz-Gaspà S, Talks B, Sidhpura K, Pascual-Reguant A, Hauser AE, Haniffa M, Prosper F, Küppers R, Gut IG, Campo E, Martin-Subero JI, Heyn H. An atlas of cells in the human tonsil. Immunity 2024; 57:379-399.e18. [PMID: 38301653 PMCID: PMC10869140 DOI: 10.1016/j.immuni.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/07/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Palatine tonsils are secondary lymphoid organs (SLOs) representing the first line of immunological defense against inhaled or ingested pathogens. We generated an atlas of the human tonsil composed of >556,000 cells profiled across five different data modalities, including single-cell transcriptome, epigenome, proteome, and immune repertoire sequencing, as well as spatial transcriptomics. This census identified 121 cell types and states, defined developmental trajectories, and enabled an understanding of the functional units of the tonsil. Exemplarily, we stratified myeloid slan-like subtypes, established a BCL6 enhancer as locally active in follicle-associated T and B cells, and identified SIX5 as putative transcriptional regulator of plasma cell maturation. Analyses of a validation cohort confirmed the presence, annotation, and markers of tonsillar cell types and provided evidence of age-related compositional shifts. We demonstrate the value of this resource by annotating cells from B cell-derived mantle cell lymphomas, linking transcriptional heterogeneity to normal B cell differentiation states of the human tonsil.
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Affiliation(s)
| | | | - Juan C Nieto
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Paula Soler-Vila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | | | - Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Amaia Vilas-Zornoza
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marco Matteo Bühler
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain
| | - Sonal Rashmi
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Clara Alsinet
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Ginevra Caratù
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Catia Moutinho
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Sara Ruiz
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Patricia Lorden
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Giulia Lunazzi
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Gerard Frigola
- Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain
| | - Will Blevins
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Lucia Romero-Rivero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Anna Vidal
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Judith Mateos-Jaimez
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Alba Maiques-Diaz
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sara Ovejero
- Department of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France; Department of Clinical Hematology, CHU Montpellier, Montpellier, France
| | - Sara Palomino
- Translational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - David Gomez-Cabrero
- Translational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain; Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Xabier Agirre
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Hamish W King
- Epigenetics and Development Division, Walter and Eliza Hall Institute, Parkville, Australia
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany; Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Peter M Baptista
- Department of Otorhinolaryngology, University of Navarra, Pamplona, Spain
| | - Isabel Vilaseca
- Otorhinolaryngology Head-Neck Surgery Department, Hospital Clínic, IDIBAPS Universitat de Barcelona, Barcelona, Spain
| | - Cecilia Rosales
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Silvia Ruiz-Gaspà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Benjamin Talks
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Department of Otolaryngology, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Keval Sidhpura
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Anna Pascual-Reguant
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
| | - Anja E Hauser
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Felipe Prosper
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Departamento de Hematología, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Ivo Glynne Gut
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - José Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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3
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Nakamura S, Ohuchida K, Ohtsubo Y, Yamada Y, Tsutsumi C, Okuda S, Hisano K, Mochida Y, Shinkawa T, Iwamoto C, Torata N, Mizuuchi Y, Shindo K, Nakata K, Moriyama T, Torisu T, Nagai E, Morisaki T, Kitazono T, Oda Y, Nakamura M. Single-cell transcriptome analysis reveals functional changes in tumour-infiltrating B lymphocytes after chemotherapy in oesophageal squamous cell carcinoma. Clin Transl Med 2023; 13:e1181. [PMID: 36650114 PMCID: PMC9845121 DOI: 10.1002/ctm2.1181] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Tumour immune microenvironment is related with carcinogenesis and efficacy of immunotherapy. B cells play major roles in humoral immunity, but detailed functions of tumour-infiltrating B lymphocytes (TIL-Bs) are unknown. Therefore, our aim was to investigate the functional heterogeneity of TIL-Bs in oesophageal squamous cell carcinoma (ESCC) and lymph nodes (LNs) during chemotherapy. METHODS Single-cell transcriptome analysis was performed on 23 specimens. We also performed immunohistochemical analysis of immunoglobulin κ C (IGKC), an antibody-secreting cell (ASC) marker, in 166 ESCC samples and evaluated the implication of IGKC in 2-year recurrence free survival (RFS) and 3-year overall survival (OS). RESULTS A total of 81,246 cells were grouped into 24 clusters. We extracted B cell clusters based on canonical markers and identified 12 TIL-B subtypes in ESCC. We found that several functions, such as co-stimulation and CD40 signalling, were enhanced in TIL-Bs after chemotherapy. The proportion of naive B cells (NBCs) decreased and B cell activation genes were up-regulated in NBCs after chemotherapy. The proportion of ASCs in tumours increased with the loss of migratory abilities and antibody production in ASCs was promoted after chemotherapy. Differentially expressed genes up-regulated with chemotherapy in ASCs correlated with prolonged survival with oesophageal cancer (p = .028). In a metastatic LN, the ASC proportion increased and B cell differentiation was enhanced. In immunohistochemical analysis, RFS and OS of high IGKC expression cases were significantly better than those of low IGKC expression cases (RFS: p < .0001, OS: p < .0001). And in multivariable analysis, the expression of IGKC was an independent favourable prognostic factor for RFS (hazard ratio (HR): 0.23, 95% confidence interval (CI): 0.12-0.45, p < .0001) and OS (HR: 0.20, 95% CI: 0.086-0.47, p = .0002) in ESCC. CONCLUSIONS Our findings provide novel insights for the heterogeneity of TIL-Bs during chemotherapy and will be useful to understand the clinical importance of TIL-Bs.
