title: Investigation of 3D Chromatin Architecture Rewiring During Muscle Satellite Cells activation and aging [HIC PAX7KD]

status: Public on Feb 03 2023

city: Hong Kong

first: Yingzhe

last: Ding

state: Shatin NT.

address: Rm503,Li Ka Shing Medical Science Build.,Prince of Wales Hosp.,30-32 Ngan SHing St.

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: 3D genome architecture rewiring is known to influence spatiotemporal expression of lineage-specific genes and cell fate transition during multiple lineage progression and cell differentiation. However, it is yet unknown how nuclear architecture remodels and effects transcription changes during muscle stem cell (SC) development and ageing process. Here, we comprehensively map the 3D chromatin reorganization and integrate genome topology with transcriptional and epigenetic change during muscle SC lineage development and ageing process. Rewiring of compartmentalization is most pronounced when SC become activated, while striking loss in insulation of TAD borders and chromatin looping during early activation process. Meanwhile, super-enhancer containing TAD cluster reorganize in nuclear space and orchestrate stage-specific gene expression. In depth analysis identifies and verifies cis-regulatory elements at Pax7 locus controlling the local chromatin interactions and Pax7 expression. Geriatric cells display a more prominent gain in long-range contacts and loss insulation of TAD borders. Moreover, genome compartmentalization and chromatin loop has already altered for aged SC while geriatric SC display a more prominent loss in strength of TAD borders. Together, our results implicate 3D chromatin extensively reorganizes at multiple architectural levels and underpin the transcriptome remodeling and SC behaviors during SC lineage development and SC aging.

overall_design: The in situ Hi-C libraries were prepared as previously reported. Briefly, isolated SCs were digested using 100U DpnII overnight at 37 °C and then filled in with biotin for 1.5 hours at 37 °C; ligated for 4.5 hours at room temperature. DNA was purified by ethanol precipitation, and then sheared into 300-400bp fragments using Covaris S220. DNA fragments containing biotin were enriched by Dynabeads MyOne Streptavidin C1 (Invitrogen 65001) for 15min at room temperature, followed by end repairing, adaptor ligation and PCR amplification as described. The libraries were then sequenced via the Illumina HiSeq X Ten system at Genewiz company.

first: Ding

last: Yingzhe

first: He

last: Liangqiang

first: Zhao

last: Yu

first: Wang

last: Huating

first: Sun

last: Hao


title: Molecular mechanisms of coronary artery disease risk at the PDGFD locus

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary: Smooth muscle cells (SMCs) go through pehnotypic transition during atherosclerosis progression. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of SMCs in aorta tissuee.

overall_design: Aortic SMCs of ApoE-/-, Myh11-Cre, Rosa-TdTomato mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of TdTomato signal and analyzed using scRNAseq.

first: Hyun-Jung

last: Kim

first: Paul

last: Cheng

first: Disha

last: Sharma


title: Effect of knockout of ALKBH5 on gene expression and m6A modifications during IRI in mice

status: Public on Feb 05 2023

city: Shanghai

first: juntao

last: chen

address: 180 Fenglin Road

country: China

institute: Zhongshan Hospital

summary: To identify the direct m6A demethylation targets of ALKBH5 at the onset of renal IRI, we performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) using RNA isolated from IRI mouse kidney of WT and KO mice 24h after I/R (WT n=3 vs. KO n=3)

overall_design: WT group (n=3) VS KO group (n=3)

first: Juntao

last: Chen

first: Cuidi

last: Xu

first: Kun

last: Yang

first: Tongyu

last: Zhu


title: Comparison of STAMP and TRIBE for identifying the targets of RNA-binding proteins in human and Drosophila cells

city: Waltham

first: Katharine

last: Abruzzi

state: MA

address: 415 South St.

department: Biology

institute: HHMI; Brandeis University

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Refer to individual Series


title: Expression data from WT and Elektra (Slfn2 mutant, loss of function) homozygous hematopoietic stem cells extracted from mice.

status: Public on Feb 09 2023

city: Lund

first: Sarah

last: Warsi

address: BMC, Sölvegatan 17

country: Sweden

institute: Lund University

summary:
Abstract copied in below, from Warsi et al. 2022 Schlafen2 is a regulator of quiescence in adult murine hematopoietic stem cells, published in Haematologica. DOI 10.3324/haematol.2021.279799
Even though hematopoietic stem cells (HSCs) are characterized by their ability to self-renew and differentiate, they primarily reside in quiescence. Despite the immense importance of this quiescent state, its maintenance and regulation is still incompletely understood. Schlafen2 (Slfn2) is a cytoplasmic protein known to be involved in cell proliferation, differentiation, quiescence, interferon response, and regulation of the immune system. Interestingly, Slfn2 is highly expressed in primitive hematopoietic cells. To investigate the role of Slfn2 in the regulation of HSCs we have studied HSC function in the elektra mouse model, where the elektra allele of the Slfn2 gene contains a point mutation causing loss of function of the Slfn2 protein. We found that homozygosity for the elektra allele caused a decrease of primitive hematopoietic compartments in murine bone marrow. We further found that transplantation of elektra bone marrow and purified HSCs resulted in a significantly reduced regenerative capacity of HSCs in competitive transplantation settings. Importantly, we found that a significantly higher fraction of elektra HSCs (as compared to WT HSCs) were actively cycling, suggesting that the mutation in Slfn2 increases HSC proliferation. This additionally caused an increased amount of apoptotic stem and progenitor cells. Taken together, our findings demonstrate that dysregulation of Slfn2 results in a functional deficiency of primitive hematopoietic cells, which is particularly reflected by a drastically impaired ability to reconstitute the hematopoietic system following transplantation and an increase in HSC proliferation. This study thus identifies Slfn2 as a novel and critical regulator of a dult HSCs and HSC quiescence.

overall_design: HSCs (LSK CD9hi CD48- CD150+) were sorted from c-kit enriched mouse bone marrow using FACS. Samples were frozen at -80 in RLT buffer and sent to KFB (Regenburg, Germany) for RNA extraction and hybridization on Affymetrix microarrays. Cells were sorted from four Elektra homozygous C57Bl/6 mice and four WT control mice (littermates). Please see further information in the associated pubilcation by Warsi et al. 2022.

first: Shamit

last: Soneji

first: Stefan

last: Karlsson


title: Investigation of 3D Chromatin Architecture Rewiring During Muscle Satellite Cells activation and aging [HIC PAX7KO]

first: Yingzhe

last: Ding

first: Ding

last: Yingzhe

first: He

last: Liangqiang


title: A Y374X TDP43 truncation leads to an altered fibroblast metabolic profile in amyotrophic lateral sclerosis driven by pyruvate and TCA cycle intermediate alterations

city: Sheffield

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

summary:
Microarray and metabolomic analysis has been applied to the study of ALS in order to investigate how a Y374X TDP43 truncation mutation  leads to an altered metabolic profile in fibroblasts driven by pyruvate and TCA cycle intermediate alterations
The aim of the present study is to combine transcriptomics, metabolic flux analysis and protein expression analysis in fibroblasts in order to investigate how the Y34X truncation mutation in the TDP43 gene causes metabolic dysfunction

overall_design: Fibroblasts from three truncation mutation patients, three sporadic ALS cases and three neurologically normal controls were used for transcriptomic analysis

first: Scott

middle: P

last: Allen

first: Afnan

last: Al Sultan

first: K

middle: K

last: Elaine

first: Erin

last: Tonkiss

first: Lydia

last: Castelli

first: Nikalaos

middle: Y

last: Stefanidis

first: Robin

middle: J

last: Highley

first: Jonathan

last: Cooper-Knock

first: Janine

last: Kirby

first: Pamela

last: Shaw


title: Investigation of 3D Chromatin Architecture Rewiring During Muscle Satellite Cells activation and aging [RNA-seq aging]

overall_design: RNA-seq was performed in freshly isolated muscle stem cell for 2 month,23-24 month and 28-32 month.

first: Zhao

last: Yu

first: Wang

last: Huating

first: Sun

last: Hao


title: Investigation of 3D Chromatin Architecture Rewiring During Muscle Satellite Cells activation and aging [HIC_aging]

last: Ding

overall_design: The in situ Hi-C libraries were prepared as previously reported. Briefly, isolated SCs were digested using 100U DpnII overnight at 37 °C and then filled in with biotin for 1.5 hours at 37 °C; ligated for 4.5 hours at room temperature. DNA was purified by ethanol precipitation, and then sheared into 300-400bp fragments using Covaris S220. DNA fragments containing biotin were enriched by Dynabeads MyOne Streptavidin C1 (Invitrogen 65001) for 15min at room temperature, followed by end repairing, adaptor ligation and PCR amplification as described. At least two biological replicates were performed for both control and sgMyc groups. The libraries were then sequenced via the Illumina HiSeq X Ten system at Genewiz company.


