Evaluating Eosinophilic Colitis as a Unique Disease Using Colonic Molecular Profiles: A Multi-Site Study

Shoda, Tetsuo; Rochman, Mark; Wen, Ting; Caldwell, Julie M.; Mack, Lydia E; Osswald, G. A.; Besse, John A.; Haberman, Yael; Denson, Lee A.; Abonia, J. Pablo; Aceves, Seema S.; Almonte, Samuel; Andrews, Rachel; Anvari, Sara; Arrington, Ashley; Arva, Nicoleta C.; Atkins, Fred M.; Bailey, Dominique D.; Berry, Andrea; Besl, Bridget; Bolton, Scott M.; Bonis, Peter A; Book, Wendy; Bray, Kimberly; Brown, Teresa; Burger, Cassandra; Burke, Deirdre; Cahoon, Jonathon; Capocelli, Kelley E.; Chehade, Mirna; Chiou, Eric; Collins, Margaret H.; Davis, Carla M.; Dellon, Evan S.; DeMarshall, Maureen; DiTommaso, Lauren A.; Dohil, Ranjan; Eby, Michael D.; Falk, Gary W.; Fleischer, David E.; Foote, Heather; Foss, Kelci; Friedlander, Joel A.; Fulkerson, Patricia C.; Furuta, Glenn T.; Geno, Debra M.; Gonsalves, Nirmala; Greuter, Thomas; Gupta, Sandeep K.; Hamilton, Frank A.; Harris, Kirk; Harris, Jennifer W.; Hirano, Ikuo; Hiremath, Girish; Holland-Thomas, Nicole; Jacinto, Lea; Kagalwalla, Amir F.; Kaseta, Timothy; Katzka, David A.; Keeley, Kaitlin; Khosh-Hemmat, Emad; Khoury, Paneez; King, Eileen; Kliewer, Kara; Klion, Amy D.; Knowles, Jennifer; Kocher, Kendra; Kodroff, Ellyn; Krischer, Jeffrey P.; Kyle, Shay; Leung, John; Levy, Meredith; Liacouras, Chris A.; Mack, Denise; Martin, Lisa J.; Martín, E; McCright-Gill, Talaya; Menard‐Katcher, Paul; Menard‐Katcher, Calies; Mendoza, Gabriela; Mingler, Melissa K.; Minnicozzi, Mike; Muir, Amanda B.; Mukkada, Vincent A.; Murray-Petzold, Cristin; Newbury, Robert; Nhu, Quan M.; Olivé, Anthony; Oyibo, Oghenekpaobor; Paliana, Allisa; Pan, Zhaoxing; Pesek, Robbie D.; Peterson, Kathryn A.; Poppendeck, Heidi; Putnam, Philip E.; Rivera, Fabian de Labastida; Rothenberg, Marc E.; Spergel, Amanda Rudman; Sable, Kathleen; Schoepfer, Alain; Scott, Melissa; Sheridan, Rachel; Sinanović, Selma; Spergel, Jonathan M.; Strobel, Mary Jo; Sun, Kiki; Tasco, Amy; Tholen, Crystal; Thompson, Katherine A.; Tomkinson, Tiffany; Tran, Daisy; Tylicki, Alexandra E.; Urv, Tiina K.; Wang, Mei-Lun; Wechsler, Joshua B.; Wershil, Barry K.; Wheatley, L Lojero; Wilkey, Leah; Yang, Guang–Yu; Zalewski, Angelika; Zicarelli, Amy

doi:10.1053/j.gastro.2022.01.022

Cited by 25 publications

(10 citation statements)

References 52 publications

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“…Western blot experiments showed that FOSB expression was downregulated in U87 and U251 cell lines, which indicated that FOSB had been knocked down successfully and that stable transfection cell lines had been successfully established ( ** P < 0.01; Figures 2A , B ). Activation of caspase 3 is central to apoptosis (Shoda et al, 2022 ). The regulatory steps of mitochondrial apoptosis are mediated by the Bcl-2 family of proteins.…”

Section: Resultsmentioning

confidence: 99%

Expression and potential role of FOSB in glioma

Sun

Zheng

et al. 2022

Front. Mol. Neurosci.

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BackgroundFOSB is reported to be an oncogene in a variety of tumors. However, the expression and role of FOSB in glioma remain obscure. In this study, we aimed to explore the expression of FOSB in glioma and its biological role in glioblastoma multiforme (GBM).MethodsWestern blot, immunohistochemical staining, and quantitative real-time polymerase chain reaction (RT-qPCR) were used to detect the expression of FOSB in clinical samples. FOSB was knocked down in cells to determine the effects of FOSB on the phenotypic changes of tumors by plate cloning, CCK-8 assay, and Transwell assay. Finally, subcutaneous tumorigenesis in nude mice was used to observe the tumorigenesis of glioma cell lines after the knockdown of the FOSB gene.ResultsFOSB expression was higher in glioma compared with normal brain tissue. After the downregulation of FOSB, the expression of cleaved caspase-3 increased. Plate cloning and CCK-8 experiments showed that the proliferation of glioma cell lines decreased. The Transwell assay demonstrated that the glioblastoma cell lines had lower migration ability after the knockdown of FOSB. Finally, the tumor volume of U87 glioma cells in group sh-FOSB was smaller than that in the control group. The TUNEL staining in vitro showed that the apoptosis of sh-FOSB glioma cells increased.ConclusionFOSB was highly expressed in glioma tissues. The viability of glioma cells decreased, and the ability of glioma cells to proliferate and migrate was reduced when FOSB was downregulated. Hence, FOSB may promote the development and migration of gliomas.

