Shayan C. Avanessian
A5076296892- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Ferroptosis and cancer prognosis
- Advanced Proteomics Techniques and Applications
- Immune Cell Function and Interaction
- Ubiquitin and proteasome pathways
- Lung Cancer Treatments and Mutations
- Gene expression and cancer classification
- Biomedical Text Mining and Ontologies
- Cancer, Hypoxia, and Metabolism
- 3D Printing in Biomedical Research
- Machine Learning in Bioinformatics
- Immune cells in cancer
- Bioinformatics and Genomic Networks
- Epigenetics and DNA Methylation
- interferon and immune responses
- Lung Cancer Research Studies
Brotman Baty Institute
2024
University of Washington
2024
Fred Hutch Cancer Center
2023-2024
Broad Institute
2019-2021
Massachusetts Institute of Technology
2019-2021
To explore the biology of lung adenocarcinoma (LUAD) and identify new therapeutic opportunities, we performed comprehensive proteogenomic characterization 110 tumors 101 matched normal adjacent tissues (NATs) incorporating genomics, epigenomics, deep-scale proteomics, phosphoproteomics, acetylproteomics. Multi-omics clustering revealed four subgroups defined by key driver mutations, country, gender. Proteomic phosphoproteomic data illuminated downstream copy number aberrations, somatic...
The integration of mass spectrometry-based proteomics with next-generation DNA and RNA sequencing profiles tumors more comprehensively. Here this "proteogenomics" approach was applied to 122 treatment-naive primary breast cancers accrued preserve post-translational modifications, including protein phosphorylation acetylation. Proteogenomics challenged standard cancer diagnoses, provided detailed analysis the ERBB2 amplicon, defined tumor subsets that could benefit from immune checkpoint...
Isobaric stable isotope labeling using, for example, tandem mass tags (TMTs) is increasingly being applied large-scale proteomic studies. Experiments focusing on proteoform analysis in drug time course or perturbation studies large patient cohorts greatly benefit from the reproducible quantification of single peptides across samples. However, such often require hundreds micrograms that cost reagents represents a major contribution to overall an experiment. Here, we describe and evaluate...
Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape LSCC, providing deeper exposition LSCC biology potential implications. identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 overexpressing target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such LSD1 EZH2 to SOX2-overexpressing tumors. Our data support...
We present a proteogenomic study of 108 human papilloma virus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs). Proteomic analysis systematically catalogs HNSCC-associated proteins phosphosites, prioritizes copy number drivers, highlights an oncogenic role for RNA processing genes. investigation mutual exclusivity between FAT1 truncating mutations 11q13.3 amplifications reveals dysregulated actin dynamics as common functional consequence. Phosphoproteomics characterizes two...
The accuracy of crucial nuclear processes such as transcription, replication, and repair, depends on the local composition chromatin regulatory proteins that reside there. Understanding these DNA-protein interactions at level specific genomic loci has remained challenging due to technical limitations. Here, we introduce a method termed “DNA O-MAP”, which uses programmable peroxidase-conjugated oligonucleotide probes biotinylate nearby proteins. We show DNA O-MAP can be coupled with sample...
The accuracy of crucial nuclear processes such as transcription, replication, and repair, depends on the local composition chromatin regulatory proteins that reside there. Understanding these DNA-protein interactions at level specific genomic loci has remained challenging due to technical limitations. Here, we introduce a method termed "DNA O-MAP", which uses programmable peroxidase-conjugated oligonucleotide probes biotinylate nearby proteins. We show DNA O-MAP can be coupled with sample...
Abstract Natural killer (NK) cells are an innate lymphocyte population that have inherent ability to recognize and eliminate malignant without requiring prior sensitization. However, NK more than just a of killers—they prominent producers cytokines chemokines, lending them pivotal orchestrate robust immune responses involving other cell types. We previously shown in the tumor microenvironment (TME) critical regulators type one conventional dendritic (cDC1s), which required for protective...
The accuracy of crucial nuclear processes such as transcription, replication, and repair, depends on the local composition chromatin regulatory proteins that reside there. Understanding these DNA-protein interactions at level specific genomic loci has remained challenging due to technical limitations. Here, we introduce a method termed “DNA O-MAP”, which uses programmable peroxidase-conjugated oligonucleotide probes biotinylate nearby proteins. We show DNA O-MAP can be coupled with sample...
Abstract Natural killer (NK) cell abundance in the tumor correlates with increased immunotherapy responses and better survival cancer patients. As their name suggests, NK cells can control tumors through direct cytotoxicity, but also play an important part regulating immune immunomodulatory production of cytokines chemokines. We recently discovered that a cytokine called FMS-like tyrosine kinase 3 ligand (Flt3L) tumor, which regulates type 1 conventional dendritic (cDC1) abundance. However,...