title: Investigation of 3D Chromatin Architecture Rewiring During Muscle Satellite Cells activation and aging [HiC SC]

last: Yingzhe


title: Investigation of 3D Chromatin Architecture Rewiring During Muscle Satellite Cells activation and aging [HIC_PAX7KO]

last: Liangqiang


title: Investigation of 3D Chromatin Architecture Rewiring During Muscle Satellite Cells activation and aging

type: Genome binding/occupancy profiling by high throughput sequencing


title: Lung lymphatic endothelial cells

status: Public on Feb 02 2023

city: Beijing

first: Siling

last: Fu

address: No. 7, Science Park Road

institute: National Institute of Biological Sciences, Beijing.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcriptomic analysis of P0 mouse lung lymphatic endothelial cells

summary: Fluid clearance mediated by lymphatic vessels is known to be essential for lung inflation and gas exchange function during the transition from prenatal to postnatal life, yet the molecular mechanisms that regulate lymphatic function remain unclear. Here, we profiled the molecular features of lymphatic endothelial cells (LECs) in embryonic and postnatal day (P) 0 lungs by single-cell RNA-seq analysis. We identified that the expression of c-JUN is transiently upregulated in P0 LECs. Conditional knockout of Jun in LECs impairs the opening of lung lymphatic vessels at birth, leading to fluid retention in the lungs and neonatal death. We further demonstrated that increased mechanical pressure induces the expression of c-JUN in LECs. c-JUN regulates the opening of lymphatic vessels by modulating remodeling of the actin cytoskeleton in LECs. Our study established the essential regulatory function of c-JUN-mediated transcriptional responses in facilitating lung lymphatic fluid clearance at birth.

overall_design: Control and Jun knockout LECs from Prox1-GFP mouse lungs were isolated at P0  by FACS. LECs isolated from three replicates of each group were identically mixed and then processed to RNA amplification following the protocol of Arcturus RiboAmp HS PLUS RNA ampliﬁcation kit before RNA sequencing. Datasets were generated named as "Jun-Ctrl", and "Jun-cKO".

first: Ennan

last: Bin

last: Tang


title: Single-cell transcriptomics of mouse lung lymphatic endothelial cells

overall_design: GFP+ CD31+ LECs from Prox1-GFP mouse lungs were isolated at E14.5, E16.5, E18.5, and P0  by FACS. LECs isolated from three to five replicates of each group were identically mixed and then processed to sc-RNA seq following the 10X Genomics protocol. Four single-cell RNA sequencing datasets were generated named as "E14","E16","E18", and "P0".

first: Huanwei

last: Huang


title: Cleavage Under Targets and Tagmentation analysis of human lung lymphatic endothelial cells

overall_design: Cultured human lung LECs (CC-2527,Lonza) treated with scramble or JUN siRNAs were harvested and the CUT&Tag technology was performed as previously described and performed using a kit (TD902, Vazyme) according to manufacturer’s instructions.


title: Circle-Seq for extrachromosomal circular DNA in PLC-PRF-5 cells after treatment with 25OHD

status: Public on Feb 01 2023

city: Tianjin

first: Heng

last: Zhang

address: 38 Rd.Tongyan

institute: Nankai University

summary: It has been verified that extrachromosomal circular DNA (ecDNA) has important clinical significance, and the formation process of ecDNA, its immunogenicity, and its other functions have also been described. However, the balancing mechanism by which cells respond to ecDNA, i.e., how ecDNA degrades within cells, is unclear. Here, by using Circle-Seq method conducted on PLC-PRF-5 HCC Cells, ecDNA was purified and the samples were used for DNA Library Preparation and Next Generation Paired-End Sequencing using Illumina MiSeq Technology, We found that some ecDNAs disappeared after VD treatment compared with the DMSO group, and these disappearing ecDNA were related to EMT, proliferation, cell cycle, focal adhesion and other malignant behaviors. Moreover, Circle-seq peaks narrowed after VD treatment, and the coverage over the whole gene was significantly reduced, suggesting that ecDNA after VD treatment carried smaller DNA fragments, which may cause them not to function as a whole gene. Importantly, we demonstrate that VD can cause a continuous and steady decrease in ecDNA in HCC cells.

overall_design: We purified ecDNA from PLC-PRF-5 cells treated with DMSO or 25OHD (100nM and 500nM) for 48 h owing to the remarkably higher level of ecDNA content among HCC cell lines. The obtained genomic DNA was treated with Plasmid-Safe ATP-dependent DNase to eliminate linear chromosomal DNA and then DNAs were eluted and digested with PacI to eliminate mitochondrial DNA. we employed rolling-circle amplification of the purified eccDNA by MDA using φ29 DNA polymerase and random hexamer primers. We than sequenced the purified eccDNA using Illumina paired-end sequencing.

first: Zhang

last: Heng

first: Qin

last: Lu-ning

first: Feng

last: Yi-qian

last: Lei


title: Investigation of 3D Chromatin Architecture Rewiring During Muscle Satellite Cells activation and aging [CTCF ChIP-Seq]

first: Yingzhe

first: Ding

first: He


title: Yeast meiotic transcriptional profile [Kfc1p mutant]

city: DC

first: Zachory

last: Park

state: Washington DC

address: 37th and O Streets NW

institute: Georgetown University

summary: RNAseq across a time course of meiosis of cells with and without Kfc1p. The overexpression of either IME1 or both IME1 and RIM4 was used to determine how overexpression of the two genes functions to resuce the meiotic defect associated with the loss of Kar4p.

overall_design: Samples were induced to sporulated and harvested across the first 12 to 48 hours of meiosis at 2-4 hour intervals. Each sample has two biological replicates.

first: Mark

last: Rose


title: Sequence data for annotation and scaffolding of the Lathyrus sativus LS007 Rbp1.0 genome assembly

status: Public on Jan 31 2023

city: Norwich

first: Martin

last: Vickers

state: Norfolk

address: Colney Ln

institute: John Innes Centre

summary: This dataset includes RNAseq data of 7 tissues/developmental stages of Lathyrus sativus genotype LSWT11 and 2 tissues with drought- and well-watered treatments of Lathyrus sativus genotypes LS007 and Mahateora. These data were used in the functional annotation pipeline of the Rbp1.0 genome assembly of LS007. The multi-tissue transcriptome was also used to support gene candidate identification by mRNA abundance. Also included is Hi-C sequencing data used to scaffold the assembly into pseudochromosomes

overall_design: RNAseq data to inform a genome annotation pipeline - replication of multi-tissue transcriptome as shown below, three replicates for each genotype/treatment combination in drought experiment; RNAseq for RNA read counting to support gene candidate identification, replication as shown below, HiC for scaffolding of genome assembly

first: Peter

last: Emmrich

first: Abhimanyu

last: Sarkar

first: Roland

last: Wouters

first: Jonathan

last: Moore

first: Janet

last: Higgins

first: Gemy

middle: G

last: Kaithakottil


title: RNA sequencing of postmortem-fibroblast derived cell lines and postmortem human Brodmann Area 9 from Cocaine Use Disorder Subjects in the University of Texas Health Science Center at Houston Brain Collection

city: Houston

first: Consuelo

last: Walss-Bass

state: Texas

address: 1941 East Road Rm. 3110

department: Louis A. Faillace Department of Psychiatry and Behavioral Sciences

summary: Introduction: Human-derived induced pluripotent stem cell (iPSC) models of brain promise to advance our understanding of neurotoxic consequences of drug use. However, how well these models recapitulate the actual genomic landscape and cell function, as well as the drug-induced alterations, remains to be established. New in vitro models of drug exposure are needed to advance our understanding of how to protect or reverse molecular changes related to substance use disorders.  Methods: We engineered a novel induced pluripotent stem cell-derived model of neural progenitor cells and neurons from cultured postmortem human skin fibroblasts, and directly compared these to isogenic brain tissue from the donor source. We assessed the maturity of the cell models across differentiation from stem cells to neurons using RNA cell type and maturity deconvolution analyses as well as DNA methylation epigenetic clocks trained on adult and fetal human tissue. As proof-of-concept of this model’s utility for substance use disorder studies, we compared morphine- and cocaine-treated neurons to gene expression signatures in postmortem Opioid Use Disorder (OUD) and Cocaine Use Disorder (CUD) brains, respectively.   Results: Within each human subject (N = 2, 2 clones each), brain frontal cortex epigenetic age parallels that of skin fibroblasts and closely approximates the donor’s chronological age; stem cell induction from fibroblast cells effectively sets the epigenetic clock to an embryonic age; and differentiation of stem cells to neural progenitor cells and then to neurons progressively matures the cells via DNA methylation and RNA gene expression readouts. In neurons derived from an individual who died of opioid overdose, morphine treatment induced alterations in gene expression similar to those previously observed in OUD ex-vivo brain tissue, including differential expression of the immediate early gene EGR1, which is known to be dysregulated by opioid use.   Discussion: In summary, we introduce an iPSC model generated from human postmortem fibroblasts that can be directly compared to corresponding isogenic brain tissue and can be used to model perturbagen exposure such as that seen in opioid use disorder. Future studies with this and other postmortem-derived brain cellular models, including cerebral organoids, can be an invaluable tool for understanding mechanisms of drug-induced brain alterations.

