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Iwahashi N, Umakoshi H, Fujita M, Fukumoto T, Ogasawara T, Yokomoto-Umakoshi M, Kaneko H, Nakao H, Kawamura N, Uchida N, Matsuda Y, Sakamoto R, Seki M, Suzuki Y, Nakatani K, Izumi Y, Bamba T, Oda Y, Ogawa Y. Single-cell and spatial transcriptomics analysis of human adrenal aging. Mol Metab 2024; 84:101954. [PMID: 38718896 PMCID: PMC11101872 DOI: 10.1016/j.molmet.2024.101954] [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: 01/09/2024] [Revised: 03/30/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
OBJECTIVE The human adrenal cortex comprises three functionally and structurally distinct layers that produce layer-specific steroid hormones. With aging, the human adrenal cortex undergoes functional and structural alteration or "adrenal aging", leading to the unbalanced production of steroid hormones. Given the marked species differences in adrenal biology, the underlying mechanisms of human adrenal aging have not been sufficiently studied. This study was designed to elucidate the mechanisms linking the functional and structural alterations of the human adrenal cortex. METHODS We conducted single-cell RNA sequencing and spatial transcriptomics analysis of the aged human adrenal cortex. RESULTS The data of this study suggest that the layer-specific alterations of multiple signaling pathways underlie the abnormal layered structure and layer-specific changes in steroidogenic cells. We also highlighted that macrophages mediate age-related adrenocortical cell inflammation and senescence. CONCLUSIONS This study is the first detailed analysis of the aged human adrenal cortex at single-cell resolution and helps to elucidate the mechanism of human adrenal aging, thereby leading to a better understanding of the pathophysiology of age-related disorders associated with adrenal aging.
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Affiliation(s)
- Norifusa Iwahashi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hironobu Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Masamichi Fujita
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tazuru Fukumoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tatsuki Ogasawara
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Maki Yokomoto-Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroki Kaneko
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroshi Nakao
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Namiko Kawamura
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naohiro Uchida
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yayoi Matsuda
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryuichi Sakamoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kohta Nakatani
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takeshi Bamba
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
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2
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Li X, Turaga D, Li RG, Tsai CR, Quinn JN, Zhao Y, Wilson R, Carlson K, Wang J, Spinner JA, Hickey EJ, Adachi I, Martin JF. The Macrophage Landscape Across the Lifespan of a Human Cardiac Allograft. Circulation 2024; 149:1650-1666. [PMID: 38344825 PMCID: PMC11105989 DOI: 10.1161/circulationaha.123.065294] [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: 04/25/2023] [Accepted: 01/16/2024] [Indexed: 05/22/2024]
Abstract
BACKGROUND Much of our knowledge of organ rejection after transplantation is derived from rodent models. METHODS We used single-nucleus RNA sequencing to investigate the inflammatory myocardial microenvironment in human pediatric cardiac allografts at different stages after transplantation. We distinguished donor- from recipient-derived cells using naturally occurring genetic variants embedded in single-nucleus RNA sequencing data. RESULTS Donor-derived tissue resident macrophages, which accompany the allograft into the recipient, are lost over time after transplantation. In contrast, monocyte-derived macrophages from the recipient populate the heart within days after transplantation and form 2 macrophage populations: recipient MP1 and recipient MP2. Recipient MP2s have cell signatures similar to donor-derived resident macrophages; however, they lack signatures of pro-reparative phagocytic activity typical of donor-derived resident macrophages and instead express profibrotic genes. In contrast, recipient MP1s express genes consistent with hallmarks of cellular rejection. Our data suggest that recipient MP1s activate a subset of natural killer cells, turning them into a cytotoxic cell population through feed-forward signaling between recipient MP1s and natural killer cells. CONCLUSIONS Our findings reveal an imbalance of donor-derived and recipient-derived macrophages in the pediatric cardiac allograft that contributes to allograft failure.
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Affiliation(s)
- Xiao Li
- The Texas Heart Institute, Houston, TX, USA
| | - Diwakar Turaga
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Division of Critical Care Medicine, Texas Children’s Hospital, Houston TX, USA
| | - Rich G. Li
- The Texas Heart Institute, Houston, TX, USA
| | - Chang-Ru Tsai
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Julianna N. Quinn
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, TX, USA
| | - Yi Zhao
- The Texas Heart Institute, Houston, TX, USA
| | | | - Katherine Carlson
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Jun Wang
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, TX, USA
| | - Joseph A. Spinner
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Division of Cardiology, Texas Children’s Hospital, Houston, TX, USA
| | - Edward J. Hickey
- Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
- Division of Congenital Heart Surgery, Texas Children’s Hospital, Houston, TX, USA
| | - Iki Adachi
- Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
- Division of Congenital Heart Surgery, Texas Children’s Hospital, Houston, TX, USA
| | - James F. Martin
- The Texas Heart Institute, Houston, TX, USA
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
- Center for Organ Repair and Renewal, Baylor College of Medicine, Houston, TX, USA
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3
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Iida K, Okada M. Identifying Key Regulatory Genes in Drug Resistance Acquisition: Modeling Pseudotime Trajectories of Breast Cancer Single-Cell Transcriptome. Cancers (Basel) 2024; 16:1884. [PMID: 38791962 PMCID: PMC11119661 DOI: 10.3390/cancers16101884] [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: 04/28/2024] [Revised: 05/11/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) technology has provided significant insights into cancer drug resistance at the single-cell level. However, understanding dynamic cell transitions at the molecular systems level remains limited, requiring a systems biology approach. We present an approach that combines mathematical modeling with a pseudotime analysis using time-series scRNA-seq data obtained from the breast cancer cell line MCF-7 treated with tamoxifen. Our single-cell analysis identified five distinct subpopulations, including tamoxifen-sensitive and -resistant groups. Using a single-gene mathematical model, we discovered approximately 560-680 genes out of 6000 exhibiting multistable expression states in each subpopulation, including key estrogen-receptor-positive breast cancer cell survival genes, such as RPS6KB1. A bifurcation analysis elucidated their regulatory mechanisms, and we mapped these genes into a molecular network associated with cell survival and metastasis-related pathways. Our modeling approach comprehensively identifies key regulatory genes for drug resistance acquisition, enhancing our understanding of potential drug targets in breast cancer.
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Affiliation(s)
- Keita Iida
- Institute for Protein Research, Osaka University, Suita 565-0871, Osaka, Japan;
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4
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Gong X, He W, Jin W, Ma H, Wang G, Li J, Xiao Y, Zhao Y, Chen Q, Guo H, Yang J, Qi Y, Dong W, Fu M, Li X, Liu J, Liu X, Yin A, Zhang Y, Wei Y. Disruption of maternal vascular remodeling by a fetal endoretrovirus-derived gene in preeclampsia. Genome Biol 2024; 25:117. [PMID: 38715110 PMCID: PMC11075363 DOI: 10.1186/s13059-024-03265-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Preeclampsia, one of the most lethal pregnancy-related diseases, is associated with the disruption of uterine spiral artery remodeling during placentation. However, the early molecular events leading to preeclampsia remain unknown. RESULTS By analyzing placentas from preeclampsia, non-preeclampsia, and twin pregnancies with selective intrauterine growth restriction, we show that the pathogenesis of preeclampsia is attributed to immature trophoblast and maldeveloped endothelial cells. Delayed epigenetic reprogramming during early extraembryonic tissue development leads to generation of excessive immature trophoblast cells. We find reduction of de novo DNA methylation in these trophoblast cells results in selective overexpression of maternally imprinted genes, including the endoretrovirus-derived gene PEG10 (paternally expressed gene 10). PEG10 forms virus-like particles, which are transferred from the trophoblast to the closely proximate endothelial cells. In normal pregnancy, only a low amount of PEG10 is transferred to maternal cells; however, in preeclampsia, excessive PEG10 disrupts maternal vascular development by inhibiting TGF-beta signaling. CONCLUSIONS Our study reveals the intricate epigenetic mechanisms that regulate trans-generational genetic conflict and ultimately ensure proper maternal-fetal interface formation.
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Affiliation(s)
- Xiaoli Gong
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Wei He
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wan Jin
- Euler Technology, Beijing, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongwei Ma
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Gang Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiaxin Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yangyu Zhao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | | | | | - Jiexia Yang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yiming Qi
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wei Dong
- Maternity Ward, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Meng Fu
- Department of Obstetrics and Gynecology, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Xiaojuan Li
- Euler Technology, Beijing, China
- Present Address: International Max Planck Research School for Genome Science, and University of Göttingen, Göttingen Center for Molecular Biosciences, Göttingen, Germany
| | | | - Xinghui Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China.
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
| | - Aihua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China.
| | - Yi Zhang
- Euler Technology, Beijing, China.
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
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5
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Tao W, Yu Z, Han JDJ. Single-cell senescence identification reveals senescence heterogeneity, trajectory, and modulators. Cell Metab 2024; 36:1126-1143.e5. [PMID: 38604170 DOI: 10.1016/j.cmet.2024.03.009] [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: 08/18/2023] [Revised: 12/15/2023] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
Cellular senescence underlies many aging-related pathologies, but its heterogeneity poses challenges for studying and targeting senescent cells. We present here a machine learning program senescent cell identification (SenCID), which accurately identifies senescent cells in both bulk and single-cell transcriptome. Trained on 602 samples from 52 senescence transcriptome datasets spanning 30 cell types, SenCID identifies six major senescence identities (SIDs). Different SIDs exhibit different senescence baselines, stemness, gene functions, and responses to senolytics. SenCID enables the reconstruction of senescent trajectories under normal aging, chronic diseases, and COVID-19. Additionally, when applied to single-cell Perturb-seq data, SenCID helps reveal a hierarchy of senescence modulators. Overall, SenCID is an essential tool for precise single-cell analysis of cellular senescence, enabling targeted interventions against senescent cells.
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Affiliation(s)
- Wanyu Tao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Zhengqing Yu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China; Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China.
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6
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Nguyen TH, Vicidomini R, Choudhury SD, Han TH, Maric D, Brody T, Serpe M. scRNA-seq data from the larval Drosophila ventral cord provides a resource for studying motor systems function and development. Dev Cell 2024; 59:1210-1230.e9. [PMID: 38569548 PMCID: PMC11078614 DOI: 10.1016/j.devcel.2024.03.016] [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: 06/27/2023] [Revised: 12/05/2023] [Accepted: 03/06/2024] [Indexed: 04/05/2024]
Abstract
The Drosophila larval ventral nerve cord (VNC) shares many similarities with the spinal cord of vertebrates and has emerged as a major model for understanding the development and function of motor systems. Here, we use high-quality scRNA-seq, validated by anatomical identification, to create a comprehensive census of larval VNC cell types. We show that the neural lineages that comprise the adult VNC are already defined, but quiescent, at the larval stage. Using fluorescence-activated cell sorting (FACS)-enriched populations, we separate all motor neuron bundles and link individual neuron clusters to morphologically characterized known subtypes. We discovered a glutamate receptor subunit required for basal neurotransmission and homeostasis at the larval neuromuscular junction. We describe larval glia and endorse the general view that glia perform consistent activities throughout development. This census represents an extensive resource and a powerful platform for future discoveries of cellular and molecular mechanisms in repair, regeneration, plasticity, homeostasis, and behavioral coordination.
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Affiliation(s)
| | | | | | | | - Dragan Maric
- Flow and Imaging Cytometry Core, NINDS, NIH, Bethesda, MD 20892, USA
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7
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Neff LS, Biggs RM, Zhang Y, Van Laer AO, Baicu CF, Subramanian S, Berto S, DeLeon-Pennell K, Zile MR, Bradshaw AD. Role of macrophages in regression of myocardial fibrosis following alleviation of left ventricular pressure overload. Am J Physiol Heart Circ Physiol 2024; 326:H1204-H1218. [PMID: 38363214 DOI: 10.1152/ajpheart.00240.2023] [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: 04/25/2023] [Revised: 01/30/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
Sustained hemodynamic pressure overload (PO) produced by murine transverse aortic constriction (TAC) causes myocardial fibrosis; removal of TAC (unTAC) returns left ventricle (LV) hemodynamic load to normal and results in significant, but incomplete regression of myocardial fibrosis. However, the cellular mechanisms that result in these outcomes have not been defined. The objective was to determine temporal changes in myocardial macrophage phenotype in TAC and unTAC and determine whether macrophage depletion alters collagen degradation after unTAC. Myocardial macrophage abundance and phenotype were assessed by immunohistochemistry, flow cytometry, and gene expression by RT-PCR in control (non-TAC), 2 wk, 4 wk TAC, and 2 wk, 4 wk, and 6 wk unTAC. Myocardial cytokine profiles and collagen-degrading enzymes were determined by immunoassay and immunoblots. Initial collagen degradation was detected with collagen-hybridizing peptide (CHP). At unTAC, macrophages were depleted with clodronate liposomes, and endpoints were measured at 2 wk unTAC. Macrophage number had a defined temporal pattern: increased in 2 wk and 4 wk TAC, followed by increases at 2 wk unTAC (over 4 wk TAC) that then decreased at 4 wk and 6 wk unTAC. At 2 wk unTAC, macrophage area was significantly increased and was regionally associated with CHP reactivity. Cytokine profiles in unTAC reflected a proinflammatory milieu versus the TAC-induced profibrotic milieu. Single-cell sequencing analysis of 2 wk TAC versus 2 and 6 wk unTAC revealed distinct macrophage gene expression profiles at each time point demonstrating unique macrophage populations in unTAC versus TAC myocardium. Clodronate liposome depletion at unTAC reduced CHP reactivity and decreased cathepsin K and proMMP2. We conclude that temporal changes in number and phenotype of macrophages play a critical role in both TAC-induced development and unTAC-mediated partial, but incomplete, regression of myocardial fibrosis.NEW & NOTEWORTHY Our novel findings highlight the dynamic changes in myocardial macrophage populations that occur in response to PO and after alleviation of PO. Our data demonstrated, for the first time, a potential benefit of macrophages in contributing to collagen degradation and the partial regression of interstitial fibrosis following normalization of hemodynamic load.
