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Tian Y, Wu X, Luo S, Xiong D, Liu R, Hu L, Yuan Y, Shi G, Yao J, Huang Z, Fu F, Yang X, Tang Z, Zhang J, Hu K. A multi-omic single-cell landscape of cellular diversification in the developing human cerebral cortex. Comput Struct Biotechnol J 2024; 23:2173-2189. [PMID: 38827229 PMCID: PMC11141146 DOI: 10.1016/j.csbj.2024.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 06/04/2024] Open
Abstract
The vast neuronal diversity in the human neocortex is vital for high-order brain functions, necessitating elucidation of the regulatory mechanisms underlying such unparalleled diversity. However, recent studies have yet to comprehensively reveal the diversity of neurons and the molecular logic of neocortical origin in humans at single-cell resolution through profiling transcriptomic or epigenomic landscapes, owing to the application of unimodal data alone to depict exceedingly heterogeneous populations of neurons. In this study, we generated a comprehensive compendium of the developing human neocortex by simultaneously profiling gene expression and open chromatin from the same cell. We computationally reconstructed the differentiation trajectories of excitatory projection neurons of cortical origin and inferred the regulatory logic governing lineage bifurcation decisions for neuronal diversification. We demonstrated that neuronal diversity arises from progenitor cell lineage specificity and postmitotic differentiation at distinct stages. Our data paves the way for understanding the primarily coordinated regulatory logic for neuronal diversification in the neocortex.
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Affiliation(s)
- Yuhan Tian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Xia Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Songhao Luo
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Dan Xiong
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Rong Liu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Lanqi Hu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuchen Yuan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Guowei Shi
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Junjie Yao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhiwei Huang
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Fang Fu
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 511436, China
| | - Xin Yang
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 511436, China
| | - Zhonghui Tang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiajun Zhang
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Kunhua Hu
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
- Public Platform Laboratory, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
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2
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Li YR, Ling LB, Chao A, Fugmann SD, Yang SY. Transient chromatin decompaction at the start of D. melanogaster male embryonic germline development. Life Sci Alliance 2024; 7:e202302401. [PMID: 38991729 PMCID: PMC11239976 DOI: 10.26508/lsa.202302401] [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: 09/27/2023] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
Embryonic germ cells develop rapidly to establish the foundation for future developmental trajectories, and in this process, they make critical lineage choices including the configuration of their unique identity and a decision on sex. Here, we use single-cell genomics patterns for the entire embryonic germline in Drosophila melanogaster along with the somatic gonadal precursors after embryonic gonad coalescence to investigate molecular mechanisms involved in the setting up and regulation of the germline program. Profiling of the early germline chromatin landscape revealed sex- and stage-specific features. In the male germline immediately after zygotic activation, the chromatin structure underwent a brief remodeling phase during which nucleosome density was lower and deconcentrated from promoter regions. These findings echoed enrichment analysis results of our genomics data in which top candidates were factors with the ability to mediate large-scale chromatin reorganization. Together, they point to the importance of chromatin regulation in the early germline and raise the possibility of a conserved epigenetic reprogramming-like process required for proper initiation of germline development.
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Affiliation(s)
- Yi-Ru Li
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Li Bin Ling
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Angel Chao
- https://ror.org/02dnn6q67 Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Sebastian D Fugmann
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/00d80zx46 Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/02dnn6q67 Department of Nephrology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shu Yuan Yang
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/00d80zx46 Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/02dnn6q67 Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
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3
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Wu Z, Zhao Z, Li Y, Wang C, Cheng C, Li H, Zhao M, Li J, Law Wen Xin E, Zhang N, Zhao Y, Yang X. Identification of key genes and immune infiltration in peripheral blood biomarker analysis of delayed cerebral ischemia: Valproic acid as a potential therapeutic drug. Int Immunopharmacol 2024; 137:112408. [PMID: 38897129 DOI: 10.1016/j.intimp.2024.112408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/29/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Delayed cerebral ischemia (DCI) is a common and serious complication of subarachnoid hemorrhage (SAH). Its pathogenesis is not fully understood. Here, we developed a predictive model based on peripheral blood biomarkers and validated the model using several bioinformatic multi-analysis methods. METHODS Six datasets were obtained from the GEO database. Characteristic genes were screened using weighted correlation network analysis (WGCNA) and differentially expressed genes. Three machine learning algorithms, elastic networks-LASSO, support vector machines (SVM-RFE) and random forests (RF), were also used to construct diagnostic prediction models for key genes. To further evaluate the performance and predictive value of the diagnostic models, nomogram model were constructed, and the clinical value of the models was assessed using Decision Curve Analysis (DCA), Area Under the Check Curve (AUC), Clinical Impact Curve (CIC), and validated in the mouse single-cell RNA-seq dataset. Mendelian randomization(MR) analysis explored the causal relationship between SAH and stroke, and the intermediate influencing factors. We validated this by retrospectively analyzing the qPCR levels of the most relevant genes in SAH and SAH-DCI patients. This experiment demonstrated a statistically significant difference between SAH and SAH-DCI and normal group controls. Finally, potential small molecule compounds interacting with the selected features were screened from the Comparative Toxicogenomics Database (CTD). RESULTS The fGSEA results showed that activation of Toll-like receptor signaling and leukocyte transendothelial cell migration pathways were positively correlated with the DCI phenotype, whereas cytokine signaling pathways and natural killer cell-mediated cytotoxicity were negatively correlated. Consensus feature selection of DEG genes using WGCNA and three machine learning algorithms resulted in the identification of six genes (SPOCK2, TRRAP, CIB1, BCL11B, PDZD8 and LAT), which were used to predict DCI diagnosis with high accuracy. Three external datasets and the mouse single-cell dataset showed high accuracy of the diagnostic model, in addition to high performance and predictive value of the diagnostic model in DCA and CIC. MR analysis looked at stroke after SAH independent of SAH, but associated with multiple intermediate factors including Hypertensive diseases, Total triglycerides levels in medium HDL and Platelet count. qPCR confirmed that significant differences in DCI signature genes were observed between the SAH and SAH-DCI groups. Finally, valproic acid became a potential therapeutic agent for DCI based on the results of target prediction and molecular docking of the characterized genes. CONCLUSION This diagnostic model can identify SAH patients at high risk for DCI and may provide potential mechanisms and therapeutic targets for DCI. Valproic acid may be an important future drug for the treatment of DCI.
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Affiliation(s)
- Zhuolin Wu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Zilin Zhao
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Yang Li
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Cong Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Chunchao Cheng
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Hongwen Li
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Mingyu Zhao
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Jia Li
- Neurosurgery Third Department, Baoding NO.1 Central Hospital, 320 Changcheng North Street, Baoding City, Hebei Province, China
| | - Elethea Law Wen Xin
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Nai Zhang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Yan Zhao
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China.
| | - Xinyu Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China.
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4
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Santoni G, Astori S, Leleu M, Glauser L, Zamora SA, Schioppa M, Tarulli I, Sandi C, Gräff J. Chromatin plasticity predetermines neuronal eligibility for memory trace formation. Science 2024; 385:eadg9982. [PMID: 39052786 DOI: 10.1126/science.adg9982] [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: 02/03/2023] [Revised: 03/01/2024] [Accepted: 05/24/2024] [Indexed: 07/27/2024]
Abstract
Memories are encoded by sparse populations of neurons but how such sparsity arises remains largely unknown. We found that a neuron's eligibility to be recruited into the memory trace depends on its epigenetic state prior to encoding. Principal neurons in the mouse lateral amygdala display intrinsic chromatin plasticity, which when experimentally elevated favors neuronal allocation into the encoding ensemble. Such chromatin plasticity occurred at genomic regions underlying synaptic plasticity and was accompanied by increased neuronal excitability in single neurons in real time. Lastly, optogenetic silencing of the epigenetically altered neurons prevented memory expression, revealing a cell-autonomous relationship between chromatin plasticity and memory trace formation. These results identify the epigenetic state of a neuron as a key factor enabling information encoding.
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Affiliation(s)
- Giulia Santoni
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Simone Astori
- Laboratory of Behavioural Genetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Marion Leleu
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Liliane Glauser
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Simon A Zamora
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Myriam Schioppa
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- The institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Isabella Tarulli
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Carmen Sandi
- Laboratory of Behavioural Genetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Johannes Gräff
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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5
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Borrelli C, Roberts M, Eletto D, Hussherr MD, Fazilaty H, Valenta T, Lafzi A, Kretz JA, Guido Vinzoni E, Karakatsani A, Adivarahan S, Mannhart A, Kimura S, Meijs A, Baccouche Mhamedi F, Acar IE, Handler K, Ficht X, Platt RJ, Piscuoglio S, Moor AE. In vivo interaction screening reveals liver-derived constraints to metastasis. Nature 2024:10.1038/s41586-024-07715-3. [PMID: 39048831 DOI: 10.1038/s41586-024-07715-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 06/14/2024] [Indexed: 07/27/2024]
Abstract
It is estimated that only 0.02% of disseminated tumour cells are able to seed overt metastases1. While this suggests the presence of environmental constraints to metastatic seeding, the landscape of host factors controlling this process remains largely unclear. Here, combining transposon technology2 and fluorescence niche labelling3, we developed an in vivo CRISPR activation screen to systematically investigate the interactions between hepatocytes and metastatic cells. We identify plexin B2 as a critical host-derived regulator of liver colonization in colorectal and pancreatic cancer and melanoma syngeneic mouse models. We dissect a mechanism through which plexin B2 interacts with class IV semaphorins on tumour cells, leading to KLF4 upregulation and thereby promoting the acquisition of epithelial traits. Our results highlight the essential role of signals from the liver parenchyma for the seeding of disseminated tumour cells before the establishment of a growth-promoting niche. Our findings further suggest that epithelialization is required for the adaptation of CRC metastases to their new tissue environment. Blocking the plexin-B2-semaphorin axis abolishes metastatic colonization of the liver and therefore represents a therapeutic strategy for the prevention of hepatic metastases. Finally, our screening approach, which evaluates host-derived extrinsic signals rather than tumour-intrinsic factors for their ability to promote metastatic seeding, is broadly applicable and lays a framework for the screening of environmental constraints to metastasis in other organs and cancer types.
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Affiliation(s)
- Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Morgan Roberts
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Davide Eletto
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Hassan Fazilaty
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Tomas Valenta
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Atefeh Lafzi
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Jonas A Kretz
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Elena Guido Vinzoni
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | | | - Ardian Mannhart
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Shoichiro Kimura
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ab Meijs
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Ilhan E Acar
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Kristina Handler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Xenia Ficht
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Salvatore Piscuoglio
- IRCCS Humanitas Research Hospital, Milan, Italy
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
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Wang HC, Chen R, Yang W, Li Y, Muthukumar R, Patel RM, Casey EB, Denby E, Magee JA. Kmt2c restricts G-CSF-driven HSC mobilization and granulocyte production in a methyltransferase-independent manner. Cell Rep 2024; 43:114542. [PMID: 39046877 DOI: 10.1016/j.celrep.2024.114542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 06/10/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024] Open
Abstract
Granulocyte colony-stimulating factor (G-CSF) is widely used to enhance myeloid recovery after chemotherapy and to mobilize hematopoietic stem cells (HSCs) for transplantation. Unfortunately, through the course of chemotherapy, cancer patients can acquire leukemogenic mutations that cause therapy-related myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). This raises the question of whether therapeutic G-CSF might potentiate therapy-related MDS/AML by disproportionately stimulating mutant HSCs and other myeloid progenitors. A common mutation in therapy-related MDS/AML involves chromosome 7 deletions that inactivate many tumor suppressor genes, including KMT2C. Here, we show that Kmt2c deletions hypersensitize murine HSCs and myeloid progenitors to G-CSF, as evidenced by increased HSC mobilization and enhanced granulocyte production from granulocyte-monocyte progenitors (GMPs). Furthermore, Kmt2c attenuates the G-CSF response independently from its SET methyltransferase function. Altogether, the data raise concerns that monosomy 7 can hypersensitize progenitors to G-CSF, such that clinical use of G-CSF may amplify the risk of therapy-related MDS/AML.
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Affiliation(s)
- Helen C Wang
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Ran Chen
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Wei Yang
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Yanan Li
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Rohini Muthukumar
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Riddhi M Patel
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Emily B Casey
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Elisabeth Denby
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Jeffrey A Magee
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA.
