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Bilous M, Hérault L, Gabriel AA, Teleman M, Gfeller D. Building and analyzing metacells in single-cell genomics data. Mol Syst Biol 2024; 20:744-766. [PMID: 38811801 PMCID: PMC11220014 DOI: 10.1038/s44320-024-00045-6] [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: 02/04/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024] Open
Abstract
The advent of high-throughput single-cell genomics technologies has fundamentally transformed biological sciences. Currently, millions of cells from complex biological tissues can be phenotypically profiled across multiple modalities. The scaling of computational methods to analyze and visualize such data is a constant challenge, and tools need to be regularly updated, if not redesigned, to cope with ever-growing numbers of cells. Over the last few years, metacells have been introduced to reduce the size and complexity of single-cell genomics data while preserving biologically relevant information and improving interpretability. Here, we review recent studies that capitalize on the concept of metacells-and the many variants in nomenclature that have been used. We further outline how and when metacells should (or should not) be used to analyze single-cell genomics data and what should be considered when analyzing such data at the metacell level. To facilitate the exploration of metacells, we provide a comprehensive tutorial on the construction and analysis of metacells from single-cell RNA-seq data ( https://github.com/GfellerLab/MetacellAnalysisTutorial ) as well as a fully integrated pipeline to rapidly build, visualize and evaluate metacells with different methods ( https://github.com/GfellerLab/MetacellAnalysisToolkit ).
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Affiliation(s)
- Mariia Bilous
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Léonard Hérault
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Aurélie Ag Gabriel
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Matei Teleman
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 1011, Lausanne, Switzerland.
- Agora Cancer Research Centre, 1011, Lausanne, Switzerland.
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland.
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2
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Wang W, Liu D, Yao J, Yuan Z, Yan L, Cao B. ANXA5: A Key Regulator of Immune Cell Infiltration in Hepatocellular Carcinoma. Med Sci Monit 2024; 30:e943523. [PMID: 38824386 PMCID: PMC11155417 DOI: 10.12659/msm.943523] [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: 12/16/2023] [Accepted: 04/10/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) poses a significant threat to human life and is the most prevalent form of liver cancer. The intricate interplay between apoptosis, a common form of programmed cell death, and its role in immune regulation stands as a crucial mechanism influencing tumor metastasis. MATERIAL AND METHODS Utilizing HCC samples from the TCGA database and 61 anoikis-related genes (ARGs) sourced from GeneCards, we analyzed the relationship between ARGs and immune cell infiltration in HCC. Subsequently, we identified long non-coding RNAs (lncRNAs) associated with ARGs, using the least absolute shrinkage and selection operator (LASSO) regression analysis to construct a robust prognostic model. The predictive capabilities of the model were then validated through examination in a single-cell dataset. RESULTS Our constructed prognostic model, derived from lncRNAs linked to ARGs, comprised 11 significant lncRNAs: NRAV, MCM3AP-AS1, OTUD6B-AS1, AC026356.1, AC009133.1, DDX11-AS1, AC108463.2, MIR4435-2HG, WARS2-AS1, LINC01094, and HCG18. The risk score assigned to HCC samples demonstrated associations with immune indicators and the infiltration of immune cells. Further, we identified Annexin A5 (ANXA5) as the pivotal gene among ARGs, with it exerting a prominent role in regulating the lncRNA gene signature. Our validation in a single-cell database elucidated the involvement of ANXA5 in immune cell infiltration, specifically in the regulation of mononuclear cells. CONCLUSIONS This study delves into the intricate correlation between ARGs and immune cell infiltration in HCC, culminating in the development of a novel prognostic model reliant on 11 ARGs-associated lncRNAs. Furthermore, our findings highlight ANXA5 as a promising target for immune regulation in HCC, offering new perspectives for immune therapy in the context of HCC.