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Affiliation(s)
- Lily S Neff
- Division of Cardiology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Rachel M Biggs
- Division of Cardiology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Yuhua Zhang
- Division of Cardiology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
| | - An O Van Laer
- Division of Cardiology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Catalin F Baicu
- Division of Cardiology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Suganya Subramanian
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Stefano Berto
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Kristine DeLeon-Pennell
- Division of Cardiology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
- The Ralph H. Johnson Department of Veteran's Affairs Medical Center, Charleston, South Carolina, United States
| | - Michael R Zile
- Division of Cardiology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
- The Ralph H. Johnson Department of Veteran's Affairs Medical Center, Charleston, South Carolina, United States
| | - Amy D Bradshaw
- Division of Cardiology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
- The Ralph H. Johnson Department of Veteran's Affairs Medical Center, Charleston, South Carolina, United States
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Fukumoto T, Umakoshi H, Iwahashi N, Ogasawara T, Yokomoto-Umakoshi M, Kaneko H, Fujita M, Uchida N, Nakao H, Kawamura N, Matsuda Y, Sakamoto R, Miyazawa T, Seki M, Eto M, Oda Y, Suzuki Y, Ogawa S, Ogawa Y. Steroids-producing nodules: a two-layered adrenocortical nodular structure as a precursor lesion of cortisol-producing adenoma. EBioMedicine 2024; 103:105087. [PMID: 38570222 PMCID: PMC11121169 DOI: 10.1016/j.ebiom.2024.105087] [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: 10/29/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND The human adrenal cortex consists of three functionally and structurally distinct layers; zona glomerulosa, zona fasciculata (zF), and zona reticularis (zR), and produces adrenal steroid hormones in a layer-specific manner; aldosterone, cortisol, and adrenal androgens, respectively. Cortisol-producing adenomas (CPAs) occur mostly as a result of somatic mutations associated with the protein kinase A pathway. However, how CPAs develop after adrenocortical cells acquire genetic mutations, remains poorly understood. METHODS We conducted integrated approaches combining the detailed histopathologic studies with genetic, RNA-sequencing, and spatially resolved transcriptome (SRT) analyses for the adrenal cortices adjacent to human adrenocortical tumours. FINDINGS Histopathological analysis revealed an adrenocortical nodular structure that exhibits the two-layered zF- and zR-like structure. The nodular structures harbour GNAS somatic mutations, known as a driver mutation of CPAs, and confer cell proliferative and autonomous steroidogenic capacities, which we termed steroids-producing nodules (SPNs). RNA-sequencing coupled with SRT analysis suggests that the expansion of the zF-like structure contributes to the formation of CPAs, whereas the zR-like structure is characterised by a macrophage-mediated immune response. INTERPRETATION We postulate that CPAs arise from a precursor lesion, SPNs, where two distinct cell populations might contribute differently to adrenocortical tumorigenesis. Our data also provide clues to the molecular mechanisms underlying the layered structures of human adrenocortical tissues. FUNDING KAKENHI, The Uehara Memorial Foundation, Daiwa Securities Health Foundation, Kaibara Morikazu Medical Science Promotion Foundation, Secom Science and Technology Foundation, ONO Medical Research Foundation, and Japan Foundation for Applied Enzymology.
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Affiliation(s)
- Tazuru Fukumoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hironobu Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Norifusa Iwahashi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tatsuki Ogasawara
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Maki Yokomoto-Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroki Kaneko
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masamichi Fujita
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naohiro Uchida
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroshi Nakao
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Namiko Kawamura
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yayoi Matsuda
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryuichi Sakamoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takashi Miyazawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Masatoshi Eto
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
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9
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Wang W, Zheng S, Shin SC, Yuan GC. Characterizing Spatially Continuous Variations in Tissue Microenvironment through Niche Trajectory Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590827. [PMID: 38712255 PMCID: PMC11071437 DOI: 10.1101/2024.04.23.590827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Recent technological developments have made it possible to map the spatial organization of a tissue at the single-cell resolution. However, computational methods for analyzing spatially continuous variations in tissue microenvironment are still lacking. Here we present ONTraC as a strategy that constructs niche trajectories using a graph neural network-based modeling framework. Our benchmark analysis shows that ONTraC performs more favorably than existing methods for reconstructing spatial trajectories. Applications of ONTraC to public spatial transcriptomics datasets successfully recapitulated the underlying anatomical structure, and further enabled detection of tissue microenvironment-dependent changes in gene regulatory networks and cell-cell interaction activities during embryonic development. Taken together, ONTraC provides a useful and generally applicable tool for the systematic characterization of the structural and functional organization of tissue microenvironments.
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Affiliation(s)
- Wen Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shiwei Zheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sujung Crystal Shin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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10
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Kumar N, Prakash PG, Wentland C, Kurian SM, Jethva G, Brinkmann V, Mollenkopf HJ, Krammer T, Toussaint C, Saliba AE, Biebl M, Jürgensen C, Wiedenmann B, Meyer TF, Gurumurthy RK, Chumduri C. Decoding spatiotemporal transcriptional dynamics and epithelial fibroblast crosstalk during gastroesophageal junction development through single cell analysis. Nat Commun 2024; 15:3064. [PMID: 38594232 PMCID: PMC11004180 DOI: 10.1038/s41467-024-47173-z] [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: 04/13/2023] [Accepted: 03/22/2024] [Indexed: 04/11/2024] Open
Abstract
The gastroesophageal squamocolumnar junction (GE-SCJ) is a critical tissue interface between the esophagus and stomach, with significant relevance in the pathophysiology of gastrointestinal diseases. Despite this, the molecular mechanisms underlying GE-SCJ development remain unclear. Using single-cell transcriptomics, organoids, and spatial analysis, we examine the cellular heterogeneity and spatiotemporal dynamics of GE-SCJ development from embryonic to adult mice. We identify distinct transcriptional states and signaling pathways in the epithelial and mesenchymal compartments of the esophagus and stomach during development. Fibroblast-epithelial interactions are mediated by various signaling pathways, including WNT, BMP, TGF-β, FGF, EGF, and PDGF. Our results suggest that fibroblasts predominantly send FGF and TGF-β signals to the epithelia, while epithelial cells mainly send PDGF and EGF signals to fibroblasts. We observe differences in the ligands and receptors involved in cell-cell communication between the esophagus and stomach. Our findings provide insights into the molecular mechanisms underlying GE-SCJ development and fibroblast-epithelial crosstalk involved, paving the way to elucidate mechanisms during adaptive metaplasia development and carcinogenesis.
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Affiliation(s)
- Naveen Kumar
- Laboratory of Infections, Carcinogenesis and Regeneration, Medical Biotechnology Section, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
- Department of Microbiology, University of Würzburg, Würzburg, Germany
| | | | | | | | - Gaurav Jethva
- Department of Microbiology, University of Würzburg, Würzburg, Germany
| | - Volker Brinkmann
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Hans-Joachim Mollenkopf
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Tobias Krammer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Christophe Toussaint
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Institute of Molecular Infection Biology (IMIB), Würzburg, Germany
| | - Matthias Biebl
- Surgical Clinic Campus Charité Mitte, Charité University Medicine, Berlin, Germany
| | - Christian Jürgensen
- Department of Hepatology and Gastroenterology, Charité University Medicine, Berlin, Germany
| | - Bertram Wiedenmann
- Department of Hepatology and Gastroenterology, Charité University Medicine, Berlin, Germany
| | - Thomas F Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Rajendra Kumar Gurumurthy
- Department of Microbiology, University of Würzburg, Würzburg, Germany
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Cindrilla Chumduri
- Laboratory of Infections, Carcinogenesis and Regeneration, Medical Biotechnology Section, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark.
- Department of Microbiology, University of Würzburg, Würzburg, Germany.
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany.
- Department of Hepatology and Gastroenterology, Charité University Medicine, Berlin, Germany.
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11
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Xiao Y, Jin W, Qian K, Ju L, Wang G, Wu K, Cao R, Chang L, Xu Z, Luo J, Shan L, Yu F, Chen X, Liu D, Cao H, Wang Y, Cao X, Zhou W, Cui D, Tian Y, Ji C, Luo Y, Hong X, Chen F, Peng M, Zhang Y, Wang X. Integrative Single Cell Atlas Revealed Intratumoral Heterogeneity Generation from an Adaptive Epigenetic Cell State in Human Bladder Urothelial Carcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308438. [PMID: 38582099 DOI: 10.1002/advs.202308438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/22/2024] [Indexed: 04/08/2024]
Abstract
Intratumor heterogeneity (ITH) of bladder cancer (BLCA) contributes to therapy resistance and immune evasion affecting clinical prognosis. The molecular and cellular mechanisms contributing to BLCA ITH generation remain elusive. It is found that a TM4SF1-positive cancer subpopulation (TPCS) can generate ITH in BLCA, evidenced by integrative single cell atlas analysis. Extensive profiling of the epigenome and transcriptome of all stages of BLCA revealed their evolutionary trajectories. Distinct ancestor cells gave rise to low-grade noninvasive and high-grade invasive BLCA. Epigenome reprograming led to transcriptional heterogeneity in BLCA. During early oncogenesis, epithelial-to-mesenchymal transition generated TPCS. TPCS has stem-cell-like properties and exhibited transcriptional plasticity, priming the development of transcriptionally heterogeneous descendent cell lineages. Moreover, TPCS prevalence in tumor is associated with advanced stage cancer and poor prognosis. The results of this study suggested that bladder cancer interacts with its environment by acquiring a stem cell-like epigenomic landscape, which might generate ITH without additional genetic diversification.
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Affiliation(s)
- Yu Xiao
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Wan Jin
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Euler Technology, Beijing, 102206, China
| | - Kaiyu Qian
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Lingao Ju
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Gang Wang
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Kai Wu
- Euler Technology, Beijing, 102206, China
| | - Rui Cao
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | | | - Zilin Xu
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jun Luo
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | | | - Fang Yu
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | | | | | - Hong Cao
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Yejinpeng Wang
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xinyue Cao
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Clinical Trial Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Wei Zhou
- Hubei Key Laboratory of Medical Technology on Transplantation, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Wuhan, 430071, China
| | - Diansheng Cui
- Department of Urology, Hubei Cancer Hospital, Wuhan, 430079, China
| | - Ye Tian
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Chundong Ji
- Department of Urology, The Affiliated Hospital of Panzhihua University, Panzhihua, 617099, China
| | - Yongwen Luo
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xin Hong
- Department of Urology, Peking University International Hospital, Beijing, 102206, China
| | - Fangjin Chen
- Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, 100091, China
| | - Minsheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming College of Life Science, University of Academy of Sciences, Kunming, 650201, China
| | - Yi Zhang
- Euler Technology, Beijing, 102206, China
| | - Xinghuan Wang
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Medical Research Institute, Wuhan University, Wuhan, 430071, China
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12
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Liu S, Zhang Y, Peng J, Shang X. An improved hierarchical variational autoencoder for cell-cell communication estimation using single-cell RNA-seq data. Brief Funct Genomics 2024; 23:118-127. [PMID: 36752035 DOI: 10.1093/bfgp/elac056] [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: 07/22/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 02/09/2023] Open
Abstract
Analysis of cell-cell communication (CCC) in the tumor micro-environment helps decipher the underlying mechanism of cancer progression and drug tolerance. Currently, single-cell RNA-Seq data are available on a large scale, providing an unprecedented opportunity to predict cellular communications. There have been many achievements and applications in inferring cell-cell communication based on the known interactions between molecules, such as ligands, receptors and extracellular matrix. However, the prior information is not quite adequate and only involves a fraction of cellular communications, producing many false-positive or false-negative results. To this end, we propose an improved hierarchical variational autoencoder (HiVAE) based model to fully use single-cell RNA-seq data for automatically estimating CCC. Specifically, the HiVAE model is used to learn the potential representation of cells on known ligand-receptor genes and all genes in single-cell RNA-seq data, respectively, which are then utilized for cascade integration. Subsequently, transfer entropy is employed to measure the transmission of information flow between two cells based on the learned representations, which are regarded as directed communication relationships. Experiments are conducted on single-cell RNA-seq data of the human skin disease dataset and the melanoma dataset, respectively. Results show that the HiVAE model is effective in learning cell representations, and transfer entropy could be used to estimate the communication scores between cell types.
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Affiliation(s)
- Shuhui Liu
- School of Computer Science, Northwestern Polytechnical University, Xi'an 710129, Shaanxi, China
| | - Yupei Zhang
- School of Computer Science, Northwestern Polytechnical University, Xi'an 710129, Shaanxi, China
- Key Laboratory of Big Data Storage and Management, MIIT, Ministry of Industry and Information Technology, Xi'an 710129, Shaanxi, China
| | - Jiajie Peng
- School of Computer Science, Northwestern Polytechnical University, Xi'an 710129, Shaanxi, China
- Key Laboratory of Big Data Storage and Management, MIIT, Ministry of Industry and Information Technology, Xi'an 710129, Shaanxi, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi'an 710129, Shaanxi, China
- Key Laboratory of Big Data Storage and Management, MIIT, Ministry of Industry and Information Technology, Xi'an 710129, Shaanxi, China
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13
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Kazer SW, Match CM, Langan EM, Messou MA, LaSalle TJ, O’Leary E, Marbourg J, Naughton K, von Andrian UH, Ordovas-Montanes J. Primary nasal viral infection rewires the tissue-scale memory response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.11.539887. [PMID: 38562902 PMCID: PMC10983857 DOI: 10.1101/2023.05.11.539887] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The nasal mucosa is frequently the initial site of respiratory viral infection, replication, and transmission. Recent work has started to clarify the independent responses of epithelial, myeloid, and lymphoid cells to viral infection in the nasal mucosa, but their spatiotemporal coordination and relative contributions remain unclear. Furthermore, understanding whether and how primary infection shapes tissue-scale memory responses to secondary challenge is critical for the rational design of nasal-targeting therapeutics and vaccines. Here, we generated a single-cell RNA-sequencing (scRNA-seq) atlas of the murine nasal mucosa sampling three distinct regions before and during primary and secondary influenza infection. Primary infection was largely restricted to respiratory mucosa and induced stepwise changes in cell type, subset, and state composition over time. Type I Interferon (IFN)-responsive neutrophils appeared 2 days post infection (dpi) and preceded transient IFN-responsive/cycling epithelial cell responses 5 dpi, which coincided with broader antiviral monocyte and NK cell accumulation. By 8 dpi, monocyte-derived macrophages (MDMs) expressing Cxcl9 and Cxcl16 arose alongside effector cytotoxic CD8 and Ifng-expressing CD4 T cells. Following viral clearance (14 dpi), rare, previously undescribed Krt13+ nasal immune-interacting floor epithelial (KNIIFE) cells expressing multiple genes with immune communication potential increased concurrently with tissue-resident memory T (TRM)-like cells and early IgG+/IgA+ plasmablasts. Proportionality analysis coupled with cell-cell communication inference, alongside validation by in situ microscopy, underscored the CXCL16-CXCR6 signaling axis between MDMs and effector CD8 T cells 8dpi and KNIIFE cells and TRM cells 14 dpi. Secondary influenza challenge with a homologous or heterologous strain administered 60 dpi induced an accelerated and coordinated myeloid and lymphoid response without epithelial proliferation, illustrating how tissue-scale memory to natural infection engages both myeloid and lymphoid cells to reduce epithelial regenerative burden. Together, this atlas serves as a reference for viral infection in the upper respiratory tract and highlights the efficacy of local coordinated memory responses upon rechallenge.
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Affiliation(s)
- Samuel W. Kazer
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Colette Matysiak Match
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Erica M. Langan
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marie-Angèle Messou
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Thomas J. LaSalle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Health Sciences and Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA
| | - Elise O’Leary
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | | | | | - Ulrich H. von Andrian
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
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14
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Liao Y, Rao Z, Huang S, Zhao D. Protocol to analyze immune cells in the tumor microenvironment by transcriptome using machine learning. STAR Protoc 2024; 5:102684. [PMID: 38219153 PMCID: PMC10826422 DOI: 10.1016/j.xpro.2023.102684] [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: 08/01/2023] [Revised: 09/15/2023] [Accepted: 10/10/2023] [Indexed: 01/16/2024] Open
Abstract
Immunotherapy is a promising strategy to treat cancer. Here, we present a protocol for analyzing the transcriptome-based phenotypic alterations and immune cell infiltration in the tumor microenvironment. We describe steps for integrating single-cell RNA sequencing (scRNA-seq) data, comparing phenotypes and origins of mononuclear phagocytes, inferring the differentiation trajectory and infiltration process, and identifying infiltration-associated genes using machine learning. We then detail procedures for exploring the impact of these genes in prognosis through the integrated microarray and bulk RNA-seq data to obtain potential drug targets. For complete details on the use and execution of this protocol, please refer to Liao et al.1.
