Event Title

Analyzing the Differential Expression of OPTN during Herpes Simplex Virus-2 Infection

Session Number

Project ID: MEDH 23

Advisor(s)

Dr. Deepak Shukla; University of Illinois at Chicago

Dr. Tejabhiram Yadavalli; University of Illinois at Chicago

Discipline

Medical and Health Sciences

Start Date

20-4-2022 10:25 AM

End Date

20-4-2022 10:40 AM

Abstract

Herpes Simplex Virus Type 2 (HSV-2) is one of the most widespread sexually transmitted infections in the world today, infecting more than 500 million people worldwide. In a recent article, we showed that OPTN, a gene that codes for the Optineurin protein, selectively marks essential HSV proteins for degradation in an autophagy-dependent manner and that an essential chemokine, CCL5, positively correlated with OPTN expression during human genital HSV-2 infection when screened through the Gene Expression Omnibus (GEO) functional genomics data repository.GEO2R is a software that allows users to compare multiple groups of samples in a GEO Series across different experimental conditions and identify differentially expressed (upregulated or downregulated) genes across those conditions based on author-normalized expression values (log2 scale). In this study, we analyzed the aforementioned HSV-2 dataset using GEO2R for other potential correlation partners of OPTN. We took the 46 genes with the highest Pearson correlation coefficients with OPTN during the “lesion” (active) state and calculated their correlation coefficients in the “control” condition. We then subjected those 46 genes to STRING analysis and discovered that 7 of the 46 genes -- TMEM186, PCMTD1, LAMP3, RNF149, APOL3, FLVCR2, and SMAP2 -- did not have any known experimental correlations with OPTN prior.

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Apr 20th, 10:25 AM Apr 20th, 10:40 AM

Analyzing the Differential Expression of OPTN during Herpes Simplex Virus-2 Infection

Herpes Simplex Virus Type 2 (HSV-2) is one of the most widespread sexually transmitted infections in the world today, infecting more than 500 million people worldwide. In a recent article, we showed that OPTN, a gene that codes for the Optineurin protein, selectively marks essential HSV proteins for degradation in an autophagy-dependent manner and that an essential chemokine, CCL5, positively correlated with OPTN expression during human genital HSV-2 infection when screened through the Gene Expression Omnibus (GEO) functional genomics data repository.GEO2R is a software that allows users to compare multiple groups of samples in a GEO Series across different experimental conditions and identify differentially expressed (upregulated or downregulated) genes across those conditions based on author-normalized expression values (log2 scale). In this study, we analyzed the aforementioned HSV-2 dataset using GEO2R for other potential correlation partners of OPTN. We took the 46 genes with the highest Pearson correlation coefficients with OPTN during the “lesion” (active) state and calculated their correlation coefficients in the “control” condition. We then subjected those 46 genes to STRING analysis and discovered that 7 of the 46 genes -- TMEM186, PCMTD1, LAMP3, RNF149, APOL3, FLVCR2, and SMAP2 -- did not have any known experimental correlations with OPTN prior.