251
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Liu HX, Feng J, Jiang JJ, Shen WJ, Zheng Y, Liu G, Gao XY. Integrated single-cell and bulk RNA sequencing revealed an epigenetic signature predicts prognosis and tumor microenvironment colorectal cancer heterogeneity. World J Gastrointest Oncol 2024; 16:3032-3054. [PMID: 39072180 PMCID: PMC11271797 DOI: 10.4251/wjgo.v16.i7.3032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/23/2024] [Accepted: 05/07/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) prognosis prediction is currently a major challenge. Epigenetic regulation has been widely reported for its role in cancer development. AIM To construct a robust prognostic signature, we used developed and validated across datasets. METHODS After constructing the signature, the prognostic value of the signature was evaluated in the TCGA cohort and six independent datasets (GSE17526, GSE17537, GSE33113, GSE37892, GSE39048 and GSE39582). The clinical, genomic and transcriptomic features related to the signature were identified. The correlations of the signature score with immune cell infiltration and cell-cell interactions were analyzed. The correlations between the signature score and the sensitivity to different drugs were also predicted. RESULTS In the TCGA cohort, patients in the low-risk group according to the signature score had longer survival than those in the high-risk group, and this finding was validated in the validation datasets. The signature was a prognostic factor independent of age and sex and was correlated with stage and PD-1/PD-L1 expression. Area under the receiving operating characteristic curve was 0.72. Genomic association analyses revealed that samples from high-risk patients exhibited chromosomal instability. Transcriptomic analyses revealed that the signature score was significantly associated with multiple cellular pathways. Bulk RNA-seq and single-cell sequencing data revealed that the signature reflected differences in infiltrating immune cell-tumor cell interactions, especially for macrophages. The signature also predicted the putative drug sensitivity of CRC samples. CONCLUSION The signature is a valuable biomarker for predicting CRC prognosis and reflects multiple features of CRC, especially macrophage infiltration in the microenvironment.
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Affiliation(s)
- Han-Xuan Liu
- Beijing Jinghua Anliang Technology, Beijing 102627, China
| | - Jie Feng
- Department of Clinical Laboratory, The First Medical Centre of Chinese PLA General Hospital, Beijing 100853, China
| | - Jing-Jing Jiang
- Clinical Biological Sample Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China
| | - Wan-Jun Shen
- Department of Nephrology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Yu Zheng
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Gang Liu
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xiang-Yang Gao
- The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
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252
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Li K, Song Z, Yue Q, Wang Q, Li Y, Zhu Y, Chen H. Disease-specific transcriptional programs govern airway goblet cell metaplasia. Heliyon 2024; 10:e34105. [PMID: 39071568 PMCID: PMC11283004 DOI: 10.1016/j.heliyon.2024.e34105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/02/2024] [Accepted: 07/03/2024] [Indexed: 07/30/2024] Open
Abstract
Hypersecretion of airway mucus caused by goblet cell metaplasia is a characteristic of chronic pulmonary inflammatory diseases including asthma, cystic fibrosis (CF), and chronic obstructive pulmonary disease (COPD). Goblet cells originate from airway progenitor club cells. However, the molecular mechanisms and features of goblet cell metaplasia in lung disease are poorly understood. Herein, public single-cell RNA sequencing datasets of human lungs were reanalyzed to explore the transitional phase as club cells differentiate into goblet cells in asthma, CF, and COPD. We found that changes in club and goblet cells during pathogenesis and cellular transition were associated with signalling pathways related to immune response, oxidative stress, and apoptosis. Moreover, other key drivers of goblet cell specification appeared to be pathologically specific, with interleukin (IL)-13 and hypoxia inducible factor 1 (HIF-1)-induced genetic changes in asthma, cystic fibrosis transmembrane conductance regulator (CFTR) mutation being present in CF, and interactions with CD8+ T cells, mitophagy, and mitochondria-induced apoptosis in COPD. In conclusion, this study revealed the similarities and differences in goblet cell metaplasia in asthma, CF, and COPD at the transcriptome level, thereby providing insights into possible novel therapeutic approaches for these diseases.
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Affiliation(s)
- Kuan Li
- Department of Respiratory Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Tianjin Institute of Respiratory Diseases, 300350, Tianjin, China
| | - Zhaoyu Song
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Department of Clinical Lab, Tianjin First Central Hospital, 300192, Tianjin, China
| | - Qing Yue
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
| | - Qi Wang
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
| | - Yu Li
- Department of Respiratory Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Department of Tuberculosis, Haihe Clinical School, Tianjin Medical University, 300350, Tianjin, China
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Tianjin Institute of Respiratory Diseases, 300350, Tianjin, China
| | - Yu Zhu
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Department of Clinical Laboratory, Haihe Hospital, Tianjin University, 300350, Tianjin, China
| | - Huaiyong Chen
- Department of Respiratory Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Department of Tuberculosis, Haihe Clinical School, Tianjin Medical University, 300350, Tianjin, China
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Tianjin Institute of Respiratory Diseases, 300350, Tianjin, China
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253
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Quach H, Farrell S, Wu MJM, Kanagarajah K, Leung JWH, Xu X, Kallurkar P, Turinsky AL, Bear CE, Ratjen F, Kalish B, Goyal S, Moraes TJ, Wong AP. Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity. Nat Commun 2024; 15:5898. [PMID: 39003323 PMCID: PMC11246468 DOI: 10.1038/s41467-024-50281-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 07/05/2024] [Indexed: 07/15/2024] Open
Abstract
Studying human fetal lungs can inform how developmental defects and disease states alter the function of the lungs. Here, we sequenced >150,000 single cells from 19 healthy human pseudoglandular fetal lung tissues ranging between gestational weeks 10-19. We capture dynamic developmental trajectories from progenitor cells that express abundant levels of the cystic fibrosis conductance transmembrane regulator (CFTR). These cells give rise to multiple specialized epithelial cell types. Combined with spatial transcriptomics, we show temporal regulation of key signalling pathways that may drive the temporal and spatial emergence of specialized epithelial cells including ciliated and pulmonary neuroendocrine cells. Finally, we show that human pluripotent stem cell-derived fetal lung models contain CFTR-expressing progenitor cells that capture similar lineage developmental trajectories as identified in the native tissue. Overall, this study provides a comprehensive single-cell atlas of the developing human lung, outlining the temporal and spatial complexities of cell lineage development and benchmarks fetal lung cultures from human pluripotent stem cell differentiations to similar developmental window.
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Affiliation(s)
- Henry Quach
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Spencer Farrell
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Ming Jia Michael Wu
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kayshani Kanagarajah
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Joseph Wai-Hin Leung
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xiaoqiao Xu
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Prajkta Kallurkar
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrei L Turinsky
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christine E Bear
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Felix Ratjen
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brian Kalish
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Neonatology, Department of Paediatrics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sidhartha Goyal
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Theo J Moraes
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amy P Wong
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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254
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Berdnikovs S, Newcomb DC, McKernan KE, Kuehnle SN, Haruna NF, Gebretsadik T, McKennan C, Ma S, Cephus JY, Rosas-Salazar C, Anderson LJ, Gern JE, Hartert T. Single cell profiling to determine influence of wheeze and early-life viral infection on developmental programming of airway epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602506. [PMID: 39026695 PMCID: PMC11257436 DOI: 10.1101/2024.07.08.602506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Although childhood asthma is in part an airway epithelial disorder, the development of the airway epithelium in asthma is not understood. We sought to characterize airway epithelial developmental phenotypes in those with and without recurrent wheeze and the impact of infant infection with respiratory syncytial virus (RSV). Nasal airway epithelial cells (NAECs) were collected at age 2-3 years from an a priori designed nested birth cohort of children from four mutually exclusive groups of wheezers/non-wheezers and RSV-infected/uninfected in the first year of life. NAECs were cultured in air-liquid interface differentiation conditions followed by a combined analysis of single cell RNA sequencing (scRNA-seq) and in vitro infection with respiratory syncytial virus (RSV). NAECs from children with a wheeze phenotype were characterized by abnormal differentiation and basal cell activation of developmental pathways, plasticity in precursor differentiation and a delayed onset of maturation. NAECs from children with wheeze also had increased diversity of currently known RSV receptors and blunted anti-viral immune responses to in vitro infection. The most dramatic changes in differentiation of cultured epithelium were observed in NAECs derived from children that had both wheeze and RSV in the first year of life. Together this suggests that airway epithelium in children with wheeze is developmentally reprogrammed and characterized by increased barrier permeability, decreased antiviral response, and increased RSV receptors, which may predispose to and amplify the effects of RSV infection in infancy and susceptibility to other asthma risk factors that interact with the airway mucosa. SUMMARY Nasal airway epithelial cells from children with wheeze are characterized by altered development and increased susceptibility to RSV infection.
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255
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Eaton AF, Danielson EC, Capen D, Merkulova M, Brown D. Dmxl1 Is an Essential Mammalian Gene that Is Required for V-ATPase Assembly and Function In Vivo. FUNCTION 2024; 5:zqae025. [PMID: 38984989 PMCID: PMC11237898 DOI: 10.1093/function/zqae025] [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: 04/16/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 07/11/2024] Open
Abstract
The proton pumping V-ATPase drives essential biological processes, such as acidification of intracellular organelles. Critically, the V-ATPase domains, V1 and VO, must assemble to produce a functional holoenzyme. V-ATPase dysfunction results in cancer, neurodegeneration, and diabetes, as well as systemic acidosis caused by reduced activity of proton-secreting kidney intercalated cells (ICs). However, little is known about the molecular regulation of V-ATPase in mammals. We identified a novel interactor of the mammalian V-ATPase, Drosophila melanogaster X chromosomal gene-like 1 (Dmxl1), aka Rabconnectin-3A. The yeast homologue of Dmxl1, Rav1p, is part of a complex that catalyzes the reversible assembly of the domains. We, therefore,hypothesized that Dmxl1 is a mammalian V-ATPase assembly factor. Here, we generated kidney IC-specific Dmxl1 knockout (KO) mice, which had high urine pH, like B1 V-ATPase KO mice, suggesting impaired V-ATPase function. Western blotting showed decreased B1 expression and B1 (V1) and a4 (VO) subunits were more intracellular and less colocalized in Dmxl1 KO ICs. In parallel, subcellular fractionation revealed less V1 associated B1 in the membrane fraction of KO cells relative to the cytosol. Furthermore, a proximity ligation assay performed using probes against B1 and a4 V-ATPase subunits also revealed decreased association. We propose that loss of Dmxl1 reduces V-ATPase holoenzyme assembly, thereby inhibiting proton pumping function. Dmxl1 may recruit the V1 domain to the membrane and facilitate assembly with the VO domain and in its absence V1 may be targeted for degradation. We conclude that Dmxl1 is a bona fide mammalian V-ATPase assembly factor.
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Affiliation(s)
- Amity F Eaton
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Elizabeth C Danielson
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Diane Capen
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Maria Merkulova
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Dennis Brown
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
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256
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Reedy JL, Jensen KN, Crossen AJ, Basham KJ, Ward RA, Reardon CM, Brown Harding H, Hepworth OW, Simaku P, Kwaku GN, Tone K, Willment JA, Reid DM, Stappers MHT, Brown GD, Rajagopal J, Vyas JM. Fungal melanin suppresses airway epithelial chemokine secretion through blockade of calcium fluxing. Nat Commun 2024; 15:5817. [PMID: 38987270 PMCID: PMC11237042 DOI: 10.1038/s41467-024-50100-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Respiratory infections caused by the human fungal pathogen Aspergillus fumigatus are a major cause of mortality for immunocompromised patients. Exposure to these pathogens occurs through inhalation, although the role of the respiratory epithelium in disease pathogenesis has not been fully defined. Employing a primary human airway epithelial model, we demonstrate that fungal melanins potently block the post-translational secretion of the chemokines CXCL1 and CXCL8 independent of transcription or the requirement of melanin to be phagocytosed, leading to a significant reduction in neutrophil recruitment to the apical airway both in vitro and in vivo. Aspergillus-derived melanin, a major constituent of the fungal cell wall, dampened airway epithelial chemokine secretion in response to fungi, bacteria, and exogenous cytokines. Furthermore, melanin muted pathogen-mediated calcium fluxing and hindered actin filamentation. Taken together, our results reveal a critical role for melanin interaction with airway epithelium in shaping the host response to fungal and bacterial pathogens.
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Affiliation(s)
- Jennifer L Reedy
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kirstine Nolling Jensen
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Arianne J Crossen
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Kyle J Basham
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Rebecca A Ward
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher M Reardon
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Hannah Brown Harding
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Olivia W Hepworth
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Patricia Simaku
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Geneva N Kwaku
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Kazuya Tone
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
- Division of Respiratory Diseases, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Janet A Willment
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Delyth M Reid
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Mark H T Stappers
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Gordon D Brown
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Jatin M Vyas
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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257
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Zaidi S, Park J, Chan JM, Roudier MP, Zhao JL, Gopalan A, Wadosky KM, Patel RA, Sayar E, Karthaus WR, Kates DH, Chaudhary O, Xu T, Masilionis I, Mazutis L, Chaligné R, Obradovic A, Linkov I, Barlas A, Jungbluth AA, Rekhtman N, Silber J, Manova-Todorova K, Watson PA, True LD, Morrissey C, Scher HI, Rathkopf DE, Morris MJ, Goodrich DW, Choi J, Nelson PS, Haffner MC, Sawyers CL. Single-cell analysis of treatment-resistant prostate cancer: Implications of cell state changes for cell surface antigen-targeted therapies. Proc Natl Acad Sci U S A 2024; 121:e2322203121. [PMID: 38968122 PMCID: PMC11252802 DOI: 10.1073/pnas.2322203121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/09/2024] [Indexed: 07/07/2024] Open
Abstract
Targeting cell surface molecules using radioligand and antibody-based therapies has yielded considerable success across cancers. However, it remains unclear how the expression of putative lineage markers, particularly cell surface molecules, varies in the process of lineage plasticity, wherein tumor cells alter their identity and acquire new oncogenic properties. A notable example of lineage plasticity is the transformation of prostate adenocarcinoma (PRAD) to neuroendocrine prostate cancer (NEPC)-a growing resistance mechanism that results in the loss of responsiveness to androgen blockade and portends dismal patient survival. To understand how lineage markers vary across the evolution of lineage plasticity in prostate cancer, we applied single-cell analyses to 21 human prostate tumor biopsies and two genetically engineered mouse models, together with tissue microarray analysis on 131 tumor samples. Not only did we observe a higher degree of phenotypic heterogeneity in castrate-resistant PRAD and NEPC than previously anticipated but also found that the expression of molecules targeted therapeutically, namely PSMA, STEAP1, STEAP2, TROP2, CEACAM5, and DLL3, varied within a subset of gene-regulatory networks (GRNs). We also noted that NEPC and small cell lung cancer subtypes shared a set of GRNs, indicative of conserved biologic pathways that may be exploited therapeutically across tumor types. While this extreme level of transcriptional heterogeneity, particularly in cell surface marker expression, may mitigate the durability of clinical responses to current and future antigen-directed therapies, its delineation may yield signatures for patient selection in clinical trials, potentially across distinct cancer types.
