Article
Biochemistry & Molecular Biology
Ullas Valiya Chembazhi, Wesley S. Tung, Hyojeong Hwang, Yuexi Wang, Aryan Lalwani, Ka Lam Nguyen, Sushant Bangru, Danielle Yee, Kristy Chin, Jing Yang, Auinash Kalsotra, Wenyan Mei
Summary: Intestinal epithelial regeneration is driven by intestinal stem cells. Upon the loss of intestinal stem cells, differentiated intestinal epithelial cells, such as Paneth cells, are capable of acquiring multipotency and contributing to regeneration. Depletion of an RNA-binding protein named PTBP1 in mouse intestinal epithelial cells leads to intestinal stem cell death and epithelial regeneration failure.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Immunology
Gustavo Ulises Martinez-Ruiz, Abigail Morales-Sanchez, Avinash Bhandoola
Summary: The thymus is crucial for the development of T cell subsets, with interest in manipulating thymic function for therapeutic purposes in various conditions. Thymic epithelial cells play essential roles in directing T cell development and are regulated by several transcription factors. While some transcription factors have been studied in detail, the roles of many others remain unclear, suggesting potential for new discoveries in this field.
IMMUNOLOGICAL REVIEWS
(2022)
Article
Chemistry, Multidisciplinary
Li-jun Liang, Di Wang, Hong Yu, Jun Wang, Hui Zhang, Bei-bei Sun, Fu-ying Yang, Zheng Wang, Da-wei Xie, Rui-E Feng, Kai-feng Xu, Gui-zhen Wang, Guang-biao Zhou
Summary: In this study, the researchers evaluated the transcription factors that regulate ACE2 expression and identified 24 potential regulators, with Stat3 being the most significant one. They also found that a compound called 6-OAP could effectively inhibit ACE2 expression and reduce IL-6 production. Moreover, 6-OAP was found to inhibit the entry of SARS-CoV-2 into target cells.
ACTA PHARMACOLOGICA SINICA
(2022)
Article
Gastroenterology & Hepatology
Nga Le, Claire Mazahery, Kien Nguyen, Alan D. Levine
Summary: The study reveals that communication between T cells and the intestinal epithelium can impact epithelial barrier function by regulating the assembly of tight junction complex. Activated T cells have different effects on ion flux and cell morphology, ultimately leading to cell death or disruption.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2021)
Review
Dermatology
Yinglu Guan, Youn Joo Yang, Priyadharsini Nagarajan, Yejing Ge
Summary: Epithelial stem cells play crucial roles in maintaining skin homeostasis, wound repair, and cancer, with their function tightly controlled by various transcriptional and signaling mechanisms. After injury, stem cells exhibit lineage plasticity and adjust their differentiation fate according to damage signals.
EXPERIMENTAL DERMATOLOGY
(2021)
Article
Immunology
Nongthombam Boby, Xuewei Cao, Alyssa Ransom, Barcley T. Pace, Christopher Mabee, Monica N. Shroyer, Arpita Das, Peter J. Didier, Sudesh K. Srivastav, Edith Porter, Qiuying Sha, Bapi Pahar
Summary: Research has shown that under SIV infection, intestinal epithelial regeneration decreases, certain cell types increase, and differentially expressed genes in important pathways are downregulated. Despite the lack of significant reduction in stem cell population, dysregulation of intestinal stem cell niche factors, presence of inflammatory factors, and loss of epithelial barrier function, suggest that SIV infection impacts epithelial cell proliferation and intestinal homeostasis.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Cell Biology
Digvijay Singh, Rohit K. Deshmukh, Amitava Das
Summary: The study identified the crucial role of SNAI1 in inducing the expression of differentially expressed genes in breast cancer cells, leading to increased migration, invasion, and in vitro tumorigenesis, comparable to TNBC. The activation of breast cancer stem cell (CSC) phenotypes mediated by SNAI1 was perturbed by inhibiting downstream target MMPs, highlighting the importance of MMPs in SNAI1-mediated EMT regulation.
CELLULAR SIGNALLING
(2021)
Article
Multidisciplinary Sciences
Siranart Jeerawattanawart, Adithap Hansakon, Sittiruk Roytrakul, Pornpimon Angkasekwinai
Summary: Adiponectin expression is increased in the small intestine following helminth infection, and it is strongly associated with the expression of IL-25, IL-33, and TSLP. Adiponectin enhances intestinal epithelial cell responses and improves barrier function. Adiponectin also promotes IL-13 secretion and worm clearance in vivo.
