bioRxiv Channel: SCORCH https://biorxiv.org This feed contains articles for bioRxiv Channel "SCORCH" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Morphine Suppresses Peripheral Responses and Transforms Brain Myeloid Gene Expression to Favor Neuropathogenesis in SIV Infection ]]> https://biorxiv.org/cgi/content/short/2022.07.25.501436v1?rss=1" Fox, H. S. Niu, M. Morsey, B. M. Lamberty, B. G. Emanuel, K. Periyasamy, P. Callen, S. Acharya, A. Kubik, G. Eudy, J. D. Guda, C. Dyavar, S. R. Fletcher, C. V. Byrareddy, S. Buch, S. 2022-07-27 doi:10.1101/2022.07.25.501436 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ ScISOr-ATAC reveals convergent and divergent splicing and chromatin specificities between matched cell types across cortical regions, evolution, and in Alzheimer's disease. ]]> https://biorxiv.org/cgi/content/short/2024.02.24.581897v1?rss=1" Hu, W. Foord, C. Hsu, J. Fan, L. Corley, M. J. Bhatia, T. N. Xu, S. Belchikov, N. He, Y. Pang, A. P. Lanjewar, S. N. Jarroux, J. Joglekar, A. Milner, T. A. Ndhlovu, L. Zhang, J. Butelman, E. Sloan, S. A. Lee, V. M. Gan, L. Tilgner, H. U. 2024-02-28 doi:10.1101/2024.02.24.581897 Cold Spring Harbor Laboratory Press 2024-02-28 <![CDATA[ Principled PCA separates signal from noise in omics count data ]]> https://biorxiv.org/cgi/content/short/2025.02.03.636129v1?rss=1" Stanley, J. S. Yang, J. Li, R. Lindenbaum, O. Kobak, D. Landa, B. Kluger, Y. 2025-02-07 doi:10.1101/2025.02.03.636129 Cold Spring Harbor Laboratory Press 2025-02-07 <![CDATA[ Transcriptional impacts of substance use disorder and HIV on human ventral midbrain neurons and microglia ]]> https://biorxiv.org/cgi/content/short/2025.02.05.636667v1?rss=1" Wilson, A. M. Jacobs, M. M. Lambert, T. Y. Valada, A. Meloni, G. Gilmore, E. Murray, J. Morgello, S. Akbarian, S. 2025-02-06 doi:10.1101/2025.02.05.636667 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ Multi-omic Characterization of HIV Effects at Single Cell Level across Human Brain Regions ]]> https://biorxiv.org/cgi/content/short/2025.02.05.636707v1?rss=1" Yang, J. Agrawal, K. Stanley, J. S. Li, R. Jacobs, N. Wang, H. Lu, C. Qu, R. Clarke, D. Chen, Y. Jiang, Y. Bai, D. Zheng, S. Fox, H. Ho, Y.-C. Huttner, A. Gerstein, M. Kluger, Y. Zhang, L. Spudich, S. 2025-02-08 doi:10.1101/2025.02.05.636707 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Microglia and macrophages alterations in the CNS during acute SIV infection: a single-cell analysis in rhesus macaques ]]> https://biorxiv.org/cgi/content/short/2024.04.04.588047v1?rss=1" View larger version (13K): org.highwire.dtl.DTLVardef@1d9fadcorg.highwire.dtl.DTLVardef@1e491daorg.highwire.dtl.DTLVardef@1238f91org.highwire.dtl.DTLVardef@1a6a548_HPS_FORMAT_FIGEXP M_FIG C_FIG HIVs entry into the central nervous system (CNS) can lead to neurological dysfunction, including HIV-associated neurocognitive disorders (HAND), and the establishment of a viral reservoir. While microglia and CNS-associated macrophages (CAMs) are the primary targets of HIV in the CNS, their responses during acute HIV infection remain poorly defined. To address this, we employed the scRNA-seq technique to study microglial and CAM populations in rhesus macaques during acute SIV infection. By identifying signature genes associated with different