Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection

AbstractAnalyzing host transcriptional changes in response to SARS-CoV-2 infection will help delineate biological processes underlying viral pathogenesis. Comparison of expression profiles of lung cell lines A549 (infected with either SARS-CoV-2 (with ACE2 expression)) or Influenza A virus (IAV)) and Calu3 (infected with SARS-CoV-2 or MERS-CoV) revealed upregulation of the antiviral interferon signaling in all three viral infections. However, perturbations in inflammatory, mitochondrial, and autophagy processes were specifically observed in SARS-CoV-2 infected cells. Validation of findings from cell line data revealed perturbations in autophagy and mitochondrial processes in the infected human nasopharyngeal samples. Specifically, downregulation of mTOR expression, mitochondrial ribosomal, mitochondrial complex I, and lysosome acidification genes were concurrently observed in both infected cell lines and human datasets. Furthermore, SARS-CoV-2 infection impedes autophagic flux by upregulating GSK3B in lung cell lines, or by downregulating autophagy genes, SNAP29 and lysosome acidification genes in human samples, contributing to increased viral replication. Therefore, drugs targeting lysosome acidification or autophagic flux could be tested as intervention strategies. Additionally, downregulation of MTFP1 (in cell lines) or SOCS6 (in human samples) results in hyperfused mitochondria and impede proper interferon response. Coexpression networks analysis identifies correlated clusters of genes annotated to inflammation and mitochondrial processes that are misregulated in SARS-CoV-2 infected cells. Finally, comparison of age stratified human gene expression data revealed impaired upregulation of chemokines, interferon stimulated and tripartite motif genes that are critical for antiviral signaling. Together, this analysis has revealed specific aspects of autophagic and mitochondrial function that are uniquely perturbed in SARS-CoV-2 infection.

Download Full-text

Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection

Frontiers in Genetics ◽

10.3389/fgene.2021.599261 ◽

2021 ◽

Vol 12 ◽

Author(s):

Komudi Singh ◽

Yun-Ching Chen ◽

Shahin Hassanzadeh ◽

Kim Han ◽

Jennifer T. Judy ◽

...

Keyword(s):

Cell Lines ◽

Influenza A ◽

Expression Profiles ◽

Mitochondrial Fission ◽

Transcriptional Response ◽

Transcriptome Profiling ◽

Host Cells ◽

Autophagic Flux ◽

Interferon Stimulated Genes ◽

Human Samples

Analyzing host cells' transcriptional response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection will help delineate biological processes underlying viral pathogenesis. First, analysis of expression profiles of lung cell lines A549 and Calu3 revealed upregulation of antiviral interferon signaling genes in response to all three SARS-CoV-2, MERS-CoV, or influenza A virus (IAV) infections. However, perturbations in expression of genes involved in inflammatory, mitochondrial, and autophagy processes were specifically observed in SARS-CoV-2-infected cells. Next, a validation study in infected human nasopharyngeal samples also revealed perturbations in autophagy and mitochondrial processes. Specifically, mTOR expression, mitochondrial ribosomal, mitochondrial complex I, lysosome acidification, and mitochondrial fission promoting genes were concurrently downregulated in both infected cell lines and human samples. SARS-CoV-2 infection impeded autophagic flux either by upregulating GSK3B in lung cell lines or by downregulating autophagy genes, SNAP29, and lysosome acidification genes in human samples, contributing to increased viral replication. Therefore, drugs targeting lysosome acidification or autophagic flux could be tested as intervention strategies. Finally, age-stratified SARS-CoV-2-positive human data revealed impaired upregulation of chemokines, interferon-stimulated genes, and tripartite motif genes that are critical for antiviral signaling. Together, this analysis has revealed specific aspects of autophagic and mitochondrial function that are uniquely perturbed in SARS-CoV-2-infected host cells.

Download Full-text

Robust Metabolic Transcriptional Components in 34,494 Patient-Derived Samples and Cell Lines

10.21203/rs.3.rs-659596/v1 ◽

2021 ◽

Author(s):

Vincent Christiaan Leeuwenburgh ◽

Carlos G. Urzúa-Traslaviña ◽

Arkajyoti Bhattacharya ◽

Marthe T.C. Walvoort ◽

Mathilde Jalving ◽

...

