Joshua K. Stone
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View article: Urinary Metabolites and Survival in Malignant Mesothelioma
Urinary Metabolites and Survival in Malignant Mesothelioma Open
Background Malignant mesothelioma is a rare and aggressive malignancy with limited treatment options and poor survival outcomes. Current biomarkers such as MESOMARK, fibulin-3, and osteopontin show diagnostic potential but remain hampered …
View article: Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes
Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes Open
The study of the tumor microbiome has been garnering increased attention. We developed a computational pipeline (CSI-Microbes) for identifying microbial reads from single-cell RNA sequencing (scRNA-seq) data and for analyzing differential …
View article: Acidovorax temperans skews neutrophil maturation and polarizes Th17 cells to promote lung adenocarcinoma development
Acidovorax temperans skews neutrophil maturation and polarizes Th17 cells to promote lung adenocarcinoma development Open
Change within the intratumoral microbiome is a common feature in lung and other cancers and may influence inflammation and immunity in the tumor microenvironment, affecting growth and metastases. We previously characterized the lung cancer…
View article: <i>Acidovorax temperans</i>polarizes T17 cells and skews neutrophil maturation to promote lung adenocarcinoma development
<i>Acidovorax temperans</i>polarizes T17 cells and skews neutrophil maturation to promote lung adenocarcinoma development Open
SUMMARY Dysbiosis, or changes within the microbiome, is a common feature of solid tumors, however whether this dysbiosis directly contributes to tumor development is largely unknown. We previously characterized the lung cancer microbiome a…
View article: SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity
SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity Open
While dysregulation of RNA splicing has been recognized as an emerging target for cancer therapy, the functional significance of RNA splicing and individual splicing factors in brain tumors is poorly understood. Here, we identify SON as a …
View article: eNEMAL, an enhancer RNA transcribed from a distal MALAT1 enhancer, promotes NEAT1 long isoform expression
eNEMAL, an enhancer RNA transcribed from a distal MALAT1 enhancer, promotes NEAT1 long isoform expression Open
Emerging evidence has shown that active enhancers are abundantly transcribed, generating long non-coding RNAs, called enhancer RNAs (eRNAs). While putative eRNAs are often observed from RNA sequencing, the roles of most eRNAs remain largel…
View article: SON inhibits megakaryocytic differentiation via repressing RUNX1 and the megakaryocytic gene expression program in acute megakaryoblastic leukemia
SON inhibits megakaryocytic differentiation via repressing RUNX1 and the megakaryocytic gene expression program in acute megakaryoblastic leukemia Open
View article: Cancer-Type-Specific Bacteria: Freeloaders or Partners?
Cancer-Type-Specific Bacteria: Freeloaders or Partners? Open
View article: scRNA-seq analysis of colon and esophageal tumors uncovers abundant microbial reads in myeloid cells undergoing proinflammatory transcriptional alterations
scRNA-seq analysis of colon and esophageal tumors uncovers abundant microbial reads in myeloid cells undergoing proinflammatory transcriptional alterations Open
The study of the tumor microbiome has been garnering increased attention. We developed a computational pipeline (CSI-Microbes) for identifying microbial reads from single-cell RNA sequencing (scRNA-seq) data. Using a series of controlled e…
View article: Hypoxia induces cancer cell-specific chromatin interactions and increases MALAT1 expression in breast cancer cells
Hypoxia induces cancer cell-specific chromatin interactions and increases MALAT1 expression in breast cancer cells Open
View article: SON haploinsufficiency causes impaired pre-mRNA splicing of CAKUT genes and heterogeneous renal phenotypes
SON haploinsufficiency causes impaired pre-mRNA splicing of CAKUT genes and heterogeneous renal phenotypes Open
View article: Burkholderia humptydooensis sp. nov., a New Species Related to Burkholderia thailandensis and the Fifth Member of the Burkholderia pseudomallei Complex
Burkholderia humptydooensis sp. nov., a New Species Related to Burkholderia thailandensis and the Fifth Member of the Burkholderia pseudomallei Complex Open
During routine screening for Burkholderia pseudomallei from water wells in northern Australia in areas where it is endemic, Gram-negative bacteria (strains MSMB43 T , MSMB121, and MSMB122) with a similar morphology and biochemical pattern …
View article: Immunological Patterns from Four Melioidosis Cases: Constant and Variable Protein Antigens
Immunological Patterns from Four Melioidosis Cases: Constant and Variable Protein Antigens Open
Burkholderia pseudomallei is the causative agent of the melioidosis and is endemic to Southeast Asia and northern Australia. There is no available vaccine and accurate diagnosis is difficult, time-consuming and labor intensive. Early diagn…
View article: De Novo Mutations in SON Disrupt RNA Splicing of Genes Essential for Brain Development and Metabolism, Causing an Intellectual-Disability Syndrome
De Novo Mutations in SON Disrupt RNA Splicing of Genes Essential for Brain Development and Metabolism, Causing an Intellectual-Disability Syndrome Open
View article: SON and Its Alternatively Spliced Isoforms Control MLL Complex-Mediated H3K4me3 and Transcription of Leukemia-Associated Genes
SON and Its Alternatively Spliced Isoforms Control MLL Complex-Mediated H3K4me3 and Transcription of Leukemia-Associated Genes Open
View article: Pangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates
Pangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates Open
The pangenomic diversity in Burkholderia pseudomallei is high, with approximately 5.8% of the genome consisting of genomic islands. Genomic islands are known hotspots for recombination driven primarily by site-specific recombination associ…