SCIENTIFIC REPORTS
(2023)
Article
Agriculture, Dairy & Animal Science
Pengfei Hou, Caihong Wang, Miaomiao Zhou, Hongyun Liu
Summary: This study investigated the regulation, uptake, and transport of dipeptides in bovine intestinal epithelial cells, finding that temperature, pH, other dipeptides, and the PI3K/AKT signaling pathway significantly affect the absorption and transport of the dipeptide Gly-Sar-FITC.
JOURNAL OF ANIMAL PHYSIOLOGY AND ANIMAL NUTRITION
(2022)
Article
Cell Biology
Zachary K. Criss, Nobel Bhasin, Sara C. Di Rienzi, Anubama Rajan, Kali Deans-Fielder, Ganesh Swaminathan, Nabiollah Kamyabi, Xi-Lei Zeng, Harsha Doddapaneni, Vipin K. Menon, Deepavali Chakravarti, Clarissa Estrella, Xiaomin Yu, Ketki Patil, Joseph F. Petrosino, James C. Fleet, Michael P. Verzi, Sylvia Christakos, Michael A. Helmrath, Sumimasa Arimura, Ronald A. DePinho, Robert A. Britton, Anthony W. Maresso, K. Jane Grande-Allen, Sarah E. Blutt, Sue E. Crawford, Mary K. Estes, Sasirekha Ramani, Noah F. Shroyer
Summary: The study investigated the impact of common variations in culture methods on the transcriptome of human intestinal epithelial organoids, finding that substrate and format had the largest effects on transcriptomic variation, while patient heterogeneity and specific experimental manipulations had smaller effects. Results show that variations in culture conditions can significantly influence intestinal organoids and should be considered when designing experiments and comparing results between laboratories.
PHYSIOLOGICAL GENOMICS
(2021)
Review
Immunology
Joshua Oluoch Amimo, Sergei Alekseevich Raev, Juliet Chepngeno, Alfred Omwando Mainga, Yusheng Guo, Linda Saif, Anastasia N. Vlasova
Summary: Rotavirus is a major pathogen causing severe diarrheal illness in young children and animals worldwide, infecting mature enterocytes in the intestinal epithelium. The immune system of intestinal epithelial cells plays a crucial role in countering rotavirus invasion, while rotavirus has evolved mechanisms to evade host immunity. Understanding the mechanisms of rotavirus-IECs interactions is essential for developing strategies to control infections.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Cell Biology
Wei Yu, V. Praveen Chakravarthi, Shaon Borosha, Iman Dilower, Eun Bee Lee, Anamika Ratri, Rebekah R. Starks, Patrick E. Fields, Michael W. Wolfe, M. Omar Faruque, Geetu Tuteja, M. A. Karim Rumi
Summary: The study reveals that trophoblast-specific Satb1 expression is regulated by long-range chromatin looping mediated by an enhancer that interacts with ELF5 and SATB proteins, contributing to the maintenance of cell state.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Spela Konjar, Miha Pavsic, Marc Veldhoen
Summary: The unique biology of the intestinal epithelial barrier is linked to low oxygen pressure and hypoxia-inducible factor-dependent signaling; communication between microbiota and the gut plays a crucial role in maintaining oxygen homeostasis and intestinal health.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell & Tissue Engineering
Semir Beyaz, Charlie Chung, Haiwei Mou, Khristian E. Bauer-Rowe, Michael E. Xifaras, Ilgin Ergin, Lenka Dohnalova, Moshe Biton, Karthik Shekhar, Onur Eskiocak, Katherine Papciak, Kadir Ozler, Mohammad Almeqdadi, Brian Yueh, Miriam Fein, Damodaran Annamalai, Eider Valle-Encinas, Aysegul Erdemir, Karoline Dogum, Vyom Shah, Aybuke Alici-Garipcan, Hannah V. Meyer, Deniz M. Ozata, Eran Elinav, Alper Kucukural, Pawan Kumar, Jeremy P. McAleer, James G. Fox, Christoph A. Thaiss, Aviv Regev, Jatin Roper, Stuart H. Orkin, Omer H. Yilmaz
Summary: A high-fat diet reduces MHC class II gene expression in intestinal epithelial cells, affecting microbiome diversity. The expression of epithelial MHC class II is regulated by intestinal flora through PRR and IFNg signaling. MHC-II-ISCs have greater tumor-initiating capacity compared to MHC-II+ counterparts under the influence of a high-fat diet, showing the role of immune surveillance in suppressing tumorigenesis.
Article
Medicine, Research & Experimental
Harleen Kaur, Anjeza Erickson, Regis Moreau
Summary: mTORC1 plays a differential role in the immune responses of THP-1-derived macrophages and Caco-2 epithelial cells in a pro-inflammatory microenvironment, impacting cytokine gene expression through manipulation of mTORC1 activity.