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Affiliation(s)
- Shoichi Nakamura
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Kenoki Ohuchida
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yoshiki Ohtsubo
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yutaka Yamada
- Department of Anatomic PathologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Chikanori Tsutsumi
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Sho Okuda
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Kyoko Hisano
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yuki Mochida
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Tomohiko Shinkawa
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Chika Iwamoto
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
- Department of HematologyClinical Immunology and Infectious DiseasesGraduate School of MedicineEhime UniversityEhimeJapan
| | - Nobuhiro Torata
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yusuke Mizuuchi
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Koji Shindo
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Kohei Nakata
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Taiki Moriyama
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Takehiro Torisu
- Department of Medicine and Clinical ScienceGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Eishi Nagai
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
- Department of SurgeryFukuoka Red Cross HospitalFukuokaJapan
| | - Takashi Morisaki
- Department of Cancer ImmunotherapyFukuoka General Cancer ClinicFukuokaJapan
| | - Takanari Kitazono
- Department of Medicine and Clinical ScienceGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yoshinao Oda
- Department of Anatomic PathologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Masafumi Nakamura
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
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4
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Zhuang Y, Che J, Wu M, Guo Y, Xu Y, Dong X, Yang H. Altered pathways and targeted therapy in double hit lymphoma. J Hematol Oncol 2022; 15:26. [PMID: 35303910 PMCID: PMC8932183 DOI: 10.1186/s13045-022-01249-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/07/2022] [Indexed: 12/20/2022] Open
Abstract
High-grade B-cell lymphoma with translocations involving MYC and BCL2 or BCL6, usually referred to as double hit lymphoma (DHL), is an aggressive hematological malignance with distinct genetic features and poor clinical prognosis. Current standard chemoimmunotherapy fails to confer satisfying outcomes and few targeted therapeutics are available for the treatment against DHL. Recently, the delineating of the genetic landscape in tumors has provided insight into both biology and targeted therapies. Therefore, it is essential to understand the altered signaling pathways of DHL to develop treatment strategies with better clinical benefits. Herein, we summarized the genetic alterations in the two DHL subtypes (DHL-BCL2 and DHL-BCL6). We further elucidate their implications on cellular processes, including anti-apoptosis, epigenetic regulations, B-cell receptor signaling, and immune escape. Ongoing and potential therapeutic strategies and targeted drugs steered by these alterations were reviewed accordingly. Based on these findings, we also discuss the therapeutic vulnerabilities that coincide with these genetic changes. We believe that the understanding of the DHL studies will provide insight into this disease and capacitate the finding of more effective treatment strategies.
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Affiliation(s)
- Yuxin Zhuang
- Department of Lymphoma, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People’s Republic of China
| | - Jinxin Che
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People’s Republic of China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, People’s Republic of China
| | - Meijuan Wu
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
| | - Yu Guo
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, People’s Republic of China
| | - Yongjin Xu
- Department of Lymphoma, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People’s Republic of China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, People’s Republic of China
- Cancer Center, Zhejiang University, Hangzhou, People’s Republic of China
| | - Haiyan Yang
- Department of Lymphoma, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
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5
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King HW, Wells KL, Shipony Z, Kathiria AS, Wagar LE, Lareau C, Orban N, Capasso R, Davis MM, Steinmetz LM, James LK, Greenleaf WJ. Integrated single-cell transcriptomics and epigenomics reveals strong germinal center-associated etiology of autoimmune risk loci. Sci Immunol 2021; 6:eabh3768. [PMID: 34623901 DOI: 10.1126/sciimmunol.abh3768] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Hamish W King
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - Kristen L Wells
- Barbara Davis Center for Diabetes and RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Zohar Shipony
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Arwa S Kathiria
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Lisa E Wagar
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Caleb Lareau
- Department of Genetics, Stanford University, Stanford, CA, USA.,Department of Pathology, University of California Irvine, Irvine, CA, USA
| | - Nara Orban
- Barts Health Ear, Nose and Throat Service, The Royal London Hospital, London, UK
| | - Robson Capasso
- Division of Sleep Surgery, Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Lars M Steinmetz
- Department of Genetics, Stanford University, Stanford, CA, USA.,Stanford Genome Technology Center, Stanford University, Stanford, CA, USA.,Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Louisa K James
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
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6
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Meng J, Wen H, Li X, Luan B, Gong S, Wen J, Wang Y, Wang L. POU class 2 homeobox associating factor 1 (POU2AF1) participates in abdominal aortic aneurysm enlargement based on integrated bioinformatics analysis. Bioengineered 2021; 12:8980-8993. [PMID: 34637689 PMCID: PMC8806937 DOI: 10.1080/21655979.2021.1990822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abdominal aortic aneurysm (AAA) is life-threatening, its natural course is progressively sac expansion and rupture. Elegant studies have been conducted to investigate the molecular markers associated with AAA growth and expansion, this topic however, still needs to be further elucidated. This study aimed to identify potential genes for AAA growth and expansion based on comprehensive bioinformatics approaches. Firstly, 29 up-regulated genes were identified through DEGs analysis between large AAA and small AAA in GSE57691. Secondly, signed WGCNA analysis was conducted based on GSE57691 and the green module was found to exhibit the topmost correlation with large AAA as well as AAA, 133 WGCNA hub genes were further identified. Merged gene set including 29 up-regulated DEGs and 858 green module genes was subjected to constructing a PPI network where 195 PPI hub genes were identified. Subsequently, 4 crucial genes including POU2AF1, FCRLA, CD79B, HLA-DOB were recognized by Venn plot. In addition, by using GSE7084 and GSE98278 for verification, POU2AF1 showed potential diagnostic value between AAA and normal groups, and exhibited a significant higher expression level in large AAA samples compared with small AAA samples. Furthermore, immunohistochemistry results indicated up-regulation of POU2AF1 in large AAA samples than small AAA samples, which implies POU2AF1 may be a key regulator in AAA enlargement and growth. In summary, this study indicates that POU2AF1 has great predictive value for the expansion of AAA, and may contribute to the further exploration of pathogenesis and progression of AAA.
