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Liu X, Shi J, Jiao Y, An J, Tian J, Yang Y, Zhuo L. Integrated multi-omics with machine learning to uncover the intricacies of kidney disease. Brief Bioinform 2024; 25:bbae364. [PMID: 39082652 PMCID: PMC11289682 DOI: 10.1093/bib/bbae364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/20/2024] [Accepted: 07/17/2024] [Indexed: 08/03/2024] Open
Abstract
The development of omics technologies has driven a profound expansion in the scale of biological data and the increased complexity in internal dimensions, prompting the utilization of machine learning (ML) as a powerful toolkit for extracting knowledge and understanding underlying biological patterns. Kidney disease represents one of the major growing global health threats with intricate pathogenic mechanisms and a lack of precise molecular pathology-based therapeutic modalities. Accordingly, there is a need for advanced high-throughput approaches to capture implicit molecular features and complement current experiments and statistics. This review aims to delineate strategies for integrating multi-omics data with appropriate ML methods, highlighting key clinical translational scenarios, including predicting disease progression risks to improve medical decision-making, comprehensively understanding disease molecular mechanisms, and practical applications of image recognition in renal digital pathology. Examining the benefits and challenges of current integration efforts is expected to shed light on the complexity of kidney disease and advance clinical practice.
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Affiliation(s)
| | | | | | | | | | | | - Li Zhuo
- Corresponding author. Department of Nephrology, China-Japan Friendship Hospital, Beijing 100029, China; China-Japan Friendship Clinic Medical College, Beijing University of Chinese Medicine, 100029 Beijing, China. E-mail:
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2
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Choi J, Butcher SK, Angel PW, Bransfield J, Barry J, Faux N, Shaban B, Pillai P, Michalewicz A, Wells CA. Stemformatics data portal enables transcriptional benchmarking of lab-derived myeloid cells. Stem Cell Reports 2024; 19:922-932. [PMID: 38788723 DOI: 10.1016/j.stemcr.2024.04.012] [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: 01/07/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Stemformatics.org has been serving the stem cell research community for over a decade, by making it easy for users to find and view transcriptional profiles of pluripotent and adult stem cells and their progeny, comparing data derived from multiple tissues and derivation methods. In recent years, Stemformatics has shifted its focus from curation to collation and integration of public data with shared phenotypes. It now hosts several integrated expression atlases based on human myeloid cells, which allow for easy cross-dataset comparisons and discovery of emerging cell subsets and activation properties. The atlases are designed for external users to benchmark their own data against a common reference. Here, we use case studies to illustrate how to find and explore previously published datasets of relevance and how in-vitro-derived cells can be transcriptionally matched to cells in the integrated atlas to highlight phenotypes of interest.
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Affiliation(s)
- Jarny Choi
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia.
| | - Suzanne K Butcher
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Paul W Angel
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jack Bransfield
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jake Barry
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Noel Faux
- Melbourne Data Analytics Platform, University of Melbourne, Parkville, VIC 3010, Australia; Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia
| | - Bobbie Shaban
- Melbourne Data Analytics Platform, University of Melbourne, Parkville, VIC 3010, Australia
| | - Priyanka Pillai
- Melbourne Data Analytics Platform, University of Melbourne, Parkville, VIC 3010, Australia; Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC 3010, Australia
| | - Aleks Michalewicz
- Melbourne Data Analytics Platform, University of Melbourne, Parkville, VIC 3010, Australia
| | - Christine A Wells
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia.
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3
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Macri C, Paxman M, Jenika D, Lin XP, Elahi Z, Gleeson PA, Caminschi I, Lahoud MH, Villadangos JA, Mintern JD. FcRn regulates antigen presentation in dendritic cells downstream of DEC205-targeted vaccines. NPJ Vaccines 2024; 9:76. [PMID: 38594284 PMCID: PMC11003989 DOI: 10.1038/s41541-024-00854-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/29/2024] [Indexed: 04/11/2024] Open
Abstract
Dendritic cell (DC)-targeted vaccination is a new mode of antigen delivery that relies on the use of monoclonal antibodies (mAb) to target antigen to specific DC subsets. The neonatal Fc receptor (FcRn) is a non-classical Fc receptor that binds to immunoglobulin G (IgG) in acidified endosomes and controls its intracellular transport and recycling. FcRn is known to participate in the antigen presentation of immune complexes, however its contribution to DC-targeted vaccination has not previously been examined. Here we have investigated the role of FcRn in antigen presentation using antigen conjugated to IgG mAb which target specific DC receptors, including DEC205 and Clec9A expressed by the conventional DC 1 (cDC1) subset. We show that FcRn is expressed at high levels by cDC1, both at steady-state and following activation and plays a significant role in MHC I cross-presentation and MHC II presentation of antigens that are targeted to cDC1 via mAb specific for DEC205. This effect of FcRn is intrinsic to cDC1 and FcRn impacts the efficacy of anti-DEC205-mediated vaccination against B cell lymphoma. In contrast, FcRn does not impact presentation of antigens targeted to Clec9A and does not regulate presentation of cell-associated antigen. These data highlight a new and unique role of FcRn in controlling the immunogenicity of anti-DEC205-based vaccination, with consequences for exploiting this pathway to improve DC-targeted vaccine outcomes.
