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López-Tobón A, Shyti R, Villa CE, Cheroni C, Fuentes-Bravo P, Trattaro S, Caporale N, Troglio F, Tenderini E, Mihailovich M, Skaros A, Gibson WT, Cuomo A, Bonaldi T, Mercurio C, Varasi M, Osborne L, Testa G. GTF2I dosage regulates neuronal differentiation and social behavior in 7q11.23 neurodevelopmental disorders. Sci Adv 2023; 9:eadh2726. [PMID: 38019906 PMCID: PMC10686562 DOI: 10.1126/sciadv.adh2726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Copy number variations at 7q11.23 cause neurodevelopmental disorders with shared and opposite manifestations. Deletion causes Williams-Beuren syndrome featuring hypersociability, while duplication causes 7q11.23 microduplication syndrome (7Dup), frequently exhibiting autism spectrum disorder (ASD). Converging evidence indicates GTF2I as key mediator of the cognitive-behavioral phenotypes, yet its role in cortical development and behavioral hallmarks remains largely unknown. We integrated proteomic and transcriptomic profiling of patient-derived cortical organoids, including longitudinally at single-cell resolution, to dissect 7q11.23 dosage-dependent and GTF2I-specific disease mechanisms. We observed dosage-dependent impaired dynamics of neural progenitor proliferation, transcriptional imbalances, and highly specific alterations in neuronal output, leading to precocious excitatory neuron production in 7Dup, which was rescued by restoring physiological GTF2I levels. Transgenic mice with Gtf2i duplication recapitulated progenitor proliferation and neuronal differentiation defects alongside ASD-like behaviors. Consistently, inhibition of lysine demethylase 1 (LSD1), a GTF2I effector, was sufficient to rescue ASD-like phenotypes in transgenic mice, establishing GTF2I-LSD1 axis as a molecular pathway amenable to therapeutic intervention in ASD.
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Affiliation(s)
- Alejandro López-Tobón
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Reinald Shyti
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Carlo Emanuele Villa
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Cristina Cheroni
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Patricio Fuentes-Bravo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Sebastiano Trattaro
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Nicolò Caporale
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Flavia Troglio
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Erika Tenderini
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Marija Mihailovich
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Adrianos Skaros
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - William T. Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Ciro Mercurio
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), 20139 Milan, Italy
| | - Mario Varasi
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), 20139 Milan, Italy
| | - Lucy Osborne
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Giuseppe Testa
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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Smith NP, Yan Y, Pan Y, Williams JB, Manakongtreecheep K, Pant S, Zhao J, Tian T, Pan T, Stingley C, Wu K, Zhang J, Kley AL, Sorger PK, Villani AC, Kupper TS. Resident memory T cell development is associated with AP-1 transcription factor upregulation across anatomical niches. bioRxiv 2023:2023.09.29.560006. [PMID: 37873428 PMCID: PMC10592877 DOI: 10.1101/2023.09.29.560006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Tissue-resident memory T (T RM ) cells play a central role in immune responses to pathogens across all barrier tissues after infection. However, the underlying mechanisms that drive T RM differentiation and priming for their recall effector function remains unclear. In this study, we leveraged both newly generated and publicly available single-cell RNA-sequencing (scRNAseq) data generated across 10 developmental time points to define features of CD8 T RM across both skin and small-intestine intraepithelial lymphocytes (siIEL). We employed linear modeling to capture temporally-associated gene programs that increase their expression levels in T cell subsets transitioning from an effector to a memory T cell state. In addition to capturing tissue-specific gene programs, we defined a consensus T RM signature of 60 genes across skin and siIEL that can effectively distinguish T RM from circulating T cell populations, providing a more specific T RM signature than what was previously generated by comparing bulk T RM to naïve or non-tissue resident memory populations. This updated T RM signature included the AP-1 transcription factor family members Fos, Fosb and Fosl2 . Moreover, ATACseq analysis detected an enrichment of AP-1-specific motifs at open chromatin sites in mature T RM . CyCIF tissue imaging detected nuclear co-localization of AP-1 members Fosb and Junb in resting CD8 T RM >100 days post-infection. Taken together, these results reveal a critical role of AP-1 transcription factor members in T RM biology and suggests a novel mechanism for rapid reactivation of resting T RM in tissue upon antigen encounter.