overall_design: RNAseq of postmortem fibroblast-derived induced pluripotent stem cells (iPSCs), Neural Progenitor Cells (NPCs) and Neurons from one subject with opioid use disorder and one subject with cocaine use disorder. Each iPSC, NPC and Neuron line has one clonal replicate, for a total of 4 lines. Also contains RNAseq from Postmortem Brain Brodmann Area 9 for 8 cocaine use disorder subjects from the UTHealth Brain Collection. Please see GEO Accession GSE182321 for control subject data used in study

first: Emily

last: Mendez

first: Sandra

last: Grimm

first: Laura

last: Stertz

first: Preethi

last: Gunaratne

first: Cristian

last: Coarfa


title: Hepatocyte-derived DPP4 regulates portal GLP-1 bioactivity, glucose production and its absence alters liver disease progression (F480+ CELLS)

city: Ottawa

first: Erin

last: Mulvihill

state: On

address: 40 Ruskin Street

country: Canada

institute: UOHI

summary: Elevated circulating dipeptidyl-peptidase 4 (DPP4) is a biomarker for liver disease, but its involvement in gluconeogenesis and metabolic associated fatty liver disease (MAFLD) progression remains unclear. Here we identified that DPP4 in hepatocytes but not Tie2+ endothelial cells regulates the local bioactivity of incretin hormones and gluconeogenesis. However, the complete absence of DPP4 (Dpp4-/-) in aged mice with metabolic syndrome accelerates liver fibrosis without altering dyslipidemia and steatosis. Analysis of transcripts from the livers of Dpp4-/- mice displayed enrichment for inflammasome, p53, and senescence programs compared to littermate controls. High-fat high-cholesterol (HFHC)-feeding decreased Dpp4 expression in F4/80+ cells, with only minor changes in immune signaling.

overall_design: Aged mice were fed a HFHC diet for 6 months, liver tissue was collected and F4/80+ cells were isolated using the liver dissociation kit from Miltenyi Biotech. Total RNA was isolated using Trizol as permanufacturer's protocol, and processed for NanoString analysis using manufacturer's protocol, lastly analyzed using nSolver

middle: E

first: Natasha

middle: A

last: Trzaskalski


title: Hepatocyte-derived DPP4 regulates portal GLP-1 bioactivity, glucose production and its absence alters liver disease progression (LIVER)

overall_design: Aged mice were fed a HFHC diet for 6 months, liver tissue was collected. Total RNA was isolated using Trizol as permanufacturer's protocol, and processed for NanoString analysis using manufacturer's protocol, lastly analyzed using nSolver


title: Repair of airway epithelia requires metabolic rewiring towards fatty acid oxidation

city: London

first: Andreas

last: Wack

address: 1 Midland Road

institute: The Francis Crick Institute

overall_design: Comparative gene expression profiling analysis of RNA-seq data from CD49f+NGFR+ (Basal Cells), CD49f-NGFR- SiRTubulin + (ciliated) and CD49f-NGFR- SiRTubulin - (secretory) cell sorted from differentiated MTEC cultures collected at ALI day 10,

first: Stefania

last: Crotta

first: Matteo

last: Villa


title: Repair of airway epithelia requires metabolic rewiring towards fatty acid oxidation [II]

summary: To test  the role of FAO in epithelium differentiation, we assessed genome-wide transcriptional changes in Cpt1a+/- and Cpt1a-/- primary mouse tracheal epithelial cell (mTEC) cultures analysed at the end of the expansion phase (ALI day 0) or at day 5 and 7 post air-exposure by RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Cpt1a+/- and Cpt1a-/- mTEC cells taken at ALI day 0, 5 and 7

first: Crotta

last: Stefania

first: Villa

last: Matteo

first: Wack

last: Andreas


title: Hepatocyte-derived DPP4 regulates portal GLP-1 bioactivity, glucose production and its absence alters liver disease progression


title: The tRNA derived fragments  (tRFs) expression profiles in human aortic  smooth muscle cells (HASMCs)

first: zhihua

last: Rong

address: dongdan

institute: peking union medical college hospital

summary: To explore the potential involvement of tRNA derived fragments (tRFs) in the human aortic vascular smooth muscle cells (HASMCs), we conducted tRFs profiling in three pairs of differentiated HASMCs (treated with PBS) and dedifferentiated HASMCs (treated with PDGF-BB 50 ng/ml) by microarray. Our results showed that tRFs were aberrantly expressed in dedifferentiated HASMCs compared with differentiated HASMCs and provided potential targets for novel insights into VSMC differentiation or vascular remodeling diseases.

overall_design: The tRFs expression profiles of three paired differentiated HASMCs (treated with PBS) and dedifferentiated HASMCs (treated with PDGF-BB 50 ng/ml)were analyzed using the microarray platform.

first: Zhihua

first: Fengshi

last: Li

first: Leng

last: Ni

first: Changwei

last: Liu


title: Investigation of 3D Chromatin Architecture Rewiring During Muscle Satellite Cells activation and aging [RNA-seq SC]

first: Yingzhe

last: Ding

overall_design: RNA-seq was performed in quiescent muscle stem cells, freshly isolated or cultured muscle stem cell.

first: Ding

last: Yingzhe

first: Zhao

last: Yu

first: He

last: Liangqiang

first: Wang

last: Huating

first: Sun

last: Hao


title: Repair of airway epithelia requires metabolic rewiring towards fatty acid oxidation [I]

first: Andreas

summary: Comparative gene expression profiling analysis of RNA-seq data from CD49f+NGFR+, CD49f-NGFR- cell sorted from differentiated MTEC cultures collected at ALI day 10, and MTEC culture taken at ALI t0

overall_design:
Primary cells isolated from tracheas by enzymatic treatment were seeded onto 0.4 μm pore size clear polyester membrane  coated with a collagen solution. At confluence, media was removed from the upper chamber to establish an air- liquid interface (ALI). Cells were collected at day 10 post air-exposure.
Cultures were trypzinazed and sorted into CD49f+NGFR+ and CD49f-NGFR- subsets


title: microRNA Expression in Normal and Diabetic Pancreatic Islets

status: Public on Jan 29 2023

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

summary: Genetic studies have identified ≥240 loci associated with type 2 diabetes (T2D), yet most of these loci lie in  non-coding regions, masking the underlying molecular mechanisms. Recent studies investigating gene  expression in pancreatic islets have provided key insights into the molecular drivers of T2D pathophysiology  through comprehensive genetic and genomic analyses. However, similar studies investigating microRNA  (miRNA) expression remain limited. Here, we present the largest genetic and genomic analysis of miRNA  expression in human islets to date, spanning 63 participants. We characterize the genetic regulation of miRNA  expression by decomposing the expression of highly heritable miRNAs into cis- and trans- genetic components  and mapping cis loci associated with miRNA expression (miRNA-eQTLs). We find (a) 81 heritable miRNAs,  which we show are primarily regulated by trans-acting genetic effects, and (b) 5 miRNA-eQTLs. To evaluate  the impact of miRNA expression on T2D, we use several different strategies to nominate T2D-associated  miRNAs. First, we colocalize miRNA-eQTLs with genetic studies of T2D and several T2D-related traits and  identify one miRNA, miR-1908, that shares genetic signals for blood glucose and HbA1c. Next, we intersect  miRNA seed regions with credible set SNPs from T2D and T2D-related genetic studies and find 46 miRNAs  that may have altered binding and function due to disrupted seed regions. Finally, we perform differential  expression analysis and identify 38 miRNAs associated with either T2D status, body mass index, sex, or a  polygenic score for HbA1c levels. To validate identified miRNAs, we perform chromatin run-on sequencing and  confirm differential transcription of T2D-associated miRNAs.

overall_design: Multi-omic comparison of small RNAseq and ChROseq data from patients that are either non-diabetic or have type2 diabetes.

first: Leland

last: Taylor

first: Matt

last: Kanke


title: Integration of parallel metabolomics and transcriptomics reveals metabolic patterns in porcine oocytes during maturation

status: Public on Jan 25 2023

city: Nanjing

first: Qiuzhen

last: Chen

address: 101 Longmian Rd, Nanjing, Jiangsu, 211166 China

institute: Nanjing Medical University

summary: Well-balanced and timed metabolism is the prerequisite for optimal oocyte development. To date, numerous studies have focused on the utilization of exogenous substrates by oocytes, whereas the underlying mechanism of intrinsic regulation during meiotic maturation is less characterized. Herein, we performed an integrated analysis of parallel metabolomics and transcriptomics by isolating porcine oocytes at three time points, cooperatively depicting the global picture of the metabolic patterns during oocyte maturation. In particular, we identified the metabolic features of porcine oocytes during meiotic maturation, such as the fall in bile acids, the active one-carbon metabolism and a progressive decline in nucleotide metabolism. Collectively, the current study not only provide a comprehensive multiple omics data resource, but also may promote the discovery of biomarkers in the prediction and improvement of oocyte quality.

overall_design: To explore the expression of the enzymes related to metabolism, we simultaneously conducted transcriptional profiling of oocytes during in vitro maturation at three key time points 0h (GV), 24h (Pre-MI), and 46h (MII).

first: Ming

last: Gao

first: Minjian

first: Shuai

last: Zhu

first: Hengjie

last: Wang

first: Weizheng

last: Yang

first: Xi

first: Qiang

first: Ling

last: Gu


title: OMICS Analyses Unraveling Related Gene and Protein Driven Molecular Mechanisms Underlying PACAP 38 Induced Neurite Outgrowth in PC12 Cells

