Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “ctDNA”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

165 records · Page 10Linked to original sources

Identification of a nifDK-like gene (ORF467) involved in the biosynthesis of chlorophyll in the cyanobacterium Plectonema boryanum.

The frxC gene, which is found in chloroplast DNA (ctDNA) and in cyanobacteria, encodes a protein that is required for the light-independent reduction of protochlorophyllide (Pchlide) to chlorophyllide a (Chlide). A DNA fragment downstream of frxC in the filamentous cyanobacterium Plectonema boryanum was cloned and analyzed. Sequencing of the DNA fragment revealed an open reading frame (ORF) that encoded a protein of 467 amino acid residues (designated ORF467), which showed extensive homology to the proteins encoded by genes on ctDNAs (ORF465 in liverwort, gidA in pine and chlN in Chlamydomonas reinhardtii) and to ORF469 protein of the cyanobacterium Synechocystis sp. strain PCC 6803. We isolated a targeted mutant YFM6D-3 in which ORF467 was inactivated by the insertion of a kanamycin-resistance gene into the coding region. YFM6D-3 exhibited a phenotype similar to that of YFC1004, an frxC-disrupted mutant, which did not synthesize chlorophyll (Chl) and accumulated Pchlide, a precursor to Chl, in the dark. These phenotypic characteristics of YFM6D-3 indicate that the light-independent reduction of Pchlide requires not only the FrxC protein but also the ORF467 protein. The amino acid sequences of the homologues of ORF467 exhibit low but significant similarity to those of the alpha and beta subunits of nitrogenase MoFe-protein, suggesting a phylogenetic relationship between the light-independent Pchlide reductase and nitrogenase, as is observed between the FrxC protein and the Fe-protein of nitrogenase.

Amino Acid Sequence↗

Associations of neighborhood deprivation with breast cancer tumor genomics, targeted treatment use, and survival.

PURPOSE: Neighborhood environments appear to influence breast cancer biology and outcomes. This study evaluated somatic, treatment, and outcome differences by Area Deprivation Index in patients with metastatic breast cancer. METHODS: Retrospective, population-based cohort study using clinical and genomic data gathered between 2015 and 2024 at four academic institutions in the United States. The outcomes were differences in circulating tumor DNA mutation profiles, PI3K inhibitor use, and survival between patients with metastatic breast cancer living in high deprivation (Area Deprivation Index&#x2009;&#x2265;&#x2009;60 by national rank) and low deprivation (<&#x2009;60) neighborhoods. RESULTS: Among 1127 patients with metastatic breast cancer, 335 (29.7%) lived in high deprivation areas. These patients were more likely to have TP53 mutations (Odds ratio 1.49, 95% Confidence Interval 1.07-2.08, P&#x2009;=&#x2009;0.018). Among hormone receptor-positive, HER2-negative patients eligible for PI3K inhibitors, those from high deprivation areas were less likely to receive them (17.4% vs. 36.7%, p&#x2009;=&#x2009;0.02). Median survival from the time of circulating tumor DNA testing was significantly shorter in the high deprivation group (24 months versus 28 months, p&#x2009;=&#x2009;0.04) and for Black patients in the high deprivation group versus Black patients in low deprivation group and all White patients (15 months versus 25-28 months, p&#x2009;=&#x2009;0.02). CONCLUSIONS: We found that patients with metastatic breast cancer living in high deprivation neighborhoods were more likely to have TP53 mutations, an indicator of aggressive disease biology, less likely to receive PI3K inhibitors, and had shorter overall survival compared to patients living in low deprivation neighborhoods by Area Deprivation Index.

Humans↗

Liquid biopsy: a new window on the BRCA genes.

The Breast Cancer Susceptibility Gene (BRCA)-associated tumors represent a constantly evolving and intriguing scenario in oncology, in which the availability of novel systemic treatment, mainly including the poly (ADP-ribose) polymerase (PARP) inhibitors, has enabled an improved survival benefit in clinical subgroups. The expanding regulatory approvals of PARP inhibitors have inevitably reshaped the clinical indications for BRCA testing, moving the BRCA1/2 profiling from the traditional and preventive workflows to therapeutic paths. Despite advances in technology and treatment, substantial limitations remain in current genetic and genomic tools for the detection of deleterious BRCA1/2 variants. Germline and tumor tissue testing provide only a snapshot of a patient's disease, failing to capture the dynamic and longitudinal aspects of tumor clonal evolution. In this scenario, liquid biopsy (LB) profiling of BRCA1/2 genes, primarily as circulating tumor DNA, represents a highly active area of research potentially affecting many aspects of cancer screening, diagnosis, and monitoring in individuals who are carriers of BRCA1/2 deleterious variants. Beyond the attractive potential to surrogate the tumor tissue testing, to overcome the cancer spatial and temporal heterogeneity, and to monitor the tumor mutational profile over time, accurately detecting all clinically relevant BRCA genetic variants and epigenetic modifications using LB remains technically challenging.

BRCA1/2↗