Thursday, April 25, 2024: Sixue Chen – “Redox proteomics and metabolomics of guard cell immunity and CO2 response”

Dr Chen joins us from the University of Mississippi, where he is a professor and the chair of the Department of Biology. This event was co-sponsored by the Cornell University School of Integrative Plant Science, Plant Biology Section.

Redox proteomics and metabolomics of guard cell immunity and CO2 response

Pathogen infection and other environmental stresses have posed grand challenges to crop production and food security. Stomatal pores are major entry points of bacteria pathogens.How stomatal guard cells respond to pathogen invasion and other environmental factors(e.g., rising CO2) is an important question. Recently, we have reported a new redox proteomics method called cysTMTRAQ that combines two types of isobaric tags, isobaric tag for relative and absolute quantification (iTRAQ) and cysteine tandem mass tag (cysTMT) in one experiment. The method not only enables simultaneous analysis of cysteine redox changes and total protein level changes, but also allows determination of bona fide redox modified cysteines in proteins through correction of protein turnover. This technology has recently been applied to discover potential redox proteins in stomatal guard cells in response to a 22-aa peptide (flg22) of Pseudomonas syringae. cysTMTRAQ revealed 677 proteins containing cysteines with cysTMT labels, and 57 showing significant redox changes after flg22 treatment. As CO2 levels affect stomatal immunity, we studied CO2 signaling using metabolomics. A new signaling pathway involving jasmonic acid was discovered.

Thursday, March 28, 2024: Alexey Nesvizhskii – “FragPipe: A comprehensive computational platform for proteomics“

Dr Nesvizhskii joined us from the University of Michigan, where he is the Professor of Bioinformatics, Computational Medicine, Pathology and is the Director of the Proteomics Resource Facility.This event was co-sponsored by the Cornell University Department of Computational Biology.

FragPipe: A comprehensive computational platform for proteomics

I have been fascinated with the subject of the “dark proteome” since my entry in the field of proteomics in 2001. What are all those spectra that we cannot identify in a typical proteomics experiment, and how do we design efficient computational strategies to move beyond standard analyses. To this end, we have created a highly efficient peptide indexing algorithm and implemented it in an ultrafast peptide identification tool MSFragger, which has become the engine behind our widely used FragPipe computational platform. MSFragger have empowered new strategies for faster and more sensitive identification of biologically or chemically modified peptides. I will describe recent computational advances and applications of our algorithms, including methods for the identification of N- and O-linked glycopeptides, labile PTMs, as well as collaborative studies in the areas of single-cell proteomics and chemical proteomics. I will illustrate the power of our algorithms for the analysis of large-scale proteomics and immunopeptidomics datasets. I will also provide an overview of the various quantification workflows (DIA, TMT, LFQ-MBR) available in FragPipe supporting analysis of data across all major instrument platforms.

Thursday, February 22, 2024: Yonghao Yu – “Targeting Protein Poly-ADP-Ribosylation for the Development of Next Generation PARP Inhibitors”

Dr. Yu joined us from Columbia University Irving Medical Center, where he is a professor in the department of Molecular Pharmacology and Therapeutics. This event was co-sponsored by the Cornell University College of Veterinary Medicine.

Thursday, November 9, 2023: Savas Tay – “Understanding and modeling signaling networks by single-cell proteomics”

Dr Tay joined us from the Pritzker School of Molecular Engineering at the University of Chicago.

Understanding and modeling signaling networks by single-cell proteomics

Signaling pathways process a wide range of inputs whose type, concentration and dynamics constantly fluctuate [1], and aberrant signaling leads to inflammation, infection and cancer. We use microfluidic live cell imaging, single cell analysis and computational modeling to study spatial and temporal characteristics of signaling. I will show our recent results on how immune pathway NF-κB processes complex, combinatorial and dynamically changing pathogen and cytokine signals in single cells [2]. We found that single cell transcription factor dynamics leads to spatial “patterning” of pro and anti-inflammatory gene expression across a cell population [2]. Furthermore, I will introduce a new single cell proteomics technology, called proximity sequencing (Prox-seq), which enables simultaneous measurement of proteins, protein complexes and mRNA in thousands of individual cells [3, 4]. Prox-seq combines proximity ligation assay with single-cell sequencing to measure proteins and their complexes from all pairwise combinations of targeted proteins, providing quadratically-scaled multiplexing. We studied human peripheral blood mononuclear cells using Prox-seq, identified various cell types using protein readouts, and discovered that naïve CD8 T cells display a new protein complex CD8:CD9. We also studied protein interactions during toll-like receptor (TLR) signaling in human macrophages. We observe the formation and dissociation of signal-specific protein complexes and co-receptor activity, quantify signal integration under joint TLR4 and TLR2 stimulation, and show that quantification of protein complexes identifies signaling inputs received by single macrophages. Prox-seq provides access to an untapped measurement modality for single-cells, is practical and broadly applicable, and can discover new protein interactions in different cell types.

Thursday, October 26, 2023: Jacob Geri – “Photocatalytic Proximity Labeling”

Dr Geri joined us from Weill Cornell Medicine in New York City, where he is an Assistant Professor of Pharmacology and a member or the Meyer Cancer Center.

Photocatalytic Proximity Labeling

Interactions between proteins and other molecules are central to the architecture of life, and a lack of effective technologies for mapping these interactions is a major bottleneck in identifying actionable therapeutic targets. Widely used approaches for protein-protein interaction discovery suffer from a high rate of false positives (enzymatic proximity labeling) and false negatives (coIP-MS, crosslink-MS), while small molecule target-ID with photoaffinity labeling demands extensive empirical optimization of probe design. Photocatalytic proximity labeling, in which an iridium based photocatalyst generates reactive carbene-biotin conjugates via Dexter energy transfer, bypasses these limitations by affording high resolution (<4 nm) labeling of nearby biomolecules. Any targeting modality can be used to localize the photocatalyst, including small molecules, peptides, proteins, and antibodies, and the flexibility of the photocatalytic platform allows a user to dial in a desired labeling radius from nanometer to micrometer distance scales. The Geri lab at Weill Cornell Medicine focuses on the further development of μMap technology and its application towards currently inaccessible biological spaces, including single-cell interactomics, high throughput small molecule target identification, and expanding the activity based protein profiling concept beyond irreversibly reactive warheads.