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Classification of psychedelics and psychoactive drugs based on brain-wide imaging of cellular c-Fos expression. 根据细胞 c-Fos 表达的全脑成像对迷幻药进行分类。
bioRxiv : the preprint server for biology Pub Date : 2024-11-07 DOI: 10.1101/2024.05.23.590306
Farid Aboharb, Pasha A Davoudian, Ling-Xiao Shao, Clara Liao, Gillian N Rzepka, Cassandra Wojtasiewicz, Mark Dibbs, Jocelyne Rondeau, Alexander M Sherwood, Alfred P Kaye, Alex C Kwan
{"title":"Classification of psychedelics and psychoactive drugs based on brain-wide imaging of cellular c-Fos expression.","authors":"Farid Aboharb, Pasha A Davoudian, Ling-Xiao Shao, Clara Liao, Gillian N Rzepka, Cassandra Wojtasiewicz, Mark Dibbs, Jocelyne Rondeau, Alexander M Sherwood, Alfred P Kaye, Alex C Kwan","doi":"10.1101/2024.05.23.590306","DOIUrl":"10.1101/2024.05.23.590306","url":null,"abstract":"<p><p>Psilocybin, ketamine, and MDMA are psychoactive compounds that exert behavioral effects with distinguishable but also overlapping features. The growing interest in using these compounds as therapeutics necessitates preclinical assays that can accurately screen psychedelics and related analogs. We posit that a promising approach may be to measure drug action on markers of neural plasticity in native brain tissues. We therefore developed a pipeline for drug classification using light sheet fluorescence microscopy of immediate early gene expression at cellular resolution followed by machine learning. We tested male and female mice with a panel of drugs, including psilocybin, ketamine, 5-MeO-DMT, 6-fluoro-DET, MDMA, acute fluoxetine, chronic fluoxetine, and vehicle. In one-versus-rest classification, the exact drug was identified with 67% accuracy, significantly above the chance level of 12.5%. In one-versus-one classifications, psilocybin was discriminated from 5-MeO-DMT, ketamine, MDMA, or acute fluoxetine with >95% accuracy. We used Shapley additive explanation to pinpoint the brain regions driving the machine learning predictions. Our results support a novel approach for characterizing and validating psychoactive drugs with psychedelic properties.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11142187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141201443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
moPepGen: Rapid and Comprehensive Identification of Non-canonical Peptides. moPepGen:快速、全面的蛋白质形式鉴定。
bioRxiv : the preprint server for biology Pub Date : 2024-11-05 DOI: 10.1101/2024.03.28.587261
Chenghao Zhu, Lydia Y Liu, Annie Ha, Takafumi N Yamaguchi, Helen Zhu, Rupert Hugh-White, Julie Livingstone, Yash Patel, Thomas Kislinger, Paul C Boutros
{"title":"moPepGen: Rapid and Comprehensive Identification of Non-canonical Peptides.","authors":"Chenghao Zhu, Lydia Y Liu, Annie Ha, Takafumi N Yamaguchi, Helen Zhu, Rupert Hugh-White, Julie Livingstone, Yash Patel, Thomas Kislinger, Paul C Boutros","doi":"10.1101/2024.03.28.587261","DOIUrl":"10.1101/2024.03.28.587261","url":null,"abstract":"<p><p>Gene expression is a multi-step transformation of biological information from its storage form (DNA) into functional forms (protein and some RNAs). Regulatory activities at each step of this transformation multiply a single gene into a myriad of proteoforms. Proteogenomics is the study of how genomic and transcriptomic variation creates this proteomic diversity, and is limited by the challenges of modeling the complexities of gene-expression. We therefore created moPepGen, a graph-based algorithm that comprehensively generates non-canonical peptides in linear time. moPepGen works with multiple technologies, in multiple species and on all types of genetic and transcriptomic data. In human cancer proteomes, it enumerates previously unobservable noncanonical peptides arising from germline and somatic genomic variants, noncoding open reading frames, RNA fusions and RNA circularization. By enabling efficient detection and quantitation of previously hidden proteins in both existing and new proteomic data, moPepGen facilitates all proteogenomics applications. It is available at: https://github.com/uclahs-cds/package-moPepGen.