phenotypes and mapping them to various biological and pathological pathways, we discovered two myeloid cell clusters strongly linked to neurodegenerative disorders. Additionally, other clusters were associated with inflammatory pathways, suggesting varying degrees of activation among different myeloid cell populations in the brain, possibly mediated by distinct signaling pathways. All microglia clusters developed signs of the cellular senescence pathway. These findings shed light on the immunological and pathological effects of different myeloid phenotypes in the brain during acute SIV infection, providing valuable insights for future therapeutic strategies targeting this critical stage and aiming to eliminate the viral reservoir. ]]> Xu, X. Niu, M. Lamberty, B. G. Emanuel, K. Trease, A. J. Tabassum, M. Lifson, J. D. Fox, H. S. 2024-04-04 doi:10.1101/2024.04.04.588047 Cold Spring Harbor Laboratory Press 2024-04-04 <![CDATA[ BACH2-driven tissue resident memory programs promote HIV-1 persistence ]]> https://biorxiv.org/cgi/content/short/2024.12.16.628794v1?rss=1" Wei, Y. Ma, H. K. Wang, M. E. Papasavvas, E. Konnikova, L. Tebas, P. Morgenstern, R. Montaner, L. J. Ho, Y.-C. 2024-12-20 doi:10.1101/2024.12.16.628794 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ A Transcriptional Signature of Induced Neurons Differentiates Virologically Suppressed People Living With HIV from People Without HIV ]]> https://biorxiv.org/cgi/content/short/2024.10.22.619617v1?rss=1" Ostermann, P. N. Wu, Y. Bowler, S. A. Siddiqui, M. A. Herrera, A. Sidharta, M. Ramnarine, K. Martinez-Meza, S. St. Bernard, L. A. Nixon, D. F. Jones, R. B. Yamashita, M. Ndhlovu, L. C. Zhou, T. Evering, T. H. 2024-10-22 doi:10.1101/2024.10.22.619617 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Drug Metabolism and Transport Capacity of Endothelial Cells, Pericytes, and Astrocytes: Implications for CNS Drug Disposition ]]> https://biorxiv.org/cgi/content/short/2024.08.01.606165v1?rss=1" Wilkins, H. N. Knerler, S. A. Warshanna, A. Ortiz, R. C. Haas, K. Orsburn, B. C. Williams, D. W. 2024-08-05 doi:10.1101/2024.08.01.606165 Cold Spring Harbor Laboratory Press 2024-08-05 <![CDATA[ Cocaine Regulates Antiretroviral Therapy CNS Access Through Pregnane-X Receptor-Mediated Drug Transporter and Metabolizing Enzyme Modulation at the Blood Brain Barrier ]]> https://biorxiv.org/cgi/content/short/2023.07.28.551042v1?rss=1" Fridman, L. B. Knerler, S. Price, A.-S. Colon Ortiz, R. Mercado, A. Wilkins, H. Flores, B. R. Orsburn, B. Williams, D. 2023-07-29 doi:10.1101/2023.07.28.551042 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform variability in brain cell types ]]> https://biorxiv.org/cgi/content/short/2025.06.25.661563v1?rss=1" Michielsen, L. Prjibelski, A. D. Foord, C. Hu, W. Jarroux, J. Hsu, J. Tomescu, A. I. Hajirasouliha, I. Tilgner, H. U. 2025-06-25 doi:10.1101/2025.06.25.661563 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Quantitative Economon Model of Transactions for Drugs and Other Commodities ]]> https://biorxiv.org/cgi/content/short/2025.07.08.663082v1?rss=1" Haynes, J. M. Correa da Rosa, J. M. Butelman, E. Hursh, S. R. Negus, S. S. 2025-07-11 doi:10.1101/2025.07.08.663082 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ SIMVI reveals intrinsic