122 results on '"McCabe, Cristin"'
Search Results
2. Correction of age-associated defects in dendritic cells enables CD4+ T cells to eradicate tumors
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Zhivaki, Dania, Kennedy, Stephanie N., Park, Josh, Boriello, Francesco, Devant, Pascal, Cao, Anh, Bahleda, Kristin M., Murphy, Shane, McCabe, Cristin, Evavold, Charles L., Chapman, Kate L., Zanoni, Ivan, Ashenberg, Orr, Xavier, Ramnik J., and Kagan, Jonathan C.
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- 2024
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3. Multicellular communities are perturbed in the aging human brain and Alzheimer’s disease
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Cain, Anael, Taga, Mariko, McCabe, Cristin, Green, Gilad S., Hekselman, Idan, White, Charles C., Lee, Dylan I., Gaur, Pallavi, Rozenblatt-Rosen, Orit, Zhang, Feng, Yeger-Lotem, Esti, Bennett, David A., Yang, Hyun-Sik, Regev, Aviv, Menon, Vilas, Habib, Naomi, and De Jager, Philip L.
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- 2023
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4. The effect of background noise and its removal on the analysis of single-cell expression data
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Janssen, Philipp, Kliesmete, Zane, Vieth, Beate, Adiconis, Xian, Simmons, Sean, Marshall, Jamie, McCabe, Cristin, Heyn, Holger, Levin, Joshua Z., Enard, Wolfgang, and Hellmann, Ines
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- 2023
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5. Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility
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Patsopoulos, Nikolaos A, Baranzini, Sergio E, Santaniello, Adam, Shoostari, Parisa, Cotsapas, Chris, Wong, Garrett, Beecham, Ashley H, James, Tojo, Replogle, Joseph, Vlachos, Ioannis S, McCabe, Cristin, Pers, Tune H, Brandes, Aaron, White, Charles, Keenan, Brendan, Cimpean, Maria, Winn, Phoebe, Panteliadis, Ioannis-Pavlos, Robbins, Allison, Andlauer, Till FM, Zarzycki, Onigiusz, Dubois, Bénédicte, Goris, An, Søndergaard, Helle Bach, Sellebjerg, Finn, Sorensen, Per Soelberg, Ullum, Henrik, Thørner, Lise Wegner, Saarela, Janna, Cournu-Rebeix, Isabelle, Damotte, Vincent, Fontaine, Bertrand, Guillot-Noel, Lena, Lathrop, Mark, Vukusic, Sandra, Berthele, Achim, Pongratz, Viola, Buck, Dorothea, Gasperi, Christiane, Graetz, Christiane, Grummel, Verena, Hemmer, Bernhard, Hoshi, Muni, Knier, Benjamin, Korn, Thomas, Lill, Christina M, Luessi, Felix, Mühlau, Mark, Zipp, Frauke, Dardiotis, Efthimios, Agliardi, Cristina, Amoroso, Antonio, Barizzone, Nadia, Benedetti, Maria D, Bernardinelli, Luisa, Cavalla, Paola, Clarelli, Ferdinando, Comi, Giancarlo, Cusi, Daniele, Esposito, Federica, Ferrè, Laura, Galimberti, Daniela, Guaschino, Clara, Leone, Maurizio A, Martinelli, Vittorio, Moiola, Lucia, Salvetti, Marco, Sorosina, Melissa, Vecchio, Domizia, Zauli, Andrea, Santoro, Silvia, Mancini, Nicasio, Zuccalà, Miriam, Mescheriakova, Julia, van Duijn, Cornelia, Bos, Steffan D, Celius, Elisabeth G, Spurkland, Anne, Comabella, Manuel, Montalban, Xavier, Alfredsson, Lars, Bomfim, Izaura L, Gomez-Cabrero, David, Hillert, Jan, Jagodic, Maja, Lindén, Magdalena, Piehl, Fredrik, Jelčić, Ilijas, Martin, Roland, Sospedra, Mirela, Baker, Amie, Ban, Maria, Hawkins, Clive, Hysi, Pirro, Kalra, Seema, Karpe, Fredrik, Khadake, Jyoti, Lachance, Genevieve, Molyneux, Paul, and Neville, Matthew
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Neurosciences ,Brain Disorders ,Multiple Sclerosis ,Human Genome ,Autoimmune Disease ,Clinical Research ,Genetics ,Neurodegenerative ,Aetiology ,2.1 Biological and endogenous factors ,Inflammatory and immune system ,Neurological ,Case-Control Studies ,Cell Cycle Proteins ,Chromosome Mapping ,Chromosomes ,Human ,X ,GTPase-Activating Proteins ,Gene Frequency ,Genetic Loci ,Genome-Wide Association Study ,Genomics ,Humans ,Inheritance Patterns ,Major Histocompatibility Complex ,Microglia ,Polymorphism ,Single Nucleotide ,Quantitative Trait Loci ,RNA-Seq ,Transcriptome ,International Multiple Sclerosis Genetics Consortium ,General Science & Technology - Abstract
We analyzed genetic data of 47,429 multiple sclerosis (MS) and 68,374 control subjects and established a reference map of the genetic architecture of MS that includes 200 autosomal susceptibility variants outside the major histocompatibility complex (MHC), one chromosome X variant, and 32 variants within the extended MHC. We used an ensemble of methods to prioritize 551 putative susceptibility genes that implicate multiple innate and adaptive pathways distributed across the cellular components of the immune system. Using expression profiles from purified human microglia, we observed enrichment for MS genes in these brain-resident immune cells, suggesting that these may have a role in targeting an autoimmune process to the central nervous system, although MS is most likely initially triggered by perturbation of peripheral immune responses.
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- 2019
6. Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection
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Ye, Chun Jimmie, Chen, Jenny, Villani, Alexandra-Chloé, Gate, Rachel E, Subramaniam, Meena, Bhangale, Tushar, Lee, Mark N, Raj, Towfique, Raychowdhury, Raktima, Li, Weibo, Rogel, Noga, Simmons, Sean, Imboywa, Selina H, Chipendo, Portia I, McCabe, Cristin, Lee, Michelle H, Frohlich, Irene Y, Stranger, Barbara E, De Jager, Philip L, Regev, Aviv, Behrens, Tim, and Hacohen, Nir
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Biological Sciences ,Genetics ,Infectious Diseases ,Biotechnology ,Human Genome ,Pneumonia & Influenza ,Influenza ,Aetiology ,2.1 Biological and endogenous factors ,Infection ,Adolescent ,Adult ,Alternative Splicing ,Aminopeptidases ,Chromosome Mapping ,Computational Biology ,Dendritic Cells ,Female ,Gene Expression Profiling ,Gene Expression Regulation ,Gene Ontology ,Genetic Predisposition to Disease ,Genetic Testing ,Genetic Variation ,Host-Pathogen Interactions ,Humans ,Influenza A virus ,Influenza ,Human ,Interferon Type I ,Male ,Middle Aged ,Models ,Biological ,Molecular Sequence Annotation ,Monocytes ,Quantitative Trait Loci ,Transcriptome ,Young Adult ,Medical and Health Sciences ,Bioinformatics - Abstract
While genetic variants are known to be associated with overall gene abundance in stimulated immune cells, less is known about their effects on alternative isoform usage. By analyzing RNA-seq profiles of monocyte-derived dendritic cells from 243 individuals, we uncovered thousands of unannotated isoforms synthesized in response to influenza infection and type 1 interferon stimulation. We identified more than a thousand quantitative trait loci (QTLs) associated with alternate isoform usage (isoQTLs), many of which are independent of expression QTLs (eQTLs) for the same gene. Compared with eQTLs, isoQTLs are enriched for splice sites and untranslated regions, but depleted of sequences upstream of annotated transcription start sites. Both eQTLs and isoQTLs explain a significant proportion of the disease heritability attributed to common genetic variants. At the ERAP2 locus, we shed light on the function of the gene and how two frequent, highly differentiated haplotypes with intermediate frequencies could be maintained by balancing selection. At baseline and following type 1 interferon stimulation, the major haplotype is associated with low ERAP2 expression caused by nonsense-mediated decay, while the minor haplotype, known to increase Crohn's disease risk, is associated with high ERAP2 expression. In response to influenza infection, we found two uncharacterized isoforms expressed from the major haplotype, likely the result of multiple perfectly linked variants affecting the transcription and splicing at the locus. Thus, genetic variants at a single locus could modulate independent gene regulatory processes in innate immune responses and, in the case of ERAP2, may confer a historical fitness advantage in response to virus.
