Here is an update on the RF1 meeting from August 21, 2023. If you have any questions, please reach out to Susana Valente and Doug Nixon.
Susana Valente – Schedule a meeting with Cedric to go over DUX4 data
Roan Lab – Look for DUX4 expression in single-cell RNAseq tonsil datasets (+/- HIV)
(In progress) Luisa Mori, Ana Leda, and Susana Valente considering writing a review/summary of all the HIV latency models
We heard updates from Quentin Gibaut (Valente Lab) on FUBP3 data, Qifan Wang (Valente Lab) on p32 data, and Nick Dopkins (Nixon Lab) on transposable element expression.
Quentin Gibaut (Valente Lab) presented on the host factor FUBP3 promotes HIV transcription. Quentin went into the background of identifying FUBP3 as an HIV transcriptional activator. The chaperone protein p32 was recently discovered to interact with Tat and promote HIV transcription. There are 161 proteins identified through ChAP-MS. ChAP-MS is a new technique to identify proteins involved in the HIV machinery. The goal is to identify the enrichment or loss of proteins in transcriptionally active or silenced HIV promoter loci. The advantages of this are it is selective for HIV and has unbiased detection of multiple proteins associated with the DNA target. FUBP3 was identified by ChAP-MS as an HIV activator.
He shared validation data of FUBP3 as an HIV transcription activator and the mechanistic studies of FUBP3 in the HIV transcription machinery. For future studies, the Valente lab will try to find stimulation pathways and run ChipSeq to share a global overview of the infections. They will try to determine which part of the proteins are required for this, run MD stimulation of FUBP3 to Tat, Chip in JLat -10.6, and the effects of FUBP3 overexpression.
Qifan Wang (Valente Lab) shared the activity of prohibitin-2 in HIV-1 transcriptional regulation and reactivation. He shared data on the prohibitin 2 (PHB2) function. PHB2 expression decreases after HIV infection in primary CD4+ T cells and expression is reduced in the HIV GFP population. PHB2 overexpression inhibits HIV production in 293T cells. PHB2 reduces HIV LTR activity and restricts HIV reactivation in Jurkat 10.6 cells. The preliminary data evidence shows PHB2 plays a negative role in primary CD4+T cell infected with HIV. He shared a paper in Nature, Global landscape of HIV-human protein complexes that shows The PHB2 Co-IPs with Tat.
Qifan summarized that PHB2 expression was decreased during HIV transactivation. CHip-PCR showed PHB2 binding to the LTR and its loss during reactivation. PHB2 OE reduces HIV LTR transactivation driven by Tat and PMA. PHB2 restricts HIV reactivation in Jurkat 10.6 cells. PHB2 binds to tat, likely via the basic and core domains. For future studies, they plan to construct a series of PHB2 deletion variants and deliver them into J-Lat cells with the endogenous PHB2 depleted by shRNAs to define PHB2 domains involved in LTR binding. They will perform RNAseq after PHB2 knockdown in HIV-infected primary CD4+ T cells and study if there is an indirect activity of PHB2 on HIV activity. Lastly, they will perform ChIP studies to confirm the epigenetic outcome of each of the factors recruited by PHB2.
Nick Dopkins from the Nixon Lab shared updates on the transposable element (TEs) expression in the gut microenvironment of people living with HIV (PLWH). The TEs comprise a substantial fraction of the human genome. They looked at the activation of human endogenous retroviruses and its physiological consequences. He shared the paper from Plos Pathogens, Qualitative Differences Between the IFNα subtypes and IFNβ Influence Chronic Mucosal HIV-1 Pathogenesis. The data shows gut biopsies and interferome analysis of gut CD4+ T cells. TEs are modulated in the gut and influence the HIV status on TE expression in the gut. There is an impact of type 1 interferons on TE expression in gut CD4+ T cells. He shared 6 of his favorite HERV lines that interplay between interferons and HIV status on TE expression in the gut microenvironment.
In summary, they are testing the expression of certain HERV elements, such as LTR19_12p13.31. This is indicative of an overabundant antiviral response observed in the hit microenvironment of PLWH pre-ART. Antigen-presenting mDCs and CD4 populations seem primarily unchanged in the gut. The HERV activity in the gut microenvironment is modulated in PLWH, with TYPE 1 interferons processing shared and differential induction in their expression. The incorporation of HERV activity to interferon-centric studies could explain the heterogeneity of prognostic outcomes in PLWH. In the future, they will work to quantify the expression of differentially expressed TEs in the PBMC data from the same patients and define physiological roles for differentially expressed TEs.
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The next RF1 standing meeting will be Oct 16th, 2023
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“Research reported in this publication was supported by the NIAID of the National Institutes of Health under award number UM1AI164559, with co-funding support from NIDA, NIMH, NHLBI, the NIDDK, and the NINDS. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.”
“This research was supported by NIAID award number UM1AI164559, co-funded by NHLBI, NIDA, NIMH, NINDS, and NIDDK.”