Article
Neurosciences
Matthew J. Armstrong, Yulin Jin, Selina M. Vattathil, Yanting Huang, Jason P. Schroeder, David A. Bennet, Zhaohui S. Qin, Thomas S. Wingo, Peng Jin
Summary: Alzheimer's disease (AD) is a neurodegenerative disorder influenced by a complex interplay of environmental, epigenetic, and genetic factors. This study suggests that TET enzymes, particularly TET1, may contribute to AD pathogenesis by regulating the methylome. The loss of TET1 function increases AD-associated pathology.
NEUROBIOLOGY OF DISEASE
(2023)
Article
Neurosciences
Daniel Felsky, Ismael Santa-Maria, Mehmet Ilyas Cosacak, Leon French, Julie A. Schneider, David A. Bennett, Philip L. De Jager, Caghan Kizil, Giuseppe Tosto
Summary: Identifying ancestry-specific molecular profiles of late-onset Alzheimer's Disease (LOAD) in brain tissue is crucial to understand novel mechanisms and develop effective interventions in non-European, high-risk populations. We performed gene differential expression (DE) and consensus network-based analyses in RNA-sequencing data of postmortem brain tissue from 39 Caribbean Hispanics (CH). Our findings provide insights into the shared and specific genetic factors associated with LOAD in different ancestral populations.
NEUROBIOLOGY OF DISEASE
(2023)
Article
Microbiology
Joshua M. Wang, Andrew L. Woodruff, Matthew J. Dunn, Robert J. Fillinger, Richard J. Bennett, Matthew Z. Anderson
Summary: The research on 21 clinical isolates of Candida albicans showed extensive genetic and phenotypic variation, with strain-specific gene expression patterns and linkages between gene expression and phenotypic traits. The study highlights the importance of transcriptional profiling in understanding the genetic basis for phenotypic diversity and identifies new genes and pathways associated with pathogenic processes. These findings underscore the need for personalized treatment strategies based on individual strains of infectious fungi.
Article
Biochemistry & Molecular Biology
Eimi Yamaguchi, Tatsuya Akutsu, Jose C. Nacher
Summary: This study investigated age-related changes in the brain from a controllability perspective by analyzing gene expression profiles of individuals aged 20-99 years across four brain regions. A new algorithm was developed to efficiently identify critical proteins in probabilistic protein networks, revealing significant enrichment of well-known ageing genes among the identified critical proteins. In particular, potential new ageing gene candidates were identified in the hippocampal region for male samples involved in replicative and premature senescence processes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Benjamin D. Harris, Megan Crow, Stephan Fischer, Jesse Gillis
Summary: Gene co-expression networks reveal functional and co-regulatory relationships between genes, with single-cell RNA sequencing datasets offering insights into how gene-gene relationships shape cell identity. Comparison between single-cell and bulk RNA-seq data shows consistent topologies reflecting shared co-regulatory signals, with differential signals between broad cell classes persisting at finer levels. Convergent regulatory processes impact cell phenotype at multiple scales.
Article
Biochemistry & Molecular Biology
Liao Peng, Xi Jin, Bo-ya Li, Xiao Zeng, Bang-hua Liao, Tao Jin, Jia-wei Chen, Xiao-shuai Gao, Wei Wang, Qing He, Guo Chen, Li-na Gong, Hong Shen, Kun-jie Wang, Hong Li, De-yi Luo
Summary: Interstitial cystitis is a debilitating chronic disorder with unclear etiology and pathophysiology. Immune cells in the bladders of IC patients undergo significant changes, including increased immune cell populations and a virus-related response.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Article
Clinical Neurology
Hong-Dong Li, Cory C. Funk, Karen McFarland, Eric B. Dammer, Mariet Allen, Minerva M. Carrasquillo, Yona Levites, Paramita Chakrabarty, Jeremy D. Burgess, Xue Wang, Dennis Dickson, Nicholas T. Seyfried, Duc M. Duong, James J. Lah, Steven G. Younkin, Allan Levey, Gilbert S. Omenn, Nilufer Ertekin-Taner, Todd E. Golde, Nathan D. Price
Summary: In this study, intron retention (IR) was found to play a role in Alzheimer's disease (AD) through genome-wide analysis of genetic, transcriptomic, and proteomic data. Thousands of IR events were identified, along with differentially expressed genes associated with AD and splicing-related genes that may regulate IR. The findings provide a new resource for exploring new AD biomarkers and pathological mechanisms.