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- 2018
7. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
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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
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- 2021
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8. Atlas of RNA editing events affecting protein expression in aged and Alzheimer’s disease human brain tissue
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Ma, Yiyi, Dammer, Eric B., Felsky, Daniel, Duong, Duc M., Klein, Hans-Ulrich, White, Charles C., Zhou, Maotian, Logsdon, Benjamin A., McCabe, Cristin, Xu, Jishu, Wang, Minghui, Wingo, Thomas S., Lah, James J., Zhang, Bin, Schneider, Julie, Allen, Mariet, Wang, Xue, Ertekin-Taner, Nilüfer, Seyfried, Nicholas T., Levey, Allan I., Bennett, David A., and De Jager, Philip L.
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- 2021
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9. Disease-associated astrocytes in Alzheimer’s disease and aging
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Habib, Naomi, McCabe, Cristin, Medina, Sedi, Varshavsky, Miriam, Kitsberg, Daniel, Dvir-Szternfeld, Raz, Green, Gilad, Dionne, Danielle, Nguyen, Lan, Marshall, Jamie L., Chen, Fei, Zhang, Feng, Kaplan, Tommy, Regev, Aviv, and Schwartz, Michal
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- 2020
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10. Intersection of population variation and autoimmunity genetics in human T cell activation
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Ye, Chun Jimmie, Feng, Ting, Kwon, Ho-Keun, Raj, Towfique, Wilson, Michael T, Asinovski, Natasha, McCabe, Cristin, Lee, Michelle H, Frohlich, Irene, Paik, Hyun-il, Zaitlen, Noah, Hacohen, Nir, Stranger, Barbara, De Jager, Philip, Mathis, Diane, Regev, Aviv, and Benoist, Christophe
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Human Genome ,Genetics ,Clinical Research ,Biotechnology ,Autoimmune Disease ,2.1 Biological and endogenous factors ,Aetiology ,Inflammatory and immune system ,Asians ,Autoimmunity ,Blacks ,CD4-Positive T-Lymphocytes ,Cytokines ,Gene Expression Regulation ,Genetic Variation ,Genome-Wide Association Study ,Humans ,Lymphocyte Activation ,Multigene Family ,Quantitative Trait Loci ,Th17 Cells ,Whites ,Asian People ,White People ,Black People ,General Science & Technology - Abstract
T lymphocyte activation by antigen conditions adaptive immune responses and immunopathologies, but we know little about its variation in humans and its genetic or environmental roots. We analyzed gene expression in CD4(+) T cells during unbiased activation or in T helper 17 (T(H)17) conditions from 348 healthy participants representing European, Asian, and African ancestries. We observed interindividual variability, most marked for cytokine transcripts, with clear biases on the basis of ancestry, and following patterns more complex than simple T(H)1/2/17 partitions. We identified 39 genetic loci specifically associated in cis with activated gene expression. We further fine-mapped and validated a single-base variant that modulates YY1 binding and the activity of an enhancer element controlling the autoimmune-associated IL2RA gene, affecting its activity in activated but not regulatory T cells. Thus, interindividual variability affects the fundamental immunologic process of T helper activation, with important connections to autoimmune disease.
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- 2014
11. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci
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De Jager, Philip L, Srivastava, Gyan, Lunnon, Katie, Burgess, Jeremy, Schalkwyk, Leonard C, Yu, Lei, Eaton, Matthew L, Keenan, Brendan T, Ernst, Jason, McCabe, Cristin, Tang, Anna, Raj, Towfique, Replogle, Joseph, Brodeur, Wendy, Gabriel, Stacey, Chai, High S, Younkin, Curtis, Younkin, Steven G, Zou, Fanggeng, Szyf, Moshe, Epstein, Charles B, Schneider, Julie A, Bernstein, Bradley E, Meissner, Alex, Ertekin-Taner, Nilufer, Chibnik, Lori B, Kellis, Manolis, Mill, Jonathan, and Bennett, David A
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Neurosciences ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Brain Disorders ,Alzheimer's Disease ,Human Genome ,Genetics ,Dementia ,Neurodegenerative ,Acquired Cognitive Impairment ,Aging ,2.1 Biological and endogenous factors ,Aetiology ,Neurological ,Adaptor Proteins ,Signal Transducing ,Aged ,Aged ,80 and over ,Alzheimer Disease ,Amyloidosis ,Ankyrins ,Brain ,Carrier Proteins ,CpG Islands ,DNA Methylation ,Female ,Genetic Predisposition to Disease ,Genome-Wide Association Study ,Humans ,Intracellular Signaling Peptides and Proteins ,Male ,Middle Aged ,Nuclear Proteins ,Protein Interaction Maps ,Tumor Suppressor Proteins ,Psychology ,Cognitive Sciences ,Neurology & Neurosurgery - Abstract
We used a collection of 708 prospectively collected autopsied brains to assess the methylation state of the brain's DNA in relation to Alzheimer's disease (AD). We found that the level of methylation at 71 of the 415,848 interrogated CpGs was significantly associated with the burden of AD pathology, including CpGs in the ABCA7 and BIN1 regions, which harbor known AD susceptibility variants. We validated 11 of the differentially methylated regions in an independent set of 117 subjects. Furthermore, we functionally validated these CpG associations and identified the nearby genes whose RNA expression was altered in AD: ANK1, CDH23, DIP2A, RHBDF2, RPL13, SERPINF1 and SERPINF2. Our analyses suggest that these DNA methylation changes may have a role in the onset of AD given that we observed them in presymptomatic subjects and that six of the validated genes connect to a known AD susceptibility gene network.
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- 2014
12. Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer’s human brains
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Klein, Hans-Ulrich, McCabe, Cristin, Gjoneska, Elizabeta, Sullivan, Sarah E., Kaskow, Belinda J., Tang, Anna, Smith, Robert V., Xu, Jishu, Pfenning, Andreas R., Bernstein, Bradley E., Meissner, Alexander, Schneider, Julie A., Mostafavi, Sara, Tsai, Li-Huei, Young-Pearse, Tracy L., Bennett, David A., and De Jager, Philip L.
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- 2019
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13. Author Correction: Nuclei multiplexing with barcoded antibodies for single-nucleus genomics
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Gaublomme, Jellert T., Li, Bo, McCabe, Cristin, Knecht, Abigail, Yang, Yiming, Drokhlyansky, Eugene, Van Wittenberghe, Nicholas, Waldman, Julia, Dionne, Danielle, Nguyen, Lan, De Jager, Philip L., Yeung, Bertrand, Zhao, Xinfang, Habib, Naomi, Rozenblatt-Rosen, Orit, and Regev, Aviv
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- 2020
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14. A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease
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Mostafavi, Sara, Gaiteri, Chris, Sullivan, Sarah E., White, Charles C., Tasaki, Shinya, Xu, Jishu, Taga, Mariko, Klein, Hans-Ulrich, Patrick, Ellis, Komashko, Vitalina, McCabe, Cristin, Smith, Robert, Bradshaw, Elizabeth M., Root, David E., Regev, Aviv, Yu, Lei, Chibnik, Lori B., Schneider, Julie A., Young-Pearse, Tracy L., Bennett, David A., and De Jager, Philip L.