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10996593/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140867388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Joint representation and visualization of derailed cell states with Decipher. 深度生成模型解读急性髓性白血病的脱轨轨迹。
bioRxiv : the preprint server for biology Pub Date : 2024-11-05 DOI: 10.1101/2023.11.11.566719
Achille Nazaret, Joy Linyue Fan, Vincent-Philippe Lavallée, Cassandra Burdziak, Andrew E Cornish, Vaidotas Kiseliovas, Robert L Bowman, Ignas Masilionis, Jaeyoung Chun, Shira E Eisman, James Wang, Justin Hong, Lingting Shi, Ross L Levine, Linas Mazutis, David Blei, Dana Pe'er, Elham Azizi
{"title":"Joint representation and visualization of derailed cell states with Decipher.","authors":"Achille Nazaret, Joy Linyue Fan, Vincent-Philippe Lavallée, Cassandra Burdziak, Andrew E Cornish, Vaidotas Kiseliovas, Robert L Bowman, Ignas Masilionis, Jaeyoung Chun, Shira E Eisman, James Wang, Justin Hong, Lingting Shi, Ross L Levine, Linas Mazutis, David Blei, Dana Pe'er, Elham Azizi","doi":"10.1101/2023.11.11.566719","DOIUrl":"10.1101/2023.11.11.566719","url":null,"abstract":"<p><p>Biological insights often depend on comparing conditions such as disease and health, yet we lack effective computational tools for integrating single-cell genomics data across conditions or characterizing transitions from normal to deviant cell states. Here, we present Decipher, a deep generative model that characterizes derailed cell-state trajectories. Decipher jointly models and visualizes gene expression and cell state from normal and perturbed single-cell RNA-seq data, revealing shared and disrupted dynamics. We demonstrate its superior performance across diverse contexts, including in pancreatitis with oncogene mutation, acute myeloid leukemia, and gastric cancer.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10680623/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138447756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis. iPSC衍生神经元的CRISPR筛选揭示了tau蛋白稳定的原理。
bioRxiv : the preprint server for biology Pub Date : 2024-11-04 DOI: 10.1101/2023.06.16.545386
Avi J Samelson, Nabeela Ariqat, Justin McKetney, Gita Rohanitazangi, Celeste Parra Bravo, Rudra Bose, Kyle J Travaglini, Victor L Lam, Darrin Goodness, Gary Dixon, Emily Marzette, Julianne Jin, Ruilin Tian, Eric Tse, Romany Abskharon, Henry Pan, Emma C Carroll, Rosalie E Lawrence, Jason E Gestwicki, David Eisenberg, Nicholas M Kanaan, Daniel R Southworth, John D Gross, Li Gan, Danielle L Swaney, Martin Kampmann
{"title":"CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis.","authors":"Avi J Samelson, Nabeela Ariqat, Justin McKetney, Gita Rohanitazangi, Celeste Parra Bravo, Rudra Bose, Kyle J Travaglini, Victor L Lam, Darrin Goodness, Gary Dixon, Emily Marzette, Julianne Jin, Ruilin Tian, Eric Tse, Romany Abskharon, Henry Pan, Emma C Carroll, Rosalie E Lawrence, Jason E Gestwicki, David Eisenberg, Nicholas M Kanaan, Daniel R Southworth, John D Gross, Li Gan, Danielle L Swaney, Martin Kampmann","doi":"10.1101/2023.06.16.545386","DOIUrl":"10.1101/2023.06.16.545386","url":null,"abstract":"<p><p>Aggregation of the protein tau defines tauopathies, which include Alzheimer's disease and frontotemporal dementia. Specific neuronal subtypes are selectively vulnerable to tau aggregation and subsequent dysfunction and death, but the underlying mechanisms are unknown. To systematically uncover the cellular factors controlling the accumulation of tau aggregates in