Article
Gastroenterology & Hepatology
Takahiro Utsumi, Shin'ichi Miyamoto, Takahiro Shimizu, Kasumi Yokogawa, Yuki Nakanishi, Mitsuhiro Nikaido, Ayako Hirata, Miyu Nishida, Ikuo Aoyama, Tomoko Okuno, Akihiko Yoshizawa, Akihiro Kaneda, Yoshiharu Sakai, Chiharu Kawanami, Hiroshi Seno
Summary: Spontaneous regression in colorectal cancer is rare and often associated with specific endoscopic characteristics, lack of DNA mismatch repair proteins, and a deficiency in mismatch repair (dMMR). The activation of anti-tumor host immune responses through increased tumor-infiltrating lymphocytes may play a role in the spontaneous regression of colorectal cancer.
DIGESTIVE ENDOSCOPY
(2021)
Article
Oncology
Rikke Lovendahl Eefsen, Jim S. S. Larsen, Louise L. L. Klarskov, Rahim Altaf, Estrid Hogdall, Peter Ingeholm, Jakob Lykke, Dorte L. L. Nielsen, Per Pfeiffer, Laurids O. Poulsen, Camilla Qvortrup, Jakob V. V. Schou, Morten Mau-Sorensen, Kell Osterlind, Benny V. V. Jensen
Summary: Therapy with immune checkpoint inhibitors has shown effectiveness in patients with metastatic mismatch-repair deficient colorectal cancer. However, the data on neoadjuvant ICI treatment in locally advanced CRC patients are limited. A study in Danish oncological centers evaluated the use of preoperative pembrolizumab in 10 treatment-naive dMMR CRC patients, demonstrating feasibility and effectiveness.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Microbiology
Min Jin, Jingjing Wu, Linli Shi, Bin Zhou, Fumei Shang, Xiaona Chang, Xiaochuan Dong, Shenghe Deng, Li Liu, Kailin Cai, Xiu Nie, Tao Zhang, Jun Fan, Hongli Liu
Summary: CRC patients with different MMR status have distinct gut bacterial community richness, compositions, and related metabolic pathways.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Health Care Sciences & Services
Abdul K. Siraj, Sandeep Kumar Parvathareddy, Padmanaban Annaiyappanaidu, Wael Haqawi, Maha Al-Rasheed, Hadeel M. AlManea, Hussah F. AlHussaini, Fouad Al-Dayel, Khawla S. Al-Kuraya
Summary: This study in Middle Eastern CRC patients showed that PD-L1 expression is associated with aggressive clinic-pathological features, MMR deficiency, and BRAF mutation, and it serves as an independent prognostic marker for overall survival. These findings suggest that PD-L1 expression could be a useful biomarker for predicting poor prognosis in Middle Eastern CRC patients, particularly those with MMR deficient tumors.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Oncology
Helena de Castro e Gloria, Laura Jesuino Nogueira, Patricia Bencke Grudzinski, Paola Victoria da Costa Ghignatti, Temenouga Nikolova Guecheva, Natalia Motta Leguisamo, Jenifer Saffi
Summary: Our study demonstrated that Olaparib enhances the cytotoxicity of 5-FU in MMR-deficient CRC cells, while it reduces clonogenic survival and induces DNA damage in MMR-proficient CRC cells. Combined therapy with Olaparib could be a strategy to overcome 5-FU chemotherapeutic resistance in MMR-deficient CRC.
Article
Medicine, General & Internal
Wu Jiang, Wei-Jian Mei, Shuo-Yu Xu, Yi-Hong Ling, Wei-Rong Li, Jin-Bo Kuang, Hao-Sen Li, Hui Hui, Ji-Bin Li, Mu-Yan Cai, Zhi-Zhong Pan, Hui-Zhong Zhang, Li Li, Pei-Rong Ding
Summary: A DL model was developed to predict MMR status in CRC patients based on WSI, achieving high accuracy and establishing a dual-threshold strategy for patient triage, which is significant for avoiding unnecessary IHC testing.