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- 2018
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15. Cellular dynamics across aged human brains uncover a multicellular cascade leading to Alzheimer’s disease
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Green, Gilad Sahar, primary, Fujita, Masashi, additional, Yang, Hyun-Sik, additional, Taga, Mariko, additional, McCabe, Cristin, additional, Cain, Anael, additional, White, Charles C., additional, Schmidtner, Anna K., additional, Zeng, Lu, additional, Wang, Yangling, additional, Regev, Aviv, additional, Menon, Vilas, additional, Bennett, David A., additional, Habib, Naomi, additional, and De Jager, Philip L., additional
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- 2023
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16. Multi-region brain transcriptomes uncover two subtypes of aging individuals with differences in Alzheimer risk and the impact ofAPOEε4
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Lee, Annie J., primary, Ma, Yiyi, additional, Yu, Lei, additional, Dawe, Robert J., additional, McCabe, Cristin, additional, Arfanakis, Konstantinos, additional, Mayeux, Richard, additional, Bennett, David A., additional, Klein, Hans-Ulrich, additional, and De Jager, Philip L., additional
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- 2023
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17. An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome
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Ng, Bernard, White, Charles C, Klein, Hans-Ulrich, Sieberts, Solveig K, McCabe, Cristin, Patrick, Ellis, Xu, Jishu, Yu, Lei, Gaiteri, Chris, Bennett, David A, Mostafavi, Sara, and De Jager, Philip L
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- 2017
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18. Nuclei multiplexing with barcoded antibodies for single-nucleus genomics
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Gaublomme, Jellert T., Li, Bo, McCabe, Cristin, Knecht, Abigail, Yang, Yiming, Drokhlyansky, Eugene, Van Wittenberghe, Nicholas, Waldman, Julia, Dionne, Danielle, Nguyen, Lan, De Jager, Philip L., Yeung, Bertrand, Zhao, Xinfang, Habib, Naomi, Rozenblatt-Rosen, Orit, and Regev, Aviv
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- 2019
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19. Cellular network perturbations point to a new microglia‐astrocyte community accelerating Alzheimer’s disease progression
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Green, Gilad Sahar, primary, Fujita, Masashi, additional, Yang, Hyun‐Sik, additional, McCabe, Cristin, additional, Taga, Mariko, additional, Cain, Anael, additional, Zeng, Lu, additional, Regev, Aviv, additional, Bennett, David A, additional, Menon, Vilas, additional, Habib, Naomi, additional, and De Jager, Philip L, additional
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- 2022
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20. The effect of background noise and its removal on the analysis of single-cell expression data
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Janssen, Philipp, primary, Kliesmete, Zane, additional, Vieth, Beate, additional, Adiconis, Xian, additional, Simmons, Sean, additional, Marshall, Jamie, additional, McCabe, Cristin, additional, Heyn, Holger, additional, Levin, Joshua Z., additional, Enard, Wolfgang, additional, and Hellmann, Ines, additional
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- 2022
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21. Cell-subtype specific effects of genetic variation in the aging and Alzheimer cortex
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Fujita, Masashi, primary, Gao, Zongmei, additional, Zeng, Lu, additional, McCabe, Cristin, additional, White, Charles C., additional, Ng, Bernard, additional, Green, Gilad Sahar, additional, Rozenblatt-Rosen, Orit, additional, Phillips, Devan, additional, Amir-Zilberstein, Liat, additional, Lee, Hyo, additional, Pearse, Richard V., additional, Khan, Atlas, additional, Vardarajan, Badri N., additional, Kiryluk, Krzysztof, additional, Ye, Chun Jimmie, additional, Klein, Hans-Ulrich, additional, Wang, Gao, additional, Regev, Aviv, additional, Habib, Naomi, additional, Schneider, Julie A., additional, Wang, Yanling, additional, Young-Pearse, Tracy, additional, Mostafavi, Sara, additional, Bennett, David A., additional, Menon, Vilas, additional, and De Jager, Philip L., additional
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- 2022
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22. Cell type- and state- resolved immune transcriptomic profiling identifies glucocorticoid-responsive molecular defects in multiple sclerosis T cells
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Roostaei, Tina, primary, Sabrin, Afsana, additional, Kivisäkk, Pia, additional, McCabe, Cristin, additional, Nejad, Parham, additional, Felsky, Daniel, additional, Touil, Hanane, additional, Vlachos, Ioannis S., additional, Hui, Daniel, additional, Fransson, Jennifer, additional, Patsopoulos, Nikolaos A., additional, Kuchroo, Vijay K., additional, Zujovic, Violetta, additional, Weiner, Howard L., additional, Klein, Hans-Ulrich, additional, and De Jager, Philip L., additional
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- 2022
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23. Genetic architecture of age-related cognitive decline in African Americans
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Raj, Towfique, Chibnik, Lori B., McCabe, Cristin, Wong, Andus, Replogle, Joseph M., Yu, Lei, Gao, Sujuan, Unverzagt, Frederick W., Stranger, Barbara, Murrell, Jill, Barnes, Lisa, Hendrie, Hugh C., Foroud, Tatiana, Krichevsky, Anna, Bennett, David A., Hall, Kathleen S., Evans, Denis A., and De Jager, Philip L.
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- 2017
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24. Abstract SY12-04: Multicellular spatial community featuring a novel neuronal-like malignant phenotype is enriched in pancreatic cancer after neoadjuvant chemotherapy and radiotherapy
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Hwang, William L., primary, Jagadeesh, Karthik A., additional, Guo, Jimmy A., additional, Hoffman, Hannah I., additional, Shiau, Carina, additional, Su, Jennifer, additional, Yadollahpour, Payman, additional, Reeves, Jason W., additional, Kim, Youngmi, additional, Kim, Sean, additional, Gregory, Mark, additional, Divakar, Prajan, additional, Miller, Eric, additional, Rhodes, Michael, additional, Warren, Sarah, additional, Rueckert, Erroll, additional, Fuhrman, Kit, additional, Zollinger, Daniel R., additional, Fropf, Robin, additional, Beechem, Joseph M., additional, Mehta, Arnav, additional, Delorey, Toni, additional, McCabe, Cristin, additional, Barth, Jaimie L., additional, Zelga, Piotr, additional, Ferrone, Cristina R., additional, Qadan, Motaz, additional, Lillemoe, Keith D., additional, Jain, Rakesh K., additional, Wo, Jennifer Y., additional, Hong, Theodore S., additional, Xavier, Ramnik, additional, Rozenblatt-Rosen, Orit, additional, Aguirre, Andrew J., additional, Castillo, Carlos Fernandez-Del, additional, Liss, Andrew S., additional, Mino-Kenudson, Mari, additional, Ting, David T., additional, Jacks, Tyler, additional, and Regev, Aviv, additional
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- 2022
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25. Genes and Environment in Multiple Sclerosis Project: A Platform to Investigate Multiple Sclerosis Risk
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Xia, Zongqi, White, Charles C., Owen, Emily K., Von Korff, Alina, Clarkson, Sarah R., McCabe, Cristin A., Cimpean, Maria, Winn, Phoebe A., Hoesing, Ashley, Steele, Sonya U., Cortese, Irene C. M., Chitnis, Tanuja, Weiner, Howard L., Reich, Daniel S., Chibnik, Lori B., and De Jager, Philip L.