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Keyes TJ, Koladiya A, Lo YC, Nolan GP, Davis KL. tidytof: a user-friendly framework for scalable and reproducible high-dimensional cytometry data analysis. Bioinform Adv 2023; 3:vbad071. [PMID: 37351311 PMCID: PMC10281957 DOI: 10.1093/bioadv/vbad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/03/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023]
Abstract
Summary While many algorithms for analyzing high-dimensional cytometry data have now been developed, the software implementations of these algorithms remain highly customized-this means that exploring a dataset requires users to learn unique, often poorly interoperable package syntaxes for each step of data processing. To solve this problem, we developed {tidytof}, an open-source R package for analyzing high-dimensional cytometry data using the increasingly popular 'tidy data' interface. Availability and implementation {tidytof} is available at https://github.com/keyes-timothy/tidytof and is released under the MIT license. It is supported on Linux, MS Windows and MacOS. Additional documentation is available at the package website (https://keyes-timothy.github.io/tidytof/). Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Timothy J Keyes
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Abhishek Koladiya
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yu-Chen Lo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Keeler AB, Van Deusen AL, Gadani IC, Williams CM, Goggin SM, Hirt AK, Vradenburgh SA, Fread KI, Puleo EA, Jin L, Calhan OY, Deppmann CD, Zunder ER. A developmental atlas of somatosensory diversification and maturation in the dorsal root ganglia by single-cell mass cytometry. Nat Neurosci 2022; 25:1543-1558. [PMID: 36303068 PMCID: PMC10691656 DOI: 10.1038/s41593-022-01181-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 09/08/2022] [Indexed: 01/13/2023]
Abstract
Precisely controlled development of the somatosensory system is essential for detecting pain, itch, temperature, mechanical touch and body position. To investigate the protein-level changes that occur during somatosensory development, we performed single-cell mass cytometry on dorsal root ganglia from C57/BL6 mice of both sexes, with litter replicates collected daily from embryonic day 11.5 to postnatal day 4. Measuring nearly 3 million cells, we quantified 30 molecularly distinct somatosensory glial and 41 distinct neuronal states across all timepoints. Analysis of differentiation trajectories revealed rare cells that co-express two or more Trk receptors and over-express stem cell markers, suggesting that these neurotrophic factor receptors play a role in cell fate specification. Comparison to previous RNA-based studies identified substantial differences between many protein-mRNA pairs, demonstrating the importance of protein-level measurements to identify functional cell states. Overall, this study demonstrates that mass cytometry is a high-throughput, scalable platform to rapidly phenotype somatosensory tissues.
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Affiliation(s)
- Austin B Keeler
- Department of Biology, College of Arts and Sciences, Charlottesville, VA, USA
| | - Amy L Van Deusen
- Department of Biology, College of Arts and Sciences, Charlottesville, VA, USA
- Neuroscience Graduate Program, School of Medicine, University of Virginia, Charlottesville, VA, USA
- Department of Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, VA, USA
| | - Irene C Gadani
- Department of Biology, College of Arts and Sciences, Charlottesville, VA, USA
- Neuroscience Graduate Program, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Corey M Williams
- Department of Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, VA, USA
| | - Sarah M Goggin
- Neuroscience Graduate Program, School of Medicine, University of Virginia, Charlottesville, VA, USA
- Department of Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, VA, USA
| | - Ashley K Hirt
- Department of Biology, College of Arts and Sciences, Charlottesville, VA, USA
| | - Shayla A Vradenburgh
- Department of Biology, College of Arts and Sciences, Charlottesville, VA, USA
- Neuroscience Graduate Program, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Kristen I Fread
- Department of Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, VA, USA
| | - Emily A Puleo
- Department of Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, VA, USA
| | - Lucy Jin
- Department of Biology, College of Arts and Sciences, Charlottesville, VA, USA
| | - O Yipkin Calhan
- Department of Biology, College of Arts and Sciences, Charlottesville, VA, USA
| | - Christopher D Deppmann
- Department of Biology, College of Arts and Sciences, Charlottesville, VA, USA.
- Department of Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, VA, USA.
- Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA, USA.
- Department of Cell Biology, School of Medicine, University of Virginia, Charlottesville, VA, USA.
- Program in Fundamental Neuroscience, College of Arts and Sciences, Charlottesville, VA, USA.
| | - Eli R Zunder
- Neuroscience Graduate Program, School of Medicine, University of Virginia, Charlottesville, VA, USA.
- Department of Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, VA, USA.
- Program in Fundamental Neuroscience, College of Arts and Sciences, Charlottesville, VA, USA.