Article
Oncology
Dung T. Le, Luis A. Diaz Jr, Tae Won Kim, Eric Van Cutsem, Ravit Geva, Dirk Jaeger, Hiroki Hara, Matthew Burge, Bert H. O'Neil, Petr Kavan, Takayuki Yoshino, Rosine Guimbaud, Hiroya Taniguchi, Elena Elez, Salah-Eddin Al-Batran, Patrick M. Boland, Yi Cui, Pierre Leconte, Patricia Marinello, Thierry Andre
Summary: The study demonstrated that Pembrolizumab had durable clinical benefit and manageable safety in previously treated MSI-H/dMMR colorectal cancer patients. It showed persistent antitumor activity, prolonged overall survival, and tolerable safety profile.
EUROPEAN JOURNAL OF CANCER
(2023)
Article
Medicine, Research & Experimental
Wuteng Cao, Huabin Hu, Jirui Guo, Qiyuan Qin, Yanbang Lian, Jiao Li, Qianyu Wu, Junhong Chen, Xinhua Wang, Yanhong Deng
Summary: This study aimed to develop and validate a deep learning model based on pre-treatment CT images for predicting DNA mismatch repair (MMR) status in patients with colorectal cancer (CRC). The results showed that the deep learning model had good predictive ability and could serve as a noninvasive tool for predicting MMR status in patients with CRC.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Gastroenterology & Hepatology
Tomotaka Ugai, Naohiko Akimoto, Koichiro Haruki, Tabitha A. Harrison, Yin Cao, Conghui Qu, Andrew T. Chan, Peter T. Campbell, Sonja Berndt, Daniel D. Buchanan, Amanda J. Cross, Brenda Diergaarde, Steven J. Gallinger, Marc J. Gunter, Sophia Harlid, Akihisa Hidaka, Michael Hoffmeister, Hermann Brenner, Jenny Chang-Claude, Li Hsu, Mark A. Jenkins, Yi Lin, Roger L. Milne, Victor Moreno, Polly A. Newcomb, Reiko Nishihara, Mireia Obon-Santacana, Rish K. Pai, Lori C. Sakoda, Robert E. Schoen, Martha L. Slattery, Wei Sun, Efrat L. Amitay, Elizabeth Alwers, Stephen N. Thibodeau, Amanda E. Toland, Bethany Van Guelpen, Syed H. Zaidi, John D. Potter, Jeffrey A. Meyerhardt, Marios Giannakis, Mingyang Song, Jonathan A. Nowak, Ulrike Peters, Amanda Phipps, Shuji Ogino
Summary: This study analyzed 13,101 colorectal cancer cases and found a significant association between tumor location and molecular features. The detailed colonic location and tumor molecular features play an important role in the prognostication and precision medicine of colon cancer.
JOURNAL OF GASTROENTEROLOGY
(2023)
Article
Medicine, Research & Experimental
Jing Wang, Ruiyu Li, Junjie Li, Yuting Yi, Xiaoding Liu, Jingci Chen, Hui Zhang, Junliang Lu, Cami Li, Huanwen Wu, Zhiyong Liang
Summary: This study utilized DNA and RNA sequencing to detect fusion genes in dMMR CRCs, revealing that fusion-positive tumors tend to occur in older patients, are predominantly right-sided, and display mutations in key WNT pathway components.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
Article
Oncology
Raphael Colle, Anna Radzik, Romain Cohen, Anna Pellat, Daniel Lopez-Tabada, Marine Cachanado, Alex Duval, Magali Svrcek, Yves Menu, Thierry Andre
Summary: The study found that 10% of patients with MSI/dMMR mCRC treated with ICIs experienced PSPD, with most of them occurring within the first 3 months, representing the majority of primary radiological PDs. There were almost no occurrences of PSPD after 3 months.