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Affiliation(s)
- Christophe Macri
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Rd, Parkville, The University of Melbourne, Victoria, 3010, Australia
| | - Matthew Paxman
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Rd, Parkville, The University of Melbourne, Victoria, 3010, Australia
| | - Devi Jenika
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Rd, Parkville, The University of Melbourne, Victoria, 3010, Australia
| | - Xiao Peng Lin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Rd, Parkville, The University of Melbourne, Victoria, 3010, Australia
| | - Zahra Elahi
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Paul A Gleeson
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Rd, Parkville, The University of Melbourne, Victoria, 3010, Australia
| | - Irina Caminschi
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, 3010, Australia
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
| | - Mireille H Lahoud
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
| | - Jose A Villadangos
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Rd, Parkville, The University of Melbourne, Victoria, 3010, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Justine D Mintern
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Rd, Parkville, The University of Melbourne, Victoria, 3010, Australia.
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4
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Maggi F, Morelli MB, Aguzzi C, Zeppa L, Nabissi M, Polidori C, Santoni G, Amantini C. Calcium influx, oxidative stress, and apoptosis induced by TRPV1 in chronic myeloid leukemia cells: Synergistic effects with imatinib. Front Mol Biosci 2023; 10:1129202. [PMID: 36876044 PMCID: PMC9975599 DOI: 10.3389/fmolb.2023.1129202] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
Introduction: Calcium flux is the master second messenger that influences the proliferation-apoptosis balance. The ability of calcium flux alterations to reduce cell growth makes ion channels interesting targets for therapy. Among all, we focused on transient receptor potential vanilloid 1, a ligand-gated cation channel with selectivity for calcium. Its involvement in hematological malignancies is poorly investigated, especially in the field of chronic myeloid leukemia, a malignancy characterized by the accumulation of immature cells. Methods: FACS analysis, Western blot analysis, gene silencing, and cell viability assay were performed to investigate the activation of transient receptor potential vanilloid 1, by N-oleoyl-dopamine, in chronic myeloid leukemia cell lines. Results: We demonstrated that the triggering of transient receptor potential vanilloid 1 inhibits cell growth and promotes apoptosis of chronic myeloid leukemia cells. Its activation induced calcium influx, oxidative stress, ER stress, mitochondria dysfunction, and caspase activation. Interestingly, a synergistic effect exerted by N-oleoyl-dopamine and the standard drug imatinib was found. Conclusion: Overall, our results support that transient receptor potential vanilloid 1 activation could be a promising strategy to enhance conventional therapy and improve the management of chronic myeloid leukemia.
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Affiliation(s)
- Federica Maggi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | | | | | - Laura Zeppa
- School of Pharmacy, University of Camerino, Camerino, Italy
| | | | - Carlo Polidori
- School of Pharmacy, University of Camerino, Camerino, Italy
| | | | - Consuelo Amantini
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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5
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Elahi Z, Angel PW, Butcher SK, Rajab N, Choi J, Deng Y, Mintern JD, Radford K, Wells CA. The Human Dendritic Cell Atlas: An Integrated Transcriptional Tool to Study Human Dendritic Cell Biology. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:2352–2361. [PMID: 36427009 PMCID: PMC9719841 DOI: 10.4049/jimmunol.2200366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/09/2022] [Indexed: 12/24/2022]
Abstract
Dendritic cells (DCs) are functionally diverse and are present in most adult tissues, but deep understanding of human DC biology is hampered by relatively small numbers of these in circulation and their short lifespan in human tissues. We built a transcriptional atlas of human DCs by combining samples from 14 expression profiling studies derived from 10 laboratories. We identified significant gene expression variation of DC subset-defining markers across tissue type and upon viral or bacterial stimulation. We further highlight critical gaps between in vitro-derived DC subsets and their in vivo counterparts and provide evidence that monocytes or cord blood progenitor in vitro-differentiated DCs fail to capture the repertoire of primary DC subsets or behaviors. In constructing a reference DC atlas, we provide an important resource for the community wishing to identify and annotate tissue-specific DC subsets from single-cell datasets, or benchmark new in vitro models of DC biology.