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

summary: Recently, our group has shown that the pituitary adenylate cyclase-activating polypeptide (PACAP)-induced neurite projection elongation in rat adrenal-derived pheochromocytoma cell line (PC12) is mediated via PAC1 receptor-mediated dephosphorylation of CRMP2 majorly through PI3K/AKT and MEK/ERK pathways. However, the mechanism of neuronal outgrowth by PACAP, including CRMP2 dephosphorylation, remains unclear. In our previous report, we found that GSK-3β, CDK5, and Rho/ROCK dephosphorylated CRMP2 within 3 hours after the addition of PACAP, but the early dephosphorylation of CRMP2 by PACAP remains unclear. Thus, we considered it important to identify early factors in PACAP-induced neurite projection elongation and performed omics-based transcriptomic (whole genome DNA microarray) and proteomic (TMT-labeling in conjunction with liquid chromatography-tandem mass spectrometry) analyses of gene and protein expression profiles from 5-120 minutes after PACAP addition. Results surprisingly revealed a number of key regulators involved in neurite outgrowth, including known ones. We also identified factors that may be involved in CRMP2 dephosphorylation. Cross-referencing previous research, we tried to map these molecular components onto potential pathways. The results of this comprehensive analysis may provide important new information on the molecular mechanisms of neuronal differentiation induced by PACAP.

overall_design: Whole genome DNA microarray was carried out on the PC12 cells treated with PACAP38 (10⁻⁷ M) for the respective time points (5 – 120 minutes) and washed cells were stored at -80°C until RNA isolation. Total RNA was extracted from PC12 cells cultured in a 10 cm culture dish using the RNeasy Mini Kit (74104, Qiagen). Total RNA extracted from PC12 cells for each control and treatment (n=6) was pooled in each group, prior to DNA microarray analysis.

first: Junko

last: Shibato

first: Fumiko

last: Takenoya

first: Seiji

last: Shioda

first: Randeep

last: Rakwal


title: Molecular and Physiological Functions of PACAP in Sweat Secretion

status: Public on Jan 23 2023

summary: Sweat has a critical role in human body, including thermoregulation and maintenance of skin environment and health. Hyperhidrosis and anhidrosis are caused by abnormalities in sweat secretion resulting in severe skin conditions (pruritus and erythema). Bioactive peptide, pituitary adenylate cyclase-activating polypeptide (PACAP) was isolated and identified to activate adenylate cyclase in pituitary cells. In recent years, it was reported that PACAP increases sweat secretion via PAC1R in mice and promotes the translocation of AQP5 to the cell membrane through increasing intercellular [Ca2+] via PAC1R in NCL-SG3 cells. However, the intracellular signaling mechanisms by PACAP are poorly clarified. In this study, we used PAC1R knockout (KO) mice and wild-type (WT) mice to observe changes in AQP5 localization and gene expression in sweat gland by PACAP treatment. Immunohistochemistry revealed that PACAP promotes the translocation of AQP5 to lumen side in eccrine gland via PAC1R. Furthermore, PACAP up-regulates gene expression (Ptgs2, Kcnn2, Cacna1s) involved in sweat secretion in WT mice. Further, PACAP treatment down-regulated Chrna1 gene expression in PAC1R KO mice. These genes were found to be involved in multiple pathways related to sweating. Overall our data provide a solid basis for future research initiatives to develop new therapies to treat sweating disorders.

overall_design: After intradermal injection of PACAP to six WT mice and PAC1R KO mice each, the skin of the paws was sampled at 30 and 60 minutes later, which were immersed immediately post-dissection in liquid nitrogen and thereafter transferred to an -80°C deep freezer. The samples were individually ground in liquid nitrogen to prepare very fine powders for subsequent downstream gene expression analyses. The Agilent mouse whole genome 4 × 44 K (G4122F) DNA slide (composed of 4 chips on one slide) was used for the microarray analysis, which was performed according to manufacturer’s instructions.

first: Michio

last: Yamashita


title: Single-cell discovery and multi-omic characterization of therapeutic targets in multiple myeloma [scRNA-seq]

status: Public on Jan 17 2023

city: St. Louis

first: Ravi

last: Vij

state: MO

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St. Louis

summary: Multiple myeloma (MM) is a highly refractory hematological cancer. Targeted immunotherapy has shown promise in MM but remains hindered by the challenge of identifying specific yet broadly representative tumor markers. We analyzed 53 bone marrow (BM) aspirates from 41 MM patients using an unbiased, high-throughput pipeline for therapeutic target discovery via single cell transcriptomic profiling, yielding 38 MM marker genes encoding cell-surface proteins and 15 encoding intracellular proteins. Of these, 20 candidate genes were highlighted that are not yet under clinical study, 11 of which are previously uncharacterized as therapeutic targets. The findings were cross-validated using bulk RNA-sequencing, flow cytometry, and proteomic mass spectrometry of MM cell lines and patient BM, demonstrating high overall concordance across data types. Independent discovery using bulk RNA-sequencing reiterated top candidates, further affirming the ability of single cell transcriptomics to accurately capture marker expression despite limitations in sample size or sequencing depth. Target dynamics and heterogeneity were further examined using both transcriptomic and immuno-imaging methods. In summary, this study presents a robust and broadly applicable strategy for identifying tumor markers to better inform the development of targeted cancer therapy.

overall_design:
We used scRNA-seq to perform an unbiased search for genes with specific expression in plasma cells and/or B cells (relative to other detected cell types) on 53 bone marrow mononuclear cell (BMMC) samples taken from 41 patients.

Submitter states: raw data will be submitted to dbGaP due to patient privacy concerns. ND* samples already have raw data available in dbGaP:  accession number phs000159

first: Li

last: Ding

first: John

middle: F

last: DiPersio


title: Overdominant expression of genes plays a key role in root growth of tobacco hybrids

status: Public on Jan 22 2023

city: Guiyang

first: kai

last: pi

state: Guizhou

department: Key Laboratory for Tobacco Quality Research Guizhou Province

institute: Guizhou University

summary: Heterosis has greatly improved the yield and quality of crops. However, previous studies often focused on improving the yield and quality of the shoot system, while research on the root system was neglected. We determined the root numbers of 12 F1 hybrids, all of which showed strong heterosis, indicating that tobacco F1 hybrids have general heterosis. To understand its molecular mechanism, we selected two hybrids with strong heterosis, GJ (G70 × Jiucaiping No.2) and KJ (K326 × Jiucaiping No.2), and their parents for transcriptome analysis. There were 84.22% and 90.25% of the differentially expressed genes were overdominantly expressed. The enrichment analysis of these overdominantly expressed genes showed that "Plant hormone signal transduction", "Phenylpropanoid biosynthesis", "MAPK signaling pathway - plant", and "Starch and sucrose metabolism" pathways were associated with root development. We focused on the analysis of the biosynthetic pathways of auxin(AUX), cytokinins(CTK), abscisic acid(ABA), ethylene(ET), and salicylic acid(SA), suggesting that overdominant expression of these hormone signaling pathway genes may enhance root development in hybrids.

overall_design: 15 samples were analyzed, including 5 plant materials, each with three replicates.

first: Kai

last: Pi


title: A Virus-Packageable CRISPR System Identifies Host Dependency Factors Co-opted by Multiple HIV-1 Strains

status: Public on Jan 26 2023

city: SEATTLE

first: Vanessa

last: Montoya

state: Washington

address: 1100 Fairview Ave

institute: Fred Hutchinson Cancer Center

summary: The goal of this CRISPR-based screen (HIV-CRISPR) is to identify HIV-1 dependency factors by evaluating multiple pathways simultaneously. Here are Illumina sequencing data and counts files from HIV-CRISPR screens using a guide RNA library targeting the whole genome (TKOv3), a custom guide RNA library targeting human epigenome genes (HuEpi), a custom guide RNA library targeting interferon-stimulated genes (PIKA), and a custom guide RNA library of genes containing of a subset of each of the aforementioned libraries designed to target human dependency factors (HIVDEP). The HIV-CRISPR screens described here were performed in clonal ZAP knockout Jurkat cell lines as ZAP inhibition of the HIV-CRISPR vector has been previously described (PMID: 30520725).

overall_design: These HIV-CRISPR screens were performed by generating a pool of ZAP-knockout Jurkat cells engineered to stably overexpress CCR5 and that are each knocked out for human genes using the TKOv3, HuEpi, PIKA, or HIVDEP guide RNA libraries. Each screen was performed in two biological replicates. Afterwards, for each condition, the cell pellets were harvested, genomic DNA (gDNA) was extracted, and sequencing was performed to evaluate the single guide RNA (sgRNA) representation of the library. Simultaneously, the viral supernatant was harvested, viral RNA (vRNA) was extracted, and sequencing was performed. By comparing the sgRNA representation of the viral RNA to the library representation of the genomic DNA, the sgRNAs that are depleted in the viral population are associated with potential HIV-1 dependency factors. The plasmid library of the HIV-CRISPR HIVDEP guide RNA library was also sequenced and included here. The plasmid guide libraries of the guide RNA libraries TKOv3, PIKA, and HuEpi have been sequenced before and are not included here.