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5
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Uzquiano A, Kedaigle AJ, Pigoni M, Paulsen B, Adiconis X, Kim K, Faits T, Nagaraja S, Antón-Bolaños N, Gerhardinger C, Tucewicz A, Murray E, Jin X, Buenrostro J, Chen F, Velasco S, Regev A, Levin JZ, Arlotta P. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell 2022; 185:3770-3788.e27. [PMID: 36179669 PMCID: PMC9990683 DOI: 10.1016/j.cell.2022.09.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 03/25/2022] [Accepted: 09/01/2022] [Indexed: 01/26/2023]
Abstract
Realizing the full utility of brain organoids to study human development requires understanding whether organoids precisely replicate endogenous cellular and molecular events, particularly since acquisition of cell identity in organoids can be impaired by abnormal metabolic states. We present a comprehensive single-cell transcriptomic, epigenetic, and spatial atlas of human cortical organoid development, comprising over 610,000 cells, from generation of neural progenitors through production of differentiated neuronal and glial subtypes. We show that processes of cellular diversification correlate closely to endogenous ones, irrespective of metabolic state, empowering the use of this atlas to study human fate specification. We define longitudinal molecular trajectories of cortical cell types during organoid development, identify genes with predicted human-specific roles in lineage establishment, and uncover early transcriptional diversity of human callosal neurons. The findings validate this comprehensive atlas of human corticogenesis in vitro as a resource to prime investigation into the mechanisms of human cortical development.
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Affiliation(s)
- Ana Uzquiano
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amanda J Kedaigle
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Martina Pigoni
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bruna Paulsen
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xian Adiconis
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kwanho Kim
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tyler Faits
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Surya Nagaraja
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Noelia Antón-Bolaños
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chiara Gerhardinger
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ashley Tucewicz
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Evan Murray
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xin Jin
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Society of Fellows, Harvard University, Cambridge, MA 02138, USA
| | - Jason Buenrostro
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fei Chen
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Silvia Velasco
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paola Arlotta
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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6
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Hsieh WC, Lai EY, Liu YT, Wang YF, Tzeng YS, Cui L, Lai YJ, Huang HC, Huang JH, Ni HC, Tsai DY, Liang JJ, Liao CC, Lu YT, Jiang L, Liu MT, Wang JT, Chang SY, Chen CY, Tsai HC, Chang YM, Wernig G, Li CW, Lin KI, Lin YL, Tsai HK, Huang YT, Chen SY. NK cell receptor and ligand composition influences the clearance of SARS-CoV-2. J Clin Invest 2021; 131:e146408. [PMID: 34720095 PMCID: PMC8553551 DOI: 10.1172/jci146408] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 09/16/2021] [Indexed: 12/30/2022] Open
Abstract
To explore how the immune system controls clearance of SARS-CoV-2, we used a single-cell, mass cytometry-based proteomics platform to profile the immune systems of 21 patients who had recovered from SARS-CoV-2 infection without need for admission to an intensive care unit or for mechanical ventilation. We focused on receptors involved in interactions between immune cells and virus-infected cells. We found that the diversity of receptor repertoires on natural killer (NK) cells was negatively correlated with the viral clearance rate. In addition, NK subsets expressing the receptor DNAM1 were increased in patients who more rapidly recovered from infection. Ex vivo functional studies revealed that NK subpopulations with high DNAM1 expression had cytolytic activities in response to target cell stimulation. We also found that SARS-CoV-2 infection induced the expression of CD155 and nectin-4, ligands of DNAM1 and its paired coinhibitory receptor TIGIT, which counterbalanced the cytolytic activities of NK cells. Collectively, our results link the cytolytic immune responses of NK cells to the clearance of SARS-CoV-2 and show that the DNAM1 pathway modulates host-pathogen interactions during SARS-CoV-2 infection.