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- 2016
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26. A cellular and spatial map of the choroid plexus across brain ventricles and ages
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Dani, Neil, primary, Herbst, Rebecca H., additional, McCabe, Cristin, additional, Green, Gilad S., additional, Kaiser, Karol, additional, Head, Joshua P., additional, Cui, Jin, additional, Shipley, Frederick B., additional, Jang, Ahram, additional, Dionne, Danielle, additional, Nguyen, Lan, additional, Rodman, Christopher, additional, Riesenfeld, Samantha J., additional, Prochazka, Jan, additional, Prochazkova, Michaela, additional, Sedlacek, Radislav, additional, Zhang, Feng, additional, Bryja, Vitezslav, additional, Rozenblatt-Rosen, Orit, additional, Habib, Naomi, additional, Regev, Aviv, additional, and Lehtinen, Maria K., additional
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- 2021
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27. IMMUNOGENETICS: Intersection of population variation and autoimmunity genetics in human T cell activation
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Ye, Chun Jimmie, Feng, Ting, Kwon, Ho-Keun, Raj, Towfique, Wilson, Michael, Asinovski, Natasha, McCabe, Cristin, Lee, Michelle H., Frohlich, Irene, Paik, Hyun-il, Zaitlen, Noah, Hacohen, Nir, Stranger, Barbara, Jager, Philip De, Mathis, Diane, Regev, Aviv, and Benoist, Christophe
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- 2014
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28. A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2
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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
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- 2021
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29. Multi-cellular communities are perturbed in the aging human brain and Alzheimer’s disease
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Cain, Anael, primary, Taga, Mariko, additional, McCabe, Cristin, additional, Green, Gilad, additional, Hekselman, Idan, additional, White, Charles C., additional, Lee, Dylan I., additional, Gaur, Pallavi, additional, Rozenblatt-Rosen, Orit, additional, Zhang, Feng, additional, Yeger-Lotem, Esti, additional, Bennett, David A., additional, Yang, Hyun-Sik, additional, Regev, Aviv, additional, Menon, Vilas, additional, Habib, Naomi, additional, and De Jager, Philip L., additional
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- 2020
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- View/download PDF
30. Low-Frequency and Rare-Coding Variation Contributes to Multiple Sclerosis Risk
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Mitrovič, Mitja, primary, Patsopoulos, Nikolaos A., additional, Beecham, Ashley H., additional, Dankowski, Theresa, additional, Goris, An, additional, Dubois, Bénédicte, additional, D’hooghe, Marie B., additional, Lemmens, Robin, additional, Van Damme, Philip, additional, Søndergaard, Helle Bach, additional, Sellebjerg, Finn, additional, Sorensen, Per Soelberg, additional, Ullum, Henrik, additional, Thørner, Lise W., additional, Werge, Thomas, additional, Saarela, Janna, additional, Cournu-Rebeix, Isabelle, additional, Damotte, Vincent, additional, Fontaine, Bertrand, additional, Guillot-Noel, Lena, additional, Lathrop, Mark, additional, Vukusik, Sandra, additional, Gourraud, Pierre-Antoine, additional, Andlauer, Till F.M., additional, Pongratz, Viola, additional, Buck, Dorothea, additional, Gasperi, Christiane, additional, Bayas, Antonios, additional, Heesen, Christoph, additional, Kümpfel, Tania, additional, Linker, Ralf, additional, Paul, Friedemann, additional, Stangel, Martin, additional, Tackenberg, Björn, additional, Bergh, Florian Then, additional, Warnke, Clemens, additional, Wiendl, Heinz, additional, Wildemann, Brigitte, additional, Zettl, Uwe, additional, Ziemann, Ulf, additional, Tumani, Hayrettin, additional, Gold, Ralf, additional, Grummel, Verena, additional, Hemmer, Bernhard, additional, Knier, Benjamin, additional, Lill, Christina M., additional, Luessi, Felix, additional, Dardiotis, Efthimios, additional, Agliardi, Cristina, additional, Barizzone, Nadia, additional, Mascia, Elisabetta, additional, Bernardinelli, Luisa, additional, Comi, Giancarlo, additional, Cusi, Daniele, additional, Esposito, Federica, additional, Ferrè, Laura, additional, Comi, Cristoforo, additional, Galimberti, Daniela, additional, Leone, Maurizio A., additional, Sorosina, Melissa, additional, Mescheriakova, Julia, additional, Hintzen, Rogier, additional, van Duijn, Cornelia, additional, Teunissen, Charlotte E., additional, Bos, Steffan D., additional, Myhr, Kjell-Morten, additional, Celius, Elisabeth G., additional, Lie, Benedicte A., additional, Spurkland, Anne, additional, Comabella, Manuel, additional, Montalban, Xavier, additional, Alfredsson, Lars, additional, Stridh, Pernilla, additional, Hillert, Jan, additional, Jagodic, Maja, additional, Piehl, Fredrik, additional, Jelčić, Ilijas, additional, Martin, Roland, additional, Sospedra, Mireia, additional, Ban, Maria, additional, Hawkins, Clive, additional, Hysi, Pirro, additional, Kalra, Seema, additional, Karpe, Fredrik, additional, Khadake, Jyoti, additional, Lachance, Genevieve, additional, Neville, Matthew, additional, Santaniello, Adam, additional, Caillier, Stacy J., additional, Calabresi, Peter A., additional, Cree, Bruce A.C., additional, Cross, Anne, additional, Davis, Mary F., additional, Haines, Jonathan L., additional, de Bakker, Paul I.W., additional, Delgado, Silvia, additional, Dembele, Marieme, additional, Edwards, Keith, additional, Fitzgerald, Kathryn C., additional, Hakonarson, Hakon, additional, Konidari, Ioanna, additional, Lathi, Ellen, additional, Manrique, Clara P., additional, Pericak-Vance, Margaret A., additional, Piccio, Laura, additional, Schaefer, Cathy, additional, McCabe, Cristin, additional, Weiner, Howard, additional, Goldstein, Jacqueline, additional, Olsson, Tomas, additional, Hadjigeorgiou, Georgios, additional, Taylor, Bruce, additional, Tajouri, Lotti, additional, Charlesworth, Jac, additional, Booth, David R., additional, Harbo, Hanne F., additional, Ivinson, Adrian J., additional, Hauser, Stephen L., additional, Compston, Alastair, additional, Stewart, Graeme, additional, Zipp, Frauke, additional, Barcellos, Lisa F., additional, Baranzini, Sergio E., additional, Martinelli-Boneschi, Filippo, additional, D’Alfonso, Sandra, additional, Ziegler, Andreas, additional, Oturai, Annette, additional, McCauley, Jacob L., additional, Sawcer, Stephen J., additional, Oksenberg, Jorge R., additional, De Jager, Philip L., additional, Kockum, Ingrid, additional, Hafler, David A., additional, and Cotsapas, Chris, additional
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- 2020
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31. Low-Frequency and Rare-Coding Variation Contributes to Multiple Sclerosis Risk
