Project description:Objective was to identify urine cell-free microRNAs enabling early non-invasive detection of bladder cancer. Total RNA enriched for fraction of short RNAs was isolated using Urine microRNA purification kit (Norgen corp.). miRNA profiles were determined using the Affymetrix GeneChip miRNA 3.0 array and analyzed to identify differentially deregulated miRNA in bladder cancer patients compared with helathy controls.
Project description:While it is well known that cell-free RNA (cfRNA) can be isolated from urine, the diagnostic potential of this urine cfRNA, especially in comparison to plasma cfRNA, remains underexplored. Here, we directly compared the utility of urine cfRNA and plasma cfRNA for the monitoring of systemic and urinary tract related complications. We analyzed 272 matched plasma and urine cfRNA isolates obtained from three cohorts of patients: Hematopoietic Stem Cell Transplant (HSCT) recipients, patients with acute kidney injury (AKI), and healthy volunteers. The data highlight the unique cellular origins and properties of urinary and plasma RNA. Most importantly, we find that although plasma cfRNA is a superior analyte for monitoring immune and systemic complications, urinary cfRNA is more sensitive to complications of the urinary tract, including cell-type specific injury in the kidney. These findings highlight the potential of urine cfRNA as a novel analyte in diagnostic medicine.
Project description:Human neural stem cells (NSCs) hold great promise in reparative therapy for neural diseases and injuries. However, the isolation of NSCs from either fetal or adult tissue and their application remain difficult due to ethical and immune-rejection concerns. One promising solution is to generate patient specific induced pluripotent stem cells (iPSCs) and subsequently differentiate them into NSCs. Alternatively, induced neurons (iN) can be generated directly from fibroblasts by retroviral delivery of neural specific transcription factors or miroRNAs. The later two approaches remain inefficient and with safety concerns. Here, we describe a process to generate, from epithelial-like cells present in human urine, integration free and engraftable NSCs (UiNSC) efficiently. Using an episomal system to deliver reprogramming factors and microRNAs into human urine cells and subsequently culture them in a chemically defined medium supplemented with a cocktail of small molecules, we generated UiNSCs capable of proliferation and without the transgenes upon prolonged expansion. These transgene free UiNSCs express typical neural stem cell markers and are able to differentiate into all neuronal subtypes and glial cells in vitro and more importantly could engraft and differentiate in vivo upon transplantation into the brain of new born rat. Thus, our work provides an efficient and highly practical platform to generate patient specific NSCs for regenerative medicine. This is a general expression microarray design (NimbleGen platform). It includes 6 samples.
Project description:Cell-free lncRNA expression signatures in urine serve as novel noninvasive biomarkers for diagnosis and recurrence prediction of bladder cancer
Project description:We analyzed cell-free microRNAs (cfmiRs) in blood, tissue, and urine samples of melanoma patients to find potential biomarkers for monitoring and assessing early detection of melanoma metastasis. This study demonstrates that identifying cfmiR signatures in body fluids may allow for detection and assessment of melanoma brain metastasis (MBM) and metastatic melanoma patients undergoing checkpoint inhibitor immunotherapy treatments.
Project description:Human neural stem cells (NSCs) hold great promise in reparative therapy for neural diseases and injuries. However, the isolation of NSCs from either fetal or adult tissue and their application remain difficult due to ethical and immune-rejection concerns. One promising solution is to generate patient specific induced pluripotent stem cells (iPSCs) and subsequently differentiate them into NSCs. Alternatively, induced neurons (iN) can be generated directly from fibroblasts by retroviral delivery of neural specific transcription factors or miroRNAs. The later two approaches remain inefficient and with safety concerns. Here, we describe a process to generate, from epithelial-like cells present in human urine, integration free and engraftable NSCs (UiNSC) efficiently. Using an episomal system to deliver reprogramming factors and microRNAs into human urine cells and subsequently culture them in a chemically defined medium supplemented with a cocktail of small molecules, we generated UiNSCs capable of proliferation and without the transgenes upon prolonged expansion. These transgene free UiNSCs express typical neural stem cell markers and are able to differentiate into all neuronal subtypes and glial cells in vitro and more importantly could engraft and differentiate in vivo upon transplantation into the brain of new born rat. Thus, our work provides an efficient and highly practical platform to generate patient specific NSCs for regenerative medicine.
Project description:Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality globally, with particularly high burdens among people living with HIV (PLWH) in low-resource settings like Nigeria. Effective early detection remains a major challenge due to limited access to imaging-based surveillance and the low sensitivity of current biomarkers such as alpha-fetoprotein (AFP). We conducted an epigenome-wide association study (EWAS) of circulating cell-free DNA (ccfDNA) methylation in a Nigerian cohort of HIV-positive individuals (n = 245), spanning HCC, cirrhosis, fibrosis, and HCC-free groups. Using random forest modeling, we developed and evaluated a ccfDNA methylation classifier (ccfDNAmRF) for HCC risk prediction. We identified 73 CpG sites significantly associated with HCC (false discovery rate <0.01). The ccfDNAmRF model demonstrated strong discriminatory power, achieving 100% sensitivity and 81–91% specificity for distinguishing HCC from cirrhosis, fibrosis, and HCC-free groups (area under the curve [AUC]: 92–97%). Combining ccfDNA methylation risk scores with AFP further improved classification accuracy (AUC up to 98.5%). Notably, ccfDNA methylation patterns displayed clear dose–response relationships across the disease spectrum, supporting their utility for early-stage detection and risk stratification. Our findings highlight the promise of ccfDNA methylation biomarkers as a minimally invasive, blood-based screening tool for improving early HCC detection among PLWH in resource-limited settings. These biomarkers may help address critical gaps in current surveillance strategies, offering scalable solutions adaptable to high-risk populations.