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Affiliation(s)
- Yunxi Liao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Ziyan Rao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Shaodong Huang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Dongyu Zhao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China.
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15
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Brand J, Haro M, Lin X, Rimel B, McGregor SM, Lawrenson K, Dinh HQ. Fallopian tube single cell analysis reveals myeloid cell alterations in high-grade serous ovarian cancer. iScience 2024; 27:108990. [PMID: 38384837 PMCID: PMC10879678 DOI: 10.1016/j.isci.2024.108990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/23/2024] Open
Abstract
Most high-grade serous ovarian cancers (HGSCs) likely initiate from fallopian tube (FT) epithelia. While epithelial subtypes have been characterized using single-cell RNA-sequencing (scRNA-Seq), heterogeneity of other compartments and their involvement in tumor progression are poorly defined. Integrated analysis of human FT scRNA-Seq and HGSC-related tissues, including tumors, revealed greater immune and stromal transcriptional diversity than previously reported. We identified abundant monocytes in FTs across two independent cohorts. The ratio of macrophages to monocytes is similar between benign FTs, ovaries, and adjacent normal tissues but significantly greater in tumors. FT-defined monocyte and macrophage signatures, cell-cell communication, and gene set enrichment analyses identified monocyte- and macrophage-specific interactions and functional pathways in paired tumors and adjacent normal tissues. Further reanalysis of HGSC scRNA-Seq identified monocyte and macrophage subsets associated with neoadjuvant chemotherapy. Taken together, our work provides data that an altered FT myeloid cell composition could inform the discovery of early detection markers for HGSC.
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Affiliation(s)
- Joshua Brand
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin – Madison, Madison, WI 53705, USA
| | - Marcela Haro
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Xianzhi Lin
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- RNA Biology Group, Division of Natural and Applied Sciences and Global Health Research Center, Duke Kunshan University, Kunshan 215316, Jiangsu Province, China
| | - B.J. Rimel
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Stephanie M. McGregor
- Department of Pathology and Laboratory Medicine, University of Wisconsin – Madison, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Kate Lawrenson
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Huy Q. Dinh
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin – Madison, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin – Madison, Madison, WI 53705, USA
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16
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Zhang W, Sen A, Pena JK, Reitsma A, Alexander OC, Tajima T, Martinez OM, Krams SM. Application of Mass Cytometry Platforms to Solid Organ Transplantation. Transplantation 2024:00007890-990000000-00687. [PMID: 38467594 DOI: 10.1097/tp.0000000000004925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Transplantation serves as the cornerstone of treatment for patients with end-stage organ disease. The prevalence of complications, such as allograft rejection, infection, and malignancies, underscores the need to dissect the complex interactions of the immune system at the single-cell level. In this review, we discuss studies using mass cytometry or cytometry by time-of-flight, a cutting-edge technology enabling the characterization of immune populations and cell-to-cell interactions in granular detail. We review the application of mass cytometry in human and experimental animal studies in the context of transplantation, uncovering invaluable contributions of the tool to understanding rejection and other transplant-related complications. We discuss recent innovations that have the potential to streamline and standardize mass cytometry workflows for application to multisite clinical trials. Additionally, we introduce imaging mass cytometry, a technique that couples the power of mass cytometry with spatial context, thereby mapping cellular interactions within tissue microenvironments. The synergistic integration of mass cytometry and imaging mass cytometry data with other omics data sets and high-dimensional data platforms to further define immune dynamics is discussed. In conclusion, mass cytometry technologies, when integrated with other tools and data, shed light on the intricate landscape of the immune response in transplantation. This approach holds significant potential for enhancing patient outcomes by advancing our understanding and facilitating the development of new diagnostics and therapeutics.
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Affiliation(s)
- Wenming Zhang
- Department of Surgery, Stanford University, Stanford, CA
| | - Ayantika Sen
- Department of Surgery, Stanford University, Stanford, CA
| | | | - Andrea Reitsma
- Department of Surgery, Stanford University, Stanford, CA
| | - Oliver C Alexander
- Department of Surgery, Stanford University, Stanford, CA
- Meharry Medical College, School of Medicine, Nashville, TN
| | - Tetsuya Tajima
- Department of Surgery, Stanford University, Stanford, CA
| | | | - Sheri M Krams
- Department of Surgery, Stanford University, Stanford, CA
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17
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Chatterjee N, Komaravolu RK, Durant CP, Wu R, McSkimming C, Drago F, Kumar S, Valentin-Guillama G, Miller YI, McNamara CA, Ley K, Taylor A, Alimadadi A, Hedrick CC. Single Cell High Dimensional Analysis of Human Peripheral Blood Mononuclear Cells Reveals Unique Intermediate Monocyte Subsets Associated with Sex Differences in Coronary Artery Disease. Int J Mol Sci 2024; 25:2894. [PMID: 38474140 PMCID: PMC10932111 DOI: 10.3390/ijms25052894] [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: 01/17/2024] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Monocytes are associated with human cardiovascular disease progression. Monocytes are segregated into three major subsets: classical (cMo), intermediate (iMo), and nonclassical (nMo). Recent studies have identified heterogeneity within each of these main monocyte classes, yet the extent to which these subsets contribute to heart disease progression is not known. Peripheral blood mononuclear cells (PBMC) were obtained from 61 human subjects within the Coronary Assessment of Virginia (CAVA) Cohort. Coronary atherosclerosis severity was quantified using the Gensini Score (GS). We employed high-dimensional single-cell transcriptome and protein methods to define how human monocytes differ in subjects with low to severe coronary artery disease. We analyzed 487 immune-related genes and 49 surface proteins at the single-cell level using Antibody-Seq (Ab-Seq). We identified six subsets of myeloid cells (cMo, iMo, nMo, plasmacytoid DC, classical DC, and DC3) at the single-cell level based on surface proteins, and we associated these subsets with coronary artery disease (CAD) incidence based on Gensini score (GS) in each subject. Only frequencies of iMo were associated with high CAD (GS > 32), adj.p = 0.024. Spearman correlation analysis with GS from each subject revealed a positive correlation with iMo frequencies (r = 0.314, p = 0.014) and further showed a robust sex-dependent positive correlation in female subjects (r = 0.663, p = 0.004). cMo frequencies did not correlate with CAD severity. Key gene pathways differed in iMo among low and high CAD subjects and between males and females. Further single-cell analysis of iMo revealed three iMo subsets in human PBMC, distinguished by the expression of HLA-DR, CXCR3, and CD206. We found that the frequency of immunoregulatory iMo_HLA-DR+CXCR3+CD206+ was associated with CAD severity (adj.p = 0.006). The immunoregulatory iMo subset positively correlated with GS in both females (r = 0.660, p = 0.004) and males (r = 0.315, p = 0.037). Cell interaction analyses identified strong interactions of iMo with CD4+ effector/memory T cells and Tregs from the same subjects. This study shows the importance of iMo in CAD progression and suggests that iMo may have important functional roles in modulating CAD risk, particularly among females.
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Affiliation(s)
- Nandini Chatterjee
- La Jolla Institute of Immunology, La Jolla, CA 92037, USA; (N.C.); (K.L.)
| | - Ravi K. Komaravolu
- Department of Medicine, Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA; (R.K.K.)
| | | | - Runpei Wu
- La Jolla Institute of Immunology, La Jolla, CA 92037, USA; (N.C.); (K.L.)
| | - Chantel McSkimming
- Beirne Carter Immunology Center, University of Virginia, Charlottesville, VA 22904, USA (A.T.)
| | - Fabrizio Drago
- Beirne Carter Immunology Center, University of Virginia, Charlottesville, VA 22904, USA (A.T.)
| | - Sunil Kumar
- Department of Medicine, Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA; (R.K.K.)
| | - Gabriel Valentin-Guillama
- Department of Medicine, Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA; (R.K.K.)
| | - Yury I. Miller
- Division of Endocrinology, University of California San Diego, La Jolla, CA 92093, USA
| | - Coleen A. McNamara
- Beirne Carter Immunology Center, University of Virginia, Charlottesville, VA 22904, USA (A.T.)
| | - Klaus Ley
- La Jolla Institute of Immunology, La Jolla, CA 92037, USA; (N.C.); (K.L.)
- Department of Medicine, Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA; (R.K.K.)
| | - Angela Taylor
- Beirne Carter Immunology Center, University of Virginia, Charlottesville, VA 22904, USA (A.T.)
| | - Ahmad Alimadadi
- La Jolla Institute of Immunology, La Jolla, CA 92037, USA; (N.C.); (K.L.)
- Department of Medicine, Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA; (R.K.K.)
| | - Catherine C. Hedrick
- La Jolla Institute of Immunology, La Jolla, CA 92037, USA; (N.C.); (K.L.)
- Department of Medicine, Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA; (R.K.K.)
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18
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Puvogel S, Alsema A, North HF, Webster MJ, Weickert CS, Eggen BJL. Single-Nucleus RNA-Seq Characterizes the Cell Types Along the Neuronal Lineage in the Adult Human Subependymal Zone and Reveals Reduced Oligodendrocyte Progenitor Abundance with Age. eNeuro 2024; 11:ENEURO.0246-23.2024. [PMID: 38351133 PMCID: PMC10913050 DOI: 10.1523/eneuro.0246-23.2024] [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: 07/12/2023] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 03/06/2024] Open
Abstract
The subependymal zone (SEZ), also known as the subventricular zone (SVZ), constitutes a neurogenic niche that persists during postnatal life. In humans, the neurogenic potential of the SEZ declines after the first year of life. However, studies discovering markers of stem and progenitor cells highlight the neurogenic capacity of progenitors in the adult human SEZ, with increased neurogenic activity occurring under pathological conditions. In the present study, the complete cellular niche of the adult human SEZ was characterized by single-nucleus RNA sequencing, and compared between four youth (age 16-22) and four middle-aged adults (age 44-53). We identified 11 cellular clusters including clusters expressing marker genes for neural stem cells (NSCs), neuroblasts, immature neurons, and oligodendrocyte progenitor cells. The relative abundance of NSC and neuroblast clusters did not differ between the two age groups, indicating that the pool of SEZ NSCs does not decline in this age range. The relative abundance of oligodendrocyte progenitors and microglia decreased in middle-age, indicating that the cellular composition of human SEZ is remodeled between youth and adulthood. The expression of genes related to nervous system development was higher across different cell types, including NSCs, in youth as compared with middle-age. These transcriptional changes suggest ongoing central nervous system plasticity in the SEZ in youth, which declined in middle-age.
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Affiliation(s)
- Sofía Puvogel
- Section Molecular Neurobiology, Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen 9700 AD, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen 6500 HB, The Netherlands
| | - Astrid Alsema
- Section Molecular Neurobiology, Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen 9700 AD, The Netherlands
| | - Hayley F North
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney, New South Wales 2031, Australia
- School of Psychiatry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Maree J Webster
- Laboratory of Brain Research, Stanley Medical Research Institute, Rockville 20850, Maryland
| | - Cynthia Shannon Weickert
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney, New South Wales 2031, Australia
- School of Psychiatry, University of New South Wales, Sydney, New South Wales 2052, Australia
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, New York 13201
| | - Bart J L Eggen
- Section Molecular Neurobiology, Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen 9700 AD, The Netherlands
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19
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Hu J, Wang SG, Hou Y, Chen Z, Liu L, Li R, Li N, Zhou L, Yang Y, Wang L, Wang L, Yang X, Lei Y, Deng C, Li Y, Deng Z, Ding Y, Kuang Y, Yao Z, Xun Y, Li F, Li H, Hu J, Liu Z, Wang T, Hao Y, Jiao X, Guan W, Tao Z, Ren S, Chen K. Multi-omic profiling of clear cell renal cell carcinoma identifies metabolic reprogramming associated with disease progression. Nat Genet 2024; 56:442-457. [PMID: 38361033 PMCID: PMC10937392 DOI: 10.1038/s41588-024-01662-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a complex disease with remarkable immune and metabolic heterogeneity. Here we perform genomic, transcriptomic, proteomic, metabolomic and spatial transcriptomic and metabolomic analyses on 100 patients with ccRCC from the Tongji Hospital RCC (TJ-RCC) cohort. Our analysis identifies four ccRCC subtypes including De-clear cell differentiated (DCCD)-ccRCC, a subtype with distinctive metabolic features. DCCD cancer cells are characterized by fewer lipid droplets, reduced metabolic activity, enhanced nutrient uptake capability and a high proliferation rate, leading to poor prognosis. Using single-cell and spatial trajectory analysis, we demonstrate that DCCD is a common mode of ccRCC progression. Even among stage I patients, DCCD is associated with worse outcomes and higher recurrence rate, suggesting that it cannot be cured by nephrectomy alone. Our study also suggests a treatment strategy based on subtype-specific immune cell infiltration that could guide the clinical management of ccRCC.
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Affiliation(s)
- Junyi Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shao-Gang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaxin Hou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhaohui Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lilong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ruizhi Li
- Shanghai Luming Biotech, Shanghai, China
| | - Nisha Li
- Shanghai Luming Biotech, Shanghai, China
- Shanghai OE Biotech, Shanghai, China
| | - Lijie Zhou
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Yang
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Liping Wang
- Department of Pathology, Baylor Scott & White Medical Center, Temple, TX, USA
| | - Liang Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiong Yang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yichen Lei
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Changqi Deng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyao Deng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhong Ding
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingchun Kuang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhipeng Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Xun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fan Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Hao
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuanmao Jiao
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Philadelphia, PA, USA
| | - Wei Guan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Zhen Tao
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Tianjin's Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Shancheng Ren
- Department of Urology, Second Affiliated Hospital of Naval Medical University, Shanghai, China.
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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20
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Nakanoh S, Sham K, Ghimire S, Mohorianu I, Rayon T, Vallier L. Human surface ectoderm and amniotic ectoderm are sequentially specified according to cellular density. SCIENCE ADVANCES 2024; 10:eadh7748. [PMID: 38427729 PMCID: PMC10906920 DOI: 10.1126/sciadv.adh7748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 01/29/2024] [Indexed: 03/03/2024]
Abstract
Mechanisms specifying amniotic ectoderm and surface ectoderm are unresolved in humans due to their close similarities in expression patterns and signal requirements. This lack of knowledge hinders the development of protocols to accurately model human embryogenesis. Here, we developed a human pluripotent stem cell model to investigate the divergence between amniotic and surface ectoderms. In the established culture system, cells differentiated into functional amnioblast-like cells. Single-cell RNA sequencing analyses of amnioblast differentiation revealed an intermediate cell state with enhanced surface ectoderm gene expression. Furthermore, when the differentiation started at the confluent condition, cells retained the expression profile of surface ectoderm. Collectively, we propose that human amniotic ectoderm and surface ectoderm are specified along a common nonneural ectoderm trajectory based on cell density. Our culture system also generated extraembryonic mesoderm-like cells from the primed pluripotent state. Together, this study provides an integrative understanding of the human nonneural ectoderm development and a model for embryonic and extraembryonic human development around gastrulation.