middle: R

first: Michael

last: Emerman


title: Selective and brain-penetrant lanosterol synthase inhibitors target glioma stem-like cells by activating a shunt pathway that generates the toxic metabolite 24(S),25-epoxycholesterol

city: Dallas

first: Deepak

last: Nijhawan

address: 5323 Harry Hines Blvd

department: Biochemistry

institute: UT Southwestern

summary: Glioblastoma (GBM) is a common and aggressive adult brain cancer with few treatment options due in part to the challenges of identifying brain-penetrant drugs. Here, we investigated the mechanism of a tetracyclic dicarboximide (referred to as MM0299) identified in a screen for compounds with anti-glioblastoma activity. MM0299 inhibits lanosterol synthase (LSS) and diverts sterol flux away from cholesterol into a “shunt” pathway that culminates in 24(S),25-epoxycholesterol (EPC). EPC synthesis following MM0299 treatment is both necessary and sufficient to block the growth of mouse and human glioma stem-like cells by depleting cellular cholesterol. In comparison to a known LSS inhibitor, MM0299 exhibits superior selectivity for LSS over other sterol biosynthetic enzymes. Critical for its application in the brain, we report an MM0299 derivative that is orally bioavailable, brain-penetrant and induces the production of EPC in orthotopic GBM tumors but not normal mouse brain. These studies have implications for the development of an LSS inhibitor to treat GBM or other neurologic indications.

overall_design: Spontaneous glioblastoma tumors from genetically engineered mouse model were pooled together to generate mouse GBM Mut6 cell line. Mut6 cells were treated with DMSO or 100 nM MM0299 for 24 hours. Total RNA was collected from these samples.

first: Thu

last: Nguyen


title: Retinol Dehydrogenase 10 Reduction Mediated Retinol Metabolism Disorder Promotes Diabetic Cardiomyopathy

status: Public on Jan 15 2023

city: Guangzhou

first: Yandi

last: Wu

address: Zhongshan Road

institute: Sun Yat-sen University

summary: Diabetic cardiomyopathy (DCM) is a primary myocardial injury induced by diabetes mellitus (DM) with a complex pathogenesis. In this study, we identified disordered cardiac retinol metabolism in T2DM mice and patients characterized by retinol (vitamin A, Rol) overload, all-trans retinoic acid (atRA) deficiency and retinoic acid receptors (RARs) reduction, and demonstrated that both cardiac Rol overload and atRA deficiency promote DCM by supplementing T2DM mice with Rol or atRA. Mechanically, by constructing cardiomyocyte-specific conditional RDH10-knockout mice and overexpressing RDH10 in T2DM mice via adeno-associated virus, we verified that the reduction in cardiac retinol dehydrogenase 10 (RDH10) is the initiating factor for cardiac retinol metabolism disorder and its resulting DCM. Additionally, lipotoxicity and ferroptosis contribute to the effect of retinol metabolism disorder on DCM. Based on these results, we suggest that the reduction of cardiac RDH10 and its mediated disorder of cardiac retinol metabolism is a new mechanism underlying DCM.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for db/m and db/db miceat 4, 24, and 32 weeks of age.

first: Weibin

last: Cai

first: Tongsheng

last: Huang

first: Xinghui

last: Li


title: VGLL2-NCOA2 leverages developmental programs for pediatric sarcomagenesis

status: Public on Jan 16 2023

city: Columbus

first: Genevieve

last: Kendall

state: OH

address: 700 Children's Drive, WA5014

institute: Nationwide Children's Hospital / The Ohio State University

summary: Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators, VGLL2-NCOA2, found in infantile rhabdomyosarcoma. To delineate VGLL2-NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities, we implemented a cross-species comparative oncology approach with zebrafish, mouse allograft, and patient samples. We found that VGLL2-NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2-NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2-NCOA2 developmental targets, including a RAS family GTPase, arf6/ARF6. In VGLL2-NCOA2 zebrafish, mouse allograft, and patient tumors, arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover, ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2-NCOA2 is an oncogene which leverages developmental programs for tumorigenesis, and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: Examination of RNA-seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2-NCOA2 expression, and a comparison to mature  zebrafish skeletal muscle and CIC-DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2-NCOA2, and allografted to generate tumor models. These are compared to allografts of C2C12-empty controls.

first: James

last: Amatruda

first: Olivier

last: Delattre

first: Franck

last: Tirode

first: Matthew

last: Cannon

first: Lin

last: Xu

first: Sarah

last: Watson

first: Didier

last: Surdez


title: RNA-Seq analysis was performed with total RNA isolated from mature axillary bud of Fielder and tfl1-5 mutant

status: Public on Jan 13 2023

city: 泰安

first: 孙

last: 静

address: 山东农业大学岱宗校区

institute: 山东农业大学

summary: To establish the regulatory roles of TaTFL1-5 in wheat axillary bud development , we identified the regulated genes whose transcriptional activities are associated with relative abundance of TaTFL1-5 transcripts by transcriptomic analysis. Differentially expressed genes are mainly enriched in the metabolic pathway and the lifetime metabolic pathway, but also in many plant hormone signal transduction pathways such as auxin, gibberellin, brassinosteroids and cytokinin.

overall_design: Three biological repeats of the wheat axillary bud from tfl1-5(Mutant-1, Mutant-2, Mutant-3) and Fielder (Fielder-1, Fielder-2, Fielder-3) were used for RNA sequencing.

first: Xin

middle: Q

last: Gao

first: Jing

last: Sun


title: Circular RNA expression profile in mitochondria fractions of liver tumour-initiating cells

city: Zhengzhou

first: Pingping

last: Zhu

address: 100 Kexue Road

institute: Zhengzhou University

summary: Tumour-initiating cells (TICs), also termed as cancer stem cells, contribute to tumour initiation, metastasis, progression and drug resistance. Metabolic reprogramming is a cancer hallmark and plays vital roles in liver tumorigenesis. However, the role of metabolic reprogramming in TICs remains poorly explored.Here we isolated mitochondria from liver TICs and non-TICs, and detected the expression levels of mitochondrial encoded circRNAs in TICs and non-TICs.

overall_design: Liver TICs were enriched from oncospheres. Liver TICs and non-TICs were used for mitochondria isolation, and mitochondrial encoded circRNAs (mecirc) were identified through circRNA sequencing.

first: Z

last: Chen

first: Q

last: He

first: T

last: Lu

first: P


title: Developmental Deficits of MGE-derived Interneurons in the Cntnap2 Knockout Mouse Model of Autism Spectrum Disorder

status: Public on Jan 12 2023

city: Acton

first: Lixinyu

last: Liu

state: ACT

address: 131 Garran road

country: Australia

institute: John Curtin School of Medical Research

summary: Interneurons are fundamental cells for maintaining the excitation-inhibition balance in the brain in health and disease. While interneurons have been shown to play a key role in the pathophysiology of autism spectrum disorder (ASD) in adult mice, little is known about how their maturation is altered in the developing striatum in ASD. Here, we aimed to track striatal developing interneurons and elucidate the molecular and physiological alterations in the Cntnap2 knockout mouse model. Using Stereo-seq and single-cell RNA sequencing data, we first characterized the pattern of expression of Cntnap2 in the adult brain and at embryonic stages in the medial ganglionic eminence (MGE), a transitory structure producing most cortical and striatal interneurons. We found that Cntnap2 is enriched in the striatum, compared to the cortex, particularly in the developing striatal cholinergic interneurons. We then revealed enhanced MGE-derived cell proliferation, followed by increased cell loss during the canonical window of developmental cell death in the Cntnap2 knockout mice. We uncovered specific cellular and molecular alterations in the developing Lhx6-expressing cholinergic interneurons of the striatum, which impacts interneuron firing properties during the first postnatal week. Overall, our work unveils some of the mechanisms underlying the shift in the developmental trajectory of striatal interneurons which greatly contribute to the ASD pathogenesis.

overall_design: control adult mouse brain

first: Noorya

last: Ahmed

first: Rhys

last: Knowles

first: Yiming

last: Yan

first: Xiaohan

first: Ulrike

last: Schumann

first: Yumeng

last: Wang

first: Yovina

last: Sontani

first: Nathan

last: Reynolds

first: Riccardo

last: Natoli

first: Jiayu

last: Wen

first: Isabel

last: Del Pino

first: Da

last: Mi

first: Nathalie

last: Dehorter


title: Genetic screens reveal new targetable vulnerabilities in BAP1-deficient Mesothelioma

city: Amsterdam

first: Jitendra

last: Badhai

address: Plesmanlaan 121

department: Division Molecular Genetics

country: Netherlands

institute: Netherlands Cancer Institute

summary: More than half of malignant mesothelioma patients show alterations in the BAP1 tumour suppressor gene. Being a member of the Polycomb repressive deubiquitinating (PR-DUB) complex, BAP1 loss results in an altered epigenome which may create new vulnerabilities that remain largely unknown. Here we performed a CRISPR/Cas9-kinome screen in mesothelioma cells that identified two kinases in the Mevalonate/Cholesterol biosynthesis pathway. Furthermore, our analysis of chromatin, expression and genetic perturbation data in mesothelioma cells suggests a dependency on Polycomb repressive complex 2 (PRC2) mediated silencing. Pharmacological inhibition of PRC2 elevates the expression of cholesterol biosynthesis genes only in BAP1-deficient mesothelioma, thereby sensitizing these cells to the combined targeting of PRC2 and the mevalonate pathway. Finally, by subjecting autochthonous Bap1-deficient mesothelioma mice or xenografts to mevalonate pathway inhibition (Zoledronic Acid) and PRC2 inhibition (Tazemetostat), we demonstrate a potent anti-tumour effect, suggesting a targeted combination therapy for Bap1-deficient mesothelioma

overall_design: mRNA profiles of BNC and NC mesothelioma and H2810, MSTO-211H and H2731 human mesothelioma cells

first: Nick

last: Landman

first: Gaurav

last: Pandey


title: Improved salt tolerance of Synechococcus elongatus PCC 7942 by heterologous synthesis of compatible solute ectoine

status: Public on Jan 08 2023

city: Tianjin

first: Zhengxin

last: Dong

address: No. 135 Yaguan Road

institute: Tianjin University

summary:
In order to explore the effect of introducing the ectoine synthesis module in Synechococcus elongatus PCC 7942 on the global regulation of the strain under high-salt environment.
The ectoine synthesis module was introduced at the Synpcc7942_0808 locus to obtain the Syn7942/Δsps-ect strain that lacked sucrose synthesis and could synthesize ectoine.
Comparative transcriptomic analysis was performed on WT and Syn7942/Δsps-ect under 0 mM and 300 mM NaCl conditions.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: WT and Syn7942/Δsps-ect were cultured in BG11 medium with 0 mM as control-1 and control-2 and 300 mM NaCl as experimental-1 and experimental-2, respectively. On the fourth day, samples were collected for transcriptome sequencing and data analysis.