human neurons, we conducted a genome-wide CRISPRi-based modifier screen in iPSC-derived neurons. The screen uncovered expected pathways, including autophagy, but also unexpected pathways, including UFMylation and GPI anchor synthesis. We discover that the E3 ubiquitin ligase CUL5<sup>SOCS4</sup> is a potent modifier of tau levels in human neurons, ubiquitinates tau, and is a correlated with vulnerability to tauopathies in mouse and human. Disruption of mitochondrial function promotes proteasomal misprocessing of tau, which generates tau proteolytic fragments like those in disease and changes tau aggregation <i>in vitro</i>. These results reveal new principles of tau proteostasis in human neurons and pinpoint potential therapeutic targets for tauopathies.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10131792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Discovery of a multipotent cell type from the term human placenta. 从人胎盘中发现一种多能细胞。
bioRxiv : the preprint server for biology Pub Date : 2024-11-03 DOI: 10.1101/2023.08.02.551028
Sangeetha Vadakke-Madathil, Esmaa Bouhamida, Bingyan Wang, Prabhu Mathiyalagan, Micayla Oniskey, Carlos Santos-Gallego, Michael Hadley, Lori Croft, Fumiko Dekio, Rachel Brody, Shari Gelber, Rhoda Sperling, Hina W Chaudhry
{"title":"Discovery of a multipotent cell type from the term human placenta.","authors":"Sangeetha Vadakke-Madathil, Esmaa Bouhamida, Bingyan Wang, Prabhu Mathiyalagan, Micayla Oniskey, Carlos Santos-Gallego, Michael Hadley, Lori Croft, Fumiko Dekio, Rachel Brody, Shari Gelber, Rhoda Sperling, Hina W Chaudhry","doi":"10.1101/2023.08.02.551028","DOIUrl":"10.1101/2023.08.02.551028","url":null,"abstract":"<p><p>We report a population of multipotent cells isolated from term human placentas, for the first time, that differentiates into cardiomyocytes and vascular cells with clonal ability, migratory ability, and trancriptomic evidence of immune privilege. Caudal-type homeobox-2 (CDX2) is a conserved factor that regulates trophectoderm formation and placentation during early embryonic development but has not previously been implicated in developmentally conserved regenerative mechanisms. We earlier reported that murine Cdx2 cells restored cardiac function after intravenous delivery in male mice with experimental myocardial infarction (MI). Here we demonstrate that CDX2 cells found in human chorion are poised for cardiovascular differentiation. We isolated CDX2 cells from term placentas of 150 healthy patients and showed that they spontaneously differentiate into cardiomyocytes, functional vascular cells, and retain homing ability in vitro with a transcriptome that supports enhanced cardiogenesis, vasculogenesis, immune modulation, and chemotaxis gene signatures. They restore cardiac function when administered to NOD/SCID mice subjected to MI. CDX2 cells can be clonally propagated in culture with retention of cardiovascular differentiation. Our data compels further use of this ethically feasible cell source in the design of therapeutic strategies for cardiovascular disease.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10418244/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9991211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Regulation of NRF2 by Phosphoinositides and Small Heat Shock Proteins. 磷酸肌苷和小热休克蛋白对NRF2的调控。
bioRxiv : the preprint server for biology Pub Date : 2024-11-01 DOI: 10.1101/2023.10.26.564194
Changliang Chen, Mo Chen, Tianmu Wen, Poorwa Awasthi, Noah D Carrillo, Richard A Anderson, Vincent L Cryns