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7
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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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8
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Shah MM, Layhadi JA, Hourcade DE, Fulton WT, Tan TJ, Dunham D, Chang I, Vel MS, Fernandes A, Lee AS, Liu J, Arunachalam PS, Galli SJ, Boyd SD, Pulendran B, Davis MM, O'Hara R, Park H, Mitchell LM, Akk A, Patterson A, Jerath MR, Monroy JM, Ren Z, Kendall PL, Durham SR, Fedina A, Gibbs BF, Agache I, Chinthrajah S, Sindher SB, Heider A, Akdis CA, Shamji MH, Pham CTN, Nadeau KC. Elucidating allergic reaction mechanisms in response to SARS-CoV-2 mRNA vaccination in adults. Allergy 2024. [PMID: 39033312 DOI: 10.1111/all.16231] [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: 03/13/2024] [Revised: 05/31/2024] [Accepted: 06/18/2024] [Indexed: 07/23/2024]
Abstract
BACKGROUND During the COVID-19 pandemic, novel nanoparticle-based mRNA vaccines were developed. A small number of individuals developed allergic reactions to these vaccines although the mechanisms remain undefined. METHODS To understand COVID-19 vaccine-mediated allergic reactions, we enrolled 19 participants who developed allergic events within 2 h of vaccination and 13 controls, nonreactors. Using standard hemolysis assays, we demonstrated that sera from allergic participants induced stronger complement activation compared to nonallergic subjects following ex vivo vaccine exposure. RESULTS Vaccine-mediated complement activation correlated with anti-polyethelyne glycol (PEG) IgG (but not IgM) levels while anti-PEG IgE was undetectable in all subjects. Depletion of total IgG suppressed complement activation in select individuals. To investigate the effects of vaccine excipients on basophil function, we employed a validated indirect basophil activation test that stratified the allergic populations into high and low responders. Complement C3a and C5a receptor blockade in this system suppressed basophil response, providing strong evidence for complement involvement in vaccine-mediated basophil activation. Single-cell multiome analysis revealed differential expression of genes encoding the cytokine response and Toll-like receptor (TLR) pathways within the monocyte compartment. Differential chromatin accessibility for IL-13 and IL-1B genes was found in allergic and nonallergic participants, suggesting that in vivo, epigenetic modulation of mononuclear phagocyte immunophenotypes determines their subsequent functional responsiveness, contributing to the overall physiologic manifestation of vaccine reactions. CONCLUSION These findings provide insights into the mechanisms underlying allergic reactions to COVID-19 mRNA vaccines, which may be used for future vaccine strategies in individuals with prior history of allergies or reactions and reduce vaccine hesitancy.
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Affiliation(s)
- Mihir M Shah
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, California, USA
| | - Janice A Layhadi
- Immunomodulation and Tolerance Group, Allergy and Clinical Immunology, Department of National Heart and Lung Institute, Imperial College London, London, UK
| | - Dennis E Hourcade
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - William T Fulton
- Immunomodulation and Tolerance Group, Allergy and Clinical Immunology, Department of National Heart and Lung Institute, Imperial College London, London, UK
| | - Tiak Ju Tan
- Immunomodulation and Tolerance Group, Allergy and Clinical Immunology, Department of National Heart and Lung Institute, Imperial College London, London, UK
| | - Diane Dunham
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, California, USA
| | - Iris Chang
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, California, USA
| | - Monica S Vel
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, California, USA
| | - Andrea Fernandes
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, California, USA
| | - Alexandra S Lee
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, California, USA
| | - James Liu
- Stanford Health Library, Stanford, California, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, California, USA
| | - Stephen J Galli
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Scott D Boyd
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Ruth O'Hara
- Department of Veteran's Administration and Dean's Office, Stanford University, Stanford, California, USA
| | - Helen Park
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
| | - Lynne M Mitchell
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Antonina Akk
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alexander Patterson
- Department of Medicine, Division of Allergy and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Maya R Jerath
- Department of Medicine, Division of Allergy and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jennifer M Monroy
- Department of Medicine, Division of Allergy and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Zhen Ren
- Department of Medicine, Division of Allergy and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Peggy L Kendall
- Department of Medicine, Division of Allergy and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Stephen R Durham
- Immunomodulation and Tolerance Group, Allergy and Clinical Immunology, Department of National Heart and Lung Institute, Imperial College London, London, UK
| | - Aleksandra Fedina
- Immunomodulation and Tolerance Group, Allergy and Clinical Immunology, Department of National Heart and Lung Institute, Imperial College London, London, UK
| | - Bernhard F Gibbs
- Department of Human Medicine, School of Medicine and Health Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Canterbury Christ Church University, Canterbury, UK
| | - Ioana Agache
- Faculty of Medicine, Transilvania University, Brasov, Romania
| | - Sharon Chinthrajah
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, California, USA
| | - Sayantani B Sindher
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, California, USA
| | - Anja Heider
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Mohamed H Shamji
- Immunomodulation and Tolerance Group, Allergy and Clinical Immunology, Department of National Heart and Lung Institute, Imperial College London, London, UK
| | - Christine T N Pham
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kari C Nadeau
- Harvard T.H. Chan School of Public Health, Harvard University, Cambridge, Massachusetts, USA
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9
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Stuart T. Progress in multifactorial single-cell chromatin profiling methods. Biochem Soc Trans 2024:BST20231471. [PMID: 39023855 DOI: 10.1042/bst20231471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024]
Abstract
Chromatin states play a key role in shaping overall cellular states and fates. Building a complete picture of the functional state of chromatin in cells requires the co-detection of several distinct biochemical aspects. These span DNA methylation, chromatin accessibility, chromosomal conformation, histone posttranslational modifications, and more. While this certainly presents a challenging task, over the past few years many new and creative methods have been developed that now enable co-assay of these different aspects of chromatin at single cell resolution. This field is entering an exciting phase, where a confluence of technological improvements, decreased sequencing costs, and computational innovation are presenting new opportunities to dissect the diversity of chromatin states present in tissues, and how these states may influence gene regulation. In this review, I discuss the spectrum of current experimental approaches for multifactorial chromatin profiling, highlight some of the experimental and analytical challenges, as well as some areas for further innovation.
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Affiliation(s)
- Tim Stuart
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
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10
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Dong C, Meng X, Zhang T, Guo Z, Liu Y, Wu P, Chen S, Zhou F, Ma Y, Xiong H, Shu S, He A. Single-cell EpiChem jointly measures drug-chromatin binding and multimodal epigenome. Nat Methods 2024:10.1038/s41592-024-02360-0. [PMID: 39025969 DOI: 10.1038/s41592-024-02360-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 06/25/2024] [Indexed: 07/20/2024]
Abstract
Studies of molecular and cellular functions of small-molecule inhibitors in cancer treatment, eliciting effects by targeting genome and epigenome associated proteins, requires measurement of drug-target engagement in single-cell resolution. Here we present EpiChem for in situ single-cell joint mapping of small molecules and multimodal epigenomic landscape. We demonstrate single-cell co-assays of three small molecules together with histone modifications, chromatin accessibility or target proteins in human colorectal cancer (CRC) organoids. Integrated multimodal analysis reveals diverse drug interactions in the context of chromatin states within heterogeneous CRC organoids. We further reveal drug genomic binding dynamics and adaptive epigenome across cell types after small-molecule drug treatment in CRC organoids. This method provides a unique tool to exploit the mechanisms of cell type-specific drug actions.
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Affiliation(s)
- Chao Dong
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiaoxuan Meng
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Tong Zhang
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhifang Guo
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
- Peking University International Cancer Institute, Beijing, China
- Peking University-Yunnan Baiyao International Medical Research Center, Beijing, China
| | - Yaxi Liu
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Peihuang Wu
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Shiwei Chen
- Peking University International Cancer Institute, Beijing, China
- Peking University-Yunnan Baiyao International Medical Research Center, Beijing, China
| | - Fanqi Zhou
- State Key Laboratory of Medical Molecular Biology, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yanni Ma
- State Key Laboratory of Medical Molecular Biology, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Haiqing Xiong
- 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
- Tianjin Institutes of Health Science, Tianjin, China
| | - Shaokun Shu
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China.
- Peking University International Cancer Institute, Beijing, China.
- Peking University-Yunnan Baiyao International Medical Research Center, Beijing, China.
| | - Aibin He
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Key laboratory of Carcinogenesis and Translational Research of Ministry of Education of China, Peking University Cancer Hospital & Institute, Beijing, China.
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China.
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11
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Pérez RF, Tezanos P, Peñarroya A, González-Ramón A, Urdinguio RG, Gancedo-Verdejo J, Tejedor JR, Santamarina-Ojeda P, Alba-Linares JJ, Sainz-Ledo L, Roberti A, López V, Mangas C, Moro M, Cintado Reyes E, Muela Martínez P, Rodríguez-Santamaría M, Ortea I, Iglesias-Rey R, Castilla-Silgado J, Tomás-Zapico C, Iglesias-Gutiérrez E, Fernández-García B, Sanchez-Mut JV, Trejo JL, Fernández AF, Fraga MF. A multiomic atlas of the aging hippocampus reveals molecular changes in response to environmental enrichment. Nat Commun 2024; 15:5829. [PMID: 39013876 PMCID: PMC11252340 DOI: 10.1038/s41467-024-49608-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: 09/12/2023] [Accepted: 06/10/2024] [Indexed: 07/18/2024] Open
Abstract
Aging involves the deterioration of organismal function, leading to the emergence of multiple pathologies. Environmental stimuli, including lifestyle, can influence the trajectory of this process and may be used as tools in the pursuit of healthy aging. To evaluate the role of epigenetic mechanisms in this context, we have generated bulk tissue and single cell multi-omic maps of the male mouse dorsal hippocampus in young and old animals exposed to environmental stimulation in the form of enriched environments. We present a molecular atlas of the aging process, highlighting two distinct axes, related to inflammation and to the dysregulation of mRNA metabolism, at the functional RNA and protein level. Additionally, we report the alteration of heterochromatin domains, including the loss of bivalent chromatin and the uncovering of a heterochromatin-switch phenomenon whereby constitutive heterochromatin loss is partially mitigated through gains in facultative heterochromatin. Notably, we observed the multi-omic reversal of a great number of aging-associated alterations in the context of environmental enrichment, which was particularly linked to glial and oligodendrocyte pathways. In conclusion, our work describes the epigenomic landscape of environmental stimulation in the context of aging and reveals how lifestyle intervention can lead to the multi-layered reversal of aging-associated decline.
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Affiliation(s)
- Raúl F Pérez
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Patricia Tezanos
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
- Programa de Doctorado en Neurociencia, Universidad Autónoma de Madrid-Instituto Cajal, 28002, Madrid, Spain
| | - Alfonso Peñarroya
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - Alejandro González-Ramón
- Laboratory of Functional Epi-Genomics of Aging and Alzheimer's disease, Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550, Alicante, Spain
| | - Rocío G Urdinguio
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Javier Gancedo-Verdejo
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Pablo Santamarina-Ojeda
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Juan José Alba-Linares
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Lidia Sainz-Ledo
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - Annalisa Roberti
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - Virginia López
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Cristina Mangas
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - María Moro
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
| | - Elisa Cintado Reyes
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
- Programa de Doctorado en Neurociencia, Universidad Autónoma de Madrid-Instituto Cajal, 28002, Madrid, Spain
| | - Pablo Muela Martínez
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
- Programa de Doctorado en Neurociencia, Universidad Autónoma de Madrid-Instituto Cajal, 28002, Madrid, Spain
| | - Mar Rodríguez-Santamaría
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Bioterio y unidad de imagen preclínica, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Ignacio Ortea
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Proteomics Unit, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), 33011, Oviedo, Spain
| | - Ramón Iglesias-Rey
- Neuroimaging and Biotechnology Laboratory (NOBEL), Clinical Neurosciences Research Laboratory (LINC), Health Research Institute of Santiago de Compostela (IDIS), 15706, Santiago de Compostela, Spain
| | - Juan Castilla-Silgado
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Cristina Tomás-Zapico
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Eduardo Iglesias-Gutiérrez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Benjamín Fernández-García
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Jose Vicente Sanchez-Mut
- Laboratory of Functional Epi-Genomics of Aging and Alzheimer's disease, Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550, Alicante, Spain
| | - José Luis Trejo
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
| | - Agustín F Fernández
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain.
| | - Mario F Fraga
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain.
- Departamento de Biología de Organismos y Sistemas, Área de Fisiología Vegetal, Universidad de Oviedo, 33006, Oviedo, Spain.
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12
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Yang Y, Chen X, Pan J, Ning H, Zhang Y, Bo Y, Ren X, Li J, Qin S, Wang D, Chen MM, Zhang Z. Pan-cancer single-cell dissection reveals phenotypically distinct B cell subtypes. Cell 2024:S0092-8674(24)00712-8. [PMID: 39047727 DOI: 10.1016/j.cell.2024.06.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 04/25/2024] [Accepted: 06/26/2024] [Indexed: 07/27/2024]
Abstract
Characterizing the compositional and phenotypic characteristics of tumor-infiltrating B cells (TIBs) is important for advancing our understanding of their role in cancer development. Here, we establish a comprehensive resource of human B cells by integrating single-cell RNA sequencing data of B cells from 649 patients across 19 major cancer types. We demonstrate substantial heterogeneity in their total abundance and subtype composition and observe immunoglobulin G (IgG)-skewness of antibody-secreting cell isotypes. Moreover, we identify stress-response memory B cells and tumor-associated atypical B cells (TAABs), two tumor-enriched subpopulations with prognostic potential, shared in a pan-cancer manner. In particular, TAABs, characterized by a high clonal expansion level and proliferative capacity as well as by close interactions with activated CD4 T cells in tumors, are predictive of immunotherapy response. Our integrative resource depicts distinct clinically relevant TIB subsets, laying a foundation for further exploration of functional commonality and diversity of B cells in cancer.
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Affiliation(s)
- Yu Yang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jieying Pan
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Huiheng Ning
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yaojun Zhang
- State Key Laboratory of Oncology in South China, Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yufei Bo
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xianwen Ren
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jiesheng Li
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Shishang Qin
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dongfang Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China.
| | - Min-Min Chen
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China.