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Pichol-Thievend C, Anezo O, Pettiwala AM, Bourmeau G, Montagne R, Lyne AM, Guichet PO, Deshors P, Ballestín A, Blanchard B, Reveilles J, Ravi VM, Joseph K, Heiland DH, Julien B, Leboucher S, Besse L, Legoix P, Dingli F, Liva S, Loew D, Giani E, Ribecco V, Furumaya C, Marcos-Kovandzic L, Masliantsev K, Daubon T, Wang L, Diaz AA, Schnell O, Beck J, Servant N, Karayan-Tapon L, Cavalli FMG, Seano G. VC-resist glioblastoma cell state: vessel co-option as a key driver of chemoradiation resistance. Nat Commun 2024; 15:3602. [PMID: 38684700 PMCID: PMC11058782 DOI: 10.1038/s41467-024-47985-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: 11/10/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Glioblastoma (GBM) is a highly lethal type of cancer. GBM recurrence following chemoradiation is typically attributed to the regrowth of invasive and resistant cells. Therefore, there is a pressing need to gain a deeper understanding of the mechanisms underlying GBM resistance to chemoradiation and its ability to infiltrate. Using a combination of transcriptomic, proteomic, and phosphoproteomic analyses, longitudinal imaging, organotypic cultures, functional assays, animal studies, and clinical data analyses, we demonstrate that chemoradiation and brain vasculature induce cell transition to a functional state named VC-Resist (vessel co-opting and resistant cell state). This cell state is midway along the transcriptomic axis between proneural and mesenchymal GBM cells and is closer to the AC/MES1-like state. VC-Resist GBM cells are highly vessel co-opting, allowing significant infiltration into the surrounding brain tissue and homing to the perivascular niche, which in turn induces even more VC-Resist transition. The molecular and functional characteristics of this FGFR1-YAP1-dependent GBM cell state, including resistance to DNA damage, enrichment in the G2M phase, and induction of senescence/stemness pathways, contribute to its enhanced resistance to chemoradiation. These findings demonstrate how vessel co-option, perivascular niche, and GBM cell plasticity jointly drive resistance to therapy during GBM recurrence.
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Affiliation(s)
- Cathy Pichol-Thievend
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Oceane Anezo
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Aafrin M Pettiwala
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
- Institut Curie, PSL University, 75005, Paris, France
| | - Guillaume Bourmeau
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Remi Montagne
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Anne-Marie Lyne
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Pierre-Olivier Guichet
- Université de Poitiers, CHU Poitiers, ProDiCeT, F-86000, Poitiers, France
- CHU Poitiers, Laboratoire de Cancérologie Biologique, F-86000, Poitiers, France
| | - Pauline Deshors
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Alberto Ballestín
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Benjamin Blanchard
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Juliette Reveilles
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Vidhya M Ravi
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Kevin Joseph
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Dieter H Heiland
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Boris Julien
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | | | - Laetitia Besse
- Institut Curie, PSL University, Université Paris-Saclay, CNRS UMS2016, INSERM US43, Multimodal Imaging Center, 91400, Orsay, France
| | - Patricia Legoix
- Institut Curie, PSL University, ICGex Next-Generation Sequencing Platform, 75005, Paris, France
| | - Florent Dingli
- Institut Curie, PSL University, CurieCoreTech Spectrométrie de Masse Protéomique, 75005, Paris, France
| | - Stephane Liva
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Damarys Loew
- Institut Curie, PSL University, CurieCoreTech Spectrométrie de Masse Protéomique, 75005, Paris, France
| | - Elisa Giani
- Department of Biomedical Sciences, Humanitas University, 20072, Pieve Emanuele, Italy
| | - Valentino Ribecco
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Charita Furumaya
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Laura Marcos-Kovandzic
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Konstantin Masliantsev
- Université de Poitiers, CHU Poitiers, ProDiCeT, F-86000, Poitiers, France
- CHU Poitiers, Laboratoire de Cancérologie Biologique, F-86000, Poitiers, France
| | - Thomas Daubon
- Université Bordeaux, CNRS, IBGC, UMR5095, Bordeaux, France
| | - Lin Wang
- Department of Computational and Quantitative Medicine, Hematologic Malignancies Research Institute and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Aaron A Diaz
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Oliver Schnell
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Jürgen Beck
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Nicolas Servant
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Lucie Karayan-Tapon
- Université de Poitiers, CHU Poitiers, ProDiCeT, F-86000, Poitiers, France
- CHU Poitiers, Laboratoire de Cancérologie Biologique, F-86000, Poitiers, France
| | - Florence M G Cavalli
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Giorgio Seano
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France.
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4
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Kim H, Chang W, Chae SJ, Park JE, Seo M, Kim JK. scLENS: data-driven signal detection for unbiased scRNA-seq data analysis. Nat Commun 2024; 15:3575. [PMID: 38678050 DOI: 10.1038/s41467-024-47884-3] [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: 10/18/2023] [Accepted: 04/14/2024] [Indexed: 04/29/2024] Open
Abstract
High dimensionality and noise have limited the new biological insights that can be discovered in scRNA-seq data. While dimensionality reduction tools have been developed to extract biological signals from the data, they often require manual determination of signal dimension, introducing user bias. Furthermore, a common data preprocessing method, log normalization, can unintentionally distort signals in the data. Here, we develop scLENS, a dimensionality reduction tool that circumvents the long-standing issues of signal distortion and manual input. Specifically, we identify the primary cause of signal distortion during log normalization and effectively address it by uniformizing cell vector lengths with L2 normalization. Furthermore, we utilize random matrix theory-based noise filtering and a signal robustness test to enable data-driven determination of the threshold for signal dimensions. Our method outperforms 11 widely used dimensionality reduction tools and performs particularly well for challenging scRNA-seq datasets with high sparsity and variability. To facilitate the use of scLENS, we provide a user-friendly package that automates accurate signal detection of scRNA-seq data without manual time-consuming tuning.