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Affiliation(s)
- Jinze Meng
- Department of Pharmacology, China Medical University, Shenyang, China
| | - Hao Wen
- Department of Trauma Center, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xintong Li
- Department of Vascular Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm in Liaoning Province, Shenyang, China
| | - Boyang Luan
- Department of Trauma Center, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Shiqiang Gong
- Department of Pharmacology, China Medical University, Shenyang, China
| | - Jie Wen
- Department of Ultrasonography, Inner Mongolia Baotou City Central Hospital, Baotou, China
| | - Yifei Wang
- Department of Pharmacology, China Medical University, Shenyang, China
| | - Lei Wang
- Department of Vascular Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm in Liaoning Province, Shenyang, China
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7
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Loss of synergistic transcriptional feedback loops drives diverse B-cell cancers. EBioMedicine 2021; 71:103559. [PMID: 34461601 PMCID: PMC8403728 DOI: 10.1016/j.ebiom.2021.103559] [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: 05/25/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/30/2022] Open
Abstract
Background The most common B-cell cancers, chronic lymphocytic leukemia/lymphoma (CLL), follicular and diffuse large B-cell (FL, DLBCL) lymphomas, have distinct clinical courses, yet overlapping “cell-of-origin”. Dynamic changes to the epigenome are essential regulators of B-cell differentiation. Therefore, we reasoned that these distinct cancers may be driven by shared mechanisms of disruption in transcriptional circuitry. Methods We compared purified malignant B-cells from 52 patients with normal B-cell subsets (germinal center centrocytes and centroblasts, naïve and memory B-cells) from 36 donor tonsils using >325 high-resolution molecular profiling assays for histone modifications, open chromatin (ChIP-, FAIRE-seq), transcriptome (RNA-seq), transcription factor (TF) binding, and genome copy number (microarrays). Findings From the resulting data, we identified gains in active chromatin in enhancers/super-enhancers that likely promote unchecked B-cell receptor signaling, including one we validated near the immunoglobulin superfamily receptors FCMR and PIGR. More striking and pervasive was the profound loss of key B-cell identity TFs, tumor suppressors and their super-enhancers, including EBF1, OCT2(POU2F2), and RUNX3. Using a novel approach to identify transcriptional feedback, we showed that these core transcriptional circuitries are self-regulating. Their selective gain and loss form a complex, iterative, and interactive process that likely curbs B-cell maturation and spurs proliferation. Interpretation Our study is the first to map the transcriptional circuitry of the most common blood cancers. We demonstrate that a critical subset of B-cell TFs and their cognate enhancers form self-regulatory transcriptional feedback loops whose disruption is a shared mechanism underlying these diverse subtypes of B-cell lymphoma. Funding National Institute of Health, Siteman Cancer Center, Barnes-Jewish Hospital Foundation, Doris Duke Foundation.
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8
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Imran S, Neeland MR, Koplin J, Dharmage S, Tang MLK, Sawyer S, Dang T, McWilliam V, Peters R, Perrett KP, Novakovic B, Saffery R. Epigenetic programming underpins B-cell dysfunction in peanut and multi-food allergy. Clin Transl Immunology 2021; 10:e1324. [PMID: 34466226 PMCID: PMC8384135 DOI: 10.1002/cti2.1324] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/07/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Rates of IgE-mediated food allergy (FA) have increased over the last few decades, and mounting evidence implicates disruption of epigenetic profiles in various immune cell types in FA development. Recent data implicate B-cell dysfunction in FA; however, few studies have examined epigenetic changes within these cells. METHODS We assessed epigenetic and transcriptomic profiles in purified B cells from adolescents with FA, comparing single-food-allergic (peanut only), multi-food-allergic (peanut and ≥1 other food) and non-allergic (control) individuals. Adolescents represent a phenotype of persistent and severe FA indicative of a common immune deviation. RESULTS We identified 144 differentially methylated probes (DMPs) and 116 differentially expressed genes (DEGs) that distinguish B cells of individuals with FA from controls, including differential methylation of the PM20D1 promoter previously associated with allergic disorders. Subgroup comparisons found 729 DMPs specific to either single-food- or multi-food-allergic individuals, suggesting epigenetic distinctions between allergy groups. This included two regions with increased methylation near three S100 genes in multi-food-allergic individuals. Ontology results of DEGs specific to multi-food-allergic individuals revealed enrichment of terms associated with myeloid cell activation. Motif enrichment analysis of promoters associated with DMPs and DEGs showed differential enrichment for motifs recognised by transcription factors regulating B- and T-cell development, B-cell lineage determination and TGF-β signalling pathway between the multi-food-allergic and single-food-allergic groups. CONCLUSION Our data highlight epigenetic changes in B cells associated with peanut allergy, distinguishing features of the epigenome between single-food- and multi-food-allergic individuals and revealing differential developmental pathways potentially underpinning these distinct phenotypes.
