7 results on '"Pita-Juárez, Yered H."'
Search Results
2. Serine and arginine rich splicing factor 1 deficiency alters pathways involved in IL-17A expression and is implicated in human psoriasis
- Author
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Su, Shi, Katopodi, Xanthi-Lida, Pita-Juarez, Yered H., Maverakis, Emanual, Vlachos, Ioannis S., and Adamopoulos, Iannis E.
- Published
- 2022
- Full Text
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3. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
- Author
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Delorey, Toni M., Ziegler, Carly G. K., Heimberg, Graham, Normand, Rachelly, Yang, Yiming, Segerstolpe, Åsa, Abbondanza, Domenic, Fleming, Stephen J., Subramanian, Ayshwarya, Montoro, Daniel T., Jagadeesh, Karthik A., Dey, Kushal K., Sen, Pritha, Slyper, Michal, Pita-Juárez, Yered H., Phillips, Devan, Biermann, Jana, Bloom-Ackermann, Zohar, Barkas, Nikolaos, Ganna, Andrea, Gomez, James, Melms, Johannes C., Katsyv, Igor, Normandin, Erica, Naderi, Pourya, Popov, Yury V., Raju, Siddharth S., Niezen, Sebastian, Tsai, Linus T.-Y., Siddle, Katherine J., Sud, Malika, Tran, Victoria M., Vellarikkal, Shamsudheen K., Wang, Yiping, Amir-Zilberstein, Liat, Atri, Deepak S., Beechem, Joseph, Brook, Olga R., Chen, Jonathan, Divakar, Prajan, Dorceus, Phylicia, Engreitz, Jesse M., Essene, Adam, Fitzgerald, Donna M., Fropf, Robin, Gazal, Steven, Gould, Joshua, Grzyb, John, Harvey, Tyler, Hecht, Jonathan, Hether, Tyler, Jané-Valbuena, Judit, Leney-Greene, Michael, Ma, Hui, McCabe, Cristin, McLoughlin, Daniel E., Miller, Eric M., Muus, Christoph, Niemi, Mari, Padera, Robert, Pan, Liuliu, Pant, Deepti, Pe’er, Carmel, Pfiffner-Borges, Jenna, Pinto, Christopher J., Plaisted, Jacob, Reeves, Jason, Ross, Marty, Rudy, Melissa, Rueckert, Erroll H., Siciliano, Michelle, Sturm, Alexander, Todres, Ellen, Waghray, Avinash, Warren, Sarah, Zhang, Shuting, Zollinger, Daniel R., Cosimi, Lisa, Gupta, Rajat M., Hacohen, Nir, Hibshoosh, Hanina, Hide, Winston, Price, Alkes L., Rajagopal, Jayaraj, Tata, Purushothama Rao, Riedel, Stefan, Szabo, Gyongyi, Tickle, Timothy L., Ellinor, Patrick T., Hung, Deborah, Sabeti, Pardis C., Novak, Richard, Rogers, Robert, Ingber, Donald E., Jiang, Z. Gordon, Juric, Dejan, Babadi, Mehrtash, Farhi, Samouil L., Izar, Benjamin, Stone, James R., Vlachos, Ioannis S., Solomon, Isaac H., Ashenberg, Orr, Porter, Caroline B. M., Li, Bo, Shalek, Alex K., Villani, Alexandra-Chloé, Rozenblatt-Rosen, Orit, and Regev, Aviv
- Published
- 2021
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4. Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci.
- Author
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Miliotis, Christos, Ma, Yuling, Katopodi, Xanthi-Lida, Karagkouni, Dimitra, Kanata, Eleni, Mattioli, Kaia, Kalavros, Nikolas, Pita-Juárez, Yered H., Batalini, Felipe, Ramnarine, Varune R., Nanda, Shivani, Slack, Frank J., and Vlachos, Ioannis S.