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Affiliation(s)
- Hyun Kim
- Biomedical Mathematics Group, Pioneer Research Center for Mathematical and Computational Sciences, Institute for Basic Science, Daejeon, 34126, Republic of Korea
| | - Won Chang
- Division of Statistics and Data Science, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Seok Joo Chae
- Biomedical Mathematics Group, Pioneer Research Center for Mathematical and Computational Sciences, Institute for Basic Science, Daejeon, 34126, Republic of Korea
- Department of Mathematical Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Jong-Eun Park
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Minseok Seo
- Department of Computer and Information Science, Korea University, Sejong, 30019, Republic of Korea
| | - Jae Kyoung Kim
- Biomedical Mathematics Group, Pioneer Research Center for Mathematical and Computational Sciences, Institute for Basic Science, Daejeon, 34126, Republic of Korea.
- Department of Mathematical Sciences, KAIST, Daejeon, 34141, Republic of Korea.
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5
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Chang PC, Yuan X, Zampieri A, Towns C, Yoo SP, Engstrom C, Tsai S, Robles CR, Zhu Y, Lopez S, Montel-Hagen A, Seet CS, Crooks GM. Generation of antigen-specific mature T cells from RAG1 -/-RAG2 -/-B2M -/- stem cells by engineering their microenvironment. Nat Biomed Eng 2024; 8:461-478. [PMID: 38062131 PMCID: PMC11087257 DOI: 10.1038/s41551-023-01146-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/25/2023] [Indexed: 02/03/2024]
Abstract
Pluripotent stem cells (PSCs) are a promising source of allogeneic T cells for off-the-shelf immunotherapies. However, the process of differentiating genetically engineered PSCs to generate mature T cells requires that the same molecular elements that are crucial for the selection of these cells be removed to prevent alloreactivity. Here we show that antigen-restricted mature T cells can be generated in vitro from PSCs edited via CRISPR to lack endogenous T cell receptors (TCRs) and class I major histocompatibility complexes. Specifically, we used T cell precursors from RAG1-/-RAG2-/-B2M-/- human PSCs expressing a single TCR, and a murine stromal cell line providing the cognate human major histocompatibility complex molecule and other critical signals for T cell maturation. Possibly owing to the absence of TCR mispairing, the generated T cells showed substantially better tumour control in mice than T cells with an intact endogenous TCR. Introducing the T cell selection components into the stromal microenvironment of the PSCs overcomes inherent biological challenges associated with the development of T cell immunotherapies from allogeneic PSCs.
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Affiliation(s)
- Patrick C Chang
- Molecular Biology Interdepartmental Program, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Xuegang Yuan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Alexandre Zampieri
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Chloe Towns
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Sang Pil Yoo
- Molecular Biology Interdepartmental Program, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Claire Engstrom
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Steven Tsai
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Yuhua Zhu
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Shawn Lopez
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Amelie Montel-Hagen
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Christopher S Seet
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA
| | - Gay M Crooks
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA.
- Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA.
- Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
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6
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Lobón-Iglesias MJ, Andrianteranagna M, Han ZY, Chauvin C, Masliah-Planchon J, Manriquez V, Tauziede-Espariat A, Turczynski S, Bouarich-Bourimi R, Frah M, Dufour C, Blauwblomme T, Cardoen L, Pierron G, Maillot L, Guillemot D, Reynaud S, Bourneix C, Pouponnot C, Surdez D, Bohec M, Baulande S, Delattre O, Piaggio E, Ayrault O, Waterfall JJ, Servant N, Beccaria K, Dangouloff-Ros V, Bourdeaut F. Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups. Nat Commun 2023; 14:6669. [PMID: 37863903 PMCID: PMC10589300 DOI: 10.1038/s41467-023-42371-7] [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: 06/10/2022] [Accepted: 10/09/2023] [Indexed: 10/22/2023] Open
Abstract
Atypical teratoid rhabdoid tumors (ATRT) are divided into MYC, TYR and SHH subgroups, suggesting diverse lineages of origin. Here, we investigate the imaging of human ATRT at diagnosis and the precise anatomic origin of brain tumors in the Rosa26-CreERT2::Smarcb1flox/flox model. This cross-species analysis points to an extra-cerebral origin for MYC tumors. Additionally, we clearly distinguish SHH ATRT emerging from the cerebellar anterior lobe (CAL) from those emerging from the basal ganglia (BG) and intra-ventricular (IV) regions. Molecular characteristics point to the midbrain-hindbrain boundary as the origin of CAL SHH ATRT, and to the ganglionic eminence as the origin of BG/IV SHH ATRT. Single-cell RNA sequencing on SHH ATRT supports these hypotheses. Trajectory analyses suggest that SMARCB1 loss induces a de-differentiation process mediated by repressors of the neuronal program such as REST, ID and the NOTCH pathway.