Article
Microbiology
Lihua Ye, Munhyung Bae, Chelsi D. Cassilly, Sairam Jabba, Daniel W. Thorpe, Alyce M. Martin, Hsiu-Yi Lu, Jinhu Wang, John D. Thompson, Colin R. Lickwar, Kenneth D. Poss, Damien J. Keating, Sven-Eric Jordt, Jon Clardy, Rodger A. Liddle, John F. Rawls
Summary: This study demonstrates that epithelial sensory enteroendocrine cells (EEC) in the intestinal epithelium can sense and respond to microbial stimuli through the Trpa1 receptor, leading to activation of vagal neuronal pathways and increased intestinal motility. Furthermore, indole derivatives of tryptophan catabolism also play a role in this process by activating Trpa1 signaling and stimulating intestinal serotonin secretion.
CELL HOST & MICROBE
(2021)
Article
Endocrinology & Metabolism
Jessica R. McCann, Nathan A. Bihlmeyer, Kimberly Roche, Cameron Catherine, Jayanth Jawahar, Lydia Coulter Kwee, Noelle E. Younge, Justin Silverman, Olga Ilkayeva, Charles Sarria, Alexandra Zizzi, Janet Wootton, Lisa Poppe, Paul Anderson, Michelle Arlotto, Zhengzheng Wei, Joshua A. Granek, Raphael H. Valdivia, Lawrence A. David, Holly K. Dressman, Christopher B. Newgard, Svati H. Shah, Patrick C. Seed, John F. Rawls, Sarah C. Armstrong
Summary: The study aimed to establish a biorepository of samples from adolescents with obesity undergoing lifestyle modification. Initial findings suggest a unique metabolic signature of obesity in adolescents, as well as confirmation of previously reported metabolic and microbiome markers.
Article
Multidisciplinary Sciences
Chuyi Chen, Yuyang Gu, Julien Philippe, Peiran Zhang, Hunter Bachman, Jinxin Zhang, John Mai, Joseph Rufo, John F. Rawls, Erica E. Davis, Nicholas Katsanis, Tony Jun Huang
Summary: A novel acoustofluidic rotational tweezing platform has been developed for contactless, high-speed, 3D multispectral imaging and digital reconstruction of zebrafish larvae, allowing quantitative phenotypic analysis. This technology has the potential to be a valuable asset in various fields, especially in biomedical research, biochemistry screening, and preclinical drug development.
NATURE COMMUNICATIONS
(2021)
Article
Ecology
Matthew S. Kelly, Catherine Plunkett, Yahe Yu, Jhoanna N. Aquino, Sweta M. Patel, Jillian H. Hurst, Rebecca R. Young, Marek Smieja, Andrew P. Steenhoff, Tonya Arscott-Mills, Kristen A. Feemster, Sefelani Boiditswe, Tirayaone Leburu, Tiny Mazhani, Mohamed Z. Patel, John F. Rawls, Jayanth Jawahar, Samir S. Shah, Christopher R. Polage, Coleen K. Cunningham, Patrick C. Seed
Summary: This study conducted in sub-Saharan Africa examined the nasopharyngeal microbiome of 179 mother-infant dyads to investigate the relationship between Corynebacterium abundance and Streptococcus pneumoniae colonization in infants. Results showed a negative correlation between Corynebacterium abundance and S. pneumoniae colonization, with in vitro experiments demonstrating growth inhibition of S. pneumoniae by secreted factors from Corynebacterium strains isolated from infants. Additionally, antibiotic exposure and seasonal variations were associated with changes in Corynebacterium abundance, suggesting potential implications for preventing pneumococcal infections.
Article
Physiology
Adelaide Tovar, Wesley L. Crouse, Gregory J. Smith, Joseph M. Thomas, Benjamin P. Keith, Kathryn M. McFadden, Timothy P. Moran, Terrence S. Furey, Samir N. P. Kelada
Summary: This study aimed to explore the effects of strain, exposure, and strain-by-O3 exposure interactions on airway macrophage (AM) gene expression, as well as to identify transcriptional correlates of O3-induced inflammation and injury. The results showed that O3 exposure resulted in airway neutrophilia and lung injury, with differences in gene expression between different strains likely contributing to their varying responses to O3.
AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY
(2022)
Article
Pediatrics
Lilianna Suarez, Asheley C. Skinner, Tracy Truong, Jessica R. McCann, John F. Rawls, Patrick C. Seed, Sarah C. Armstrong
Summary: In a specialized healthcare setting, a significant number of adolescents opt for new and advanced obesity treatments, particularly those at higher risk for developing diabetes.
