The emergence of highly resistant and hypervirulent Klebsiella pneumoniae CC14 clone in a tertiary hospital over 8 years
ConclusionsOverall, these results demonstrate the clinical significance of ST2096 clones and illustrate the rapid evolution of an emerging hypervirulent and MDRK. pneumoniae in a clinical setting. (Source: Genome Medicine)
Source: Genome Medicine - April 18, 2024 Category: Genetics & Stem Cells Source Type: research
National genomic epidemiology investigation revealed the spread of carbapenem-resistant Escherichia coli in healthy populations and the impact on public health
ConclusionsOur findings underscore the significance of healthy populations-derived CRECs as a crucial reservoir of antibiotic resistance genes (ARGs). This highlights the need for ongoing monitoring of CREC isolates in healthy populations to accurately assess the potential risks posed by clinical CREC isolates. (Source: Genome Medicine)
Source: Genome Medicine - April 16, 2024 Category: Genetics & Stem Cells Source Type: research
PheSeq, a Bayesian deep learning model to enhance and interpret the gene-disease association studies
AbstractDespite the abundance of genotype-phenotype association studies, the resulting association outcomes often lack robustness and interpretations. To address these challenges, we introduce PheSeq, a Bayesian deep learning model that enhances and interprets association studies through the integration and perception of phenotype descriptions. By implementing the PheSeq model in three case studies on Alzheimer ’s disease, breast cancer, and lung cancer, we identify 1024 priority genes for Alzheimer’s disease and 818 and 566 genes for breast cancer and lung cancer, respectively. Benefiting from data fusion, these findi...
Source: Genome Medicine - April 16, 2024 Category: Genetics & Stem Cells Source Type: research
Single cell lineage tracing reveals clonal dynamics of anti-EGFR therapy resistance in triple negative breast cancer
ConclusionsOur strategy proved effective in reconstructing the complex signalling network driving EGFR-targeted therapy resistance, offering new insights for the development of individualized treatment strategies in TNBC. (Source: Genome Medicine)
Source: Genome Medicine - April 11, 2024 Category: Genetics & Stem Cells Source Type: research
Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk
ConclusionsOur results provide initial evidence for germline-mediated personalized smoke injury response and risk in the general population, with potential implications for managing long-term lung cancer incidence and mortality. (Source: Genome Medicine)
Source: Genome Medicine - April 8, 2024 Category: Genetics & Stem Cells Source Type: research
Burden of Mendelian disorders in a large Middle Eastern biobank
ConclusionsThis study on the first phase of the growing Qatar Genome Program cohort provides a comprehensive resource from a Middle Eastern population to understand the global mutational burden in Mendelian genes and their impact on traits in seemingly healthy individuals in high consanguinity settings. (Source: Genome Medicine)
Source: Genome Medicine - April 8, 2024 Category: Genetics & Stem Cells Source Type: research
NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy
ConclusionOur data further support a role for rare deleterious variants inNODAL as a cause for sporadic human laterality defects, expand the repertoire of observed anatomical complexity of potential cardiovascular anomalies, and implicate an allele specific gene dosage model. (Source: Genome Medicine)
Source: Genome Medicine - April 3, 2024 Category: Genetics & Stem Cells Source Type: research
Single-cell profiling of response to neoadjuvant chemo-immunotherapy in surgically resectable esophageal squamous cell carcinoma
ConclusionsThis pioneering study unveiled an intriguing association between cancer cell differentiation and pathological response in esophageal cancer patients, revealing distinct subgroups of tumors for which neoadjuvant chemo-immunotherapy might be effective. We also delineated the immune landscape of ESCC tumors in the context of clinical response to NAT, which provides clinical insights for better understanding how patients respond to the treatment and further identifying novel therapeutic targets for ESCC patients in the future. (Source: Genome Medicine)
Source: Genome Medicine - April 2, 2024 Category: Genetics & Stem Cells Source Type: research
Conserved methylation signatures associate with the tumor immune microenvironment and immunotherapy response
ConclusionsOur findings demonstrated that the methylation signatures of distinct biological processes are associated with immune activity in the cancer microenvironment and predict immunotherapy response. (Source: Genome Medicine)
Source: Genome Medicine - April 2, 2024 Category: Genetics & Stem Cells Source Type: research
Full-spectral genome analysis of natural killer/T cell lymphoma highlights impacts of genome instability in driving its progression
ConclusionsThe striking differences underlying the mutational landscapes between the primary and relapsed/refractory NKTCL patients highlight the importance of genomic instability in driving the progression of NKTCL. Our newly proposed molecular subtyping system is valuable in assisting patient stratification and novel treatment design towards a better prognosis in the age of precision medicine. (Source: Genome Medicine)
Source: Genome Medicine - April 2, 2024 Category: Genetics & Stem Cells Source Type: research
Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts
ConclusionsOur data provide novel insights into the phenotypic adaptation of the heterogeneous TME instructed by GBM tumors. We show the key role of microglial phenotypic states in supporting GBM tumor growth and response to treatment. Our data place PDOXs as relevant models to assess the functionality of the TME and changes in the GBM ecosystem upon treatment.Graphical Abstract (Source: Genome Medicine)
Source: Genome Medicine - April 2, 2024 Category: Genetics & Stem Cells Source Type: research
Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma
ConclusionsOur new frameworks promote the characterization of mtDNA features, which enables the elucidation of the landscapes and roles of mtDNA in ESCC essential for extending the current understanding of ESCC etiology. dMTLV and fNUMT are freely available fromhttps://github.com/sunnyzxh/dMTLV andhttps://github.com/sunnyzxh/fNUMT, respectively. (Source: Genome Medicine)
Source: Genome Medicine - April 2, 2024 Category: Genetics & Stem Cells Source Type: research
Race-specific coregulatory and transcriptomic profiles associated with DNA methylation and androgen receptor in prostate cancer
ConclusionsOur study reveals unique signaling networks underlying prostate cancer biology in AA and EA men, offering potential insights for clinical management strategies tailored to specific racial groups. Targeting AR and associated pathways could be particularly beneficial in addressing the disparities observed in prostate cancer outcomes in the context of AA and EA men. Further investigation into these identified pathways may lead to the development of personalized therapeutic approaches to improve outcomes for prostate cancer patients across different racial backgrounds. (Source: Genome Medicine)
Source: Genome Medicine - April 2, 2024 Category: Genetics & Stem Cells Source Type: research
Deep learning in cancer genomics and histopathology
AbstractHistopathology and genomic profiling are cornerstones of precision oncology and are routinely obtained for patients with cancer. Traditionally, histopathology slides are manually reviewed by highly trained pathologists. Genomic data, on the other hand, is evaluated by engineered computational pipelines. In both applications, the advent of modern artificial intelligence methods, specifically machine learning (ML) and deep learning (DL), have opened up a fundamentally new way of extracting actionable insights from raw data, which could augment and potentially replace some aspects of traditional evaluation workflows. ...
Source: Genome Medicine - March 27, 2024 Category: Genetics & Stem Cells Source Type: research
Systematic immune cell dysregulation and molecular subtypes revealed by single-cell RNA-seq of subjects with type 1 diabetes
ConclusionsOur study reveals a surprisingly strong systemic dimension at the level of immune cell network in T1DM, defines disease-relevant molecular subtypes, and has the potential to guide non-invasive test development and patient stratification. (Source: Genome Medicine)
Source: Genome Medicine - March 27, 2024 Category: Genetics & Stem Cells Source Type: research