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MESH Headings
- Male
- Humans
- Single-Cell Analysis/methods
- Animals
- Mice
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Prostatic Neoplasms/drug therapy
- Antigens, Surface/metabolism
- Antigens, Surface/genetics
- Antigens, Neoplasm/metabolism
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Biomarkers, Tumor/metabolism
- Biomarkers, Tumor/genetics
- Adenocarcinoma/genetics
- Adenocarcinoma/pathology
- Adenocarcinoma/metabolism
- Adenocarcinoma/drug therapy
- Carcinoma, Neuroendocrine/genetics
- Carcinoma, Neuroendocrine/pathology
- Carcinoma, Neuroendocrine/metabolism
- Carcinoma, Neuroendocrine/drug therapy
- Gene Expression Regulation, Neoplastic
- Prostatic Neoplasms, Castration-Resistant/metabolism
- Prostatic Neoplasms, Castration-Resistant/pathology
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/drug therapy
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Affiliation(s)
- Samir Zaidi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- Department of Medicine, Division of Solid Tumor Oncology, Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Jooyoung Park
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul02841, Korea
| | - Joseph M. Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | | | | | - Anuradha Gopalan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Kristine M. Wadosky
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY14263
| | - Radhika A. Patel
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98195
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98195
| | - Erolcan Sayar
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98195
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98195
| | - Wouter R. Karthaus
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne1015, Switzerland
| | - D. Henry Kates
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Ojasvi Chaudhary
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Tianhao Xu
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Ignas Masilionis
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Linas Mazutis
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Ronan Chaligné
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Aleksandar Obradovic
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY10032
| | - Irina Linkov
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Afsar Barlas
- Molecular Cytology Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New YorkNY10065
| | - Achim A. Jungbluth
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Natasha Rekhtman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Joachim Silber
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Katia Manova-Todorova
- Molecular Cytology Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New YorkNY10065
| | - Philip A. Watson
- Research Outreach and Compliance, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA98195
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA98195
| | - Howard I. Scher
- Department of Medicine, Division of Solid Tumor Oncology, Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Dana E. Rathkopf
- Department of Medicine, Division of Solid Tumor Oncology, Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Michael J. Morris
- Department of Medicine, Division of Solid Tumor Oncology, Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - David W. Goodrich
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY14263
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul02841, Korea
- Department of Genetics, Yale University School of Medicine, New Haven, CT06510
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98195
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98195
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98195
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98195
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA98195
| | - Charles L. Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- HHMI, Memorial Sloan Kettering Cancer Center, New York, NY10065
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258
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Hung CT, Ma C, Panda SK, Trsan T, Hodel M, Frein J, Foster A, Sun S, Wu HT, Kern J, Mishra R, Jain U, Ho YC, Colonna M, Stappenbeck TS, Liu TC. Western diet reduces small intestinal intraepithelial lymphocytes via FXR-Interferon pathway. Mucosal Immunol 2024:S1933-0219(24)00067-9. [PMID: 38992433 DOI: 10.1016/j.mucimm.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/13/2024]
Abstract
The prevalence of obesity in the United States has continued to increase over the past several decades. Understanding how diet-induced obesity modulates mucosal immunity is of clinical relevance. We previously showed that consumption of a high fat, high sugar "Western" diet (WD) reduces the density and function of small intestinal Paneth cells, a small intestinal epithelial cell type with innate immune function. We hypothesized that obesity could also result in repressed gut adaptive immunity. Using small intestinal intraepithelial lymphocytes (IEL) as a readout, we found that in non-inflammatory bowel disease (IBD) subjects, high body mass index correlated with reduced IEL density. We recapitulated this in wild type (WT) mice fed with WD. A 4-week WD consumption was able to reduce IEL but not splenic, blood, or bone marrow lymphocytes, and the effect was reversible after another 2 weeks of standard diet (SD) washout. Importantly, WD-associated IEL reduction was not dependent on the presence of gut microbiota, as WD-fed germ-free mice also showed IEL reduction. We further found that WD-mediated Farnesoid X Receptor (FXR) activation in the gut triggered IEL reduction, and this was partially mediated by intestinal phagocytes. Activated FXR signaling stimulated phagocytes to secrete type I IFN, and inhibition of either FXR or type I IFN signaling within the phagocytes prevented WD-mediated IEL loss. Therefore, WD consumption represses both innate and adaptive immunity in the gut. These findings have significant clinical implications in the understanding of how diet modulates mucosal immunity.
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Affiliation(s)
- Chen-Ting Hung
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Changqing Ma
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Santosh K Panda
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Tihana Trsan
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Miki Hodel
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Jennifer Frein
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Amanda Foster
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Shengxiang Sun
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Hung-Ting Wu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Justin Kern
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Richa Mishra
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, United States
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, United States
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States.
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259
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Collier CA, Salikhova A, Sabir S, Foncerrada S, Raghavan SA. Crisis in the gut: navigating gastrointestinal challenges in Gulf War Illness with bioengineering. Mil Med Res 2024; 11:45. [PMID: 38978144 PMCID: PMC11229309 DOI: 10.1186/s40779-024-00547-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/26/2024] [Indexed: 07/10/2024] Open
Abstract
Gulf War Illness (GWI) is characterized by a wide range of symptoms that manifests largely as gastrointestinal symptoms. Among these gastrointestinal symptoms, motility disorders are highly prevalent, presenting as chronic constipation, stomach pain, indigestion, diarrhea, and other conditions that severely impact the quality of life of GWI veterans. However, despite a high prevalence of gastrointestinal impairments among these veterans, most research attention has focused on neurological disturbances. This perspective provides a comprehensive overview of current in vivo research advancements elucidating the underlying mechanisms contributing to gastrointestinal disorders in GWI. Generally, these in vivo and in vitro models propose that neuroinflammation alters gut motility and drives the gastrointestinal symptoms reported in GWI. Additionally, this perspective highlights the potential and challenges of in vitro bioengineering models, which could be a crucial contributor to understanding and treating the pathology of gastrointestinal related-GWI.
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Affiliation(s)
- Claudia A Collier
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Aelita Salikhova
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Sufiyan Sabir
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Steven Foncerrada
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Shreya A Raghavan
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA.
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260
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Chen Y, Wang D, Li Y, Qi L, Si W, Bo Y, Chen X, Ye Z, Fan H, Liu B, Liu C, Zhang L, Zhang X, Li Z, Zhu L, Wu A, Zhang Z. Spatiotemporal single-cell analysis decodes cellular dynamics underlying different responses to immunotherapy in colorectal cancer. Cancer Cell 2024; 42:1268-1285.e7. [PMID: 38981439 DOI: 10.1016/j.ccell.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 04/10/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
Abstract
Expanding the efficacy of immune checkpoint blockade (ICB) in colorectal cancer (CRC) presses for a comprehensive understanding of treatment responsiveness. Here, we analyze multiple sequential single-cell samples from 22 patients undergoing PD-1 blockade to map the evolution of local and systemic immunity of CRC patients. In tumors, we identify coordinated cellular programs exhibiting distinct response associations. Specifically, exhausted T (Tex) or tumor-reactive-like CD8+ T (Ttr-like) cells are closely related to treatment efficacy, and Tex cells show correlated proportion changes with multiple other tumor-enriched cell types following PD-1 blockade. In addition, we reveal the less-exhausted phenotype of blood-associated Ttr-like cells in tumors and find that their higher abundance suggests better treatment outcomes. Finally, a higher major histocompatibility complex (MHC) II-related signature in circulating CD8+ T cells at baseline is linked to superior responses. Our study provides insights into the spatiotemporal cellular dynamics following neoadjuvant PD-1 blockade in CRC.
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Affiliation(s)
- Yuqing Chen
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dongfang Wang
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China.
| | - Yingjie Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Gastrointestinal Cancer Center, Unit III, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Lu Qi
- Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing, China
| | - Wen Si
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Yufei Bo
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhaochen Ye
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Hongtao Fan
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Baolin Liu
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Chang Liu
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Li Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Pathology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xiaoyan Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Radiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Zhongwu Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Pathology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Linna Zhu
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Aiwen Wu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Gastrointestinal Cancer Center, Unit III, Peking University Cancer Hospital & Institute, Beijing 100142, China.
| | - Zemin Zhang
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China.
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261
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Liang L, Yang Y, Deng K, Wu Y, Li Y, Bai L, Wang Y, Lu C. Type I Interferon Activates PD-1 Expression through Activation of the STAT1-IRF2 Pathway in Myeloid Cells. Cells 2024; 13:1163. [PMID: 38995014 PMCID: PMC11240780 DOI: 10.3390/cells13131163] [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: 04/30/2024] [Revised: 06/18/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024] Open
Abstract
PD-1 (Programmed cell death protein 1) regulates the metabolic reprogramming of myeloid-derived suppressor cells and myeloid cell differentiation, as well as the type I interferon (IFN-I) signaling pathway in myeloid cells in the tumor microenvironment. PD-1, therefore, is a key inhibitory receptor in myeloid cells. However, the regulation of PD-1 expression in myeloid cells is unknown. We report that the expression level of PDCD1, the gene that encodes the PD-1 protein, is positively correlated with the levels of IFNB1 and IFNAR1 in myeloid cells in human colorectal cancer. Treatment of mouse myeloid cell lines with recombinant IFNβ protein elevated PD-1 expression in myeloid cells in vitro. Knocking out IFNAR1, the gene that encodes the IFN-I-specific receptor, diminished the inductive effect of IFNβ on PD-1 expression in myeloid cells in vitro. Treatment of tumor-bearing mice with a lipid nanoparticle-encapsulated IFNβ-encoding plasmid (IFNBCOL01) increased IFNβ expression, resulting in elevated PD-1 expression in tumor-infiltrating myeloid cells. At the molecular level, we determined that IFNβ activates STAT1 (signal transducer and activator of transcription 1) and IRFs (interferon regulatory factors) in myeloid cells. Analysis of the cd279 promoter identified IRF2-binding consensus sequence elements. ChIP (chromatin immunoprecipitation) analysis determined that the pSTAT1 directly binds to the irf2 promoter and that IRF2 directly binds to the cd279 promoter in myeloid cells in vitro and in vivo. In colon cancer patients, the expression levels of STAT1, IRF2 and PDCD1 are positively correlated in tumor-infiltrating myeloid cells. Our findings determine that IFNβ activates PD-1 expression at least in part by an autocrine mechanism via the stimulation of the pSTAT1-IRF2 axis in myeloid cells.
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Affiliation(s)
- Liyan Liang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (L.L.); (Y.Y.); (K.D.); (Y.W.); (Y.L.)
| | - Yingcui Yang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (L.L.); (Y.Y.); (K.D.); (Y.W.); (Y.L.)
| | - Kaidi Deng
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (L.L.); (Y.Y.); (K.D.); (Y.W.); (Y.L.)
| | - Yanmin Wu
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (L.L.); (Y.Y.); (K.D.); (Y.W.); (Y.L.)
| | - Yan Li
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (L.L.); (Y.Y.); (K.D.); (Y.W.); (Y.L.)
| | - Liya Bai
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China; (L.B.); (Y.W.)
| | - Yinsong Wang
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China; (L.B.); (Y.W.)
| | - Chunwan Lu
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (L.L.); (Y.Y.); (K.D.); (Y.W.); (Y.L.)
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262
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Bakht MK, Beltran H. Biological determinants of PSMA expression, regulation and heterogeneity in prostate cancer. Nat Rev Urol 2024:10.1038/s41585-024-00900-z. [PMID: 38977769 DOI: 10.1038/s41585-024-00900-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2024] [Indexed: 07/10/2024]
Abstract
Prostate-specific membrane antigen (PSMA) is an important cell-surface imaging biomarker and therapeutic target in prostate cancer. The PSMA-targeted theranostic 177Lu-PSMA-617 was approved in 2022 for men with PSMA-PET-positive metastatic castration-resistant prostate cancer. However, not all patients respond to PSMA-radioligand therapy, in part owing to the heterogeneity of PSMA expression in the tumour. The PSMA regulatory network is composed of a PSMA transcription complex, an upstream enhancer that loops to the FOLH1 (PSMA) gene promoter, intergenic enhancers and differentially methylated regions. Our understanding of the PSMA regulatory network and the mechanisms underlying PSMA suppression is evolving. Clinically, molecular imaging provides a unique window into PSMA dynamics that occur on therapy and with disease progression, although challenges arise owing to the limited resolution of PET. PSMA regulation and heterogeneity - including intertumoural and inter-patient heterogeneity, temporal changes, lineage dynamics and the tumour microenvironment - affect PSMA theranostics. PSMA response and resistance to radioligand therapy are mediated by a number of potential mechanisms, and complementary biomarkers beyond PSMA are under development. Understanding the biological determinants of cell surface target regulation and heterogeneity can inform precision medicine approaches to PSMA theranostics as well as other emerging therapies.
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Affiliation(s)
- Martin K Bakht
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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263
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Ávila-Arres IE, Rodríguez Hernández E, Gómez Rosales S, Reis de Souza TC, Mariscal-Landín G. Proteomic Identification and Quantification of Basal Endogenous Proteins in the Ileal Digesta of Growing Pigs. Animals (Basel) 2024; 14:2000. [PMID: 38998112 PMCID: PMC11240675 DOI: 10.3390/ani14132000] [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: 05/27/2024] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024] Open
Abstract
The accurate estimation of basal endogenous losses (BEL) of amino acids at the ileum is indispensable to improve nutrient utilization efficiency. This study used a quantitative proteomic approach to identify variations in BEL in the ileal digesta of growing pigs fed a nitrogen-free diet (NFD) or a casein diet (CAS). Eight barrow pigs (39.8 ± 6.3 kg initial body weight (BW)) were randomly assigned to a 2 × 2 crossover design. A total of 348 proteins were identified and quantified in both treatments, of which 101 showed a significant differential abundance between the treatments (p < 0.05). Functional and pathway enrichment analyses revealed that the endogenous proteins were associated with intestinal metabolic function. Furthermore, differentially abundant proteins (DAPs) in the digesta of pigs fed the NFD enriched terms and pathways that suggest intestinal inflammation, the activation of innate antimicrobial host defense, an increase in cellular autophagy and epithelial turnover, and reduced synthesis of pancreatic and intestinal secretions. These findings suggest that casein diets may provide a more accurate estimation of BEL because they promote normal gastrointestinal secretions. Overall, proteomic and bioinformatic analyses provided valuable insights into the composition of endogenous proteins in the ileal digesta and their relationship with the functions, processes, and pathways modified by diet composition.
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Affiliation(s)
- Iris Elisa Ávila-Arres
- Posgrado en Ciencias de la Producción y de la Salud Animal, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
| | - Elba Rodríguez Hernández
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Km 1 Carretera a Colón, Querétaro 76280, Mexico; (E.R.H.); (S.G.R.)
| | - Sergio Gómez Rosales
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Km 1 Carretera a Colón, Querétaro 76280, Mexico; (E.R.H.); (S.G.R.)
| | - Tércia Cesária Reis de Souza
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias s/n, Querétaro 76230, Mexico;
| | - Gerardo Mariscal-Landín
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Km 1 Carretera a Colón, Querétaro 76280, Mexico; (E.R.H.); (S.G.R.)