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Affiliation(s)
- Zahra Elahi
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul W. Angel
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Suzanne K. Butcher
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Nadia Rajab
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Jarny Choi
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Yidi Deng
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Justine D. Mintern
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia; and
| | - Kristen Radford
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Christine A. Wells
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
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6
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Urh K, Zidar N, Boštjančič E. Bioinformatics Analysis of RNA-seq Data Reveals Genes Related to Cancer Stem Cells in Colorectal Cancerogenesis. Int J Mol Sci 2022; 23:ijms232113252. [PMID: 36362041 PMCID: PMC9654446 DOI: 10.3390/ijms232113252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Cancer stem cells (CSC) play one of the crucial roles in the pathogenesis of various cancers, including colorectal cancer (CRC). Although great efforts have been made regarding our understanding of the cancerogenesis of CRC, CSC involvement in CRC development is still poorly understood. Using bioinformatics and RNA-seq data of normal mucosa, colorectal adenoma, and carcinoma (n = 106) from GEO and TCGA, we identified candidate CSC genes and analyzed pathway enrichment analysis (PEI) and protein–protein interaction analysis (PPI). Identified CSC-related genes were validated using qPCR and tissue samples from 47 patients with adenoma, adenoma with early carcinoma, and carcinoma without and with lymph node metastasis and were compared to normal mucosa. Six CSC-related genes were identified: ANLN, CDK1, ECT2, PDGFD, TNC, and TNXB. ANLN, CDK1, ECT2, and TNC were differentially expressed between adenoma and adenoma with early carcinoma. TNC was differentially expressed in CRC without lymph node metastases whereas ANLN, CDK1, and PDGFD were differentially expressed in CRC with lymph node metastases compared to normal mucosa. ANLN and PDGFD were differentially expressed between carcinoma without and with lymph node metastasis. Our study identified and validated CSC-related genes that might be involved in early stages of CRC development (ANLN, CDK1, ECT2, TNC) and in development of metastasis (ANLN, PDGFD).
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7
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Choi S, Ferrari G, Moyle LA, Mackinlay K, Naouar N, Jalal S, Benedetti S, Wells C, Muntoni F, Tedesco FS. Assessing and enhancing migration of human myogenic progenitors using directed iPS cell differentiation and advanced tissue modelling. EMBO Mol Med 2022; 14:e14526. [PMID: 36161772 PMCID: PMC9549733 DOI: 10.15252/emmm.202114526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/19/2022] [Accepted: 08/19/2022] [Indexed: 02/05/2023] Open
Abstract
Muscle satellite stem cells (MuSCs) are responsible for skeletal muscle growth and regeneration. Despite their differentiation potential, human MuSCs have limited in vitro expansion and in vivo migration capacity, limiting their use in cell therapies for diseases affecting multiple skeletal muscles. Several protocols have been developed to derive MuSC-like progenitors from human induced pluripotent stem (iPS) cells (hiPSCs) to establish a source of myogenic cells with controllable proliferation and differentiation. However, current hiPSC myogenic derivatives also suffer from limitations of cell migration, ultimately delaying their clinical translation. Here we use a multi-disciplinary approach including bioinformatics and tissue engineering to show that DLL4 and PDGF-BB improve migration of hiPSC-derived myogenic progenitors. Transcriptomic analyses demonstrate that this property is conserved across species and multiple hiPSC lines, consistent with results from single cell motility profiling. Treated cells showed enhanced trans-endothelial migration in transwell assays. Finally, increased motility was detected in a novel humanised assay to study cell migration using 3D artificial muscles, harnessing advanced tissue modelling to move hiPSCs closer to future muscle gene and cell therapies.
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Affiliation(s)
- SungWoo Choi
- The Francis Crick InstituteLondonUK
- Department of Cell and Developmental BiologyUniversity College LondonLondonUK
| | - Giulia Ferrari
- Department of Cell and Developmental BiologyUniversity College LondonLondonUK
| | - Louise A Moyle
- Department of Cell and Developmental BiologyUniversity College LondonLondonUK
- Present address:
Institute of Biomedical EngineeringUniversity of TorontoTorontoONCanada
| | - Kirsty Mackinlay
- Department of Cell and Developmental BiologyUniversity College LondonLondonUK
- Present address:
Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Naira Naouar
- Institut de Biologie Paris Seine FR3631, Plateforme de Bioinformatique ARTbioSorbonne UniversitéParisFrance
| | - Salma Jalal
- The Francis Crick InstituteLondonUK
- Department of Cell and Developmental BiologyUniversity College LondonLondonUK
| | - Sara Benedetti
- UCL Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
- National Institute for Health Research Great Ormond Street Hospital Biomedical Research CentreLondonUK
| | - Christine Wells
- Centre for Stem Cell SystemsThe University of MelbourneMelbourneVICAustralia
| | - Francesco Muntoni
- National Institute for Health Research Great Ormond Street Hospital Biomedical Research CentreLondonUK
- Dubowitz Neuromuscular CentreUCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital for ChildrenLondonUK
| | - Francesco Saverio Tedesco
- The Francis Crick InstituteLondonUK
- Department of Cell and Developmental BiologyUniversity College LondonLondonUK
- Dubowitz Neuromuscular CentreUCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital for ChildrenLondonUK
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8
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Survivin Inhibition by Piperine Sensitizes Glioblastoma Cancer Stem Cells and Leads to Better Drug Response. Int J Mol Sci 2022; 23:ijms23147604. [PMID: 35886952 PMCID: PMC9323232 DOI: 10.3390/ijms23147604] [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: 05/15/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
Glioblastoma multiforme (GBM) cancer stem cells (GSCs) are one of the strongest contributing factors to treatment resistance in GBM. Identification of biomarkers capable of directly affecting these cells within the bulk tumor is a major challenge associated with the development of new targeting strategies. In this study, we focus on understanding the potential of the multifunctional extraordinaire survivin as a biomarker for GSCs. We analyzed the expression profiles of this gene using various publicly available datasets to understand its importance in stemness and other cancer processes. The findings from these studies were further validated using human GSCs isolated from a GBM cell line. In these GSCs, survivin was inhibited using the dietary phytochemical piperine (PIP) and the subsequent effects on stemness, cancer processes and Temozolomide were investigated. In silico analysis identified survivin to be one of the most significant differentially regulated gene in GSCs, in comparison to common stemness markers. Further validation studies on the isolated GSCs showed the importance of survivin in stemness, cancer progression and therapy resistance. Taken together, our study identifies survivin as a more consistent GSC marker and also suggests the possibility of using survivin inhibitors along with standard of care drugs for better therapeutic outcomes.