Article
Biotechnology & Applied Microbiology
Jayanth Jawahar, Alexander W. McCumber, Colin R. Lickwar, Caroline R. Amoroso, Sol Gomez de la Torre Canny, Sandi Wong, Margaret Morash, James H. Thierer, Steven A. Farber, Brendan J. M. Bohannan, Karen Guillemin, John F. Rawls
Summary: This study reveals the effects of long-term starvation and refeeding on the intestinal transcriptome and microbiome in zebrafish. Starvation leads to changes in intestinal microbiome composition and host gene expression, which are rapidly reversed after refeeding.
Article
Immunology
Jillian H. Hurst, Alexander W. McCumber, Jhoanna N. Aquino, Javier Rodriguez, Sarah M. Heston, Debra J. Lugo, Alexandre T. Rotta, Nicholas A. Turner, Trevor S. Pfeiffer, Thaddeus C. Gurley, M. Anthony Moody, Thomas N. Denny, John F. Rawls, James S. Clark, Christopher W. Woods, Matthew S. Kelly
Summary: The upper respiratory microbiome features are associated with SARS-CoV-2 infection susceptibility and symptoms among children, adolescents, and young adults, and the relationship is influenced by age.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Gastroenterology & Hepatology
Colin R. Lickwar, James M. Davison, Cecelia Kelly, Gilberto Padilla Mercado, Jia Wen, Briana R. Davis, Matthew C. Tillman, Ivana Semova, Sarah F. Andres, Goncalo Vale, Jeffrey G. McDonald, John F. Rawls
Summary: This study reveals that the combination of microbiota and high-fat diet may suppress the expression of hepatocyte nuclear factor 4 alpha, leading to the preferential activation of intestinal epithelial cell proliferation programs, which in turn affects intestinal lipid absorption, epithelial cell renewal, and systemic energy balance.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2022)
Article
Gastroenterology & Hepatology
Ismael Gomez-Martinez, R. Jarrett Bliton, Keith A. Breau, Michael J. Czerwinski, Ian A. Williamson, Jia Wen, John F. Rawls, Scott T. Magness
Summary: Through single-cell RNA sequencing, it was found that the expression of lipid-handling genes increases as absorptive enterocytes mature. Culture conditions promote differentiation of intestinal stem cells into dense absorptive enterocyte monolayers. Fatty acid oxidation modulation affects fatty acid export, while short-chain fatty acids are unaffected.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2022)
Review
Immunology
Jean-Pierre Levraud, John F. Rawls, Anne E. Clatworthy
Summary: Animals rely on their nervous and immune systems to perceive and adapt to their environment, with microorganisms playing a significant role. The zebrafish serves as a model organism for studying the interactions between the immune and nervous systems, the nervous system and the microbiota, and the microbiota and immune system.
JOURNAL OF NEUROINFLAMMATION
(2022)
Article
Biochemistry & Molecular Biology
Wenxin Tong, Sarah A. Hannou, You Wang, Inna Astapova, Ashot Sargsyan, Ruby Monn, Venkataramana Thiriveedi, Diana Li, Jessica R. McCann, John F. Rawls, Jatin Roper, Guo-fang Zhang, Mark A. Herman
Summary: The tricarboxylic acid (TCA) cycle plays a crucial role in cellular aerobic metabolism, producing energy and precursor molecules while also acting as a signaling pathway. Research shows that the gut is a major contributor to circulating TCA cycle metabolites, with endogenous succinate production being a key physiological source.
Article
Genetics & Heredity
Jennifer K. Heppert, Colin R. Lickwar, Matthew C. Tillman, Briana R. Davis, James M. Davison, Hsiu-Yi Lu, Wei Chen, Elisabeth M. Busch-Nentwich, David L. Corcoran, John F. Rawls
Summary: Transcription factors hnf4a and hnf4g play important roles in the development and function of the intestinal epithelium, showing partial genetic redundancy.
Article
Biochemical Research Methods
Nolan H. Hamilton, Terrence S. Furey
Summary: ROCCO is a novel method that determines consensus open chromatin regions across multiple samples simultaneously. It utilizes robust summary statistics and solves a constrained optimization problem to consider both the enrichment and spatial dependence of open chromatin signal data. We demonstrate that this method has attractive theoretical and conceptual properties and shows superior empirical performance compared to current methodology.
Meeting Abstract
Gastroenterology & Hepatology
Cecelia Kelly, Lauren Davey, Jayanth Jawahar, Jeffrey I. Everitt, Joseph Galanko, Jonathan E. Avendano, Jessica R. McCann, R. Balfour Sartor, Raphael H. Valdivia, John F. Rawls