EUROPEAN JOURNAL OF CANCER
(2021)
Review
Immunology
Wei-Jian Mei, Mi Mi, Jing Qian, Nan Xiao, Ying Yuan, Pei-Rong Ding
Summary: Colorectal cancers with high microsatellite instability and deficient mismatch repair have different characteristics compared to normal CRC, but the testing rates for MSI and MMR remain low in clinical practice. Insufficient testing fails to identify patients with these types of CRC who could benefit from immunotherapy. Understanding the importance of MMR/MSI status in the clinical characteristics and prognosis of CRC may help improve testing rates and guide the development of more effective therapies.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Microbiology
Yaping Yan, Xiaoyan Yi, Yanchao Duan, Bin Jiang, Tianzhuang Huang, Briauna Marie Inglis, Bingrong Zheng, Wei Si
Summary: This study found differences in intestinal microbiota between monkeys with OA and normal monkeys, identified potential biomarkers related to OA, and predicted microbiota metabolic pathways associated with cartilage damage. The research provides a reference for the development of drugs for the treatment of OA based on the close relationship between non-human primates and humans.
Article
Oncology
Shuai Chen, Wenzhe Du, Yuhai Cao, Jixia Kong, Xin Wang, Yisen Wang, Yang Lu, Xiang Li
Summary: This study investigates the correlation between preoperative CT and clinicopathologic characteristics of colorectal cancer (CRC) according to different mismatch repair (MMR) statuses. The results show that the combination of pre-operative CT and clinicopathological characteristics of CRC correlates with MMR status, providing possible non-invasive MMR prediction.
Article
Oncology
Takayuki Yoshino, Thierry Andre, Tae Won Kim, Wei Peng Yong, Kai-Keen Shiu, Benny Vittrup Jensen, Lars Henrik Jensen, Cornelis J. A. Punt, Denis Smith, Rocio Garcia-Carbonero, Julia Alcaide-Garcia, Peter Gibbs, Christelle de la Fouchardiere, Fernando Rivera, Elena Elez, Dung T. Le, Noriaki Adachi, David Fogelman, Patricia Marinello, Luis A. Jr Jr Diaz
Summary: The phase 3 KEYNOTE-177 study compared pembrolizumab with chemotherapy in newly diagnosed MSI-H/dMMR mCRC patients. The study showed that pembrolizumab as a first-line treatment was effective for patients from Asia with MSI-H/dMMR mCRC.
Article
Gastroenterology & Hepatology
Elias Orouji, Ayush T. Raman, Anand K. Singh, Alexey Sorokin, Emre Arslan, Archit K. Ghosh, Jonathan Schulz, Christopher Terranova, Shan Jiang, Ming Tang, Mayinuer Maitituoheti, Scot C. Callahan, Praveen Barrodia, Katarzyna Tomczak, Yingda Jiang, Zhiqin Jiang, Jennifer S. Davis, Sukhen Ghosh, Hey Min Lee, Laura Reyes-Uribe, Kyle Chang, Yusha Liu, Huiqin Chen, Ali Azhdarinia, Jeffrey Morris, Eduardo Vilar, Kendra S. Carmon, Scott E. Kopetz, Kunal Rai
Summary: Enhancer aberrations are key epigenetic features in colorectal cancers, with active enhancer dynamics underlying tumor progression and potential for precision combination therapy. By mapping chromatin profiles and identifying distinct enhancer subtypes, combinatorial therapeutic strategies targeting specific pathways based on enhancer patterns have been proposed for different CRC subgroups, potentially improving patient outcomes.
Article
Mathematical & Computational Biology
Nan Deng, Canglin Wu, Ashraf Yaseen, Hulin Wu
Summary: ImmuneData is a data discovery system for the immunology research community, which provides integrated access to five immunology data repositories and restructures their metadata using domain experts' knowledge and Natural Language Processing (NLP) technologies. It comes with a user-friendly web interface and a Google-like search engine, making it easy for researchers to find and access data.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
Article
Biochemical Research Methods
Luis F. Paulin, Muthuswamy Raveendran, R. Alan Harris, Jeffrey Rogers, Arndt von Haeseler, Fritz J. Sedlazeck
Summary: In population or species diversity studies, predicting regions with unseen variations can enhance the analysis for potentially missed variants. SVhound is a method that can identify these regions and ensure high quality of SV call sets.