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9
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Deng Y, Choi J, Lê Cao KA. Sincast: a computational framework to predict cell identities in single-cell transcriptomes using bulk atlases as references. Brief Bioinform 2022; 23:6561437. [PMID: 35362513 PMCID: PMC9155616 DOI: 10.1093/bib/bbac088] [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: 11/29/2021] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 11/23/2022] Open
Abstract
Characterizing the molecular identity of a cell is an essential step in single-cell RNA sequencing (scRNA-seq) data analysis. Numerous tools exist for predicting cell identity using single-cell reference atlases. However, many challenges remain, including correcting for inherent batch effects between reference and query data andinsufficient phenotype data from the reference. One solution is to project single-cell data onto established bulk reference atlases to leverage their rich phenotype information. Sincast is a computational framework to query scRNA-seq data by projection onto bulk reference atlases. Prior to projection, single-cell data are transformed to be directly comparable to bulk data, either with pseudo-bulk aggregation or graph-based imputation to address sparse single-cell expression profiles. Sincast avoids batch effect correction, and cell identity is predicted along a continuum to highlight new cell states not found in the reference atlas. In several case study scenarios, we show that Sincast projects single cells into the correct biological niches in the expression space of the bulk reference atlas. We demonstrate the effectiveness of our imputation approach that was specifically developed for querying scRNA-seq data based on bulk reference atlases. We show that Sincast is an efficient and powerful tool for single-cell profiling that will facilitate downstream analysis of scRNA-seq data.
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Affiliation(s)
- Yidi Deng
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, 3010, VIC, Australia.,Centre for Stem Cell Systems, School of Biomedical Sciences, The University of Melbourne, Parkville, 3010, VIC, Country
| | - Jarny Choi
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, 3010, VIC, Australia
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10
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Francia M, Stortz M, Echegaray CV, Oses C, Verneri P, Petrone MV, Toro A, Waisman A, Miriuka S, Cosentino MS, Levi V, Guberman A. SUMO conjugation susceptibility of Akt/protein kinase B affects the expression of the pluripotency transcription factor Nanog in embryonic stem cells. PLoS One 2021; 16:e0254447. [PMID: 34242346 PMCID: PMC8270172 DOI: 10.1371/journal.pone.0254447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/27/2021] [Indexed: 12/24/2022] Open
Abstract
Akt/PKB is a kinase involved in the regulation of a wide variety of cell processes. Its activity is modulated by diverse post-translational modifications (PTMs). Particularly, conjugation of the small ubiquitin-related modifier (SUMO) to this kinase impacts on multiple cellular functions, such as proliferation and splicing. In embryonic stem (ES) cells, this kinase is key for pluripotency maintenance. Among other functions, Akt is known to promote the expression of Nanog, a central pluripotency transcription factor (TF). However, the relevance of this specific PTM of Akt has not been previously analyzed in this context. In this work, we study the effect of Akt1 variants with differential SUMOylation susceptibility on the expression of Nanog. Our results demonstrate that both, the Akt1 capability of being modified by SUMO conjugation and a functional SUMO conjugase activity are required to induce Nanog gene expression. Likewise, we found that the common oncogenic E17K Akt1 mutant affected Nanog expression in ES cells also in a SUMOylatability dependent manner. Interestingly, this outcome takes places in ES cells but not in a non-pluripotent heterologous system, suggesting the presence of a crucial factor for this induction in ES cells. Remarkably, the two major candidate factors to mediate this induction, GSK3-β and Tbx3, are non-essential players of this effect, suggesting a complex mechanism probably involving non-canonical pathways. Furthermore, we found that Akt1 subcellular distribution does not depend on its SUMOylatability, indicating that Akt localization has no influence on the effect on Nanog, and that besides the membrane localization of E17K Akt mutant, SUMOylation is also required for its hyperactivity. Our results highlight the impact of SUMO conjugation in the function of a kinase relevant for a plethora of cellular processes, including the control of a key pluripotency TF.
