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Article ; Online: Identification of gene classifier and modules associated with SARS-CoV-2 ARI in nasal swab

Pandikannan Krishnamoorthy / Athira S. Raj / Himanshu Kumar

Genes and Diseases, Vol 11, Iss 1, Pp 38-

2024 Volume 41

Keywords	Medicine (General) ; R5-920 ; Genetics ; QH426-470
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	KeAi Communications Co., Ltd.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of gene classifier and modules associated with SARS-CoV-2 ARI in nasal swab.

Krishnamoorthy, Pandikannan / Raj, Athira S / Kumar, Himanshu

Genes & diseases

2023

Language	English
Publishing date	2023-04-05
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2821806-1
ISSN	2352-3042 ; 2352-3042
ISSN (online)	2352-3042
ISSN	2352-3042
DOI	10.1016/j.gendis.2023.03.004
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Interplay of host and viral factors in inflammatory pathway mediated cytokine storm during RNA virus infection

Riya Chaudhary / Aparna Meher / Pandikannan Krishnamoorthy / Himanshu Kumar

Current Research in Immunology, Vol 4, Iss , Pp 100062- (2023)

2023

Abstract: RNA viruses always have been a serious concern for human health by causing several outbreaks, often pandemics. The excessive mortality and deaths associated with the outbreaks caused by these viruses were due to the excessive induction of pro- ... ...

Abstract	RNA viruses always have been a serious concern for human health by causing several outbreaks, often pandemics. The excessive mortality and deaths associated with the outbreaks caused by these viruses were due to the excessive induction of pro-inflammatory cytokines leading to cytokine storm. Cytokines are important for cell-to-cell communication to maintain cell homeostasis. Disturbances of this homeostasis can lead to intricate chain reactions resulting in a massive release of cytokines. This could lead to a severe self-reinforcement of several feedback processes, which could eventually cause systemic harm, multiple organ failure, or death. Multiple inflammation-associated pathways were involved in the cytokine production and its regulation. Different RNA viruses induce these pathways through the interplay with their viral factors and host proteins and miRNAs regulating these pathways. This review will discuss the interplay of host proteins and miRNAs that can play an important role in the regulation of cytokine storm and the possible therapeutic potential of these molecules for the treatment and the challenges associated with the clinical translation.
Keywords	Cytokine storm ; RNA viruses ; Innate immunity ; miRNAs ; Antiviral therapeutics ; Inflammation ; Specialties of internal medicine ; RC581-951
Subject code	610
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Interplay of host and viral factors in inflammatory pathway mediated cytokine storm during RNA virus infection.

Chaudhary, Riya / Meher, Aparna / Krishnamoorthy, Pandikannan / Kumar, Himanshu

Current research in immunology

2023 Volume 4, Page(s) 100062

Abstract	RNA viruses always have been a serious concern for human health by causing several outbreaks, often pandemics. The excessive mortality and deaths associated with the outbreaks caused by these viruses were due to the excessive induction of pro-inflammatory cytokines leading to cytokine storm. Cytokines are important for cell-to-cell communication to maintain cell homeostasis. Disturbances of this homeostasis can lead to intricate chain reactions resulting in a massive release of cytokines. This could lead to a severe self-reinforcement of several feedback processes, which could eventually cause systemic harm, multiple organ failure, or death. Multiple inflammation-associated pathways were involved in the cytokine production and its regulation. Different RNA viruses induce these pathways through the interplay with their viral factors and host proteins and miRNAs regulating these pathways. This review will discuss the interplay of host proteins and miRNAs that can play an important role in the regulation of cytokine storm and the possible therapeutic potential of these molecules for the treatment and the challenges associated with the clinical translation.
Language	English
Publishing date	2023-05-26
Publishing country	Netherlands
Document type	Journal Article ; Review
ISSN	2590-2555
ISSN (online)	2590-2555
DOI	10.1016/j.crimmu.2023.100062
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Machine learning-driven blood transcriptome-based discovery of SARS-CoV-2 specific severity biomarkers.