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Affiliation(s)
- Samira Imran
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
| | - Melanie R Neeland
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
| | - Jennifer Koplin
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
| | - Shyamali Dharmage
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
- Allergy and Lung Health UnitMelbourne School of Population and Global HealthUniversity of MelbourneCarltonVICAustralia
| | - Mimi LK Tang
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
- Department of Allergy and ImmunologyRoyal Children's HospitalMelbourneVICAustralia
| | - Susan Sawyer
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
- Centre for Adolescent HealthRoyal Children's HospitalMelbourneVICAustralia
| | - Thanh Dang
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
| | - Vicki McWilliam
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
- Department of Allergy and ImmunologyRoyal Children's HospitalMelbourneVICAustralia
| | - Rachel Peters
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
| | - Kirsten P Perrett
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
- Department of Allergy and ImmunologyRoyal Children's HospitalMelbourneVICAustralia
| | - Boris Novakovic
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
| | - Richard Saffery
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
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9
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OBF1 and Oct factors control the germinal center transcriptional program. Blood 2021; 137:2920-2934. [PMID: 33512466 DOI: 10.1182/blood.2020010175] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022] Open
Abstract
OBF1 is a specific coactivator of the POU family transcription factors OCT1 and OCT2. OBF1 and OCT2 are B cell-specific and indispensable for germinal center (GC) formation, but their mechanism of action is unclear. Here, we show by chromatin immunoprecipitation-sequencing that OBF1 extensively colocalizes with OCT1 and OCT2. We found that these factors also often colocalize with transcription factors of the ETS family. Furthermore, we showed that OBF1, OCT2, and OCT1 bind widely to the promoters or enhancers of genes involved in GC formation in mouse and human GC B cells. Short hairpin RNA knockdown experiments demonstrated that OCT1, OCT2, and OBF1 regulate each other and are essential for proliferation of GC-derived lymphoma cell lines. OBF1 downregulation disrupts the GC transcriptional program: genes involved in GC maintenance, such as BCL6, are downregulated, whereas genes related to exit from the GC program, such as IRF4, are upregulated. Ectopic expression of BCL6 does not restore the proliferation of GC-derived lymphoma cells depleted of OBF1 unless IRF4 is also depleted, indicating that OBF1 controls an essential regulatory node in GC differentiation.
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10
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Shen S, Wei Y, Li Y, Duan W, Dong X, Lin L, You D, Tardon A, Chen C, Field JK, Hung RJ, Liu G, Zhu D, Amos CI, Su L, Zhao Y, Hu Z, Shen H, Zhang R, Chen F, Christiani DC. A multi-omics study links TNS3 and SEPT7 to long-term former smoking NSCLC survival. NPJ Precis Oncol 2021; 5:39. [PMID: 34002017 PMCID: PMC8128887 DOI: 10.1038/s41698-021-00182-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/19/2021] [Indexed: 11/15/2022] Open
Abstract
The genetic architecture of non-small cell lung cancer (NSCLC) is relevant to smoking status. However, the genetic contribution of long-term smoking cessation to the prognosis of NSCLC patients remains largely unknown. We conducted a genome-wide association study primarily on the prognosis of 1299 NSCLC patients of long-term former smokers from independent discovery (n = 566) and validation (n = 733) sets, and used in-silico function prediction and multi-omics analysis to identify single nucleotide polymorphisms (SNPs) on prognostics with NSCLC. We further detected SNPs with at least moderate association strength on survival within each group of never, short-term former, long-term former, and current smokers, and compared their genetic similarity at the SNP, gene, expression quantitative trait loci (eQTL), enhancer, and pathway levels. We identified two SNPs, rs34211819TNS3 at 7p12.3 (P = 3.90 × 10-9) and rs1143149SEPT7 at 7p14.2 (P = 9.75 × 10-9), were significantly associated with survival of NSCLC patients who were long-term former smokers. Both SNPs had significant interaction effects with years of smoking cessation (rs34211819TNS3: Pinteraction = 8.0 × 10-4; rs1143149SEPT7: Pinteraction = 0.003). In addition, in silico function prediction and multi-omics analysis provided evidence that these QTLs were associated with survival. Moreover, comparison analysis found higher genetic similarity between long-term former smokers and never-smokers, compared to short-term former smokers or current smokers. Pathway enrichment analysis indicated a unique pattern among long-term former smokers that was related to immune pathways. This study provides important insights into the genetic architecture associated with long-term former smoking NSCLC.