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264
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Yuan X, Ma Y, Gao R, Cui S, Wang Y, Fa B, Ma S, Wei T, Ma S, Yu Z. HEARTSVG: a fast and accurate method for identifying spatially variable genes in large-scale spatial transcriptomics. Nat Commun 2024; 15:5700. [PMID: 38972896 PMCID: PMC11228050 DOI: 10.1038/s41467-024-49846-1] [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: 06/29/2023] [Accepted: 06/19/2024] [Indexed: 07/09/2024] Open
Abstract
Identifying spatially variable genes (SVGs) is crucial for understanding the spatiotemporal characteristics of diseases and tissue structures, posing a distinctive challenge in spatial transcriptomics research. We propose HEARTSVG, a distribution-free, test-based method for fast and accurately identifying spatially variable genes in large-scale spatial transcriptomic data. Extensive simulations demonstrate that HEARTSVG outperforms state-of-the-art methods with higherF 1 scores (averageF 1 Score=0.948), improved computational efficiency, scalability, and reduced false positives (FPs). Through analysis of twelve real datasets from various spatial transcriptomic technologies, HEARTSVG identifies a greater number of biologically significant SVGs (average AUC = 0.792) than other comparative methods without prespecifying spatial patterns. Furthermore, by clustering SVGs, we uncover two distinct tumor spatial domains characterized by unique spatial expression patterns, spatial-temporal locations, and biological functions in human colorectal cancer data, unraveling the complexity of tumors.
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Affiliation(s)
- Xin Yuan
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China
| | - Yanran Ma
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ruitian Gao
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuya Cui
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China
| | - Yifan Wang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Botao Fa
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Shiyang Ma
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ting Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangge Ma
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China.
- Department of Biostatistics, Yale University, New Haven, USA.
| | - Zhangsheng Yu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China.
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Center for Biomedical Data Science, Translational Science Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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265
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Sabbaghian M, Gheitasi H, Fadaee M, Javadi Henafard H, Tavakoli A, Shekarchi AA, Poortahmasebi V. Human cytomegalovirus microRNAs: strategies for immune evasion and viral latency. Arch Virol 2024; 169:157. [PMID: 38969819 DOI: 10.1007/s00705-024-06080-w] [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: 12/11/2023] [Accepted: 05/17/2024] [Indexed: 07/07/2024]
Abstract
Viruses use various strategies and mechanisms to deal with cells and proteins of the immune system that form a barrier against infection. One of these mechanisms is the encoding and production of viral microRNAs (miRNAs), whose function is to regulate the gene expression of the host cell and the virus, thus creating a suitable environment for survival and spreading viral infection. miRNAs are short, single-stranded, non-coding RNA molecules that can regulate the expression of host and viral proteins, and due to their non-immunogenic nature, they are not eliminated by the cells of the immune system. More than half of the viral miRNAs are encoded and produced by Orthoherpesviridae family members. Human cytomegalovirus (HCMV) produces miRNAs that mediate various processes in infected cells to contribute to HCMV pathogenicity, including immune escape, viral latency, and cell apoptosis. Here, we discuss which cellular and viral proteins or cellular pathways and processes these mysterious molecules target to evade immunity and support viral latency in infected cells. We also discuss current evidence that their function of bypassing the host's innate and adaptive immune system is essential for the survival and multiplication of the virus and the spread of HCMV infection.
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Affiliation(s)
- Mohammad Sabbaghian
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamidreza Gheitasi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Manouchehr Fadaee
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran
| | | | - Ahmad Tavakoli
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Akbar Shekarchi
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahdat Poortahmasebi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
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266
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Alayoubi Y, Bentsen M, Looso M. Scanpro is a tool for robust proportion analysis of single-cell resolution data. Sci Rep 2024; 14:15581. [PMID: 38971877 PMCID: PMC11227528 DOI: 10.1038/s41598-024-66381-7] [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: 09/21/2023] [Accepted: 07/01/2024] [Indexed: 07/08/2024] Open
Abstract
In higher organisms, individual cells respond to signals and perturbations by epigenetic regulation and transcriptional adaptation. However, in addition to shifting the expression level of individual genes, the adaptive response of cells can also lead to shifts in the proportions of different cell types. Recent methods such as scRNA-seq allow for the interrogation of expression on the single-cell level, and can quantify individual cell type clusters within complex tissue samples. In order to identify clusters showing differential composition between different biological conditions, differential proportion analysis has recently been introduced. However, bioinformatics tools for robust proportion analysis of both replicated and unreplicated single-cell datasets are critically missing. In this manuscript, we present Scanpro, a modular tool for proportion analysis, seamlessly integrating into widely accepted frameworks in the Python environment. Scanpro is fast, accurate, supports datasets without replicates, and is intended to be used by bioinformatics experts and beginners alike.
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Affiliation(s)
- Yousef Alayoubi
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mette Bentsen
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
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267
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Coulton A, Murai J, Qian D, Thakkar K, Lewis CE, Litchfield K. Using a pan-cancer atlas to investigate tumour associated macrophages as regulators of immunotherapy response. Nat Commun 2024; 15:5665. [PMID: 38969631 PMCID: PMC11226649 DOI: 10.1038/s41467-024-49885-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/24/2024] [Indexed: 07/07/2024] Open
Abstract
The paradigm for macrophage characterization has evolved from the simple M1/M2 dichotomy to a more complex model that encompasses the broad spectrum of macrophage phenotypic diversity, due to differences in ontogeny and/or local stimuli. We currently lack an in-depth pan-cancer single cell RNA-seq (scRNAseq) atlas of tumour-associated macrophages (TAMs) that fully captures this complexity. In addition, an increased understanding of macrophage diversity could help to explain the variable responses of cancer patients to immunotherapy. Our atlas includes well established macrophage subsets as well as a number of additional ones. We associate macrophage composition with tumour phenotype and show macrophage subsets can vary between primary and metastatic tumours growing in sites like the liver. We also examine macrophage-T cell functional cross talk and identify two subsets of TAMs associated with T cell activation. Analysis of TAM signatures in a large cohort of immune checkpoint inhibitor-treated patients (CPI1000 + ) identify multiple TAM subsets associated with response, including the presence of a subset of TAMs that upregulate collagen-related genes. Finally, we demonstrate the utility of our data as a resource and reference atlas for mapping of novel macrophage datasets using projection. Overall, these advances represent an important step in both macrophage classification and overcoming resistance to immunotherapies in cancer.
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Affiliation(s)
- Alexander Coulton
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK
| | - Jun Murai
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK
| | - Danwen Qian
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK
| | - Krupa Thakkar
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK
| | - Claire E Lewis
- Department of Oncology and Metabolism, University of Sheffield Medical School, Beech Hill Road, Sheffield, Yorkshire, S10 2RX, UK.
| | - Kevin Litchfield
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK.
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Robinson W, Stone JK, Schischlik F, Gasmi B, Kelly MC, Seibert C, Dadkhah K, Gertz EM, Lee JS, Zhu K, Ma L, Wang XW, Sahinalp SC, Patro R, Leiserson MDM, Harris CC, Schäffer AA, Ruppin E. Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes. SCIENCE ADVANCES 2024; 10:eadj7402. [PMID: 38959321 PMCID: PMC11221508 DOI: 10.1126/sciadv.adj7402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 05/29/2024] [Indexed: 07/05/2024]
Abstract
The study of the tumor microbiome has been garnering increased attention. We developed a computational pipeline (CSI-Microbes) for identifying microbial reads from single-cell RNA sequencing (scRNA-seq) data and for analyzing differential abundance of taxa. Using a series of controlled experiments and analyses, we performed the first systematic evaluation of the efficacy of recovering microbial unique molecular identifiers by multiple scRNA-seq technologies, which identified the newer 10x chemistries (3' v3 and 5') as the best suited approach. We analyzed patient esophageal and colorectal carcinomas and found that reads from distinct genera tend to co-occur in the same host cells, testifying to possible intracellular polymicrobial interactions. Microbial reads are disproportionately abundant within myeloid cells that up-regulate proinflammatory cytokines like IL1Β and CXCL8, while infected tumor cells up-regulate antigen processing and presentation pathways. These results show that myeloid cells with bacteria engulfed are a major source of bacterial RNA within the tumor microenvironment (TME) and may inflame the TME and influence immunotherapy response.
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Affiliation(s)
- Welles Robinson
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20910, USA
- Department of Computer Science, University of Maryland, College Park, MD 20910, USA
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
- Tumour Immunogenomics and Immunosurveillance Laboratory, Department of Oncology, University College London, London, UK
| | - Joshua K. Stone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Fiorella Schischlik
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Billel Gasmi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael C. Kelly
- Center for Cancer Research Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Bethesda, MD 20701, USA
| | - Charlie Seibert
- Center for Cancer Research Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Bethesda, MD 20701, USA
| | - Kimia Dadkhah
- Center for Cancer Research Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Bethesda, MD 20701, USA
| | - E. Michael Gertz
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Joo Sang Lee
- Department of Artificial Intelligence and Department of Precision Medicine, School of Medicine, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Kaiyuan Zhu
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
- Department of Computer Science, Indiana University, Bloomington, IN 47408, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lichun Ma
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - S. Cenk Sahinalp
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Rob Patro
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20910, USA
- Department of Computer Science, University of Maryland, College Park, MD 20910, USA
| | - Mark D. M. Leiserson
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20910, USA
- Department of Computer Science, University of Maryland, College Park, MD 20910, USA
| | - Curtis C. Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alejandro A. Schäffer
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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269
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Singh PNP, Gu W, Madha S, Lynch AW, Cejas P, He R, Bhattacharya S, Muñoz Gomez M, Oser MG, Brown M, Long HW, Meyer CA, Zhou Q, Shivdasani RA. Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation. Cell Stem Cell 2024; 31:1038-1057.e11. [PMID: 38733993 DOI: 10.1016/j.stem.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024]
Abstract
Enteroendocrine cells (EECs) secrete serotonin (enterochromaffin [EC] cells) or specific peptide hormones (non-EC cells) that serve vital metabolic functions. The basis for terminal EEC diversity remains obscure. By forcing activity of the transcription factor (TF) NEUROG3 in 2D cultures of human intestinal stem cells, we replicated physiologic EEC differentiation and examined transcriptional and cis-regulatory dynamics that culminate in discrete cell types. Abundant EEC precursors expressed stage-specific genes and TFs. Before expressing pre-terminal NEUROD1, post-mitotic precursors oscillated between transcriptionally distinct ASCL1+ and HES6hi cell states. Loss of either factor accelerated EEC differentiation substantially and disrupted EEC individuality; ASCL1 or NEUROD1 deficiency had opposing consequences on EC and non-EC cell features. These TFs mainly bind cis-elements that are accessible in undifferentiated stem cells, and they tailor subsequent expression of TF combinations that underlie discrete EEC identities. Thus, early TF oscillations retard EEC maturation to enable accurate diversity within a medically important cell lineage.
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Affiliation(s)
- Pratik N P Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Wei Gu
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shariq Madha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Allen W Lynch
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ruiyang He
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Swarnabh Bhattacharya
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Miguel Muñoz Gomez
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Clifford A Meyer
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Qiao Zhou
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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270
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Gilliland T, Dron JS, Selvaraj MS, Trinder M, Paruchuri K, Urbut SM, Haidermota S, Bernardo R, Uddin MM, Honigberg MC, Peloso GM, Natarajan P. Genetic Architecture and Clinical Outcomes of Combined Lipid Disturbances. Circ Res 2024; 135:265-276. [PMID: 38828614 PMCID: PMC11223949 DOI: 10.1161/circresaha.123.323973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Dyslipoproteinemia often involves simultaneous derangements of multiple lipid traits. We aimed to evaluate the phenotypic and genetic characteristics of combined lipid disturbances in a general population-based cohort. METHODS Among UK Biobank participants without prevalent coronary artery disease, we used blood lipid and apolipoprotein B concentrations to ascribe individuals into 1 of 6 reproducible and mutually exclusive dyslipoproteinemia subtypes. Incident coronary artery disease risk was estimated for each subtype using Cox proportional hazards models. Phenome-wide analyses and genome-wide association studies were performed for each subtype, followed by in silico causal gene prioritization and heritability analyses. Additionally, the prevalence of disruptive variants in causal genes for Mendelian lipid disorders was assessed using whole-exome sequence data. RESULTS Among 450 636 UK Biobank participants: 63 (0.01%) had chylomicronemia; 40 005 (8.9%) had hypercholesterolemia; 94 785 (21.0%) had combined hyperlipidemia; 13 998 (3.1%) had remnant hypercholesterolemia; 110 389 (24.5%) had hypertriglyceridemia; and 49 (0.01%) had mixed hypertriglyceridemia and hypercholesterolemia. Over a median (interquartile range) follow-up of 11.1 (10.4-11.8) years, incident coronary artery disease risk varied across subtypes, with combined hyperlipidemia exhibiting the largest hazard (hazard ratio, 1.92 [95% CI, 1.84-2.01]; P=2×10-16), even when accounting for non-HDL-C (hazard ratio, 1.45 [95% CI, 1.30-1.60]; P=2.6×10-12). Genome-wide association studies revealed 250 loci significantly associated with dyslipoproteinemia subtypes, of which 72 (28.8%) were not detected in prior single lipid trait genome-wide association studies. Mendelian lipid variant carriers were rare (2.0%) among individuals with dyslipoproteinemia, but polygenic heritability was high, ranging from 23% for remnant hypercholesterolemia to 54% for combined hyperlipidemia. CONCLUSIONS Simultaneous assessment of multiple lipid derangements revealed nuanced differences in coronary artery disease risk and genetic architectures across dyslipoproteinemia subtypes. These findings highlight the importance of looking beyond single lipid traits to better understand combined lipid and lipoprotein phenotypes and implications for disease risk.