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Affiliation(s)
- María-Jesús Lobón-Iglesias
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Mamy Andrianteranagna
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
- INSERM U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, Mines Paris Tech, PSL Research University, Institut Curie Research Center, Paris, France
| | - Zhi-Yan Han
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Céline Chauvin
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Julien Masliah-Planchon
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Valeria Manriquez
- INSERM U932, Immunity and Cancer, PSL Research University, Institut Curie Research Center, Paris, France
| | - Arnault Tauziede-Espariat
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
- Paris Psychiatry and Neurosciences Institute (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Sandrina Turczynski
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Rachida Bouarich-Bourimi
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Magali Frah
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Christelle Dufour
- Department of Children and Adolescents Oncology, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Thomas Blauwblomme
- Department of Pediatric Neurosurgery-AP-HP, Necker Sick Kids Hospital, Université de Paris, Paris, France
| | | | - Gaelle Pierron
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Laetitia Maillot
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Delphine Guillemot
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Stéphanie Reynaud
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Christine Bourneix
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Célio Pouponnot
- CNRS UMR 3347, INSERM U1021, Institut Curie, PSL Research University, Université Paris-Saclay, Orsay, France
| | - Didier Surdez
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Mylene Bohec
- Institut Curie, PSL University, Single Cell Initiative, ICGex Next-Generation Sequencing Platform, PSL University, 75005, Paris, France
| | - Sylvain Baulande
- Institut Curie, PSL University, Single Cell Initiative, ICGex Next-Generation Sequencing Platform, PSL University, 75005, Paris, France
| | - Olivier Delattre
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Eliane Piaggio
- INSERM U932, Immunity and Cancer, PSL Research University, Institut Curie Research Center, Paris, France
| | - Olivier Ayrault
- CNRS UMR 3347, INSERM U1021, Institut Curie, PSL Research University, Université Paris-Saclay, Orsay, France
| | - Joshua J Waterfall
- INSERM U830, Integrative Functional Genomics of Cancer Lab, PSL Research University, Institut Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Nicolas Servant
- INSERM U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, Mines Paris Tech, PSL Research University, Institut Curie Research Center, Paris, France
| | - Kevin Beccaria
- Department of Pediatric Neurosurgery-AP-HP, Necker Sick Kids Hospital, Université de Paris, Paris, France
| | - Volodia Dangouloff-Ros
- Pediatric Radiology Department, AP-HP, Necker Sick Kids Hospital and Paris Cite Universiy INSERM 1299 and UMR 1163, Institut Imagine, Paris, France
| | - Franck Bourdeaut
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France.
- Department of Pediatric Oncology, SIREDO Oncology Center, Institut Curie Hospital, Paris, and Université de Paris, Paris, France.
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7
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Leary JR, Xu Y, Morrison AB, Jin C, Shen EC, Kuhlers PC, Su Y, Rashid NU, Yeh JJ, Peng XL. Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in single-cell RNA-sequencing. Bioinformatics 2023; 39:btad449. [PMID: 37498558 PMCID: PMC10412410 DOI: 10.1093/bioinformatics/btad449] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/30/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023] Open
Abstract
MOTIVATION Single-cell RNA-sequencing (scRNA-seq) has enabled the molecular profiling of thousands to millions of cells simultaneously in biologically heterogenous samples. Currently, the common practice in scRNA-seq is to determine cell type labels through unsupervised clustering and the examination of cluster-specific genes. However, even small differences in analysis and parameter choosing can greatly alter clustering results and thus impose great influence on which cell types are identified. Existing methods largely focus on determining the optimal number of robust clusters, which can be problematic for identifying cells of extremely low abundance due to their subtle contributions toward overall patterns of gene expression. RESULTS Here, we present a carefully designed framework, SCISSORS, which accurately profiles subclusters within broad cluster(s) for the identification of rare cell types in scRNA-seq data. SCISSORS employs silhouette scoring for the estimation of heterogeneity of clusters and reveals rare cells in heterogenous clusters by a multi-step semi-supervised reclustering process. Additionally, SCISSORS provides a method for the identification of marker genes of high specificity to the cell type. SCISSORS is wrapped around the popular Seurat R package and can be easily integrated into existing Seurat pipelines. AVAILABILITY AND IMPLEMENTATION SCISSORS, including source code and vignettes, are freely available at https://github.com/jr-leary7/SCISSORS.