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13
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Song L, Li Q, Xia L, Sahay AE, Qiu Q, Li Y, Li H, Sasaki K, Susztak K, Wu H, Wan L. Single-cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape. Nat Commun 2024; 15:5937. [PMID: 39009564 PMCID: PMC11250843 DOI: 10.1038/s41467-024-50171-w] [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: 10/31/2023] [Accepted: 07/02/2024] [Indexed: 07/17/2024] Open
Abstract
How disruptions to normal cell differentiation link to tumorigenesis remains incompletely understood. Wilms tumor, an embryonal tumor associated with disrupted organogenesis, often harbors mutations in epigenetic regulators, but their role in kidney development remains unexplored. Here, we show at single-cell resolution that a Wilms tumor-associated mutation in the histone acetylation reader ENL disrupts kidney differentiation in mice by rewiring the gene regulatory landscape. Mutant ENL promotes nephron progenitor commitment while restricting their differentiation by dysregulating transcription factors such as Hox clusters. It also induces abnormal progenitors that lose kidney-associated chromatin identity. Furthermore, mutant ENL alters the transcriptome and chromatin accessibility of stromal progenitors, resulting in hyperactivation of Wnt signaling. The impacts of mutant ENL on both nephron and stroma lineages lead to profound kidney developmental defects and postnatal mortality in mice. Notably, a small molecule inhibiting mutant ENL's histone acetylation binding activity largely reverses these defects. This study provides insights into how mutations in epigenetic regulators disrupt kidney development and suggests a potential therapeutic approach.
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Affiliation(s)
- Lele Song
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Qinglan Li
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lingbo Xia
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of the School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Arushi Eesha Sahay
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Kotaro Sasaki
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Katalin Susztak
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Liling Wan
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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14
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Kong W, He J, Zhou Q, Zhou X, Wei X, Yang Y, Mei Y, Wang S, Zhang X, Yao B, Yue Y, Xu J, Jiang M, Xu C. Histone lactylation-related genes correlate with the molecular patterns and functions of cancer-associated fibroblasts and have significant clinical implications in clear cell renal cell carcinoma. Heliyon 2024; 10:e33554. [PMID: 39035489 PMCID: PMC11259888 DOI: 10.1016/j.heliyon.2024.e33554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 06/22/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
Recent research emphasised the indispensable role of histone lactylation in the activation of hepatic stellate cells. The VHL mutation is extremely common in clear cell renal cell carcinoma, which normally causes a metabolic shift in cancer cells and increases lactate production, eventually creating a lactate-enriched tumour microenvironment. Cancer-associated fibroblasts (CAFs) promote tumour progression, which is also vital in clear cell renal cell carcinoma. Therefore, this study investigated histone lactylation in CAFs and its impact on patient survival. Multiomics technology was employed to determine the role of histone lactylation-related genes in the evolution of CAFs which correlated with the function and molecular signatures of CAFs. The results suggested that TIMP1 was the hub gene of histone lactylation-related genes in clear cell renal cell carcinoma.
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Affiliation(s)
- Weiyu Kong
- Department of Urology, Suzhou Ninth People's Hospital, Soochow University, Suzhou, 215000, China
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jiaxin He
- National Experimental Teaching Center of Basic Medical Science, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Qinyao Zhou
- National Experimental Teaching Center of Basic Medical Science, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xin Zhou
- National Experimental Teaching Center of Basic Medical Science, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xiyi Wei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yonglin Yang
- The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, China
| | - Yiwen Mei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Shuai Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xi Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Bing Yao
- National Experimental Teaching Center of Basic Medical Science, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yulin Yue
- Department of Clinical Laboratory, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jiali Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Minjun Jiang
- Department of Urology, Suzhou Ninth People's Hospital, Soochow University, Suzhou, 215000, China
| | - Chen Xu
- Department of Urology, Suzhou Ninth People's Hospital, Soochow University, Suzhou, 215000, China
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15
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Le N, Vu TD, Palazzo I, Pulya R, Kim Y, Blackshaw S, Hoang T. Robust reprogramming of glia into neurons by inhibition of Notch signaling and nuclear factor I (NFI) factors in adult mammalian retina. SCIENCE ADVANCES 2024; 10:eadn2091. [PMID: 38996013 PMCID: PMC11244444 DOI: 10.1126/sciadv.adn2091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/10/2024] [Indexed: 07/14/2024]
Abstract
Generation of neurons through direct reprogramming has emerged as a promising therapeutic approach for treating neurodegenerative diseases. In this study, we present an efficient method for reprogramming retinal glial cells into neurons. By suppressing Notch signaling by disrupting either Rbpj or Notch1/2, we induced mature Müller glial cells to reprogram into bipolar- and amacrine-like neurons. We demonstrate that Rbpj directly activates both Notch effector genes and genes specific to mature Müller glia while indirectly repressing expression of neurogenic basic helix-loop-helix (bHLH) factors. Combined loss of function of Rbpj and Nfia/b/x resulted in conversion of nearly all Müller glia to neurons. Last, inducing Müller glial proliferation by overexpression of dominant-active Yap promotes neurogenesis in both Rbpj- and Nfia/b/x/Rbpj-deficient Müller glia. These findings demonstrate that Notch signaling and NFI factors act in parallel to inhibit neurogenic competence in mammalian Müller glia and help clarify potential strategies for regenerative therapies aimed at treating retinal dystrophies.
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Affiliation(s)
- Nguyet Le
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Trieu-Duc Vu
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI 48105
- Michigan Neuroscience Institute, University of Michigan School of Medicine, Ann Arbor, MI 48105, USA
| | - Isabella Palazzo
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ritvik Pulya
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yehna Kim
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Seth Blackshaw
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thanh Hoang
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI 48105
- Michigan Neuroscience Institute, University of Michigan School of Medicine, Ann Arbor, MI 48105, USA
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, MI 48105, USA
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16
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Simats A, Zhang S, Messerer D, Chong F, Beşkardeş S, Chivukula AS, Cao J, Besson-Girard S, Montellano FA, Morbach C, Carofiglio O, Ricci A, Roth S, Llovera G, Singh R, Chen Y, Filser S, Plesnila N, Braun C, Spitzer H, Gokce O, Dichgans M, Heuschmann PU, Hatakeyama K, Beltrán E, Clauss S, Bonev B, Schulz C, Liesz A. Innate immune memory after brain injury drives inflammatory cardiac dysfunction. Cell 2024:S0092-8674(24)00702-5. [PMID: 39043180 DOI: 10.1016/j.cell.2024.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 04/22/2024] [Accepted: 06/21/2024] [Indexed: 07/25/2024]
Abstract
The medical burden of stroke extends beyond the brain injury itself and is largely determined by chronic comorbidities that develop secondarily. We hypothesized that these comorbidities might share a common immunological cause, yet chronic effects post-stroke on systemic immunity are underexplored. Here, we identify myeloid innate immune memory as a cause of remote organ dysfunction after stroke. Single-cell sequencing revealed persistent pro-inflammatory changes in monocytes/macrophages in multiple organs up to 3 months after brain injury, notably in the heart, leading to cardiac fibrosis and dysfunction in both mice and stroke patients. IL-1β was identified as a key driver of epigenetic changes in innate immune memory. These changes could be transplanted to naive mice, inducing cardiac dysfunction. By neutralizing post-stroke IL-1β or blocking pro-inflammatory monocyte trafficking with a CCR2/5 inhibitor, we prevented post-stroke cardiac dysfunction. Such immune-targeted therapies could potentially prevent various IL-1β-mediated comorbidities, offering a framework for secondary prevention immunotherapy.
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Affiliation(s)
- Alba Simats
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany; Cerebrovascular Research Laboratory, Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Sijia Zhang
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Denise Messerer
- Medizinische Klinik und Poliklinik I, University Hospital, LMU Munich, Munich, Germany
| | - Faye Chong
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Sude Beşkardeş
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Jiayu Cao
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Simon Besson-Girard
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Felipe A Montellano
- Department of Neurology, University Hospital Würzburg, Würzburg, Germany; Institute of Clinical Epidemiology and Biometry, Julius-Maximilian-University Würzburg, Würzburg, Germany
| | - Caroline Morbach
- Department Clinical Research & Epidemiology, Comprehensive Heart Failure Center, and Department Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Olga Carofiglio
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Alessio Ricci
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Stefan Roth
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Gemma Llovera
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Rashween Singh
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Yiming Chen
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Severin Filser
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Nikolaus Plesnila
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Christian Braun
- Institute of Legal Medicine, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Hannah Spitzer
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Ozgun Gokce
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Partner Sites Munich and Bonn, Germany; Department of Old Age Psychiatry and cognitive Disorders, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Partner Sites Munich and Bonn, Germany
| | - Peter U Heuschmann
- Institute of Clinical Epidemiology and Biometry, Julius-Maximilian-University Würzburg, Würzburg, Germany; Institute for Medical Data Sciences, University Hospital Würzburg, Würzburg, Germany; Clinical Trial Centre Würzburg, University Hospital Würzburg, Würzburg, Germany
| | - Kinta Hatakeyama
- Department of Pathology, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Eduardo Beltrán
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany; Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Sebastian Clauss
- Medizinische Klinik und Poliklinik I, University Hospital, LMU Munich, Munich, Germany; Institute of Surgical Research at the Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; Interfaculty Center for Endocrine and Cardiovascular Disease Network Modelling and Clinical Transfer (ICONLMU), LMU Munich, Munich, Germany
| | - Boyan Bonev
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany; Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christian Schulz
- Medizinische Klinik und Poliklinik I, University Hospital, LMU Munich, Munich, Germany; Institute of Surgical Research at the Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; Department of Immunopharmacology, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Arthur Liesz
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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17
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Rodrigues PF, Trsan T, Cvijetic G, Khantakova D, Panda SK, Liu Z, Ginhoux F, Cella M, Colonna M. Progenitors of distinct lineages shape the diversity of mature type 2 conventional dendritic cells. Immunity 2024; 57:1567-1585.e5. [PMID: 38821051 DOI: 10.1016/j.immuni.2024.05.007] [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: 08/29/2023] [Revised: 02/15/2024] [Accepted: 05/07/2024] [Indexed: 06/02/2024]
Abstract
Conventional dendritic cells (cDC) are antigen-presenting cells comprising cDC1 and cDC2, responsible for priming naive CD8+ and CD4+ T cells, respectively. Recent studies have unveiled cDC2 heterogeneity and identified various cDC2 progenitors beyond the common DC progenitor (CDP), hinting at distinct cDC2 lineages. By generating Cd300ciCre-hCD2R26tdTomato reporter mice, we identified a bone marrow pro-cDC2 progenitor exclusively generating cDC2 in vitro and in vivo. Single-cell analyses and multiparametric flow cytometry demonstrated that pro-cDC2 encompasses myeloid-derived pre-cDC2 and lymphoid-derived plasmacytoid DC (pDC)-like precursors differentiating into a transcriptionally convergent cDC2 phenotype. Cd300c-traced cDC2 had distinct transcriptomic profiles, phenotypes, and tissue distributions compared with Ms4a3CreR26tdTomato lineage-traced DC3, a monocyte-DC progenitor (MDP)-derived subset that bypasses CDP. Mice with reduced Cd300c-traced cDC2 showed impaired humoral responses to T cell-dependent antigens. We conclude that progenitors of distinct lineages shape the diversity of mature cDC2 across tissues. Thus, ontogenesis may impact tissue immune responses.
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Affiliation(s)
- Patrick Fernandes Rodrigues
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - Tihana Trsan
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - Grozdan Cvijetic
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Darya Khantakova
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - Santosh K Panda
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - Zhaoyuan Liu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Florent Ginhoux
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Institut Gustave Roussy, INSERM U1015, Bâtiment de Médecine Moléculaire 114 rue Edouard Vaillant, 94800 Villejuif, France; Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA.
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18
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Warns J, Kim YI, O'Rourke R, Sagerström CG. scMultiome analysis identifies a single caudal hindbrain compartment in the developing zebrafish nervous system. Neural Dev 2024; 19:12. [PMID: 38970093 PMCID: PMC11225431 DOI: 10.1186/s13064-024-00189-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: 05/17/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND A key step in nervous system development involves the coordinated control of neural progenitor specification and positioning. A long-standing model for the vertebrate CNS postulates that transient anatomical compartments - known as neuromeres - function to position neural progenitors along the embryonic anteroposterior neuraxis. Such neuromeres are apparent in the embryonic hindbrain - that contains six rhombomeres with morphologically apparent boundaries - but other neuromeres lack clear morphological boundaries and have instead been defined by different criteria, such as differences in gene expression patterns and the outcomes of transplantation experiments. Accordingly, the caudal hindbrain (CHB) posterior to rhombomere (r) 6 has been variably proposed to contain from two to five 'pseudo-rhombomeres', but the lack of comprehensive molecular data has precluded a detailed definition of such structures. METHODS We used single-cell Multiome analysis, which allows simultaneous characterization of gene expression and chromatin state of individual cell nuclei, to identify and characterize CHB progenitors in the developing zebrafish CNS. RESULTS We identified CHB progenitors as a transcriptionally distinct population, that also possesses a unique profile of accessible transcription factor binding motifs, relative to both r6 and the spinal cord. This CHB population can be subdivided along its dorsoventral axis based on molecular characteristics, but we do not find any molecular evidence that it contains multiple pseudo-rhombomeres. We further observe that the CHB is closely related to r6 at the earliest embryonic stages, but becomes more divergent over time, and that it is defined by a unique gene regulatory network. CONCLUSIONS We conclude that the early CHB represents a single neuromere compartment that cannot be molecularly subdivided into pseudo-rhombomeres and that it may share an embryonic origin with r6.