- Subjects
LOCUS (Genetics) ,STOMACH cancer ,GENE expression ,T cell receptors ,PHENOTYPES - Abstract
The landscape of non-coding mutations in cancer progression and immune evasion is largely unexplored. Here, we identify transcrptome-wide somatic and germline 3′ untranslated region (3′-UTR) variants from 375 gastric cancer patients from The Cancer Genome Atlas. By performing gene expression quantitative trait loci (eQTL) and immune landscape QTL (ilQTL) analysis, we discover 3′-UTR variants with cis effects on expression and immune landscape phenotypes, such as immune cell infiltration and T cell receptor diversity. Using a massively parallel reporter assay, we distinguish between causal and correlative effects of 3′-UTR eQTLs in immune-related genes. Our approach identifies numerous 3′-UTR eQTLs and ilQTLs, providing a unique resource for the identification of immunotherapeutic targets and biomarkers. A prioritized ilQTL variant signature predicts response to immunotherapy better than standard-of-care PD-L1 expression in independent patient cohorts, showcasing the untapped potential of non-coding mutations in cancer. The role of non-coding mutations in cancer progression and immune evasion needs to be further explored. Here, the authors investigate the potential of common somatic and germline 3′ untranslated region variants in predicting response to immunotherapy in gastric patients. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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5. Genetic Variation in the Mitochondrial Glycerol‐3‐Phosphate Acyltransferase Is Associated With Liver Injury
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Hakim, Aaron, primary, Moll, Matthew, additional, Brancale, Joseph, additional, Liu, Jiangyuan, additional, Lasky‐Su, Jessica A., additional, Silverman, Edwin K., additional, Vilarinho, Silvia, additional, Jiang, Z. Gordon, additional, Pita‐Juárez, Yered H., additional, Vlachos, Ioannis S., additional, Zhang, Xuehong, additional, Åberg, Fredrik, additional, Afdhal, Nezam H., additional, Hobbs, Brian D., additional, and Cho, Michael H., additional
- Published
- 2021
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6. A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2
- Author
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Delorey, Toni M., primary, Ziegler, Carly G. K., additional, Heimberg, Graham, additional, Normand, Rachelly, additional, Yang, Yiming, additional, Segerstolpe, Asa, additional, Abbondanza, Domenic, additional, Fleming, Stephen J., additional, Subramanian, Ayshwarya, additional, Montoro, Daniel T., additional, Jagadeesh, Karthik A., additional, Dey, Kushal K., additional, Sen, Pritha, additional, Slyper, Michal, additional, Pita-Juárez, Yered H., additional, Phillips, Devan, additional, Bloom-Ackerman, Zohar, additional, Barkas, Nick, additional, Ganna, Andrea, additional, Gomez, James, additional, Normandin, Erica, additional, Naderi, Pourya, additional, Popov, Yury V., additional, Raju, Siddharth S., additional, Niezen, Sebastian, additional, Tsai, Linus T.-Y., additional, Siddle, Katherine J., additional, Sud, Malika, additional, Tran, Victoria M., additional, Vellarikkal, Shamsudheen K., additional, Amir-Zilberstein, Liat, additional, Atri, Deepak S., additional, Beechem, Joseph, additional, Brook, Olga R., additional, Chen, Jonathan, additional, Divakar, Prajan, additional, Dorceus, Phylicia, additional, Engreitz, Jesse M., additional, Essene, Adam, additional, Fitzgerald, Donna M., additional, Fropf, Robin, additional, Gazal, Steven, additional, Gould, Joshua, additional, Grzyb, John, additional, Harvey, Tyler, additional, Hecht, Jonathan, additional, Hether, Tyler, additional, Jane-Valbuena, Judit, additional, Leney-Greene, Michael, additional, Ma, Hui, additional, McCabe, Cristin, additional, McLoughlin, Daniel E., additional, Miller, Eric M., additional, Muus, Christoph, additional, Niemi, Mari, additional, Padera, Robert, additional, Pan, Liuliu, additional, Pant, Deepti, additional, Pe’er, Carmel, additional, Pfiffner-Borges, Jenna, additional, Pinto, Christopher J., additional, Plaisted, Jacob, additional, Reeves, Jason, additional, Ross, Marty, additional, Rudy, Melissa, additional, Rueckert, Erroll H., additional, Siciliano, Michelle, additional, Sturm, Alexander, additional, Todres, Ellen, additional, Waghray, Avinash, additional, Warren, Sarah, additional, Zhang, Shuting, additional, Zollinger, Daniel R., additional, Cosimi, Lisa, additional, Gupta, Rajat M., additional, Hacohen, Nir, additional, Hide, Winston, additional, Price, Alkes L., additional, Rajagopal, Jayaraj, additional, Tata, Purushothama Rao, additional, Riedel, Stefan, additional, Szabo, Gyongyi, additional, Tickle, Timothy L., additional, Hung, Deborah, additional, Sabeti, Pardis C., additional, Novak, Richard, additional, Rogers, Robert, additional, Ingber, Donald E., additional, Gordon Jiang, Z., additional, Juric, Dejan, additional, Babadi, Mehrtash, additional, Farhi, Samouil L., additional, Stone, James R., additional, Vlachos, Ioannis S., additional, Solomon, Isaac H., additional, Ashenberg, Orr, additional, Porter, Caroline B.M., additional, Li, Bo, additional, Shalek, Alex K., additional, Villani, Alexandra-Chloé, additional, Rozenblatt-Rosen, Orit, additional, and Regev, Aviv, additional
