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About my research

I am fascinated by the design principles governing biological systems and firmly believe that a profound understanding of these principles holds the key to significant scientific breakthroughs. During my PhD and postdoctoral research, I have been developing high-throughput techniques to unravel the mechanisms underlying the recruitment of ribosomes to mRNA, decipher determinants of transcriptional regulation, and uncover "hidden" T cell epitopes within viral genomes

Approaching fundamental questions in virology through the lens of systems biology offers a new perspective and the potential to address long-standing questions in the field. By employing interdisciplinary approaches encompassing computational biology, viral genomics, synthetic biology, immunology, and molecular genetics, I build new tools to systematically investigate virology, aiming to illuminate biological processes in hundreds of human-pathogenic viruses.

Viral immunology

T cell-mediated immunity plays a crucial role in controlling viral infections. While current vaccine design strategies primarily focus on T cell epitopes derived from well-known viral proteins, the significance of microproteins originating from non-canonical open reading frames (ORFs) in T cell immunity remains largely unexplored. Unveiling this 'hidden source' of T cell epitopes will enhance our understanding of the immune response to viruses and provide novel targets for vaccine development. During my postdoctoral research, I utilized immunopeptidome profiling to identify viral peptides that are naturally processed and presented on human leukocyte antigen (HLA) molecules to T cells in infected cells. I adapted this protocol to study high-containment viruses and led a multi-institutional team, providing the first comprehensive view of SARS-CoV-2 HLA-I and HLA-II peptides. Our untargeted approach revealed a remarkable enrichment of peptides derived from viral non-canonical ORFs bound to the HLA-I complex. Notably, some of these peptides elicited stronger T cell responses than the most immunogenic T cell epitopes known to date, underscoring the importance of considering this previously overlooked source as potential viral immune targets.

Relevant publications:

Weingarten-Gabbay S*✉, Klaeger S*✉, Sarkizova S*, Pearlman LR, Chen D-Y, …, Hacohen N, Carr SA, Abelin JG, Saeed M✉, Sabeti PC. Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs. Cell. 2021

> Featured on Cell’s cover, HFSP highlight, Broad Institute news, Boston University news

Weingarten-Gabbay S*✉, Chen D-Y*, Sarkizova S*, Taylor HB, Gentili M, Pearlman LR, Bauer MR, Rice CM, Clauser KR, Hachoen N, Carr SA, Abelin JG, Saeed M, Sabeti PC. The HLA-II immunopeptidome of SARS-CoV-2. Cell Reports. 2023

Weingarten-Gabbay S*✉, Pearlman LR*, Chen D-Y, Klaeger S, Taylor HB, Welch NL, Keskin DB, Carr SA, Abelin JG, Saeed M, Sabeti PC. HLA-I immunopeptidome profiling of human cells infected with high-containment enveloped viruses. STAR protocols. 2022

Taylor HB, Klaeger S, Clauser KR, Sarkizova S, Weingarten-Gabbay S, Graham DB, Carr SA, Abelin JG. MS-based HLA-II peptidomics combined with multi-omics will aid the development of future immunotherapies. Mol Cell Proteomics. 2021

Translational control

In addition to the recognized "cap" structure at the beginning of eukaryotic mRNAs, ribosomes can initiate translation independently using an RNA element called internal ribosome entry site (IRES). IRESs play crucial roles in synthesizing human and viral proteins, but only handful of IRESs were detected and their recruitment mechanisms were largely unknown. During my PhD, I developed a high-throughput reporter assay to quantify IRES activity across 55,000 designed sequences in a single experiment. This led to the discovery of thousands of cellular and viral IRESs, greatly expanding our knowledge in this area. I characterized three mechanisms of IRES regulation: secondary structure formation, local sequence motifs, and complementarity to the 18S rRNA. Surprisingly, IRESs were found to be enriched in human 3'UTRs and the polyprotein region of RNA viruses. By employing machine learning, we identified sequence motifs governing IRES activity and revealed the spatial organization of these features in RNA.

Relevant publications:

Weingarten-Gabbay S, Elias-Kirma S, Nir R, Gritsenko AA, Yakhini Z, Stern-Ginossar N, Weinberger A and Segal E. Systematic discovery of cap-independent translation sequences in human and viral genomes. Science. 2016

>Perspective in Science, Highlight in Cell Systems, Faculty of 1000 review

Weingarten-Gabbay S and Segal E. Toward a systematic understanding of translational regulatory elements in human and viruses. RNA Biology. 2016.

Gritsenko AA*, Weingarten-Gabbay S*, Elias-Kirma S, Nir R, de Ridder D and Segal E. Sequence features of viral and human internal ribosome entry sites predictive of their activity. PLoS Comp Biol. 2017

Weingarten-Gabbay S*, Khan D*, Liberman N, Yoffe Y, Bialik S, Das S, Oren M and Kimchi A. The translation initiation factor DAP5 promotes IRES-driven translation of p53 mRNA. Oncogene. 2013

Hernández G, García A, Weingarten-Gabbay S, Mishra RK, Hussain T, Amiri M, Moreno-Hagelsieb G, Montiel-Dávalos A, Lasko P, Sonenberg N. Functional analysis of the AUG initiator codon context reveals novel conserved sequences that disfavor mRNA translation in eukaryotes. NAR. 2023

Finkel Y*, Mizrahi O*, Nachshon A, Weingarten-Gabbay S, Yahalom-Ronen Y, Tamir H, Achdout H, Melamed S, Weiss S, Israely T, Paran N, Schwartz M and Stern-Ginossar N. The coding capacity of SARS-CoV-2. Nature. 2020

David M, Olender T, Mizrahi O, Weingarten-Gabbay S, Friedlander G, Savidor A, Levin Y, Salomon V, Stern-Ginossar N, Bialik S and Kimchi A. DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells. RNA. 2022


Chen CK, Cheng R, Demeter J, Chen J, Weingarten-Gabbay S, Jiang L, Snyder MP, Weissman JS, Segal E, Jackson PK and Chang HY. Structured elements drive extensive circular RNA translation. Molecular Cell. 2021.

Transcriptional regulation

Despite progress in identifying DNA elements involved in transcriptional regulation, a key remaining question is how the arrangement and combination of these elements orchestrate a transcriptional output. During my PhD, I developed a Massively Parallel Reporter Assay (MPRA) to quantify transcription levels of synthetic promoters at a fixed location in the human genome. Utilizing a set of 15,000 designed promoters, I extensively investigated the 'grammatical rules' of transcriptional regulation. Through this study, I characterized various cis-regulatory elements, including core promoter elements, TF binding sites, and nucleosome-disfavoring sequences. By exploring diverse configurations and distances, I precisely quantified the individual effects of each element on gene expression and analyzed their spatial interactions. Furthermore, I conducted a comprehensive screening of hundreds of TF binding sites, uncovering the factor-specific impact of binding site numbers on gene expression. These findings shed light on the organizational principles of homotypic clusters in the human genome.

Relevant publications:

Weingarten-Gabbay S*✉, Nir R*, Lubliner S, Sharon E, Kalma Y, Weinberger A and Segal E✉. Systematic interrogation of human promoters. Genome Research. 2019

Weingarten-Gabbay S and Segal E. The grammar of transcriptional regulation. Human Genetics. 2014

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