Krishnamoorthy, Pandikannan / Raj, Athira S / Kumar, Himanshu

Journal of medical virology

2023 Volume 95, Issue 2, Page(s) e28488

Abstract: The Coronavirus disease 2019 (COVID-19) pandemic, caused by rapidly evolving variants of severe acute respiratory syndrome coronavirus (SARS-CoV-2), continues to be a global health threat. SARS-CoV-2 infection symptoms often intersect with other ... ...

Abstract	The Coronavirus disease 2019 (COVID-19) pandemic, caused by rapidly evolving variants of severe acute respiratory syndrome coronavirus (SARS-CoV-2), continues to be a global health threat. SARS-CoV-2 infection symptoms often intersect with other nonsevere respiratory infections, making early diagnosis challenging. There is an urgent need for early diagnostic and prognostic biomarkers to predict severity and reduce mortality when a sudden outbreak occurs. This study implemented a novel approach of integrating bioinformatics and machine learning algorithms over publicly available clinical COVID-19 transcriptome data sets. The robust 7-gene biomarker identified through this analysis can not only discriminate SARS-CoV-2 associated acute respiratory illness (ARI) from other types of ARIs but also can discriminate severe COVID-19 patients from nonsevere COVID-19 patients. Validation of the 7-gene biomarker in an independent blood transcriptome data set of longitudinal analysis of COVID-19 patients across various stages of the disease showed that the dysregulation of the identified biomarkers during severe disease is restored during recovery, showing their prognostic potential. The blood biomarkers identified in this study can serve as potential diagnostic candidates and help reduce COVID-19-associated mortality.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19/epidemiology ; Transcriptome ; Biomarkers ; Machine Learning
Chemical Substances	Biomarkers
Language	English
Publishing date	2023-01-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.28488
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Article ; Online: MicroRNA-30e-5p Regulates SOCS1 and SOCS3 During Bacterial Infection.

Mishra, Richa / Krishnamoorthy, Pandikannan / Kumar, Himanshu

Frontiers in cellular and infection microbiology

2021 Volume 10, Page(s) 604016

Abstract: Host innate immunity is the major player against continuous microbial infection. Various pathogenic bacteria adopt the strategies to evade the immunity and show resistance toward the various established therapies. Despite the advent of many antibiotics ... ...

Abstract	Host innate immunity is the major player against continuous microbial infection. Various pathogenic bacteria adopt the strategies to evade the immunity and show resistance toward the various established therapies. Despite the advent of many antibiotics for bacterial infections, there is a substantial need for the host-directed therapies (HDTs) to combat the infection. HDTs are recently being adopted to be useful in eradicating intracellular bacterial infection. Changing the innate immune responses of the host cells alters pathogen's ability to reside inside the cell. MicroRNAs are the small non-coding endogenous molecules and post-transcriptional regulators to target the 3'UTR of the messenger RNA. They are reported to modulate the host's immune responses during bacterial infections. Exploiting microRNAs as a therapeutic candidate in HDTs upon bacterial infection is still in its infancy. Here, initially, we re-analyzed the publicly available transcriptomic dataset of macrophages, infected with
MeSH term(s)	Bacterial Infections ; Humans ; Immunity, Innate ; Macrophages ; MicroRNAs/genetics ; Signal Transduction ; Suppressor of Cytokine Signaling 1 Protein/genetics ; Suppressor of Cytokine Signaling 3 Protein/genetics
Chemical Substances	MIRN30e microRNA, human ; MicroRNAs ; SOCS1 protein, human ; SOCS3 protein, human ; Suppressor of Cytokine Signaling 1 Protein ; Suppressor of Cytokine Signaling 3 Protein
Language	English
Publishing date	2021-01-27
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2020.604016
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Article ; Online: Host and viral non-coding RNAs in dengue pathogenesis.

Krishnamoorthy, Pandikannan / Raj, Athira S / Kumar, Pramod / Das, Nilanjana / Kumar, Himanshu

Reviews in medical virology

2022 Volume 32, Issue 6, Page(s) e2360

Abstract: Dengue virus (DENV) is a mosquito-borne flavivirus that causes frequent outbreaks in tropical countries. Due to the four different serotypes and ever-mutating RNA genome, it is challenging to develop efficient therapeutics. Early diagnosis is crucial to ... ...