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Affiliation(s)
- Jack R Leary
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, United States
| | - Yi Xu
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Ashley B Morrison
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Chong Jin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Emily C Shen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Peyton C Kuhlers
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Ye Su
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Naim U Rashid
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Jen Jen Yeh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Xianlu Laura Peng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
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8
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Zehentmeier S, Lim VY, Ma Y, Fossati J, Ito T, Jiang Y, Tumanov AV, Lee HJ, Dillinger L, Kim J, Csomos K, Walter JE, Choi J, Pereira JP. Dysregulated stem cell niches and altered lymphocyte recirculation cause B and T cell lymphopenia in WHIM syndrome. Sci Immunol 2022; 7:eabo3170. [PMID: 36149943 PMCID: PMC9614684 DOI: 10.1126/sciimmunol.abo3170] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Gain-of-function (GOF) mutations in CXCR4 cause WHIM (warts, hypogammaglobulinemia, infections, and myelokathexis) syndrome, characterized by infections, leukocyte retention in bone marrow (BM), and blood leukopenias. B lymphopenia is evident at early progenitor stages, yet why do CXCR4 GOF mutations that cause B (and T) lymphopenia remain obscure? Using a CXCR4 R334X GOF mouse model of WHIM syndrome, we showed that lymphopoiesis is reduced because of a dysregulated mesenchymal stem cell (MSC) transcriptome characterized by a switch from an adipogenic to an osteolineage-prone program with limited lymphopoietic activity. We identify lymphotoxin beta receptor (LTβR) as a critical pathway promoting interleukin-7 (IL-7) down-regulation in MSCs. Blocking LTβR or CXCR4 signaling restored IL-7 production and B cell development in WHIM mice. LTβR blocking also increased production of IL-7 and B cell activating factor (BAFF) in secondary lymphoid organs (SLOs), increasing B and T cell numbers in the periphery. These studies revealed that LTβR signaling in BM MSCs and SLO stromal cells limits the lymphocyte compartment size.
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Affiliation(s)
- Sandra Zehentmeier
- Department of Immunobiology and Yale Stem Cell Center, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, USA
| | - Vivian Y Lim
- Department of Immunobiology and Yale Stem Cell Center, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, USA
| | - Yifan Ma
- Department of Immunobiology and Yale Stem Cell Center, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, USA
| | - Julia Fossati
- Department of Immunobiology and Yale Stem Cell Center, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, USA
| | - Takeshi Ito
- Department of Immunobiology and Yale Stem Cell Center, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, USA
| | - Yawen Jiang
- Department of Immunobiology and Yale Stem Cell Center, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, USA
| | - Alexei V Tumanov
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Ho-Joon Lee
- Department of Genetics and Yale Center for Genome Analysis, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | - Lukas Dillinger
- X4 Pharmaceuticals Inc., Cambridge, MA, USA
- X4 Pharmaceuticals Inc., Vienna, Austria
| | - Jihyun Kim
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Krisztian Csomos
- Division of Allergy and Immunology, Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jolan E Walter
- Division of Allergy and Immunology, Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Division Allergy and Immunology, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA
| | - Jungmin Choi
- Department of Genetics and Yale Center for Genome Analysis, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - João P Pereira
- Department of Immunobiology and Yale Stem Cell Center, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, USA
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9
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Thennavan A, Garcia-Recio S, Liu S, He X, Perou CM. Molecular signatures of in situ to invasive progression for basal-like breast cancers: An integrated mouse model and human DCIS study. NPJ Breast Cancer 2022; 8:83. [PMID: 35851387 PMCID: PMC9293914 DOI: 10.1038/s41523-022-00450-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 06/24/2022] [Indexed: 11/08/2022] Open
Abstract
Ductal carcinoma in situ (DCIS) of the breast is a non-obligate precursor of Invasive Ductal Carcinoma (IDC) and thus the identification of features that may predict DCIS progression would be of potential clinical value. Experimental mouse models can be used to address this challenge by studying DCIS-to-IDC biology. Here we utilize single cell RNA sequencing (scRNAseq) on the C3Tag genetically engineered mouse model that forms DCIS-like precursor lesions and for which many lesions progress into end-stage basal-like molecular subtype IDC. We also perform bulk RNAseq analysis on 10 human synchronous DCIS-IDC pairs comprised of estrogen receptor (ER) positive and ER-negative subsets and utilize 2 additional public human DCIS data sets for comparison to our mouse model. By identifying malignant cells using inferred DNA copy number changes from the murine C3Tag scRNAseq data, we show the existence of cancer cells within the C3Tag pre-DCIS, DCIS, and IDC-like tumor specimens. These cancer cells were further classified into proliferative, hypoxic, and inflammatory subpopulations, which change in frequency in DCIS versus IDC. The C3Tag tumor progression model was also associated with increase in Cancer-Associated Fibroblasts and decrease in activated T cells in IDC. Importantly, we translate the C3Tag murine genomic findings into human DCIS where we find common features only with human basal-like DCIS, suggesting there are intrinsic subtype unique DCIS features. This study identifies several tumor and microenvironmental features associated with DCIS progression and may also provide genomic signatures that can identify progression-prone DCIS within the context of human basal-like breast cancers.