Keyword(s):

Cell Lines ◽

Expression Profiles ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Metabolic Processes ◽

Gene Sets ◽

Transcriptional Changes ◽

Cancer Tissues ◽

Tumor Biopsies ◽

Transcriptional Landscape

Abstract Background: Patient-derived bulk expression profiles of cancers can provide insight into transcriptional changes that underlie reprogrammed metabolism in cancer. These profiles represent the average expression pattern of all heterogeneous tumor and non-tumor cells present in biopsies of tumor lesions. Hence, subtle transcriptional footprints of metabolic processes can be concealed by other biological processes and experimental artifacts. However, consensus Independent Component Analyses (c-ICA) can capture statistically independent transcriptional footprints, of both subtle and more pronounced metabolic processes. Methods: We performed c-ICA with 34,494 bulk expression profiles of patient-derived tumor biopsies, non-cancer tissues, and cell lines. Gene set enrichment analysis with 608 gene sets that describe metabolic processes was performed to identify transcriptional components enriched for metabolic processes (mTCs). The activity of these mTCs were determined in all samples to create a metabolic transcriptional landscape. Results: A set of 555 mTCs were identified of which many were robust across different datasets, platforms, and patient-derived tissues and cell lines. We demonstrate how the metabolic transcriptional landscape defined by the activity of these mTCs in samples can be used to explore associations between the metabolic transcriptome and drug sensitivities, patient outcomes, and the composition of the immune tumor microenvironment. Conclusions: To facilitate the use of our transcriptional metabolic landscape, we have provided access to all data via a web portal ( www.themetaboliclandscapeofcancer.com ). We believe this resource will contribute to the formulation of new hypotheses on how to metabolically engage the tumor or its (immune) microenvironment.

Download Full-text

Caffeoylquinic Acids Are Major Constituents with Potent Anti-Influenza Effects in Brazilian Green Propolis Water Extract

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2011/254914 ◽

2011 ◽

Vol 2011 ◽

pp. 1-7 ◽

Cited By ~ 16

Author(s):

Tomohiko Urushisaki ◽

Tomoaki Takemura ◽

Shigemi Tazawa ◽

Mayuko Fukuoka ◽

Junji Hosokawa-Muto ◽

...

Keyword(s):

Influenza Virus ◽

Influenza A ◽

Viral Infections ◽

Influenza Virus Infection ◽

Water Extract ◽

H1n1 Influenza ◽

Caffeoylquinic Acids ◽

Cytoprotective Activity ◽

Infected Cells ◽

Brazilian Green Propolis

Influenza A viral infections reached pandemic levels in 1918, 1957, 1968, and, most recently, in 2009 with the emergence of the swine-origin H1N1 influenza virus. The development of novel therapeutics or prophylactics for influenza virus infection is urgently needed. We examined the evaluation of the anti-influenza virus (A/WSN/33 (H1N1)) activity of Brazilian green propolis water extract (PWE) and its constituents by cell viability and real-time PCR assays. Our findings showed strong evidence that PWE has an anti-influenza effect and demonstrate that caffeoylquinic acids are the active anti-influenza components of PWE. Furthermore, we have found that the amount of viral RNA per cell remained unchanged even in the presence of PWE, suggesting that PWE has no direct impact on the influenza virus but may have a cytoprotective activity by affecting internal cellular process. These findings indicate that caffeoylquinic acids are the active anti-influenza components of PWE. Above findings might facilitate the prophylactic application of natural products and the realization of novel anti-influenza drugs based on caffeoylquinic acids, as well as further the understanding of cytoprotective intracellular mechanisms in influenza virus-infected cells.

Download Full-text

Elucidation of the antiviral mechanism of cystine and theanine through transcriptome analysis of mice and comparison with COVID-19 gene set data

10.1101/2020.06.25.149427 ◽

2020 ◽

Author(s):

Akira Mitsui ◽

Ryosei Sakai ◽

Kiyoshi Miwa ◽

Susumu Shibahara ◽

Shigekazu Kurihara ◽

...