first: Tao

last: Sun

first: Weiwen

last: Zhang

first: Lei

last: Chen


title: Factors influencing the nitrogen-source dependent flucytosine resistance in Cryptococcus species

status: Public on Jan 11 2023

city: Bethesda

first: Yun

last: Chang

address: 9000 Rockville pike

institute: NIH

summary: Flucytosine (5-FC) is an antifungal drug commonly used for treatment of cryptococcosis and several other systemic mycoses. In fungal species, cytosine permease and cytosine deaminase are known to play major roles in flucytosine resistance by regulating uptake and deamination of 5-FC, respectively. Cryptococcus species have three paralogs of cytosine permease (FCY2, FCY3, and FCY4) and three paralogs of cytosine deaminase (FCY1, FCY5, and FCY6). Like in other fungi, we found Fcy1 and Fcy2 to be the primary cytosine deaminase and permease respectively in C. neoformans H99 (VNI), C. gattii R265 (VGIIa), and WM276 (VGI). However, when different amino acids were used as the sole nitrogen source, Fcy3 and Fcy6 functioned as the secondary cytosine permease and deaminase respectively in C. gattii. Transcriptome analysis using RNA-seq under three different nitrogen sources (NH4, Asn, and Pro) revealed that these permease and deaminase genes as well as two GATA family transcription factor genes, GAT1 and CIR1, were differentially expressed in WM276. In addition, deletion studies of GAT1 and CIR1 demonstrated that the expression of each permease and deaminase genes was under the regulation of GAT1 and CIR1 individually. Furthermore, the expression levels of FCY3 and FCY6 regulated by GAT1 and CIR1 contributed to the 5-FC susceptibility in fcy2Δ or fcy1Δ background under different amino acid conditions. This study offers an insight into the mechanism of 5-FC resistance in C. gattii which is orchestrated by cytosine permease and deaminase genes, and two GATA family transcription factor genes, GAT1 and CIR1, under diverse nitrogen conditions.

overall_design: Total RNAs from Cryptococcus gattii WM276 strain grown on YNB media with 2% glucose containing NH4, Asn, or Pro as sole nitrogen source. Three biological replicates were prepared for the RNA-seq.

first: Dong-Hoon

last: Yang

first: Ami

last: Khanal Lamichhane

first: Kyung

last: Kwon-Chung

middle: C


title: Mapping quantitative trait loci and developing their KASP markers for Pre-harvest Sprouting resistance of Henan wheat varieties in China

city: Xianyang

first: Cheng

last: Kou

address: 3 Tai Cheng Road, Yangling District, Xianyang City, Shaanxi Province, China

institute: Northwest A&F University

summary: Introduction: Pre-harvest Sprouting (PHS) seriously affects wheat quality and yield. However, to date there have been limited reports. It is of great urgency to breed resistance varieties via quantitative trait nucleotides (QTNs) or genes for PHS resistance in white-grained wheat.    Methods: 629 Chinese wheat varieties, including 373 local wheat varieties from 70 years ago and 256 improved wheat varieties were phenotyped for spike sprouting (SS) in two environments and genotyped by wheat 660K microarray. These phenotypes were used to associate with 314,548 SNP markers for identifying QTNs for PHS resistance using several multi-locus genome-wide association study (GWAS) methods. Their candidate genes were verified by RNA-seq, and the validated candidate genes were further exploited in wheat breeding.    Results: As a result, variation coefficients of 50% and 47% for PHS in 629 wheat varieties, respectively, in 2020-2021 and 2021-2022 indicated large phenotypic variation, in particular, 38 white grain varieties appeared at least medium resistance, such as Baipimai, Fengchan 3, and Jimai 20. In GWAS, 22 significant QTNs, with the sizes of 0.06% ~ 38.11%, for PHS resistance were stably identified by multiple multi-locus methods in two environments, e.g., AX-95124645 (chr3D:571.35Mb), with the sizes of 36.390% and 45.850% in 2020-2021 and 2021-2022, respectively, was detected by several multi-locus methods in two environments. As compared with previous studies, the AX-95124645 was used to develop Kompetitive Allele-Specific PCR marker QSS.TAF9-3D (chr3D:569.17Mb~573.55Mb) for the first time, especially, it is available in white-grain wheat varieties. Around this locus, nine genes were significantly differentially expressed, and two of them (TraesCS3D01G466100 and TraesCS3D01G468500) were found by GO annotation to be related to PHS resistance and determined as candidate genes.    Discussion: The QTN and two new candidate genes related to PHS resistance were identified in this study. The QTN can be used to effectively identify the PHS resistance materials, especially, all the white-grained varieties with QSS.TAF9-3D-TT haplotype are resistant to spike sprouting. Thus, this study provides candidate genes, materials, and methodological basis for breeding wheat PHS resistance in the future.

overall_design:
Spike of wheat wax ripe stage

Time: 0 hour, 48hour and 96 hour represents the time the sample was processed at a temperature of 22 plus or minus 1 degrees C and a relative humidity of 95% plus or minus 5%.

first: ChaoJun

last: Peng

first: HaiBin

first: Lin

last: HU

first: WeiGang

last: Xu


title: DEtail-seq profiled meiotic DSBs in Mus musculus

city: Beijing

first: li

last: kuan

address: zhongguancun

institute: Tsinghua University

summary: SPO11-promoted DNA double-strand breaks (DSBs) formation is a crucial step for meiotic recombination, and it is indispensable to detect the broken DNA ends accurately for dissecting the molecular mechanisms behind. Here, we report a novel technique, named DEtail-seq (DNA End tailing followed by sequencing), that can directly and quantitatively capture the meiotic DSB 3’ overhang hotspots at single-nucleotide resolution.

overall_design: Profiled mammalian meiotic DNA breaks by performing DEtail-seq in mouse sertoli cells (SC), testicular cells at leptotene/zygotene stages (L/Z), and pachytene stage (Pac)

first: Wei

first: Chao

last: Liu

first: Kuan

last: Li

first: Qin

first: Zhuo

first: Qianwen


title: A comprehensive platform for analyzing longitudinal multi-omics data

city: Seattle

first: Allen Institute

last: For Immunology

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

summary: We profiled four healthy individuals with age between 25 to 38 years old over 10-week period longitudinally using high throughput analysis. We measured blood count, flow-based cell populations, plasma proteome, transcriptome at single cell level, and genomic region accessibility using single cell ATAC to infer immune variations in healthy individuals.

overall_design:
Peripheral blood mononuclear cells from 4 healthy individuals were profiled using multi-modal single cell RNAseq and scATACseq using the 10x Genomics Chromium system. Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium 3’ Single Cell Gene Expression assay and Chromium Controller Instrument according to the manufacturer’s published protocol with modifications for cell hashing. Final libraries were quantified using Picogreen and their quality was assessed via capillary electrophoresis using the Agilent Fragment Analyzer HS DNA fragment kit and/or Agilent Bioanalyzer High Sensitivity chips. Libraries were sequenced on the Illumina NovaSeq platform using S4 flow cells. Read lengths were 28bp read1, 8bp i7 index read, 91bp read2.  For scATACseq PBMC samples were sorted by fluorescence activated cell sorting (FACS) prior to cell permeabilization. Permeabilized-cell scATAC-seq was performed as described previously (Swanson et al. 2021). scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC v1.1 Reagent Kits. Final libraries were quantified using a Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) on a SpectraMax iD3 (Molecular Devices). Library quality and average fragment size was assessed using a Bioanalyzer (Agilent, G2939A) High Sensitivity DNA chip (Agilent, 5067-4626). Libraries were sequenced on the Illumina NovaSeq platform with the following read lengths: 51nt read 1, 8nt i7 index, 16nt i5 index, 51nt read 2. scATAC based fragments were submitted to ArchR package to create ArchR object. The QC analysis shows FRiP score (the fraction of reads that fall into a peak) >0.25.
-----------------------------------
Authors state "Raw files from human subjects will be submitted to dbGaP."