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Affiliation(s)
- Sipeng Shen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Yongyue Wei
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Yi Li
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Weiwei Duan
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Xuesi Dong
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA
| | - Lijuan Lin
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA
| | - Dongfang You
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA
| | - Adonina Tardon
- University of Oviedo and CIBERESP, Faculty of Medicine, Oviedo, 33003, Spain
| | - Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - John K Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System and University of Toronto, Toronto, ON, M5T 3L9, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Dakai Zhu
- Department of Medicine, Epidemiology Section, Institute for Clinical and Translational Research, Baylor Medical College, Houston, TX, 77030, USA
| | - Christopher I Amos
- Department of Medicine, Epidemiology Section, Institute for Clinical and Translational Research, Baylor Medical College, Houston, TX, 77030, USA
| | - Li Su
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA
| | - Yang Zhao
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Hongbing Shen
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Ruyang Zhang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
| | - Feng Chen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA.
- Pulmonary and Critical Care Division, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Boston, MA, 02114, USA.
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11
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Abstract
Memory B cells (MBCs) are critical for the rapid development of protective immunity following re-infection. MBCs capable of neutralizing distinct subclasses of pathogens, such as influenza and HIV, have been identified in humans. However, efforts to develop vaccines that induce broadly protective MBCs to rapidly mutating pathogens have not yet been successful. Better understanding of the signals regulating MBC development and function are essential to overcome current challenges hindering successful vaccine development. Here, we discuss recent advancements regarding the signals and transcription factors regulating germinal centre-derived MBC development and function.
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Affiliation(s)
- Brian J Laidlaw
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
| | - Jason G Cyster
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
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12
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King HW, Orban N, Riches JC, Clear AJ, Warnes G, Teichmann SA, James LK. Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics. Sci Immunol 2021; 6:6/56/eabe6291. [PMID: 33579751 DOI: 10.1126/sciimmunol.abe6291] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/14/2021] [Indexed: 12/21/2022]
Abstract
Protective humoral memory forms in secondary lymphoid organs where B cells undergo affinity maturation and differentiation into memory or plasma cells. Here, we provide a comprehensive roadmap of human B cell maturation with single-cell transcriptomics matched with bulk and single-cell antibody repertoires to define gene expression, antibody repertoires, and clonal sharing of B cell states at single-cell resolution, including memory B cell heterogeneity that reflects diverse functional and signaling states. We reconstruct gene expression dynamics during B cell activation to reveal a pre-germinal center state primed to undergo class switch recombination and dissect how antibody class-dependent gene expression in germinal center and memory B cells is linked with a distinct transcriptional wiring with potential to influence their fate and function. Our analyses reveal the dynamic cellular states that shape human B cell-mediated immunity and highlight how antibody isotype may play a role during their antibody-based selection.
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Affiliation(s)
- Hamish W King
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK. .,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Nara Orban
- Barts Health Ear, Nose and Throat Service, Royal London Hospital, London E1 1BB, UK
| | - John C Riches
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK.,Francis Crick Institute, London NW1 1AT, UK
| | - Andrew J Clear
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Gary Warnes
- Flow Cytometry Core Facility, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0EH, UK
| | - Louisa K James
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK.
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13
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Figueiredo CR, Kalirai H, Sacco JJ, Azevedo RA, Duckworth A, Slupsky JR, Coulson JM, Coupland SE. Loss of BAP1 expression is associated with an immunosuppressive microenvironment in uveal melanoma, with implications for immunotherapy development. J Pathol 2020; 250:420-439. [PMID: 31960425 PMCID: PMC7216965 DOI: 10.1002/path.5384] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/28/2019] [Accepted: 01/14/2020] [Indexed: 12/22/2022]
Abstract
Immunotherapy using immune checkpoint inhibitors (ICIs) induces durable responses in many metastatic cancers. Metastatic uveal melanoma (mUM), typically occurring in the liver, is one of the most refractory tumours to ICIs and has dismal outcomes. Monosomy 3 (M3), polysomy 8q, and BAP1 loss in primary uveal melanoma (pUM) are associated with poor prognoses. The presence of tumour-infiltrating lymphocytes (TILs) within pUM and surrounding mUM - and some evidence of clinical responses to adoptive TIL transfer - strongly suggests that UMs are indeed immunogenic despite their low mutational burden. The mechanisms that suppress TILs in pUM and mUM are unknown. We show that BAP1 loss is correlated with upregulation of several genes associated with suppressive immune responses, some of which build an immune suppressive axis, including HLA-DR, CD38, and CD74. Further, single-cell analysis of pUM by mass cytometry confirmed the expression of these and other markers revealing important functions of infiltrating immune cells in UM, most being regulatory CD8+ T lymphocytes and tumour-associated macrophages (TAMs). Transcriptomic analysis of hepatic mUM revealed similar immune profiles to pUM with BAP1 loss, including the expression of IDO1. At the protein level, we observed TAMs and TILs entrapped within peritumoural fibrotic areas surrounding mUM, with increased expression of IDO1, PD-L1, and β-catenin (CTNNB1), suggesting tumour-driven immune exclusion and hence the immunotherapy resistance. These findings aid the understanding of how the immune response is organised in BAP1 - mUM, which will further enable functional validation of detected biomarkers and the development of focused immunotherapeutic approaches. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Carlos R Figueiredo