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Affiliation(s)
- Marcos Francia
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN, CONICET-UBA), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Martin Stortz
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN, CONICET-UBA), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Camila Vazquez Echegaray
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN, CONICET-UBA), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Camila Oses
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN, CONICET-UBA), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Verneri
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN, CONICET-UBA), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Victoria Petrone
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN, CONICET-UBA), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ayelen Toro
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN, CONICET-UBA), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ariel Waisman
- Laboratorio de Investigación Aplicada a las Neurociencias Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (LIAN, FLENI-CONICET), Escobar, Provincia de Buenos Aires, Argentina
| | - Santiago Miriuka
- Laboratorio de Investigación Aplicada a las Neurociencias Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (LIAN, FLENI-CONICET), Escobar, Provincia de Buenos Aires, Argentina
| | - María Soledad Cosentino
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN, CONICET-UBA), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Valeria Levi
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN, CONICET-UBA), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Alejandra Guberman
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN, CONICET-UBA), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
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11
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An integrated analysis of human myeloid cells identifies gaps in in vitro models of in vivo biology. Stem Cell Reports 2021; 16:1629-1643. [PMID: 33989517 PMCID: PMC8190595 DOI: 10.1016/j.stemcr.2021.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 12/13/2022] Open
Abstract
The Stemformatics myeloid atlas is an integrated transcriptome atlas of human macrophages and dendritic cells that systematically compares freshly isolated tissue-resident, cultured, and pluripotent stem cell–derived myeloid cells. Three classes of tissue-resident macrophage were identified: Kupffer cells and microglia; monocyte-associated; and tumor-associated macrophages. Culture had a major impact on all primary cell phenotypes. Pluripotent stem cell–derived macrophages were characterized by atypical expression of collagen and a highly efferocytotic phenotype. Myeloid subsets, and phenotypes associated with derivation, were reproducible across experimental series including data projected from single-cell studies, demonstrating that the atlas provides a robust reference for myeloid phenotypes. Implementation in Stemformatics.org allows users to visualize patterns of sample grouping or gene expression for user-selected conditions and supports temporary upload of your own microarray or RNA sequencing samples, including single-cell data, to benchmark against the atlas. A reference transcriptome atlas for human macrophage biology Culture alters primary myeloid phenotypes Pluripotent stem cell–derived macrophages retain a common stromal signature FLT3L-derived cord blood DCs lack expression of key pattern recognition receptors
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12
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Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis. Cell Discov 2021; 7:30. [PMID: 33947837 PMCID: PMC8096850 DOI: 10.1038/s41421-021-00259-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 03/10/2021] [Indexed: 12/11/2022] Open
Abstract
Pannexin1 (PANX1) is a large-pore ATP efflux channel with a broad distribution, which allows the exchange of molecules and ions smaller than 1 kDa between the cytoplasm and extracellular space. In this study, we show that in human macrophages PANX1 expression is upregulated by diverse stimuli that promote pyroptosis, which is reminiscent of the previously reported lipopolysaccharide-induced upregulation of PANX1 during inflammasome activation. To further elucidate the function of PANX1, we propose the full-length human Pannexin1 (hPANX1) model through cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulation studies, establishing hPANX1 as a homo-heptamer and revealing that both the N-termini and C-termini protrude deeply into the channel pore funnel. MD simulations also elucidate key energetic features governing the channel that lay a foundation to understand the channel gating mechanism. Structural analyses, functional characterizations, and computational studies support the current hPANX1-MD model, suggesting the potential role of hPANX1 in pyroptosis during immune responses.
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13
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Lai HC, James A, Luff J, De Souza P, Quek H, Ho U, Lavin MF, Roberts TL. Regulation of RNA degradation pathways during the lipopolysaccharide response in Macrophages. J Leukoc Biol 2021; 109:593-603. [PMID: 32829531 DOI: 10.1002/jlb.2ab0420-151rr] [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: 06/25/2019] [Revised: 04/01/2020] [Accepted: 05/26/2020] [Indexed: 11/09/2022] Open
Abstract
The innate immune response to LPS is highly dynamic yet tightly regulated. The majority of studies of gene expression have focussed on transcription. However, it is also important to understand how post-transcriptional pathways are regulated in response to inflammatory stimuli as the rate of RNA degradation relative to new transcription is important for overall expression. RNA decay pathways include nonsense-mediated decay, the RNA decay exosome, P-body localized deadenylation, decapping and degradation, and AU-rich element targeted decay mediated by tristetraprolin. Here, bone marrow-derived Mϕs were treated with LPS over a time course of 0, 2, 6, and 24 h and the transcriptional profiles were analyzed by RNA sequencing. The data show that components of RNA degradation pathways are regulated during an LPS response. Processing body associated decapping enzyme DCP2 and regulatory subunit DCP1A, and 5' exonuclease XRN1 and sequence specific RNA decay pathways were upregulated. Nonsense mediated decay was also increased in response to LPS induced signaling, initially by increased activation and at later timepoints at the mRNA and protein levels. This leads to increased nonsense mediated decay efficiency across the 24 h following LPS treatment. These findings suggest that LPS activation of Mϕs results in targeted regulation of RNA degradation pathways in order to change how subsets of mRNAs are degraded during an inflammatory response.