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Section: Resultsmentioning

confidence: 99%

Expression and potential role of FOSB in glioma

Sun

Zheng

et al. 2022

Front. Mol. Neurosci.

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“…Since its inception in 2019, it has demonstrated its utility at the local laboratory level and beyond such as by generating interest from collaborators in academia and industry. At least 12 publications have already been facilitated by EGIDExpress 15, 16, 17, 18, 19,20, 21, 14, 22, 23, 24, 25 . Datasets will continue to be added to EGIDExpress as they are generated, and we remain flexible to adding new data formats or modes of visualization as new dataset types arise, and we are open to developing new functionalities within the app.…”

Section: Resultsmentioning

confidence: 99%

“…A pharmaceutical company has already written an article based on the data derived EGIDExpress, proving that we are accelerating hypothesis generation and new data analysis 13 . Deposition of a dataset on EGIDExpress has already in one case satisfied a journal's requirement for data deposition in a publicly available repository 14 . Published data are freely available for individuals who have personal interest in learning about EGIDs and the research occurring in the Rothenberg CURED Lab, such as patients or patient advocacy groups; they can browse the site for their own scientific efforts or to see the progress being made in the lab.…”

Section: Resultsmentioning

confidence: 99%

EGIDExpress: An Interactive Shiny Web App to Visualize and Share Large Biological Datasets

Besse

Osswald

Ballaban

et al. 2022

Preprint

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Biomedical research on rare diseases faces challenges such as low availability of biological specimens to study and limited funding. Eosinophilic gastrointestinal diseases (EGIDs) are rare conditions associated with inappropriate inflammation and the accumulation of eosinophils in various segments of the gastrointestinal tract. We aimed to build a repository of large datasets related to EGIDs that would be easily browsable, interpretable, and accessible in order to facilitate data sharing and hypothesis generation. Using the R-code based package Shiny, we built a website that allows visualization of multiple types of datasets including microarray, RNAseq, protein array, single-cell RNAseq, and ChIPseq. Users can access EGIDExpress (https://egidexpress.research.cchmc.org/) to browse data on a per-gene basis and to generate graphic representation of the data. Additionally, users can download the processed data to initiate their own analyses. Within 34 months of launching EGIDExpress, over 2400 users from 37 countries and 37 states within the United States accessed the site. Overall, EGIDExpress is accelerating research on EGIDs and provides a prototypic platform for broad research data sharing.

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“…Any segment of the GI tract may be affected and symptoms are usually related to the segment and depth of bowel involved [2]. The common underlying pathophysiology for EGIDs is thought to be immune-mediated chronic inflammation strongly linked with food allergen triggers and genetic factors [2,3 ▪ ,4 ▪▪ ]. Therapeutic strategies involve medications targeting inflammatory pathways and/or dietary elimination of potential food allergens [5].…”

Section: Introductionmentioning

confidence: 99%

“…Eosinophilic esophagitis (EoE) is the most common and best characterized EGID, with detailed understanding of pathophysiologic mechanisms developed over several decades leading to clear diagnostic criteria and society guideline recommendations for management [6–8]. The following review will focus on recent updates in non-EoE EGIDs, which have been increasingly studied to develop better understanding of disease pathophysiology, epidemiology, accurate diagnosis and nomenclature, and therapeutic options [2,3 ▪ ,9–11,12 ▪▪ ,13 ▪▪ ]…”

Section: Introductionmentioning

confidence: 99%

“Tickle me pink”: update in eosinophilic gastrointestinal disorders

Lam¹,

Gonsalves²

2022

Current Opinion in Gastroenterology

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Purpose of reviewEosinophilic gastrointestinal diseases (EGIDs) outside of the esophagus have been previously enigmatic and rare diagnoses. Fortunately, increasing research over the past few decades has led to an improved understanding of disease pathophysiology and epidemiology. This has been foundational for developing accurate nomenclature, diagnostic criteria, and therapeutics. Recent findingsThis article will review recent updates in nonesophageal EGIDs. Accurate disease classification and nomenclature developed from international consensus are now available, as well as data challenging the notion that abnormal endoscopic findings are rare in this population. Studies on natural history, outcomes, and impact on patient quality of life are reviewed. Lastly, retrospective studies and clinical trials on EGID therapies are summarized.

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Evaluating Eosinophilic Colitis as a Unique Disease Using Colonic Molecular Profiles: A Multi-Site Study

Cited by 25 publications

References 52 publications

Expression and potential role of FOSB in glioma

Expression and potential role of FOSB in glioma

EGIDExpress: An Interactive Shiny Web App to Visualize and Share Large Biological Datasets

“Tickle me pink”: update in eosinophilic gastrointestinal disorders

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