- Department of Molecular and Clinical Cancer Medicine, ITMUniversity of LiverpoolLiverpoolUK
- Department of the Faculty of Medicine, MediCity Research Laboratory and Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Helen Kalirai
- Department of Molecular and Clinical Cancer Medicine, ITMUniversity of LiverpoolLiverpoolUK
| | - Joseph J Sacco
- Department of Molecular and Clinical Cancer Medicine, ITMUniversity of LiverpoolLiverpoolUK
- Department of Medical OncologyThe Clatterbridge Cancer CentreWirralUK
| | - Ricardo A Azevedo
- Department of Cancer BiologyThe University of Texas–MD Anderson Cancer CenterHoustonTXUSA
| | - Andrew Duckworth
- Department of Molecular and Clinical Cancer Medicine, ITMUniversity of LiverpoolLiverpoolUK
| | - Joseph R Slupsky
- Department of Molecular and Clinical Cancer Medicine, ITMUniversity of LiverpoolLiverpoolUK
| | - Judy M Coulson
- Department of Cellular and Molecular PhysiologyUniversity of LiverpoolLiverpoolUK
| | - Sarah E Coupland
- Department of Molecular and Clinical Cancer Medicine, ITMUniversity of LiverpoolLiverpoolUK
- Liverpool Clinical LaboratoriesRoyal Liverpool University HospitalLiverpoolUK
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14
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Wu Y, Chang YM, Stell AJ, Priestnall SL, Sharma E, Goulart MR, Gribben J, Xia D, Garden OA. Phenotypic characterisation of regulatory T cells in dogs reveals signature transcripts conserved in humans and mice. Sci Rep 2019; 9:13478. [PMID: 31530890 PMCID: PMC6748983 DOI: 10.1038/s41598-019-50065-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/05/2019] [Indexed: 12/12/2022] Open
Abstract
Regulatory T cells (Tregs) are a double-edged regulator of the immune system. Aberrations of Tregs correlate with pathogenesis of inflammatory, autoimmune and neoplastic disorders. Phenotypically and functionally distinct subsets of Tregs have been identified in humans and mice on the basis of their extensive portfolios of monoclonal antibodies (mAb) against Treg surface antigens. As an important veterinary species, dogs are increasingly recognised as an excellent model for many human diseases. However, insightful study of canine Tregs has been restrained by the limited availability of mAb. We therefore set out to characterise CD4+CD25high T cells isolated ex vivo from healthy dogs and showed that they possess a regulatory phenotype, function, and transcriptomic signature that resembles those of human and murine Tregs. By launching a cross-species comparison, we unveiled a conserved transcriptomic signature of Tregs and identified that transcript hip1 may have implications in Treg function.
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Affiliation(s)
- Ying Wu
- Royal Veterinary College, London, UK
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Eshita Sharma
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Michelle R Goulart
- Royal Veterinary College, London, UK
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - John Gribben
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Dong Xia
- Royal Veterinary College, London, UK
| | - Oliver A Garden
- Royal Veterinary College, London, UK.
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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15
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Hong CC, Sucheston-Campbell LE, Liu S, Hu Q, Yao S, Lunetta KL, Haddad SA, Ruiz-Narváez EA, Bensen JT, Cheng TYD, Bandera EV, Rosenberg LA, Haiman CA, Lee K, Evans SS, Abrams SI, Repasky EA, Olshan AF, Palmer JR, Ambrosone CB. Genetic Variants in Immune-Related Pathways and Breast Cancer Risk in African American Women in the AMBER Consortium. Cancer Epidemiol Biomarkers Prev 2018; 27:321-330. [PMID: 29339359 PMCID: PMC5835191 DOI: 10.1158/1055-9965.epi-17-0434] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/23/2017] [Accepted: 01/02/2018] [Indexed: 11/16/2022] Open
Abstract
Background: Constitutional immunity shaped by exposure to endemic infectious diseases and parasitic worms in Sub-Saharan Africa may play a role in the etiology of breast cancer among African American (AA) women.Methods: A total of 149,514 gene variants in 433 genes across 45 immune pathways were analyzed in the AMBER consortium among 3,663 breast cancer cases and 4,687 controls. Gene-based pathway analyses were conducted using the adaptive rank truncated product statistic for overall breast cancer risk, and risk by estrogen receptor (ER) status. Unconditional logistic regression analysis was used to estimate ORs and 95% confidence intervals (CIs) for single variants.Results: The top pathways were Interleukin binding (P = 0.01), Biocarta TNFR2 (P = 0.005), and positive regulation of cytokine production (P = 0.024) for overall, ER+, and ER- cancers, respectively. The most significant gene was IL2RB (P = 0.001) for overall cancer, with rs228952 being the top variant identified (OR = 0.85; 95% CI, 0.79-0.92). Only BCL3 contained a significant variant for ER+ breast cancer. Variants in IL2RB, TLR6, IL8, PRKDC, and MAP3K1 were associated with ER- disease. The only genes showing heterogeneity between ER- and ER+ cancers were TRAF1, MAP3K1, and MAPK3 (P ≤ 0.02). We also noted genes associated with autoimmune and atopic disorders.Conclusions: Findings from this study suggest that genetic variants in immune pathways are relevant to breast cancer susceptibility among AA women, both for ER+ and ER- breast cancers.Impact: Results from this study extend our understanding of how inherited genetic variation in immune pathways is relevant to breast cancer susceptibility. Cancer Epidemiol Biomarkers Prev; 27(3); 321-30. ©2018 AACR.