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Affiliation(s)
- Thomas Gilliland
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Jacqueline S. Dron
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Margaret Sunitha Selvaraj
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Mark Trinder
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC
| | - Kaavya Paruchuri
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Sarah M. Urbut
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Sara Haidermota
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Rachel Bernardo
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Md Mesbah Uddin
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Michael C. Honigberg
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Gina M. Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
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271
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Xu C, Yang L, Cheng T, Wang Z, Liu C, Shao J. Sodium Houttuyfonate Ameliorates DSS-induced Colitis Aggravated by Candida albicans through Dectin-1/NF-κB/miR-32-5p/NFKBIZ Axis Based on Intestinal microRNA Profiling. Inflammation 2024:10.1007/s10753-024-02091-6. [PMID: 38963571 DOI: 10.1007/s10753-024-02091-6] [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: 05/14/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
Our previous research indicated that Sodium houttuyfonate (SH) can effectively ameliorate dextran sulfate sodium (DSS)-induced colitis exacerbated by Candida albicans. However, the underlying protective mechanism of SH remains unclear. Therefore, in this study, a mice colitis model was infected with C. albicans, and the total colonic miRNAs were assessed. Furthermore, the differentially expressed miRNAs were enriched, clustered, and analyzed. Moreover, based on the dual luciferase analysis of NFKBIZ modulation by miR-32-5p, the in vitro and in vivo therapeutic effects of SH on inflammatory response, fungal burden, oxidative stress, and apoptosis were assessed at transcriptional and translational levels in the presence of agonist and antagonist. A total of 1157 miRNAs were identified, 84 of which were differentially expressed. Furthermore, qRT-PCR validated that SH treatment improved 17 differentially expressed miRNAs with > fourfold upregulation or > sixfold downregulation. Similar to most differentially altered miRNA, C. albicans significantly increased Dectin-1, NF-κB, TNF-α, IL-1β, IL-17A, and decreased miR-32-5p which negatively targeted NFKBIZ. In addition, SH treatment reduced inflammatory response and fungal burden in a colitis model with C. albicans infection. Further analyses indicated that in C. albicans infected Caco2 cells, SH inhibited fungal growth, oxidative stress, and apoptosis by increasing Dectin-1, NF-κB, NFKBIZ, TNF-α, IL-1β, IL-17A, and decreasing miR-32-5p. Therefore, SH can ameliorate the severity of colitis aggravated by C. albicans via the Dectin-1/NF-κB/miR-32-5p/NFKBIZ axis.
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Affiliation(s)
- Chen Xu
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Liu Yang
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Ting Cheng
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Zixu Wang
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Chengcheng Liu
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Jing Shao
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China.
- Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China.
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272
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Weine E, Carbonetto P, Stephens M. Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.23.586420. [PMID: 38585920 PMCID: PMC10996495 DOI: 10.1101/2024.03.23.586420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Summary Motivated by theoretical and practical issues that arise when applying Principal Components Analysis (PCA) to count data, Townes et al introduced "Poisson GLM-PCA", a variation of PCA adapted to count data, as a tool for dimensionality reduction of single-cell RNA sequencing (RNA-seq) data. However, fitting GLM-PCA is computationally challenging. Here we study this problem, and show that a simple algorithm, which we call "Alternating Poisson Regression" (APR), produces better quality fits, and in less time, than existing algorithms. APR is also memory-efficient, and lends itself to parallel implementation on multi-core processors, both of which are helpful for handling large single-cell RNA-seq data sets. We illustrate the benefits of this approach in two published single-cell RNA-seq data sets. The new algorithms are implemented in an R package, fastglmpca. Availability and implementation The fastglmpca R package is released on CRAN for Windows, macOS and Linux, and the source code is available at github.com/stephenslab/fastglmpca under the open source GPL-3 license. Scripts to reproduce the results in this paper are also available in the GitHub repository. Contact mstephens@uchicago.edu. Supplementary information Supplementary data are available on BioRxiv online.
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273
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Yamashita T, Kaplan U, Chakraborty A, Marden G, Gritli S, Roh D, Bujor A, Trojanowski M, Ligresti G, Browning JL, Trojanowska M. ERG Regulates Lymphatic Vessel Specification Genes and Its Deficiency Impairs Wound Healing-Associated Lymphangiogenesis. Arthritis Rheumatol 2024. [PMID: 38965683 DOI: 10.1002/art.42944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/30/2024] [Accepted: 06/20/2024] [Indexed: 07/06/2024]
Abstract
OBJECTIVE Rarefaction of blood and lymphatic vessels in the skin has been reported in systemic sclerosis (SSc) (scleroderma). E26 transformation-specific-related factor (ERG) and Friend leukemia virus-induced erythroleukemia 1 (FLI-1) are important regulators of angiogenesis, but their role in lymphatic vasculature is lesser known. The goal of this study was to determine the role of ERG and FLI-1 in postnatal lymphangiogenesis and SSc lymphatic system defects. METHODS Immunofluorescence was used to detect ERG and FLI-1 in skin biopsy samples from patients with SSc and healthy controls. Transcriptional analysis of ERG or FLI-1-silenced human dermal lymphatic endothelial cells (LECs) was performed using microarrays. Effects of ERG and FLI-1 deficiency on in vitro tubulogenesis in human dermal LECs were examined using a Matrigel assay. ERG and FLI-1 endothelial-specific knockouts and ERG lymphatic-specific knockouts were generated to examine vessel regeneration in mice. RESULTS ERG and FLI-1 protein levels were reduced in the blood and lymphatic vasculature in SSc skin biopsy samples. ERG levels were shown to regulate genes involved in lymphatic vessel specification, including vascular endothelial growth factor receptor 3/FLT-4, lymphatic vessel endothelial hyaluronan receptor 1, SOX-18, and prospero homeobox 1 (PROX-1), whereas FLI-1 enhanced the function of ERG. The ERG-FLT-4 pathway regulated in vitro tubulogenesis in human LECs. Deficiency of ERG or FLI-1 similarly impaired the function of blood vessels in mice. However, only ERG deficiency affected the regeneration of lymphatic vessels during wound healing. CONCLUSION ERG and FLI-1 are essential regulators of blood and lymphatic vessel regeneration. Deficiency of ERG and FLI-1 in SSc endothelial cells may contribute to the impairment of blood and lymphatic vasculature in patients with SSc.
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Affiliation(s)
| | | | | | | | | | - Daniel Roh
- Boston University, Boston, Massachusetts
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274
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Luan X, Zhang X, Luan Q, Gan J, Wang Y, Zhao Y. Traditional Chinese Medicine Integrated Multifunctional Responsive Core-Shell Microneedles for Dermatosis Treatment. RESEARCH (WASHINGTON, D.C.) 2024; 7:0420. [PMID: 38966748 PMCID: PMC11223756 DOI: 10.34133/research.0420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 06/09/2024] [Indexed: 07/06/2024]
Abstract
Microneedles have demonstrated value in targeted treatment of dermatosis. Current investigation aims to enhance the functions and optimize substance delivery to improve therapeutic effects. Here, we present innovative shell-core microneedles with light-pH dual responsiveness for spatiotemporal sequential release of multiple Chinese herb drugs to treat scleroderma. By using a stepwise template-assisted method, we effectively prepare a hydrogel-based core layer containing polydopamine-MXene (P-MXene) loaded with triptolide (TP), and a shell layer composed of polyvinyl alcohol (PVA) encapsulating paeoniflorin (Pae). P-MXene can adsorb the sparingly soluble TP to ensure its encapsulation efficiency and contribute to the synergistic photothermal effect benefitting from its excellent photothermal conversion ability. Besides, PVA can rapidly dissolve upon microneedle piercing into the skin and quickly release the anti-inflammatory and detoxifying Pae, establishing a favorable low-acid subcutaneous environment. In response to pH changes and near-infrared effects, TP is sustainably released from P-MXene and delivered through the swollen pores of the hydrogel. On the basis of these characteristics, we demonstrate that these microneedles could effectively reduce profibrotic key cytokines interleukin-1β and transforming growth factor-β, thereby reducing collagen deposition and decreasing epidermal thickness, ameliorating skin fibrosis and capillary lesion in scleroderma mouse models. These findings highlight the important clinical potential of these microneedles in the treatment of skin diseases.
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Affiliation(s)
- Xi Luan
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Pharmacy, Clinical College of Traditional Chinese and Western Medicine,
Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiaoxuan Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering,
Southeast University, Nanjing 210096, China
| | - Qichen Luan
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Pharmacy, Clinical College of Traditional Chinese and Western Medicine,
Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jingjing Gan
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Pharmacy, Clinical College of Traditional Chinese and Western Medicine,
Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yu Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering,
Southeast University, Nanjing 210096, China
| | - Yuanjin Zhao
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Pharmacy, Clinical College of Traditional Chinese and Western Medicine,
Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering,
Southeast University, Nanjing 210096, China
- Shenzhen Research Institute,
Southeast University, Shenzhen 518071, China
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275
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Wu C, Yu H, Liang F, Huang X, Jiang B, Lou Z, Liu Y, Wu Z, Wang Q, Shen H, Chen M, Wu P, Wu M. Hypoxia inhibits the iMo/cDC2/CD8+ TRMs immune axis in the tumor microenvironment of human esophageal cancer. J Immunother Cancer 2024; 12:e008889. [PMID: 38964786 PMCID: PMC11227851 DOI: 10.1136/jitc-2024-008889] [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] [Accepted: 05/22/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Esophageal cancer (ESCA) is a form of malignant tumor associated with chronic inflammation and immune dysregulation. However, the specific immune status and key mechanisms of immune regulation in this disease require further exploration. METHODS To investigate the features of the human ESCA tumor immune microenvironment and its possible regulation, we performed mass cytometry by time of flight, single-cell RNA sequencing, multicolor fluorescence staining of tissue, and flow cytometry analyses on tumor and paracancerous tissue from treatment-naïve patients. RESULTS We depicted the immune landscape of the ESCA and revealed that CD8+ (tissue-resident memory CD8+ T cells (CD8+ TRMs) were closely related to disease progression. We also revealed the heterogeneity of CD8+ TRMs in the ESCA tumor microenvironment (TME), which was associated with their differentiation and function. Moreover, the subset of CD8+ TRMs in tumor (called tTRMs) that expressed high levels of granzyme B and immune checkpoints was markedly decreased in the TME of advanced ESCA. We showed that tTRMs are tumor effector cells preactivated in the TME. We then demonstrated that conventional dendritic cells (cDC2s) derived from intermediate monocytes (iMos) are essential for maintaining the proliferation of CD8+ TRMs in the TME. Our preliminary study showed that hypoxia can promote the apoptosis of iMos and impede the maturation of cDC2s, which in turn reduces the proliferative capacity of CD8+ TRMs, thereby contributing to the progression of cancer. CONCLUSIONS Our study revealed the essential antitumor roles of CD8+ TRMs and preliminarily explored the regulation of the iMo/cDC2/CD8+ TRM immune axis in the human ESCA TME.
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Affiliation(s)
- Chuanqiang Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Laboratory of Clinical Research Center of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Huan Yu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Fuxiang Liang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Xiancong Huang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang Province, People's Republic of China
| | - Bin Jiang
- Department of Thoracic Surgery, Shandong Provincial Hospital, Jinan, Shandong Province, People's Republic of China
| | - Zhiling Lou
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Yafei Liu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Zixiang Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Qi Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Hong Shen
- Department of Medical Oncology, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Pin Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Ming Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Laboratory of Clinical Research Center of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
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276
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Zeng Y, Ma Q, Chen J, Kong X, Chen Z, Liu H, Liu L, Qian Y, Wang X, Lu S. Single-cell sequencing: Current applications in various tuberculosis specimen types. Cell Prolif 2024:e13698. [PMID: 38956399 DOI: 10.1111/cpr.13698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/21/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
Tuberculosis (TB) is a chronic disease caused by Mycobacterium tuberculosis (M.tb) and responsible for millions of deaths worldwide each year. It has a complex pathogenesis that primarily affects the lungs but can also impact systemic organs. In recent years, single-cell sequencing technology has been utilized to characterize the composition and proportion of immune cell subpopulations associated with the pathogenesis of TB disease since it has a high resolution that surpasses conventional techniques. This paper reviews the current use of single-cell sequencing technologies in TB research and their application in analysing specimens from various sources of TB, primarily peripheral blood and lung specimens. The focus is on how these technologies can reveal dynamic changes in immune cell subpopulations, genes and proteins during disease progression after M.tb infection. Based on the current findings, single-cell sequencing has significant potential clinical value in the field of TB research. Next, we will focus on the real-world applications of the potential targets identified through single-cell sequencing for diagnostics, therapeutics and the development of effective vaccines.
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Affiliation(s)
- Yuqin Zeng
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Quan Ma
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Jinyun Chen
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Xingxing Kong
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Zhanpeng Chen
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Huazhen Liu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Lanlan Liu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Yan Qian
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Xiaomin Wang
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Shuihua Lu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
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277
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Reddy BL, Reddy VS, Saier MH. Health Benefits of Intermittent Fasting. Microb Physiol 2024; 34:142-152. [PMID: 38955141 PMCID: PMC11262566 DOI: 10.1159/000540068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 05/27/2024] [Indexed: 07/04/2024]
Abstract
We propose that intermittent fasting (time-restricted eating), in agreement with the conclusions of other biologists, as revealed in recent publications, promotes the achievement of numerous health benefits including the extension of human and animal lifespans. Background: There is evidence, obtained both with animal model systems and with humans, that intermittent fasting has health benefits. These benefits include extended longevity, weight loss, and counteracting various disease conditions. Such procedures positively influence the benefits of human tissue-specific microbiomes and minimize the consequences of organellar apoptosis. Key Messages: In this review, we attempt to summarize the predominant evidence, published in the scientific literature, relevant to the conclusions that in general, and in many specific instances, intermittent fasting has long-term benefits to animals, including humans, with respect to overall and specific organismal health and longevity.
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Affiliation(s)
- B. Lakshmi Reddy
- Department of Molecular Biology, University of California at San Diego 9500 Gilman Dr. La Jolla, CA 92093-0116 USA
| | | | - Milton H. Saier
- Department of Molecular Biology, University of California at San Diego 9500 Gilman Dr. La Jolla, CA 92093-0116 USA
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278
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Kolski-Andreaco A, Taiclet S, Myerburg MM, Sembrat J, Bridges RJ, Straub AC, Wills ZP, Butterworth MB, Devor DC. Potentiation of BKCa channels by cystic fibrosis transmembrane conductance regulator correctors VX-445 and VX-121. J Clin Invest 2024; 134:e176328. [PMID: 38954478 PMCID: PMC11324306 DOI: 10.1172/jci176328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
Cystic fibrosis results from mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel, ultimately leading to diminished transepithelial anion secretion and mucociliary clearance. CFTR correctors are therapeutics that restore the folding/trafficking of mutated CFTR to the plasma membrane. The large-conductance calcium-activated potassium channel (BKCa, KCa1.1) is also critical for maintaining lung airway surface liquid (ASL) volume. Here, we show that the class 2 (C2) CFTR corrector VX-445 (elexacaftor) induces K+ secretion across WT and F508del CFTR primary human bronchial epithelial cells (HBEs), which was entirely inhibited by the BKCa antagonist paxilline. Similar results were observed with VX-121, a corrector under clinical evaluation. Whole-cell patch-clamp recordings verified that CFTR correctors potentiated BKCa activity from both primary HBEs and HEK cells stably expressing the α subunit (HEK-BK cells). Furthermore, excised patch-clamp recordings from HEK-BK cells verified direct action on the channel and demonstrated a significant increase in open probability. In mouse mesenteric artery, VX-445 induced a paxilline-sensitive vasorelaxation of preconstricted arteries. VX-445 also reduced firing frequency in primary rat hippocampal and cortical neurons. We raise the possibilities that C2 CFTR correctors gain additional clinical benefit by activation of BKCa in the lung yet may lead to adverse events through BKCa activation elsewhere.