ALZHEIMERS & DEMENTIA
(2021)
Article
Plant Sciences
Lars H. Kruse, Benjamin Fehr, Jason D. Chobirko, Gaurav D. Moghe
Summary: This study provides insights into the functional evolution and prediction of the BAHD acyltransferase family in flowering plants. The expansion of BAHDs in land plants is associated with significant changes in gene features, and different plant groups exhibit clade expansions related to specific metabolite classes. Co-expression analysis and metabolic pathway models contribute to the recovery of metabolic processes and novel functional predictions for BAHD acyltransferases.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Cell Biology
Jingqi Wang, Maciej Daniszewski, Marlene M. Hao, Damian Hernandez, Alice Pebay, Paul A. Gleeson, Lou Fourriere
Summary: This study investigates the secretory pathways within dendrites of human neurons. It finds that the entire Golgi apparatus transiently translocates into dendrites during early neuronal development. In mature neurons, dynamic Golgi structures are transported along dendrites, showing bidirectional movement. This study reveals the presence of dynamic, functional Golgi structures in dendrites and provides insights into dendrite trafficking in human neurons.
Article
Biochemical Research Methods
Tamara Raschka, Meemansa Sood, Bruce Schultz, Aybuge Altay, Christian Ebeling, Holger Froehlich
Summary: This study proposes a novel hybrid AI approach named iVAMBN, which combines clinical and patient level gene expression data with a disease focused knowledge graph to develop a validated multi-scale model connecting molecular mechanisms with clinical outcomes in the field of Alzheimer's Disease (AD).
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yoonbee Kim, Jong-Hoon Park, Young-Rae Cho
Summary: Network-based computational approaches are used for efficient disease-gene association prediction. This survey provides an overview of network-based disease-gene association prediction methods and shows that integrative methods perform better.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Thomas Depuydt, Klaas Vandepoele
Summary: This study introduces a novel automated function prediction method that leverages complementary information from gene co-expression networks to successfully predict biological process annotations for Arabidopsis thaliana genes. Using experimental data validation, high-confidence functional annotations were obtained for unknown genes and genes with computational annotations, shedding light on a variety of developmental processes and molecular responses in Arabidopsis.
Article
Biology
Monica Leticia Martinez-Pacheco, Enrique Hernandez-Lemus, Carmen Mejia
Summary: Neuroblastoma is a common solid tumor that occurs in the nerve cells of children, most commonly in the adrenal glands. Current treatments have a low survival rate and are not tailored to individual genetic features. This study identified 104 genes that are shared by high-risk neuroblastoma patients and are involved in crucial cellular processes for cancer development.
Article
Multidisciplinary Sciences
Kosaku Masuda, Naohiro Kon, Kosuke Iizuka, Yoshitaka Fukada, Takeshi Sakurai, Arisa Hirano
Summary: The authors establish a method for estimating circadian entrainment characteristics using simple experiments and mathematical modeling. They demonstrate that singularity response analysis can be employed to unveil entrainment mechanisms with diverse stimuli in multiscale mammalian clocks.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Fangyuan Ding, Christina J. Su, KeHuan Kuo Edmonds, Guohao Liang, Michael B. Elowitz
Summary: A study has found that negative autoregulatory splicing of the splicing factor SRSF1 plays a critical role in gene regulation. It establishes an upper limit for SRSF1 protein concentration, reduces cell-to-cell variability in SRSF1 levels, and buffers transcriptional variation. Furthermore, this negative autoregulatory splicing adapts SRSF1 splicing activity to variations in demand from other pre-mRNA substrates.
Article
Biochemistry & Molecular Biology
Nikki K. Lytle, L. Paige Ferguson, Nirakar Rajbhandari, Kathryn Gilroy, Raymond G. Fox, Anagha Deshpande, Christian M. Schurch, Michael Hamilton, Neil Robertson, Pawan Noel, Martin Wartenberg, Inti Zlobec, Micha Eichmann, Jose A. Galvan, Eva Karamitopoulou, Tami Gilderman, Lourdes Adriana Esparza, Yutaka Shima, Philipp Spahn, Randall French, Nathan E. Lewis, Kathleen M. Fisch, Roman Sasik, Sara Brin Rosenthal, Marcie Kritzik, Daniel Von Hoff, Haiyong Han, Trey Ideker, Aniruddha J. Deshpande, Andrew M. Lowy, Peter D. Adams, Tannishtha Reya, Wei Lin