Keyword(s):

Viral Infection ◽

Influenza A ◽

Influenza Virus Infection ◽

Transcriptome Profiling ◽

Cytokine Storm ◽

Gene Signatures ◽

Gene Set ◽

Unique Gene ◽

Infected Cells ◽

Intracellular Redox

ABSTRACTWe previously showed that oral administration of cystine and theanine (CT) to mice confers resistance to influenza virus infection. In human studies, CT prevented colds in healthy subjects and enhanced antibody production after influenza vaccination in elderly individuals with a poor nutritional status. The mechanism of action of CT is thought to be glutathione (GSH)-mediated regulation of intracellular redox, which might affect innate immune systems such as macrophages to exert physiological effects. The effect of CT on influenza is independent of viral type, and this treatment has a broad range of antiviral activities. To explore the mechanisms of CT in viral infection, we performed transcriptome profiling of spleen tissues isolated from influenza A virus (IAV)-infected mice. We identified unique gene signatures in response to CT in the IAV-infected mice. Genes upregulated by CT included redox-regulated genes such as GCLC/GCLM (subunits of glutamate cysteine ligase, a rate-limiting enzyme of GSH biosynthesis), TXN1, TXN2, TXNRD2, and SOD1, suggesting that the intracellular redox environment is substantially altered by CT. However, genes downregulated in response to CT included chemokine/chemokine receptor genes (CCL5, CCL19, CXCL9, CXCL12, CXCR3, CXCR4, and ACKR3), some of which are related to cytokine storm. A comparison with public COVID-19-related gene set data showed that the upregulated gene signature was highly similar to the downregulated gene sets of SARS-CoV/SARS-CoV-2-infected cells and the upregulated gene set of attenuated SARS-CoV-infected cells. In conclusion, the unique gene signatures observed in response to orally administered CT in IAV-infected mouse spleen tissues suggested that CT may attenuate viral infection, replication and associated symptoms such as cytokine storm.

Download Full-text

The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells

10.1101/186056 ◽

2017 ◽

Author(s):

Kimberly C. Olney ◽

David B. Nyer ◽

Daniel A. Vargas ◽

Melissa A. Wilson Sayres ◽

Karmella A. Haynes

Keyword(s):

Breast Cancer ◽

Cell Lines ◽

Transcriptional Response ◽

Transcriptome Profiling ◽

Interferon Response ◽

Breast Cancer Cell Lines ◽

Binding Motif ◽

Histone Marks ◽

Model Cell ◽

Treated Breast

ABSTRACTMounting evidence from genome-wide studies of cancer show that chromatin-mediated epigenetic silencing at large cohorts of genes is strongly linked to a poor prognosis. This mechanism is thought to prevent cell differentiation and enable evasion of the immune system. Drugging the cancer epigenome with small molecule inhibitors to release silenced genes from the repressed state has emerged as a powerful approach for cancer research and drug development. Targets of these inhibitors include chromatin-modifying enzymes that can acquire drug-resistant mutations. In order to directly target a generally conserved feature, elevated trimethyl-lysine 27 on histone H3 (H3K27me3), we developed the Polycomb-based Transcription Factor (PcTF), a fusion activator that targets methyl-histone marks via its N-terminal H3K27me3-binding motif, and co-regulates sets of silenced genes. Here, we report transcriptome profiling analyses of PcTF-treated breast cancer model cell lines. We identified a set of 19 PcTF-upregulated genes, or PUGs, that were consistent across three distinct breast cancer cell lines. These genes are associated with the interferon response pathway. Our results demonstrate for the first time a chromatin-mediated interferon-related transcriptional response driven by an engineered fusion protein that physically links repressive histone marks with active transcription.

Download Full-text

Porcine Reproductive and Respiratory Syndrome Virus Interferes with Swine Influenza A Virus Infection of Epithelial Cells

Vaccines ◽

10.3390/vaccines8030508 ◽

2020 ◽

Vol 8 (3) ◽

pp. 508

Author(s):

Georges Saade ◽

Déborah Ménard ◽

Caroline Hervet ◽

Patricia Renson ◽

Erika Hue ◽

...