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Affiliation(s)
- Wan-Chen Hsieh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
| | - En-Yu Lai
- Institute of Statistical Science, and
| | - Yu-Ting Liu
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Yi-Fu Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Shiuan Tzeng
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Lu Cui
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, California, USA
| | - Yun-Ju Lai
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Solomont School of Nursing, Zuckerberg College of Health Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Hsiang-Chi Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jia-Hsin Huang
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
- National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Hung-Chih Ni
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Dong-Yan Tsai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Jian-Jong Liang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chun-Che Liao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ya-Ting Lu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Laurence Jiang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | | | - Jann-Tay Wang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chung-Yu Chen
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsing-Chen Tsai
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yao-Ming Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Gerlinde Wernig
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, California, USA
| | - Chia-Wei Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Kuo-I Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Huai-Kuang Tsai
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Yen-Tsung Huang
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
- Institute of Statistical Science, and
- Department of Mathematics, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Shih-Yu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
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7
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Lee SW, Choi HY, Lee GW, Kim T, Cho HJ, Oh IJ, Song SY, Yang DH, Cho JH. CD8 + TILs in NSCLC differentiate into TEMRA via a bifurcated trajectory: deciphering immunogenicity of tumor antigens. J Immunother Cancer 2021; 9:jitc-2021-002709. [PMID: 34593620 PMCID: PMC8487216 DOI: 10.1136/jitc-2021-002709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2021] [Indexed: 01/21/2023] Open
Abstract
Background CD8+ tumor-infiltrating lymphocytes (TILs) comprise phenotypically and functionally heterogeneous subpopulations. Of these, effector memory CD45RA re-expressing CD8+ T cells (Temra) have been discovered and characterized as the most terminally differentiated subset. However, their exact ontogeny and physiological importance in association with tumor progression remain poorly understood. Methods We analyzed primary tumors and peripheral blood samples from 26 patients with non-small cell lung cancer and analyzed their phenotypes and functional characteristics using flow cytometry, RNA-sequencing, and bioinformatics. Results We found that tumor-infiltrating Temra (tilTemra) cells largely differ from peripheral blood Temra (pTemra), with distinct transcriptomes and functional properties. Notably, although majority of the pTemra was CD27−CD28− double-negative (DN), a large fraction of tilTemra population was CD27+CD28+ double-positive (DP), a characteristic of early-stage, less differentiated effector cells. Trajectory analysis revealed that CD8+ TILs undergo a divergent sequence of events for differentiation into either DP or DN tilTemra. Such a differentiation toward DP tilTemra relied on persistent expression of CD27 and CD28 and was associated with weak T cell receptor engagement. Thus, a higher proportion of DP Temra was correlated with lower immunogenicity of tumor antigens and consequently lower accumulation of CD8+ TILs. Conclusions These data suggest a complex interplay between CD8+ T cells and tumors and define DP Temra as a unique subset of tumor-specific CD8+ TILs that are produced in patients with relatively low immunogenic cancer types, predicting immunogenicity of tumor antigens and CD8+ TIL counts, a reliable biomarker for successful cancer immunotherapy.
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Affiliation(s)
- Sung-Woo Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongsangbukdo, Republic of Korea
| | - He Yun Choi
- Department of Internal Medicine, Chonnam National University Medical School, Hwasun Hospital, Hwasunup, Jeollanamdo, Republic of Korea
| | - Gil-Woo Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongsangbukdo, Republic of Korea
| | - Therasa Kim
- Department of Internal Medicine, Chonnam National University Medical School, Hwasun Hospital, Hwasunup, Jeollanamdo, Republic of Korea
| | - Hyun-Ju Cho
- Department of Internal Medicine, Chonnam National University Medical School, Hwasun Hospital, Hwasunup, Jeollanamdo, Republic of Korea
| | - In-Jae Oh
- Department of Internal Medicine, Chonnam National University Medical School, Hwasun Hospital, Hwasunup, Jeollanamdo, Republic of Korea
| | - Sang Yun Song
- Department of Thoracic and Cardiovascular Surgery, Chonnam National University Medical School, Hwasun Hospital, Hwasunup, Jeollanamdo, Republic of Korea
| | - Deok Hwan Yang
- Department of Internal Medicine, Chonnam National University Medical School, Hwasun Hospital, Hwasunup, Jeollanamdo, Republic of Korea
| | - Jae-Ho Cho
- Department of Microbiology and Immunology, Chonnam National University Medical School, Hwasunup, Jeollanamdo, Republic of Korea .,Medical Research Center for Combinatorial Tumor Immunotherapy, Chonnam National University Medical School, Hwasunup, Jeollanamdo, Republic of Korea.,Immunotherapy Innovation Center, Chonnam National University Medical School, Hwasunup, Jeollanamdo, Republic of Korea.,BioMedical Sciences Graduate Program, Chonnam National University Medical School, Hwasunup, Jeollanamdo, Republic of Korea
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Stassen SV, Yip GGK, Wong KKY, Ho JWK, Tsia KK. Generalized and scalable trajectory inference in single-cell omics data with VIA. Nat Commun 2021; 12:5528. [PMID: 34545085 PMCID: PMC8452770 DOI: 10.1038/s41467-021-25773-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/31/2021] [Indexed: 11/08/2022] Open
Abstract
Inferring cellular trajectories using a variety of omic data is a critical task in single-cell data science. However, accurate prediction of cell fates, and thereby biologically meaningful discovery, is challenged by the sheer size of single-cell data, the diversity of omic data types, and the complexity of their topologies. We present VIA, a scalable trajectory inference algorithm that overcomes these limitations by using lazy-teleporting random walks to accurately reconstruct complex cellular trajectories beyond tree-like pathways (e.g., cyclic or disconnected structures). We show that VIA robustly and efficiently unravels the fine-grained sub-trajectories in a 1.3-million-cell transcriptomic mouse atlas without losing the global connectivity at such a high cell count. We further apply VIA to discovering elusive lineages and less populous cell fates missed by other methods across a variety of data types, including single-cell proteomic, epigenomic, multi-omics datasets, and a new in-house single-cell morphological dataset.