{"title":"Regulation of NRF2 by Phosphoinositides and Small Heat Shock Proteins.","authors":"Changliang Chen, Mo Chen, Tianmu Wen, Poorwa Awasthi, Noah D Carrillo, Richard A Anderson, Vincent L Cryns","doi":"10.1101/2023.10.26.564194","DOIUrl":"10.1101/2023.10.26.564194","url":null,"abstract":"<p><p>Reactive oxygen species (ROS) are generated by aerobic metabolism, and their deleterious effects are buffered by the cellular antioxidant response, which prevents oxidative stress. The nuclear factor erythroid 2-related factor 2 (NRF2) is a master transcriptional regulator of the antioxidant response. Basal levels of NRF2 are kept low by ubiquitin-dependent degradation of NRF2 by E3 ligases, including the Kelch-like ECH-associated protein 1 (KEAP1). Here, we show that the stability and function of NRF2 is regulated by the type I phosphatidylinositol phosphate kinase γ (PIPKIγ), which binds NRF2 and transfers its product phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P <sub>2</sub> ) to NRF2. PtdIns(4,5)P <sub>2</sub> binding recruits the small heat shock protein HSP27 to the complex. Silencing PIPKIγ or HSP27 destabilizes NRF2, reduces expression of its target gene HO-1, and sensitizes cells to oxidative stress. These data demonstrate an unexpected role of phosphoinositides and HSP27 in regulating NRF2 and point to PIPKIγ and HSP27 as drug targets to destabilize NRF2 in cancer.</p><p><strong>In brief: </strong>Phosphoinositides are coupled to NRF2 by PIPKIγ, and HSP27 is recruited and stabilizes NRF2, promoting stress-resistance.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10634847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92157925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Phenotypic complexities of rare heterozygous neurexin-1 deletions. 不同NRXN1+/-突变的精确治疗靶向。
bioRxiv : the preprint server for biology Pub Date : 2024-11-01 DOI: 10.1101/2023.10.28.564543
Michael B Fernando, Yu Fan, Yanchun Zhang, Alex Tokolyi, Aleta N Murphy, Sarah Kammourh, P J Michael Deans, Sadaf Ghorbani, Ryan Onatzevitch, Adriana Pero, Christopher Padilla, Sarah Williams, Erin K Flaherty, Iya A Prytkova, Lei Cao, David A Knowles, Gang Fang, Paul A Slesinger, Kristen J Brennand
{"title":"Phenotypic complexities of rare heterozygous neurexin-1 deletions.","authors":"Michael B Fernando, Yu Fan, Yanchun Zhang, Alex Tokolyi, Aleta N Murphy, Sarah Kammourh, P J Michael Deans, Sadaf Ghorbani, Ryan Onatzevitch, Adriana Pero, Christopher Padilla, Sarah Williams, Erin K Flaherty, Iya A Prytkova, Lei Cao, David A Knowles, Gang Fang, Paul A Slesinger, Kristen J Brennand","doi":"10.1101/2023.10.28.564543","DOIUrl":"10.1101/2023.10.28.564543","url":null,"abstract":"<p><p>Given the large number of genes significantly associated with risk for neuropsychiatric disorders, a critical unanswered question is the extent to which diverse mutations --sometimes impacting the same gene-- will require tailored therapeutic strategies. Here we consider this in the context of rare neuropsychiatric disorder-associated copy number variants (2p16.3) resulting in heterozygous deletions in <i>NRXN1</i>, a pre-synaptic cell adhesion protein that serves as a critical synaptic organizer in the brain. Complex patterns of <i>NRXN1</i> alternative splicing are fundamental to establishing diverse neurocircuitry, vary between the cell types of the brain, and are differentially impacted by unique (non-recurrent) deletions. We contrast the cell-type-specific impact of patient-specific mutations in <i>NRXN1</i> using human induced pluripotent stem cells, finding that perturbations in <i>NRXN1</i> splicing result in divergent cell-type-specific synaptic outcomes. Via distinct loss-of-function (LOF) and gain-of-function (GOF) mechanisms, <i>NRXN1</i> <sup>+/-</sup> deletions cause decreased synaptic activity in glutamatergic neurons, yet increased synaptic activity in GABAergic neurons. Reciprocal isogenic manipulations causally demonstrate that aberrant splicing drives these changes in synaptic activity. For <i>NRXN1</i> deletions, and perhaps more broadly, precision medicine will require stratifying patients based on whether their gene mutations act through LOF or GOF mechanisms, in order to achieve individualized restoration of <i>NRXN1</i> isoform repertoires by increasing wildtype, or ablating mutant isoforms. Given the increasing number of mutations predicted to engender both LOF and GOF mechanisms in brain disorders, our findings add nuance to future considerations of precision medicine.