Article
Gastroenterology & Hepatology
Takahiro Nishio, Ronglin Hu, Yukinori Koyama, Shuang Liang, Sara B. Rosenthal, Gen Yamamoto, Daniel Karin, Jacopo Baglieri, Hsiao-Yen Ma, Jun Xu, Xiao Liu, Debanjan Dhar, Keiko Iwaisako, Kojiro Taura, David A. Brenner, Tatiana Kisseleva
JOURNAL OF HEPATOLOGY
(2019)
Article
Multidisciplinary Sciences
Sara Brin Rosenthal, Kevin T. Bush, Sanjay K. Nigam
SCIENTIFIC REPORTS
(2019)
Article
Gastroenterology & Hepatology
Xiao Liu, Jun Xu, Sara Rosenthal, Ling-juan Zhang, Ryan McCubbin, Nairika Meshgin, Linshan Shang, Yukinori Koyama, Hsiao-Yen Ma, Sonia Sharma, Sven Heinz, Chris K. Glass, Chris Benner, David A. Brenner, Tatiana Kisseleva
Article
Gastroenterology & Hepatology
Hsiao-Yen Ma, Gen Yamamoto, Jun Xu, Xiao Liu, Daniel Karin, Ju Youn Kim, Ludmil B. Alexandrov, Yukinori Koyama, Takahiro Nishio, Chris Benner, Sven Heinz, Sara B. Rosenthal, Shuang Liang, Mengxi Sun, Gabriel Karin, Peng Zhao, Pnina Brodt, Lain H. Mckillop, Oswald Quehenberger, Ed Dennis, Alan Saltiel, Hidekazu Tsukamoto, Bin Gao, Michael Karin, David A. Brenner, Tatiana Kisseleva
JOURNAL OF HEPATOLOGY
(2020)
Article
Multidisciplinary Sciences
David E. Gordon, Gwendolyn M. Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Kris M. White, Matthew J. O'Meara, Veronica V. Rezelj, Jeffrey Z. Guo, Danielle L. Swaney, Tia A. Tummino, Ruth Huttenhain, Robyn M. Kaake, Alicia L. Richards, Beril Tutuncuoglu, Helene Foussard, Jyoti Batra, Kelsey Haas, Maya Modak, Minkyu Kim, Paige Haas, Benjamin J. Polacco, Hannes Braberg, Jacqueline M. Fabius, Manon Eckhardt, Margaret Soucheray, Melanie J. Bennett, Merve Cakir, Michael J. McGregor, Qiongyu Li, Bjoern Meyer, Ferdinand Roesch, Thomas Vallet, Alice Mac Kain, Lisa Miorin, Elena Moreno, Zun Zar Chi Naing, Yuan Zhou, Shiming Peng, Ying Shi, Ziyang Zhang, Wenqi Shen, Ilsa T. Kirby, James E. Melnyk, John S. Chorba, Kevin Lou, Shizhong A. Dai, Inigo Barrio-Hernandez, Danish Memon, Claudia Hernandez-Armenta, Jiankun Lyu, Christopher J. P. Mathy, Tina Perica, Kala Bharath Pilla, Sai J. Ganesan, Daniel J. Saltzberg, Ramachandran Rakesh, Xi Liu, Sara B. Rosenthal, Lorenzo Calviello, Srivats Venkataramanan, Jose Liboy-Lugo, Yizhu Lin, Xi-Ping Huang, YongFeng Liu, Stephanie A. Wankowicz, Markus Bohn, Maliheh Safari, Fatima S. Ugur, Cassandra Koh, Nastaran Sadat Savar, Quang Dinh Tran, Djoshkun Shengjuler, Sabrina J. Fletcher, Michael C. O'Neal, Yiming Cai, Jason C. J. Chang, David J. Broadhurst, Saker Klippsten, Phillip P. Sharp, Nicole A. Wenzell, Duygu Kuzuoglu-Ozturk, Hao-Yuan Wang, Raphael Trenker, Janet M. Young, Devin A. Cavero, Joseph Hiatt, Theodore L. Roth, Ujjwal Rathore, Advait Subramanian, Julia Noack, Mathieu Hubert, Robert M. Stroud, Alan D. Frankel, Oren S. Rosenberg, Kliment A. Verba, David A. Agard, Melanie Ott, Michael Emerman, Natalia Jura, Mark von Zastrow, Eric Verdin, Alan Ashworth, Olivier Schwartz, Christophe D'Enfert, Shaeri Mukherjee, Matt Jacobson, Harmit S. Malik, Danica G. Fujimori, Trey Ideker, Charles S. Craik, Stephen N. Floor, James S. Fraser, John D. Gross, Andrej Sali, Bryan L. Roth, Davide Ruggero, Jack Taunton, Tanja Kortemme, Pedro Beltrao, Marco Vignuzzi, Adolfo Garcia-Sastre, Kevan M. Shokat, Brian K. Shoichet, Nevan J. Krogan
Article
Psychiatry
Elise Koch, Brin Rosenthal, Anders Lundquist, Chi-Hua Chen, Karolina Kauppi
SCHIZOPHRENIA RESEARCH
(2020)
Article
Immunology
Tongfei Liu, Bing Zhu, Yan Liu, Xiaoming Zhang, Jun Yin, Xiaoguang Li, LuLin Jiang, Andrew P. Hodges, Sara Brin Rosenthal, Lisa Zhou, Joel Yancey, Amanda McQuade, Mathew Blurton-Jones, Rudolph E. Tanzi, Timothy Y. Huang, Huaxi Xu
JOURNAL OF EXPERIMENTAL MEDICINE
(2020)
Article
Gastroenterology & Hepatology
Sara Brin Rosenthal, Xiao Liu, Souradipta Ganguly, Debanjan Dhar, Martina P. Pasillas, Eugenia Ricciardelli, Rick Z. Li, Ty D. Troutman, Tatiana Kisseleva, Christopher K. Glass, David A. Brenner
Summary: This study utilized single-cell RNA sequencing to characterize the phenotypic changes of hepatic stellate cells (HSCs) in a NASH model, revealing unexpected heterogeneity of HSC phenotypes under normal and injured states. The NASH livers showed four distinct HSC clusters, including one representing the classic fibrogenic myofibroblast, while livers with NASH regression had one cluster of inactivated HSCs similar to quiescent HSCs.