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Int Multiple Sclerosis Genetics, Mitrovic, Mitja, Patsopoulos, Nikoloas, Beecham, Ashley, Dankowski, Theresa, Goris, An, Dubois, Bénédicte, D'hooghe, Marie B, Lemmens, Robin, Van Damme, Philip, Bach Sondergaard, Helle, Sellebjerg, Finn, Soelberg Sorensen, Per, Ullum, Henrik, Thorner, Lise W, Werge, Thomas, Saarela, Janna, Cournu-Rebeix, Isabelle, Damotte, Vincent, Fontaine, Bertrand, Guillot-Noel, Lena, Lathrop, Mark, Vukusik, Sandra, Gourraud, Pierre-Antoine, Andlauer, Till FM, Pongratz, Viola, Buck, Dorothea, Gasperi, Christiane, Bayas, Antonios, Heesen, Christoph, Kümpfel, Tania, Linker, Ralf, Friedemann, Paul, Stangel, Martin, Tackenberg, Björn, Then Bergh, Florian, Warnke, Clemens, Wiendl, Heinz, Wildemann, Brigitte, Zettl, Uwe, Ziemann, Ulf, Tumani, Hayrettin, Gold, Ralf, Grummel, Verena, Hemmer, Bernhard, Knier, Benjamin, Lill, Christina, Luessi, Felix, Dardiotis, Efthimios, Agliardi, Cristina, Barizzone, Nadia, Mascia, Elisabetta, Bernardinelli, Luisa, Comi, Giancarlo, Cusi, Daniele, Esposito, Federica, Ferrè, Laura, Comi, Cristoforo, Galimberti, Daniela, Leone, Maurizio A, Sorosina, Melissa, Mescheriakova, Julia, Hintzen, Rogier, van Duijn, Cornelia, Theunissen, Charlotte E, Bos, Steffan D, Myhr, Kjell-Morten, Celius, Elisabeth G, Lie, Benedicte A, Spurkland, Anne, Comabella, Manuel, Montalban, Xavier, Alfredsson, Lars, Stridh, Pernilla, Hillert, Jan, Jagodic, Maja, Piehl, Fredrik, Jelcic, Ilijas, Martin, Roland, Sospedra, Mireia, Ban, Maria, Hawkins, Clive, Hysi, Pirro, Kalra, Seema, Karpe, Fredrik, Khadake, Jyoti, Lachance, Genevieve, Neville, Matthew, Santaniello, Adam, Caillier, Stacy J, Calavresi, Peter A, Cree, Bruce AC, Cross, Anne, Davis, Mary F, Haines, Jonathan L, de Bakker, Paul IW, Delgado, Silvia, Dembele, Marieme, Edwards, Keith, Fitzgerald, Kathryn C, Hakonarson, Hakon, Konidari, Ioanna, Lathi, Ellen, Manrique, Clara P, Pericak-Vance, Margaret A, Piccio, Laura, Schaefer, Cathy, McCabe, Cristin, Weiner, Howard, Goldstein, Jacqueline, Olsson, Tomas, Hadjigeorgiou, Georgios, Taylor, Bruce, Tajouri, Lotti, Charlesworth, Jac, Booth, David R, HArbo, Hanne F, Ivinson, Adrian J, Hauser, Stephen L, Compston, Alistair, Stewart, Graeme, Zipp, Frauke, Barcellos, Lisa F, Baranzini, Sergio E, Martinelli-Boneschi, Filippo, D'Alfonso, Sandra, Ziegler, Andreas, Oturai, Annette, McCauley, Jacob L, Sawcer, Stephen J, Oksenberg, Jorge R, De Jager, Philip L, Kockum, Ingrid, Hafler, David A, and Cotsapas, Chris
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Biochemistry & Molecular Biology ,Science & Technology ,REPLICATION ,LINKAGE ,Cell Biology ,GENETIC RISK ,GENOME-WIDE ASSOCIATION ,VARIANTS ,Life Sciences & Biomedicine ,METAANALYSIS ,POPULATION - Abstract
Multiple sclerosis is a complex neurological disease, with ∼20% of risk heritability attributable to common genetic variants, including >230 identified by genome-wide association studies. Multiple strands of evidence suggest that much of the remaining heritability is also due to additive effects of common variants rather than epistasis between these variants or mutations exclusive to individual families. Here, we show in 68,379 cases and controls that up to 5% of this heritability is explained by low-frequency variation in gene coding sequence. We identify four novel genes driving MS risk independently of common-variant signals, highlighting key pathogenic roles for regulatory T cell homeostasis and regulation, IFNγ biology, and NFκB signaling. As low-frequency variants do not show substantial linkage disequilibrium with other variants, and as coding variants are more interpretable and experimentally tractable than non-coding variation, our discoveries constitute a rich resource for dissecting the pathobiology of MS. ispartof: CELL vol:175 issue:6 pages:1679-1695 ispartof: location:United States status: published
- Published
- 2018
32. Low-Frequency and Rare-Coding Variation Contributes to Multiple Sclerosis Risk
- Author
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Mitrovič, Mitja, Patsopoulos, Nikolaos, Beecham, Ashley, Dankowski, Theresa, Goris, An, Dubois, Bénédicte, D’hooghe, Marie, Lemmens, Robin, Van Damme, Philip, Søndergaard, Helle Bach, Sellebjerg, Finn, Sorensen, Per Soelberg, Ullum, Henrik, Thørner, Lise, Werge, Thomas, Saarela, Janna, Cournu-Rebeix, Isabelle, Damotte, Vincent, Fontaine, Bertrand, Guillot-Noel, Lena, Lathrop, Mark, Vukusik, Sandra, Gourraud, Pierre-Antoine, Andlauer, Till F.M., Pongratz, Viola, Buck, Dorothea, Gasperi, Christiane, Bayas, Antonios, Heesen, Christoph, Kümpfel, Tania, Linker, Ralf, Paul, Friedemann, Stangel, Martin, Tackenberg, Björn, Bergh, Florian Then, Warnke, Clemens, Wiendl, Heinz, Wildemann, Brigitte, Zettl, Uwe, Ziemann, Ulf, Tumani, Hayrettin, Gold, Ralf, Grummel, Verena, Hemmer, Bernhard, Knier, Benjamin, Lill, Christina, Luessi, Felix, Dardiotis, Efthimios, Agliardi, Cristina, Barizzone, Nadia, Mascia, Elisabetta, Bernardinelli, Luisa, Comi, Giancarlo, Cusi, Daniele, Esposito, Federica, Ferrè, Laura, Comi, Cristoforo, Galimberti, Daniela, Leone, Maurizio, Sorosina, Melissa, Mescheriakova, Julia, Hintzen, Rogier, Van Duijn, Cornelia, Teunissen, Charlotte, Bos, Steffan, Myhr, Kjell-Morten, Celius, Elisabeth, Lie, Benedicte, Spurkland, Anne, Comabella, Manuel, Montalban, Xavier, Alfredsson, Lars, Stridh, Pernilla, Hillert, Jan, Jagodic, Maja, Piehl, Fredrik, Jelčić, Ilijas, Martin, Roland, Sospedra, Mireia, Ban, Maria, Hawkins, Clive, Hysi, Pirro, Kalra, Seema, Karpe, Fredrik, Khadake, Jyoti, Lachance, Genevieve, Neville, Matthew, Santaniello, Adam, Caillier, Stacy, Calabresi, Peter, Cree, Bruce A.C., Cross, Anne, Davis, Mary, Haines, Jonathan, de Bakker, Paul I.W., Delgado, Silvia, Dembele, Marieme, Edwards, Keith, Fitzgerald, Kathryn, Hakonarson, Hakon, Konidari, Ioanna, Lathi, Ellen, Manrique, Clara, Pericak-Vance, Margaret, Piccio, Laura, Schaefer, Cathy, McCabe, Cristin, Weiner, Howard, Goldstein, Jacqueline, Olsson, Tomas, Hadjigeorgiou, Georgios, Taylor, Bruce, Tajouri, Lotti, Charlesworth, Jac, Booth, David, Harbo, Hanne, Ivinson, Adrian, Hauser, Stephen, Compston, Alastair, Stewart, Graeme, Zipp, Frauke, Barcellos, Lisa, Baranzini, Sergio, Martinelli-Boneschi, Filippo, D’Alfonso, Sandra, Ziegler, Andreas, Oturai, Annette, McCauley, Jacob, Sawcer, Stephen, Oksenberg, Jorge, De Jager, Philip, Kockum, Ingrid, Hafler, David, Cotsapas, Chris, Søndergaard, Helle, Sorensen, Per, Andlauer, Till, Bergh, Florian, Cree, Bruce, De Bakker, Paul, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Centre de recherche en Myologie – U974 SU-INSERM, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), and Centre de Recherche en Myologie
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[SDV.MHEP.AHA]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO] - Abstract
International audience; Multiple sclerosis is a complex neurological disease, with ∼20% of risk heritability attributable to common genetic variants, including >230 identified by genome-wide association studies. Multiple strands of evidence suggest that much of the remaining heritability is also due to additive effects of common variants rather than epistasis between these variants or mutations exclusive to individual families. Here, we show in 68,379 cases and controls that up to 5% of this heritability is explained by low-frequency variation in gene coding sequence. We identify four novel genes driving MS risk independently of common-variant signals, highlighting key pathogenic roles for regulatory T cell homeostasis and regulation, IFNγ biology, and NFκB signaling. As low-frequency variants do not show substantial linkage disequilibrium with other variants, and as coding variants are more interpretable and experimentally tractable than non-coding variation, our discoveries constitute a rich resource for dissecting the pathobiology of MS.
