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Kassis G, Palshikar MG, Hilchey SP, Zand MS, Thakar J. Discrete-state models identify pathway specific B cell states across diseases and infections at single-cell resolution. J Theor Biol 2024; 583:111769. [PMID: 38423206 PMCID: PMC11046450 DOI: 10.1016/j.jtbi.2024.111769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 02/10/2024] [Accepted: 02/17/2024] [Indexed: 03/02/2024]
Abstract
Oxygen (O2) regulated pathways modulate B cell activation, migration and proliferation during infection, vaccination, and other diseases. Modeling these pathways in health and disease is critical to understand B cell states and ways to mediate them. To characterize B cells by their activation of O2 regulated pathways we develop pathway specific discrete state models using previously published single-cell RNA-sequencing (scRNA-seq) datasets from isolated B cells. Specifically, Single Cell Boolean Omics Network Invariant-Time Analysis (scBONITA) was used to infer logic gates for known pathway topologies. The simplest inferred set of logic gates that maximized the number of "OR" interactions between genes was used to simulate B cell networks involved in oxygen sensing until they reached steady network states (attractors). By focusing on the attractors that best represented sequenced cells, we identified genes critical in determining pathway specific cellular states that corresponded to diseased and healthy B cell phenotypes. Specifically, we investigate the transendothelial migration, regulation of actin cytoskeleton, HIF1A, and Citrate Cycle pathways. Our analysis revealed attractors that resembled the state of B cell exhaustion in HIV+ patients as well as attractors that promoted anerobic metabolism, angiogenesis, and tumorigenesis in breast cancer patients, which were eliminated after neoadjuvant chemotherapy (NACT). Finally, we investigated the attractors to which the Azimuth-annotated B cells mapped and found that attractors resembling B cells from HIV+ patients encompassed a significantly larger number of atypical memory B cells than HIV- attractors. Meanwhile, attractors resembling B cells from breast cancer patients post NACT encompassed a reduced number of atypical memory B cells compared to pre-NACT attractors.
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Affiliation(s)
- George Kassis
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, USA
| | - Mukta G Palshikar
- Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry, Rochester, USA
| | - Shannon P Hilchey
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY, USA
| | - Martin S Zand
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY, USA
| | - Juilee Thakar
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, USA; Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry, Rochester, USA; Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, USA; Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, USA.
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2
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Jeon H, Lim Y, Lee IG, Kim DI, Kim KP, Hong SH, Kim J, Jung YS, Seo YJ. Inhibition of KIF20A suppresses the replication of influenza A virus by inhibiting viral entry. J Microbiol 2022; 60:1113-1121. [PMID: 36318360 DOI: 10.1007/s12275-022-2436-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
The influenza A virus (IAV) has caused several pandemics, and therefore there are many ongoing efforts to identify novel antiviral therapeutic strategies including vaccines and antiviral drugs. However, influenza viruses continuously undergo antigenic drift and shift, resulting in the emergence of mutated viruses. In turn, this decreases the efficiency of existing vaccines and antiviral drugs to control IAV infection. Therefore, this study sought to identify alternative therapeutic strategies targeting host cell factors rather than viruses to avoid infection by mutated viruses. Particularly, we investigated the role of KIF20A that is one of kinesin superfamily proteins in the replication of IAV. The KIF20A increased viral protein levels in IAV-infected cells by regulating the initial entry stage during viral infection. Furthermore, the KIF20A inhibitor significantly suppressed viral replication, which protected mice from morbidity and mortality. Therefore, our findings demonstrated that KIF20A is highly involved in the viral replication process and viral propagation both in vitro and in vivo, and could thus be used as a target for the development of novel antiviral drugs.
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Affiliation(s)
- Hoyeon Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Younghyun Lim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - In-Gu Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dong-In Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Keun Pil Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - So-Hee Hong
- Department of Microbiology, College of Medicine, Ewha Womans University, Seoul, 07804, Republic of Korea
| | - Jeongkyu Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Youn-Sang Jung
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Young-Jin Seo
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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3
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Sala MA, Balderas-Martínez YI, Buendía-Roldan I, Abdala-Valencia H, Nam K, Jain M, Bhorade S, Bharat A, Reyfman PA, Ridge KM, Pardo A, Sznajder JI, Budinger GRS, Misharin AV, Selman M. Inflammatory pathways are upregulated in the nasal epithelium in patients with idiopathic pulmonary fibrosis. Respir Res 2018; 19:233. [PMID: 30477498 PMCID: PMC6257973 DOI: 10.1186/s12931-018-0932-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/07/2018] [Indexed: 12/12/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by progressive scarring of the lung parenchyma, leading to respiratory failure and death. High resolution computed tomography of the chest is often diagnostic for IPF, but its cost and the risk of radiation exposure limit its use as a screening tool even in patients at high risk for the disease. In patients with lung cancer, investigators have detected transcriptional signatures of disease in airway and nasal epithelial cells distal to the site of disease that are clinically useful as screening tools. Here we assessed the feasibility of distinguishing patients with IPF from age-matched controls through transcriptomic profiling of nasal epithelial curettage samples, which can be safely and repeatedly sampled over the course of a patient's illness. We recruited 10 patients with IPF and 23 age-matched healthy control subjects. Using 3' messenger RNA sequencing (mRNA-seq), we identified 224 differentially expressed genes, most of which were upregulated in patients with IPF compared with controls. Pathway enrichment analysis revealed upregulation of pathways related to immune response and inflammatory signaling in IPF patients compared with controls. These findings support the concept that fibrosis is associated with upregulation of inflammatory pathways across the respiratory epithelium with possible implications for disease detection and pathobiology.