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Affiliation(s)
- Aatish Thennavan
- Oral and Craniofacial Biomedicine Program, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, 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, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Siyao Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Xiaping He
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, 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.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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10
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Ye J, Calvo IA, Cenzano I, Vilas A, Martinez-de-Morentin X, Lasaga M, Alignani D, Paiva B, Viñado AC, San Martin-Uriz P, Romero JP, Quilez Agreda D, Miñana Barrios M, Sancho-González I, Todisco G, Malcovati L, Planell N, Saez B, Tegner JN, Prosper F, Gomez-Cabrero D. Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation. iScience 2022; 25:104225. [PMID: 35494238 PMCID: PMC9046238 DOI: 10.1016/j.isci.2022.104225] [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: 11/17/2021] [Revised: 02/14/2022] [Accepted: 04/05/2022] [Indexed: 11/28/2022] Open
Abstract
Understanding the regulation of normal and malignant human hematopoiesis requires comprehensive cell atlas of the hematopoietic stem cell (HSC) regulatory microenvironment. Here, we develop a tailored bioinformatic pipeline to integrate public and proprietary single-cell RNA sequencing (scRNA-seq) datasets. As a result, we robustly identify for the first time 14 intermediate cell states and 11 stages of differentiation in the endothelial and mesenchymal BM compartments, respectively. Our data provide the most comprehensive description to date of the murine HSC-regulatory microenvironment and suggest a higher level of specialization of the cellular circuits than previously anticipated. Furthermore, this deep characterization allows inferring conserved features in human, suggesting that the layers of microenvironmental regulation of hematopoiesis may also be shared between species. Our resource and methodology is a stepping-stone toward a comprehensive cell atlas of the BM microenvironment.
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Affiliation(s)
- Jin Ye
- Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal 23955, Saudi Arabia
| | - Isabel A. Calvo
- Universidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
| | - Itziar Cenzano
- Universidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain
| | - Amaia Vilas
- Universidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
| | - Xabier Martinez-de-Morentin
- Navarrabiomed, ComplejoHospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, 31008 Navarra, Spain
| | - Miren Lasaga
- Navarrabiomed, ComplejoHospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, 31008 Navarra, Spain
| | - Diego Alignani
- Universidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
| | - Bruno Paiva
- Universidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
| | - Ana C. Viñado
- Universidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
| | - Patxi San Martin-Uriz
- Universidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain
| | - Juan P. Romero
- Universidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain
| | | | | | | | - Gabriele Todisco
- Department of Molecular Medicine, University of Pavia & Unit of Precision Hematology Oncology, IRCCS S. Matteo Hospital Foundation, 27100 Pavia, Italy
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia & Unit of Precision Hematology Oncology, IRCCS S. Matteo Hospital Foundation, 27100 Pavia, Italy
| | - Nuria Planell
- Navarrabiomed, ComplejoHospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, 31008 Navarra, Spain
| | - Borja Saez
- Universidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
| | - Jesper N. Tegner
- Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal 23955, Saudi Arabia
- Department of Medicine, Centre for Molecular Medicine, Karolinska Institutet, 17177 Stockholm, Stockholm, Sweden
- Computer, Electrical, and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology KAUST, Thuwal 23955, Saudi Arabia
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal 23955, Saudi Arabia
| | - Felipe Prosper
- Universidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain
- Service of Hematology and Cell Therapy, Clínica Universidad de Navarra; CCUN, Pamplona, Navarra, 31008; Spain
| | - David Gomez-Cabrero
- Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal 23955, Saudi Arabia
- Navarrabiomed, ComplejoHospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, 31008 Navarra, Spain
- Department of Medicine, Centre for Molecular Medicine, Karolinska Institutet, 17177 Stockholm, Stockholm, Sweden
- Centre for Host Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College, London WC2R 2LS, UK
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal 23955, Saudi Arabia
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11
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Zeng Y, Wei Z, Zhong F, Pan Z, Lu Y, Yang Y. A parameter-free deep embedded clustering method for single-cell RNA-seq data. Brief Bioinform 2022; 23:6582003. [PMID: 35524494 DOI: 10.1093/bib/bbac172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/25/2022] [Accepted: 04/18/2022] [Indexed: 11/12/2022] Open
Abstract
Clustering analysis is widely used in single-cell ribonucleic acid (RNA)-sequencing (scRNA-seq) data to discover cell heterogeneity and cell states. While many clustering methods have been developed for scRNA-seq analysis, most of these methods require to provide the number of clusters. However, it is not easy to know the exact number of cell types in advance, and experienced determination is not always reliable. Here, we have developed ADClust, an automatic deep embedding clustering method for scRNA-seq data, which can accurately cluster cells without requiring a predefined number of clusters. Specifically, ADClust first obtains low-dimensional representation through pre-trained autoencoder and uses the representations to cluster cells into initial micro-clusters. The clusters are then compared in between by a statistical test, and similar micro-clusters are merged into larger clusters. According to the clustering, cell representations are updated so that each cell will be pulled toward centers of its assigned cluster and similar clusters, while cells are separated to keep distances between clusters. This is accomplished through jointly optimizing the carefully designed clustering and autoencoder loss functions. This merging process continues until convergence. ADClust was tested on 11 real scRNA-seq datasets and was shown to outperform existing methods in terms of both clustering performance and the accuracy on the number of the determined clusters. More importantly, our model provides high speed and scalability for large datasets.