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Affiliation(s)
- Shota Nakanoh
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
- Epigenetics & Signalling Programmes, Babraham Institute, Cambridge CB22 3AT, UK
| | - Kendig Sham
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Sabitri Ghimire
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Irina Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Teresa Rayon
- Epigenetics & Signalling Programmes, Babraham Institute, Cambridge CB22 3AT, UK
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
- Berlin Institute of Health Centre for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany
- Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
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21
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Hu B, Jin H, Shi Y, Yu H, Wu X, Wang S, Zhang K. Single-cell RNA-Seq reveals the earliest lineage specification and X chromosome dosage compensation in bovine preimplantation embryos. FASEB J 2024; 38:e23492. [PMID: 38363564 DOI: 10.1096/fj.202302035rr] [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: 10/08/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
Lineage specification and X chromosome dosage compensation are two crucial biological processes that occur during preimplantation embryonic development. Although extensively studied in mice, the timing and regulation of these processes remain elusive in other species, including humans. Previous studies have suggested conserved principles of human and bovine early development. This study aims to provide fundamental insights into these programs and the regulation using a bovine embryo model by employing single-cell transcriptomics and genome editing approaches. The study analyzes the transcriptomes of 286 individual cells and reveals that bovine trophectoderm/inner cell mass transcriptomes diverge at the early blastocyst stage, after cavitation but before blastocyst expansion. The study also identifies transcriptomic markers and provides the timing of lineage specification events in the bovine embryo. Importantly, we find that SOX2 is required for the first cell decision program in bovine embryos. Moreover, the study shows the occurrence of X chromosome dosage compensation from morula to late blastocyst and reveals that this compensation results from downregulation of X-linked genes in female embryonic cells. The transcriptional atlas generated by this study is expected to be widely useful in improving our understanding of mammalian early embryo development.
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Affiliation(s)
- Bingjie Hu
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Jin
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Shi
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haotian Yu
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaotong Wu
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shaohua Wang
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kun Zhang
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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22
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Taelman J, Czukiewska SM, Moustakas I, Chang YW, Hillenius S, van der Helm T, van der Meeren LE, Mei H, Fan X, Chuva de Sousa Lopes SM. Characterization of the human fetal gonad and reproductive tract by single-cell transcriptomics. Dev Cell 2024; 59:529-544.e5. [PMID: 38295793 PMCID: PMC10898717 DOI: 10.1016/j.devcel.2024.01.006] [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: 02/12/2022] [Revised: 09/05/2023] [Accepted: 01/08/2024] [Indexed: 02/29/2024]
Abstract
During human fetal development, sex differentiation occurs not only in the gonads but also in the adjacent developing reproductive tract. However, while the cellular composition of male and female human fetal gonads is well described, that of the adjacent developing reproductive tract remains poorly characterized. Here, we performed single-cell transcriptomics on male and female human fetal gonads together with the adjacent developing reproductive tract from first and second trimesters, highlighting the morphological and molecular changes during sex differentiation. We validated different cell populations of the developing reproductive tract and gonads and compared the molecular signatures between the first and second trimesters, as well as between sexes, to identify conserved and sex-specific features. Together, our study provides insights into human fetal sex-specific gonadogenesis and development of the reproductive tract beyond the gonads.
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Affiliation(s)
- Jasin Taelman
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Sylwia M Czukiewska
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Ioannis Moustakas
- Sequencing Analysis Support Core, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Yolanda W Chang
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Sanne Hillenius
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Talia van der Helm
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Lotte E van der Meeren
- Department of Pathology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands; Department of Pathology, Erasmus Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Xueying Fan
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands.
| | - Susana M Chuva de Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands; Department for Reproductive Medicine, Ghent University Hospital, 9000 Ghent, Belgium.
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23
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Fisher J, Verhagen M, Long Z, Moissidis M, Yan Y, He C, Wang J, Micoli E, Alastruey CM, Moors R, Marín O, Mi D, Lim L. Cortical somatostatin long-range projection neurons and interneurons exhibit divergent developmental trajectories. Neuron 2024; 112:558-573.e8. [PMID: 38086373 DOI: 10.1016/j.neuron.2023.11.013] [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: 11/07/2022] [Revised: 08/22/2023] [Accepted: 11/10/2023] [Indexed: 02/24/2024]
Abstract
The mammalian cerebral cortex contains an extraordinary diversity of cell types that emerge by implementing different developmental programs. Delineating when and how cellular diversification occurs is particularly challenging for cortical inhibitory neurons because they represent a small proportion of all cortical cells and have a protracted development. Here, we combine single-cell RNA sequencing and spatial transcriptomics to characterize the emergence of neuronal diversity among somatostatin-expressing (SST+) cells in mice. We found that SST+ inhibitory neurons segregate during embryonic stages into long-range projection (LRP) neurons and two types of interneurons, Martinotti cells and non-Martinotti cells, following distinct developmental trajectories. Two main subtypes of LRP neurons and several subtypes of interneurons are readily distinguishable in the embryo, although interneuron diversity is likely refined during early postnatal life. Our results suggest that the timing for cellular diversification is unique for different subtypes of SST+ neurons and particularly divergent for LRP neurons and interneurons.
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Affiliation(s)
- Josephine Fisher
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE1 1UL London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL, London, UK
| | - Marieke Verhagen
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Zhen Long
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Monika Moissidis
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE1 1UL London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL, London, UK
| | - Yiming Yan
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chenyi He
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingyu Wang
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Elia Micoli
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Clara Milían Alastruey
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Rani Moors
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE1 1UL London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL, London, UK.
| | - Da Mi
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Lynette Lim
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium.
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24
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De Blander H, Tonon L, Fauvet F, Pommier RM, Lamblot C, Benhassoun R, Angileri F, Gibert B, Rodriguez R, Ouzounova M, Morel AP, Puisieux A. Cooperative pro-tumorigenic adaptation to oncogenic RAS through epithelial-to-mesenchymal plasticity. SCIENCE ADVANCES 2024; 10:eadi1736. [PMID: 38354248 PMCID: PMC10866563 DOI: 10.1126/sciadv.adi1736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
In breast cancers, aberrant activation of the RAS/MAPK pathway is strongly associated with mesenchymal features and stemness traits, suggesting an interplay between this mitogenic signaling pathway and epithelial-to-mesenchymal plasticity (EMP). By using inducible models of human mammary epithelial cells, we demonstrate herein that the oncogenic activation of RAS promotes ZEB1-dependent EMP, which is necessary for malignant transformation. Notably, EMP is triggered by the secretion of pro-inflammatory cytokines from neighboring RAS-activated senescent cells, with a prominent role for IL-6 and IL-1α. Our data contrast with the common view of cellular senescence as a tumor-suppressive mechanism and EMP as a process promoting late stages of tumor progression in response to signals from the tumor microenvironment. We highlighted here a pro-tumorigenic cooperation of RAS-activated mammary epithelial cells, which leverages on oncogene-induced senescence and EMP to trigger cellular reprogramming and malignant transformation.
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Affiliation(s)
- Hadrien De Blander
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
| | - Laurie Tonon
- Synergie Lyon Cancer, Plateforme de Bioinformatique ‘Gilles Thomas’, Centre Léon Bérard, Lyon, France
| | - Frédérique Fauvet
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
| | - Roxane M. Pommier
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
- Synergie Lyon Cancer, Plateforme de Bioinformatique ‘Gilles Thomas’, Centre Léon Bérard, Lyon, France
| | - Christelle Lamblot
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
| | - Rahma Benhassoun
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
| | - Francesca Angileri
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
| | - Benjamin Gibert
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
- Gastroenterology and Technologies for Health Group, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS5286, Université Lyon 1, 69008, Lyon, France
| | - Raphaël Rodriguez
- Equipe Labellisée Ligue Contre le Cancer, CNRS UMR 3666, INSERM U1143, Paris, France
- Institut Curie, PSL Research University, Paris, France
| | - Maria Ouzounova
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
| | - Anne-Pierre Morel
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
| | - Alain Puisieux
- Equipe Labellisée Ligue Contre le Cancer, CNRS UMR 3666, INSERM U1143, Paris, France
- Institut Curie, PSL Research University, Paris, France
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25
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Zhang K, Zemke NR, Armand EJ, Ren B. A fast, scalable and versatile tool for analysis of single-cell omics data. Nat Methods 2024; 21:217-227. [PMID: 38191932 PMCID: PMC10864184 DOI: 10.1038/s41592-023-02139-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/23/2023] [Indexed: 01/10/2024]
Abstract
Single-cell omics technologies have revolutionized the study of gene regulation in complex tissues. A major computational challenge in analyzing these datasets is to project the large-scale and high-dimensional data into low-dimensional space while retaining the relative relationships between cells. This low dimension embedding is necessary to decompose cellular heterogeneity and reconstruct cell-type-specific gene regulatory programs. Traditional dimensionality reduction techniques, however, face challenges in computational efficiency and in comprehensively addressing cellular diversity across varied molecular modalities. Here we introduce a nonlinear dimensionality reduction algorithm, embodied in the Python package SnapATAC2, which not only achieves a more precise capture of single-cell omics data heterogeneities but also ensures efficient runtime and memory usage, scaling linearly with the number of cells. Our algorithm demonstrates exceptional performance, scalability and versatility across diverse single-cell omics datasets, including single-cell assay for transposase-accessible chromatin using sequencing, single-cell RNA sequencing, single-cell Hi-C and single-cell multi-omics datasets, underscoring its utility in advancing single-cell analysis.
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Affiliation(s)
- Kai Zhang
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, China
| | - Nathan R Zemke
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Ethan J Armand
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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26
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Umeda M, Ma J, Westover T, Ni Y, Song G, Maciaszek JL, Rusch M, Rahbarinia D, Foy S, Huang BJ, Walsh MP, Kumar P, Liu Y, Yang W, Fan Y, Wu G, Baker SD, Ma X, Wang L, Alonzo TA, Rubnitz JE, Pounds S, Klco JM. A new genomic framework to categorize pediatric acute myeloid leukemia. Nat Genet 2024; 56:281-293. [PMID: 38212634 PMCID: PMC10864188 DOI: 10.1038/s41588-023-01640-3] [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: 05/11/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024]
Abstract
Recent studies on pediatric acute myeloid leukemia (pAML) have revealed pediatric-specific driver alterations, many of which are underrepresented in the current classification schemas. To comprehensively define the genomic landscape of pAML, we systematically categorized 887 pAML into 23 mutually distinct molecular categories, including new major entities such as UBTF or BCL11B, covering 91.4% of the cohort. These molecular categories were associated with unique expression profiles and mutational patterns. For instance, molecular categories characterized by specific HOXA or HOXB expression signatures showed distinct mutation patterns of RAS pathway genes, FLT3 or WT1, suggesting shared biological mechanisms. We show that molecular categories were strongly associated with clinical outcomes using two independent cohorts, leading to the establishment of a new prognostic framework for pAML based on these updated molecular categories and minimal residual disease. Together, this comprehensive diagnostic and prognostic framework forms the basis for future classification of pAML and treatment strategies.
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Affiliation(s)
- Masayuki Umeda
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yonghui Ni
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jamie L Maciaszek
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Delaram Rahbarinia
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Benjamin J Huang
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Michael P Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Priyadarshini Kumar
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sharyn D Baker
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lu Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Todd A Alonzo
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeffrey E Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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27
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Wang T, Peng J, Fan J, Tang N, Hua R, Zhou X, Wang Z, Wang L, Bai Y, Quan X, Wang Z, Zhang L, Luo C, Zhang W, Kang X, Liu J, Li L, Li L. Single-cell multi-omics profiling of human preimplantation embryos identifies cytoskeletal defects during embryonic arrest. Nat Cell Biol 2024; 26:263-277. [PMID: 38238450 DOI: 10.1038/s41556-023-01328-0] [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: 03/01/2023] [Accepted: 12/01/2023] [Indexed: 02/16/2024]
Abstract
Human in vitro fertilized embryos exhibit low developmental capabilities, and the mechanisms that underlie embryonic arrest remain unclear. Here using a single-cell multi-omics sequencing approach, we simultaneously analysed alterations in the transcriptome, chromatin accessibility and the DNA methylome in human embryonic arrest due to unexplained reasons. Arrested embryos displayed transcriptome disorders, including a distorted microtubule cytoskeleton, increased genomic instability and impaired glycolysis, which were coordinated with multiple epigenetic reprogramming defects. We identified Aurora A kinase (AURKA) repression as a cause of embryonic arrest. Mechanistically, arrested embryos induced through AURKA inhibition resembled the reprogramming abnormalities of natural embryonic arrest in terms of the transcriptome, the DNA methylome, chromatin accessibility and H3K4me3 modifications. Mitosis-independent sequential activation of the zygotic genome in arrested embryos showed that YY1 contributed to human major zygotic genome activation. Collectively, our study decodes the reprogramming abnormalities and mechanisms of human embryonic arrest and the key regulators of zygotic genome activation.
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Affiliation(s)
- Teng Wang
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Junhua Peng
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Jiaqi Fan
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Ni Tang
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Rui Hua
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, P. R. China
| | - Xueliang Zhou
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Zhihao Wang
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Longfei Wang
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Yanling Bai
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Xiaowan Quan
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Zimeng Wang
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Li Zhang
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Chen Luo
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, P. R. China
| | - Weiqing Zhang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, P. R. China
| | - Xiangjin Kang
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Jianqiao Liu
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Lei Li
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China.
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China.
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China.
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China.
| | - Lin Li
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China.
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28
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Van Haver S, Fan Y, Bekaert SL, Everaert C, Van Loocke W, Zanzani V, Deschildre J, Maestre IF, Amaro A, Vermeirssen V, De Preter K, Zhou T, Kentsis A, Studer L, Speleman F, Roberts SS. Human iPSC modeling recapitulates in vivo sympathoadrenal development and reveals an aberrant developmental subpopulation in familial neuroblastoma. iScience 2024; 27:108096. [PMID: 38222111 PMCID: PMC10784699 DOI: 10.1016/j.isci.2023.108096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/12/2023] [Accepted: 09/26/2023] [Indexed: 01/16/2024] Open
Abstract
Studies defining normal and disrupted human neural crest cell development have been challenging given its early timing and intricacy of development. Consequently, insight into the early disruptive events causing a neural crest related disease such as pediatric cancer neuroblastoma is limited. To overcome this problem, we developed an in vitro differentiation model to recapitulate the normal in vivo developmental process of the sympathoadrenal lineage which gives rise to neuroblastoma. We used human in vitro pluripotent stem cells and single-cell RNA sequencing to recapitulate the molecular events during sympathoadrenal development. We provide a detailed map of dynamically regulated transcriptomes during sympathoblast formation and illustrate the power of this model to study early events of the development of human neuroblastoma, identifying a distinct subpopulation of cell marked by SOX2 expression in developing sympathoblast obtained from patient derived iPSC cells harboring a germline activating mutation in the anaplastic lymphoma kinase (ALK) gene.