and spatial-induced states in spatial omics data ]]> https://biorxiv.org/cgi/content/short/2023.08.28.554970v1?rss=1" Dong, M. Kluger, H. Fan, R. Kluger, Y. 2023-08-30 doi:10.1101/2023.08.28.554970 Cold Spring Harbor Laboratory Press 2023-08-30 <![CDATA[ Deep identifiable modeling of single-cell atlases enables zero-shot query of cellular states ]]> https://biorxiv.org/cgi/content/short/2023.11.11.566161v1?rss=1" Dong, M. Kluger, Y. 2023-11-15 doi:10.1101/2023.11.11.566161 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ FABEL: Forecasting Animal Behavioral Events with Deep Learning-Based Computer Vision ]]> https://biorxiv.org/cgi/content/short/2024.03.15.584610v1?rss=1" Catto, A. O'Connor, R. Braunscheidel, K. M. Kenny, P. J. Shen, L. 2024-03-17 doi:10.1101/2024.03.15.584610 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ Cell type-specific contributions to impaired blood-brain barrier and cerebral metabolism in presymptomatic 5XFAD mice ]]> https://biorxiv.org/cgi/content/short/2025.04.23.650260v1?rss=1" Yao, M. Sun, N. Linville, R. Wei, Z. Kakazu, A. Ouyang, Y. Li, R. Du, L. Wang, H. Zhou, Y. Jiang, Y. Zhang, Z. Li, A. Lu, H. Xu, J. Kellis, M. Heiman, M. Duan, W. 2025-04-29 doi:10.1101/2025.04.23.650260 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types. ]]> https://biorxiv.org/cgi/content/short/2025.06.10.658877v1?rss=1" Foord, C. Prjibelski, A. D. Hu, W. Michielsen, L. Vandelli, A. Narykov, O. Evans, B. Hsu, J. Belchikov, N. Jarroux, J. He, Y. Ross, M. E. Hajirasouliha, I. Tartaglia, G. G. Korkin, D. Tomescu, A. I. Tilgner, H. U. 2025-06-10 doi:10.1101/2025.06.10.658877 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development ]]> https://biorxiv.org/cgi/content/short/2023.04.02.535281v1?rss=1" Joglekar, A. Hu, W. Zhang, B. Narykov, O. Diekhans, M. Balacco, J. Ndhlovu, L. Milner, T. A. Fedrigo, O. Jarvis, E. D. Sheynkman, G. M. Korkin, D. Ross, M. E. Tilgner, H. U. 2023-04-04 doi:10.1101/2023.04.02.535281 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Roadmap for Canonical and Extended Endocannabinoid System Receptors in Peripheral Organs of Preclinical Animal Models ]]> https://biorxiv.org/cgi/content/short/2023.06.10.544455v1?rss=1" Rosado-Franco, J. J. Ellison, A. L. White, C. J. Price, A. S. Moore, C. F. Williams, R. E. Fridman, L. B. Weerts, E. M. Williams, D. W. 2023-06-10 doi:10.1101/2023.06.10.544455 Cold Spring Harbor Laboratory Press 2023-06-10 <![CDATA[ Antiviral and Anti-inflammatory Effects of Cannabidiol in HIV/SIV Infection ]]> https://biorxiv.org/cgi/content/short/2025.09.25.678534v1?rss=1" Ellison, A. L. Rosado-Franco, J. J. Mamun, L. Knerler, S. Daniali, M. Mehta, K. Williams-McLeod, S. Alvarez, J. Joyner, S. S. Vandrey, R. Weerts, E. M. Gaskill, P. J. Corley, M. J. Ndhlovu, L. C. Williams, D. W. 2025-09-25 doi:10.1101/2025.09.25.678534 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Investigation of CNS damage following HIV infection and methamphetamine exposure using human iPSC-derived microglia and 3D cerebral assembloid models ]]> https://biorxiv.org/cgi/content/short/2025.12.06.692767v1?rss=1" Tiwari, S. K. Baidwan, G. Trescott, S. Jakhmola, S. Coufal, N. G. Rana, T. M. 2025-12-10 doi:10.64898/2025.12.06.692767 Cold Spring Harbor Laboratory Press 2025-12-10