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Affiliation(s)
- Jessica Warns
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
- Department of Science and Math, Northern State University, 1200 S. Jay St, Aberdeen, SD, 57401, USA
| | - Yong-Ii Kim
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Rebecca O'Rourke
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Charles G Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, 12801 E. 17th Avenue, Aurora, CO, 80045, USA.
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19
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Oguchi A, Suzuki A, Komatsu S, Yoshitomi H, Bhagat S, Son R, Bonnal RJP, Kojima S, Koido M, Takeuchi K, Myouzen K, Inoue G, Hirai T, Sano H, Takegami Y, Kanemaru A, Yamaguchi I, Ishikawa Y, Tanaka N, Hirabayashi S, Konishi R, Sekito S, Inoue T, Kere J, Takeda S, Takaori-Kondo A, Endo I, Kawaoka S, Kawaji H, Ishigaki K, Ueno H, Hayashizaki Y, Pagani M, Carninci P, Yanagita M, Parrish N, Terao C, Yamamoto K, Murakawa Y. An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases. Science 2024; 385:eadd8394. [PMID: 38963856 DOI: 10.1126/science.add8394] [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: 07/17/2022] [Accepted: 05/01/2024] [Indexed: 07/06/2024]
Abstract
Transcribed enhancer maps can reveal nuclear interactions underpinning each cell type and connect specific cell types to diseases. Using a 5' single-cell RNA sequencing approach, we defined transcription start sites of enhancer RNAs and other classes of coding and noncoding RNAs in human CD4+ T cells, revealing cellular heterogeneity and differentiation trajectories. Integration of these datasets with single-cell chromatin profiles showed that active enhancers with bidirectional RNA transcription are highly cell type-specific and that disease heritability is strongly enriched in these enhancers. The resulting cell type-resolved multimodal atlas of bidirectionally transcribed enhancers, which we linked with promoters using fine-scale chromatin contact maps, enabled us to systematically interpret genetic variants associated with a range of immune-mediated diseases.
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Affiliation(s)
- Akiko Oguchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shuichiro Komatsu
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Hiroyuki Yoshitomi
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shruti Bhagat
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Raku Son
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Shohei Kojima
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masaru Koido
- Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuhiro Takeuchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keiko Myouzen
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Gyo Inoue
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomoya Hirai
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Hiromi Sano
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | | | | | - Yuki Ishikawa
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Nao Tanaka
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shigeki Hirabayashi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Riyo Konishi
- Inter-Organ Communication Research Team, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sho Sekito
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie University, Tsu, Japan
| | - Takahiro Inoue
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie University, Tsu, Japan
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhalsan Research Center, Helsinki, Finland
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Shinpei Kawaoka
- Inter-Organ Communication Research Team, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Integrative Bioanalytics, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Science, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hideki Ueno
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihide Hayashizaki
- K.K. DNAFORM, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Massimiliano Pagani
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi, Milan, Italy
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Motoko Yanagita
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nicholas Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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20
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Singh PNP, Gu W, Madha S, Lynch AW, Cejas P, He R, Bhattacharya S, Muñoz Gomez M, Oser MG, Brown M, Long HW, Meyer CA, Zhou Q, Shivdasani RA. Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation. Cell Stem Cell 2024; 31:1038-1057.e11. [PMID: 38733993 DOI: 10.1016/j.stem.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024]
Abstract
Enteroendocrine cells (EECs) secrete serotonin (enterochromaffin [EC] cells) or specific peptide hormones (non-EC cells) that serve vital metabolic functions. The basis for terminal EEC diversity remains obscure. By forcing activity of the transcription factor (TF) NEUROG3 in 2D cultures of human intestinal stem cells, we replicated physiologic EEC differentiation and examined transcriptional and cis-regulatory dynamics that culminate in discrete cell types. Abundant EEC precursors expressed stage-specific genes and TFs. Before expressing pre-terminal NEUROD1, post-mitotic precursors oscillated between transcriptionally distinct ASCL1+ and HES6hi cell states. Loss of either factor accelerated EEC differentiation substantially and disrupted EEC individuality; ASCL1 or NEUROD1 deficiency had opposing consequences on EC and non-EC cell features. These TFs mainly bind cis-elements that are accessible in undifferentiated stem cells, and they tailor subsequent expression of TF combinations that underlie discrete EEC identities. Thus, early TF oscillations retard EEC maturation to enable accurate diversity within a medically important cell lineage.
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Affiliation(s)
- Pratik N P Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Wei Gu
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shariq Madha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Allen W Lynch
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ruiyang He
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Swarnabh Bhattacharya
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Miguel Muñoz Gomez
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Clifford A Meyer
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Qiao Zhou
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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21
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Sethi R, Ang KS, Li M, Long Y, Ling J, Chen J. ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists. Nat Commun 2024; 15:5600. [PMID: 38961061 PMCID: PMC11222513 DOI: 10.1038/s41467-024-48188-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/22/2024] [Indexed: 07/05/2024] Open
Abstract
ezSingleCell is an interactive and easy-to-use application for analysing various single-cell and spatial omics data types without requiring prior programing knowledge. It combines the best-performing publicly available methods for in-depth data analysis, integration, and interactive data visualization. ezSingleCell consists of five modules, each designed to be a comprehensive workflow for one data type or task. In addition, ezSingleCell allows crosstalk between different modules within a unified interface. Acceptable input data can be in a variety of formats while the output consists of publication ready figures and tables. In-depth manuals and video tutorials are available to guide users on the analysis workflows and parameter adjustments to suit their study aims. ezSingleCell's streamlined interface can analyse a standard scRNA-seq dataset of 3000 cells in less than five minutes. ezSingleCell is available in two forms: an installation-free web application ( https://immunesinglecell.org/ezsc/ ) or a software package with a shinyApp interface ( https://github.com/JinmiaoChenLab/ezSingleCell2 ) for offline analysis.
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Affiliation(s)
- Raman Sethi
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
| | - Kok Siong Ang
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Mengwei Li
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Yahui Long
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Jingjing Ling
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Singapore, 138648, Singapore
| | - Jinmiao Chen
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix, Singapore, 138671, Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
- Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 5 Science Drive 2, Blk MD4, Level 3, Singapore, 117545, Singapore.
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22
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Wang X, Lian Q, Dong H, Xu S, Su Y, Wu X. Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae014. [PMID: 39049508 DOI: 10.1093/gpbjnl/qzae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 07/27/2024]
Abstract
Gene set scoring (GSS) has been routinely conducted for gene expression analysis of bulk or single-cell RNA sequencing (RNA-seq) data, which helps to decipher single-cell heterogeneity and cell type-specific variability by incorporating prior knowledge from functional gene sets. Single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) is a powerful technique for interrogating single-cell chromatin-based gene regulation, and genes or gene sets with dynamic regulatory potentials can be regarded as cell type-specific markers as if in single-cell RNA-seq (scRNA-seq). However, there are few GSS tools specifically designed for scATAC-seq, and the applicability and performance of RNA-seq GSS tools on scATAC-seq data remain to be investigated. Here, we systematically benchmarked ten GSS tools, including four bulk RNA-seq tools, five scRNA-seq tools, and one scATAC-seq method. First, using matched scATAC-seq and scRNA-seq datasets, we found that the performance of GSS tools on scATAC-seq data was comparable to that on scRNA-seq, suggesting their applicability to scATAC-seq. Then, the performance of different GSS tools was extensively evaluated using up to ten scATAC-seq datasets. Moreover, we evaluated the impact of gene activity conversion, dropout imputation, and gene set collections on the results of GSS. Results show that dropout imputation can significantly promote the performance of almost all GSS tools, while the impact of gene activity conversion methods or gene set collections on GSS performance is more dependent on GSS tools or datasets. Finally, we provided practical guidelines for choosing appropriate preprocessing methods and GSS tools in different application scenarios.
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Affiliation(s)
- Xi Wang
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
- Department of Automation, Xiamen University, Xiamen 361005, China
| | - Qiwei Lian
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
- Department of Automation, Xiamen University, Xiamen 361005, China
| | - Haoyu Dong
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
| | - Shuo Xu
- Department of Automation, Xiamen University, Xiamen 361005, China
| | - Yaru Su
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou 350116, China
| | - Xiaohui Wu
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
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23
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Qadir MMF, Elgamal RM, Song K, Kudtarkar P, Sakamuri SS, Katakam PV, El-Dahr SS, Kolls JK, Gaulton KJ, Mauvais-Jarvis F. Single cell regulatory architecture of human pancreatic islets suggests sex differences in β cell function and the pathogenesis of type 2 diabetes. RESEARCH SQUARE 2024:rs.3.rs-4607352. [PMID: 39011095 PMCID: PMC11247939 DOI: 10.21203/rs.3.rs-4607352/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Type 2 and type 1 diabetes (T2D, T1D) exhibit sex differences in insulin secretion, the mechanisms of which are unknown. We examined sex differences in human pancreatic islets from 52 donors with and without T2D combining single cell RNA-seq (scRNA-seq), single nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq), hormone secretion, and bioenergetics. In nondiabetic (ND) donors, sex differences in islet cells gene accessibility and expression predominantly involved sex chromosomes. Islets from T2D donors exhibited similar sex differences in sex chromosomes differentially expressed genes (DEGs), but also exhibited sex differences in autosomal genes. Comparing β cells from T2D vs. ND donors, gene enrichment of female β cells showed suppression in mitochondrial respiration, while male β cells exhibited suppressed insulin secretion. Thus, although sex differences in gene accessibility and expression of ND β cells predominantly affect sex chromosomes, the transition to T2D reveals sex differences in autosomes highlighting mitochondrial failure in females.
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Affiliation(s)
- Mirza Muhammad Fahd Qadir
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
- Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA
| | - Ruth M. Elgamal
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Keijing Song
- Center for Translational Research in Infection and Inflammation, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Parul Kudtarkar
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Siva S.V.P Sakamuri
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Prasad V. Katakam
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Samir S. El-Dahr
- Department of Pediatrics, Tulane University, School of Medicine, New Orleans, LA, USA
| | - Jay K. Kolls
- Center for Translational Research in Infection and Inflammation, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Franck Mauvais-Jarvis
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
- Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA
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24
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Shwab EK, Gingerich DC, Man Z, Gamache J, Garrett ME, Crawford GE, Ashley-Koch AE, Serrano GE, Beach TG, Lutz MW, Chiba-Falek O. Single-nucleus multi-omics of Parkinson's disease reveals a glutamatergic neuronal subtype susceptible to gene dysregulation via alteration of transcriptional networks. Acta Neuropathol Commun 2024; 12:111. [PMID: 38956662 PMCID: PMC11218415 DOI: 10.1186/s40478-024-01803-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
The genetic architecture of Parkinson's disease (PD) is complex and multiple brain cell subtypes are involved in the neuropathological progression of the disease. Here we aimed to advance our understanding of PD genetic complexity at a cell subtype precision level. Using parallel single-nucleus (sn)RNA-seq and snATAC-seq analyses we simultaneously profiled the transcriptomic and chromatin accessibility landscapes in temporal cortex tissues from 12 PD compared to 12 control subjects at a granular single cell resolution. An integrative bioinformatic pipeline was developed and applied for the analyses of these snMulti-omics datasets. The results identified a subpopulation of cortical glutamatergic excitatory neurons with remarkably altered gene expression in PD, including differentially-expressed genes within PD risk loci identified in genome-wide association studies (GWAS). This was the only neuronal subtype showing significant and robust overexpression of SNCA. Further characterization of this neuronal-subpopulation showed upregulation of specific pathways related to axon guidance, neurite outgrowth and post-synaptic structure, and downregulated pathways involved in presynaptic organization and calcium response. Additionally, we characterized the roles of three molecular mechanisms in governing PD-associated cell subtype-specific dysregulation of gene expression: (1) changes in cis-regulatory element accessibility to transcriptional machinery; (2) changes in the abundance of master transcriptional regulators, including YY1, SP3, and KLF16; (3) candidate regulatory variants in high linkage disequilibrium with PD-GWAS genomic variants impacting transcription factor binding affinities. To our knowledge, this study is the first and the most comprehensive interrogation of the multi-omics landscape of PD at a cell-subtype resolution. Our findings provide new insights into a precise glutamatergic neuronal cell subtype, causal genes, and non-coding regulatory variants underlying the neuropathological progression of PD, paving the way for the development of cell- and gene-targeted therapeutics to halt disease progression as well as genetic biomarkers for early preclinical diagnosis.
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Affiliation(s)
- E Keats Shwab
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Daniel C Gingerich
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Zhaohui Man
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Julia Gamache
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Melanie E Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, 27701, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, 27708, USA
- Center for Advanced Genomic Technologies, Duke University Medical Center, Durham, NC, 27708, USA
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, 27701, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27708, USA
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Michael W Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA.