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Affiliation(s)
- Stéphane Van Haver
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Yujie Fan
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
- Developmental Biology Program, MSKCC, New York, NY 10065, USA
- Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065, USA
| | - Sarah-Lee Bekaert
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Celine Everaert
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Vittorio Zanzani
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Joke Deschildre
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Inés Fernandez Maestre
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adrianna Amaro
- Department of Pediatrics, MSKCC, New York, NY 10065, USA
| | - Vanessa Vermeirssen
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Ting Zhou
- The SKI Stem Cell Research Facility, The Center for Stem Cell Biology and Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Alex Kentsis
- Department of Pediatrics, MSKCC, New York, NY 10065, USA
- Molecular Pharmacology Program, MSKCC, New York, NY, USA
- Tow Center for Developmental Oncology, MSKCC, New York, NY 10065, USA
- Departments of Pediatrics, Pharmacology and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
- Developmental Biology Program, MSKCC, New York, NY 10065, USA
| | - Frank Speleman
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
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29
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Ng MS, Kwok I, Tan L, Shi C, Cerezo-Wallis D, Tan Y, Leong K, Yang K, Zhang Y, Jing J, Liong KH, Wu D, He R, Liu D, Teh YC, Bleriot C, Caronni N, Liu Z, Duan K, Narang V, Li M, Chen J, Liu Y, Liu L, Qi J, Liu Y, Jiang L, Shen B, Cheng H, Cheng T, Angeli V, Sharma A, Loh YH, Tey HL, Chong SZ, Ostuni R, Hidalgo A, Ginhoux F, Ng LG. Deterministic reprogramming of neutrophils within tumors. Science 2024; 383:eadf6493. [PMID: 38207030 PMCID: PMC11087151 DOI: 10.1126/science.adf6493] [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: 11/09/2022] [Accepted: 11/27/2023] [Indexed: 01/13/2024]
Abstract
Neutrophils are increasingly recognized as key players in the tumor immune response and are associated with poor clinical outcomes. Despite recent advances characterizing the diversity of neutrophil states in cancer, common trajectories and mechanisms governing the ontogeny and relationship between these neutrophil states remain undefined. Here, we demonstrate that immature and mature neutrophils that enter tumors undergo irreversible epigenetic, transcriptional, and proteomic modifications to converge into a distinct, terminally differentiated dcTRAIL-R1+ state. Reprogrammed dcTRAIL-R1+ neutrophils predominantly localize to a glycolytic and hypoxic niche at the tumor core and exert pro-angiogenic function that favors tumor growth. We found similar trajectories in neutrophils across multiple tumor types and in humans, suggesting that targeting this program may provide a means of enhancing certain cancer immunotherapies.
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Affiliation(s)
- Melissa S.F. Ng
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
| | - Immanuel Kwok
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
| | - Leonard Tan
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
| | - Changming Shi
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital; Shanghai, China
| | - Daniela Cerezo-Wallis
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III; Madrid, Spain
- Vascular Biology and Therapeutics Program and Department of Immunobiology, Yale University School of Medicine; New Haven, USA
| | - Yingrou Tan
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
- National Skin Centre, National Healthcare Group; Singapore
| | - Keith Leong
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
| | - Katharine Yang
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
| | - Yuning Zhang
- Department of Microbiology and Immunology, National University of Singapore (NUS); Singapore
| | - Jingsi Jing
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital; Shanghai, China
| | - Ka Hang Liong
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
| | - Dandan Wu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine; Shanghai, China
| | - Rui He
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital; Shanghai, China
| | - Dehua Liu
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
| | - Ye Chean Teh
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
| | - Camille Bleriot
- INSERM U1015, Institut Gustave Roussy; Villejuif, France
- CNRS UMR8253, Institut Necker des Enfants Malades; Paris, France
| | - Nicoletta Caronni
- Genomics of the Innate Immune System Unit, San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute; Milan, Italy
| | - Zhaoyuan Liu
- Genomics of the Innate Immune System Unit, San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute; Milan, Italy
| | - Kaibo Duan
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
| | - Vipin Narang
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
| | - Mengwei Li
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
| | - Jinmiao Chen
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
| | | | - Lianxin Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China; Anhui, China
| | - Jingjing Qi
- Department of Biliary and Pancreatic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine; Shanghai, China
- Shanghai Institute of Cancer Biology, Renji Hospital, Shanghai Jiao Tong University School of Medicine; Shanghai, China
| | - Yingbin Liu
- Department of Biliary and Pancreatic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine; Shanghai, China
- Shanghai Institute of Cancer Biology, Renji Hospital, Shanghai Jiao Tong University School of Medicine; Shanghai, China
| | - Lingxi Jiang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine; Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiaotong University School of Medicine; Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University; Shanghai, China
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine; Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiaotong University School of Medicine; Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University; Shanghai, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin, China
| | - Veronique Angeli
- Department of Microbiology and Immunology, National University of Singapore (NUS); Singapore
| | - Ankur Sharma
- Harry Perkins Institute of Medical Research, QEII Medical Centre; Nedlands, Western Australia, Australia
- Curtin Medical School, Curtin University; Bentley, Western Australia, Australia
- Curtin Health Innovation Research Institute, Curtin University; Bentley, Western Australia, Australia
| | - Yuin-han Loh
- Genome Institute of Singapore (GIS), A*STAR (Agency for Science, Technology and Research); Singapore
| | - Hong Liang Tey
- National Skin Centre, National Healthcare Group; Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University; Singapore
- Yong Loo Lin School of Medicine, National University of Singapore; Singapore
| | - Shu Zhen Chong
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
- Department of Microbiology and Immunology, National University of Singapore (NUS); Singapore
| | - Renato Ostuni
- Genomics of the Innate Immune System Unit, San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute; Milan, Italy
- Vita-Salute San Raffaele University, Milan; Italy
| | - Andrés Hidalgo
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III; Madrid, Spain
- Vascular Biology and Therapeutics Program and Department of Immunobiology, Yale University School of Medicine; New Haven, USA
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine; Shanghai, China
- INSERM U1015, Institut Gustave Roussy; Villejuif, France
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre; Singapore
| | - Lai Guan Ng
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research); Singapore
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital; Shanghai, China
- Department of Microbiology and Immunology, National University of Singapore (NUS); Singapore
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30
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Gisch DL, Brennan M, Lake BB, Basta J, Keller MS, Melo Ferreira R, Akilesh S, Ghag R, Lu C, Cheng YH, Collins KS, Parikh SV, Rovin BH, Robbins L, Stout L, Conklin KY, Diep D, Zhang B, Knoten A, Barwinska D, Asghari M, Sabo AR, Ferkowicz MJ, Sutton TA, Kelly KJ, De Boer IH, Rosas SE, Kiryluk K, Hodgin JB, Alakwaa F, Winfree S, Jefferson N, Türkmen A, Gaut JP, Gehlenborg N, Phillips CL, El-Achkar TM, Dagher PC, Hato T, Zhang K, Himmelfarb J, Kretzler M, Mollah S, Jain S, Rauchman M, Eadon MT. The chromatin landscape of healthy and injured cell types in the human kidney. Nat Commun 2024; 15:433. [PMID: 38199997 PMCID: PMC10781985 DOI: 10.1038/s41467-023-44467-6] [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: 06/15/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. Comprehensive integration of gene expression with epigenetic features that define regulatory elements remains a significant challenge. We measure dual single nucleus RNA expression and chromatin accessibility, DNA methylation, and H3K27ac, H3K4me1, H3K4me3, and H3K27me3 histone modifications to decipher the chromatin landscape and gene regulation of the kidney in reference and adaptive injury states. We establish a spatially-anchored epigenomic atlas to define the kidney's active, silent, and regulatory accessible chromatin regions across the genome. Using this atlas, we note distinct control of adaptive injury in different epithelial cell types. A proximal tubule cell transcription factor network of ELF3, KLF6, and KLF10 regulates the transition between health and injury, while in thick ascending limb cells this transition is regulated by NR2F1. Further, combined perturbation of ELF3, KLF6, and KLF10 distinguishes two adaptive proximal tubular cell subtypes, one of which manifested a repair trajectory after knockout. This atlas will serve as a foundation to facilitate targeted cell-specific therapeutics by reprogramming gene regulatory networks.
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Affiliation(s)
- Debora L Gisch
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Blue B Lake
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Jeannine Basta
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | | | | | | | - Reetika Ghag
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Charles Lu
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Ying-Hua Cheng
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Samir V Parikh
- Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Brad H Rovin
- Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Lynn Robbins
- St. Louis Veteran Affairs Medical Center, St. Louis, MO, 63106, USA
| | - Lisa Stout
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Kimberly Y Conklin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Dinh Diep
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Bo Zhang
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Amanda Knoten
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Daria Barwinska
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mahla Asghari
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Angela R Sabo
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Timothy A Sutton
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | | | - Sylvia E Rosas
- Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
| | | | | | | | - Seth Winfree
- University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Nichole Jefferson
- Kidney Precision Medicine Project Community Engagement Committee, Dallas, TX, USA
| | - Aydın Türkmen
- Istanbul School of Medicine, Division of Nephrology, Istanbul, Turkey
| | - Joseph P Gaut
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | | | | | - Pierre C Dagher
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Takashi Hato
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Shamim Mollah
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Sanjay Jain
- Washington University in Saint Louis, St. Louis, MO, 63103, USA.
| | - Michael Rauchman
- Washington University in Saint Louis, St. Louis, MO, 63103, USA.
| | - Michael T Eadon
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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Grall E, Feregrino C, Fischer S, De Courten A, Sacher F, Hiscock TW, Tschopp P. Self-organized BMP signaling dynamics underlie the development and evolution of digit segmentation patterns in birds and mammals. Proc Natl Acad Sci U S A 2024; 121:e2304470121. [PMID: 38175868 PMCID: PMC10786279 DOI: 10.1073/pnas.2304470121] [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: 03/17/2023] [Accepted: 11/03/2023] [Indexed: 01/06/2024] Open
Abstract
Repeating patterns of synovial joints are a highly conserved feature of articulated digits, with variations in joint number and location resulting in diverse digit morphologies and limb functions across the tetrapod clade. During the development of the amniote limb, joints form iteratively within the growing digit ray, as a population of distal progenitors alternately specifies joint and phalanx cell fates to segment the digit into distinct elements. While numerous molecular pathways have been implicated in this fate choice, it remains unclear how they give rise to a repeating pattern. Here, using single-cell RNA sequencing and spatial gene expression profiling, we investigate the transcriptional dynamics of interphalangeal joint specification in vivo. Combined with mathematical modeling, we predict that interactions within the BMP signaling pathway-between the ligand GDF5, the inhibitor NOGGIN, and the intracellular effector pSMAD-result in a self-organizing Turing system that forms periodic joint patterns. Our model is able to recapitulate the spatiotemporal gene expression dynamics observed in vivo, as well as phenocopy digit malformations caused by BMP pathway perturbations. By contrasting in silico simulations with in vivo morphometrics of two morphologically distinct digits, we show how changes in signaling parameters and growth dynamics can result in variations in the size and number of phalanges. Together, our results reveal a self-organizing mechanism that underpins amniote digit segmentation and its evolvability and, more broadly, illustrate how Turing systems based on a single molecular pathway may generate complex repetitive patterns in a wide variety of organisms.
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Affiliation(s)
- Emmanuelle Grall
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Christian Feregrino
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Sabrina Fischer
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Aline De Courten
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Fabio Sacher
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Tom W. Hiscock
- Institute of Medical Sciences, University of Aberdeen, AberdeenAB25 2ZD, Scotland, United Kingdom
| | - Patrick Tschopp
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
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Kaczanowska S, Murty T, Alimadadi A, Contreras CF, Duault C, Subrahmanyam PB, Reynolds W, Gutierrez NA, Baskar R, Wu CJ, Michor F, Altreuter J, Liu Y, Jhaveri A, Duong V, Anbunathan H, Ong C, Zhang H, Moravec R, Yu J, Biswas R, Van Nostrand S, Lindsay J, Pichavant M, Sotillo E, Bernstein D, Carbonell A, Derdak J, Klicka-Skeels J, Segal JE, Dombi E, Harmon SA, Turkbey B, Sahaf B, Bendall S, Maecker H, Highfill SL, Stroncek D, Glod J, Merchant M, Hedrick CC, Mackall CL, Ramakrishna S, Kaplan RN. Immune determinants of CAR-T cell expansion in solid tumor patients receiving GD2 CAR-T cell therapy. Cancer Cell 2024; 42:35-51.e8. [PMID: 38134936 PMCID: PMC10947809 DOI: 10.1016/j.ccell.2023.11.011] [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: 01/10/2023] [Revised: 09/18/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Chimeric antigen receptor T cells (CAR-Ts) have remarkable efficacy in liquid tumors, but limited responses in solid tumors. We conducted a Phase I trial (NCT02107963) of GD2 CAR-Ts (GD2-CAR.OX40.28.z.iC9), demonstrating feasibility and safety of administration in children and young adults with osteosarcoma and neuroblastoma. Since CAR-T efficacy requires adequate CAR-T expansion, patients were grouped into good or poor expanders across dose levels. Patient samples were evaluated by multi-dimensional proteomic, transcriptomic, and epigenetic analyses. T cell assessments identified naive T cells in pre-treatment apheresis associated with good expansion, and exhausted T cells in CAR-T products with poor expansion. Myeloid cell assessment identified CXCR3+ monocytes in pre-treatment apheresis associated with good expansion. Longitudinal analysis of post-treatment samples identified increased CXCR3- classical monocytes in all groups as CAR-T numbers waned. Together, our data uncover mediators of CAR-T biology and correlates of expansion that could be utilized to advance immunotherapies for solid tumor patients.
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Affiliation(s)
- Sabina Kaczanowska
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tara Murty
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ahmad Alimadadi
- La Jolla Institute for Immunology, La Jolla, CA, USA; Immunology Center of Georgia, Augusta University, Augusta, GA, USA; Georgia Cancer Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Cristina F Contreras
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Oncology, University of Oxford, Oxford, UK
| | - Caroline Duault
- Stanford Human Immune Monitoring Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Priyanka B Subrahmanyam
- Stanford Human Immune Monitoring Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Warren Reynolds
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Reema Baskar
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Catherine J Wu
- Broad Institute, Cambridge, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Yang Liu
- Broad Institute, Cambridge, MA, USA
| | | | - Vandon Duong
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hima Anbunathan
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Claire Ong
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hua Zhang
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Radim Moravec
- Cancer Therapy Evaluation Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joyce Yu
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | - Mina Pichavant
- Immunology Center of Georgia, Augusta University, Augusta, GA, USA
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Donna Bernstein
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amanda Carbonell
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joanne Derdak
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jacquelyn Klicka-Skeels
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Julia E Segal
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eva Dombi
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie A Harmon
- Artificial Intelligence Resource, Molecular Imaging Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Baris Turkbey
- Artificial Intelligence Resource, Molecular Imaging Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bita Sahaf
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean Bendall
- Georgia Cancer Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Holden Maecker
- Immunology Center of Georgia, Augusta University, Augusta, GA, USA
| | - Steven L Highfill
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - David Stroncek
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - John Glod
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Melinda Merchant
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Catherine C Hedrick
- La Jolla Institute for Immunology, La Jolla, CA, USA; Immunology Center of Georgia, Augusta University, Augusta, GA, USA; Georgia Cancer Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Sneha Ramakrishna
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
| | - Rosandra N Kaplan
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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Lochs SJA, van der Weide RH, de Luca KL, Korthout T, van Beek RE, Kimura H, Kind J. Combinatorial single-cell profiling of major chromatin types with MAbID. Nat Methods 2024; 21:72-82. [PMID: 38049699 PMCID: PMC10776404 DOI: 10.1038/s41592-023-02090-9] [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: 12/16/2022] [Accepted: 10/17/2023] [Indexed: 12/06/2023]
Abstract
Gene expression programs result from the collective activity of numerous regulatory factors. Studying their cooperative mode of action is imperative to understand gene regulation, but simultaneously measuring these factors within one sample has been challenging. Here we introduce Multiplexing Antibodies by barcode Identification (MAbID), a method for combinatorial genomic profiling of histone modifications and chromatin-binding proteins. MAbID employs antibody-DNA conjugates to integrate barcodes at the genomic location of the epitope, enabling combined incubation of multiple antibodies to reveal the distributions of many epigenetic markers simultaneously. We used MAbID to profile major chromatin types and multiplexed measurements without loss of individual data quality. Moreover, we obtained joint measurements of six epitopes in single cells of mouse bone marrow and during mouse in vitro differentiation, capturing associated changes in multifactorial chromatin states. Thus, MAbID holds the potential to gain unique insights into the interplay between gene regulatory mechanisms, especially for low-input samples and in single cells.
