Project description:FAM134B is a reticulon-homology domain (RHD)-containing protein that participates in membrane-shaping of the endoplasmic reticulum (ER)8 13. It also functions as a mammalian ER-phagy receptor, mediating the fragmentation and selective degradation of ER sheets in multiple cell types8. However, little is known about the molecular and biophysical mechanisms that control and/or switch between these two FAM134B functions.
Project description:Rheumatic heart disease (RHD) remains a major source of morbidity and mortality in developing countries. A deeper insight into the pathogenetic mechanisms underlying RHD could provide opportunities for drug repurposing, guide recommendations for secondary penicillin prophylaxis, and/or inform development of near-patient diagnostics. We performed quantitative proteomics using Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectrometry (SWATH-MS) to screen protein expression in 215 African patients with severe RHD, and 230 controls. A machine learning (ML) approach was applied to feature selection among the 366 proteins quantifiable in at least 40% of samples, using the Boruta wrapper algorithm. The case-control differences and contribution to AUC of the ROC for each of the 56 proteins identified by the Boruta algorithm were calculated by Logistic Regression adjusted for age, sex and BMI. Adiponectin, complement component C7 and fibulin-1, a component of heart valve matrix, were each higher in cases when compared with controls. Ficolin-3, a protein with calcium-independent lectin activity that activates the complement pathway, was lower in cases than controls. The top six biomarkers from the Boruta analyses conferred an AUC of 0.90 indicating excellent discriminatory capacity between RHD cases and controls.
Project description:Transcriptome of N2a cells carrying a GFAT-1 gain-of-function point mutation that results in a G451E amino acid substitution were compared to WT N2a transcriptome profiles. Three replicates of both cell lines were analyzed. Additionally WT N2a cells were treated with 10 mM GlcNAc for 24h prior to transcriptome analysis resulting in a third dataset with 3 replicates.
Project description:Effects of TET2 on repressing inflammation have been assigned to its methylcytosine dioxygenase activity, but also to its ability to recruit HDAC-mediated repressor activity to pro-inflammatory genes. To discriminate between the two above-proposed functions of TET2, we asked how inhibition of its enzymatic activity, by administration of octyl-(R)-2hydroxyglutarate (2HG), and its ability to recruit HDAC-activity, by administration of the HDAC-inhibitor MS275 (Entinostat), affected the transcriptional profile of CSF3R-d715 RUNX1-D171N (RHD) expressing SCN-iPSC derived CD34+CD45+ HPCs. HPCs were generated from CRISPR-Cas9 genome edited CSF3R-d715 SCN-derived iPSCs with the STEMdiff™ Hematopoietic Kit (STEMCELL Technologies). The RUNX1-D171N (RHD) mutation was lentivirally introduced to the hematopoietic induction cultures 60 hours before harvesting the floating cells. DMSO (solvent control), 0.1 mM Octyl-(R)-2HG (Sigma-Aldrich) or 2 µM MS275 (Santa Cruz) was added for 16 hours to the hematopoietic induction cultures before harvesting the floating cells. Floating cells were harvested at Day 12 of the hematopoietic induction protocol. CD34+CD45+ HPCs were FACS sorted in TRIzol and RNA was isolated according to the manufacturer’s protocol. SMARTer Ultra Low Input RNA kit for sequencing (Clontech, v4 Cat# 634891) was used to generate cDNA. Sequencing libraries were generated using TruSeq Nano DNA Sample Preparation kits (Illumina, Cat# 20015964), according to the low sample protocol and paired-end sequenced on a Novaseq 6000 (Illumina).