Article
Multidisciplinary Sciences
Carolina Makowski, Dennis van der Meer, Weixiu Dong, Hao Wang, Yan Wu, Jingjing Zou, Cin Liu, Sara B. Rosenthal, Donald J. Hagler, Chun Chieh Fan, William S. Kremen, Ole A. Andreassen, Terry L. Jernigan, Anders M. Dale, Kun Zhang, Peter M. Visscher, Jian Yang, Chi-Hua Chen
Summary: Genetic variants affecting regional cortical surface area and thickness in the brain were studied in adults and children, revealing 440 significant loci. The genetic variations in adulthood were found to already be present in childhood, showing signs of negative selection and associations with early neurodevelopment and neuropsychiatric risk.
Article
Gastroenterology & Hepatology
Nidhi P. Goyal, Sara B. Rosenthal, Chanod Nasamran, Cynthia A. Behling, Jorge E. Angeles, Mark H. Fishbein, Kathryn E. Harlow, Ajay K. Jain, Jean P. Mollewston, Kimberly P. Newton, Patricia Ugalde-Nicalo, Stavra A. Xanthankos, Katherine Yates, Nicholas J. Schork, Kathleen M. Fisch, Jeffrey B. Schwimmer
Summary: This study identified disease-associated SNPs in children with NAFLD, particularly rs6006473 which was highly associated with fibrosis severity. These hypothesis-generating results support future mechanistic studies of the development of adverse outcomes such as fibrosis and the generation of therapeutic targets for children with NAFLD.
Article
Medicine, Research & Experimental
Jun Xu, Hsiao-Yen Ma, Xiao Liu, Sara Rosenthal, Jacopo Baglieri, Ryan McCubbin, Mengxi Sun, Yukinori Koyama, Cedric G. Geoffroy, Kaoru Saijo, Linshan Shang, Takahiro Nishio, Igor Maricic, Max Kreifeldt, Praveen Kusumanchi, Amanda Roberts, Binhai Zheng, Vipin Kumar, Karsten Zengler, Donald P. Pizzo, Mojgan Hosseini, Candice Contet, Christopher K. Glass, Suthat Liangpunsakul, Hidekazu Tsukamoto, Bin Gao, Michael Karin, David A. Brenner, George F. Koob, Tatiana Kisseleva
Article
Gastroenterology & Hepatology
Xiao Liu, Sara Brin Rosenthal, Nairika Meshgin, Jacopo Baglieri, Sami G. Musallam, Karin Diggle, Kevin Lam, Raymond Wu, Stephanie Q. Pan, Yibu Chen, Ken Dorko, Sharon Presnell, Chris Benner, Mojgan Hosseini, Hidekazu Tsukamoto, David Brenner, Tatiana Kisseleva
HEPATOLOGY COMMUNICATIONS
(2020)
Article
Rheumatology
Roxana Coras, Arthur Kavanaugh, Tristan Boyd, Doquyen Huynh, Kim A. Lagerborg, Yong-Jiang Xu, Sarah B. Rosenthal, Mohit Jain, Monica Guma
CLINICAL AND EXPERIMENTAL RHEUMATOLOGY
(2019)
Article
Gastroenterology & Hepatology
Sara Brin Rosenthal, Xiao Liu, Souradipta Ganguly, Debanjan Dhar, Martina P. Pasillas, Eugenia Ricciardelli, Rick Z. Li, Ty D. Troutman, Tatiana Kisseleva, Christopher K. Glass, David A. Brenner
Summary: The phenotypic changes of hepatic stellate cells (HSCs) were studied in a NASH model using foz/foz mice, revealing unexpected heterogeneity in HSC populations under normal and injured states.