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Affiliation(s)
- Silke J A Lochs
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Robin H van der Weide
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Kim L de Luca
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Tessy Korthout
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Ramada E van Beek
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Jop Kind
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands.
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34
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Carmona EG, Callejas-Rubio JL, Raya E, Ríos-Fernández R, Villanueva-Martín G, Cid MC, Hernández-Rodríguez J, Ballestar E, Timmermann B, Ortego-Centeno N, Martín J, Márquez A. Single-cell transcriptomic profiling reveals a pathogenic role of cytotoxic CD4 + T cells in giant cell arteritis. J Autoimmun 2024; 142:103124. [PMID: 37952293 DOI: 10.1016/j.jaut.2023.103124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 11/14/2023]
Abstract
Giant cell arteritis (GCA) is a systemic vasculitis mediated by an aberrant immunological response against the blood vessel wall. Although the pathogenic mechanisms that drive GCA have not yet been elucidated, there is strong evidence that CD4+ T cells are key drivers of the inflammatory process occurring in this vasculitis. The aim of this study was to further delineate the role of CD4+ T cells in GCA by applying single-cell RNA sequencing and T cell receptor (TCR) repertoire profiling to 114.799 circulating CD4+ T cells from eight GCA patients in two different clinical states, active and in remission, and eight healthy controls. Our results revealed an expansion of cytotoxic CD4+ T lymphocytes (CTLs) in active GCA patients, which expressed higher levels of cytotoxic and chemotactic genes when compared to patients in remission and controls. Accordingly, differentially expressed genes in CTLs of active patients were enriched in pathways related to granzyme-mediated apoptosis, inflammation, and the recruitment of different immune cells, suggesting a role of this cell type in the inflammatory and vascular remodelling processes occurring in GCA. CTLs also exhibited a higher clonal expansion in active patients with respect to those in remission. Drug repurposing analysis prioritized maraviroc, which targeted CTLs, as potentially repositionable for this vasculitis. In addition, effector regulatory T cells (Tregs) were decreased in GCA and showed lower expression of genes involved in their suppressive activity. These findings provide further insights into the pathogenic role of CD4+ T cells in GCA and suggest targeting CTLs as a potential therapeutic option.
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Affiliation(s)
- Elio G Carmona
- Institute of Parasitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain; Systemic Autoimmune Diseases Unit, Hospital Universitario Clínico San Cecilio, Instituto de Investigación Biosanitaria de Granada ibs.GRANADA, Granada, Spain
| | - José Luis Callejas-Rubio
- Systemic Autoimmune Diseases Unit, Hospital Universitario Clínico San Cecilio, Instituto de Investigación Biosanitaria de Granada ibs.GRANADA, Granada, Spain
| | - Enrique Raya
- Rheumatology Department, Hospital Universitario Clínico San Cecilio, Instituto de Investigación Biosanitaria de Granada ibs.GRANADA, Granada, Spain
| | - Raquel Ríos-Fernández
- Systemic Autoimmune Diseases Unit, Hospital Universitario Clínico San Cecilio, Instituto de Investigación Biosanitaria de Granada ibs.GRANADA, Granada, Spain
| | - Gonzalo Villanueva-Martín
- Institute of Parasitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - María C Cid
- Vasculitis Research Unit, Department of Autoimmune Diseases, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - José Hernández-Rodríguez
- Vasculitis Research Unit, Department of Autoimmune Diseases, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Badalona, Barcelona, Spain
| | | | - Norberto Ortego-Centeno
- Department of Medicine, University of Granada, Instituto de Investigación Biosanitaria de Granada ibs.GRANADA, Granada, Spain
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - Ana Márquez
- Institute of Parasitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain.
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35
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Bravo González-Blas C, Matetovici I, Hillen H, Taskiran II, Vandepoel R, Christiaens V, Sansores-García L, Verboven E, Hulselmans G, Poovathingal S, Demeulemeester J, Psatha N, Mauduit D, Halder G, Aerts S. Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation. Nat Cell Biol 2024; 26:153-167. [PMID: 38182825 PMCID: PMC10791584 DOI: 10.1038/s41556-023-01316-4] [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: 11/22/2022] [Accepted: 11/15/2023] [Indexed: 01/07/2024]
Abstract
In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based on their location within the liver lobule. However, it is unclear whether this spatial variation, called zonation, is governed by a well-defined gene regulatory code. Here, using a combination of single-cell multiomics, spatial omics, massively parallel reporter assays and deep learning, we mapped enhancer-gene regulatory networks across mouse liver cell types. We found that zonation affects gene expression and chromatin accessibility in hepatocytes, among other cell types. These states are driven by the repressors TCF7L1 and TBX3, alongside other core hepatocyte transcription factors, such as HNF4A, CEBPA, FOXA1 and ONECUT1. To examine the architecture of the enhancers driving these cell states, we trained a hierarchical deep learning model called DeepLiver. Our study provides a multimodal understanding of the regulatory code underlying hepatocyte identity and their zonation state that can be used to engineer enhancers with specific activity levels and zonation patterns.
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Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irina Matetovici
- VIB Center for Brain & Disease Research, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
| | - Hanne Hillen
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Roel Vandepoel
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Leticia Sansores-García
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Elisabeth Verboven
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | | | - Jonas Demeulemeester
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nikoleta Psatha
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - David Mauduit
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Georg Halder
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium.
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36
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Cao Y, Tran A, Kim H, Robertson N, Lin Y, Torkel M, Yang P, Patrick E, Ghazanfar S, Yang J. Thinking process templates for constructing data stories with SCDNEY. F1000Res 2023; 12:261. [PMID: 38434622 PMCID: PMC10905113 DOI: 10.12688/f1000research.130623.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/08/2023] [Indexed: 03/05/2024] Open
Abstract
Background Globally, scientists now have the ability to generate a vast amount of high throughput biomedical data that carry critical information for important clinical and public health applications. This data revolution in biology is now creating a plethora of new single-cell datasets. Concurrently, there have been significant methodological advances in single-cell research. Integrating these two resources, creating tailor-made, efficient, and purpose-specific data analysis approaches can assist in accelerating scientific discovery. Methods We developed a series of living workshops for building data stories, using Single-cell data integrative analysis (scdney). scdney is a wrapper package with a collection of single-cell analysis R packages incorporating data integration, cell type annotation, higher order testing and more. Results Here, we illustrate two specific workshops. The first workshop examines how to characterise the identity and/or state of cells and the relationship between them, known as phenotyping. The second workshop focuses on extracting higher-order features from cells to predict disease progression. Conclusions Through these workshops, we not only showcase current solutions, but also highlight critical thinking points. In particular, we highlight the Thinking Process Template that provides a structured framework for the decision-making process behind such single-cell analyses. Furthermore, our workshop will incorporate dynamic contributions from the community in a collaborative learning approach, thus the term 'living'.
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Affiliation(s)
- Yue Cao
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Andy Tran
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Hani Kim
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
- Children's Medical Research Institute, The University of Sydney, Westmead, NSW, 2145, Australia
| | - Nick Robertson
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Yingxin Lin
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Marni Torkel
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Pengyi Yang
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
- Children's Medical Research Institute, The University of Sydney, Westmead, NSW, 2145, Australia
| | - Ellis Patrick
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Shila Ghazanfar
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jean Yang
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
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37
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Cao X, Ma T, Fan R, Yuan GC. Broad H3K4me3 Domain Is Associated with Spatial Coherence during Mammalian Embryonic Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.570452. [PMID: 38168252 PMCID: PMC10760050 DOI: 10.1101/2023.12.11.570452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
It is well known that the chromatin states play a major role in cell-fate decision and cell-identity maintenance; however, the spatial variation of chromatin states in situ remains poorly characterized. Here, by leveraging recently available spatial-CUT&Tag data, we systematically characterized the global spatial organization of the H3K4me3 profiles in a mouse embryo. Our analysis identified a subset of genes with spatially coherent H3K4me3 patterns, which together delineate the tissue boundaries. The spatially coherent genes are strongly enriched with tissue-specific transcriptional regulators. Remarkably, their corresponding genomic loci are marked by broad H3K4me3 domains, which is distinct from the typical H3K4me3 signature. Spatial transition across tissue boundaries is associated with continuous shortening of the broad H3K4me3 domains as well as expansion of H3K27me3 domains. Our analysis reveals a strong connection between the genomic and spatial variation of chromatin states, which may play an important role in embryonic development.
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Affiliation(s)
- Xuan Cao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Terry Ma
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Havens, CT, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
- Lead contact
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38
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Minegishi M, Kuchimaru T, Nishikawa K, Isagawa T, Iwano S, Iida K, Hara H, Miura S, Sato M, Watanabe S, Shiomi A, Mabuchi Y, Hamana H, Kishi H, Sato T, Sawaki D, Sato S, Hanazono Y, Suzuki A, Kohro T, Kadonosono T, Shimogori T, Miyawaki A, Takeda N, Shintaku H, Kizaka-Kondoh S, Nishimura S. Secretory GFP reconstitution labeling of neighboring cells interrogates cell-cell interactions in metastatic niches. Nat Commun 2023; 14:8031. [PMID: 38052804 DOI: 10.1038/s41467-023-43855-2] [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: 09/02/2022] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
Cancer cells inevitably interact with neighboring host tissue-resident cells during the process of metastatic colonization, establishing a metastatic niche to fuel their survival, growth, and invasion. However, the underlying mechanisms in the metastatic niche are yet to be fully elucidated owing to the lack of methodologies for comprehensively studying the mechanisms of cell-cell interactions in the niche. Here, we improve a split green fluorescent protein (GFP)-based genetically encoded system to develop secretory glycosylphosphatidylinositol-anchored reconstitution-activated proteins to highlight intercellular connections (sGRAPHIC) for efficient fluorescent labeling of tissue-resident cells that neighbor on and putatively interact with cancer cells in deep tissues. The sGRAPHIC system enables the isolation of metastatic niche-associated tissue-resident cells for their characterization using a single-cell RNA sequencing platform. We use this sGRAPHIC-leveraged transcriptomic platform to uncover gene expression patterns in metastatic niche-associated hepatocytes in a murine model of liver metastasis. Among the marker genes of metastatic niche-associated hepatocytes, we identify Lgals3, encoding galectin-3, as a potential pro-metastatic factor that accelerates metastatic growth and invasion.
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Affiliation(s)
- Misa Minegishi
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
- RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Takahiro Kuchimaru
- RIKEN Cluster for Pioneering Research, Saitama, Japan.
- Graduate School of Medicine, Jichi Medical University, Tochigi, Japan.
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan.
- Data Science Center, Jichi Medical University, Tochigi, Japan.
| | | | - Takayuki Isagawa
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
- Data Science Center, Jichi Medical University, Tochigi, Japan
| | - Satoshi Iwano
- RIKEN Center for Brain Science, Saitama, Japan
- Institute for Tenure Track Promotion, University of Miyazaki, Miyazaki, Japan
| | - Kei Iida
- Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Hiromasa Hara
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Shizuka Miura
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Marika Sato
- MediGear International Corporation, Kanagawa, Japan
| | | | | | - Yo Mabuchi
- Graduate School of Medicine, Juntendo University, Tokyo, Japan
- School of Medicine, Fujita Health University, Aichi, Japan
| | - Hiroshi Hamana
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Tatsuyuki Sato
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Daigo Sawaki
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
- Clinical Pharmacology, Jichi Medical University, Tochigi, Japan
| | - Shigeru Sato
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Yutaka Hanazono
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Atsushi Suzuki
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takahide Kohro
- Data Science Center, Jichi Medical University, Tochigi, Japan
| | - Tetsuya Kadonosono
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
| | | | | | - Norihiko Takeda
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | | | - Shinae Kizaka-Kondoh
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
| | - Satoshi Nishimura
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
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Kyaw W, Chai RC, Khoo WH, Goldstein LD, Croucher PI, Murray JM, Phan TG. ENTRAIN: integrating trajectory inference and gene regulatory networks with spatial data to co-localize the receptor-ligand interactions that specify cell fate. Bioinformatics 2023; 39:btad765. [PMID: 38113422 PMCID: PMC10752580 DOI: 10.1093/bioinformatics/btad765] [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: 07/08/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023] Open
Abstract
MOTIVATION Cell fate is commonly studied by profiling the gene expression of single cells to infer developmental trajectories based on expression similarity, RNA velocity, or statistical mechanical properties. However, current approaches do not recover microenvironmental signals from the cellular niche that drive a differentiation trajectory. RESULTS We resolve this with environment-aware trajectory inference (ENTRAIN), a computational method that integrates trajectory inference methods with ligand-receptor pair gene regulatory networks to identify extracellular signals and evaluate their relative contribution towards a differentiation trajectory. The output from ENTRAIN can be superimposed on spatial data to co-localize cells and molecules in space and time to map cell fate potentials to cell-cell interactions. We validate and benchmark our approach on single-cell bone marrow and spatially resolved embryonic neurogenesis datasets to identify known and novel environmental drivers of cellular differentiation. AVAILABILITY AND IMPLEMENTATION ENTRAIN is available as a public package at https://github.com/theimagelab/entrain and can be used on both single-cell and spatially resolved datasets.