first: Adam

last: Savage

first: Troy

last: Torgeson

first: Peter

last: Skene

first: Xiaojun

first: Tom

last: Bumol

first: Suhas

middle: V

last: Vasaikar


title: DEtail-seq profiled meiotic DSBs in Homo sapiens

overall_design: Adult human testis samples were obtained from two patients with obstructive azoospermia (OA) who underwent vasoepididymostomy. The patients with OA were enrolled from Reproductive Center of Peking University Third Hospital. We excluded patients with chromosomal abnormalities, Y-chromosome microdeletions, varicocele, metabolic disorders such as diabetes and hepatic disease, occupational exposure to the agents, and other known factors related to male infertility.

last: Sun


status: Public on Jan 27 2023

city: Bunkyoku

first: Takahiro

last: Seimiya

state: Tokyo

address: 7-3-1 Hongo

institute: The university of Tokyo

summary: comprehensive evaluation of microRNA expression in KrasG12D+Tgfbr2-/- mouse pancreatic cancer

overall_design: To generate a genetically modified pancreatic cancer mouse model, Tgfbr2flox/flox, Ptf1acre/+ and LSL-KrasG12D/+ mouse lines were intercrossed to generate Ptf1acre/+; LSL-KrasG12D/+; Tgfbr2flox/flox (KrasG12D+Tgfbr2-/-) in a > 95% C57BL/6 background. These mice developed spontaneous pancreatic cancer, as reported previously (Ijichi et al., 2006). Pancreatic cancerous tissue from a gene-modified mouse and normal pancreas tissue from a control mouse were frozen in liquid nitrogen immediately after resection and stored at −80℃. Both mice are male at 7 weeks of age.


title: Examining the Effect of Notocactus ottonis Cold Vacuum Isolated Cell Extract on Hair Growth in C57BL/6 Mice using a Combination of Physiology and OMICS analyses

status: Public on Jan 06 2023

city: Tsukuba

first: RANDEEP

last: RAKWAL

institute: University of Tsukuba

summary: This study focuses on the hair-growing effects of a cell extract (CE) obtained from the cactus Notocactus ottonis by a cold vacuum extraction protocol, with the aim of investigating its hair-growing effects and relevant mechanisms and potential factors therein. In an experiment using male C57BL/6 mice, a vehicle control group (VC: propylene glycol : ethanol : water), a positive control group (MXD : 3% minoxidil), and an experimental group (N-CE: 10% N. ottonis CE) were applied topically to the backs of mice. Results showed that 3% MXD and 10% N-CE were more effective in promoting hair growth than the VC. Furthermore, an increase in the number of hair follicles was observed with 10% N-CE in hematoxylin-eosin-stained skin tissue.

overall_design: Whole genome DNA microarray was carried out on the skin samples (the back whole skin tissue of C57BL/6J mice was ground into a fine powder in liquid nitrogen and stored at -80°C until RNA isolation, and total RNA was extracted from powdered mouse skin tissue using the RNeasy Mini Kit ) to suggest molecular factors underlying the hair-promoting effects of N-CE.  Total RNA extracted from mouse skin tissue for each control and treatment (n=6) was pooled in each group, prior to DNA microarray analysis.

first: Junko

last: Shibato

first: Fumiko

last: Takenoya

first: Ai

last: Kimura

first: Michio

last: Yamashita

first: Randeep

last: Rakwal

first: Seiji

last: Shioda


title: Increased RNA Polymerase Activity at CTCF binding sites on the Epstein Barr Virus Genome During Reactivation from Latency

city: Ithaca

first: Joel

last: Baines

address: Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

summary: We used Precision Nuclear Run-on followed by Deep Sequencing (PRO-Seq) to investigate RNA Polymerase (Pol) activity during Epstein-Barr Virus (EBV) reactivation in EBV positive Burkitt's lymphoma cell lines Mutu-I and Akata. Nuclei were harvested from latent cells and after treatment with NaB/TPA (Mutu-I) or anti-IgG (akata) to stimulate reactivation at 1 and 4 and 12h. We identified multiple sites on the EBV genome enriched with Pol displaying distinct patterns of activity, which showed an association with CTCF and open chromatin.

overall_design: PRO-Seq data from two experiments. Latent Mutu-I cells and 1, 4 and 12 h post-treatment with NaB/TPA (2/3 biological replicates per time point). Latent Akata cells and 1, 4 and 12 h post-treatment with anti-IgG (3 biological replicates per time point). All samples contain Drosophila spike-in.

first: Laura

last: Dunn

first: Fang

last: Lu

first: Paul

middle: M

last: Lieberman

middle: D


title: ZFP462 safeguards neural lineage specification by targeting G9A/GLP mediated heterochromatin to silence enhancers [ChIP-seq]

status: Public on Jan 04 2023

city: Vienna

first: Ramesh

last: Yelagandula

address: Dr.-Bohr-Gasse 3

country: Austria

institute: IMBA

summary: ZNF462 haploinsufficiency is linked to Weiss–Kruszka syndrome, a genetic disorder characterized by neurodevelopmental defects, including autism. Though conserved in vertebrates and essential for embryonic development, the molecular functions of ZNF462 remain unclear. We identified its murine homologue ZFP462 in a screen for mediators of epigenetic gene silencing. Here we show that ZFP462 safeguards neural lineage specification of mouse embryonic stem cells (ESCs) by targeting the H3K9-specific histone methyltransferase complex G9A/GLP to silence meso-endodermal genes. ZFP462 binds to transposable elements that are potential enhancers harbouring ESC-specific transcription factor binding sites. Recruiting G9A/GLP, ZFP462 seeds heterochromatin, restricting transcription factor binding. Loss of ZFP462 in ESCs results in increased chromatin accessibility at target sites and ectopic expression of meso-endodermal genes. Taken together, ZFP462 confers lineage and locus specificity to the broadly expressed epigenetic regulator G9A/GLP. Our results suggest that aberrant activation of lineage non-specific genes in the neuronal lineage underlies ZNF462-associated neurodevelopmental pathology.

overall_design: Genome-wide binding profiling by high throughput sequencing

first: Oliver

last: Bell


title: Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications

status: Public on Jan 07 2023

first: Jinshou

last: Yang

state: Beijing

address: Peking Union Medical College Hospital (Dongdan campus), No.1 Shuaifuyuan Wangfujing Dongcheng Distri

department: General Surgery

institute: Peking Union Medical College Hospital

summary:
Background
Pancreatic ductal adenocarcinoma (PDAC) tends to undergo distant metastasis, especially liver metastasis, leading to a poor prognosis. Metabolic remodelling and epigenetic reprogramming are two important hallmarks of malignant tumours and participate in regulating PDAC tumorigenesis and metastasis. However, the interaction between these two processes during PDAC metastasis has not been fully elucidated.
Methods
We performed metabolomics analysis to identify the critical metabolites associated with PDAC liver metastasis and focused on guanidinoacetic acid (GAA). Intracellular GAA content was significantly increased in liver metastatic PDAC cells compared to primary cancer cells in mouse xenograft tumour models. The effects of GAA supplementation and glycine amidinotransferase (GATM) knockdown on PDAC metastasis were assessed by analysing cell migration, filopodia formation, epithelial-mesenchymal transition (EMT), and in vivo metastasis in different cell and animal models. Next, ChIP‒qPCR, 3C‒qPCR, and CRISPRi/dCas9-KRAB experiments were used to validate the “epigenome-metabolome" mechanism. Finally, the results of in vitro approaches, including RNA-seq, CUT&RUN, RT‒qPCR, and western blot analyses, as well as luciferase reporter gene assay and transwell assay, revealed the GAA-c-Myc-HMGA axis and transcription-activating histone modifications reprogramming.
Results
A high level of intracellular GAA was associated with PDAC liver metastasis. GAA could promote the migration, EMT, and liver metastasis of pancreatic cancer cells in vitro and in vivo. Next, we explored the role of GATM-mediated de novo GAA synthesis in pancreatic cancer metastasis. High expression of GATM was positively correlated with advanced N stage in PDAC. Knockdown of GATM significantly reduced the intracellular level of GAA, suppressed EMT, and inhibited PDAC liver metastasis, and these effects were attenuated by GAA supplementation. Mechanistically, we identified the active enhancers looped to the GATM gene locus that promoted GATM expression and PDAC liver metastasis. Furthermore, we found that GAA promoted cell migration and EMT by regulating c-Myc-mediated high mobility group AT-hook protein expression. Moreover, GAA increased the H3K4me3 modification level by upregulating histone methyltransferases, which induced the transcription of metastasis-related genes, including MYC.
Conclusions
These findings revealed the critical role of the epigenome-metabolome interaction in regulating PDAC liver metastasis and suggested potential therapeutic strategies targeting GAA metabolism and epigenetic regulatory mechanisms.

overall_design: mRNA profiles of pancreatic cancer cell lines with GATM knock-down and the control group.