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Affiliation(s)
- Chi-Chen Hong
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York.
| | | | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Stephen A Haddad
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | | | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ting-Yuan David Cheng
- Department of Epidemiology, College of Public Health and Health Professions & College of Medicine, University of Florida, Gainsville, Florida
| | - Elisa V Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Lynn A Rosenberg
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California
| | - Kelvin Lee
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, New York
| | - Sharon S Evans
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, New York
| | - Scott I Abrams
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, New York
| | | | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Julie R Palmer
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
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16
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Valor LM, Rodríguez-Bayona B, Ramos-Amaya AB, Brieva JA, Campos-Caro A. The transcriptional profiling of human in vivo-generated plasma cells identifies selective imbalances in monoclonal gammopathies. PLoS One 2017; 12:e0183264. [PMID: 28817638 PMCID: PMC5560601 DOI: 10.1371/journal.pone.0183264] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022] Open
Abstract
Plasma cells (PC) represent the heterogeneous final stage of the B cells (BC) differentiation process. To characterize the transition of BC into PC, transcriptomes from human naïve BC were compared to those of three functionally-different subsets of human in vivo-generated PC: i) tonsil PC, mainly consisting of early PC; ii) PC released to the blood after a potent booster-immunization (mostly cycling plasmablasts); and, iii) bone marrow CD138+ PC that represent highly mature PC and include the long-lived PC compartment. This transcriptional transition involves subsets of genes related to key processes for PC maturation: the already known protein processing, apoptosis and homeostasis, and of new discovery including histones, macromolecule assembly, zinc-finger transcription factors and neuromodulation. This human PC signature is partially reproduced in vitro and is conserved in mouse. Moreover, the present study identifies genes that define PC subtypes (e.g., proliferation-associated genes for circulating PC and transcriptional-related genes for tonsil and bone marrow PC) and proposes some putative transcriptional regulators of the human PC signatures (e.g., OCT/POU, XBP1/CREB, E2F, among others). Finally, we also identified a restricted imbalance of the present PC transcriptional program in monoclonal gammopathies that correlated with PC malignancy.
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Affiliation(s)
- Luis M. Valor
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Beatriz Rodríguez-Bayona
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Ana B. Ramos-Amaya
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - José A. Brieva
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Antonio Campos-Caro
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
- * E-mail:
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17
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Ebersole JL, Kirakodu SS, Novak MJ, Orraca L, Martinez JG, Cunningham LL, Thomas MV, Stromberg A, Pandruvada SN, Gonzalez OA. Transcriptome Analysis of B Cell Immune Functions in Periodontitis: Mucosal Tissue Responses to the Oral Microbiome in Aging. Front Immunol 2016; 7:272. [PMID: 27486459 PMCID: PMC4947588 DOI: 10.3389/fimmu.2016.00272] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/28/2016] [Indexed: 12/18/2022] Open
Abstract
Evidence has shown activation of T and B cells in gingival tissues in experimental models and in humans diagnosed with periodontitis. The results of this adaptive immune response are noted both locally and systemically with antigenic specificity for an array of oral bacteria, including periodontopathic species, e.g., Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans. It has been recognized through epidemiological studies and clinical observations that the prevalence of periodontitis increases with age. This report describes our studies evaluating gingival tissue transcriptomes in humans and specifically exploiting the use of a non-human primate model of naturally occurring periodontitis to delineate gingival mucosal tissue gene expression profiles focusing on cells/genes critical for the development of humoral adaptive immune responses. Patterns of B cell and plasmacyte genes were altered in aging healthy gingival tissues. Substantial increases in a large number of genes reflecting antigen-dependent activation, B cell activation, B cell proliferation, and B cell differentiation/maturation were observed in periodontitis in adults and aged animals. Finally, evaluation of the relationship of these gene expression patterns with those of various tissue destructive molecules (MMP2, MMP9, CTSK, TNFα, and RANKL) showed a greater frequency of positive correlations in healthy tissues versus periodontitis tissues, with only MMP9 correlations similar between the two tissue types. These results are consistent with B cell response activities in healthy tissues potentially contributing to muting the effects of the tissue destructive biomolecules, whereas with periodontitis this relationship is adversely affected and enabling a progression of tissue destructive events.