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Affiliation(s)
- Wunna Kyaw
- Precision Immunology Program, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- St Vincent’s Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Darlinghurst, NSW 2010, Australia
| | - Ryan C Chai
- St Vincent’s Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Darlinghurst, NSW 2010, Australia
- Cancer Plasticity and Dormancy Program, Garvan Institute of Medical Research, Darlinghurst, NSW 2010Australia
| | - Weng Hua Khoo
- St Vincent’s Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Darlinghurst, NSW 2010, Australia
- Cancer Plasticity and Dormancy Program, Garvan Institute of Medical Research, Darlinghurst, NSW 2010Australia
| | - Leonard D Goldstein
- St Vincent’s Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Darlinghurst, NSW 2010, Australia
- Data Science Platform, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Peter I Croucher
- St Vincent’s Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Darlinghurst, NSW 2010, Australia
- Cancer Plasticity and Dormancy Program, Garvan Institute of Medical Research, Darlinghurst, NSW 2010Australia
| | - John M Murray
- School of Mathematics and Statistics, Faculty of Science, UNSW Sydney, Kensington, NSW 2033, Australia
| | - Tri Giang Phan
- Precision Immunology Program, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- St Vincent’s Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Darlinghurst, NSW 2010, Australia
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40
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Nale V, Chiodi A, Di Nanni N, Cifola I, Moscatelli M, Cocola C, Gnocchi M, Piscitelli E, Sula A, Zucchi I, Reinbold R, Milanesi L, Mezzelani A, Pelucchi P, Mosca E. scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis. BMC Bioinformatics 2023; 24:445. [PMID: 38012590 PMCID: PMC10680269 DOI: 10.1186/s12859-023-05563-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: 06/01/2022] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
INTRODUCTION Single-cell (SC) gene expression analysis is crucial to dissect the complex cellular heterogeneity of solid tumors, which is one of the main obstacles for the development of effective cancer treatments. Such tumors typically contain a mixture of cells with aberrant genomic and transcriptomic profiles affecting specific sub-populations that might have a pivotal role in cancer progression, whose identification eludes bulk RNA-sequencing approaches. We present scMuffin, an R package that enables the characterization of cell identity in solid tumors on the basis of a various and complementary analyses on SC gene expression data. RESULTS scMuffin provides a series of functions to calculate qualitative and quantitative scores, such as: expression of marker sets for normal and tumor conditions, pathway activity, cell state trajectories, Copy Number Variations, transcriptional complexity and proliferation state. Thus, scMuffin facilitates the combination of various evidences that can be used to distinguish normal and tumoral cells, define cell identities, cluster cells in different ways, link genomic aberrations to phenotypes and identify subtle differences between cell subtypes or cell states. We analysed public SC expression datasets of human high-grade gliomas as a proof-of-concept to show the value of scMuffin and illustrate its user interface. Nevertheless, these analyses lead to interesting findings, which suggest that some chromosomal amplifications might underlie the invasive tumor phenotype and the presence of cells that possess tumor initiating cells characteristics. CONCLUSIONS The analyses offered by scMuffin and the results achieved in the case study show that our tool helps addressing the main challenges in the bioinformatics analysis of SC expression data from solid tumors.
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Affiliation(s)
- Valentina Nale
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Alice Chiodi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Noemi Di Nanni
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ingrid Cifola
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Marco Moscatelli
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Cinzia Cocola
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Matteo Gnocchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Eleonora Piscitelli
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ada Sula
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ileana Zucchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Rolland Reinbold
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Alessandra Mezzelani
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Paride Pelucchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy.
| | - Ettore Mosca
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy.
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41
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Kaesler N, Cheng M, Nagai J, O’Sullivan J, Peisker F, Bindels EM, Babler A, Moellmann J, Droste P, Franciosa G, Dugourd A, Saez-Rodriguez J, Neuss S, Lehrke M, Boor P, Goettsch C, Olsen JV, Speer T, Lu TS, Lim K, Floege J, Denby L, Costa I, Kramann R. Mapping cardiac remodeling in chronic kidney disease. SCIENCE ADVANCES 2023; 9:eadj4846. [PMID: 38000021 PMCID: PMC10672229 DOI: 10.1126/sciadv.adj4846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023]
Abstract
Patients with advanced chronic kidney disease (CKD) mostly die from sudden cardiac death and recurrent heart failure. The mechanisms of cardiac remodeling are largely unclear. To dissect molecular and cellular mechanisms of cardiac remodeling in CKD in an unbiased fashion, we performed left ventricular single-nuclear RNA sequencing in two mouse models of CKD. Our data showed a hypertrophic response trajectory of cardiomyocytes with stress signaling and metabolic changes driven by soluble uremia-related factors. We mapped fibroblast to myofibroblast differentiation in this process and identified notable changes in the cardiac vasculature, suggesting inflammation and dysfunction. An integrated analysis of cardiac cellular responses to uremic toxins pointed toward endothelin-1 and methylglyoxal being involved in capillary dysfunction and TNFα driving cardiomyocyte hypertrophy in CKD, which was validated in vitro and in vivo. TNFα inhibition in vivo ameliorated the cardiac phenotype in CKD. Thus, interventional approaches directed against uremic toxins, such as TNFα, hold promise to ameliorate cardiac remodeling in CKD.
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Affiliation(s)
- Nadine Kaesler
- Clinic for Renal and Hypertensive Disorders, Rheumatological and Immunological Disease, University Hospital of the RWTH Aachen, Aachen, Germany
- Institute of Experimental Medicine and Systems Biology, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Mingbo Cheng
- Institute for Computational Genomics, University Hospital of the RWTH Aachen, Aachen, Germany
| | - James Nagai
- Institute for Computational Genomics, University Hospital of the RWTH Aachen, Aachen, Germany
| | - James O’Sullivan
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Fabian Peisker
- Institute of Experimental Medicine and Systems Biology, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Eric M. J. Bindels
- Department of Hematology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Anne Babler
- Institute of Experimental Medicine and Systems Biology, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Julia Moellmann
- Department of Internal Medicine I, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Patrick Droste
- Clinic for Renal and Hypertensive Disorders, Rheumatological and Immunological Disease, University Hospital of the RWTH Aachen, Aachen, Germany
- Institute of Pathology, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Aurelien Dugourd
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Sabine Neuss
- Institute of Pathology, University Hospital of the RWTH Aachen, Aachen, Germany
- Helmholtz Institute for Biomedical Engineering, Biointerface Laboratory, RWTH Aachen University, Aachen, Germany
| | - Michael Lehrke
- Department of Internal Medicine I, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Peter Boor
- Clinic for Renal and Hypertensive Disorders, Rheumatological and Immunological Disease, University Hospital of the RWTH Aachen, Aachen, Germany
- Institute of Pathology, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Claudia Goettsch
- Department of Internal Medicine I, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Jesper V. Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Thimoteus Speer
- Department of Medicine (Nephrology), Goethe University Frankfurt, Frankfurt, Germany
| | - Tzong-Shi Lu
- Brigham and Women’s Hospital, Renal Division, Boston, MA, USA
| | - Kenneth Lim
- Division of Nephrology and Hypertension, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jürgen Floege
- Clinic for Renal and Hypertensive Disorders, Rheumatological and Immunological Disease, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Laura Denby
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Ivan Costa
- Institute for Computational Genomics, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Rafael Kramann
- Clinic for Renal and Hypertensive Disorders, Rheumatological and Immunological Disease, University Hospital of the RWTH Aachen, Aachen, Germany
- Institute of Experimental Medicine and Systems Biology, University Hospital of the RWTH Aachen, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, Netherlands
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42
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Zhou PY, Zhou C, Gan W, Tang Z, Sun BY, Huang JL, Liu G, Liu WR, Tian MX, Jiang XF, Wang H, Tao CY, Fang Y, Qu WF, Huang R, Zhu GQ, Huang C, Fu XT, Ding ZB, Gao Q, Zhou J, Shi YH, Yi Y, Fan J, Qiu SJ. Single-cell and spatial architecture of primary liver cancer. Commun Biol 2023; 6:1181. [PMID: 37985711 PMCID: PMC10661180 DOI: 10.1038/s42003-023-05455-0] [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: 09/25/2022] [Accepted: 10/12/2023] [Indexed: 11/22/2023] Open
Abstract
Primary liver cancer (PLC) poses a leading threat to human health, and its treatment options are limited. Meanwhile, the investigation of homogeneity and heterogeneity among PLCs remains challenging. Here, using single-cell RNA sequencing, spatial transcriptomic and bulk multi-omics, we elaborated a molecular architecture of 3 PLC types, namely hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular-cholangiocarcinoma (CHC). Taking a high-resolution perspective, our observations revealed that CHC cells exhibit internally discordant phenotypes, whereas ICC and HCC exhibit distinct tumor-specific features. Specifically, ICC was found to be the primary source of cancer-associated fibroblasts, while HCC exhibited disrupted metabolism and greater individual heterogeneity of T cells. We further revealed a diversity of intermediate-state cells residing in the tumor-peritumor junctional zone, including a congregation of CPE+ intermediate-state endothelial cells (ECs), which harbored the molecular characteristics of tumor-associated ECs and normal ECs. This architecture offers insights into molecular characteristics of PLC microenvironment, and hints that the tumor-peritumor junctional zone could serve as a targeted region for precise therapeutical strategies.
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Affiliation(s)
- Pei-Yun Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China.
- Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
| | - Cheng Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Wei Gan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Zheng Tang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Bao-Ye Sun
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Jin-Long Huang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Gao Liu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Wei-Ren Liu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Meng-Xin Tian
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Xi-Fei Jiang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Han Wang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Chen-Yang Tao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Yuan Fang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Wei-Feng Qu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Run Huang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Gui-Qi Zhu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Cheng Huang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Xiu-Tao Fu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Zhen-Bin Ding
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Ying-Hong Shi
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Yong Yi
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China.
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China.
| | - Shuang-Jian Qiu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China.
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43
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Mavrommatis L, Jeong HW, Kindler U, Gomez-Giro G, Kienitz MC, Stehling M, Psathaki OE, Zeuschner D, Bixel MG, Han D, Morosan-Puopolo G, Gerovska D, Yang JH, Kim JB, Arauzo-Bravo MJ, Schwamborn JC, Hahn SA, Adams RH, Schöler HR, Vorgerd M, Brand-Saberi B, Zaehres H. Human skeletal muscle organoids model fetal myogenesis and sustain uncommitted PAX7 myogenic progenitors. eLife 2023; 12:RP87081. [PMID: 37963071 PMCID: PMC10645425 DOI: 10.7554/elife.87081] [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] [Indexed: 11/16/2023] Open
Abstract
In vitro culture systems that structurally model human myogenesis and promote PAX7+ myogenic progenitor maturation have not been established. Here we report that human skeletal muscle organoids can be differentiated from induced pluripotent stem cell lines to contain paraxial mesoderm and neuromesodermal progenitors and develop into organized structures reassembling neural plate border and dermomyotome. Culture conditions instigate neural lineage arrest and promote fetal hypaxial myogenesis toward limb axial anatomical identity, with generation of sustainable uncommitted PAX7 myogenic progenitors and fibroadipogenic (PDGFRa+) progenitor populations equivalent to those from the second trimester of human gestation. Single-cell comparison to human fetal and adult myogenic progenitor /satellite cells reveals distinct molecular signatures for non-dividing myogenic progenitors in activated (CD44High/CD98+/MYOD1+) and dormant (PAX7High/FBN1High/SPRY1High) states. Our approach provides a robust 3D in vitro developmental system for investigating muscle tissue morphogenesis and homeostasis.
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Affiliation(s)
- Lampros Mavrommatis
- Ruhr University Bochum, Medical Faculty, Institute of Anatomy, Department of Anatomy and Molecular EmbryologyBochumGermany
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental BiologyMünsterGermany
- Department of Neurology with Heimer Institute for Muscle Research, University Hospital BergmannsheilBochumGermany
| | - Hyun-Woo Jeong
- Max Planck Institute for Molecular Biomedicine, Sequencing Core FacilityMünsterGermany
| | - Urs Kindler
- Ruhr University Bochum, Medical Faculty, Institute of Anatomy, Department of Anatomy and Molecular EmbryologyBochumGermany
| | - Gemma Gomez-Giro
- Luxembourg Centre for Systems Biomedicine, LCSB, Developmental and Cellular Biology, University of LuxembourgBelvauxLuxembourg
| | - Marie-Cecile Kienitz
- Ruhr University Bochum, Medical Faculty, Department of Cellular PhysiologyBochumGermany
| | - Martin Stehling
- Max Planck Institute for Molecular Biomedicine, Flow Cytometry UnitMünsterGermany
| | - Olympia E Psathaki
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental BiologyMünsterGermany
- Center for Cellular Nanoanalytics Osnabrück, CellNanOs, University of OsnabrückOsnabrückGermany
| | - Dagmar Zeuschner
- Max Planck Institute for Molecular Biomedicine, Electron Microscopy UnitMünsterGermany
| | - M Gabriele Bixel
- Max Planck Institute for Molecular Biomedicine, Department of Tissue MorphogenesisMünsterGermany
| | - Dong Han
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental BiologyMünsterGermany
| | - Gabriela Morosan-Puopolo
- Ruhr University Bochum, Medical Faculty, Institute of Anatomy, Department of Anatomy and Molecular EmbryologyBochumGermany
| | - Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research InstituteSan SebastiánSpain
| | - Ji Hun Yang
- School of Mechanical Engineering, Korea UniversitySeoulRepublic of Korea
- R&D Research Center, Next & Bio IncSeoulRepublic of Korea
| | - Jeong Beom Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST)UlsanRepublic of Korea
| | - Marcos J Arauzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research InstituteSan SebastiánSpain
| | - Jens C Schwamborn
- Luxembourg Centre for Systems Biomedicine, LCSB, Developmental and Cellular Biology, University of LuxembourgBelvauxLuxembourg
| | - Stephan A Hahn
- Ruhr University Bochum, Medical Faculty, Department of Molecular GI OncologyBochumGermany
| | - Ralf H Adams
- Max Planck Institute for Molecular Biomedicine, Department of Tissue MorphogenesisMünsterGermany
- Westphalian Wilhelms University Münster, Medical FacultyMünsterGermany
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental BiologyMünsterGermany
| | - Matthias Vorgerd
- Department of Neurology with Heimer Institute for Muscle Research, University Hospital BergmannsheilBochumGermany
| | - Beate Brand-Saberi
- Ruhr University Bochum, Medical Faculty, Institute of Anatomy, Department of Anatomy and Molecular EmbryologyBochumGermany
| | - Holm Zaehres
- Ruhr University Bochum, Medical Faculty, Institute of Anatomy, Department of Anatomy and Molecular EmbryologyBochumGermany
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental BiologyMünsterGermany
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Fu R, Walters K, Kaufman ML, Koc K, Baldwin A, Clay MR, Basham KJ, Kiseljak-Vassiliades K, Fishbein L, Mukherjee N. In Situ Spatial Reconstruction of Distinct Normal and Pathological Cell Populations Within the Human Adrenal Gland. J Endocr Soc 2023; 7:bvad131. [PMID: 37953901 PMCID: PMC10638100 DOI: 10.1210/jendso/bvad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Indexed: 11/14/2023] Open
Abstract
The human adrenal gland consists of concentrically organized, functionally distinct regions responsible for hormone production. Dysregulation of adrenocortical cell differentiation alters the proportion and organization of the functional zones of the adrenal cortex leading to disease. Current models of adrenocortical cell differentiation are based on mouse studies, but there are known organizational and functional differences between human and mouse adrenal glands. This study aimed to investigate the centripetal differentiation model in the human adrenal cortex and characterize aldosterone-producing micronodules (APMs) to better understand adrenal diseases such as primary aldosteronism. We applied spatially resolved in situ transcriptomics to human adrenal tissue sections from 2 individuals and identified distinct cell populations and their positional relationships. The results supported the centripetal differentiation model in humans, with cells progressing from the outer capsule to the zona glomerulosa, zona fasciculata, and zona reticularis. Additionally, we characterized 2 APMs in a 72-year-old woman. Comparison with earlier APM transcriptomes indicated a subset of core genes, but also heterogeneity between APMs. The findings contribute to our understanding of normal and pathological cellular differentiation in the human adrenal cortex.