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25
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Hu H, Wang X, Feng S, Xu Z, Liu J, Heidrich-O'Hare E, Chen Y, Yue M, Zeng L, Rong Z, Chen T, Billiar T, Ding Y, Huang H, Duerr RH, Chen W. A unified model-based framework for doublet or multiplet detection in single-cell multiomics data. Nat Commun 2024; 15:5562. [PMID: 38956023 PMCID: PMC11220103 DOI: 10.1038/s41467-024-49448-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 06/03/2024] [Indexed: 07/04/2024] Open
Abstract
Droplet-based single-cell sequencing techniques rely on the fundamental assumption that each droplet encapsulates a single cell, enabling individual cell omics profiling. However, the inevitable issue of multiplets, where two or more cells are encapsulated within a single droplet, can lead to spurious cell type annotations and obscure true biological findings. The issue of multiplets is exacerbated in single-cell multiomics settings, where integrating cross-modality information for clustering can inadvertently promote the aggregation of multiplet clusters and increase the risk of erroneous cell type annotations. Here, we propose a compound Poisson model-based framework for multiplet detection in single-cell multiomics data. Leveraging experimental cell hashing results as the ground truth for multiplet status, we conducted trimodal DOGMA-seq experiments and generated 17 benchmarking datasets from two tissues, involving a total of 280,123 droplets. We demonstrated that the proposed method is an essential tool for integrating cross-modality multiplet signals, effectively eliminating multiplet clusters in single-cell multiomics data-a task at which the benchmarked single-omics methods proved inadequate.
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Affiliation(s)
- Haoran Hu
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Xinjun Wang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Site Feng
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Zhongli Xu
- School of Medicine, Tsinghua University, 100084, Beijing, China
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, 15224, USA
| | - Jing Liu
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, 15224, USA
| | | | - Yanshuo Chen
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
- Center of Bioinformatics and Computational Biology, College Park, MD, 20740, USA
| | - Molin Yue
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Lang Zeng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Ziqi Rong
- School of Information, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Tianmeng Chen
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Timothy Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Heng Huang
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
- Center of Bioinformatics and Computational Biology, College Park, MD, 20740, USA
| | - Richard H Duerr
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Wei Chen
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, 15224, USA.
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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26
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Pereira A, Diwakar J, Masserdotti G, Beşkardeş S, Simon T, So Y, Martín-Loarte L, Bergemann F, Vasan L, Schauer T, Danese A, Bocchi R, Colomé-Tatché M, Schuurmans C, Philpott A, Straub T, Bonev B, Götz M. Direct neuronal reprogramming of mouse astrocytes is associated with multiscale epigenome remodeling and requires Yy1. Nat Neurosci 2024; 27:1260-1273. [PMID: 38956165 PMCID: PMC11239498 DOI: 10.1038/s41593-024-01677-5] [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: 09/16/2022] [Accepted: 05/10/2024] [Indexed: 07/04/2024]
Abstract
Direct neuronal reprogramming is a promising approach to regenerate neurons from local glial cells. However, mechanisms of epigenome remodeling and co-factors facilitating this process are unclear. In this study, we combined single-cell multiomics with genome-wide profiling of three-dimensional nuclear architecture and DNA methylation in mouse astrocyte-to-neuron reprogramming mediated by Neurogenin2 (Ngn2) and its phosphorylation-resistant form (PmutNgn2), respectively. We show that Ngn2 drives multilayered chromatin remodeling at dynamic enhancer-gene interaction sites. PmutNgn2 leads to higher reprogramming efficiency and enhances epigenetic remodeling associated with neuronal maturation. However, the differences in binding sites or downstream gene activation cannot fully explain this effect. Instead, we identified Yy1, a transcriptional co-factor recruited by direct interaction with Ngn2 to its target sites. Upon deletion of Yy1, activation of neuronal enhancers, genes and ultimately reprogramming are impaired without affecting Ngn2 binding. Thus, our work highlights the key role of interactors of proneural factors in direct neuronal reprogramming.
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Affiliation(s)
- Allwyn Pereira
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
- Nantes Université, CHU Nantes, INSERM, TaRGeT - Translational Research in Gene Therapy, UMR 1089, Nantes, France
| | - Jeisimhan Diwakar
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Helmholtz Pioneer Campus, Helmholtz Center Munich, Neuherberg, Germany
| | - Giacomo Masserdotti
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
| | - Sude Beşkardeş
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Helmholtz Pioneer Campus, Helmholtz Center Munich, Neuherberg, Germany
| | - Tatiana Simon
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
| | - Younju So
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
| | - Lucía Martín-Loarte
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
| | - Franziska Bergemann
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
| | - Lakshmy Vasan
- Biological Science Platform, Sunnybrook Research Institute; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Tamas Schauer
- Biomedical Center Munich (BMC), Bioinformatic Core Facility, Faculty of Medicine, LMU Munich, Planegg, Germany
- Institute of Stem Cells and Epigenetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Anna Danese
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
| | - Riccardo Bocchi
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Maria Colomé-Tatché
- Institute of Computational Biology, Helmholtz Center Munich, Neuherberg, Germany
- Biomedical Center Munich (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg, Germany
| | - Carol Schuurmans
- Biological Science Platform, Sunnybrook Research Institute; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Anna Philpott
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Tobias Straub
- Biological Science Platform, Sunnybrook Research Institute; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Boyan Bonev
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany.
- Helmholtz Pioneer Campus, Helmholtz Center Munich, Neuherberg, Germany.
| | - Magdalena Götz
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany.
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany.
- Excellence Cluster of Systems Neurology (SYNERGY), Munich, Germany.
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27
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Taylor OB, Patel SP, Hawthorn EC, El-Hodiri HM, Fischer AJ. ID factors regulate the ability of Müller glia to become proliferating neurogenic progenitor-like cells. Glia 2024; 72:1236-1258. [PMID: 38515287 DOI: 10.1002/glia.24523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
The purpose of this study was to investigate how ID factors regulate the ability of Müller glia (MG) to reprogram into proliferating MG-derived progenitor cells (MGPCs) in the chick retina. We found that ID1 is transiently expressed by maturing MG (mMG), whereas ID4 is maintained in mMG in embryonic retinas. In mature retinas, ID4 was prominently expressed by resting MG, but following retinal damage ID4 was rapidly upregulated and then downregulated in MGPCs. By contrast, ID1, ID2, and ID3 were low in resting MG and then upregulated in MGPCs. Inhibition of ID factors following retinal damage decreased numbers of proliferating MGPCs. Inhibition of IDs, after MGPC proliferation, significantly increased numbers of progeny that differentiated as neurons. In damaged or undamaged retinas inhibition of IDs increased levels of p21Cip1 in MG. In response to damage or insulin+FGF2 levels of CDKN1A message and p21Cip1 protein were decreased, absent in proliferating MGPCs, and elevated in MG returning to a resting phenotype. Inhibition of notch- or gp130/Jak/Stat-signaling in damaged retinas increased levels of ID4 but not p21Cip1 in MG. Although ID4 is the predominant isoform expressed by MG in the chick retina, id1 and id2a are predominantly expressed by resting MG and downregulated in activated MG and MGPCs in zebrafish retinas. We conclude that ID factors have a significant impact on regulating the responses of MG to retinal damage, controlling the ability of MG to proliferate by regulating levels of p21Cip1, and suppressing the neurogenic potential of MGPCs.
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Affiliation(s)
- Olivia B Taylor
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Snehal P Patel
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Evan C Hawthorn
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Heithem M El-Hodiri
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Andy J Fischer
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
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28
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Schonfeld M, O’Neil M, Weinman SA, Tikhanovich I. Alcohol-induced epigenetic changes prevent fibrosis resolution after alcohol cessation in miceresolution. Hepatology 2024; 80:119-135. [PMID: 37943941 PMCID: PMC11078890 DOI: 10.1097/hep.0000000000000675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND AND AIMS Alcohol-associated liver disease is a major cause of alcohol-associated mortality. Recently, we identified hepatic demethylases lysine demethylase (KDM)5B and KDM5C as important epigenetic regulators of alcohol response in the liver. In this study, we aimed to investigate the role of KDM5 demethylases in alcohol-associated liver disease resolution. APPROACH AND RESULTS We showed that alcohol-induced liver steatosis rapidly resolved after alcohol cessation. In contrast, fibrosis persisted in the liver for up to 8 weeks after the end of alcohol exposure. Defects in fibrosis resolution were in part due to alcohol-induced KDM5B and KDM5C-dependent epigenetic changes in hepatocytes. Using cell-type-specific knockout mice, we found that adeno-associated virus-mediated knockout of KDM5B and KDM5C demethylases in hepatocytes at the time of alcohol withdrawal promoted fibrosis resolution. Single-cell ATAC sequencing analysis showed that during alcohol-associated liver disease resolution epigenetic cell states largely reverted to control conditions. In addition, we found unique epigenetic cell states distinct from both control and alcohol states and identified associated transcriptional regulators, including liver X receptor (LXR) alpha (α). In vitro and in vivo analysis confirmed that knockout of KDM5B and KDM5C demethylases promoted LXRα activity, likely through regulation of oxysterol biosynthesis, and this activity was critical for the fibrosis resolution process. Reduced LXR activity by small molecule inhibitors prevented fibrosis resolution in KDM5-deficient mice. CONCLUSIONS In summary, KDM5B and KDM5C demethylases prevent liver fibrosis resolution after alcohol cessation in part through suppression of LXR activity.
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Affiliation(s)
- Michael Schonfeld
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Maura O’Neil
- Department of Pathology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Steven A. Weinman
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
- Kansas City VA Medical Center, Kansas City, Missouri, USA
| | - Irina Tikhanovich
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
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29
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Verhagen MP, Joosten R, Schmitt M, Välimäki N, Sacchetti A, Rajamäki K, Choi J, Procopio P, Silva S, van der Steen B, van den Bosch TPP, Seinstra D, de Vries AC, Doukas M, Augenlicht LH, Aaltonen LA, Fodde R. Non-stem cell lineages as an alternative origin of intestinal tumorigenesis in the context of inflammation. Nat Genet 2024; 56:1456-1467. [PMID: 38902475 PMCID: PMC11250264 DOI: 10.1038/s41588-024-01801-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/15/2024] [Indexed: 06/22/2024]
Abstract
According to conventional views, colon cancer originates from stem cells. However, inflammation, a key risk factor for colon cancer, has been shown to suppress intestinal stemness. Here, we used Paneth cells as a model to assess the capacity of differentiated lineages to trigger tumorigenesis in the context of inflammation in mice. Upon inflammation, Paneth cell-specific Apc mutations led to intestinal tumors reminiscent not only of those arising in patients with inflammatory bowel disease, but also of a larger fraction of human sporadic colon cancers. The latter is possibly because of the inflammatory consequences of western-style dietary habits, a major colon cancer risk factor. Machine learning methods designed to predict the cell-of-origin of cancer from patient-derived tumor samples confirmed that, in a substantial fraction of sporadic cases, the origins of colon cancer reside in secretory lineages and not in stem cells.
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Affiliation(s)
- Mathijs P Verhagen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Rosalie Joosten
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mark Schmitt
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Institute of Pharmacology, University of Marburg, Marburg, Germany
| | - Niko Välimäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Andrea Sacchetti
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kristiina Rajamäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Jiahn Choi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Paola Procopio
- Institute of Pharmacology, University of Marburg, Marburg, Germany
| | - Sara Silva
- Institute of Pharmacology, University of Marburg, Marburg, Germany
| | - Berdine van der Steen
- Department of Otorhinolaryngology and Head & Neck Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Danielle Seinstra
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Annemarie C de Vries
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Michail Doukas
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Leonard H Augenlicht
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Riccardo Fodde
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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30
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Zenk F, Fleck JS, Jansen SMJ, Kashanian B, Eisinger B, Santel M, Dupré JS, Camp JG, Treutlein B. Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems. Nat Neurosci 2024; 27:1376-1386. [PMID: 38914828 PMCID: PMC11239525 DOI: 10.1038/s41593-024-01652-0] [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: 04/20/2023] [Accepted: 04/17/2024] [Indexed: 06/26/2024]
Abstract
Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the epigenetic mechanisms underlying human cell diversity has been difficult. In this study, we use human brain and retina organoid models and present single-cell profiling of H3K27ac, H3K27me3 and H3K4me3 histone modifications from progenitor to differentiated neural fates to reconstruct the epigenomic trajectories regulating cell identity acquisition. We capture transitions from pluripotency through neuroepithelium to retinal and brain region and cell type specification. Switching of repressive and activating epigenetic modifications can precede and predict cell fate decisions at each stage, providing a temporal census of gene regulatory elements and transcription factors. Removing H3K27me3 at the neuroectoderm stage disrupts fate restriction, resulting in aberrant cell identity acquisition. Our single-cell epigenome-wide map of human neural organoid development serves as a blueprint to explore human cell fate determination.