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Affiliation(s)
- Hui-Chi Lai
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia
- South West Sydney Clinical School, UNSW Australia, Liverpool, New South Wales, Australia
| | - Alexander James
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia
| | - John Luff
- The University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
| | - Paul De Souza
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia
- Medical Oncology Department, Liverpool Hospital, Liverpool, New South Wales, Australia
- School of Medicine, Western Sydney University, Macarthur, New South Wales, Australia
| | - Hazel Quek
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Uda Ho
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Martin F Lavin
- The University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
| | - Tara L Roberts
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia
- South West Sydney Clinical School, UNSW Australia, Liverpool, New South Wales, Australia
- The University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
- School of Medicine, Western Sydney University, Macarthur, New South Wales, Australia
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14
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Ten simple rules for navigating the computational aspect of an interdisciplinary PhD. PLoS Comput Biol 2021; 17:e1008554. [PMID: 33600411 PMCID: PMC7891742 DOI: 10.1371/journal.pcbi.1008554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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15
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Cellular Fitness Phenotypes of Cancer Target Genes from Oncobiology to Cancer Therapeutics. Cells 2021; 10:cells10020433. [PMID: 33670680 PMCID: PMC7921985 DOI: 10.3390/cells10020433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/17/2022] Open
Abstract
To define the growing significance of cellular targets and/or effectors of cancer drugs, we examined the fitness dependency of cellular targets and effectors of cancer drug targets across human cancer cells from 19 cancer types. We observed that the deletion of 35 out of 47 cellular effectors and/or targets of oncology drugs did not result in the expected loss of cell fitness in appropriate cancer types for which drugs targeting or utilizing these molecules for their actions were approved. Additionally, our analysis recognized 43 cellular molecules as fitness genes in several cancer types in which these drugs were not approved, and thus, providing clues for repurposing certain approved oncology drugs in such cancer types. For example, we found a widespread upregulation and fitness dependency of several components of the mevalonate and purine biosynthesis pathways (currently targeted by bisphosphonates, statins, and pemetrexed in certain cancers) and an association between the overexpression of these molecules and reduction in the overall survival duration of patients with breast and other hard-to-treat cancers, for which such drugs are not approved. In brief, the present analysis raised cautions about off-target and undesirable effects of certain oncology drugs in a subset of cancers where the intended cellular effectors of drug might not be good fitness genes and that this study offers a potential rationale for repurposing certain approved oncology drugs for targeted therapeutics in additional cancer types.
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16
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Rackham O, Cahan P, Mah N, Morris S, Ouyang JF, Plant AL, Tanaka Y, Wells CA. Challenges for Computational Stem Cell Biology: A Discussion for the Field. Stem Cell Reports 2021; 16:3-9. [PMID: 33440181 PMCID: PMC8486950 DOI: 10.1016/j.stemcr.2020.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The first meetup for Computational Stem Cell Biologists was held at the 2020 annual meeting of the International Society for Stem Cell Research. The discussions highlighted opportunities and barriers to computational stem cell research that require coordinated action across the stem cell sector.
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Affiliation(s)
- Owen Rackham
- Program in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Medical School, Singapore.
| | - Patrick Cahan
- Institute for Cell Engineering, Department of Biomedical Engineering, Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Nancy Mah
- Biomedical Data and Bioethics Group, Fraunhofer Institute for Biomedical Engineering (IBMT), Joseph-von-Fraunhofer-Weg 1, 66280 Sulzbach, Germany
| | - Samantha Morris
- Department of Developmental Biology, Department of Genetics, and Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Medical School, Singapore
| | - Anne L Plant
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg MD, 20899 USA
| | - Yoshiaki Tanaka
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Christine A Wells
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia.