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Affiliation(s)
- Yuansong Zeng
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China
| | - Zhuoyi Wei
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China
| | - Fengqi Zhong
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China
| | - Zixiang Pan
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China
| | - Yutong Lu
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China
| | - Yuedong Yang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China.,Key Laboratory of Machine Intelligence and Advanced Computing (MOE), Guangzhou 510000, China
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12
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Liu S, Thennavan A, Garay JP, Marron JS, Perou CM. MultiK: an automated tool to determine optimal cluster numbers in single-cell RNA sequencing data. Genome Biol 2021; 22:232. [PMID: 34412669 PMCID: PMC8375188 DOI: 10.1186/s13059-021-02445-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/29/2021] [Indexed: 01/02/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) provides new opportunities to characterize cell populations, typically accomplished through some type of clustering analysis. Estimation of the optimal cluster number (K) is a crucial step but often ignored. Our approach improves most current scRNA-seq cluster methods by providing an objective estimation of the number of groups using a multi-resolution perspective. MultiK is a tool for objective selection of insightful Ks and achieves high robustness through a consensus clustering approach. We demonstrate that MultiK identifies reproducible groups in scRNA-seq data, thus providing an objective means to estimating the number of possible groups or cell-type populations present.
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Affiliation(s)
- Siyao Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Marsico Hall, 5th floor, CB#7599, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Aatish Thennavan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Marsico Hall, 5th floor, CB#7599, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA
- Oral and Craniofacial Biomedicine Program, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joseph P Garay
- Department of Surgery, Oregon Health & Science University, Portland, OR, 97239, USA
| | - J S Marron
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Marsico Hall, 5th floor, CB#7599, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA.
- Department of Statistics and Operation Research, University of North Carolina at Chapel Hill, 352 Hanes Hall CB#3260, Chapel Hill, NC, 27599, USA.
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Marsico Hall, 5th floor, CB#7599, 125 Mason Farm Road, 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.
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13
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Abdel-Hakeem MS, Manne S, Beltra JC, Stelekati E, Chen Z, Nzingha K, Ali MA, Johnson JL, Giles JR, Mathew D, Greenplate AR, Vahedi G, Wherry EJ. Epigenetic scarring of exhausted T cells hinders memory differentiation upon eliminating chronic antigenic stimulation. Nat Immunol 2021; 22:1008-1019. [PMID: 34312545 PMCID: PMC8323971 DOI: 10.1038/s41590-021-00975-5] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/10/2021] [Indexed: 12/16/2022]
Abstract
Exhausted CD8 T cells (TEX) are a distinct state of T cell differentiation associated with failure to clear chronic viruses and cancer. Immunotherapies like PD-1 blockade can re-invigorate TEX cells, but re-invigoration is not durable. A major unanswered question is whether TEX cells differentiate into functional durable memory T cells (TMEM) upon antigen clearance. Here, using a mouse model, we found that upon eliminating chronic antigenic stimulation, TEX cells partially (re)acquire phenotypic and transcriptional features of TMEM cells. These “recovering” TEX cells originated from the T-cell factor (TCF-1+) TEX progenitor subset. Nevertheless, the recall capacity of these recovering-TEX cells remained compromised compared to TMEM cells. Chromatin-accessibility profiling revealed failure to recover core memory epigenetic circuits and maintenance of a largely exhausted open chromatin landscape. Thus, despite some phenotypic and transcriptional recovery upon antigen clearance, exhaustion leaves durable epigenetic scars constraining future immune responses. These results support epigenetic remodeling interventions for TEX cell targeted immunotherapies.
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Affiliation(s)
- Mohamed S Abdel-Hakeem
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Sasikanth Manne
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jean-Christophe Beltra
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - Erietta Stelekati
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology and Immunology, University of Miami, Miami, FL, USA
| | - Zeyu Chen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kito Nzingha
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mohammed-Alkhatim Ali
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John L Johnson
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - Divij Mathew
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Allison R Greenplate
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Golnaz Vahedi
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.,Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA. .,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA.