- Published
- 2018
33. HTAPP_EZ Nuclei Isolation from frozen tissue v1
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Habib, Naomi, primary, Mccabe, Cristin, additional, Drokhlyansky, Eugene, additional, Rozenblatt-Rosen, Orit, additional, and Regev, Aviv, additional
- Published
- 2019
- Full Text
- View/download PDF
34. Low-Frequency and Rare-Coding Variation Contributes to Multiple Sclerosis Risk
- Author
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Mitrovič, Mitja, primary, Patsopoulos, Nikolaos A., additional, Beecham, Ashley H., additional, Dankowski, Theresa, additional, Goris, An, additional, Dubois, Bénédicte, additional, D’hooghe, Marie B., additional, Lemmens, Robin, additional, Van Damme, Philip, additional, Søndergaard, Helle Bach, additional, Sellebjerg, Finn, additional, Sorensen, Per Soelberg, additional, Ullum, Henrik, additional, Thørner, Lise W., additional, Werge, Thomas, additional, Saarela, Janna, additional, Cournu-Rebeix, Isabelle, additional, Damotte, Vincent, additional, Fontaine, Bertrand, additional, Guillot-Noel, Lena, additional, Lathrop, Mark, additional, Vukusik, Sandra, additional, Gourraud, Pierre-Antoine, additional, Andlauer, Till F.M., additional, Pongratz, Viola, additional, Buck, Dorothea, additional, Gasperi, Christiane, additional, Bayas, Antonios, additional, Heesen, Christoph, additional, Kümpfel, Tania, additional, Linker, Ralf, additional, Paul, Friedemann, additional, Stangel, Martin, additional, Tackenberg, Björn, additional, Bergh, Florian Then, additional, Warnke, Clemens, additional, Wiendl, Heinz, additional, Wildemann, Brigitte, additional, Zettl, Uwe, additional, Ziemann, Ulf, additional, Tumani, Hayrettin, additional, Gold, Ralf, additional, Grummel, Verena, additional, Hemmer, Bernhard, additional, Knier, Benjamin, additional, Lill, Christina M., additional, Luessi, Felix, additional, Dardiotis, Efthimios, additional, Agliardi, Cristina, additional, Barizzone, Nadia, additional, Mascia, Elisabetta, additional, Bernardinelli, Luisa, additional, Comi, Giancarlo, additional, Cusi, Daniele, additional, Esposito, Federica, additional, Ferrè, Laura, additional, Comi, Cristoforo, additional, Galimberti, Daniela, additional, Leone, Maurizio A., additional, Sorosina, Melissa, additional, Mescheriakova, Julia, additional, Hintzen, Rogier, additional, van Duijn, Cornelia, additional, Teunissen, Charlotte E., additional, Bos, Steffan D., additional, Myhr, Kjell-Morten, additional, Celius, Elisabeth G., additional, Lie, Benedicte A., additional, Spurkland, Anne, additional, Comabella, Manuel, additional, Montalban, Xavier, additional, Alfredsson, Lars, additional, Stridh, Pernilla, additional, Hillert, Jan, additional, Jagodic, Maja, additional, Piehl, Fredrik, additional, Jelčić, Ilijas, additional, Martin, Roland, additional, Sospedra, Mireia, additional, Ban, Maria, additional, Hawkins, Clive, additional, Hysi, Pirro, additional, Kalra, Seema, additional, Karpe, Fredrik, additional, Khadake, Jyoti, additional, Lachance, Genevieve, additional, Neville, Matthew, additional, Santaniello, Adam, additional, Caillier, Stacy J., additional, Calabresi, Peter A., additional, Cree, Bruce A.C., additional, Cross, Anne, additional, Davis, Mary F., additional, Haines, Jonathan L., additional, de Bakker, Paul I.W., additional, Delgado, Silvia, additional, Dembele, Marieme, additional, Edwards, Keith, additional, Fitzgerald, Kathryn C., additional, Hakonarson, Hakon, additional, Konidari, Ioanna, additional, Lathi, Ellen, additional, Manrique, Clara P., additional, Pericak-Vance, Margaret A., additional, Piccio, Laura, additional, Schaefer, Cathy, additional, McCabe, Cristin, additional, Weiner, Howard, additional, Goldstein, Jacqueline, additional, Olsson, Tomas, additional, Hadjigeorgiou, Georgios, additional, Taylor, Bruce, additional, Tajouri, Lotti, additional, Charlesworth, Jac, additional, Booth, David R., additional, Harbo, Hanne F., additional, Ivinson, Adrian J., additional, Hauser, Stephen L., additional, Compston, Alastair, additional, Stewart, Graeme, additional, Zipp, Frauke, additional, Barcellos, Lisa F., additional, Baranzini, Sergio E., additional, Martinelli-Boneschi, Filippo, additional, D’Alfonso, Sandra, additional, Ziegler, Andreas, additional, Oturai, Annette, additional, McCauley, Jacob L., additional, Sawcer, Stephen J., additional, Oksenberg, Jorge R., additional, De Jager, Philip L., additional, Kockum, Ingrid, additional, Hafler, David A., additional, and Cotsapas, Chris, additional
- Published
- 2019
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- View/download PDF
35. A cellular and spatial map of the choroid plexus across brain ventricles and ages
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Dani, Neil, primary, Herbst, Rebecca H., additional, Habib, Naomi, additional, Head, Joshua, additional, Dionne, Danielle, additional, Nguyen, Lan, additional, McCabe, Cristin, additional, Cui, Jin, additional, Shipley, Frederick B., additional, Jang, Ahram, additional, Rodman, Christopher, additional, Riesenfeld, Samantha J., additional, Zhang, Feng, additional, Rozenblatt-Rosen, Orit, additional, Regev, Aviv, additional, and Lehtinen, Maria K., additional
- Published
- 2019
- Full Text
- View/download PDF
36. Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer’s human brains
- Author
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Klein, Hans-Ulrich, primary, McCabe, Cristin, additional, Gjoneska, Elizabeta, additional, Sullivan, Sarah E., additional, Kaskow, Belinda J., additional, Tang, Anna, additional, Smith, Robert V., additional, Xu, Jishu, additional, Pfenning, Andreas R., additional, Bernstein, Bradley E., additional, Meissner, Alexander, additional, Schneider, Julie A., additional, Mostafavi, Sara, additional, Tsai, Li-Huei, additional, Young-Pearse, Tracy L., additional, Bennett, David A., additional, and De Jager, Philip L., additional
- Published
- 2018
- Full Text
- View/download PDF
37. Nuclei multiplexing with barcoded antibodies for single-nucleus genomics
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Gaublomme, Jellert T., primary, Li, Bo, additional, McCabe, Cristin, additional, Knecht, Abigail, additional, Drokhlyansky, Eugene, additional, Wittenberghe, Nicholas Van, additional, Waldman, Julia, additional, Dionne, Danielle, additional, Nguyen, Lan, additional, Jager, Phil De, additional, Yeung, Bertrand, additional, Zhao, Xinfang, additional, Habib, Naomi, additional, Rozenblatt-Rosen, Orit, additional, and Regev, Aviv, additional
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- 2018
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- View/download PDF
38. Additional file 1: Table S1. of Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimerâ s disease
- Author
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Patrick, Ellis, Sathyapriya Rajagopal, Hon-Kit Wong, McCabe, Cristin, Jishu Xu, Tang, Anna, Imboywa, Selina, Schneider, Julie, Pochet, Nathalie, Krichevsky, Anna, Chibnik, Lori, Bennett, David, and Jager, Philip De
- Abstract