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17
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Cahan P, Cacchiarelli D, Dunn SJ, Hemberg M, de Sousa Lopes SMC, Morris SA, Rackham OJL, Del Sol A, Wells CA. Computational Stem Cell Biology: Open Questions and Guiding Principles. Cell Stem Cell 2021; 28:20-32. [PMID: 33417869 PMCID: PMC7799393 DOI: 10.1016/j.stem.2020.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Computational biology is enabling an explosive growth in our understanding of stem cells and our ability to use them for disease modeling, regenerative medicine, and drug discovery. We discuss four topics that exemplify applications of computation to stem cell biology: cell typing, lineage tracing, trajectory inference, and regulatory networks. We use these examples to articulate principles that have guided computational biology broadly and call for renewed attention to these principles as computation becomes increasingly important in stem cell biology. We also discuss important challenges for this field with the hope that it will inspire more to join this exciting area.
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Affiliation(s)
- Patrick Cahan
- Institute for Cell Engineering, Department of Biomedical Engineering, Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy d Department of Translational Medicine, University of Naples "Federico II," Naples, Italy
| | - Sara-Jane Dunn
- DeepMind, 14-18 Handyside Street, London N1C 4DN, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | | | - Samantha A Morris
- Department of Developmental Biology, Department of Genetics, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Owen J L Rackham
- Centre for Computational Biology and The Program for Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, Belvaux 4366, Luxembourg; CIC bioGUNE, Bizkaia Technology Park, 801 Building, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Christine A Wells
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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18
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Angel PW, Rajab N, Deng Y, Pacheco CM, Chen T, Lê Cao KA, Choi J, Wells CA. A simple, scalable approach to building a cross-platform transcriptome atlas. PLoS Comput Biol 2020; 16:e1008219. [PMID: 32986694 PMCID: PMC7544119 DOI: 10.1371/journal.pcbi.1008219] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 10/08/2020] [Accepted: 08/04/2020] [Indexed: 12/21/2022] Open
Abstract
Gene expression atlases have transformed our understanding of the development, composition and function of human tissues. New technologies promise improved cellular or molecular resolution, and have led to the identification of new cell types, or better defined cell states. But as new technologies emerge, information derived on old platforms becomes obsolete. We demonstrate that it is possible to combine a large number of different profiling experiments summarised from dozens of laboratories and representing hundreds of donors, to create an integrated molecular map of human tissue. As an example, we combine 850 samples from 38 platforms to build an integrated atlas of human blood cells. We achieve robust and unbiased cell type clustering using a variance partitioning method, selecting genes with low platform bias relative to biological variation. Other than an initial rescaling, no other transformation to the primary data is applied through batch correction or renormalisation. Additional data, including single-cell datasets, can be projected for comparison, classification and annotation. The resulting atlas provides a multi-scaled approach to visualise and analyse the relationships between sets of genes and blood cell lineages, including the maturation and activation of leukocytes in vivo and in vitro. In allowing for data integration across hundreds of studies, we address a key reproduciblity challenge which is faced by any new technology. This allows us to draw on the deep phenotypes and functional annotations that accompany traditional profiling methods, and provide important context to the high cellular resolution of single cell profiling. Here, we have implemented the blood atlas in the open access Stemformatics.org platform, drawing on its extensive collection of curated transcriptome data. The method is simple, scalable and amenable for rapid deployment in other biological systems or computational workflows.
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Affiliation(s)
- Paul W. Angel
- Centre for Stem Cell Systems, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nadia Rajab
- Centre for Stem Cell Systems, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yidi Deng
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Chris M. Pacheco
- Centre for Stem Cell Systems, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tyrone Chen
- Centre for Stem Cell Systems, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jarny Choi
- Centre for Stem Cell Systems, The University of Melbourne, Melbourne, Victoria, Australia
| | - Christine A. Wells
- Centre for Stem Cell Systems, The University of Melbourne, Melbourne, Victoria, Australia
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19
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Wiese DM, Braid LR. Transcriptome profiles acquired during cell expansion and licensing validate mesenchymal stromal cell lineage genes. Stem Cell Res Ther 2020; 11:357. [PMID: 32795342 PMCID: PMC7427746 DOI: 10.1186/s13287-020-01873-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 12/31/2022] Open
Abstract
Background Mesenchymal stromal cells (MSCs) are rapidly advancing as commercial therapeutics. However, there are still no adequate tools to validate the identity of MSCs and support standardization of MSC-based products. Currently accepted metrics include cell surface marker profiling and tri-lineage differentiation assays, neither of which is definitive. Transcript profiling represents a cost- and time-effective approach amenable to MSC manufacturing processes. Two independent labs recently reported non-overlapping MSC-specific transcriptomic signatures of 489 and 16 genes. Methods Here, we interrogated our repository of transcriptome data to determine whether routine culture manipulations including cell expansion and immune activation affect expression of the reported MSC lineage genes. These data sets comprise 4 donor populations of human umbilical cord (UC) MSCs serially cultured from cryopreservation thaw through pre-senescence, and 3 donor populations each of naïve UC and bone marrow (BM) MSCs and licensed by 3 different cytokines. Results Overall, 437 of 456 proposed signature genes assessed in these data sets were reliably expressed, representing an enduring lineage profile in 96% agreement with the previous studies. Serial passaging resulted in the downregulation of 3 signature genes, and one was silenced. Cytokine stimulation downregulated expression of 16 signature genes, and 3 were uniformly silenced in one or the other MSC type. Fifteen additional genes were unreliably detected, independent of culture manipulation. Conclusion These results validate and refine the proposed transcriptomic tools for reliable identification of MSCs after isolation through cell expansion and after inflammatory activation. We propose a 24-gene signature to support standardized and accessible MSC characterization.