BMC BIOINFORMATICS
(2023)
Article
Genetics & Heredity
R. Alan Harris, Kellie J. Archer, Mark O. Goodarzi, Timothy P. York, Jeffrey Rogers, Andrea Dunaif, Jan M. McAllister, Jerome F. Strauss
Summary: This study identified significant associations between 15 single nucleotide variants (SNVs) and androgen production in theca cells from women with PCOS. The study also found functional consequences for two SNVs, one in the ERBB3 gene and one in the promoter region of the PA2G4 gene. Furthermore, the study suggests a potential signaling pathway disruption involving ERBB3 and PA2G4 in the pathophysiology of PCOS.
Article
Parasitology
Jessica Y. Rodriguez, Kevin J. Cummings, Carolyn L. Hodo, Sarah A. Hamer
Summary: The prevalence of intestinal parasites among Texas shelter dogs was estimated using centrifugal fecal flotation and saline sedimentation techniques. Risk factors for infection were identified, and the addition of fecal sedimentation increased the number of parasite species detected and the number of dogs diagnosed with common intestinal parasites. Texas shelter dogs carry a high burden of intestinal parasites, including those of zoonotic importance.
PARASITOLOGY RESEARCH
(2023)
Article
Microbiology
Juan M. Bustamante, Brooke E. White, Gregory K. Wilkerson, Carolyn L. Hodo, Lisa D. Auckland, Wei Wang, Stephanie McCain, Sarah A. Hamer, Ashley B. Saunders, Rick L. Tarleton
Summary: This study demonstrates that higher dose, intermittent administration of benznidazole can effectively treat Trypanosoma cruzi infection. Administration twice a week, for more than 4 months, provides the best chance for parasitological cure.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Multidisciplinary Sciences
Erik F. Sorensen, R. Alan Harris, Liye Zhang, Muthuswamy Raveendran, Lukas F. K. Kuderna, Jerilyn A. Walker, Jessica M. Storer, Martin Kuhlwilm, Claudia Fontsere, Lakshmi Seshadri, Christina M. Bergey, Andrew S. Burrell, Juraj Bergman, Jane E. Phillips-Conroy, Fekadu Shiferaw, Kenneth L. Chiou, Idrissa S. Chuma, Julius D. Keyyu, Julia Fischer, Marie-Claude Gingras, Sejal Salvi, Harshavardhan Doddapaneni, Mikkel H. Schierup, Mark A. Batzer, Clifford J. Jolly, Sascha Knauf, Dietmar Zinner, Kyle K. -H. Farh, Tomas Marques-Bonet, Kasper Munch, Christian Roos, Jeffrey Rogers
Summary: Baboons are a young clade of six species that exhibit diverse population structure and evolutionary history. Hybridization between baboons has been observed, and population relationships do not correspond with phenotype. This study analyzed whole-genome sequences of 225 baboons and revealed previously unknown gene flow between populations, as well as different degrees of interspecies introgression.