- Published
- 2021
- Full Text
- View/download PDF
7. A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2.
- Author
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Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe A, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Bloom-Ackerman Z, Barkas N, Ganna A, Gomez J, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LT, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jane-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe'er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CBM, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, and Regev A
- Abstract
The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients' demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung, we uncovered significantly altered transcriptional programs within the epithelial, immune, and stromal compartments and cell intrinsic changes in multiple cell types relative to lung tissue from healthy controls. We observed evidence of: alveolar type 2 (AT2) differentiation replacing depleted alveolar type 1 (AT1) lung epithelial cells, as previously seen in fibrosis; a concomitant increase in myofibroblasts reflective of defective tissue repair; and, putative TP63
+ intrapulmonary basal-like progenitor (IPBLP) cells, similar to cells identified in H1N1 influenza, that may serve as an emergency cellular reserve for severely damaged alveoli. Together, these findings suggest the activation and failure of multiple avenues for regeneration of the epithelium in these terminal lungs. SARS-CoV-2 RNA reads were enriched in lung mononuclear phagocytic cells and endothelial cells, and these cells expressed distinct host response transcriptional programs. We corroborated the compositional and transcriptional changes in lung tissue through spatial analysis of RNA profiles in situ and distinguished unique tissue host responses between regions with and without viral RNA, and in COVID-19 donor tissues relative to healthy lung. Finally, we analyzed genetic regions implicated in COVID-19 GWAS with transcriptomic data to implicate specific cell types and genes associated with disease severity. Overall, our COVID-19 cell atlas is a foundational dataset to better understand the biological impact of SARS-CoV-2 infection across the human body and empowers the identification of new therapeutic interventions and prevention strategies., Competing Interests: Competing Interests P.D., R.F., E.M.M., M.R., E.H.R., L.P., T.He., J.R., J.B., and S.W. are employees and stockholders at Nanostring Technologies Inc. D.Z., is a former employee and stockholder at NanoString Technologies. N.H., holds equity in BioNTech and Related Sciences. T.H.is an employee and stockholder of Prime Medicine as of Oct. 13, 2020. G.H. is an employee of Genentech as of Nov 16, 2020. R.N. is a founder, shareholder, and member of the board at Rhinostics Inc. A.R. is a co-founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas, and was an SAB member of ThermoFisher Scientific, Syros Pharmaceuticals, Neogene Therapeutics and Asimov until July 31, 2020. From August 1, 2020, A.R. is an employee of Genentech. From October 19, 2020, O.R.-R is an employee of Genentech. P.C.S is a co-founder and shareholder of Sherlock Biosciences, and a Board member and shareholder of Danaher Corporation. A.K.S. reports compensation for consulting and/or SAB membership from Honeycomb Biotechnologies, Cellarity, Repertoire Immune Medicines, Ochre Bio, and Dahlia Biosciences. Z.G.J. reports grant support from Gilead Science, Pfizer, compensation for consulting from Olix Pharmaceuticals. Y.V.P. reports grant support from Enanta Pharmaceuticals, CymaBay Therapeutics, Morphic Therapeutic; consulting and/or SAB in Ambys Medicines, Morphic Therapeutics, Enveda Therapeutics, BridgeBio Pharma, as well as being an Editor – American Journal of Physiology-Gastrointestinal and Liver Physiology. GS reports consultant service in Alnylam Pharmaceuticals, Merck, Generon, Glympse Bio, Inc., Mayday Foundation, Novartis Pharmaceuticals, Quest Diagnostics, Surrozen, Terra Firma, Zomagen Bioscience, Pandion Therapeutics, Inc. Durect Corporation; royalty from UpToDate Inc., and Editor service in Hepatology Communications. P.R.T. receives consulting fees from Cellarity Inc., and Surrozen Inc., for work not related to this manuscript.- Published
- 2021
- Full Text
- View/download PDF
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