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Affiliation(s)
- Danielle M Wiese
- Aurora BioSolutions Inc., Crescent Heights PO Box 21053, Medicine Hat, AB, T1A 6N0, Canada
| | - Lorena R Braid
- Aurora BioSolutions Inc., Crescent Heights PO Box 21053, Medicine Hat, AB, T1A 6N0, Canada.
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20
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Chen T, Tyagi S. Integrative computational epigenomics to build data-driven gene regulation hypotheses. Gigascience 2020; 9:giaa064. [PMID: 32543653 PMCID: PMC7297091 DOI: 10.1093/gigascience/giaa064] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Diseases are complex phenotypes often arising as an emergent property of a non-linear network of genetic and epigenetic interactions. To translate this resulting state into a causal relationship with a subset of regulatory features, many experiments deploy an array of laboratory assays from multiple modalities. Often, each of these resulting datasets is large, heterogeneous, and noisy. Thus, it is non-trivial to unify these complex datasets into an interpretable phenotype. Although recent methods address this problem with varying degrees of success, they are constrained by their scopes or limitations. Therefore, an important gap in the field is the lack of a universal data harmonizer with the capability to arbitrarily integrate multi-modal datasets. RESULTS In this review, we perform a critical analysis of methods with the explicit aim of harmonizing data, as opposed to case-specific integration. This revealed that matrix factorization, latent variable analysis, and deep learning are potent strategies. Finally, we describe the properties of an ideal universal data harmonization framework. CONCLUSIONS A sufficiently advanced universal harmonizer has major medical implications, such as (i) identifying dysregulated biological pathways responsible for a disease is a powerful diagnostic tool; (2) investigating these pathways further allows the biological community to better understand a disease's mechanisms; and (3) precision medicine also benefits from developments in this area, particularly in the context of the growing field of selective epigenome editing, which can suppress or induce a desired phenotype.
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Affiliation(s)
- Tyrone Chen
- 25 Rainforest Walk, School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Sonika Tyagi
- 25 Rainforest Walk, School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
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21
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Wells CA, Choi J. Transcriptional Profiling of Stem Cells: Moving from Descriptive to Predictive Paradigms. Stem Cell Reports 2020; 13:237-246. [PMID: 31412285 PMCID: PMC6700522 DOI: 10.1016/j.stemcr.2019.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/24/2022] Open
Abstract
Transcriptional profiling is a powerful tool commonly used to benchmark stem cells and their differentiated progeny. As the wealth of stem cell data builds in public repositories, we highlight common data traps, and review approaches to combine and mine this data for new cell classification and cell prediction tools. We touch on future trends for stem cell profiling, such as single-cell profiling, long-read sequencing, and improved methods for measuring molecular modifications on chromatin and RNA that bring new challenges and opportunities for stem cell analysis.
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Affiliation(s)
- Christine A Wells
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville 3010, Australia.
| | - Jarny Choi
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville 3010, Australia
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22
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Surujon D, van Opijnen T. ShinyOmics: collaborative exploration of omics-data. BMC Bioinformatics 2020; 21:22. [PMID: 31952481 PMCID: PMC6969480 DOI: 10.1186/s12859-020-3360-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/10/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Omics-profiling is a collection of increasingly prominent approaches that result in large-scale biological datasets, for instance capturing an organism's behavior and response in an environment. It can be daunting to manually analyze and interpret such large datasets without some programming experience. Additionally, with increasing amounts of data; management, storage and sharing challenges arise. RESULTS Here, we present ShinyOmics, a web-based application that allows rapid collaborative exploration of omics-data. By using Tn-Seq, RNA-Seq, microarray and proteomics datasets from two human pathogens, we exemplify several conclusions that can be drawn from a rich dataset. We identify a protease and several chaperone proteins upregulated under aminoglycoside stress, show that antibiotics with the same mechanism of action trigger similar transcriptomic responses, point out the dissimilarity in different omics-profiles, and overlay the transcriptional response on a metabolic network. CONCLUSIONS ShinyOmics is easy to set up and customize, and can utilize user supplied metadata. It offers several visualization and comparison options that are designed to assist in novel hypothesis generation, as well as data management, online sharing and exploration. Moreover, ShinyOmics can be used as an interactive supplement accompanying research articles or presentations.
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Affiliation(s)
- Defne Surujon
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA.
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA.
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