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14
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Guan Y, Du Y, Wang G, Gou H, Xue Y, Xu J, Li E, Chan DW, Wu D, Xu P, Ni P, Xu D, Hu Y. Overexpression of PLXDC2 in Stromal Cell-Associated M2 Macrophages Is Related to EMT and the Progression of Gastric Cancer. Front Cell Dev Biol 2021; 9:673295. [PMID: 34124056 PMCID: PMC8194078 DOI: 10.3389/fcell.2021.673295] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/04/2021] [Indexed: 12/14/2022] Open
Abstract
The tumor microenvironment (TME) comprises distinct cell types, including stromal types such as fibroblast cells and macrophage cells, which have recently become a critical factor in tumor development and progression. Here, we identified the TME-related gene, plexin domain containing 2 (PLXDC2), in a high-stromal-score population. And we revealed that this gene was related to poor survival and advanced (tumor-node-metastasis) stage in gastric cancer (GC) patients from The Cancer Genome Atlas database. An integrated gene profile and functional analysis of the proportions of tumor-infiltrating immune cells revealed that the expression of the M2 macrophages cell marker CD163 was positively correlated with PLXDC2 expression. In addition, the M2 macrophages gene signature and high PLXDC2 expression were associated with the inflammatory signaling pathway and the epithelial-to-mesenchymal transition (EMT)-related gene signature. Single-cell study of GC identified PLXDC2 was enriched specifically in fibroblasts and monocytes/macrophages populations, which supported its important role in the stroma. Furthermore, according to a tissue microarray immunohistochemistry analysis, the expression of PLXDC2 elevated in human GC stromal specimens compared to tumor tissue specimens. Moreover, PLXDC2 overexpression in the stromal compartment was associated with CD163-positive regulatory M2 macrophages, and its functions were related to the pathogenesis of GC. Multiplexed immunohistochemistry verified PLXDC2's correlation with EMT markers. Our data suggested that PLXDC2 was expressed in stromal cells and that its crosstalk with tumor-associated macrophages could contribute to cancer biology by inducing the EMT process.
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Affiliation(s)
- Yiming Guan
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuzhang Du
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guanzheng Wang
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hongquan Gou
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yilun Xue
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jingsong Xu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Enhao Li
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - David W Chan
- Department of Obstetrics and Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Di Wu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Peiqing Xu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Peihua Ni
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dakang Xu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiqun Hu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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15
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Chen YC, Suresh A, Underbayev C, Sun C, Singh K, Seifuddin F, Wiestner A, Pirooznia M. IKAP-Identifying K mAjor cell Population groups in single-cell RNA-sequencing analysis. Gigascience 2019; 8:giz121. [PMID: 31574155 PMCID: PMC6771546 DOI: 10.1093/gigascience/giz121] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/05/2019] [Accepted: 09/16/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND In single-cell RNA-sequencing analysis, clustering cells into groups and differentiating cell groups by differentially expressed (DE) genes are 2 separate steps for investigating cell identity. However, the ability to differentiate between cell groups could be affected by clustering. This interdependency often creates a bottleneck in the analysis pipeline, requiring researchers to repeat these 2 steps multiple times by setting different clustering parameters to identify a set of cell groups that are more differentiated and biologically relevant. FINDINGS To accelerate this process, we have developed IKAP-an algorithm to identify major cell groups and improve differentiating cell groups by systematically tuning parameters for clustering. We demonstrate that, with default parameters, IKAP successfully identifies major cell types such as T cells, B cells, natural killer cells, and monocytes in 2 peripheral blood mononuclear cell datasets and recovers major cell types in a previously published mouse cortex dataset. These major cell groups identified by IKAP present more distinguishing DE genes compared with cell groups generated by different combinations of clustering parameters. We further show that cell subtypes can be identified by recursively applying IKAP within identified major cell types, thereby delineating cell identities in a multi-layered ontology. CONCLUSIONS By tuning the clustering parameters to identify major cell groups, IKAP greatly improves the automation of single-cell RNA-sequencing analysis to produce distinguishing DE genes and refine cell ontology using single-cell RNA-sequencing data.
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Affiliation(s)
- Yun-Ching Chen
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, 12 South Drive, Bethesda, MD 20892, USA
| | - Abhilash Suresh
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, 12 South Drive, Bethesda, MD 20892, USA
| | - Chingiz Underbayev
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20814, USA
| | - Clare Sun
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20814, USA
| | - Komudi Singh
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, 12 South Drive, Bethesda, MD 20892, USA
| | - Fayaz Seifuddin
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, 12 South Drive, Bethesda, MD 20892, USA
| | - Adrian Wiestner
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20814, USA
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, 12 South Drive, Bethesda, MD 20892, USA
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