Abstract	Dengue virus (DENV) is a mosquito-borne flavivirus that causes frequent outbreaks in tropical countries. Due to the four different serotypes and ever-mutating RNA genome, it is challenging to develop efficient therapeutics. Early diagnosis is crucial to prevent the severe form of dengue, leading to mortality. In the past decade, rapid advancement in the high throughput sequencing technologies has shed light on the crucial regulating role of non-coding RNAs (ncRNAs), also known as the "dark matter" of the genome, in various pathological processes. In addition to the human host ncRNAs like microRNAs and circular RNAs, DENV also produces ncRNAs such as subgenomic flaviviral RNAs that can modulate the virus life cycle and regulate disease outcomes. This review outlines the advances in understanding the interplay between the human host and DENV ncRNAs, their regulation of the innate immune system of the host, and the prospects of the ncRNAs in clinical applications such as dengue diagnosis and promising therapeutics.
MeSH term(s)	Animals ; Humans ; Dengue Virus/genetics ; Flavivirus/genetics ; High-Throughput Nucleotide Sequencing ; MicroRNAs ; Dengue/diagnosis ; Dengue/genetics
Chemical Substances	MicroRNAs
Language	English
Publishing date	2022-05-05
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1086043-5
ISSN	1099-1654 ; 1052-9276
ISSN (online)	1099-1654
ISSN	1052-9276
DOI	10.1002/rmv.2360
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Article ; Online: Particulate matter (PM

Mishra, Richa / Krishnamoorthy, Pandikannan / Gangamma, S / Raut, Ashwin Ashok / Kumar, Himanshu

Environmental pollution (Barking, Essex : 1987)

2020 Volume 266, Issue Pt 1, Page(s) 115148

Abstract: Sensing of pathogens by specialized receptors is the hallmark of the innate immunity. Innate immune response also mounts a defense response against various allergens and pollutants including particulate matter present in the atmosphere. Air pollution has ...

Abstract	Sensing of pathogens by specialized receptors is the hallmark of the innate immunity. Innate immune response also mounts a defense response against various allergens and pollutants including particulate matter present in the atmosphere. Air pollution has been included as the top threat to global health declared by WHO which aims to cover more than three billion people against health emergencies from 2019 to 2023. Particulate matter (PM), one of the major components of air pollution, is a significant risk factor for many human diseases and its adverse effects include morbidity and premature deaths throughout the world. Several clinical and epidemiological studies have identified a key link between the PM existence and the prevalence of respiratory and inflammatory disorders. However, the underlying molecular mechanism is not well understood. Here, we investigated the influence of air pollutant, PM
MeSH term(s)	Air Pollutants/analysis ; Air Pollution/analysis ; Animals ; Humans ; Immunity, Innate ; Influenza A Virus, H5N1 Subtype ; Particulate Matter/analysis ; RNA Virus Infections
Chemical Substances	Air Pollutants ; Particulate Matter
Keywords	covid19
Language	English
Publishing date	2020-07-13
Publishing country	England
Document type	Journal Article
ZDB-ID	280652-6
ISSN	1873-6424 ; 0013-9327 ; 0269-7491
ISSN (online)	1873-6424
ISSN	0013-9327 ; 0269-7491
DOI	10.1016/j.envpol.2020.115148
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Article ; Online: Comparative transcriptome analysis of SARS-CoV, MERS-CoV, and SARS-CoV-2 to identify potential pathways for drug repurposing.

Krishnamoorthy, Pandikannan / Raj, Athira S / Roy, Swagnik / Kumar, Nachimuthu Senthil / Kumar, Himanshu

Computers in biology and medicine

2020 Volume 128, Page(s) 104123

Abstract: The ongoing COVID-19 pandemic caused by the coronavirus, SARS-CoV-2, has already caused in excess of 1.25 million deaths worldwide, and the number is increasing. Knowledge of the host transcriptional response against this virus and how the pathways are ... ...

