Predicting host-based, synthetic lethal antiviral targets from omics data DOI Creative Commons
Jeannette P. Staheli, M J Neal, Arti T. Navare

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 16, 2023

Traditional antiviral therapies often have limited effectiveness due to toxicity and development of drug resistance. Host-based antivirals, while an alternative, may lead non-specific effects. Recent evidence shows that virus-infected cells can be selectively eliminated by targeting synthetic lethal (SL) partners proteins disrupted viral infection. Thus, we hypothesized genes depleted in CRISPR KO screens enriched SL altered To investigate this, established a computational pipeline predicting targets infections. First, identified SARS-CoV-2-induced changes gene products via large compendium omics data. Second, for each product. Last, screened data required cell viability infected cells. Despite differences virus-induced alterations detected various data, they share many predicted targets, with significant enrichment KO-depleted datasets. Comparing from SARS-CoV-2 influenza infections, found possible broad-spectrum, host-based targets. This suggests are replete common their relationship virus-altered states such revealed analysis datasets predictions.

Language: Английский

Saliva microbiome in relation to SARS-CoV-2 infection in a prospective cohort of healthy US adults DOI Creative Commons
Abigail Armstrong, Daniel B. Horton, Tracy Andrews

et al.

EBioMedicine, Journal Year: 2023, Volume and Issue: 94, P. 104731 - 104731

Published: July 22, 2023

The clinical outcomes of SARS-CoV-2 infection vary in severity, potentially influenced by the resident human microbiota. There is limited consensus on conserved microbiome changes response to infection, with many studies focusing severely ill individuals. This study aimed assess variation upper respiratory tract using saliva specimens a cohort individuals primarily mild moderate disease.

Language: Английский

Citations

5
Predicting host-based, synthetic lethal antiviral targets from omics data DOI Creative Commons
Jeannette P. Staheli, Maxwell L. Neal, Arti T. Navare

et al.

Deleted Journal, Journal Year: 2024, Volume and Issue: 1(1)

Published: Jan. 1, 2024

Traditional antiviral therapies often have limited effectiveness due to toxicity and the emergence of drug resistance. Host-based antivirals are an alternative, but can cause nonspecific effects. Recent evidence shows that virus-infected cells be selectively eliminated by targeting synthetic lethal (SL) partners proteins disrupted viral infection. Thus, we hypothesized genes depleted in CRISPR knockout (KO) screens may enriched SL altered To investigate this, established a computational pipeline predicting targets. First, identified SARS-CoV-2-induced changes gene products via large compendium omics data. Second, for each product. Last, screened KO data required cell viability infected cells. Despite differences virus-induced alterations detected various data, they share many predicted targets, with significant enrichment KO-depleted datasets. Our comparison SARS-CoV-2 influenza infection revealed potential broad-spectrum, host-based This suggests replete common targets their relationship virus-altered states such from analysis datasets predictions.

Language: Английский

Citations

1
Comprehensive analysis of immunogenic cell death-related gene and construction of prediction model based on WGCNA and multiple machine learning in severe COVID-19 DOI Creative Commons
Chunyu Li,

Ke Wu,

Rui Yang

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: April 11, 2024

Abstract The death of coronavirus disease 2019 (COVID-19) is primarily due to from critically ill patients, especially ARDS complications caused by SARS-CoV-2. Therefore, it essential contribute an in-depth understanding the pathogenesis and identify biomarkers for predicting patients at molecular level. Immunogenic cell (ICD), as a specific variant regulatory driven stress, can induce adaptive immune responses against antigens in host. Studies have confirmed that both innate pathways are involved SARS-CoV-2 infection. However, role ICD severe COVID-19 has rarely been explored. In this study, we systematically evaluated ICD-related genes COVID-19. We conducted consensus clustering, infiltration analysis, functional enrichment analysis based on differentially expressed genes. results showed characteristics were altered non-severe addition, used multiple machine learning methods screen five risk (KLF5, NSUN7, APH1B, GRB10 CD4), which predict severity. Finally, constructed nomogram classification recognition model, validated model with external data sets. This study provides valuable direction exploration progress COVID-19, helps early identification cases reduce mortality.

Language: Английский

Citations

1
Translation Inhibition Mediated by Interferon-Stimulated Genes during Viral Infections DOI Creative Commons

Alexandria Smart,

Orian Gilmer, Neva Caliskan

et al.