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Affiliation(s)
- Marc A Sala
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Ivette Buendía-Roldan
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan 4502, CP 14080, Mexico City, Mexico
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Kiwon Nam
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Manu Jain
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sangeeta Bhorade
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ankit Bharat
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Paul A Reyfman
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,CONACYT-Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico.,Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan 4502, CP 14080, Mexico City, Mexico.,Facultad de Ciencias, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Karen M Ridge
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Annie Pardo
- Facultad de Ciencias, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Jacob I Sznajder
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Moises Selman
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan 4502, CP 14080, Mexico City, Mexico.
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Zhang Y, Topham DJ, Thakar J, Qiu X. FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis. Bioinformatics 2018; 33:1944-1952. [PMID: 28334094 PMCID: PMC5939227 DOI: 10.1093/bioinformatics/btx104] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/17/2017] [Indexed: 01/26/2023] Open
Abstract
Motivation Gene set enrichment analyses (GSEAs) are widely used in genomic research to identify underlying biological mechanisms (defined by the gene sets), such as Gene Ontology terms and molecular pathways. There are two caveats in the currently available methods: (i) they are typically designed for group comparisons or regression analyses, which do not utilize temporal information efficiently in time-series of transcriptomics measurements; and (ii) genes overlapping in multiple molecular pathways are considered multiple times in hypothesis testing. Results We propose an inferential framework for GSEA based on functional data analysis, which utilizes the temporal information based on functional principal component analysis, and disentangles the effects of overlapping genes by a functional extension of the elastic-net regression. Furthermore, the hypothesis testing for the gene sets is performed by an extension of Mann-Whitney U test which is based on weighted rank sums computed from correlated observations. By using both simulated datasets and a large-scale time-course gene expression data on human influenza infection, we demonstrate that our method has uniformly better receiver operating characteristic curves, and identifies more pathways relevant to immune-response to human influenza infection than the competing approaches. Availability and Implementation The methods are implemented in R package FUNNEL, freely and publicly available at: https://github.com/yunzhang813/FUNNEL-GSEA-R-Package. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yun Zhang
- Department of Biostatistics and Computational Biology
| | - David J Topham
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA
| | - Juilee Thakar
- Department of Biostatistics and Computational Biology.,Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA
| | - Xing Qiu
- Department of Biostatistics and Computational Biology
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A Four-Biomarker Blood Signature Discriminates Systemic Inflammation Due to Viral Infection Versus Other Etiologies. Sci Rep 2017; 7:2914. [PMID: 28588308 PMCID: PMC5460227 DOI: 10.1038/s41598-017-02325-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/10/2017] [Indexed: 02/07/2023] Open
Abstract
The innate immune system of humans and other mammals responds to pathogen-associated molecular patterns (PAMPs) that are conserved across broad classes of infectious agents such as bacteria and viruses. We hypothesized that a blood-based transcriptional signature could be discovered indicating a host systemic response to viral infection. Previous work identified host transcriptional signatures to individual viruses including influenza, respiratory syncytial virus and dengue, but the generality of these signatures across all viral infection types has not been established. Based on 44 publicly available datasets and two clinical studies of our own design, we discovered and validated a four-gene expression signature in whole blood, indicative of a general host systemic response to many types of viral infection. The signature’s genes are: Interferon Stimulated Gene 15 (ISG15), Interleukin 16 (IL16), 2′,5′-Oligoadenylate Synthetase Like (OASL), and Adhesion G Protein Coupled Receptor E5 (ADGRE5). In each of 13 validation datasets encompassing human, macaque, chimpanzee, pig, mouse, rat and all seven Baltimore virus classification groups, the signature provides statistically significant (p < 0.05) discrimination between viral and non-viral conditions. The signature may have clinical utility for differentiating host systemic inflammation (SI) due to viral versus bacterial or non-infectious causes.