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Affiliation(s)
- Shobana V Stassen
- Department of Electrical & Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Gwinky G K Yip
- Department of Electrical & Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kenneth K Y Wong
- Department of Electrical & Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Joshua W K Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
- Laboratory of Data Discovery for Health, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Kevin K Tsia
- Department of Electrical & Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong.
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Pezoulas VC, Hazapis O, Lagopati N, Exarchos TP, Goules AV, Tzioufas AG, Fotiadis DI, Stratis IG, Yannacopoulos AN, Gorgoulis VG. Machine Learning Approaches on High Throughput NGS Data to Unveil Mechanisms of Function in Biology and Disease. Cancer Genomics Proteomics 2021; 18:605-626. [PMID: 34479914 PMCID: PMC8441762 DOI: 10.21873/cgp.20284] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/21/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
In this review, the fundamental basis of machine learning (ML) and data mining (DM) are summarized together with the techniques for distilling knowledge from state-of-the-art omics experiments. This includes an introduction to the basic mathematical principles of unsupervised/supervised learning methods, dimensionality reduction techniques, deep neural networks architectures and the applications of these in bioinformatics. Several case studies under evaluation mainly involve next generation sequencing (NGS) experiments, like deciphering gene expression from total and single cell (scRNA-seq) analysis; for the latter, a description of all recent artificial intelligence (AI) methods for the investigation of cell sub-types, biomarkers and imputation techniques are described. Other areas of interest where various ML schemes have been investigated are for providing information regarding transcription factors (TF) binding sites, chromatin organization patterns and RNA binding proteins (RBPs), while analyses on RNA sequence and structure as well as 3D dimensional protein structure predictions with the use of ML are described. Furthermore, we summarize the recent methods of using ML in clinical oncology, when taking into consideration the current omics data with pharmacogenomics to determine personalized treatments. With this review we wish to provide the scientific community with a thorough investigation of main novel ML applications which take into consideration the latest achievements in genomics, thus, unraveling the fundamental mechanisms of biology towards the understanding and cure of diseases.
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Affiliation(s)
- Vasileios C Pezoulas
- Unit of Medical Technology and Intelligent Information Systems, University of Ioannina, Ioannina, Greece
| | - Orsalia Hazapis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Nefeli Lagopati
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Themis P Exarchos
- Unit of Medical Technology and Intelligent Information Systems, Department of Materials Science and Engineering, University of Ioannina, Ioannina, Greece
- Department of Informatics, Ionian University, Corfu, Greece
| | - Andreas V Goules
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios G Tzioufas
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios I Fotiadis
- Unit of Medical Technology and Intelligent Information Systems, University of Ioannina, Ioannina, Greece
| | - Ioannis G Stratis
- Department of Mathematics, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios N Yannacopoulos
- Department of Statistics, and Stochastic Modelling and Applications Laboratory, Athens University of Economics and Business (AUEB), Athens, Greece;
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece;
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester, U.K
- Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Faculty of Health and Medical Sciences, University of Surrey, Surrey, U.K
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Ton MLN, Guibentif C, Göttgens B. Single cell genomics and developmental biology: moving beyond the generation of cell type catalogues. Curr Opin Genet Dev 2020; 64:66-71. [PMID: 32629366 DOI: 10.1016/j.gde.2020.05.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/25/2020] [Indexed: 11/17/2022]
Abstract
Major developmental processes such as gastrulation and early embryogenesis rely on a complex network of cell-cell interactions, chromatin remodeling, and transcriptional regulators. This makes it challenging to study early development when using bulk populations of cells. Recent advances in single-cell technologies have allowed researchers to better understand the interactions between different molecular modalities and the heterogeneities within classically defined cell types. As new single-cell technologies mature, they have the potential of providing a step-change in our understanding of embryogenesis. In this review, we summarize recent advances in single-cell technologies with particular focus on those that lend insight into early organogenesis. We then discuss current pitfalls and implications for future research.
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Affiliation(s)
- Mai-Linh N Ton
- Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Carolina Guibentif
- Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Sahlgrenska Cancer Center, Department of Microbiology and Immunology, University of Gothenburg, Gothenburg, Sweden
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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