Keyword(s):

Epithelial Cells ◽

Influenza A ◽

Viral Infections ◽

Respiratory Infections ◽

Swine Influenza ◽

Interferon Response ◽

Respiratory Syndrome Virus ◽

Target Cells ◽

Tracheal Epithelial Cells ◽

Respiratory Epithelial

Respiratory infections are still a major concern in pigs. Amongst the involved viruses, the porcine reproductive and respiratory syndrome virus (PRRSV) and the swine influenza type A virus (swIAV) have a major impact. These viruses frequently encounter and dual infections are reported. We analyzed here the molecular interactions between viruses and porcine tracheal epithelial cells as well as lung tissue. PRRSV-1 species do not infect porcine respiratory epithelial cells. However, PRRSV-1, when inoculated simultaneously or shortly before swIAV, was able to inhibit swIAV H1N2 infection, modulate the interferon response and alter signaling protein phosphorylations (ERK, AKT, AMPK, and JAK2), in our conditions. SwIAV inhibition was also observed, although at a lower level, by inactivated PRRSV-1, whereas acid wash treatment inactivating non-penetrated viruses suppressed the interference effect. PRRSV-1 and swIAV may interact at several stages, before their attachment to the cells, when they attach to their receptors, and later on. In conclusion, we showed for the first time that PRRSV can alter the relation between swIAV and its main target cells, opening the doors to further studies on the interplay between viruses. Consequences of these peculiar interactions on viral infections and vaccinations using modified live vaccines require further investigations.

Download Full-text

Phosphatidylserine-Mediated Phagocytosis of Influenza A Virus-Infected Cells by Mouse Peritoneal Macrophages

Journal of Virology ◽

10.1128/jvi.74.19.9240-9244.2000 ◽

2000 ◽

Vol 74 (19) ◽

pp. 9240-9244 ◽

Cited By ~ 36

Author(s):

Akiko Shiratsuchi ◽

Masako Kaido ◽

Takenori Takizawa ◽

Yoshinobu Nakanishi

Keyword(s):

Influenza Virus ◽

Influenza A Virus ◽

Cell Lines ◽

Hela Cells ◽

Influenza A ◽

Peritoneal Macrophages ◽

Animal Tissues ◽

Cultured Cell ◽

Infected Cells ◽

Mouse Peritoneal Macrophages

ABSTRACT Influenza virus induces apoptosis in cultured cell lines as well as in animal tissues. HeLa cells were infected with influenza virus A/Udon/72 (H3N2) under conditions resulting in almost 100% infection. Such cells underwent typical caspase-dependent apoptosis and were efficiently phagocytosed by macrophages prepared from peritoneal fluids of thioglycolate-treated mice. The membrane phospholipid phosphatidylserine appeared on the surfaces of virus-infected cells at around the time efficient phagocytosis became detectable. In fact, the phagocytosis was almost completely inhibited in the presence of liposomes containing phosphatidylserine, which did not influence the antibody-dependent uptake of zymosan particles by the same macrophages. These results indicate that macrophages phagocytose influenza virus-infected HeLa cells in a manner mediated by phosphatidylserine that appears on the surfaces of infected cells during the process of apoptosis.

Download Full-text

Innate Immune sensing of Influenza A viral RNA through IFI16 promotes pyroptotic cell death

10.1101/2021.02.13.431067 ◽

2021 ◽

Author(s):

Shalabh Mishra ◽

Athira S Raj ◽

Akhilesh Kumar ◽

Ashwathi Rajeevan ◽

Puja Kumari ◽

...

Keyword(s):

Cell Death ◽

Programmed Cell Death ◽

Influenza A Virus ◽

Influenza A ◽

Viral Infections ◽

Inflammatory Responses ◽

Type I ◽

Cell Death Pathways ◽

Infected Cells ◽

Immune Sensing

AbstractProgrammed cell death pathways are triggered by various stresses or stimuli, including viral infections. The mechanism underlying the regulation of these pathways upon Influenza A virus IAV infection is not well characterized. We report that a cytosolic DNA sensor IFI16 is essential for the activation of programmed cell death pathways in IAV infected cells. We have identified that IFI16 functions as an RNA sensor for influenza A virus by binding to genomic RNA. The activation of IFI16 triggers the production of type I, III interferons, and also other pro-inflammatory cytokines via the STING-TBK1 and Pro-caspase-1 signaling axis, thereby promoting cell death (apoptosis and pyroptosis in IAV infected cells). Whereas, IFI16 knockdown cells showed reduced inflammatory responses and also prevented cell mortality during IAV infection. These results demonstrate the pivotal role of IFI16-mediated IAV sensing and its essential role in activating programmed cell death pathways.