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Affiliation(s)
- Jeffrey L Ebersole
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, KY, USA; Division of Periodontics, College of Dentistry, University of Kentucky, Lexington, KY, USA
| | - Sreenatha S Kirakodu
- Center for Oral Health Research, College of Dentistry, University of Kentucky , Lexington, KY , USA
| | - M John Novak
- Center for Oral Health Research, College of Dentistry, University of Kentucky , Lexington, KY , USA
| | - Luis Orraca
- Caribbean Primate Research Center , Sabana Seca, PR , USA
| | - Janis Gonzalez Martinez
- Caribbean Primate Research Center, Sabana Seca, PR, USA; Division of Oral and Maxillofacial Surgery, College of Dentistry, University of Kentucky, Lexington, KY, USA
| | - Larry L Cunningham
- Division of Oral and Maxillofacial Surgery, College of Dentistry, University of Kentucky , Lexington, KY , USA
| | - Mark V Thomas
- Division of Periodontics, College of Dentistry, University of Kentucky , Lexington, KY , USA
| | - Arnold Stromberg
- Department of Statistics, College of Arts and Sciences, University of Kentucky , Lexington, KY , USA
| | - Subramanya N Pandruvada
- Division of Orthodontics, College of Dentistry, University of Kentucky , Lexington, KY , USA
| | - Octavio A Gonzalez
- Center for Oral Health Research, College of Dentistry, University of Kentucky , Lexington, KY , USA
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18
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Yamashita K, Kawata K, Matsumiya H, Kamekura R, Jitsukawa S, Nagaya T, Ogasawara N, Takano KI, Kubo T, Kimura S, Shigehara K, Himi T, Ichimiya S. Bob1 limits cellular frequency of T-follicular helper cells. Eur J Immunol 2016; 46:1361-70. [PMID: 27080143 PMCID: PMC5084739 DOI: 10.1002/eji.201545499] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/03/2016] [Accepted: 04/08/2016] [Indexed: 12/16/2022]
Abstract
T follicular helper (Tfh) cells are involved in specific humoral immunity at initial and recall phases. The fact that the transcription repressors B‐cell lymphoma‐6 and Blimp‐1 determine lineages of Tfh cells and other types of effector CD4+ T cells, respectively, suggests that there are unique mechanisms to establish Tfh‐cell identity. In this study, we found that Tfh cells preferentially express the transcriptional coactivator Bob1. Bob1 of Tfh cells was dispensable for the expression of B‐cell lymphoma‐6 and the functional property of the cells for B cell help. However, upon initial immunization of foreign antigens, the percentages of Tfh cells in Bob1−/− mice were much higher than those in wild‐type (WT) mice. In addition, expansion of Tfh cells within Bob1−/−CD4+ T cells transferred into WT mice revealed that the high frequency of Tfh cells was caused by a T‐cell‐intrinsic mechanism. These findings were further supported by the results of in vitro studies demonstrating that Bob1−/− Tfh cells had greater proliferative activity in response to stimuli by CD3/CD28 monoclonal antibody and were also refractory to CD3‐induced cell death in comparison to WT Tfh cells. These results suggest that Tfh cells harbor a Bob1‐related mechanism to restrict numerical frequency against stimulation of TCRs.
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Affiliation(s)
- Keiji Yamashita
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan.,Department of Otolaryngology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Koji Kawata
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Matsumiya
- Department of Otolaryngology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Ryuta Kamekura
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan.,Department of Otolaryngology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Sumito Jitsukawa
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan.,Department of Otolaryngology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tomonori Nagaya
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan.,Department of Otolaryngology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Noriko Ogasawara
- Department of Otolaryngology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Ken-Ichi Takano
- Department of Otolaryngology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Terufumi Kubo
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Sachiko Kimura
- Division of Pathology and Laboratory Medicine, Hokkaido Medical Center for Child Health and Rehabilitation, Sapporo, Japan
| | - Katsunori Shigehara
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tetsuo Himi
- Department of Otolaryngology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shingo Ichimiya
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
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19
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Wen J, Leucci E, Vendramin R, Kauppinen S, Lund AH, Krogh A, Parker BJ. Transcriptome dynamics of the microRNA inhibition response. Nucleic Acids Res 2015; 43:6207-21. [PMID: 26089393 PMCID: PMC4513874 DOI: 10.1093/nar/gkv603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We report a high-resolution time series study of transcriptome dynamics following antimiR-mediated inhibition of miR-9 in a Hodgkin lymphoma cell-line—the first such dynamic study of the microRNA inhibition response—revealing both general and specific aspects of the physiological response. We show miR-9 inhibition inducing a multiphasic transcriptome response, with a direct target perturbation before 4 h, earlier than previously reported, amplified by a downstream peak at ∼32 h consistent with an indirect response due to secondary coherent regulation. Predictive modelling indicates a major role for miR-9 in post-transcriptional control of RNA processing and RNA binding protein regulation. Cluster analysis identifies multiple co-regulated gene regulatory modules. Functionally, we observe a shift over time from mRNA processing at early time points to translation at later time points. We validate the key observations with independent time series qPCR and we experimentally validate key predicted miR-9 targets. Methodologically, we developed sensitive functional data analytic predictive methods to analyse the weak response inherent in microRNA inhibition experiments. The methods of this study will be applicable to similar high-resolution time series transcriptome analyses and provides the context for more accurate experimental design and interpretation of future microRNA inhibition studies.
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Affiliation(s)
- Jiayu Wen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Eleonora Leucci
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark Laboratory for Molecular Cancer Biology, Center for the Biology of Disease, VIB, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Center of Human Genetics, VIB, 3000 Leuven, Belgium
| | - Roberto Vendramin
- Laboratory for Molecular Cancer Biology, Center for the Biology of Disease, VIB, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Center of Human Genetics, VIB, 3000 Leuven, Belgium
| | - Sakari Kauppinen
- Department of Haematology, Aalborg University Hospital, A.C. Meyers Vnge 15, 2450 Copenhagen SV, Denmark
| | - Anders H Lund
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Anders Krogh
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Brian J Parker
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis street, #07-01, Singapore 138671
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20
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Roy AL, Roeder RG. Chromatin and transcriptional tango on the immune dance floor. Front Immunol 2015; 5:631. [PMID: 25566246 PMCID: PMC4266087 DOI: 10.3389/fimmu.2014.00631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 11/25/2014] [Indexed: 11/22/2022] Open
Affiliation(s)
- Ananda L Roy
- Programs in Immunology and Genetics, Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine , Boston, MA , USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University , New York, NY , USA
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