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10634884/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92157896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mediator Subunit Med4 Enforces Metastatic Dormancy in Breast Cancer. 通过整合素信号的表观遗传控制,Med4作为转移的守门人的非典型活性。
bioRxiv : the preprint server for biology Pub Date : 2024-11-01 DOI: 10.1101/2023.11.18.566087
Seong-Yeon Bae, Hsiang-Hsi Ling, Yi Chen, Hong Chen, Dhiraj Kumar, Jiankang Zhang, Aaron D Viny, Ronald A DePinho, Filippo G Giancotti
{"title":"Mediator Subunit Med4 Enforces Metastatic Dormancy in Breast Cancer.","authors":"Seong-Yeon Bae, Hsiang-Hsi Ling, Yi Chen, Hong Chen, Dhiraj Kumar, Jiankang Zhang, Aaron D Viny, Ronald A DePinho, Filippo G Giancotti","doi":"10.1101/2023.11.18.566087","DOIUrl":"10.1101/2023.11.18.566087","url":null,"abstract":"<p><p>Long term survival of breast cancer patients is limited due to recurrence from metastatic dormant cancer cells. However, the mechanisms by which these dormant breast cancer cells survive and awaken remain poorly understood. Our unbiased genome-scale genetic screen in mice identified <i>Med4</i> as a novel cancer-cell intrinsic gatekeeper in metastatic reactivation. <i>MED4</i> haploinsufficiency is prevalent in metastatic breast cancer patients and correlates with poorer prognosis. Syngeneic xenograft models revealed that <i>Med4</i> enforces breast cancer dormancy. Contrary to the canonical function of the Mediator complex in activating gene expression, <i>Med4</i> maintains 3D chromatin compaction and enhancer landscape, by preventing enhancer priming or activation through the suppression of H3K4me1 deposition. <i>Med4</i> haploinsufficiency disrupts enhancer poise and reprograms the enhancer dynamics to facilitate extracellular matrix (ECM) gene expression and integrin-mediated mechano-transduction, driving metastatic growth. Our findings establish <i>Med4</i> as a key regulator of cellular dormancy and a potential biomarker for high-risk metastatic relapse.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10680920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138447751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Entropy Changes in Water Networks Promote Protein Denaturation. 熵驱动变性,实现蛋白质废弃物的可持续再生。
bioRxiv : the preprint server for biology Pub Date : 2024-11-01 DOI: 10.1101/2024.06.12.598657
Yichong Wang, Junlang Liu, Michael M Peters, Ryoma Ishii, Dianzhuo Wang, Sourav Chowdhury, Kevin Kit Parker, Eugene I Shakhnovich
{"title":"Entropy Changes in Water Networks Promote Protein Denaturation.","authors":"Yichong Wang, Junlang Liu, Michael M Peters, Ryoma Ishii, Dianzhuo Wang, Sourav Chowdhury, Kevin Kit Parker, Eugene I Shakhnovich","doi":"10.1101/2024.06.12.598657","DOIUrl":"10.1101/2024.06.12.598657","url":null,"abstract":"<p><p>For over a century, an explanation for how concentrated ions denature proteins has proven elusive. Here, we report a novel mechanism of protein denaturation driven by entropy changes in water networks. Experiments and simulations show that ion pairs like LiBr and LiCl localize water molecules and disrupt the water network's structure, while others exert a more global effect without compromising network integrity. This disruption reduces the entropy penalty when proteins sequester water molecules during unfolding, resulting in a peculiar yet universal \"inverse hydrophobic effect\" that potentiates protein denaturation. Through successful isolation and systematic study of indirect solute effects, our findings offer a universal approach to salt induced protein denaturation and provide a unified framework for the decoding of the protein-water-solute nexus.