Download Full-text

Robust and independent metabolic transcriptional components in 34,494 patient-derived samples and cell lines: a resource for translational cancer research

10.1101/2020.10.01.321950 ◽

2020 ◽

Author(s):

V.C. Leeuwenburgh ◽

C.G. Urzúa-Traslaviña ◽

A. Bhattacharya ◽

M.T.C. Walvoort ◽

M. Jalving ◽

...

Keyword(s):

Cell Lines ◽

Patient Outcomes ◽

Expression Profiles ◽

Biological Processes ◽

Metabolic Processes ◽

Translational Cancer Research ◽

Transcriptional Changes ◽

Cancer Tissues ◽

Tumor Biopsies ◽

Insight Into

SUMMARYPatient-derived bulk expression profiles of cancers can provide insight into transcriptional changes that underlie reprogrammed metabolism in cancer. However, these bulk profiles represent the average expression pattern of all heterogeneous tumor and non-tumor cells present in the biopsy. Therefore, subtle transcriptional footprints of metabolic processes can be concealed by other biological processes and experimental artifacts. We therefore performed consensus Independent Component Analyses (c-ICA) with 34,494 bulk expression profiles of patient-derived tumor biopsies, non-cancer tissues and cell lines. c-ICA enabled us to create a transcriptional metabolic landscape in which many robust metabolic transcriptional components (mTCs) and their activation score in individual samples were defined. Here we demonstrate that this metabolic landscape can be used to explore associations between metabolic processes and drug sensitivities, patient outcomes, and the composition of the immune tumor microenvironment. The metabolic landscape can be explored at http://www.themetaboliclandscapeofcancer.com.

Download Full-text

Robust metabolic transcriptional components in 34,494 patient-derived cancer-related samples and cell lines

Cancer & Metabolism ◽

10.1186/s40170-021-00272-7 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

V. C. Leeuwenburgh ◽

C. G. Urzúa-Traslaviña ◽

A. Bhattacharya ◽

M. T. C. Walvoort ◽

M. Jalving ◽

...

Keyword(s):

Cell Lines ◽

Expression Profiles ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Metabolic Processes ◽

Gene Sets ◽

Transcriptional Changes ◽

Cancer Tissues ◽

Tumor Biopsies ◽

Transcriptional Landscape

Abstract Background Patient-derived bulk expression profiles of cancers can provide insight into the transcriptional changes that underlie reprogrammed metabolism in cancer. These profiles represent the average expression pattern of all heterogeneous tumor and non-tumor cells present in biopsies of tumor lesions. Hence, subtle transcriptional footprints of metabolic processes can be concealed by other biological processes and experimental artifacts. However, consensus independent component analyses (c-ICA) can capture statistically independent transcriptional footprints of both subtle and more pronounced metabolic processes. Methods We performed c-ICA with 34,494 bulk expression profiles of patient-derived tumor biopsies, non-cancer tissues, and cell lines. Gene set enrichment analysis with 608 gene sets that describe metabolic processes was performed to identify the transcriptional components enriched for metabolic processes (mTCs). The activity of these mTCs was determined in all samples to create a metabolic transcriptional landscape. Results A set of 555 mTCs was identified of which many were robust across different datasets, platforms, and patient-derived tissues and cell lines. We demonstrate how the metabolic transcriptional landscape defined by the activity of these mTCs in samples can be used to explore the associations between the metabolic transcriptome and drug sensitivities, patient outcomes, and the composition of the immune tumor microenvironment. Conclusions To facilitate the use of our transcriptional metabolic landscape, we have provided access to all data via a web portal (www.themetaboliclandscapeofcancer.com). We believe this resource will contribute to the formulation of new hypotheses on how to metabolically engage the tumor or its (immune) microenvironment.

Download Full-text