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Biology subjects

Estrada, L.

Publications and source records attributed to Estrada, L..

2 recordsLinked to original sources

Chemical proteomics decrypts the kinases that shape the dynamic human phosphoproteome

Mass-spectrometry-based phosphoproteomics enables the analysis of thousands of protein phosphorylation events across the human proteome. However, there is a lack of scalable, hypothesis-free, and statistically sound approaches for discovering, evaluating, and falsifying kinase::substrate relationships (KSRs). Here, we developed a new concept termed potency-coherence analysis. By measuring and integrating 17 million peptidoform-specific dose-response curves for 133 kinase inhibitors with known targets and affinities, we could critically re-evaluate published KSRs and discover thousands of potency-coherent and motif-plausible new KSRs for 96 human kinases. Application of these high-confidence KSRs enabled the estimation of kinase and signaling pathway activities in cancer patient biopsies. This unified and extendable framework has been implemented in ProteomicsDB to aid researchers in understanding the human phosphoproteome in health and disease.

systems biology↗

Adrenergic signaling controls early transcriptional programs during CD8+ T cell responses to viral infection

Viral infections drive the expansion and differentiation of responding CD8+ T cells into variegated populations of cytolytic effector and memory cells. While pro-inflammatory cytokines and cell surface immune receptors play a key role in guiding T cell responses to infection, T cells are also markedly influenced by neurotransmitters. Norepinephrine is a key sympathetic neurotransmitter, which acts to suppress CD8 + T cell cytokine secretion and lytic activity by signaling through the {beta}2-adrenergic receptor (ADRB2). Although ADRB2 signaling is considered generally immunosuppressive, its role in regulating differentiation of effector T cells in response to infection has not been investigated. Using an adoptive transfer approach, we compared the expansion and differentiation of wild type (WT) to Adrb2-/- CD8 + T cells throughout the primary response to vesicular stomatitis virus (VSV) infection in vivo. We measured the dynamic changes in transcriptome profiles of antigen-specific CD8 + T cells as they responded to VSV. Within the first 7 days of infection, WT cells out-paced the expansion of Adrb2-/- cells, which correlated with reduced expression of IL-2 and the IL-2R in the absence of ADRB2. RNASeq analysis identified over 300 differentially expressed genes that were both temporally regulated following infection and selectively regulated in WT vs Adrb2-/- cells. These genes contributed to major transcriptional pathways including cytokine receptor activation, signaling in cancer, immune deficiency, and neurotransmitter pathways. By parsing genes within groups that were either induced or repressed over time in response to infection, we identified three main branches of genes that were differentially regulated by the ADRB2. These gene sets were predicted to be regulated by specific transcription factors involved in effector T cell development, such as Tbx21 and Eomes. Collectively, these data demonstrate a significant role for ADRB2 signaling in regulating key transcriptional pathways during CD8 + T cells responses to infection that may dramatically impact their functional capabilities and downstream memory cell development.

immunology↗