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11195181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141447688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Pharmacological inhibition of astrocytic transglutaminase 2 facilitates the expression of a neurosupportive astrocyte reactive phenotype in association with increased histone acetylation. 药理抑制星形胶质细胞转谷氨酰胺酶 2 可促进神经支持性星形胶质细胞反应表型的表达,同时增加组蛋白乙酰化。
bioRxiv : the preprint server for biology Pub Date : 2024-10-31 DOI: 10.1101/2023.02.06.527263
Thomas Delgado, Jacen Emerson, Matthew Hong, Jeffrey W Keillor, Gail Vw Johnson
{"title":"Pharmacological inhibition of astrocytic transglutaminase 2 facilitates the expression of a neurosupportive astrocyte reactive phenotype in association with increased histone acetylation.","authors":"Thomas Delgado, Jacen Emerson, Matthew Hong, Jeffrey W Keillor, Gail Vw Johnson","doi":"10.1101/2023.02.06.527263","DOIUrl":"10.1101/2023.02.06.527263","url":null,"abstract":"<p><p>Astrocytes play critical roles in supporting structural and metabolic homeostasis in the central nervous system (CNS). CNS injury leads to the development of a range of reactive phenotypes in astrocytes whose molecular determinants are poorly understood. Finding ways to modulate astrocytic injury responses and leverage a pro-recovery phenotype holds promise in treating CNS injury. Recently, it has been demonstrated that ablation of astrocytic transglutaminase 2 (TG2) modulates the phenotype of reactive astrocytes in a way that improves neuronal injury outcomes both <i>in vitro</i> and <i>in vivo</i>. In an <i>in vivo</i> mouse model, pharmacological inhibition of TG2 with the irreversible inhibitor VA4 phenocopies the neurosupportive effects of TG2 deletion in astrocytes. In this study, we provide insights into the mechanisms by which TG2 deletion or inhibition result in a more neurosupportive astrocytic phenotype. Using a neuron-astrocyte co-culture model, we show that VA4 treatment improves the ability of astrocytes to support neurite outgrowth on an injury-relevant matrix. To better understand how pharmacologically altering TG2 affects its ability to regulate reactive astrocyte phenotypes, we assessed how VA4 inhibition impacts TG2's interaction with Zbtb7a, a transcription factor we have previously identified as a functionally relevant TG2 nuclear interactor. The results of these studies demonstrate that VA4 significantly decreases the interaction of TG2 and Zbtb7a. TG2's interactions with Zbtb7a, as well as a wide range of other transcription factors and chromatin regulatory proteins, suggest that TG2 may act as an epigenetic regulator to modulate gene expression. To begin to understand if TG2-mediated epigenetic modification may impact astrocytic phenotypes in our models, we interrogated the effect of TG2 deletion and VA4 treatment on histone acetylation and found significantly greater acetylation in both experimental groups. Consistent with these findings, previous RNA-sequencing and our present proteomic analysis also supported a predominant transcriptionally suppressive role of TG2 in astrocytes. Our proteomic data additionally unveiled pronounced changes in lipid and antioxidant metabolism in astrocytes with TG2 deletion or inhibition, which likely contribute to the enhanced neurosupportive function of these astrocytes.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f4/7d/nihpp-2023.02.06.527263v1.PMC9934526.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9694622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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