Article
Multidisciplinary Sciences
Hong Gao, Tobias Hamp, Jeffrey Ede, Joshua G. Schraiber, Jeremy McRae, Moriel Singer-Berk, Yanshen Yang, Anastasia S. D. Dietrich, Petko P. Fiziev, Lukas F. K. Kuderna, Laksshman Sundaram, Yibing Wu, Aashish Adhikari, Yair Field, Chen Chen, Serafim Batzoglou, Francois Aguet, Gabrielle Lemire, Rebecca Reimers, Daniel Balick, Mareike C. Janiak, Martin Kuhlwilm, Joseph D. Orkin, Shivakumara Manu, Alejandro Valenzuela, Juraj Bergman, Marjolaine Rousselle, Felipe Ennes Silva, Lidia Agueda, Julie Blanc, Marta Gut, Dorien de Vries, Ian Goodhead, R. Alan Harris, Muthuswamy Raveendran, Axel Jensen, Idriss S. Chuma, Julie E. Horvath, Christina Hvilsom, David Juan, Peter Frandsen, Fabiano R. de Melo, Fabricio Bertuol, Hazel Byrne, Iracilda Sampaio, Izeni Farias, Joao Valsecchi do Amaral, Mariluce Messias, Maria N. F. da Silva, Mihir Trivedi, Rogerio Rossi, Tomas Hrbek, Nicole Andriaholinirina, Clement J. Rabarivola, Alphonse Zaramody, Clifford J. Jolly, Jane Phillips-Conroy, Gregory Wilkerson, Christian Abee, Joe H. Simmons, Eduardo Fernandez-Duque, Sree Kanthaswamy, Fekadu Shiferaw, Dongdong Wu, Long Zhou, Yong Shao, Guojie Zhang, Julius D. Keyyu, Sascha Knauf, Minh D. Le, Esther Lizano, Stefan Merker, Arcadi Navarro, Thomas Bataillon, Tilo Nadler, Chiea Chuen Khor, Jessica Lee, Patrick Tan, Weng Khong Lim, Andrew C. Kitchener, Dietmar Zinner, Ivo Gut, Amanda Melin, Katerina Guschanski, Mikkel Heide Schierup, Robin M. D. Beck, Govindhaswamy Umapathy, Christian Roos, Jean P. Boubli, Monkol Lek, Shamil Sunyaev, Anne O'Donnell-Luria, Heidi L. Rehm, Jinbo Xu, Jeffrey Rogers, Tomas Marques-Bonet, Kyle Kai-How Farh
Article
Pathology
Martha E. Hensel, Aline Rodrigues-Hoffmann, Beth K. Dray, Gregory K. Wilkerson, Wally B. Baze, Sarah Sulkosky, Carolyn L. Hodo
Summary: This study examines the spontaneous gastrointestinal diseases in owl monkeys and their contribution to morbidity and mortality, revealing the common diseases and tumors affecting the gastrointestinal tract in this species.
VETERINARY PATHOLOGY
(2023)
Article
Biochemistry & Molecular Biology
R. Alan Harris, Jan M. McAllister, Jerome F. Strauss III
Summary: Polycystic ovary syndrome (PCOS) is an endocrine disorder characterized by high levels of androgens, leading to anovulation/oligo-ovulation and infertility. This study used single-cell RNA sequencing to compare gene expression in theca cells from ovaries of normal ovulatory women and women with PCOS. The results identified differentially expressed genes and pathways related to cholesterol acquisition and steroidogenesis, providing insights into the molecular mechanisms underlying PCOS and potential targets for diagnosis and treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
R. Alan Harris, Muthuswamy Raveendran, Dustin T. Lyfoung, Fritz J. Sedlazeck, Medhat Mahmoud, Trent M. Prall, Julie A. Karl, Harshavardhan Doddapaneni, Qingchang Meng, Yi Han, Donna Muzny, Roger W. Wiseman, David H. O'Connor, Jeffrey Rogers
Summary: By utilizing Oxford Nanopore Technologies long-read sequencing, an improved assembly of the Syrian hamster (M. auratus) genome (BCM_Maur_2.0) was produced, resulting in a chromosome-scale assembly with a total length of 2.46 Gb. The new assembly, BCM_Maur_2.0, exhibits significantly enhanced continuity with a scaffold N50 that is 6.7 times greater than that of MesAur1.0, and it annotates 21,616 protein-coding genes and 10,459 noncoding genes as opposed to 20,495 protein-coding genes and 4,168 noncoding genes in MesAur1.0.