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Affiliation(s)
| | | | - Michael M. Myerburg
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John Sembrat
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Robert J. Bridges
- Department of Physiology and Biophysics, Chicago Medical School, North Chicago, Illinois, USA
| | | | - Zachary P. Wills
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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279
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Kunes RZ, Walle T, Land M, Nawy T, Pe'er D. Supervised discovery of interpretable gene programs from single-cell data. Nat Biotechnol 2024; 42:1084-1095. [PMID: 37735262 PMCID: PMC10958532 DOI: 10.1038/s41587-023-01940-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 08/09/2023] [Indexed: 09/23/2023]
Abstract
Factor analysis decomposes single-cell gene expression data into a minimal set of gene programs that correspond to processes executed by cells in a sample. However, matrix factorization methods are prone to technical artifacts and poor factor interpretability. We address these concerns with Spectra, an algorithm that combines user-provided gene programs with the detection of novel programs that together best explain expression covariation. Spectra incorporates existing gene sets and cell-type labels as prior biological information, explicitly models cell type and represents input gene sets as a gene-gene knowledge graph using a penalty function to guide factorization toward the input graph. We show that Spectra outperforms existing approaches in challenging tumor immune contexts, as it finds factors that change under immune checkpoint therapy, disentangles the highly correlated features of CD8+ T cell tumor reactivity and exhaustion, finds a program that explains continuous macrophage state changes under therapy and identifies cell-type-specific immune metabolic programs.
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Affiliation(s)
- Russell Z Kunes
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Statistics, Columbia University, New York, NY, USA
| | - Thomas Walle
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Max Land
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tal Nawy
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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280
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Jiang L, Han D, Hao Y, Song Z, Sun Z, Dai Z. Linking serotonin homeostasis to gut function: Nutrition, gut microbiota and beyond. Crit Rev Food Sci Nutr 2024; 64:7291-7310. [PMID: 36861222 DOI: 10.1080/10408398.2023.2183935] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Serotonin (5-HT) produced by enterochromaffin (EC) cells in the digestive tract is crucial for maintaining gut function and homeostasis. Nutritional and non-nutritional stimuli in the gut lumen can modulate the ability of EC cells to produce 5-HT in a temporal- and spatial-specific manner that toning gut physiology and immune response. Of particular interest, the interactions between dietary factors and the gut microbiota exert distinct impacts on gut 5-HT homeostasis and signaling in metabolism and the gut immune response. However, the underlying mechanisms need to be unraveled. This review aims to summarize and discuss the importance of gut 5-HT homeostasis and its regulation in maintaining gut metabolism and immune function in health and disease with special emphasis on different types of nutrients, dietary supplements, processing, and gut microbiota. Cutting-edge discoveries in this area will provide the basis for the development of new nutritional and pharmaceutical strategies for the prevention and treatment of serotonin homeostasis-related gut and systematic disorders and diseases.
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Affiliation(s)
- Lili Jiang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China
| | - Dandan Han
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China
| | - Youling Hao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China
| | - Zhuan Song
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China
| | - Zhiyuan Sun
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China
| | - Zhaolai Dai
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China
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281
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Yang J, Xiao Y, Zhao N, Pei G, Sun Y, Sun X, Yu K, Miao C, Liu R, Lv J, Chu H, Zhou L, Wang B, Yao Z, Wang Q. PIM1-HDAC2 axis modulates intestinal homeostasis through epigenetic modification. Acta Pharm Sin B 2024; 14:3049-3067. [PMID: 39027246 PMCID: PMC11252454 DOI: 10.1016/j.apsb.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/07/2024] [Accepted: 03/14/2024] [Indexed: 07/20/2024] Open
Abstract
The mucosal barrier is crucial for intestinal homeostasis, and goblet cells are essential for maintaining the mucosal barrier integrity. The proviral integration site for Moloney murine leukemia virus-1 (PIM1) kinase regulates multiple cellular functions, but its role in intestinal homeostasis during colitis is unknown. Here, we demonstrate that PIM1 is prominently elevated in the colonic epithelia of both ulcerative colitis patients and murine models, in the presence of intestinal microbiota. Epithelial PIM1 leads to decreased goblet cells, thus impairing resistance to colitis and colitis-associated colorectal cancer (CAC) in mice. Mechanistically, PIM1 modulates goblet cell differentiation through the Wnt and Notch signaling pathways. Interestingly, PIM1 interacts with histone deacetylase 2 (HDAC2) and downregulates its level via phosphorylation, thereby altering the epigenetic profiles of Wnt signaling pathway genes. Collectively, these findings investigate the unknown function of the PIM1-HDAC2 axis in goblet cell differentiation and ulcerative colitis/CAC pathogenesis, which points to the potential for PIM1-targeted therapies of ulcerative colitis and CAC.
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Affiliation(s)
- Jianming Yang
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Institute of Immunology, State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Immunology, School of Basic Medical Sciences, Tianjin Institute of Urology, the Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China
| | - Yawen Xiao
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Institute of Immunology, State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Immunology, School of Basic Medical Sciences, Tianjin Institute of Urology, the Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China
| | - Ningning Zhao
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Institute of Immunology, State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Immunology, School of Basic Medical Sciences, Tianjin Institute of Urology, the Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China
| | - Geng Pei
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center of Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center of Cancer, Tianjin 30060, China
| | - Yan Sun
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center of Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center of Cancer, Tianjin 30060, China
| | - Xinyu Sun
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Institute of Immunology, State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Immunology, School of Basic Medical Sciences, Tianjin Institute of Urology, the Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China
| | - Kaiyuan Yu
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Institute of Immunology, State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Immunology, School of Basic Medical Sciences, Tianjin Institute of Urology, the Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China
| | - Chunhui Miao
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Institute of Immunology, State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Immunology, School of Basic Medical Sciences, Tianjin Institute of Urology, the Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China
| | - Ran Liu
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Institute of Immunology, State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Immunology, School of Basic Medical Sciences, Tianjin Institute of Urology, the Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China
| | - Junqiang Lv
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Institute of Immunology, State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Immunology, School of Basic Medical Sciences, Tianjin Institute of Urology, the Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China
| | - Hongyu Chu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Lu Zhou
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Zhi Yao
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Institute of Immunology, State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Immunology, School of Basic Medical Sciences, Tianjin Institute of Urology, the Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China
| | - Quan Wang
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Institute of Immunology, State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Immunology, School of Basic Medical Sciences, Tianjin Institute of Urology, the Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China
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282
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Atreya R, Neurath MF. Biomarkers for Personalizing IBD Therapy: The Quest Continues. Clin Gastroenterol Hepatol 2024; 22:1353-1364. [PMID: 38320679 DOI: 10.1016/j.cgh.2024.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/08/2024]
Abstract
Despite recent advances in the understanding of the pathogenesis of inflammatory bowel diseases (IBD) and advent of multiple targeted therapies, approximately one-third of patients are primary non-responders to initiated treatment, and half of patients lose response over time. There is currently a lack of available biomarkers that would prognosticate therapeutic effectiveness of these advanced therapies. This is partly explained by insufficient characterization of the functional roles assumed by the chosen molecular targets during disease treatment. There is a dire need for validated objective biomarkers, which could be indicators of a biological process, that can be applied in clinical practice to assist us in assigning therapies to patients with the highest probability of response. An appropriate molecular and cellular characterization that accounts for the interindividual differences in drug efficacy and potential side effects would help to guide clinicians in the management of patients with IBD and represent a major step to tailor a more personalized approach to treatment. An appropriate combination of complementing biomarkers should ideally incorporate a multimodal analysis in which genetic, microbial, transcriptional, proteomic, metabolic, and immunologic data are combined to enable a truly personalized approach. This would classify patients into disease subgroups according to molecular characteristics, which would enable us to initiate the most appropriate therapeutic substance. Emergence of single-cell technologies to map the intestinal cellular landscape and multiomic approaches have helped to further dissect the pathogenic mechanisms of mucosal inflammation, but the clinical translation of potential biomarkers remains cumbersome, and an ongoing concerted effort by the IBD community is required.
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Affiliation(s)
- Raja Atreya
- First Department of Medicine, Erlangen University Hospital, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany.
| | - Markus F Neurath
- First Department of Medicine, Erlangen University Hospital, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
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283
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Ooi E, Xiang R, Chamberlain AJ, Goddard ME. Archetypal clustering reveals physiological mechanisms linking milk yield and fertility in dairy cattle. J Dairy Sci 2024; 107:4726-4742. [PMID: 38369117 DOI: 10.3168/jds.2023-23699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024]
Abstract
Fertility in dairy cattle has declined as an unintended consequence of single-trait selection for high milk yield. The unfavorable genetic correlation between milk yield and fertility is now well documented; however, the underlying physiological mechanisms are still uncertain. To understand the relationship between these traits, we developed a method that clusters variants with similar patterns of effects and, after the integration of gene expression data, identifies the genes through which they are likely to act. Biological processes that are enriched in the genes of each cluster were then identified. We identified several clusters with unique patterns of effects. One of the clusters included variants associated with increased milk yield and decreased fertility, where the "archetypal" variant (i.e., the one with the largest effect) was associated with the GC gene, whereas others were associated with TRIM32, LRRK2, and U6-associated snRNA. These genes have been linked to transcription and alternative splicing, suggesting that these processes are likely contributors to the unfavorable relationship between the 2 traits. Another cluster, with archetypal variant near DGAT1 and including variants associated with CDH2, BTRC, SFRP2, ZFHX3, and SLITRK5, appeared to affect milk yield but have little effect on fertility. These genes have been linked to insulin, adipose tissue, and energy metabolism. A third cluster with archetypal variant near ZNF613 and including variants associated with ROBO1, EFNA5, PALLD, GPC6, and PTPRT were associated with fertility but not milk yield. These genes have been linked to GnRH neuronal migration, embryonic development, or ovarian function. The use of archetypal clustering to group variants with similar patterns of effects may assist in identifying the biological processes underlying correlated traits. The method is hypothesis generating and requires experimental confirmation. However, we have uncovered several novel mechanisms potentially affecting milk production and fertility such as GnRH neuronal migration. We anticipate our method to be a starting point for experimental research into novel pathways, which have been previously unexplored within the context of dairy production.
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Affiliation(s)
- E Ooi
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria 3010, Australia; Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia.
| | - R Xiang
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria 3010, Australia; Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia
| | - A J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
| | - M E Goddard
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria 3010, Australia; Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia
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284
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Pellowe AS, Wu MJ, Kang TY, Chung TD, Ledesma-Mendoza A, Herzog E, Levchenko A, Odell I, Varga J, Gonzalez AL. TGF-β1 Drives Integrin-Dependent Pericyte Migration and Microvascular Destabilization in Fibrotic Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:1171-1184. [PMID: 38548268 PMCID: PMC11220919 DOI: 10.1016/j.ajpath.2024.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/08/2024] [Accepted: 02/21/2024] [Indexed: 04/10/2024]
Abstract
Interactions between endothelial cells (ECs) and mural pericytes (PCs) are critical in maintaining the stability and function of the microvascular wall. Abnormal interactions between these two cell types are a hallmark of progressive fibrotic diseases such as systemic sclerosis (also known as scleroderma). However, the role of PCs in signaling microvascular dysfunction remains underexplored. We hypothesized that integrin-matrix interactions contribute to PC migration from the vascular wall and conversion into interstitial myofibroblasts. Herein, pro-inflammatory tumor necrosis factor α (TNFα) or a fibrotic growth factor [transforming growth factor β1 (TGF-β1)] were used to evaluate human PC inflammatory and fibrotic phenotypes by assessing their migration, matrix deposition, integrin expression, and subsequent effects on endothelial dysfunction. Both TNFα and TGF-β1 treatment altered integrin expression and matrix protein deposition, but only fibrotic TGF-β1 drove PC migration in an integrin-dependent manner. In addition, integrin-dependent PC migration was correlated to changes in EC angiopoietin-2 levels, a marker of vascular instability. Finally, there was evidence of changes in vascular stability corresponding to disease state in human systemic sclerosis skin. This work shows that TNFα and TGF-β1 induce changes in PC integrin expression and matrix deposition that facilitate migration and reduce vascular stability, providing evidence that microvascular destabilization can be an early indicator of tissue fibrosis.
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Affiliation(s)
- Amanda S Pellowe
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Michelle J Wu
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Tae-Yun Kang
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Tracy D Chung
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | | | - Erica Herzog
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Andre Levchenko
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Ian Odell
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut
| | - John Varga
- Michigan Scleroderma Program, Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Anjelica L Gonzalez
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut.
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285
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Sun Q, Li H, Lv J, Shi W, Bai Y, Pan K, Chen A. Dopamine β-hydroxylase shapes intestinal inflammation through modulating T cell activation. Cell Immunol 2024; 401-402:104839. [PMID: 38850753 DOI: 10.1016/j.cellimm.2024.104839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a chronic and relapsing disease characterized by immune-mediated dysfunction of intestinal homeostasis. Alteration of the enteric nervous system and the subsequent neuro-immune interaction are thought to contribute to the initiation and progression of IBD. However, the role of dopamine beta-hydroxylase (DBH), an enzyme converting dopamine into norepinephrine, in modulating intestinal inflammation is not well defined. METHODS CD4+CD45RBhighT cell adoptive transfer, and 2,4-dinitrobenzene sulfonic acid (DNBS) or dextran sodium sulfate (DSS)-induced colitis were collectively conducted to uncover the effects of DBH inhibition by nepicastat, a DBH inhibitor, in mucosal ulceration, disease severity, and T cell function. RESULTS Inhibition of DBH by nepicastat triggered therapeutic effects on T cell adoptive transfer induced chronic mouse colitis model, which was consistent with the gene expression of DBH in multiple cell populations including T cells. Furthermore, DBH inhibition dramatically ameliorated the disease activity and colon shortening in chemically induced acute and chronic IBD models, as evidenced by morphological and histological examinations. The reshaped systemic inflammatory status was largely associated with decreased pro-inflammatory mediators, such as TNF-α, IL-6 and IFN-γ in plasma and re-balanced Th1, Th17 and Tregs in mesenteric lymph nodes (MLNs) upon colitis progression. Additionally, the conversion from dopamine (DA) to norepinephrine (NE) was inhibited resulting in increase in DA level and decrease in NE level and DA/NE showed immune-modulatory effects on the activation of immune cells. CONCLUSION Modulation of neurotransmitter levels via inhibition of DBH exerted protective effects on progression of murine colitis by modulating the neuro-immune axis. These findings suggested a promising new therapeutic strategy for attenuating intestinal inflammation.
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Affiliation(s)
- Qiaoling Sun
- Asieris Pharmaceuticals Co., Ltd, Shanghai, China.
| | - Heng Li
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117456, Singapore
| | - Jing Lv
- Asieris Pharmaceuticals Co., Ltd, Shanghai, China
| | - Weilin Shi
- Asieris Pharmaceuticals Co., Ltd, Shanghai, China
| | - Yanfeng Bai
- Asieris Pharmaceuticals Co., Ltd, Shanghai, China
| | - Ke Pan
- Asieris Pharmaceuticals Co., Ltd, Shanghai, China
| | - Alice Chen
- Asieris Pharmaceuticals Co., Ltd, Palo Alto, CA, USA.