Abstract	The ongoing COVID-19 pandemic caused by the coronavirus, SARS-CoV-2, has already caused in excess of 1.25 million deaths worldwide, and the number is increasing. Knowledge of the host transcriptional response against this virus and how the pathways are activated or suppressed compared to other human coronaviruses (SARS-CoV, MERS-CoV) that caused outbreaks previously can help in the identification of potential drugs for the treatment of COVID-19. Hence, we used time point meta-analysis to investigate available SARS-CoV and MERS-CoV in-vitro transcriptome datasets in order to identify the significant genes and pathways that are dysregulated at each time point. The subsequent over-representation analysis (ORA) revealed that several pathways are significantly dysregulated at each time point after both SARS-CoV and MERS-CoV infection. We also performed gene set enrichment analyses of SARS-CoV and MERS-CoV with that of SARS-CoV-2 at the same time point and cell line, the results of which revealed that common pathways are activated and suppressed in all three coronaviruses. Furthermore, an analysis of an in-vivo transcriptomic dataset of COVID-19 patients showed that similar pathways are enriched to those identified in the earlier analyses. Based on these findings, a drug repurposing analysis was performed to identify potential drug candidates for combating COVID-19.
MeSH term(s)	Antiviral Agents ; COVID-19/genetics ; COVID-19/metabolism ; Databases, Nucleic Acid ; Drug Repositioning ; Humans ; Middle East Respiratory Syndrome Coronavirus/genetics ; Middle East Respiratory Syndrome Coronavirus/metabolism ; Severe acute respiratory syndrome-related coronavirus/genetics ; Severe acute respiratory syndrome-related coronavirus/metabolism ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Severe Acute Respiratory Syndrome/drug therapy ; Severe Acute Respiratory Syndrome/genetics ; Severe Acute Respiratory Syndrome/metabolism ; Transcriptome ; COVID-19 Drug Treatment
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2020-11-24
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2020.104123
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Article: Particulate matter (PM10) enhances RNA virus infection through modulation of innate immune responses

Mishra, Richa / Krishnamoorthy, Pandikannan / Gangamma, S / Raut, Ashwin Ashok / Kumar, Himanshu

Environmental pollution. 2020 Nov., v. 266

2020

Abstract	Sensing of pathogens by specialized receptors is the hallmark of the innate immunity. Innate immune response also mounts a defense response against various allergens and pollutants including particulate matter present in the atmosphere. Air pollution has been included as the top threat to global health declared by WHO which aims to cover more than three billion people against health emergencies from 2019 to 2023. Particulate matter (PM), one of the major components of air pollution, is a significant risk factor for many human diseases and its adverse effects include morbidity and premature deaths throughout the world. Several clinical and epidemiological studies have identified a key link between the PM existence and the prevalence of respiratory and inflammatory disorders. However, the underlying molecular mechanism is not well understood. Here, we investigated the influence of air pollutant, PM₁₀ (particles with aerodynamic diameter less than 10 μm) during RNA virus infections using Highly Pathogenic Avian Influenza (HPAI) – H5N1 virus. We thus characterized the transcriptomic profile of lung epithelial cell line, A549 treated with PM₁₀ prior to H5N1infection, which is known to cause severe lung damage and respiratory disease. We found that PM₁₀ enhances vulnerability (by cellular damage) and regulates virus infectivity to enhance overall pathogenic burden in the lung cells. Additionally, the transcriptomic profile highlights the connection of host factors related to various metabolic pathways and immune responses which were dysregulated during virus infection. Collectively, our findings suggest a strong link between the prevalence of respiratory illness and its association with the air quality.
Keywords	Influenza A virus ; aerodynamics ; air pollutants ; air pollution ; air quality ; avian influenza ; cell lines ; epithelial cells ; humans ; innate immunity ; lungs ; morbidity ; particulates ; pathogenicity ; people ; risk factors ; transcriptomics ; viruses
Language	English
Dates of publication	2020-11
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	280652-6
ISSN	1873-6424 ; 0013-9327 ; 0269-7491
ISSN (online)	1873-6424
ISSN	0013-9327 ; 0269-7491
DOI	10.1016/j.envpol.2020.115148
Database	NAL-Catalogue (AGRICOLA)

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