Viruses, Journal Year: 2024, Volume and Issue: 16(7), P. 1097 - 1097

Published: July 8, 2024

Viruses often pose a significant threat to the host through exploitation of cellular machineries for their own benefit. In context immune responses, myriad factors are deployed target viral RNAs and inhibit protein translation, ultimately hampering replication. Understanding how “non-self” interact with translation machinery trigger responses would help in development treatment strategies infections. this review, we explore interferon-stimulated gene products RNA order induce either global or targeted inhibition.

Language: Английский

Citations

1
Coronaviral Main Protease Induces LPCAT3 Cleavage and Endoplasmic Reticulum (ER) Stress DOI Creative Commons
Jia Wang,

Meifang Zhang,

Yanli Ding

et al.

Viruses, Journal Year: 2023, Volume and Issue: 15(8), P. 1696 - 1696

Published: Aug. 5, 2023

Zoonotic coronaviruses infect mammals and birds, causing pulmonary gastrointestinal infections. Some animal coronaviruses, such as the porcine epidemic diarrhea virus (PEDV) transmissible gastroenteritis (TGEV), lead to severe deaths. Gastrointestinal symptoms were also found in COVID-19 SARS patients. However, pathogenesis of coronavirus diseases remains elusive. In this study, main protease-induced LPCAT3 cleavage was monitored by exogenous gene expression protease inhibitors, related regulation confirmed qRT-PCR knockdown. Interestingly, plays an important role lipid absorption intestines. The Mpro diarrhea, PEDV MERS-CoV, but not HCoV-OC43 HCoV-HKU1, which could induce cleavage. Mutagenesis analysis inhibitor experiments indicated that independent catalytic activity Mpro. Moreover, cells boosted CHOP GRP78 expression, biomarkers ER stress. Since is critical for intestines malabsorption may diseases, Mpro-induced might trigger during infection.

Language: Английский

Citations

3
Developing pioneering pharmacological strategies with CRISPR/Cas9 library screening to overcome cancer drug resistance DOI

Yu He,

Huan Li,

Xueming Ju

et al.

Biochimica et Biophysica Acta (BBA) - Reviews on Cancer, Journal Year: 2024, Volume and Issue: 1879(6), P. 189212 - 189212

Published: Nov. 1, 2024

Language: Английский

Citations

0
Cation Enrichment Effect Modulated Nafion/Graphene Field-Effect Transistor for Ultrasensitive RNA Detection DOI

Heqi Ma,

Shuo Chen, Xinhao Zhang

et al.

Nano Letters, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 11, 2024

The graphene field-effect transistor (GFET) biosensor serves as a foundational platform for detecting biomolecules, offering high conductivity, label-free operation, and easy integration. These features have garnered significant attention in biomarker detection. However, the presence of free cations solution often leads to electrostatic shielding negatively charged reducing GFET detection sensitivity (LOD ≥ 1 fM). Additionally, limited capacitance change restricts its use response signal. This study introduces cation enrichment electric field modulation strategy (CEEFMS) enhance Dirac voltage during cation-enriched rough Nafion/graphene FET (CENG-FET) achieves RNA at aM level. Utilizing total shift signals, CENG-FET demonstrates wide linear range from pM. findings advance dual-signal strategies, accidental inaccuracies biomolecular sensing paving way further research.

Language: Английский

Citations

0
Impact of SARS-CoV-2 on Oncogenesis: A Deep Dive into the COVID-19 and Cancer Nexus DOI
Muhammad Waqas, Rashid Bashir, Lea Nohra

et al.

Iranian Journal of Blood and Cancer, Journal Year: 2024, Volume and Issue: 16(3), P. 55 - 62

Published: Sept. 1, 2024

Language: Английский

Citations

0
Predicting host-based, synthetic lethal antiviral targets from omics data DOI Creative Commons
Jeannette P. Staheli, M J Neal, Arti T. Navare

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 16, 2023

Traditional antiviral therapies often have limited effectiveness due to toxicity and development of drug resistance. Host-based antivirals, while an alternative, may lead non-specific effects. Recent evidence shows that virus-infected cells can be selectively eliminated by targeting synthetic lethal (SL) partners proteins disrupted viral infection. Thus, we hypothesized genes depleted in CRISPR KO screens enriched SL altered To investigate this, established a computational pipeline predicting targets infections. First, identified SARS-CoV-2-induced changes gene products via large compendium omics data. Second, for each product. Last, screened data required cell viability infected cells. Despite differences virus-induced alterations detected various data, they share many predicted targets, with significant enrichment KO-depleted datasets. Comparing from SARS-CoV-2 influenza infections, found possible broad-spectrum, host-based targets. This suggests are replete common their relationship virus-altered states such revealed analysis datasets predictions.

Language: Английский

Citations

0