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Affiliation(s)
- Fides Zenk
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
- Brain Mind Institute, School of Life Sciences EPFL, Lausanne, Switzerland.
| | - Jonas Simon Fleck
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Bijan Kashanian
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Benedikt Eisinger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Małgorzata Santel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Jean-Samuel Dupré
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - J Gray Camp
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
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31
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Clark EA, Talatala ER, Ye W, Davis RJ, Collins SL, Hillel AT, Ramirez-Solano M, Sheng Q, Wanjalla CN, Mallal SA, Gelbard A. Similarity Network Analysis of the Adaptive Immune Response in the Proximal Airway. Laryngoscope 2024; 134:3245-3252. [PMID: 38450771 PMCID: PMC11182723 DOI: 10.1002/lary.31376] [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: 05/02/2023] [Revised: 01/23/2024] [Accepted: 02/12/2024] [Indexed: 03/08/2024]
Abstract
OBJECTIVES Recent immunologic study of the adaptive immune repertoire in the subglottic airway demonstrated high-frequency T cell clones that do not overlap between individuals. However, the anatomic distribution and antigenic target of the T cell repertoire in the proximal airway mucosa remain unresolved. METHODS Single-cell RNA sequencing of matched scar and unaffected mucosa from idiopathic subglottic stenosis patients (iSGS, n = 32) was performed and compared with airway mucosa from healthy controls (n = 10). T cell receptor (TCR) sequences were interrogated via similarity network analysis to explore antigenic targets using the published algorithm: Grouping of Lymphocyte Interactions by Paratope Hotspots (GLIPH2). RESULTS The mucosal T cell repertoire in healthy control airways consisted of highly expressed T cell clones conserved across anatomic subsites (trachea, bronchi, bronchioles, and lung). In iSGS, high-frequency clones were equally represented in both scar and adjacent non-scar tissue. Significant differences in repertoire structure between iSGS scar and unaffected mucosa was observed, driven by unique low-frequency clones. GLIPH2 results suggest low-frequency clones share targets between multiple iSGS patients. CONCLUSION Healthy airway mucosa has a highly conserved T cell repertoire across multiple anatomic subsites. Similarly, iSGS patients have highly expressed T cell clones present in both scar and unaffected mucosa. iSGS airway scar possesses an abundance of less highly expanded clones with predicted antigen targets shared between patients. Interrogation of these shared motifs suggests abundant adaptive immunity to viral targets in iSGS airway scar. These results provide insight into disease pathogenesis and illuminate new treatment strategies in iSGS. LEVEL OF EVIDENCE NA Laryngoscope, 134:3245-3252, 2024.
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Affiliation(s)
- Evan A. Clark
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Edward R.R. Talatala
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Wenda Ye
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Ruth J. Davis
- Department of Otolaryngology-Head & Neck Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Samuel L. Collins
- Department of Otolaryngology-Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alexander T. Hillel
- Department of Otolaryngology-Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Celestine N. Wanjalla
- Department of Medicine, Division of Infectious Disease, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Simon A. Mallal
- Department of Medicine, Division of Infectious Disease, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alexander Gelbard
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
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32
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Liu A, Citu C, Enduru N, Chen X, Manuel AM, Sinha T, Gorski D, Fernandes BS, Yu M, Schulz PE, Simon LM, Soto C, Zhao Z. Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600720. [PMID: 38979371 PMCID: PMC11230393 DOI: 10.1101/2024.06.25.600720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Sporadic early-onset Alzheimer's disease (sEOAD) represents a significant but less-studied subtype of Alzheimer's disease (AD). Here, we generated a single-nucleus multiome atlas derived from the postmortem prefrontal cortex, entorhinal cortex, and hippocampus of nine individuals with or without sEOAD. Comprehensive analyses were conducted to delineate cell type-specific transcriptomic changes and linked candidate cis- regulatory elements (cCREs) across brain regions. We prioritized seven conservative transcription factors in glial cells in multiple brain regions, including RFX4 in astrocytes and IKZF1 in microglia, which are implicated in regulating sEOAD-associated genes. Moreover, we identified the top 25 altered intercellular signaling between glial cells and neurons, highlighting their regulatory potential on gene expression in receiver cells. We reported 38 cCREs linked to sEOAD-associated genes overlapped with late-onset AD risk loci, and sEOAD cCREs enriched in neuropsychiatric disorder risk loci. This atlas helps dissect transcriptional and chromatin dynamics in sEOAD, providing a key resource for AD research.
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33
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Yang Y, Pe’er D. REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data. Bioinformatics 2024; 40:i567-i575. [PMID: 38940155 PMCID: PMC11211829 DOI: 10.1093/bioinformatics/btae234] [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] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION Profiling of gene expression and chromatin accessibility by single-cell multi-omics approaches can help to systematically decipher how transcription factors (TFs) regulate target gene expression via cis-region interactions. However, integrating information from different modalities to discover regulatory associations is challenging, in part because motif scanning approaches miss many likely TF binding sites. RESULTS We develop REUNION, a framework for predicting genome-wide TF binding and cis-region-TF-gene "triplet" regulatory associations using single-cell multi-omics data. The first component of REUNION, Unify, utilizes information theory-inspired complementary score functions that incorporate TF expression, chromatin accessibility, and target gene expression to identify regulatory associations. The second component, Rediscover, takes Unify estimates as input for pseudo semi-supervised learning to predict TF binding in accessible genomic regions that may or may not include detected TF motifs. Rediscover leverages latent chromatin accessibility and sequence feature spaces of the genomic regions, without requiring chromatin immunoprecipitation data for model training. Applied to peripheral blood mononuclear cell data, REUNION outperforms alternative methods in TF binding prediction on average performance. In particular, it recovers missing region-TF associations from regions lacking detected motifs, which circumvents the reliance on motif scanning and facilitates discovery of novel associations involving potential co-binding transcriptional regulators. Newly identified region-TF associations, even in regions lacking a detected motif, improve the prediction of target gene expression in regulatory triplets, and are thus likely to genuinely participate in the regulation. AVAILABILITY AND IMPLEMENTATION All source code is available at https://github.com/yangymargaret/REUNION.
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Affiliation(s)
- Yang Yang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, United States
| | - Dana Pe’er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, United States
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34
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Patrick R, Naval-Sanchez M, Deshpande N, Huang Y, Zhang J, Chen X, Yang Y, Tiwari K, Esmaeili M, Tran M, Mohamed AR, Wang B, Xia D, Ma J, Bayliss J, Wong K, Hun ML, Sun X, Cao B, Cottle DL, Catterall T, Barzilai-Tutsch H, Troskie RL, Chen Z, Wise AF, Saini S, Soe YM, Kumari S, Sweet MJ, Thomas HE, Smyth IM, Fletcher AL, Knoblich K, Watt MJ, Alhomrani M, Alsanie W, Quinn KM, Merson TD, Chidgey AP, Ricardo SD, Yu D, Jardé T, Cheetham SW, Marcelle C, Nilsson SK, Nguyen Q, White MD, Nefzger CM. The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening. Cell Metab 2024:S1550-4131(24)00231-6. [PMID: 38959897 DOI: 10.1016/j.cmet.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 03/28/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024]
Abstract
A mechanistic connection between aging and development is largely unexplored. Through profiling age-related chromatin and transcriptional changes across 22 murine cell types, analyzed alongside previous mouse and human organismal maturation datasets, we uncovered a transcription factor binding site (TFBS) signature common to both processes. Early-life candidate cis-regulatory elements (cCREs), progressively losing accessibility during maturation and aging, are enriched for cell-type identity TFBSs. Conversely, cCREs gaining accessibility throughout life have a lower abundance of cell identity TFBSs but elevated activator protein 1 (AP-1) levels. We implicate TF redistribution toward these AP-1 TFBS-rich cCREs, in synergy with mild downregulation of cell identity TFs, as driving early-life cCRE accessibility loss and altering developmental and metabolic gene expression. Such remodeling can be triggered by elevating AP-1 or depleting repressive H3K27me3. We propose that AP-1-linked chromatin opening drives organismal maturation by disrupting cell identity TFBS-rich cCREs, thereby reprogramming transcriptome and cell function, a mechanism hijacked in aging through ongoing chromatin opening.
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Affiliation(s)
- Ralph Patrick
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Marina Naval-Sanchez
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Nikita Deshpande
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Yifei Huang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jingyu Zhang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Xiaoli Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Ying Yang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Kanupriya Tiwari
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Mohammadhossein Esmaeili
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Minh Tran
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Amin R Mohamed
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Binxu Wang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Di Xia
- Genome Innovation Hub, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jun Ma
- Genome Innovation Hub, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jacqueline Bayliss
- Department of Anatomy and Physiology, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kahlia Wong
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Michael L Hun
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Xuan Sun
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Benjamin Cao
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Denny L Cottle
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Tara Catterall
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Hila Barzilai-Tutsch
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Institut NeuroMyoGène, University Claude Bernard Lyon 1, 69008 Lyon, France
| | - Robin-Lee Troskie
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Zhian Chen
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Andrea F Wise
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sheetal Saini
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ye Mon Soe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Snehlata Kumari
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Helen E Thomas
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Ian M Smyth
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Anne L Fletcher
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Konstantin Knoblich
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Matthew J Watt
- Department of Anatomy and Physiology, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Majid Alhomrani
- Department of Clinical Laboratories Sciences, Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia; Research Centre for Health Sciences, Taif University, Taif, Saudi Arabia
| | - Walaa Alsanie
- Department of Clinical Laboratories Sciences, Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia; Research Centre for Health Sciences, Taif University, Taif, Saudi Arabia
| | - Kylie M Quinn
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia
| | - Tobias D Merson
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann P Chidgey
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sharon D Ricardo
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Di Yu
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia; Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Thierry Jardé
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Surgery, Cabrini Monash University, Malvern, VIC 3144, Australia
| | - Seth W Cheetham
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Christophe Marcelle
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Institut NeuroMyoGène, University Claude Bernard Lyon 1, 69008 Lyon, France
| | - Susan K Nilsson
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Melanie D White
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Christian M Nefzger
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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35
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Feng C, Tie R, Xin S, Chen Y, Li S, Chen Y, Hu X, Zhou Y, Liu Y, Hu Y, Hu Y, Pan H, Wu Z, Chao H, Zhang S, Ni Q, Huang J, Luo W, Huang H, Chen M. Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition. BMC Biol 2024; 22:143. [PMID: 38937802 PMCID: PMC11209969 DOI: 10.1186/s12915-024-01939-5] [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: 08/02/2023] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND The endothelial-to-hematopoietic transition (EHT) process during definitive hematopoiesis is highly conserved in vertebrates. Stage-specific expression of transposable elements (TEs) has been detected during zebrafish EHT and may promote hematopoietic stem cell (HSC) formation by activating inflammatory signaling. However, little is known about how TEs contribute to the EHT process in human and mouse. RESULTS We reconstructed the single-cell EHT trajectories of human and mouse and resolved the dynamic expression patterns of TEs during EHT. Most TEs presented a transient co-upregulation pattern along the conserved EHT trajectories, coinciding with the temporal relaxation of epigenetic silencing systems. TE products can be sensed by multiple pattern recognition receptors, triggering inflammatory signaling to facilitate HSC emergence. Interestingly, we observed that hypoxia-related signals were enriched in cells with higher TE expression. Furthermore, we constructed the hematopoietic cis-regulatory network of accessible TEs and identified potential TE-derived enhancers that may boost the expression of specific EHT marker genes. CONCLUSIONS Our study provides a systematic vision of how TEs are dynamically controlled to promote the hematopoietic fate decisions through transcriptional and cis-regulatory networks, and pre-train the immunity of nascent HSCs.
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Affiliation(s)
- Cong Feng
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Bioinformatics Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Ruxiu Tie
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 310058, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310058, China
- Department of Hematology, The Second Clinical Medical College of Shanxi Medical University, Shanxi Medical University, Taiyuan, 030000, China
- Department of Hematology-Oncology, Taizhou Hospital of Zhejiang Province, Linhai, 317000, China
| | - Saige Xin
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yuhao Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Sida Li
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yifan Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaotian Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yincong Zhou
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yongjing Liu
- Bioinformatics Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanshi Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hang Pan
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, 310058, China
| | - Zexu Wu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shilong Zhang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qingyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinyan Huang
- Bioinformatics Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Wenda Luo
- Department of Hematology-Oncology, Taizhou Hospital of Zhejiang Province, Linhai, 317000, China.
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 310058, China.
- Institute of Hematology, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310058, China.
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- Bioinformatics Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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Mehta K, Daghsni M, Raeisossadati R, Xu Z, Davis E, Naidich A, Wang B, Tao S, Pi S, Chen W, Kostka D, Liu S, Gross JM, Kuwajima T, Aldiri I. A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis. Cell Rep 2024; 43:114291. [PMID: 38823017 PMCID: PMC11238474 DOI: 10.1016/j.celrep.2024.114291] [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: 11/15/2023] [Revised: 04/08/2024] [Accepted: 05/13/2024] [Indexed: 06/03/2024] Open
Abstract
Atoh7 is transiently expressed in retinal progenitor cells (RPCs) and is required for retinal ganglion cell (RGC) differentiation. In humans, a deletion in a distal non-coding regulatory region upstream of ATOH7 is associated with optic nerve atrophy and blindness. Here, we functionally interrogate the significance of the Atoh7 regulatory landscape to retinogenesis in mice. Deletion of the Atoh7 enhancer structure leads to RGC deficiency, optic nerve hypoplasia, and retinal blood vascular abnormalities, phenocopying inactivation of Atoh7. Further, loss of the Atoh7 remote enhancer impacts ipsilaterally projecting RGCs and disrupts proper axonal projections to the visual thalamus. Deletion of the Atoh7 remote enhancer is also associated with the dysregulation of axonogenesis genes, including the derepression of the axon repulsive cue Robo3. Our data provide insights into how Atoh7 enhancer elements function to promote RGC development and optic nerve formation and highlight a key role of Atoh7 in the transcriptional control of axon guidance molecules.