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Affiliation(s)
- Rui Fu
- RNA Biosciences Initiative and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
- Computational Biology, New York Genome Center, New York, NY 10013, USA
| | - Kathryn Walters
- RNA Biosciences Initiative and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
| | - Michael L Kaufman
- RNA Biosciences Initiative and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
| | - Katrina Koc
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
| | - Amber Baldwin
- RNA Biosciences Initiative and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
| | - Michael R Clay
- Department of Pathology, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
| | - Kaitlin J Basham
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Katja Kiseljak-Vassiliades
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
- Research Service Veterans Affairs Medical Center, Aurora, CO 80045, USA
| | - Lauren Fishbein
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
| | - Neelanjan Mukherjee
- RNA Biosciences Initiative and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
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45
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Villanueva-Martin G, Acosta-Herrera M, Carmona EG, Kerick M, Ortego-Centeno N, Callejas-Rubio JL, Mages N, Klages S, Börno S, Timmermann B, Bossini-Castillo L, Martin J. Non-classical circulating monocytes expressing high levels of microsomal prostaglandin E2 synthase-1 tag an aberrant IFN-response in systemic sclerosis. J Autoimmun 2023; 140:103097. [PMID: 37633117 DOI: 10.1016/j.jaut.2023.103097] [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: 05/18/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/28/2023]
Abstract
Systemic sclerosis (SSc) is a complex disease that affects the connective tissue, causing fibrosis. SSc patients show altered immune cell composition and activation in the peripheral blood (PB). PB monocytes (Mos) are recruited into tissues where they differentiate into macrophages, which are directly involved in fibrosis. To understand the role of CD14+ PB Mos in SSc, a single-cell transcriptome analysis (scRNA-seq) was conducted on 8 SSc patients and 8 controls. Using unsupervised clustering methods, CD14+ cells were assigned to 11 clusters, which added granularity to the known monocyte subsets: classical (cMos), intermediate (iMos) and non-classical Mos (ncMos) or type 2 dendritic cells. NcMos were significantly overrepresented in SSc patients and showed an active IFN-signature and increased expression levels of PTGES, in addition to monocyte motility and adhesion markers. We identified a SSc-related cluster of IRF7+ STAT1+ iMos with an aberrant IFN-response. Finally, a depletion of M2 polarised cMos in SSc was observed. Our results highlighted the potential of PB Mos as biomarkers for SSc and provided new possibilities for putative drug targets for modulating the innate immune response in SSc.
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Affiliation(s)
- Gonzalo Villanueva-Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Marialbert Acosta-Herrera
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain; Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Elio G Carmona
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain; Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Martin Kerick
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Norberto Ortego-Centeno
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain; Department of Medicine, University of Granada, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Jose Luis Callejas-Rubio
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Norbert Mages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Sven Klages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Stefan Börno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Lara Bossini-Castillo
- Department of Genetics and Biotechnology Institute, Biomedical Research Centre (CIBM), University of Granada, 18100, Granada, Spain; Advanced Therapies and Biomedical Technologies (TEC-14), Biosanitary Research Institute Ibs. GRANADA, 18016, Granada, Spain.
| | - Javier Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
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46
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Ben-Chetrit N, Niu X, Sotelo J, Swett AD, Rajasekhar VK, Jiao MS, Stewart CM, Bhardwaj P, Kottapalli S, Ganesan S, Loyher PL, Potenski C, Hannuna A, Brown KA, Iyengar NM, Giri DD, Lowe SW, Healey JH, Geissmann F, Sagi I, Joyce JA, Landau DA. Breast Cancer Macrophage Heterogeneity and Self-renewal are Determined by Spatial Localization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563749. [PMID: 37961223 PMCID: PMC10634790 DOI: 10.1101/2023.10.24.563749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Tumor-infiltrating macrophages support critical steps in tumor progression, and their accumulation in the tumor microenvironment (TME) is associated with adverse outcomes and therapeutic resistance across human cancers. In the TME, macrophages adopt diverse phenotypic alterations, giving rise to heterogeneous immune activation states and induction of cell cycle. While the transcriptional profiles of these activation states are well-annotated across human cancers, the underlying signals that regulate macrophage heterogeneity and accumulation remain incompletely understood. Here, we leveraged a novel ex vivo organotypic TME (oTME) model of breast cancer, in vivo murine models, and human samples to map the determinants of functional heterogeneity of TME macrophages. We identified a subset of F4/80highSca-1+ self-renewing macrophages maintained by type-I interferon (IFN) signaling and requiring physical contact with cancer-associated fibroblasts. We discovered that the contact-dependent self-renewal of TME macrophages is mediated via Notch4, and its inhibition abrogated tumor growth of breast and ovarian carcinomas in vivo, as well as lung dissemination in a PDX model of triple-negative breast cancer (TNBC). Through spatial multi-omic profiling of protein markers and transcriptomes, we found that the localization of macrophages further dictates functionally distinct but reversible phenotypes, regardless of their ontogeny. Whereas immune-stimulatory macrophages (CD11C+CD86+) populated the tumor epithelial nests, the stroma-associated macrophages (SAMs) were proliferative, immunosuppressive (Sca-1+CD206+PD-L1+), resistant to CSF-1R depletion, and associated with worse patient outcomes. Notably, following cessation of CSF-1R depletion, macrophages rebounded primarily to the SAM phenotype, which was associated with accelerated growth of mammary tumors. Our work reveals the spatial determinants of macrophage heterogeneity in breast cancer and highlights the disruption of macrophage self-renewal as a potential new therapeutic strategy.
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Affiliation(s)
- Nir Ben-Chetrit
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- These authors contributed equally
| | - Xiang Niu
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- These authors contributed equally
- Present address: Genentech, Inc., South San Francisco, CA, USA
| | - Jesus Sotelo
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Ariel D. Swett
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Vinagolu K. Rajasekhar
- Orthopedic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria S. Jiao
- Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caitlin M. Stewart
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Priya Bhardwaj
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Sanjay Kottapalli
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Saravanan Ganesan
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Pierre-Louis Loyher
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Catherine Potenski
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Assaf Hannuna
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Kristy A. Brown
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Neil M. Iyengar
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dilip D. Giri
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W. Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - John H. Healey
- Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Frederic Geissmann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Johanna A. Joyce
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Switzerland
| | - Dan A. Landau
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
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47
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Santinha AJ, Klingler E, Kuhn M, Farouni R, Lagler S, Kalamakis G, Lischetti U, Jabaudon D, Platt RJ. Transcriptional linkage analysis with in vivo AAV-Perturb-seq. Nature 2023; 622:367-375. [PMID: 37730998 PMCID: PMC10567566 DOI: 10.1038/s41586-023-06570-y] [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] [Received: 09/22/2022] [Accepted: 08/25/2023] [Indexed: 09/22/2023]
Abstract
The ever-growing compendium of genetic variants associated with human pathologies demands new methods to study genotype-phenotype relationships in complex tissues in a high-throughput manner1,2. Here we introduce adeno-associated virus (AAV)-mediated direct in vivo single-cell CRISPR screening, termed AAV-Perturb-seq, a tuneable and broadly applicable method for transcriptional linkage analysis as well as high-throughput and high-resolution phenotyping of genetic perturbations in vivo. We applied AAV-Perturb-seq using gene editing and transcriptional inhibition to systematically dissect the phenotypic landscape underlying 22q11.2 deletion syndrome3,4 genes in the adult mouse brain prefrontal cortex. We identified three 22q11.2-linked genes involved in known and previously undescribed pathways orchestrating neuronal functions in vivo that explain approximately 40% of the transcriptional changes observed in a 22q11.2-deletion mouse model. Our findings suggest that the 22q11.2-deletion syndrome transcriptional phenotype found in mature neurons may in part be due to the broad dysregulation of a class of genes associated with disease susceptibility that are important for dysfunctional RNA processing and synaptic function. Our study establishes a flexible and scalable direct in vivo method to facilitate causal understanding of biological and disease mechanisms with potential applications to identify genetic interventions and therapeutic targets for treating disease.
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Affiliation(s)
- Antonio J Santinha
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Esther Klingler
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Maria Kuhn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Pharma Research and Early Development (pRED), Roche, Basel, Switzerland
| | - Rick Farouni
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sandra Lagler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Georgios Kalamakis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Ulrike Lischetti
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Denis Jabaudon
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- Botnar Research Center for Child Health, Basel, Switzerland.
- Department of Chemistry, University of Basel, Basel, Switzerland.
- NCCR Molecular Systems Engineering, Basel, Switzerland.
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48
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Du J, Gu XR, Yu XX, Cao YJ, Hou J. Essential procedures of single-cell RNA sequencing in multiple myeloma and its translational value. BLOOD SCIENCE 2023; 5:221-236. [PMID: 37941914 PMCID: PMC10629747 DOI: 10.1097/bs9.0000000000000172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/18/2023] [Indexed: 11/10/2023] Open
Abstract
Multiple myeloma (MM) is a malignant neoplasm characterized by clonal proliferation of abnormal plasma cells. In many countries, it ranks as the second most prevalent malignant neoplasm of the hematopoietic system. Although treatment methods for MM have been continuously improved and the survival of patients has been dramatically prolonged, MM remains an incurable disease with a high probability of recurrence. As such, there are still many challenges to be addressed. One promising approach is single-cell RNA sequencing (scRNA-seq), which can elucidate the transcriptome heterogeneity of individual cells and reveal previously unknown cell types or states in complex tissues. In this review, we outlined the experimental workflow of scRNA-seq in MM, listed some commonly used scRNA-seq platforms and analytical tools. In addition, with the advent of scRNA-seq, many studies have made new progress in the key molecular mechanisms during MM clonal evolution, cell interactions and molecular regulation in the microenvironment, and drug resistance mechanisms in target therapy. We summarized the main findings and sequencing platforms for applying scRNA-seq to MM research and proposed broad directions for targeted therapies based on these findings.
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Affiliation(s)
- Jun Du
- Department of Hematology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiao-Ran Gu
- School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Xiao-Xiao Yu
- School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Yang-Jia Cao
- Department of Hematology, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shanxi 710000, China
| | - Jian Hou
- Department of Hematology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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49
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Hung CN, Chen M, DeArmond DT, Chiu CHL, Limboy CA, Tan X, Kusi M, Chou CW, Lin LL, Zhang Z, Wang CM, Chen CL, Mitsuya K, Osmulski PA, Gaczynska ME, Kirma NB, Vadlamudi RK, Gibbons DL, Warner S, Brenner AJ, Mahadevan D, Michalek JE, Huang THM, Taverna JA. AXL-initiated paracrine activation of pSTAT3 enhances mesenchymal and vasculogenic supportive features of tumor-associated macrophages. Cell Rep 2023; 42:113067. [PMID: 37659081 PMCID: PMC10577802 DOI: 10.1016/j.celrep.2023.113067] [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: 12/09/2022] [Revised: 07/14/2023] [Accepted: 08/18/2023] [Indexed: 09/04/2023] Open
Abstract
Tumor-associated macrophages (TAMs) are integral to the development of complex tumor microenvironments (TMEs) and can execute disparate cellular programs in response to extracellular cues. However, upstream signaling processes underpinning this phenotypic plasticity remain to be elucidated. Here, we report that concordant AXL-STAT3 signaling in TAMs is triggered by lung cancer cells or cancer-associated fibroblasts in the cytokine milieu. This paracrine action drives TAM differentiation toward a tumor-promoting "M2-like" phenotype with upregulation of CD163 and putative mesenchymal markers, contributing to TAM heterogeneity and diverse cellular functions. One of the upregulated markers, CD44, mediated by AXL-IL-11-pSTAT3 signaling cascade, enhances macrophage ability to interact with endothelial cells and facilitate formation of primitive vascular networks. We also found that AXL-STAT3 inhibition can impede the recruitment of TAMs in a xenograft mouse model, thereby suppressing tumor growth. These findings suggest the potential application of AXL-STAT3-related markers to quantitatively assess metastatic potential and inform therapeutic strategies in lung cancer.
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Affiliation(s)
- Chia-Nung Hung
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Meizhen Chen
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Daniel T DeArmond
- Department of Cardiothoracic Surgery, University of Texas Health Science Center, San Antonio, TX, USA
| | - Cheryl H-L Chiu
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Catherine A Limboy
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Xi Tan
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Meena Kusi
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Chih-Wei Chou
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Li-Ling Lin
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Zhao Zhang
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Chiou-Miin Wang
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Chun-Liang Chen
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA; Office of Nursing Research & Scholarship, School of Nursing, University of Texas Health Science Center, San Antonio, TX, USA
| | - Kohzoh Mitsuya
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Pawel A Osmulski
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Maria E Gaczynska
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Nameer B Kirma
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Ratna K Vadlamudi
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA; Department of Obstetrics and Gynecology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Don L Gibbons
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Andrew J Brenner
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA; Division of Hematology and Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Daruka Mahadevan
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA; Division of Hematology and Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Joel E Michalek
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA; Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA.
| | - Josephine A Taverna
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA; Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA; Division of Hematology and Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA.
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50
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Arnold W, Taylor M, Bradford M, Raymond P, Peccia J. Microbial activity contributes to spatial heterogeneity of wetland methane fluxes. Microbiol Spectr 2023; 11:e0271423. [PMID: 37728556 PMCID: PMC10580924 DOI: 10.1128/spectrum.02714-23] [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: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 09/21/2023] Open
Abstract
The emission of methane from wetlands is spatially heterogeneous, as concurrently measured surface fluxes can vary by orders of magnitude within the span of a few meters. Despite extensive study and the climatic significance of these emissions, it remains unclear what drives large, within-site variations. While geophysical factors (e.g., soil temperature) are known to correlate with methane (CH4) flux, measurable variance in these parameters often declines as spatial and temporal scales become finer. As methane emitted from wetlands is the direct, net product of microbial metabolisms which both produce and degrade CH4, it stands to reason that characterizing the spatial variability of microbial communities within a wetland-both horizontally and vertically-may help explain observed variances in flux. To that end, we surveyed microbial communities to a depth of 1 m across an ombrotrophic peat bog in Maine, USA using amplicon sequencing and gene expression techniques. Surface methane fluxes and geophysical factors were concurrently measured. Across the first meter of peat at the site, we observed significant changes in the abundance and composition of methanogenic taxa at every depth sampled, with variance in methanogen abundance explaining 70% of flux heterogeneity at a subset of plots. Among measured environmental factors, only peat depth emerged as correlated with flux, and had significant impact on the abundance and composition of methane-cycling communities. These conclusions suggest that a heightened awareness of how microbial communities are structured and spatially distributed within wetlands could offer improved insights into predicting CH4 flux dynamics. IMPORTANCE Globally, wetlands are one of the largest sources of methane (CH4), a greenhouse gas with a warming impact significantly greater than CO2. Methane produced in wetlands is the byproduct of a group of microorganisms which convert organic carbon into CH4. Despite our knowledge of how this process works, it is still unclear what drives dramatic, localized (<10 m) variance in emission rates from the surface of wetlands. While environmental conditions, like soil temperature or water table depth, correlate with methane flux when variance in these factors is large (e.g., spring vs fall), the explanatory power of these variables decline when spatial and temporal scales become smaller. As methane fluxes are the direct product of microbial activity, we profiled how the microbial community varied, both horizontally and vertically, across a peat bog in Maine, USA, finding that variance in microbial communities was likely contributing to much of the observed variance in flux.
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Affiliation(s)
- Wyatt Arnold
- Department of Chemical and Environmental Engineering, School of Engineering and Applied Science, Yale University, New Haven, Connecticut, USA
| | - Meghan Taylor
- Yale School of the Environment, Yale University, New Haven, Connecticut, USA
| | - Mark Bradford
- Yale School of the Environment, Yale University, New Haven, Connecticut, USA
| | - Peter Raymond
- Yale School of the Environment, Yale University, New Haven, Connecticut, USA
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, School of Engineering and Applied Science, Yale University, New Haven, Connecticut, USA
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