Patiño-Navarrete, Rafael Rosinski-Chupin, Isabelle Cabanel, Nicolas Gauthier, Lauraine Takissian, Julie Madec, Jean-Yves Hamze, Monzer Bonnin, Remy A. Naas, Thierry Glaser, Philippe
...
Published in
Genome Medicine
BackgroundCarbapenem-resistant Enterobacteriaceae are considered by WHO as “critical” priority pathogens for which novel antibiotics are urgently needed. The dissemination of carbapenemase-producing Escherichia coli (CP-Ec) in the community is a major public health concern. However, the global molecular epidemiology of CP-Ec isolates remains largel...
Liu, Shiyang Harmston, Nathan Glaser, Trudy Lee Wong, Yunka Zhong, Zheng Madan, Babita Virshup, David M. Petretto, Enrico
Published in
Genome Medicine
Background Wnt signaling is an evolutionarily conserved developmental pathway that is frequently hyperactivated in cancer. While multiple protein-coding genes regulated by Wnt signaling are known, the functional lncRNAs regulated by Wnt signaling have not been systematically characterized. Methods We comprehensively mapped Wnt-regulated lncRNAs fro...
Mordaunt, Charles E. Jianu, Julia M. Laufer, Benjamin I. Zhu, Yihui Hwang, Hyeyeon Dunaway, Keith W. Bakulski, Kelly M. Feinberg, Jason I. Volk, Heather E. Lyall, Kristen
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Published in
Genome Medicine
BackgroundAutism spectrum disorder (ASD) is a neurodevelopmental disorder with complex heritability and higher prevalence in males. The neonatal epigenome has the potential to reflect past interactions between genetic and environmental factors during early development and influence future health outcomes.MethodsWe performed whole-genome bisulfite s...
Binyamin, Dana Werbner, Nir Nuriel-Ohayon, Meital Uzan, Atara Mor, Hadar Abbas, Atallah Ziv, Oren Teperino, Raffaele Gutman, Roee Koren, Omry
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Published in
Genome Medicine
BackgroundDuring aging, there is a physiological decline, an increase of morbidity and mortality, and a natural change in the gut microbiome. In this study, we investigated the influence of the gut microbiome on different metabolic parameters in adult and aged mice.MethodsFecal and blood samples from adult (n = 42, 100–300 days) and aging (n = 32, ...
Petitprez, Florent Levy, Sacha Sun, Cheng-Ming Meylan, Maxime Linhard, Christophe Becht, Etienne Elarouci, Nabila Tavel, David Roumenina, Lubka T. Ayadi, Mira
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Published in
Genome Medicine
Quantifying tissue-infiltrating immune and stromal cells provides clinically relevant information for various diseases. While numerous methods can quantify immune or stromal cells in human tissue samples from transcriptomic data, few are available for mouse studies. We introduce murine Microenvironment Cell Population counter (mMCP-counter), a meth...
Lin, Wei Noel, Pawan Borazanci, Erkut H. Lee, Jeeyun Amini, Albert Han, In Woong Heo, Jin Seok Jameson, Gayle S. Fraser, Cory Steinbach, Margaux
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Published in
Genome Medicine
BackgroundSolid tumors such as pancreatic ductal adenocarcinoma (PDAC) comprise not just tumor cells but also a microenvironment with which the tumor cells constantly interact. Detailed characterization of the cellular composition of the tumor microenvironment is critical to the understanding of the disease and treatment of the patient. Single-cell...
Shi, Ming-Jun Meng, Xiang-Yu Fontugne, Jacqueline Chen, Chun-Long Radvanyi, François Bernard-Pierrot, Isabelle
Published in
Genome Medicine
BackgroundAPOBEC-driven mutagenesis and functional positive selection of mutated genes may synergistically drive the higher frequency of some hotspot driver mutations compared to other mutations within the same gene, as we reported for FGFR3 S249C. Only a few APOBEC-associated driver hotspot mutations have been identified in bladder cancer (BCa). H...
Castellani, Christina A. Longchamps, Ryan J. Sumpter, Jason A. Newcomb, Charles E. Lane, John A. Grove, Megan L. Bressler, Jan Brody, Jennifer A. Floyd, James S. Bartz, Traci M.
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Published in
Genome Medicine
BackgroundMitochondrial DNA copy number (mtDNA-CN) has been associated with a variety of aging-related diseases, including all-cause mortality. However, the mechanism by which mtDNA-CN influences disease is not currently understood. One such mechanism may be through regulation of nuclear gene expression via the modification of nuclear DNA (nDNA) me...
Ye, Youqiong Kuang, Xinwei Xie, Zuozhong Liang, Long Zhang, Zhao Zhang, Yongchang Ma, Fangyu Gao, Qian Chang, Ruimin Lee, Heng-Huan
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Published in
Genome Medicine
BackgroundImmune checkpoint blockade (ICB) therapy has demonstrated considerable clinical benefit in several malignancies, but has shown favorable response in only a small proportion of cancer patients. Recent studies have shown that matrix metalloproteinases (MMPs) are highly associated with the microenvironment of tumors and immune cells. However...
Schwartz, D. J. Langdon, A. E. Dantas, G.
Published in
Genome Medicine
The human gut microbiome is a dynamic collection of bacteria, archaea, fungi, and viruses that performs essential functions for immune development, pathogen colonization resistance, and food metabolism. Perturbation of the gut microbiome’s ecological balance, commonly by antibiotics, can cause and exacerbate diseases. To predict and successfully re...