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Affiliation(s)
- Kamakshi Mehta
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Marwa Daghsni
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Reza Raeisossadati
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Zhongli Xu
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Emily Davis
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Abigail Naidich
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Bingjie Wang
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Shiyue Tao
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Shaohua Pi
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Wei Chen
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Dennis Kostka
- Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jeffrey M Gross
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Takaaki Kuwajima
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Issam Aldiri
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
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37
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Flynn A, Pattison AD, Balachander S, Boehm E, Bowen B, Dwight T, Rosello F, Hofmann O, Martelotto L, Zethoven M, Kirschner LS, Else T, Fishbein L, Gill AJ, Tischler AS, Giordano T, Prodanov T, Noble JR, Reddel RR, Trainer AH, Ghayee HK, Bourdeau I, Elston M, Ishak D, Ngeow Yuen Yie J, Hicks RJ, Crona J, Åkerström T, Stålberg P, Dahia P, Grimmond S, Clifton-Bligh R, Pacak K, Tothill RW. Multi-omic analysis of SDHB-deficient pheochromocytomas and paragangliomas identifies metastasis and treatment-related molecular profiles. RESEARCH SQUARE 2024:rs.3.rs-4410500. [PMID: 38978571 PMCID: PMC11230496 DOI: 10.21203/rs.3.rs-4410500/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Hereditary SDHB-mutant pheochromocytomas (PC) and paragangliomas (PG) are rare tumours with a high propensity to metastasize although their clinical behaviour is unpredictable. To characterize the genomic landscape of these tumours and identify metastasis biomarkers, we performed multi-omic analysis on 94 tumours from 79 patients using seven molecular methods. Sympathetic (chromaffin cell) and parasympathetic (non-chromaffin cell) PCPG had distinct molecular profiles reflecting their cell-of-origin and biochemical profile. TERT and ATRX-alterations were associated with metastatic PCPG and these tumours had an increased mutation load, and distinct transcriptional and telomeric features. Most PCPG had quiet genomes with some rare co-operative driver events observed, including EPAS1/HIF-2α mutations. Two mechanisms of acquired resistance to DNA alkylating chemotherapies were also detected - MGMT overexpression and mismatch repair-deficiency causing hypermutation. Our comprehensive multi-omic analysis of SDHB-mutant PCPG therefore identified features of metastatic disease and treatment response, expanding our understanding of these rare neuroendocrine tumours.
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Affiliation(s)
- Aidan Flynn
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | - Andrew D. Pattison
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | - Shiva Balachander
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | - Emma Boehm
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | - Blake Bowen
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | - Trisha Dwight
- Kolling Institute of Medical Research, Royal North Shore Hospital St Leonards NSW, Australia
| | | | - Oliver Hofmann
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | - Luciano Martelotto
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | | | - Lawrence S. Kirschner
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | | | - Lauren Fishbein
- Department of Medicine, Division of Endocrinology, Metabolism, Diabetes, University of Colorado, Aurora, CO, USA
| | - Anthony J Gill
- Sydney Medical School, University of Sydney, Sydney NSW, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards NSW, Australia
| | | | | | - Tamara Prodanov
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Jane R Noble
- Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Roger R Reddel
- Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Alison H. Trainer
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC, Australia
| | - Hans Kumar Ghayee
- University of Florida and Malcom Randall VA Medical Center, Gainesville, FL, USA
| | | | - Marianne Elston
- Waikato Clinical Campus, University of Auckland, Hamilton, New Zealand
| | | | | | - Rodney J Hicks
- St Vincent’s Dept of Medicine, University of Melbourne, VIC, Australia
| | - Joakim Crona
- 18a Department of Medical Sciences, 18b Department of Surgical Sciences, Uppsala University, Sweden
| | - Tobias Åkerström
- 18a Department of Medical Sciences, 18b Department of Surgical Sciences, Uppsala University, Sweden
| | - Peter Stålberg
- 18a Department of Medical Sciences, 18b Department of Surgical Sciences, Uppsala University, Sweden
| | - Patricia Dahia
- Div. Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio (UTHSCSA), TX, USA
| | - Sean Grimmond
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | - Roderick Clifton-Bligh
- Kolling Institute of Medical Research, Royal North Shore Hospital St Leonards NSW, Australia
- Sydney Medical School, University of Sydney, Sydney NSW, Australia
| | - Karel Pacak
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Richard W Tothill
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
- Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
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38
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Baumgarth N, Prieto AC, Luo Z, Kulaga H. B cells modulate lung antiviral inflammatory responses via the neurotransmitter acetylcholine. RESEARCH SQUARE 2024:rs.3.rs-4421566. [PMID: 38978583 PMCID: PMC11230464 DOI: 10.21203/rs.3.rs-4421566/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The rapid onset of innate immune defenses is critical for early control of viral replication in an infected host, yet it can also lead to irreversible tissue damage, especially in the respiratory tract. Intricate regulatory mechanisms must exist that modulate inflammation, while controlling the infection. Here, B cells expressing choline acetyl transferase (ChAT), an enzyme required for production of the metabolite and neurotransmitter acetylcholine (ACh) are identified as such regulators of the immediate early response to influenza A virus. Lung tissue ChAT + B cells are shown to interact with a7 nicotinic Ach receptor-expressing lung interstitial macrophages in mice within 24h of infection to control their production of TNFa, shifting the balance towards reduced inflammation at the cost of enhanced viral replication. Thus, innate-stimulated B cells are key participants of an immediate-early regulatory cascade that controls lung tissue damage after viral infection.
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39
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Wu P, Yao M, Wang W. Differential impact of quiescent non-coding loci on chromatin entropy. Nucleic Acids Res 2024:gkae535. [PMID: 38908026 DOI: 10.1093/nar/gkae535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/17/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024] Open
Abstract
Non-coding regions of the human genome are important for functional regulations, but their mechanisms remain elusive. We used machine learning to guide a CRISPR screening on hubs (i.e. non-coding loci forming many 3D contacts) and significantly increased the discovery rate of hubs essential for cell growth. We found no clear genetic or epigenetic differences between essential and nonessential hubs, but we observed that some neighboring hubs in the linear genome have distinct spatial contacts and opposite effects on cell growth. One such pair in an epigenetically quiescent region showed different impacts on gene expression, chromatin accessibility and chromatin organization. We also found that deleting the essential hub altered the genetic network activity and increased the entropy of chromatin accessibility, more severe than that caused by deletion of the nonessential hub, suggesting that they are critical for maintaining an ordered chromatin structure. Our study reveals new insights into the system-level roles of non-coding regions in the human genome.
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Affiliation(s)
- Peiyao Wu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, USA
| | - Mina Yao
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, USA
- Bioinformatics and Systems Biology program, University of California, San Diego, La Jolla, CA 92093-0359, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0359, USA
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40
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Gray-Gaillard SL, Solis SM, Chen HM, Monteiro C, Ciabattoni G, Samanovic MI, Cornelius AR, Williams T, Geesey E, Rodriguez M, Ortigoza MB, Ivanova EN, Koralov SB, Mulligan MJ, Herati RS. SARS-CoV-2 inflammation durably imprints memory CD4 T cells. Sci Immunol 2024; 9:eadj8526. [PMID: 38905326 DOI: 10.1126/sciimmunol.adj8526] [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: 07/25/2023] [Accepted: 05/30/2024] [Indexed: 06/23/2024]
Abstract
Memory CD4 T cells are critical to human immunity, yet it is unclear whether viral inflammation during memory formation has long-term consequences. Here, we compared transcriptional and epigenetic landscapes of Spike (S)-specific memory CD4 T cells in 24 individuals whose first exposure to S was via SARS-CoV-2 infection or mRNA vaccination. Nearly 2 years after memory formation, S-specific CD4 T cells established by infection remained enriched for transcripts related to cytotoxicity and for interferon-stimulated genes, likely because of a chromatin accessibility landscape altered by inflammation. Moreover, S-specific CD4 T cells primed by infection had reduced proliferative capacity in vitro relative to vaccine-primed cells. Furthermore, the transcriptional state of S-specific memory CD4 T cells was minimally altered by booster immunization and/or breakthrough infection. Thus, infection-associated inflammation durably imprints CD4 T cell memory, which affects the function of these cells and may have consequences for long-term immunity.
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Affiliation(s)
- Sophie L Gray-Gaillard
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Sabrina M Solis
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Han M Chen
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Clarice Monteiro
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Grace Ciabattoni
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Marie I Samanovic
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Amber R Cornelius
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Tijaana Williams
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Emilie Geesey
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Miguel Rodriguez
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Mila Brum Ortigoza
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Ellie N Ivanova
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Sergei B Koralov
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Mark J Mulligan
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Ramin Sedaghat Herati
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
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41
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Choi JJ, Svaren J, Wang D. Single-cell multi-omics analysis reveals cooperative transcription factors for gene regulation in oligodendrocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599799. [PMID: 38948852 PMCID: PMC11213031 DOI: 10.1101/2024.06.19.599799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Oligodendrocytes are the myelinating cells within the central nervous system. Many oligodendrocyte genes have been associated with brain disorders. However, how transcription factors (TFs) cooperate for gene regulation in oligodendrocytes remains largely uncharacterized. To address this, we integrated scRNA-seq and scATAC-seq data to identify the cooperative TFs that co-regulate the target gene (TG) expression in oligodendrocytes. First, we identified co- binding TF pairs whose binding sites overlapped in oligodendrocyte-specific regulatory regions. Second, we trained a deep learning model to predict the expression level of each TG using the expression levels of co-binding TFs. Third, using the trained models, we computed the TF importance and TF-TF interaction scores for predicting TG expression by the Shapley interaction scores. We found that the co-binding TF pairs involving known important TF pairs for oligodendrocyte differentiation, such as SOX10-TCF12, SOX10-MYRF, and SOX10-OLIG2, exhibited significantly higher Shapley scores than others (t-test, p-value < 1e-4). Furthermore, we identified 153 oligodendrocyte-associated eQTLs that reside in oligodendrocyte-specific enhancers or promoters where their eGenes (TGs) are regulated by cooperative TFs, suggesting potential novel regulatory roles from genetic variants. We also experimentally validated some identified TF pairs such as SOX10-OLIG2 and SOX10-NKX2.2 by co-enrichment analysis, using ChIP-seq data from rat peripheral nerve.
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42
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Travisano SI, Lien CL. Protocol for the isolation and single-nuclei multiomic analyses of the human fetal epicardium. STAR Protoc 2024; 5:102973. [PMID: 38517898 PMCID: PMC10978535 DOI: 10.1016/j.xpro.2024.102973] [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: 11/09/2023] [Revised: 01/18/2024] [Accepted: 03/04/2024] [Indexed: 03/24/2024] Open
Abstract
The characterization of cell populations that reside in the outer layer of the heart has been hindered by difficulties in their isolation. Here, we present a protocol for isolation and single-nuclei multiomic analyses of the human fetal epicardium. We describe steps for microdissection, isolation, and enrichment of epicardial cells by mechanical dissociations and direct lysis. We then detail procedures for integrating transcriptome and chromatin accessibility datasets. This approach allows the analysis of diverse cell populations, marked by unique cis-regulatory elements. For complete details on the use and execution of this protocol, please refer to Travisano et al.1.
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Affiliation(s)
| | - Ching-Ling Lien
- The Saban Research Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Departments of Surgery, Biochemistry, and Molecular Medicine, Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Kowalski MH, Wessels HH, Linder J, Dalgarno C, Mascio I, Choudhary S, Hartman A, Hao Y, Kundaje A, Satija R. Multiplexed single-cell characterization of alternative polyadenylation regulators. Cell 2024:S0092-8674(24)00645-7. [PMID: 38925112 DOI: 10.1016/j.cell.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/12/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Most mammalian genes have multiple polyA sites, representing a substantial source of transcript diversity regulated by the cleavage and polyadenylation (CPA) machinery. To better understand how these proteins govern polyA site choice, we introduce CPA-Perturb-seq, a multiplexed perturbation screen dataset of 42 CPA regulators with a 3' scRNA-seq readout that enables transcriptome-wide inference of polyA site usage. We develop a framework to detect perturbation-dependent changes in polyadenylation and characterize modules of co-regulated polyA sites. We find groups of intronic polyA sites regulated by distinct components of the nuclear RNA life cycle, including elongation, splicing, termination, and surveillance. We train and validate a deep neural network (APARENT-Perturb) for tandem polyA site usage, delineating a cis-regulatory code that predicts perturbation response and reveals interactions between regulatory complexes. Our work highlights the potential for multiplexed single-cell perturbation screens to further our understanding of post-transcriptional regulation.
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Affiliation(s)
- Madeline H Kowalski
- New York Genome Center, New York, NY, USA; Center for Genomics and Systems Biology, New York University, New York, NY, USA; New York University Grossman School of Medicine, New York, NY, USA
| | - Hans-Hermann Wessels
- New York Genome Center, New York, NY, USA; Center for Genomics and Systems Biology, New York University, New York, NY, USA.
| | - Johannes Linder
- Department of Genetics, Stanford University, Stanford, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | - Isabella Mascio
- New York Genome Center, New York, NY, USA; Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Saket Choudhary
- New York Genome Center, New York, NY, USA; Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | | | - Yuhan Hao
- New York Genome Center, New York, NY, USA; Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Rahul Satija
- New York Genome Center, New York, NY, USA; Center for Genomics and Systems Biology, New York University, New York, NY, USA; New York University Grossman School of Medicine, New York, NY, USA.