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Khan A, Katanic D, Thakar J. Meta-analysis of cell- specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes. BMC Bioinformatics 2017; 18:295. [PMID: 28587632 PMCID: PMC5461682 DOI: 10.1186/s12859-017-1669-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/03/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Despite advances in the gene-set enrichment analysis methods; inadequate definitions of gene-sets cause a major limitation in the discovery of novel biological processes from the transcriptomic datasets. Typically, gene-sets are obtained from publicly available pathway databases, which contain generalized definitions frequently derived by manual curation. Recently unsupervised clustering algorithms have been proposed to identify gene-sets from transcriptomics datasets deposited in public domain. These data-driven definitions of the gene-sets can be context-specific revealing novel biological mechanisms. However, the previously proposed algorithms for identification of data-driven gene-sets are based on hard clustering which do not allow overlap across clusters, a characteristic that is predominantly observed across biological pathways. RESULTS We developed a pipeline using fuzzy-C-means (FCM) soft clustering approach to identify gene-sets which recapitulates topological characteristics of biological pathways. Specifically, we apply our pipeline to derive gene-sets from transcriptomic data measuring response of monocyte derived dendritic cells and A549 epithelial cells to influenza infections. Our approach apply Ward's method for the selection of initial conditions, optimize parameters of FCM algorithm for human cell-specific transcriptomic data and identify robust gene-sets along with versatile viral responsive genes. CONCLUSION We validate our gene-sets and demonstrate that by identifying genes associated with multiple gene-sets, FCM clustering algorithm significantly improves interpretation of transcriptomic data facilitating investigation of novel biological processes by leveraging on transcriptomic data available in the public domain. We develop an interactive 'Fuzzy Inference of Gene-sets (FIGS)' package (GitHub: https://github.com/Thakar-Lab/FIGS ) to facilitate use of of pipeline. Future extension of FIGS across different immune cell-types will improve mechanistic investigation followed by high-throughput omics studies.
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Affiliation(s)
- Atif Khan
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, 14642, USA
| | - Dejan Katanic
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, 14642, USA
| | - Juilee Thakar
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, 14642, USA.
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, 14642, USA.
- , 601 Elmwood Avenue, Rochester, NY, 14618, USA.
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Taye B, Chen H, Myaing MZ, Tan BH, Maurer-Stroh S, Sugrue RJ. Systems-based approach to examine the cytokine responses in primary mouse lung macrophages infected with low pathogenic avian Influenza virus circulating in South East Asia. BMC Genomics 2017; 18:420. [PMID: 28558796 PMCID: PMC5450074 DOI: 10.1186/s12864-017-3803-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/17/2017] [Indexed: 02/08/2023] Open
Abstract
Background Influenza A virus (IAV) is a major public health concern, being responsible for the death of approximately half a million people each year. Zoonotic transmissions of the virus from swine and avian origin have occurred in the past, and can potentially lead to the emgergence of new IAV stains in future pandemics. Pulmonary macrophages have been implicated in disease severity in the lower airway, and understanding the host response of macrophages infected with avian influenza viruses should provide new therapeutic strategies. Results We used a systems-based approach to investigate the transcriptome response of primary murine lung macrophages (PMФ) infected with the mouse-adapted H1N1/WSN virus and low pathogenic avian influenza (LPAI) viruses H5N2 and H5N3. The results showed that the LPAI viruses H5N2 and H5N3 can infect PMФ with similar efficiency to the H1N1/WSN virus. While all viruses induced antiviral responses, the H5N3 virus infection resulted in higher expression levels of cytokines and chemokines associated with inflammatory responses. Conclusions The LPAI H5N2 and H5N3 viruses are able to infect murine lung macrophages. However, the H5N3 virus was associated with increased expression of pro-inflammatory mediators. Although the H5N3 virus it is capable of inducing high levels of cytokines that are associated with inflammation, this property is distinct from its inability to efficiently replicate in a mammalian host. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3803-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Biruhalem Taye
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Republic of Singapore.,School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.,Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, P.O.BOX 1176, Ethiopia
| | - Hui Chen
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.,Current address Genome Institute of Singapore, A*STAR, 60 Biopolis Street, #02-01, Genome, Singapore, 138672, Republic of Singapore
| | - Myint Zu Myaing
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Boon Huan Tan
- Detection and Diagnostics Laboratory, Defence Science Organisation National Laboratories, 27 Medical Drive, Singapore, 117510, Republic of Singapore.,LKC School of Medicine, Nanyang Technological University, 50 Nanyang Ave, Singapore, 639798, Republic of Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Republic of Singapore.,National Public Health Laboratory, Ministry of Health, Singapore, Republic of Singapore.,Department of Biological Sciences, National University of Singapore, 8 Medical Drive, Singapore, 117597, Republic of Singapore
| | - Richard J Sugrue
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
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