Project description:Dysfunction in human cerebrovasculature contribute to pathogenesis of multiple neurological diseases, and the blood brain barrier (BBB), an organotypic specialization of the cerebrovasculature, impedes the delivery of systemic therapies for nearly all brain disorders.Here we developed a novel methodology to isolate fresh cells from the human cerebrovasculature with high capture efficiency and cell viability, and performed single-cell mRNA sequencing (scRNAseq) for human cerebrovascular cells from 13 surgical resected samples, including normal human brain tissue and gliomas, the most common brain malignancy. We profiled the transcriptome of 103,230 single cells, including 57,324 endothelial cells and 27,703 mural cells.We molecular defined the principle vascular cell types in the BBB, and uncovered molecular underpinning of heterogeneity in endothelial cells, mural cells and perivascular fibroblasts along the arteriovenous axis.
Project description:Recent technological advances in molecular diagnostics through liquid biopsies hold the promise to monitor tumor evolution and treatment response of brain malignancies without the need of invasive surgical tissue accrual. Here, we implemented a new mass spectrometry-based protein analysis pipeline and analyzed 251 cerebrospinal fluid (CSF) samples from patients with four types of brain malignancies (glioblastoma, lymphoma, brain metastasis and meningeal disease) as well as from healthy individuals. On average, we identified 511 ± 121 proteins per CSF sample. 169 proteins were commonly deregulated in all four types of brain malignancies compared to controls. CSF analysis of glioblastoma patients identified two proteomic clusters that correlated with tumor size and patient survival. By integrating CSF data with proteomic analyses of matching glioma tumor tissue and primary glioma cells, we identified potential CSF biomarkers for glioblastoma, in particular chitinase-3-like protein 1 (CHI3L1) and glial fibrillary acidic protein (GFAP). Results were validated in a prospective cohort with 35 glioblastoma patients. Response of a patient with meningeal disease to combinatorial drug treatment was associated with a complex shift of the proteomic signature, including detection of potential drug resistance mechanisms. Therefore, proteomic analysis of CSF in brain malignancies has the potential to reveal biomarkers for diagnosis and therapy monitoring.
Project description:We identified diffuse lesions made of BRAF V600E-mutant CD34-immunopositive stellar cells in human samples resected to cure drug-resistant focal epilepsy. We performed single-nuclei RNAseq 5' 10X on three human brain samples (two BRAF mutant samples and one BRAF wildtype sample as control) in order to identify the molecular phenotype of CD34+ cells.
Project description:Surgical samples have long been used as important subjects for cancer research. In accordance with an increase of neoadjuvant therapy, biopsy samples have recently become imperative for cancer transcriptome. On the other hand, both biopsy and surgical samples are available for expression profiling for predicting clinical outcome by adjuvant therapy; however, it is still unclear whether surgical sample expression profiles are useful for the prediction by the use of biopsy samples because little has been done about comparative gene expression profiling between the two kinds of samples. When gene expression profiles were compared between biopsy and surgical samples, artificially induced epithelial-mesenchymal transition (aiEMT) was found in the surgical samples. This study will evoke the fundamental misinterpretation including underestimation of the prognostic evaluation power of markers by overestimation of EMT in past cancer research, and will furnish some advice for the near future as follows: 1) Understanding how long the tissues were under an ischemic condition; 2) Prevalence of biopsy samples for in vivo expression profiling with low biases on basic and clinical research; and 3) Checking cancer cell contents and normal- or necrotic-tissue contamination in biopsy samples for prevalence.
Project description:Surgical samples have long been used as important subjects for cancer research. In accordance with an increase of neoadjuvant therapy, biopsy samples have recently become imperative for cancer transcriptome. On the other hand, both biopsy and surgical samples are available for expression profiling for predicting clinical outcome by adjuvant therapy; however, it is still unclear whether surgical sample expression profiles are useful for the prediction by the use of biopsy samples because little has been done about comparative gene expression profiling between the two kinds of samples. When gene expression profiles were compared between biopsy and surgical samples, artificially induced epithelial-mesenchymal transition (aiEMT) was found in the surgical samples. This study will evoke the fundamental misinterpretation including underestimation of the prognostic evaluation power of markers by overestimation of EMT in past cancer research, and will furnish some advice for the near future as follows: 1) Understanding how long the tissues were under an ischemic condition; 2) Prevalence of biopsy samples for in vivo expression profiling with low biases on basic and clinical research; and 3) Checking cancer cell contents and normal- or necrotic-tissue contamination in biopsy samples for prevalence.
Project description:Ependymoma, the 3rd most common brain tumor in children, recurs in approximately 50% of patients. There is currently no robust marker that predicts for recurrence, which is a significant clinical problem We used global gene expression profiling of 19 patient surgical samples obtained at initial diagnosis and with known clinical outcomes to discover novel prognostic markers.
Project description:Hepatic lipid accumulation is an important complication of obesity linked to risk for type 2 diabetes. To identify novel transcriptional changes in human liver which could contribute to hepatic lipid accumulation and associated insulin resistance and type 2 diabetes (DM2), we evaluated gene expression and gene set enrichment in surgical liver biopsies from 13 obese (9 with DM2) and 5 control subjects, obtained in the fasting state at the time of elective abdominal surgery for obesity or cholecystectomy. RNA was isolated for cRNA preparation and hybridized to Affymetrix U133A microarrays. Human liver samples were obtained from 5 lean control subjects undergoing elective cholecystectomy and 13 obese subjects (with or without Type 2 diabetes) undergoing gastric bypass surgery. Subjects with diabetes were classified as either well-controlled or poorly-controlled.
Project description:Surgical samples have long been used as important subjects for cancer research. In accordance with an increase of neoadjuvant therapy, biopsy samples have recently become imperative for cancer transcriptome. On the other hand, both biopsy and surgical samples are available for expression profiling for predicting clinical outcome by adjuvant therapy; however, it is still unclear whether surgical sample expression profiles are useful for the prediction by the use of biopsy samples because little has been done about comparative gene expression profiling between the two kinds of samples. When gene expression profiles were compared between biopsy and surgical samples, artificially induced epithelial-mesenchymal transition (aiEMT) was found in the surgical samples. This study will evoke the fundamental misinterpretation including underestimation of the prognostic evaluation power of markers by overestimation of EMT in past cancer research, and will furnish some advice for the near future as follows: 1) Understanding how long the tissues were under an ischemic condition; 2) Prevalence of biopsy samples for in vivo expression profiling with low biases on basic and clinical research; and 3) Checking cancer cell contents and normal- or necrotic-tissue contamination in biopsy samples for prevalence. We used microarrays to compare gene expression profiles between 20 biopsy (BPY) and 20 surgical (OPE) samples derived from the cancerous portion of the esophagus of 20 esophageal cancer patients. One biopsy sample and one surgical sample was obtained from each patient; these sample pairs have the same number.
Project description:Survival in the majority of high grade astrocytoma (HGA) patients is very poor, with only a rare population of long-term survivors. A better understanding of the biological factors associated with long-term survival in HGA would aid development of more effective therapy and prognostication. We used microarray gene expression profiling of 26 patient surgical samples with known clinical outcomes to discover novel prognostic markers.