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286
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Xiu Z, Sun L, Liu K, Cao H, Qu HQ, Glessner JT, Ding Z, Zheng G, Wang N, Xia Q, Li J, Li MJ, Hakonarson H, Liu W, Li J. Shared molecular mechanisms and transdiagnostic potential of neurodevelopmental disorders and immune disorders. Brain Behav Immun 2024; 119:767-780. [PMID: 38677625 DOI: 10.1016/j.bbi.2024.04.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/27/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024] Open
Abstract
The co-occurrence and familial clustering of neurodevelopmental disorders and immune disorders suggest shared genetic risk factors. Based on genome-wide association summary statistics from five neurodevelopmental disorders and four immune disorders, we conducted genome-wide, local genetic correlation and polygenic overlap analysis. We further performed a cross-trait GWAS meta-analysis. Pleotropic loci shared between the two categories of diseases were mapped to candidate genes using multiple algorithms and approaches. Significant genetic correlations were observed between neurodevelopmental disorders and immune disorders, including both positive and negative correlations. Neurodevelopmental disorders exhibited higher polygenicity compared to immune disorders. Around 50%-90% of genetic variants of the immune disorders were shared with neurodevelopmental disorders. The cross-trait meta-analysis revealed 154 genome-wide significant loci, including 8 novel pleiotropic loci. Significant associations were observed for 30 loci with both types of diseases. Pathway analysis on the candidate genes at these loci revealed common pathways shared by the two types of diseases, including neural signaling, inflammatory response, and PI3K-Akt signaling pathway. In addition, 26 of the 30 lead SNPs were associated with blood cell traits. Neurodevelopmental disorders exhibit complex polygenic architecture, with a subset of individuals being at a heightened genetic risk for both neurodevelopmental and immune disorders. The identification of pleiotropic loci has important implications for exploring opportunities for drug repurposing, enabling more accurate patient stratification, and advancing genomics-informed precision in the medical field of neurodevelopmental disorders.
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Affiliation(s)
- Zhanjie Xiu
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ling Sun
- Department of Child and Adolescent Psychology, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin, China
| | - Kunlun Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Haiyan Cao
- Department of Child and Adolescent Psychology, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin, China
| | - Hui-Qi Qu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Joseph T Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Zhiyong Ding
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Jinan, China
| | - Gang Zheng
- National Supercomputer Center in Tianjin (NSCC-TJ), Tianjin, China
| | - Nan Wang
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Jinan, China
| | - Qianghua Xia
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jie Li
- Laboratory of Biological Psychiatry, Institute of Mental Health, Tianjin Anding Hospital, Tianjin Medical University, Tianjin, China
| | - Mulin Jun Li
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| | - Wei Liu
- Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China; Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China.
| | - Jin Li
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Rheumatology and Immunology, Tianjin Medical University General Hospital, Tianjin, China.
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287
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Tessmann JW, Deng P, Durham J, Li C, Banerjee M, Wang Q, Goettl RA, He D, Wang C, Lee EY, Evers BM, Hennig B, Zaytseva YY. Perfluorooctanesulfonic acid exposure leads to downregulation of 3-hydroxy-3-methylglutaryl-CoA synthase 2 expression and upregulation of markers associated with intestinal carcinogenesis in mouse intestinal tissues. CHEMOSPHERE 2024; 359:142332. [PMID: 38754493 PMCID: PMC11157449 DOI: 10.1016/j.chemosphere.2024.142332] [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: 02/06/2024] [Revised: 05/06/2024] [Accepted: 05/12/2024] [Indexed: 05/18/2024]
Abstract
Perfluorooctanesulfonic acid (PFOS) is a widely recognized environment pollutant known for its high bioaccumulation potential and a long elimination half-life. Several studies have shown that PFOS can alter multiple biological pathways and negatively affect human health. Considering the direct exposure to the gastrointestinal (GI) tract to environmental pollutants, PFOS can potentially disrupt intestinal homeostasis. However, there is limited knowledge about the effect of PFOS exposure on normal intestinal tissues, and its contribution to GI-associated diseases remains to be determined. In this study, we examined the effect of PFOS exposure on the gene expression profile of intestinal tissues of C57BL/6 mice using RNAseq analysis. We found that PFOS exposure in drinking water significantly downregulates mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), a rate-limiting ketogenic enzyme, in intestinal tissues of mice. We found that diets containing the soluble fibers inulin and pectin, which are known to be protective against PFOS exposure, were ineffective in reversing the downregulation of HMGCS2 expression in vivo. Analysis of intestinal tissues also demonstrated that PFOS exposure leads to upregulation of proteins implicated in colorectal carcinogenesis, including β-catenin, c-MYC, mTOR and FASN. Consistent with the in vivo results, PFOS exposure leads to downregulation of HMGCS2 in mouse and human normal intestinal organoids in vitro. Furthermore, we show that shRNA-mediated knockdown of HMGCS2 in a human normal intestinal cell line resulted in increased cell proliferation and upregulation of key proliferation-associated proteins such as cyclin D, survivin, ERK1/2 and AKT, along with an increase in lipid accumulation. In summary, our results suggest that PFOS exposure may contribute to pathological changes in normal intestinal cells via downregulation of HMGCS2 expression and upregulation of pro-carcinogenic signaling pathways that may increase the risk of colorectal cancer development.
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Affiliation(s)
- Josiane Weber Tessmann
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA.
| | - Pan Deng
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China.
| | - Jerika Durham
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA.
| | - Chang Li
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA.
| | - Moumita Banerjee
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA.
| | - Qingding Wang
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA.
| | - Ryan A Goettl
- Markey Cancer Center Biostatistics and Bioinformatics Shared Resource Facility, University of Kentucky, Lexington, KY 40536, USA.
| | - Daheng He
- Markey Cancer Center Biostatistics and Bioinformatics Shared Resource Facility, University of Kentucky, Lexington, KY 40536, USA.
| | - Chi Wang
- Markey Cancer Center Biostatistics and Bioinformatics Shared Resource Facility, University of Kentucky, Lexington, KY 40536, USA.
| | - Eun Y Lee
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY 40536, USA.
| | - B Mark Evers
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA.
| | - Bernhard Hennig
- Department of Animal and Food Sciences, University of Kentucky, Lexington, KY 40536, USA.
| | - Yekaterina Y Zaytseva
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA.
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288
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Kubota S, Sun Y, Morii M, Bai J, Ideue T, Hirayama M, Sorin S, Eerdunduleng, Yokomizo-Nakano T, Osato M, Hamashima A, Iimori M, Araki K, Umemoto T, Sashida G. Chromatin modifier Hmga2 promotes adult hematopoietic stem cell function and blood regeneration in stress conditions. EMBO J 2024; 43:2661-2684. [PMID: 38811851 PMCID: PMC11217491 DOI: 10.1038/s44318-024-00122-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/31/2024] Open
Abstract
The molecular mechanisms governing the response of hematopoietic stem cells (HSCs) to stress insults remain poorly defined. Here, we investigated effects of conditional knock-out or overexpression of Hmga2 (High mobility group AT-hook 2), a transcriptional activator of stem cell genes in fetal HSCs. While Hmga2 overexpression did not affect adult hematopoiesis under homeostasis, it accelerated HSC expansion in response to injection with 5-fluorouracil (5-FU) or in vitro treatment with TNF-α. In contrast, HSC and megakaryocyte progenitor cell numbers were decreased in Hmga2 KO animals. Transcription of inflammatory genes was repressed in Hmga2-overexpressing mice injected with 5-FU, and Hmga2 bound to distinct regions and chromatin accessibility was decreased in HSCs upon stress. Mechanistically, we found that casein kinase 2 (CK2) phosphorylates the Hmga2 acidic domain, promoting its access and binding to chromatin, transcription of anti-inflammatory target genes, and the expansion of HSCs under stress conditions. Notably, the identified stress-regulated Hmga2 gene signature is activated in hematopoietic stem progenitor cells of human myelodysplastic syndrome patients. In sum, these results reveal a TNF-α/CK2/phospho-Hmga2 axis controlling adult stress hematopoiesis.
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Affiliation(s)
- Sho Kubota
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Department of Medicinal Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Yuqi Sun
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Department of Hematology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Mariko Morii
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jie Bai
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takako Ideue
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Mayumi Hirayama
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Supannika Sorin
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Eerdunduleng
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takako Yokomizo-Nakano
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Motomi Osato
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Department of General Internal Medicine, Kumamoto Kenhoku Hospital, Kumamoto, Japan
| | - Ai Hamashima
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Mihoko Iimori
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
- Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
| | - Terumasa Umemoto
- Laboratory of Hematopoietic Stem Cell Engineering, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Goro Sashida
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.
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289
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Korkmaz FT, Quinton LJ. Extra-pulmonary control of respiratory defense. Cell Immunol 2024; 401-402:104841. [PMID: 38878619 DOI: 10.1016/j.cellimm.2024.104841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 06/06/2024] [Indexed: 07/13/2024]
Abstract
Pneumonia persists as a public health crisis, representing the leading cause of death due to infection. Whether respiratory tract infections progress to pneumonia and its sequelae such as acute respiratory distress syndrome and sepsis depends on numerous underlying conditions related to both the causative agent and host. Regarding the former, pneumonia burden remains staggeringly high, despite the effectiveness of pathogen-targeting strategies such as vaccines and antibiotics. This demands a greater understanding of host features that collaborate to promote immune resistance and tissue resilience in the infected lung. Such features inside the pulmonary compartment have drawn much attention, where major advances have been made related to resident and recruited immune activity. By comparison, extra-pulmonary processes guiding pneumonia susceptibility are relatively elusive, constituting the focus of this review. Here we will highlight examples of when, how, and why tissues outside of the lungs dispatch signals that modulate local immunity in the airspaces. Topics include the liver, gut, bone marrow, brain and more, all of which contribute in direct and indirect ways to pneumonia outcome. When tuned appropriately, it has become clear that these responses can serve protective roles, and this will be considered distinctly from what would otherwise be aberrant responses characteristic of pneumonia-induced organ injury and sepsis. Further advances in this area may reveal novel targetable areas for clinical intervention that are not confined to the intra-pulmonary space.
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Affiliation(s)
- Filiz T Korkmaz
- Department of Medicine, Division of Immunology and Infectious Disease, UMass Chan Medical School, Worcester, MA 01602, United States.
| | - Lee J Quinton
- Department of Medicine, Division of Immunology and Infectious Disease, UMass Chan Medical School, Worcester, MA 01602, United States
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290
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Weiler P, Lange M, Klein M, Pe'er D, Theis F. CellRank 2: unified fate mapping in multiview single-cell data. Nat Methods 2024; 21:1196-1205. [PMID: 38871986 PMCID: PMC11239496 DOI: 10.1038/s41592-024-02303-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/09/2024] [Indexed: 06/15/2024]
Abstract
Single-cell RNA sequencing allows us to model cellular state dynamics and fate decisions using expression similarity or RNA velocity to reconstruct state-change trajectories; however, trajectory inference does not incorporate valuable time point information or utilize additional modalities, whereas methods that address these different data views cannot be combined or do not scale. Here we present CellRank 2, a versatile and scalable framework to study cellular fate using multiview single-cell data of up to millions of cells in a unified fashion. CellRank 2 consistently recovers terminal states and fate probabilities across data modalities in human hematopoiesis and endodermal development. Our framework also allows combining transitions within and across experimental time points, a feature we use to recover genes promoting medullary thymic epithelial cell formation during pharyngeal endoderm development. Moreover, we enable estimating cell-specific transcription and degradation rates from metabolic-labeling data, which we apply to an intestinal organoid system to delineate differentiation trajectories and pinpoint regulatory strategies.
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Affiliation(s)
- Philipp Weiler
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
| | - Marius Lange
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michal Klein
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Machine Learning Research, Apple, Paris, France
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Fabian Theis
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany.
- School of Computation, Information and Technology, Technical University of Munich, Munich, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
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291
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Holder AM, Dedeilia A, Sierra-Davidson K, Cohen S, Liu D, Parikh A, Boland GM. Defining clinically useful biomarkers of immune checkpoint inhibitors in solid tumours. Nat Rev Cancer 2024; 24:498-512. [PMID: 38867074 DOI: 10.1038/s41568-024-00705-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 06/14/2024]
Abstract
Although more than a decade has passed since the approval of immune checkpoint inhibitors (ICIs) for the treatment of melanoma and non-small-cell lung, breast and gastrointestinal cancers, many patients still show limited response. US Food and Drug Administration (FDA)-approved biomarkers include programmed cell death 1 ligand 1 (PDL1) expression, microsatellite status (that is, microsatellite instability-high (MSI-H)) and tumour mutational burden (TMB), but these have limited utility and/or lack standardized testing approaches for pan-cancer applications. Tissue-based analytes (such as tumour gene signatures, tumour antigen presentation or tumour microenvironment profiles) show a correlation with immune response, but equally, these demonstrate limited efficacy, as they represent a single time point and a single spatial assessment. Patient heterogeneity as well as inter- and intra-tumoural differences across different tissue sites and time points represent substantial challenges for static biomarkers. However, dynamic biomarkers such as longitudinal biopsies or novel, less-invasive markers such as blood-based biomarkers, radiomics and the gut microbiome show increasing potential for the dynamic identification of ICI response, and patient-tailored predictors identified through neoadjuvant trials or novel ex vivo tumour models can help to personalize treatment. In this Perspective, we critically assess the multiple new static, dynamic and patient-specific biomarkers, highlight the newest consortia and trial efforts, and provide recommendations for future clinical trials to make meaningful steps forwards in the field.
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Affiliation(s)
- Ashley M Holder
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Sonia Cohen
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - David Liu
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Aparna Parikh
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Genevieve M Boland
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
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292
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Verhagen MP, Joosten R, Schmitt M, Välimäki N, Sacchetti A, Rajamäki K, Choi J, Procopio P, Silva S, van der Steen B, van den Bosch TPP, Seinstra D, de Vries AC, Doukas M, Augenlicht LH, Aaltonen LA, Fodde R. Non-stem cell lineages as an alternative origin of intestinal tumorigenesis in the context of inflammation. Nat Genet 2024; 56:1456-1467. [PMID: 38902475 PMCID: PMC11250264 DOI: 10.1038/s41588-024-01801-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/15/2024] [Indexed: 06/22/2024]
Abstract
According to conventional views, colon cancer originates from stem cells. However, inflammation, a key risk factor for colon cancer, has been shown to suppress intestinal stemness. Here, we used Paneth cells as a model to assess the capacity of differentiated lineages to trigger tumorigenesis in the context of inflammation in mice. Upon inflammation, Paneth cell-specific Apc mutations led to intestinal tumors reminiscent not only of those arising in patients with inflammatory bowel disease, but also of a larger fraction of human sporadic colon cancers. The latter is possibly because of the inflammatory consequences of western-style dietary habits, a major colon cancer risk factor. Machine learning methods designed to predict the cell-of-origin of cancer from patient-derived tumor samples confirmed that, in a substantial fraction of sporadic cases, the origins of colon cancer reside in secretory lineages and not in stem cells.
