Electronic Thesis and Dissertation Repository

Thesis Format



Master of Science


Microbiology and Immunology


Heit, Bryan


Antigen presentation by major histocompatibility complex class II (MHC II) to the adaptive immune system is crucial for mounting sterilizing immune responses. This central role has made antigen presentation a target for antagonism by many pathogens. Notably, infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) decrease MHC II expression in several immune cells. The mechanisms responsible for this suppression are unknown but involves either redirecting MHC II molecules away from the cell surface or inhibiting MHC II expression. To understand how pathogens manipulate intracellular MHC II trafficking, we first investigated the role of the Golgi trafficking regulator, ERC1, in this pathway, which we have previously confirmed is necessary for phagosome maturation. Immunofluorescence microscopy demonstrated that ERC1 facilitates the recruitment of MHC II to phagosomes, thereby enabling antigen loading and presentation. Interestingly, SARS-CoV-2 non-structural protein 5 (NSP5) interacts with histone deacetylase 2 (HDAC2)—a regulator of MHC II transcription—suggesting that SARS-CoV-2 may antagonize antigen presentation through epigenetic reprogramming. We hypothesize that SARS-CoV-2 NSP5 downregulates MHC II expression via interactions with HDAC2. RT-qPCR and dual luciferase analyses demonstrated that NSP5 expression was sufficient to downregulate MHC II in primary human dendritic cells and RAW 264.7 macrophages. HDAC2 knockdown alleviated this suppression, indicating that NSP5 utilizes host histone deacetylation machinery to antagonize MHC II transcription. Unexpectedly, point mutations that inactivate the catalytic site of NSP5 failed to revert this phenotype, suggesting that the proteolytic ability of NSP5 is not required for this suppression. This research may identify an important mechanism used by SARS-CoV-2 to evade adaptive immune responses and may indicate a potential use of HDAC2 inhibitors as therapeutics against coronavirus disease 19 (COVID-19).

Summary for Lay Audience

Every day we constantly encounter germs that can damage our bodies and cause debilitating diseases should they continue to persist. Our immune system fights off against infections through several ways. Particularly, specialized immune cells called phagocytes can eat microbes and break these microbes down into small pieces called antigens that are displayed on an MHC II molecule to communicate with other immune cells. To hide from the immune system, bacteria and viruses try to impair this process, either by decreasing MHC II levels or preventing MHC II from reaching the organelle where antigens reside. Surprisingly, it is unclear how MHC II is delivered to the antigen-containing organelle; hence, it is unknown how pathogens block this process. We discovered a protein called ERC1 that acts like a magnet by attracting MHC II to the antigen-containing organelle and allowing antigens to be presented to other immune cells. Interestingly, the virus responsible for COVID-19—SARS-CoV-2—interacts with components involved in controlling MHC II expression, suggesting that this virus targets these proteins to block MHC II from displaying antigens. We found that one of the viral proteins expressed by SARS-CoV-2, NSP5, can target another protein called HDAC2 to decrease MHC II levels in various immune cell types. In addition, modifying cells such that they no longer express HDAC2 restored MHC II levels. Together, these experiments help us better understand the functions of our immune system and how pathogens can persist in our bodies, such is the case in COVID-19. Using this information, it may be possible to develop better treatments to combat against COVID-19 and finally put an end to the pandemic.