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44
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Zheng X, Wu B, Liu Y, Simmons SK, Kim K, Clarke GS, Ashiq A, Park J, Li J, Wang Z, Tong L, Wang Q, Rajamani KT, Muñoz-Castañeda R, Mu S, Qi T, Zhang Y, Ngiam ZC, Ohte N, Hanashima C, Wu Z, Xu X, Levin JZ, Jin X. Massively parallel in vivo Perturb-seq reveals cell-type-specific transcriptional networks in cortical development. Cell 2024; 187:3236-3248.e21. [PMID: 38772369 PMCID: PMC11193654 DOI: 10.1016/j.cell.2024.04.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/30/2023] [Accepted: 04/30/2024] [Indexed: 05/23/2024]
Abstract
Leveraging AAVs' versatile tropism and labeling capacity, we expanded the scale of in vivo CRISPR screening with single-cell transcriptomic phenotyping across embryonic to adult brains and peripheral nervous systems. Through extensive tests of 86 vectors across AAV serotypes combined with a transposon system, we substantially amplified labeling efficacy and accelerated in vivo gene delivery from weeks to days. Our proof-of-principle in utero screen identified the pleiotropic effects of Foxg1, highlighting its tight regulation of distinct networks essential for cell fate specification of Layer 6 corticothalamic neurons. Notably, our platform can label >6% of cerebral cells, surpassing the current state-of-the-art efficacy at <0.1% by lentivirus, to achieve analysis of over 30,000 cells in one experiment and enable massively parallel in vivo Perturb-seq. Compatible with various phenotypic measurements (single-cell or spatial multi-omics), it presents a flexible approach to interrogate gene function across cell types in vivo, translating gene variants to their causal function.
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Affiliation(s)
- Xinhe Zheng
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Boli Wu
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Yuejia Liu
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Sean K Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kwanho Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Grace S Clarke
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Abdullah Ashiq
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Joshua Park
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Jiwen Li
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Zhilin Wang
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Liqi Tong
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92617, USA
| | - Qizhao Wang
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92617, USA
| | - Keerthi T Rajamani
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Rodrigo Muñoz-Castañeda
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Shang Mu
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Tianbo Qi
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Yunxiao Zhang
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Zi Chao Ngiam
- Center for Advanced Biomedical Sciences, Waseda University, Tokyo 162-8480, Japan
| | - Naoto Ohte
- Center for Advanced Biomedical Sciences, Waseda University, Tokyo 162-8480, Japan
| | - Carina Hanashima
- Center for Advanced Biomedical Sciences, Waseda University, Tokyo 162-8480, Japan
| | - Zhuhao Wu
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Xiangmin Xu
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92617, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xin Jin
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA.
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45
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Wang G, Wen B, Guo M, Li E, Zhang Y, Whitsett JA, Kalin TV, Kalinichenko VV. Identification of endothelial and mesenchymal FOXF1 enhancers involved in alveolar capillary dysplasia. Nat Commun 2024; 15:5233. [PMID: 38898031 PMCID: PMC11187179 DOI: 10.1038/s41467-024-49477-6] [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: 07/26/2023] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Mutations in the FOXF1 gene, a key transcriptional regulator of pulmonary vascular development, cause Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins, a lethal lung disease affecting newborns and infants. Identification of new FOXF1 upstream regulatory elements is critical to explain why frequent non-coding FOXF1 deletions are linked to the disease. Herein, we use multiome single-nuclei RNA and ATAC sequencing of mouse and human patient lungs to identify four conserved endothelial and mesenchymal FOXF1 enhancers. We demonstrate that endothelial FOXF1 enhancers are autoactivated, whereas mesenchymal FOXF1 enhancers are regulated by EBF1 and GLI1. The cell-specificity of FOXF1 enhancers is validated by disrupting these enhancers in mouse embryonic stem cells using CRISPR/Cpf1 genome editing followed by lineage-tracing of mutant embryonic stem cells in mouse embryos using blastocyst complementation. This study resolves an important clinical question why frequent non-coding FOXF1 deletions that interfere with endothelial and mesenchymal enhancers can lead to the disease.
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Affiliation(s)
- Guolun Wang
- Division of Neonatology and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Bingqiang Wen
- Phoenix Children's Research Institute, Department of Child Health, University of Arizona, College of Medicine - Phoenix, Phoenix, AZ, USA
| | - Minzhe Guo
- Division of Neonatology and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Enhong Li
- Phoenix Children's Research Institute, Department of Child Health, University of Arizona, College of Medicine - Phoenix, Phoenix, AZ, USA
| | - Yufang Zhang
- Division of Neonatology and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Jeffrey A Whitsett
- Division of Neonatology and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Tanya V Kalin
- Phoenix Children's Research Institute, Department of Child Health, University of Arizona, College of Medicine - Phoenix, Phoenix, AZ, USA
| | - Vladimir V Kalinichenko
- Phoenix Children's Research Institute, Department of Child Health, University of Arizona, College of Medicine - Phoenix, Phoenix, AZ, USA.
- Division of Neonatology, Phoenix Children's Hospital, Phoenix, AZ, USA.
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46
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Gioacchino E, Zhang W, Koyunlar C, Zink J, de Looper H, Gussinklo KJ, Hoogenboezem R, Bosch D, Bindels E, Touw IP, de Pater E. GATA2 heterozygosity causes an epigenetic feedback mechanism resulting in myeloid and erythroid dysplasia. Br J Haematol 2024. [PMID: 38887897 DOI: 10.1111/bjh.19585] [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: 04/03/2024] [Accepted: 05/27/2024] [Indexed: 06/20/2024]
Abstract
The transcription factor GATA2 has a pivotal role in haematopoiesis. Heterozygous germline GATA2 mutations result in a syndrome characterized by immunodeficiency, bone marrow failure and predispositions to myelodysplastic syndrome (MDS) and acute myeloid leukaemia. Clinical symptoms in these patients are diverse and mechanisms driving GATA2-related phenotypes are largely unknown. To explore the impact of GATA2 haploinsufficiency on haematopoiesis, we generated a zebrafish model carrying a heterozygous mutation of gata2b (gata2b+/-), an orthologue of GATA2. Morphological analysis revealed myeloid and erythroid dysplasia in gata2b+/- kidney marrow. Because Gata2b could affect both transcription and chromatin accessibility during lineage differentiation, this was assessed by single-cell (sc) RNA-seq and single-nucleus (sn) ATAC-seq. Sn-ATAC-seq showed that the co-accessibility between the transcription start site (TSS) and a -3.5-4.1 kb putative enhancer was more robust in gata2b+/- zebrafish HSPCs compared to wild type, increasing gata2b expression and resulting in higher genome-wide Gata2b motif use in HSPCs. As a result of increased accessibility of the gata2b locus, gata2b+/- chromatin was also more accessible during lineage differentiation. scRNA-seq data revealed myeloid differentiation defects, that is, impaired cell cycle progression, reduced expression of cebpa and cebpb and increased signatures of ribosome biogenesis. These data also revealed a differentiation delay in erythroid progenitors, aberrant proliferative signatures and down-regulation of Gata1a, a master regulator of erythropoiesis, which worsened with age. These findings suggest that cell-intrinsic compensatory mechanisms, needed to obtain normal levels of Gata2b in heterozygous HSPCs to maintain their integrity, result in aberrant lineage differentiation, thereby representing a critical step in the predisposition to MDS.
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Affiliation(s)
- Emanuele Gioacchino
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Wei Zhang
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Cansu Koyunlar
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Joke Zink
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Hans de Looper
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Cancer Genome Editing Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Kirsten J Gussinklo
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Remco Hoogenboezem
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Dennis Bosch
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Eric Bindels
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Ivo P Touw
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Emma de Pater
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Cancer Genome Editing Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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Liu J, Ma J, Wen J, Zhou X. A Cell Cycle-Aware Network for Data Integration and Label Transferring of Single-Cell RNA-Seq and ATAC-Seq. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401815. [PMID: 38887194 DOI: 10.1002/advs.202401815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/22/2024] [Indexed: 06/20/2024]
Abstract
In recent years, the integration of single-cell multi-omics data has provided a more comprehensive understanding of cell functions and internal regulatory mechanisms from a non-single omics perspective, but it still suffers many challenges, such as omics-variance, sparsity, cell heterogeneity, and confounding factors. As it is known, the cell cycle is regarded as a confounder when analyzing other factors in single-cell RNA-seq data, but it is not clear how it will work on the integrated single-cell multi-omics data. Here, a cell cycle-aware network (CCAN) is developed to remove cell cycle effects from the integrated single-cell multi-omics data while keeping the cell type-specific variations. This is the first computational model to study the cell-cycle effects in the integration of single-cell multi-omics data. Validations on several benchmark datasets show the outstanding performance of CCAN in a variety of downstream analyses and applications, including removing cell cycle effects and batch effects of scRNA-seq datasets from different protocols, integrating paired and unpaired scRNA-seq and scATAC-seq data, accurately transferring cell type labels from scRNA-seq to scATAC-seq data, and characterizing the differentiation process from hematopoietic stem cells to different lineages in the integration of differentiation data.
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Affiliation(s)
- Jiajia Liu
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jian Ma
- Department of Electronic Information and Computer Engineering, The Engineering & Technical College of Chengdu University of Technology, Leshan, Sichuan, 614000, China
| | - Jianguo Wen
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
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Regner MJ, Garcia-Recio S, Thennavan A, Wisniewska K, Mendez-Giraldez R, Felsheim B, Spanheimer PM, Parker JS, Perou CM, Franco HL. Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598858. [PMID: 38948758 PMCID: PMC11212881 DOI: 10.1101/2024.06.13.598858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Annotation of the cis-regulatory elements that drive transcriptional dysregulation in cancer cells is critical to improving our understanding of tumor biology. Herein, we present a compendium of matched chromatin accessibility (scATAC-seq) and transcriptome (scRNA-seq) profiles at single-cell resolution from human breast tumors and healthy mammary tissues processed immediately following surgical resection. We identify the most likely cell-of-origin for luminal breast tumors and basal breast tumors and then introduce a novel methodology that implements linear mixed-effects models to systematically quantify associations between regions of chromatin accessibility (i.e. regulatory elements) and gene expression in malignant cells versus normal mammary epithelial cells. These data unveil regulatory elements with that switch from silencers of gene expression in normal cells to enhancers of gene expression in cancer cells, leading to the upregulation of clinically relevant oncogenes. To translate the utility of this dataset into tractable models, we generated matched scATAC-seq and scRNA-seq profiles for breast cancer cell lines, revealing, for each subtype, a conserved oncogenic gene expression program between in vitro and in vivo cells. Together, this work highlights the importance of non-coding regulatory mechanisms that underlie oncogenic processes and the ability of single-cell multi-omics to define the regulatory logic of BC cells at single-cell resolution.
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Affiliation(s)
- Matthew J. Regner
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Susana Garcia-Recio
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Aatish Thennavan
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA, 77030
| | - Kamila Wisniewska
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Raul Mendez-Giraldez
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brooke Felsheim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Philip M. Spanheimer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joel S. Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Hector L. Franco
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Division of Clinical and Translational Cancer Research, University of Puerto Rico Comprehensive Cancer Center, San Juan, PR 00935
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Schiebout C, Frost HR. CAraCAl: CAMML with the integration of chromatin accessibility. BMC Bioinformatics 2024; 25:212. [PMID: 38872103 PMCID: PMC11170880 DOI: 10.1186/s12859-024-05833-3] [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: 03/07/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND A vital step in analyzing single-cell data is ascertaining which cell types are present in a dataset, and at what abundance. In many diseases, the proportions of varying cell types can have important implications for health and prognosis. Most approaches for cell type annotation have centered around cell typing for single-cell RNA-sequencing (scRNA-seq) and have had promising success. However, reliable methods are lacking for many other single-cell modalities such as single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq), which quantifies the extent to which genes of interest in each cell are epigenetically "open" for expression. RESULTS To leverage the informative potential of scATAC-seq data, we developed CAMML with the integration of chromatin accessibility (CAraCAl), a bioinformatic method that performs cell typing on scATAC-seq data. CAraCAl performs cell typing by scoring each cell for its enrichment of cell type-specific gene sets. These gene sets are composed of the most upregulated or downregulated genes present in each cell type according to projected gene activity. CONCLUSIONS We found that CAraCAl does not improve performance beyond CAMML when scRNA-seq is present, but if only scATAC-seq is available, CAraCAl performs cell typing relatively successfully. As such, we also discuss best practices for cell typing and the strengths and weaknesses of various cell annotation options.
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Affiliation(s)
- Courtney Schiebout
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, 03766, USA.
| | - H Robert Frost
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, 03766, USA
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50
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Venkatasubramanian D, Senevirathne G, Capellini TD, Craft AM. Leveraging single cell multiomic analyses to identify factors that drive human chondrocyte cell fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598666. [PMID: 38915712 PMCID: PMC11195167 DOI: 10.1101/2024.06.12.598666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Cartilage plays a crucial role in skeletal development and function, and abnormal development contributes to genetic and age-related skeletal disease. To better understand how human cartilage develops in vivo , we jointly profiled the transcriptome and open chromatin regions in individual nuclei recovered from distal femurs at 2 fetal timepoints. We used these multiomic data to identify transcription factors expressed in distinct chondrocyte subtypes, link accessible regulatory elements with gene expression, and predict transcription factor-based regulatory networks that are important for growth plate or epiphyseal chondrocyte differentiation. We developed a human pluripotent stem cell platform for interrogating the function of predicted transcription factors during chondrocyte differentiation and used it to test NFATC2 . We expect new regulatory networks we uncovered using multiomic data to be important for promoting cartilage health and treating disease, and our platform to be a useful tool for studying cartilage development in vitro . Statement of Significance The identity and integrity of the articular cartilage lining our joints are crucial to pain-free activities of daily living. Here we identified a gene regulatory landscape of human chondrogenesis at single cell resolution, which is expected to open new avenues of research aimed at mitigating cartilage diseases that affect hundreds of millions of individuals world-wide.
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