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Affiliation(s)
- Mathijs P Verhagen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Rosalie Joosten
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mark Schmitt
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Institute of Pharmacology, University of Marburg, Marburg, Germany
| | - Niko Välimäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Andrea Sacchetti
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kristiina Rajamäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Jiahn Choi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Paola Procopio
- Institute of Pharmacology, University of Marburg, Marburg, Germany
| | - Sara Silva
- Institute of Pharmacology, University of Marburg, Marburg, Germany
| | - Berdine van der Steen
- Department of Otorhinolaryngology and Head & Neck Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Danielle Seinstra
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Annemarie C de Vries
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Michail Doukas
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Leonard H Augenlicht
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Riccardo Fodde
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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293
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Hu M, Chikina M. InstaPrism: an R package for fast implementation of BayesPrism. Bioinformatics 2024; 40:btae440. [PMID: 38970377 PMCID: PMC11245312 DOI: 10.1093/bioinformatics/btae440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/26/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024] Open
Abstract
SUMMARY Computational cell-type deconvolution is an important analytic technique for modeling the compositional heterogeneity of bulk gene expression data. A conceptually new Bayesian approach to this problem, BayesPrism, has recently been proposed and has subsequently been shown to be superior in accuracy and robustness against model misspecifications by independent studies; however, given that BayesPrism relies on Gibbs sampling, it is orders of magnitude more computationally expensive than standard approaches. Here, we introduce the InstaPrism package which re-implements BayesPrism in a derandomized framework by replacing the time-consuming Gibbs sampling step with a fixed-point algorithm. We demonstrate that the new algorithm is effectively equivalent to BayesPrism while providing a considerable speed and memory advantage. Furthermore, the InstaPrism package is equipped with a precompiled, curated set of references tailored for a variety of cancer types, streamlining the deconvolution process. AVAILABILITY AND IMPLEMENTATION The package InstaPrism is freely available at: https://github.com/humengying0907/InstaPrism. The source code and evaluation pipeline used in this paper can be found at: https://github.com/humengying0907/InstaPrismSourceCode.
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Affiliation(s)
- Mengying Hu
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, 15260, United States
- Joint Carnegie Mellon - University of Pittsburgh Computational Biology PhD Program, University of Pittsburgh, Pittsburgh, 15260, United States
| | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, 15260, United States
- Joint Carnegie Mellon - University of Pittsburgh Computational Biology PhD Program, University of Pittsburgh, Pittsburgh, 15260, United States
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294
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Li Y, Ramírez-Suástegui C, Harris R, Castañeda-Castro FE, Ascui G, Pérez-Jeldres T, Diaz A, Morong C, Giles DA, Chai J, Seumois G, Sanchez-Elsner T, Cummings F, Kronenberg M, Vijayanand P. Stem-like T cells are associated with the pathogenesis of ulcerative colitis in humans. Nat Immunol 2024; 25:1231-1244. [PMID: 38898157 DOI: 10.1038/s41590-024-01860-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 05/01/2024] [Indexed: 06/21/2024]
Abstract
To understand the role of T cells in the pathogenesis of ulcerative colitis (UC), we analyzed colonic T cells isolated from patients with UC and controls. Here we identified colonic CD4+ and CD8+ T lymphocyte subsets with gene expression profiles resembling stem-like progenitors, previously reported in several mouse models of autoimmune disease. Stem-like T cells were increased in inflamed areas compared to non-inflamed regions from the same patients. Furthermore, TCR sequence analysis indicated stem-like T cells were clonally related to proinflammatory T cells, suggesting their involvement in sustaining effectors that drive inflammation. Using an adoptive transfer colitis model in mice, we demonstrated that CD4+ T cells deficient in either BCL-6 or TCF1, transcription factors that promote T cell stemness, had decreased colon T cells and diminished pathogenicity. Our results establish a strong association between stem-like T cell populations and UC pathogenesis, highlighting the potential of targeting this population to improve clinical outcomes.
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Affiliation(s)
- Yingcong Li
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Richard Harris
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Gabriel Ascui
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Tamara Pérez-Jeldres
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Alejandro Diaz
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Carla Morong
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Daniel A Giles
- La Jolla Institute for Immunology, La Jolla, CA, USA
- Lineage Therapeutics, Carlsbad, CA, USA
| | - Jiani Chai
- La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Pathology, Albert Einstein Medical College, New York, NY, USA
| | | | - Tilman Sanchez-Elsner
- Department of Gastroenterology, University Hospital Southampton NHS FT, Southampton, UK
| | - Fraser Cummings
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Department of Gastroenterology, University Hospital Southampton NHS FT, Southampton, UK
| | - Mitchell Kronenberg
- La Jolla Institute for Immunology, La Jolla, CA, USA.
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA.
| | - Pandurangan Vijayanand
- La Jolla Institute for Immunology, La Jolla, CA, USA.
- Department of Medicine, University of California, San Diego, San Diego, CA, USA.
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
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295
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Francis L, Capon F, Smith CH, Haniffa M, Mahil SK. Inflammatory memory in psoriasis: From remission to recurrence. J Allergy Clin Immunol 2024; 154:42-50. [PMID: 38761994 DOI: 10.1016/j.jaci.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
The routine use of targeted systemic immunomodulatory therapies has transformed outcomes for people with severe psoriasis, with skin clearance (clinical remission) rates up to 60% at 1 year of biologic treatment. However, psoriasis may recur following drug withdrawal, and as a result, patients tend to continue receiving costly treatment indefinitely. Here, we review research into the "inflammatory memory" in resolved psoriasis skin and the potential mechanisms leading to psoriasis recurrence following drug withdrawal. Research has implicated immune cells such as tissue resident memory T cells, Langerhans cells, and dermal dendritic cells, and there is growing interest in keratinocytes and fibroblasts. A better understanding of the interactions between these cell populations, enabled by single cell technologies, will help to elucidate the events underpinning the shift from remission to recurrence. This may inform the development of personalized strategies for sustaining remission while reducing long-term drug burden.
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Affiliation(s)
- Luc Francis
- St John's Institute of Dermatology, King's College London and Guy's & St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Francesca Capon
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Catherine H Smith
- St John's Institute of Dermatology, King's College London and Guy's & St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom; Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Satveer K Mahil
- St John's Institute of Dermatology, King's College London and Guy's & St Thomas' NHS Foundation Trust, London, United Kingdom.
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296
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Chiou S, Al-Ani AH, Pan Y, Patel KM, Kong IY, Whitehead LW, Light A, Young SN, Barrios M, Sargeant C, Rajasekhar P, Zhu L, Hempel A, Lin A, Rickard JA, Hall C, Gangatirkar P, Yip RK, Cawthorne W, Jacobsen AV, Horne CR, Martin KR, Ioannidis LJ, Hansen DS, Day J, Wicks IP, Law C, Ritchie ME, Bowden R, Hildebrand JM, O'Reilly LA, Silke J, Giulino-Roth L, Tsui E, Rogers KL, Hawkins ED, Christensen B, Murphy JM, Samson AL. An immunohistochemical atlas of necroptotic pathway expression. EMBO Mol Med 2024; 16:1717-1749. [PMID: 38750308 PMCID: PMC11250867 DOI: 10.1038/s44321-024-00074-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 06/12/2024] Open
Abstract
Necroptosis is a lytic form of regulated cell death reported to contribute to inflammatory diseases of the gut, skin and lung, as well as ischemic-reperfusion injuries of the kidney, heart and brain. However, precise identification of the cells and tissues that undergo necroptotic cell death in vivo has proven challenging in the absence of robust protocols for immunohistochemical detection. Here, we provide automated immunohistochemistry protocols to detect core necroptosis regulators - Caspase-8, RIPK1, RIPK3 and MLKL - in formalin-fixed mouse and human tissues. We observed surprising heterogeneity in protein expression within tissues, whereby short-lived immune barrier cells were replete with necroptotic effectors, whereas long-lived cells lacked RIPK3 or MLKL expression. Local changes in the expression of necroptotic effectors occurred in response to insults such as inflammation, dysbiosis or immune challenge, consistent with necroptosis being dysregulated in disease contexts. These methods will facilitate the precise localisation and evaluation of necroptotic signaling in vivo.
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Affiliation(s)
- Shene Chiou
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Aysha H Al-Ani
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
- Royal Melbourne Hospital, Parkville, Australia
| | - Yi Pan
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Komal M Patel
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Isabella Y Kong
- Pediatric Hematology/Oncology, Weill Cornell Medical College, New York, USA
| | - Lachlan W Whitehead
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Amanda Light
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Marilou Barrios
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Callum Sargeant
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Pradeep Rajasekhar
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Leah Zhu
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Anne Hempel
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Ann Lin
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - James A Rickard
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Austin Hospital, Heidelberg, Australia
| | - Cathrine Hall
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | | | - Raymond Kh Yip
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Wayne Cawthorne
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Annette V Jacobsen
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Katherine R Martin
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Lisa J Ioannidis
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Diana S Hansen
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Australia
| | - Jessica Day
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
- Royal Melbourne Hospital, Parkville, Australia
| | - Ian P Wicks
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Charity Law
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Matthew E Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Rory Bowden
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Joanne M Hildebrand
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Lorraine A O'Reilly
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - John Silke
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Lisa Giulino-Roth
- Pediatric Hematology/Oncology, Weill Cornell Medical College, New York, USA
| | - Ellen Tsui
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Kelly L Rogers
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Edwin D Hawkins
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | - Britt Christensen
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- University of Melbourne, Parkville, Australia
- Royal Melbourne Hospital, Parkville, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.
- University of Melbourne, Parkville, Australia.
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia.
| | - André L Samson
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.
- University of Melbourne, Parkville, Australia.
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297
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Kentistou KA, Kaisinger LR, Stankovic S, Vaudel M, Mendes de Oliveira E, Messina A, Walters RG, Liu X, Busch AS, Helgason H, Thompson DJ, Santoni F, Petricek KM, Zouaghi Y, Huang-Doran I, Gudbjartsson DF, Bratland E, Lin K, Gardner EJ, Zhao Y, Jia RY, Terao C, Riggan MJ, Bolla MK, Yazdanpanah M, Yazdanpanah N, Bradfield JP, Broer L, Campbell A, Chasman DI, Cousminer DL, Franceschini N, Franke LH, Girotto G, He C, Järvelin MR, Joshi PK, Kamatani Y, Karlsson R, Luan J, Lunetta KL, Mägi R, Mangino M, Medland SE, Meisinger C, Noordam R, Nutile T, Concas MP, Polašek O, Porcu E, Ring SM, Sala C, Smith AV, Tanaka T, van der Most PJ, Vitart V, Wang CA, Willemsen G, Zygmunt M, Ahearn TU, Andrulis IL, Anton-Culver H, Antoniou AC, Auer PL, Barnes CLK, Beckmann MW, Berrington de Gonzalez A, Bogdanova NV, Bojesen SE, Brenner H, Buring JE, Canzian F, Chang-Claude J, Couch FJ, Cox A, Crisponi L, Czene K, Daly MB, Demerath EW, Dennis J, Devilee P, De Vivo I, Dörk T, Dunning AM, Dwek M, Eriksson JG, Fasching PA, Fernandez-Rhodes L, Ferreli L, Fletcher O, Gago-Dominguez M, García-Closas M, García-Sáenz JA, González-Neira A, Grallert H, Guénel P, Haiman CA, Hall P, Hamann U, Hakonarson H, Hart RJ, Hickey M, Hooning MJ, Hoppe R, Hopper JL, Hottenga JJ, Hu FB, Huebner H, Hunter DJ, Jernström H, John EM, Karasik D, Khusnutdinova EK, Kristensen VN, Lacey JV, Lambrechts D, Launer LJ, Lind PA, Lindblom A, Magnusson PKE, Mannermaa A, McCarthy MI, Meitinger T, Menni C, Michailidou K, Millwood IY, Milne RL, Montgomery GW, Nevanlinna H, Nolte IM, Nyholt DR, Obi N, O'Brien KM, Offit K, Oldehinkel AJ, Ostrowski SR, Palotie A, Pedersen OB, Peters A, Pianigiani G, Plaseska-Karanfilska D, Pouta A, Pozarickij A, Radice P, Rennert G, Rosendaal FR, Ruggiero D, Saloustros E, Sandler DP, Schipf S, Schmidt CO, Schmidt MK, Small K, Spedicati B, Stampfer M, Stone J, Tamimi RM, Teras LR, Tikkanen E, Turman C, Vachon CM, Wang Q, Winqvist R, Wolk A, Zemel BS, Zheng W, van Dijk KW, Alizadeh BZ, Bandinelli S, Boerwinkle E, Boomsma DI, Ciullo M, Chenevix-Trench G, Cucca F, Esko T, Gieger C, Grant SFA, Gudnason V, Hayward C, Kolčić I, Kraft P, Lawlor DA, Martin NG, Nøhr EA, Pedersen NL, Pennell CE, Ridker PM, Robino A, Snieder H, Sovio U, Spector TD, Stöckl D, Sudlow C, Timpson NJ, Toniolo D, Uitterlinden A, Ulivi S, Völzke H, Wareham NJ, Widen E, Wilson JF, Pharoah PDP, Li L, Easton DF, Njølstad PR, Sulem P, Murabito JM, Murray A, Manousaki D, Juul A, Erikstrup C, Stefansson K, Horikoshi M, Chen Z, Farooqi IS, Pitteloud N, Johansson S, Day FR, Perry JRB, Ong KK. Understanding the genetic complexity of puberty timing across the allele frequency spectrum. Nat Genet 2024; 56:1397-1411. [PMID: 38951643 PMCID: PMC11250262 DOI: 10.1038/s41588-024-01798-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 05/13/2024] [Indexed: 07/03/2024]
Abstract
Pubertal timing varies considerably and is associated with later health outcomes. We performed multi-ancestry genetic analyses on ~800,000 women, identifying 1,080 signals for age at menarche. Collectively, these explained 11% of trait variance in an independent sample. Women at the top and bottom 1% of polygenic risk exhibited ~11 and ~14-fold higher risks of delayed and precocious puberty, respectively. We identified several genes harboring rare loss-of-function variants in ~200,000 women, including variants in ZNF483, which abolished the impact of polygenic risk. Variant-to-gene mapping approaches and mouse gonadotropin-releasing hormone neuron RNA sequencing implicated 665 genes, including an uncharacterized G-protein-coupled receptor, GPR83, which amplified the signaling of MC3R, a key nutritional sensor. Shared signals with menopause timing at genes involved in DNA damage response suggest that the ovarian reserve might signal centrally to trigger puberty. We also highlight body size-dependent and independent mechanisms that potentially link reproductive timing to later life disease.