Demographic information. Table S3. A table of the correlations between each of the pertinent covariates, Study, Age, Sex, NNLS, PMI, RIN, NP, NFT and AD. Figure S1. Behavior of miRNAs implicated in other experiments. Figure S2. Differentially expressed miRNAs and lincRNAs. Figure S3. Validation of RIN association. (DOCX 483 kb)
- Published
- 2017
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39. A multi-omic atlas of the human frontal cortex for aging and Alzheimer’s disease research
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De Jager, Philip L., primary, Ma, Yiyi, additional, McCabe, Cristin, additional, Xu, Jishu, additional, Vardarajan, Badri N., additional, Felsky, Daniel, additional, Klein, Hans-Ulrich, additional, White, Charles C., additional, Peters, Mette A., additional, Lodgson, Ben, additional, Nejad, Parham, additional, Tang, Anna, additional, Mangravite, Lara M., additional, Yu, Lei, additional, Gaiteri, Chris, additional, Mostafavi, Sara, additional, Schneider, Julie A., additional, and Bennett, David A., additional
- Published
- 2018
- Full Text
- View/download PDF
40. Epigenome-wide study uncovers tau pathology-driven changes of chromatin organization in the aging human brain
- Author
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Klein, Hans-Ulrich, primary, McCabe, Cristin, additional, Gjoneska, Elizabeta, additional, Sullivan, Sarah E., additional, Kaskow, Belinda J., additional, Tang, Anna, additional, Smith, Robert V., additional, Xu, Jishu, additional, Pfenning, Andreas R., additional, Bernstein, Bradley E., additional, Meissner, Alexander, additional, Schneider, Julie A., additional, Mostafavi, Sara, additional, Tsai, Li-Huei, additional, Young-Pearse, Tracy L., additional, Bennett, David A., additional, and De Jager, Philip L., additional
- Published
- 2018
- Full Text
- View/download PDF
41. A multi-omic atlas of the human frontal cortex for aging and Alzheimer's disease research
- Author
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De Jager, Phillip L, primary, Ma, Yiyi, additional, McCabe, Cristin, additional, Xu, Jishu, additional, Vardarajan, Badri N., additional, Felsky, Daniel, additional, Klein, Hans-Ulrich, additional, White, Charles C., additional, Peters, Mette A., additional, Lodgson, Ben, additional, Nejad, Parham, additional, Tang, Anna, additional, Mangravite, Lara M., additional, Yu, Lei, additional, Gaiteri, Chris, additional, Mostafavi, Sara, additional, Schneider, Julie A., additional, and Bennett, David A., additional
- Published
- 2018
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- View/download PDF
42. GEMS Project: A Platform to Investigate Multiple Sclerosis Risk
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Xia, Zongqi, White, Charles C., Owen, Emily K., Von Korff, Alina, Clarkson, Sarah R., McCabe, Cristin A., Cimpean, Maria, Winn, Phoebe A., Hoesing, Ashley, Steele, Sonya U., Cortese, Irene C. M., Chitnis, Tanuja, Weiner, Howard L., Reich, Daniel S., Chibnik, Lori B., and De Jager, Philip L.
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Adult ,Male ,Multiple Sclerosis ,Incidence ,Environment ,Middle Aged ,Polymorphism, Single Nucleotide ,Risk Assessment ,Article ,United States ,Risk Factors ,Humans ,Family ,Female ,Genetic Predisposition to Disease ,Longitudinal Studies - Abstract
The Genes and Environment in Multiple Sclerosis project establishes a platform to investigate the events leading to multiple sclerosis (MS) in at-risk individuals. It has recruited 2,632 first-degree relatives from across the USA. Using an integrated genetic and environmental risk score, we identified subjects with twice the MS risk when compared to the average family member, and we report an initial incidence rate in these subjects that is 30 times greater than that of sporadic MS. We discuss the feasibility of large-scale studies of asymptomatic at-risk subjects that leverage modern tools of subject recruitment to execute collaborative projects.
- Published
- 2015
43. Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection
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Ye, Chun Jimmie, primary, Chen, Jenny, additional, Villani, Alexandra-Chloé, additional, Gate, Rachel E., additional, Subramaniam, Meena, additional, Bhangale, Tushar, additional, Lee, Mark N., additional, Raj, Towfique, additional, Raychowdhury, Raktima, additional, Li, Weibo, additional, Rogel, Noga, additional, Simmons, Sean, additional, Imboywa, Selina H., additional, Chipendo, Portia I., additional, McCabe, Cristin, additional, Lee, Michelle H., additional, Frohlich, Irene Y., additional, Stranger, Barbara E., additional, De Jager, Philip L., additional, Regev, Aviv, additional, Behrens, Tim, additional, and Hacohen, Nir, additional
- Published
- 2017
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44. Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer’s disease
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Patrick, Ellis, primary, Rajagopal, Sathyapriya, additional, Wong, Hon-Kit Andus, additional, McCabe, Cristin, additional, Xu, Jishu, additional, Tang, Anna, additional, Imboywa, Selina H., additional, Schneider, Julie A., additional, Pochet, Nathalie, additional, Krichevsky, Anna M., additional, Chibnik, Lori B., additional, Bennett, David A., additional, and De Jager, Philip L., additional
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- 2017
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45. Genetic architecture of age-related cognitive decline in African Americans
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Raj, Towfique, primary, Chibnik, Lori B., additional, McCabe, Cristin, additional, Wong, Andus, additional, Replogle, Joseph M., additional, Yu, Lei, additional, Gao, Sujuan, additional, Unverzagt, Frederick W., additional, Stranger, Barbara, additional, Murrell, Jill, additional, Barnes, Lisa, additional, Hendrie, Hugh C., additional, Foroud, Tatiana, additional, Krichevsky, Anna, additional, Bennett, David A., additional, Hall, Kathleen S., additional, Evans, Denis A., additional, and De Jager, Philip L., additional
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- 2016
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46. Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer’s disease
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Patrick, Ellis, primary, Rajagopal, Sathyapriya, additional, Wong, Hon-Kit Andus, additional, McCabe, Cristin, additional, Xu, Jishu, additional, Tang, Anna, additional, Imboywa, Selina H., additional, Schneider, Julie A., additional, Pochet, Nathalie, additional, Krichevsky, Anna M., additional, Chibnik, Lori B., additional, Bennett, David A., additional, and De Jager, Philip L., additional
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- 2016
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47. NR1H3 p.Arg415Gln Is Not Associated to Multiple Sclerosis Risk
