The Upadhyay lab focusses on understanding the HIV envelope (Env)-mediated immuno‐pathogenesis. Several interconnected projects are currently active in the lab, all geared towards one common goal, i.e. developing preventive and/or therapeutic HIV vaccines.
A major focus of our efforts has been on understanding the features of HIV envelope that are important for its function including its antigenicity and immunogenicity. Our particular interest is in the biological and functional importance of HIV-1 envelope signal peptide (SP). Although many aspects surrounding the biology of the envelope have been investigated in an exhaustive way, our understanding of the impact that the SP can have on Env functions is largely scant. A better understanding of the processes that are involved in Env glycoprotein biogenesis within the host cells compartments will address important aspects of basic glycobiology that are challenging to study and will be a useful means to modify HIV-1 Env immunogenicity, giving it value from both basic and applied perspectives.
Meet the Team
Principal Investigator
Chitra Upadhyay, PhD, is an Associate Professor of Medicine, Infectious Diseases at the Icahn School of Medicine at Mount Sinai.
Email: Chitra.Upadhyay@mssm.edu
Priyanka Rao, M.S.
Associate Researcher
Email: Priyanka.Rao@mssm.edu
Postdoctoral Fellow
Email: Alex.Boomgarden@mssm.edu
Contact us
Research
1) Understanding the role of signal peptide (SP) in altering properties of HIV Env.
Research from our lab have shown that SP can significantly influence the HIV-1 Env phenotype by altering the sugar moieties on the Env glycans, critical for HIV-1 life cycle. These studies provide a plausible mechanistic of increased/decreased virus sensitivity to neutralization by anti-Env-Abs. Being the sole antigen exposed to host milieu Env serves as a major target for developing vaccines to curb the pandemic. High sequence diversity exists among the HIV-1 isolates however, they don’t fully account for the antigenic/functional differences observed among them. The SP of HIV-1 Env impacts Env folding and glycosylation during its biogenesis through the endoplasmic reticulum and Golgi apparatus however, involvement of SP in influencing functional phenotype of Env is unexpected and is being pursued to further understand the mechanistic underpinning of these events. The lab also aims to evaluate how different SP from chronic vs transmitted/founder isolates can affect virus transmission via routes like cell-cell and across tight barrier junctions. These studies will provide us an improved perspective on understanding the factors that may be associated with the transmission fitness of HIV-1.
2) Designing novel vaccines to improve the elicitation of antibody responses to HIV Env.
Replacement with non-HIV SPs is a strategy employed for increasing immunogens yield. However, this approach may have unfavorable effects on Env glycosylation, structure, and antigenicity. The apparent advantage of increased protein yields may be offset by a higher proportion of Env immunogens with under-processed glycans due to the absence of HIV SP-mediated effects on processing. Comparing SP from acute vs chronic isolates have shown that N domain of acute SPs are enriched for neutral and basic residues, which are lost in chronic SPs, instead chronic SPs have relatively increased number of basic residues in their H domain. Thus, SP sequence is functionally connected to regulating levels of Env expression at different stages of infection. Additionally, SP of acute Env bias the mature protein to a high-mannose, low complex glycan profile while the SP of the chronic Env skew the glycan to an increased complex type. Complex type glycans represent prominent targets of several bNAbs. These data advocate important roles of SP that is beyond protein targeting. SPs are more intricately involved in protein functions than noted before, however this fact has not been much appreciated.
Recent studies published by the lab show that select SP residues can alter the sugars on N-glycans of the Env. This allows conformational changes that promote the exposure and stability of V1V2 epitopes and thus enhance the in vivo immunogenicity of these epitopes (unpublished). We utilize different HIV-1 Env SP as a strategy to direct immune responses toward epitopes of interest and towards elicitation of antibodies with Fc-mediated functions. These studies will allow us to take advantage of a particular SP or SP residue(s) in a predictable manner towards designing more effective immunogens.
3) Functional Consequences of amino acid variability in HIV-1 Vpu.
This is an interesting offshoot of the above studies. The C-terminus of HIV-1 viral protein U (Vpu) overlaps with the Env SP and affects the various functions of two cardinal viral proteins: Env and Vpu. Vpu regulates virus release by counteracting the host antiviral factors and SP influences functional phenotype of the Env. Prior studies suggest that Vpu can also be harnessed to develop novel therapeutic targets. We show that this region can impact Vpu expression and its interaction with host factors and also impacts on the virus release and gene expression of proinflammatory cytokines. The lab is expanding the study to further understand the consequences of polymorphism in this overlapping region on HIV-1 pathogenesis and life cycle.
Publications
Rao PG, Lambert GS, and Upadhyay C. Broadly Neutralizing Antibody Epitopes On HIV-1 Particles Are Exposed After Virus Interaction with Host Cells. bioRxiv. 2023 Jan 21;2023.01.20.524996. doi: 10.1101/2023.01.20.524996. Preprint.
Klingler J, Lambert GS, Bandres JC, Rozita E-G, Nadas A, Oguntuyo, KY, Amanat F, PARIS Study Team, Simon V, Lee B, Zolla-Pazner S, Upadhyay C, Hioe CE. Immune profiles to distinguish hospitalized versus ambulatory COVID-19 cases in older patients. 2022 Dec 22;25(12):105608. PMID: 36406863 PMCID: PMC9666267
Upadhyay C, Rao PG, and Feyznezhad R. Dual role of HIV-1 Envelope Signal Peptide in Immune Evasion. Viruses 2022 Apr 13;14(4):808. doi: 10.3390/v14040808. PMID: 35458538; PubMed Central PMCID: PMC9030904
Lambert GS, and Upadhyay C. HIV-1 Envelope Glycosylation and the Signal Peptide. Vaccines (Basel). 2021 Feb 19;9(2). doi: 10.3390/vaccines9020176. Review. PubMed PMID: 33669676; PubMed Central PMCID: PMC7922494.
Upadhyay C, Feyznezhad R, Cao L, Chan KW, Liu K, Yang W, Zhang H, Yolitz J, Arthos J, Nadas A, Kong XP, Zolla-Pazner S, Hioe CE. Signal peptide of HIV-1 envelope modulates glycosylation impacting exposure of V1V2 and other epitopes. PLoS Pathog. 2020 Dec;16(12):e1009185. doi: 10.1371/journal.ppat.1009185. eCollection 2020 Dec. PubMed PMID: 33370382; PubMed Central PMCID: PMC7793277.
Complete List of Published Work:
https://www.ncbi.nlm.nih.gov/sites/myncbi/chitra.upadhyay.1/collections/62448117/public/