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Affiliation(s)
- Katherine A Kentistou
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Lena R Kaisinger
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Stasa Stankovic
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Edson Mendes de Oliveira
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Andrea Messina
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Alexander S Busch
- Department of General Pediatrics, University of Münster, Münster, Germany
- Department of Growth and Reproduction, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Hannes Helgason
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Federico Santoni
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Konstantin M Petricek
- Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pharmacology, Berlin, Germany
| | - Yassine Zouaghi
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Isabel Huang-Doran
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Eirik Bratland
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Eugene J Gardner
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Yajie Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Raina Y Jia
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Marjorie J Riggan
- Department of Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Mojgan Yazdanpanah
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Nahid Yazdanpanah
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Jonathan P Bradfield
- Quantinuum Research, Wayne, PA, USA
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Linda Broer
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Diana L Cousminer
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Lude H Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Giorgia Girotto
- Institute for Maternal and Child Health-IRCCS 'Burlo Garofolo', Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Chunyan He
- Department of Internal Medicine, Division of Medical Oncology, University of Kentucky College of Medicine, Lexington, KY, USA
- Cancer Prevention and Control Research Program, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Institute of Health Sciences, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
- Department of Children and Young People and Families, National Institute for Health and Welfare, Oulu, Finland
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- NHLBI's and Boston University's Framingham Heart Study, Framingham, MA, USA
| | - Reedik Mägi
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- NIHR Biomedical Research Centre at Guy's and St. Thomas' Foundation Trust, London, UK
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Psychology, University of Queensland, Brisbane, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Christa Meisinger
- Epidemiology, Medical Faculty, University of Augsburg, University Hospital of Augsburg, Augsburg, Germany
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Teresa Nutile
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, Naples, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health-IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Ozren Polašek
- University of Split School of Medicine, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Eleonora Porcu
- Institute of Genetics and Biomedical Research, National Research Council, Sardinia, Italy
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffele Hospital, Milano, Italy
| | - Albert V Smith
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Toshiko Tanaka
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Carol A Wang
- School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam; Amsterdam Public Health (APH) Research Institute, Amsterdam, The Netherlands
| | - Marek Zygmunt
- Clinic of Gynaecology and Obstetrics, University Medicine Greifswald, Greifswald, Germany
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services Bethesda, Bethesda, MD, USA
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Catriona L K Barnes
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | | | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital Copenhagen University Hospital, Herlev, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, USA
| | - Angela Cox
- Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Laura Crisponi
- Institute of Genetics and Biomedical Research, National Research Council, Sardinia, Italy
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Miriam Dwek
- School of Life Sciences, University of Westminster, London, UK
| | - Johan G Eriksson
- Department of General Practice and Primary Healthcare, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
- Yong Loo Lin School of Medicine, Department of Obstetrics and Gynecology and Human Potential Translational Research Programme, National University Singapore, Singapore City, Singapore
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | | | - Liana Ferreli
- Institute of Genetics and Biomedical Research, National Research Council, Sardinia, Italy
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, International Cancer Genetics and Epidemiology Group Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS Santiago de Compostela, Coruña, Spain
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services Bethesda, Bethesda, MD, USA
| | - José A García-Sáenz
- Medical Oncology Department, Hospital Clínico San Carlos Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Pascal Guénel
- Team 'Exposome and Heredity', CESP, Gustave Roussy INSERM, University Paris-Saclay, UVSQ, Orsay, France
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Roger J Hart
- Division of Obstetrics and Gynaecology, University of Western Australia, Crawley, Western Australia, Australia
| | - Martha Hickey
- Department of Obstetrics and Gynaecology, University of Melbourne and The Royal Women's Hospital, Parkville, Victoria, Australia
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam; Amsterdam Public Health (APH) Research Institute, Amsterdam, The Netherlands
| | - Frank B Hu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health School of Public Health, Boston, MA, USA
| | - Hanna Huebner
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | - David J Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Helena Jernström
- Oncology, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Esther M John
- Department of Epidemiology and Population Health, Stanford University School of Medicine Stanford, Stanford, CA, USA
- Department of Medicine, Division of Oncology Stanford Cancer Institute, Stanford University School of Medicine Stanford, Stanford, CA, USA
| | - David Karasik
- Hebrew SeniorLife Institute for Aging Research, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Vessela N Kristensen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - James V Lacey
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Penelope A Lind
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Iona Y Millwood
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dale R Nyholt
- School of Biomedical Sciences, Faculty of Health, Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Nadia Obi
- Institute for Occupational Medicine and Maritime Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katie M O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH Research Triangle Park, Durham, NC, USA
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Sisse R Ostrowski
- Department of Clinical Immunology, Rigshospitalet-University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Aarno Palotie
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Ole B Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology-IBE, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Giulia Pianigiani
- Institute for Maternal and Child Health-IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', MASA, Skopje, Republic of North Macedonia
| | - Anneli Pouta
- National Institute for Health and Welfare, Helsinki, Finland
| | - Alfred Pozarickij
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Paolo Radice
- Unit of Preventive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS, Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Gad Rennert
- Faculty of Medicine, Clalit National Cancer Control Center, Carmel Medical Center and Technion, Haifa, Israel
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, Naples, Italy
- IRCCS Neuromed, Isernia, Italy
| | - Emmanouil Saloustros
- Division of Oncology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH Research Triangle Park, Durham, NC, USA
| | - Sabine Schipf
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Carsten O Schmidt
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Kerrin Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Beatrice Spedicati
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Meir Stampfer
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Genetic Epidemiology Group, School of Population and Global Health, University of Western Australia Perth, Perth, Western Australia, Australia
| | - Rulla M Tamimi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York City, NY, USA
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Emmi Tikkanen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic Rochester, Rochester, MN, USA
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre, Oulu, Finland
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Babette S Zemel
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ko W van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam; Amsterdam Public Health (APH) Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Marina Ciullo
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, Naples, Italy
- IRCCS Neuromed, Isernia, Italy
| | | | - Francesco Cucca
- Institute of Genetics and Biomedical Research, National Research Council, Sardinia, Italy
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Tõnu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ivana Kolčić
- University of Split School of Medicine, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ellen A Nøhr
- Institute of Clinical Research, University of Southern Denmark, Department of Obstetrics and Gynecology, Odense University Hospital, Odense, Denmark
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Craig E Pennell
- School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
- Department of Maternity and Gynaecology, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Antonietta Robino
- Institute for Maternal and Child Health-IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ulla Sovio
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Doris Stöckl
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- State Institute of Health, Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | - Cathie Sudlow
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Nic J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffele Hospital, Milano, Italy
| | - André Uitterlinden
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Sheila Ulivi
- Institute for Maternal and Child Health-IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing, China
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Pål R Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Adolescent Clinic, Haukeland University Hospital, Bergen, Norway
| | | | - Joanne M Murabito
- NHLBI's and Boston University's Framingham Heart Study, Framingham, MA, USA
- Boston University Chobanian and Avedisian School of Medicine, Department of Medicine, Section of General Internal Medicine, Boston, MA, USA
| | - Anna Murray
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, RILD Level 3, Royal Devon and Exeter Hospital, Exeter, UK
| | - Despoina Manousaki
- Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, University of Montreal, Montreal, Quebec, Canada
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Anders Juul
- Department of Growth and Reproduction, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Momoko Horikoshi
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Nelly Pitteloud
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Felix R Day
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK.
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK.
| | - Ken K Ong
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
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Wang Z, Zhao Y, Wo Y, Peng Y, Hu W, Wu Z, Liu P, Shang Y, Liu C, Chen X, Huang K, Chen Y, Hong H, Li F, Sun Y. The single cell immunogenomic landscape after neoadjuvant immunotherapy combined chemotherapy in esophageal squamous cell carcinoma. Cancer Lett 2024; 593:216951. [PMID: 38734159 DOI: 10.1016/j.canlet.2024.216951] [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: 11/18/2023] [Revised: 04/19/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Neoadjuvant immunotherapy represents promising strategy in the treatment of esophageal squamous cell carcinoma (ESCC). However, the mechanisms underlying its impact on treatment sensitivity or resistance remain a subject of controversy. In this study, we conducted single-cell RNA and T/B cell receptor (scTCR/scBCR) sequencing of CD45+ immune cells on samples from 10 patients who received neoadjuvant immunotherapy and chemotherapy. We also validated our findings using multiplexed immunofluorescence and analyzed bulk RNA-seq from other cohorts in public database. By integrating analysis of 87357 CD45+ cells, we found GZMK + effector memory T cells (Tem) were relatively enriched and CXCL13+ exhausted T cells (Tex) and regulator T cells (Treg) decreased among responders, indicating a persistent anti-tumor memory process. Additionally, the enhanced presence of BCR expansion and somatic hypermutation process within TNFRSF13B + memory B cells (Bmem) suggested their roles in antigen presentation. This was further corroborated by the evidence of the T-B co-stimulation pattern and CXCL13-CXCR5 axis. The complexity of myeloid cell heterogeneity was also particularly pronounced. The elevated expression of S100A7 in ESCC, as detected by bulk RNA-seq, was associated with an exhausted and immunosuppressive tumor microenvironment. In summary, this study has unveiled a potential regulatory network among immune cells and the clonal dynamics of their functions, and the mechanisms of exhaustion and memory conversion between GZMK + Tem and TNFRSF13B + Bmem from antigen presentation and co-stimulation perspectives during neoadjuvant PD-1 blockade treatment in ESCC.
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MESH Headings
- Humans
- Neoadjuvant Therapy/methods
- Esophageal Squamous Cell Carcinoma/immunology
- Esophageal Squamous Cell Carcinoma/genetics
- Esophageal Squamous Cell Carcinoma/therapy
- Esophageal Squamous Cell Carcinoma/drug therapy
- Esophageal Squamous Cell Carcinoma/pathology
- Esophageal Neoplasms/immunology
- Esophageal Neoplasms/genetics
- Esophageal Neoplasms/therapy
- Esophageal Neoplasms/drug therapy
- Esophageal Neoplasms/pathology
- Immunotherapy/methods
- Single-Cell Analysis/methods
- Female
- Male
- Tumor Microenvironment/immunology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Chemokine CXCL13/genetics
- Chemokine CXCL13/metabolism
- Middle Aged
- Aged
- Memory T Cells/immunology
- Memory T Cells/metabolism
- Leukocyte Common Antigens/metabolism
- Leukocyte Common Antigens/genetics
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/drug effects
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Receptors, Antigen, B-Cell/immunology
- Receptors, CXCR5/metabolism
- Receptors, CXCR5/genetics
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Affiliation(s)
- Zheyi Wang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yue Zhao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Wo
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yizhou Peng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weilei Hu
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China; State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Zhigang Wu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Pengcheng Liu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan Shang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chunnan Liu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kan Huang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuting Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hui Hong
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fei Li
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Yihua Sun
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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299
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Kim GD, Shin SI, Jung SW, An H, Choi SY, Eun M, Jun CD, Lee S, Park J. Cell Type- and Age-Specific Expression of lncRNAs across Kidney Cell Types. J Am Soc Nephrol 2024; 35:870-885. [PMID: 38621182 PMCID: PMC11230714 DOI: 10.1681/asn.0000000000000354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
Key Points
We constructed a single-cell long noncoding RNA atlas of various tissues, including normal and aged kidneys.We identified age- and cell type–specific expression changes of long noncoding RNAs in kidney cells.
Background
Accumulated evidence demonstrates that long noncoding RNAs (lncRNAs) regulate cell differentiation and homeostasis, influencing kidney aging and disease. Despite their versatility, the function of lncRNA remains poorly understood because of the lack of a reference map of lncRNA transcriptome in various cell types.
Methods
In this study, we used a targeted single-cell RNA sequencing method to enrich and characterize lncRNAs in individual cells. We applied this method to various mouse tissues, including normal and aged kidneys.
Results
Through tissue-specific clustering analysis, we identified cell type–specific lncRNAs that showed a high correlation with known cell-type marker genes. Furthermore, we constructed gene regulatory networks to explore the functional roles of differentially expressed lncRNAs in each cell type. In the kidney, we observed dynamic expression changes of lncRNAs during aging, with specific changes in glomerular cells. These cell type– and age-specific expression patterns of lncRNAs suggest that lncRNAs may have a potential role in regulating cellular processes, such as immune response and energy metabolism, during kidney aging.
Conclusions
Our study sheds light on the comprehensive landscape of lncRNA expression and function and provides a valuable resource for future analysis of lncRNAs (https://gist-fgl.github.io/sc-lncrna-atlas/).
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Affiliation(s)
- Gyeong Dae Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - So-I Shin
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Su Woong Jung
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Hyunsu An
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Sin Young Choi
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Minho Eun
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Chang-Duk Jun
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Sangho Lee
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
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300
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Seidelin JB, Bronze M, Poulsen A, Attauabi M, Woetmann A, Mead BE, Karp JM, Riis LB, Bjerrum JT. Non-TGFβ profibrotic signaling in ulcerative colitis after in vivo experimental intestinal injury in humans. Am J Physiol Gastrointest Liver Physiol 2024; 327:G70-G79. [PMID: 38713614 DOI: 10.1152/ajpgi.00074.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/09/2024]
Abstract
Although impaired regeneration is important in many gastrointestinal diseases including ulcerative colitis (UC), the dynamics of mucosal regeneration in humans are poorly investigated. We have developed a model to study these processes in vivo in humans. Epithelial restitution (ER) and extracellular matrix (ECM) regulation after an experimental injury of the sigmoid colonic mucosa was assessed by repeated high-resolution endoscopic imaging, histological assessment, RNA sequencing, deconvolution analysis, and 16S rDNA sequencing of the injury niche microbiome of 19 patients with UC in remission and 20 control subjects. Human ER had a 48-h lag before induction of regenerative epithelial cells [wound-associated epithelial (WAE) and transit amplifying (TA) cells] along with the increase of fibroblast-derived stem cell growth factor gremlin 1 mRNA (GREM1). However, UC deconvolution data showed rapid induction of inflammatory fibroblasts and upregulation of major structural ECM collagen mRNAs along with tissue inhibitor of metalloproteinase 1 (TIMP1), suggesting increased profibrotic ECM deposition. No change was seen in transforming growth factor β (TGFβ) mRNA, whereas the profibrotic cytokines interleukin 13 (IL13) and IL11 were upregulated in UC, suggesting that human postinjury responses could be TGFβ-independent. In conclusion, we found distinct regulatory layers of regeneration in the normal human colon and a potential targetable profibrotic dysregulation in UC that could lead to long-term end-organ failure, i.e., intestinal damage.NEW & NOTEWORTHY The study reveals the regulatory dynamics of epithelial regeneration and extracellular matrix remodeling after experimental injury of the human colon in vivo and shows that human intestinal regeneration is different from data obtained from animals. A lag phase in epithelial restitution is associated with induction of stromal cell-derived epithelial growth factors. Postinjury regeneration is transforming growth factor β-independent, and we find a profibrotic response in patients with ulcerative colitis despite being in remission.
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Affiliation(s)
- Jakob B Seidelin
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mariana Bronze
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- LEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark
| | - Anja Poulsen
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mohamed Attauabi
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Woetmann
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- LEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin E Mead
- Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Department of Chemistry; Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, United States
| | - Jeffrey M Karp
- Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States
- Harvard Medical School, Boston, Massachusetts, United States
- Department of Anesthesiology, Perioperative and Pain Medicine,Brigham and Women's Hospital, Cambridge, Massachusetts, United States
| | - Lene B Riis
- Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jacob T Bjerrum
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
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