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Antel, Jack, primary, Ban, Maria, additional, Baranzini, Sergio, additional, Barcellos, Lisa, additional, Barizzone, Nadia, additional, Beecham, Ashley, additional, Berge, Tone, additional, Bernardinelli, Luisa, additional, Booth, David, additional, Bos, Steffan, additional, Buck, Dorothea, additional, Butkiewicz, Mariusz, additional, Celius, Elisabeth G., additional, Comabella, Manuel, additional, Compston, Alastair, additional, Dedham, Katrina, additional, Cotsapas, Chris, additional, D’ Alfonso, Sandra, additional, De Jager, Phil, additional, Dubois, Benedicte, additional, Duquette, Pierre, additional, Fontaine, Bertrand, additional, Gasperi, Christiane, additional, Gil, Elia, additional, Goris, An, additional, Gourraud, Pierre Antoine, additional, Graetz, Christiane, additional, Gyllenberg, Alexandra, additional, Hadjigeorgiou, Georgios, additional, Hafler, David, additional, Hribko, Deanna, additional, Haines, Jonathan, additional, Harbo, Hanne, additional, Hauser, Stephen, additional, Warto, Shannon, additional, Hawkins, Clive, additional, Hemmer, Bernhard, additional, Henry, Roland, additional, Hintzen, Rogier, additional, Horakova, Dana, additional, Ivinson, Adrian, additional, Howard, Melissa, additional, Jelcic, Ilijas, additional, Kaskow, Belinda, additional, Kira, Jun-Ichi, additional, Kleinova, Pavlina, additional, Kockum, Ingrid, additional, Kucerova, Karolina, additional, Lill, Christina, additional, Luessi, Felix, additional, Malhotra, Sunny, additional, Martin, Roland, additional, Martinelli, Filippo, additional, Matsushita, Takuya, additional, McCabe, Cristin, additional, McCauley, Jacob, additional, Mescheriakkova, Julia, additional, Mitrovic, Mitja, additional, Moen, Stine-Marit, additional, Montalban, Xavier, additional, Muhlau, Mark, additional, Nakmura, Yuri, additional, Oksenberg, Jorge, additional, Olsson, Tomas, additional, Oturai, Annette, additional, Palotie, Aarno, additional, Patsopoulos, Nikolaos, additional, Pavlicova, Jana, additional, Pericak-Vance, Peggy, additional, Piehl, Fredrik, additional, Rebeix, Isabelle, additional, Rioux, John, additional, Saarela, Janna, additional, Sawcer, Stephen, additional, Sellebjerg, Finn, additional, Sondergaard, Helle Bach, additional, Sorensen, Per Soelberg, additional, Sospedra, Mireia, additional, Spurkland, Anne, additional, Stewart, Graeme, additional, Taylor, Bruce, additional, Uitterlinden, Andre, additional, Van Duijn, Cornelia, additional, and Zipp, Frauke, additional
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- 2016
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48. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci
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Srivastava, Gyan, Lunnon, Katie, Burgess, Jeremy, Yu, Lei, Ernst, Jason, McCabe, Cristin, Tang, Anna, Raj, Towfique, Replogle, Joseph, Brodeur, Wendy, Gabriel, Stacey, Younkin, Curtis, Zou, Fanggeng, Szyf, Moshe, Meissner, Alexander, Ertekin-Taner, Nilufer, Kellis, Manolis, Mill, Jonathan, De Jager, Philip L., Schalkwyk, Leonard C., Eaton, Matthew Lucas, Eaton, Matthew L., Keenan, Brendan T., Chai, High S., Younkin, Steven G., Epstein, Charles B., Schneider, Julie A., Bernstein, Bradley E., Chibnik, Lori B., Bennett, David A., Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Eaton, Matthew Lucas, Ernst, Jason, Meissner, Alexander, and Kellis, Manolis
- Subjects
Male ,Aging ,Genome-wide association study ,Neurodegenerative ,Alzheimer's Disease ,80 and over ,2.1 Biological and endogenous factors ,Psychology ,Protein Interaction Maps ,Aetiology ,Epigenomics ,Genetics ,Aged, 80 and over ,General Neuroscience ,Intracellular Signaling Peptides and Proteins ,Brain ,Adaptor Proteins ,Nuclear Proteins ,Methylation ,Amyloidosis ,Middle Aged ,3. Good health ,CpG site ,Neurological ,DNA methylation ,Female ,Cognitive Sciences ,Alzheimer's disease ,Ankyrins ,and over ,Biology ,Article ,Alzheimer Disease ,Acquired Cognitive Impairment ,medicine ,Humans ,Genetic Predisposition to Disease ,Gene ,Adaptor Proteins, Signal Transducing ,Aged ,Neurology & Neurosurgery ,Tumor Suppressor Proteins ,Human Genome ,Signal Transducing ,Neurosciences ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,DNA Methylation ,medicine.disease ,Brain Disorders ,Differentially methylated regions ,Dementia ,CpG Islands ,Carrier Proteins ,Genome-Wide Association Study - Abstract
We used a collection of 708 prospectively collected autopsied brains to assess the methylation state of the brain's DNA in relation to Alzheimer's disease (AD). We found that the level of methylation at 71 of the 415,848 interrogated CpGs was significantly associated with the burden of AD pathology, including CpGs in the ABCA7 and BIN1 regions, which harbor known AD susceptibility variants. We validated 11 of the differentially methylated regions in an independent set of 117 subjects. Furthermore, we functionally validated these CpG associations and identified the nearby genes whose RNA expression was altered in AD: ANK1, CDH23, DIP2A, RHBDF2, RPL13, SERPINF1 and SERPINF2. Our analyses suggest that these DNA methylation changes may have a role in the onset of AD given that we observed them in presymptomatic subjects and that six of the validated genes connect to a known AD susceptibility gene network., National Institutes of Health (U.S.) (Grant R01 AG036042), National Institutes of Health (U.S.) (Grant R01AG036836), National Institutes of Health (U.S.) (Grant R01 AG17917), National Institutes of Health (U.S.) (Grant R01AG15819), National Institutes of Health (U.S.) (Grant R01 AG032990), National Institutes of Health (U.S.) (Grant R01 AG18023), National Institutes of Health (U.S.) (Grant RC2 AG036547), National Institutes of Health (U.S.) (Grant P30 AG10161), National Institutes of Health (U.S.) (Grant P50 AG016574), National Institutes of Health (U.S.) (Grant U01 ES017155), National Institutes of Health (U.S.) (Grant KL2 RR024151), National Institutes of Health (U.S.) (Grant K25 AG041906-01)
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- 2014
49. NMNAT2:HSP90 Complex Mediates Proteostasis in Proteinopathies
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Ali, Yousuf O., primary, Allen, Hunter M., additional, Yu, Lei, additional, Li-Kroeger, David, additional, Bakhshizadehmahmoudi, Dena, additional, Hatcher, Asante, additional, McCabe, Cristin, additional, Xu, Jishu, additional, Bjorklund, Nicole, additional, Taglialatela, Giulio, additional, Bennett, David A., additional, De Jager, Philip L., additional, Shulman, Joshua M., additional, Bellen, Hugo J., additional, and Lu, Hui-Chen, additional
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- 2016
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50. Methylation profiles in peripheral blood CD4+ lymphocytes versus brain: The relation to Alzheimer's disease pathology
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Yu, Lei, primary, Chibnik, Lori B., additional, Yang, Jingyun, additional, McCabe, Cristin, additional, Xu, Jishu, additional, Schneider, Julie A., additional, De Jager, Philip L., additional, and Bennett, David A., additional
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- 2016
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