first: Bo

last: Ren


title: ZFP462 safeguards neural lineage specification by targeting G9A/GLP mediated heterochromatin to silence enhancers [ATAC-seq]

overall_design: Analyzing the chromatin accessibility in WT and ZFP462-KO mESCS. Also in WT mNSCs


title: DEtail-seq profiled meiotic DSBs in Saccharomyces cerevisiae

first: li

last: kuan

sample_organism:
Escherichia coli
Saccharomyces cerevisiae
synthetic construct

overall_design: The meiotic DSBs were strongly induced at 4 hours in synchronous meiosis, and enhanced when DMC1 was knocked out, but blocked when SPO11 was depleted. We performed DEtail-seq on the wild-type SK1 before meiosis (WT 0h), at 4 hours after meiosis (WT 4h), and DMC1 or SPO11 depleted samples at 4 hours after meiosis (DMC1KO 4h and SPO11 KO 4h, respectively).

first: Wei

last: Xu

first: Chao

last: Liu

first: Kuan

last: Li

first: Qin

first: Zhuo

first: Qianwen

last: Sun


title: SETD5 haploinsufficiency affects mitochondrial compartment in neural cells

status: Public on Jan 05 2023

city: Milan

first: Edoardo

middle: Niccolò

last: Bellini

state: Lombardia

address: Via Olgettina 58

department: Neuroscience

country: Italy

institute: San Raffaele Hospital

summary: Neurodevelopmental disorders (NDDs) are heterogeneous conditions due to alterations of a variety of molecular mechanisms and cell dysfunctions. Epigenetic basis of NDDs have been reported in an increasingly number of cases while mitochondrial dysfunctions are more common within NDD patients than in the general population. Here, we investigated experimental models of Setd5 haploinsufficiency, that leads to NDDs in humans due to chromatin defects, and uncovered that mitochondrial dysfunction participates in the pathogenesis. Mitochondrial impairment is facilitated by transcriptional aberrations that follow the decrease of SETD5 enzyme. Low levels of SETD5 resulted in fragmented mitochondria, less mitochondrial potential and ATP production both in neural precursors and neurons. Mitochondria were miss-localized in mutant neurons, with few organelles within neurites and synapses. Our study explores the epigenetics/mitochondria interplay as an important aspect of NDD pathophysiology and defines the impairments of mitochondrial functionality and dynamics as new therapeutic targets for disorders associated with loss of SETD5.

overall_design: RNA-seq of mouse Neural precursors cells cultured in High Oxygen condition

first: Mattia

last: Zaghi

first: Luca

last: Massimino

first: Alessandro

last: Sessa

first: Vania

last: Broccoli


title: High-resolution transcriptional analysis reveals stepwise fate conversion of supporting cells to hair cells in the chicken auditory epithelium

status: Public on Jan 10 2023

city: Kyoto city

first: Ryosuke

last: Yamamoto

state: Kyoto pref

address: 54 Kawahara-cho

department: Department of Otolaryngology, Head and Neck Surgery

institute: Kyoto University

summary: In contrast to mammals, the avian cochlea, specifically the basilar papilla, can regenerate sensory hair cells, which involves fate conversion of supporting cells to hair cells. To determine the mechanisms for converting supporting cells to hair cells, we used single-cell RNA sequencing during hair cell regeneration in explant cultures of chick basilar papillae. We identified dynamic changes in the gene expression of supporting cells, and the pseudotime trajectory analysis demonstrated the stepwise fate conversion from supporting cells to hair cells. Initially, supporting cell identity was erased and transition to the precursor state occurred. A subsequent gain in hair cell identity progressed together with downregulation of precursor-state genes. Transforming growth factor beta receptor 1-mediated signaling was involved in induction of the initial step, and its inhibition resulted in suppression of hair cell regeneration. Our data provide new insights for understanding fate conversion from supporting cells to hair cells in avian basilar papillae.

overall_design: Single-cell RNA-Seq of chick basilar papillae during hair cell regeneration using an explant culture model

first: Mami

last: Matsunaga

first: Tomoko

last: Kita

first: Hiroe

last: Ohnishi

first: Satoko

last: Sakamoto

first: Akira

last: Watanabe

first: Takayuki

last: Nakagawa


title: ZFP462 safeguards neural lineage specification by targeting G9A/GLP mediated heterochromatin to silence enhancers [RNA-seq]

first: Ramesh

last: Yelagandula

overall_design: Gene expression analysis in WT and ZFP462 mutant mESCs

first: Oliver

last: Bell


title: ZFP462 safeguards neural lineage specification by targeting G9A/GLP mediated heterochromatin to silence enhancers [QuantSeq]

overall_design: RNA expression analysis using QuantSeq


title: Olig1/2-expressing intermediate lineage progenitors are predisposed to PTEN/p53-loss-induced gliomagenesis and harbor specific therapeutic vulnerabilities

status: Public on Jan 03 2023

city: CINCINNATI

first: Richard

middle: Q.

last: Lu

address: 3333 Burnet Avenue

department: CBDI

institute: Cincinnati Childrens Hosp Med Ctrl

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Spontaneous firing activity in pre-hearing inner hair cells regulates the maturation of the mechanoelectrical transducer apparatus over a critical time-period

status: Public on Jan 01 2023

city: San Francisco

first: Fiorella

middle: Carla

last: Grandi

address: 1650 Owens Street

institute: Gladstone

summary: Sensory-independent Ca2+ spiking activity is crucial for the development of mammalian sensory systems. In the cochlea, spontaneous Ca2+ action potentials (APs) are present in the pre-hearing inner hair cells (IHCs), the frequency and pattern of which is modulated by ATP-dependent intercellular Ca2+ waves in the non-sensory cells. It remains unknown whether both these Ca2+-dependent signalling mechanisms in the cochlea are required for the functional maturation of the IHCs. We found that the intrinsic Ca2+ AP activity, but not that triggered by Ca2+ signalling in the non-sensory cells, regulates the maturation and maintenance of the stereociliary hair bundle in IHCs. We used a mouse model in which the potassium channel Kir2.1 is reversibly overexpressed in IHCs in vivo. Kir2.1 overexpression (Kir2.1-OE mice) prevented spontaneous Ca2+ spikes in IHCs, but not their modulation by ATP-induced signalling from non-sensory cells. Without spontaneous Ca2+ APs, mechanoelectrical transduction in IHCs disappeared prior the onset of hearing at P12 due to the progressive loss of stereocilia and their fusion. RNA-sequencing data showed that several pathways, including those involved in morphogenesis, actin-filament based processes, and Rho-GTPase signalling, were upregulated during the second postnatal week. By manipulating the in vivo expression of Kir2.1 channels, we identified the second post-natal week as the “critical point” after which spontaneous Ca2+ APs are required for proper hair bundle maintenance. We showed that the final stage of IHC maturation is finely regulated by their intrinsic electrical activity just before sound-induced sensory driven activity.

overall_design: The sensory epithelium (Kir2.1) from 4 mice were micro dissected in DNase free ice-cold PBS 1X and immediately snap frozen in liquid nitrogen.

first: Adam

last: Carlton

first: Mirna

last: Mustapha

first: Walter

last: Marcotti


title: Transit-amplifying lineage states convey the susceptibility of PTEN and P53 loss to gliomagenesis [PPO1_and PPO1_Cells_RNA-seq]

summary:
To investigate the glioma mouse model by knocking out Pten and Trp53 in embryonal Olig2 and Olig1 positive cells in glioma pathogenesis.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 PPO2, 4 PPO1 and 2 OPN cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PPO1 & PPO2 cell lines with Oligodendrocyte progenitor Cells and neural stem cells tissue from publically available datasets. And also explore transcriptomic changes of Nf1 and Trp53 knocl out in OPC with PPO1

first: Q

first: Ravinder

last: Verma

first: Dazhuan

last: Xin


title: Transit-amplifying lineage states convey the susceptibility of PTEN and P53 loss to gliomagenesis [ATAC-seq]

summary:
To investigate the glioma mouse model by knocking out Pten and Trp53 in embryonal Olig2 and Olig1 positive cells in glioma pathogenesis.
ATAC-seq

overall_design: Total 2 samples were analyzed of 1 each of PPO1 and PPO2 cell line


title: Transit-amplifying lineage states convey the susceptibility of PTEN and P53 loss to gliomagenesis [CUT&RUN]

summary:
To investigate the glioma mouse model by knocking out Pten and Trp53 in embryonal Olig2 and Olig1 positive cells in glioma pathogenesis.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27Ac  in PPO1 and PPO2 mouse glioma cell lines and compare the active enhancers with oligodendrocyte progenitor cells.

overall_design: Total of 4 biological samples were investigated 2 each of PPO1 and PPO2


title: Transit-amplifying lineage states convey the susceptibility of PTEN and P53 loss to gliomagenesis [PPO1_Bulk_RNA-seq]

summary:
To investigate the glioma mouse model by knocking out Pten and Trp53 in embryonal Olig1 positive cells in glioma pathogenesis and track its evolution over multiple time-points.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 5 PPO1 tumor tissue with 3 Control cortex tissue.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PPO1 glioma and wild type control cortex.


title: A miRNome analysis at the early postmortem interval

status: Public on Jan 02 2023

city: Ciudad de México

first: Mariano

last: Guardado Estrada

state: Ciudad de México

address: Circuito de la Investigación SN

country: Mexico

institute: UNAM

summary:
The post-mortem interval (PMI) is the time that elapses since the death of an individual until the body is found. Different molecules have been analyzed to better estimate the PMI with variable results. The miRNAs draw attention in the forensic field to estimate the PMI, since they can better support degradation. To find potential biomarkers for PMI estimation, we analyzed the miRNome at early PMI in rat skeletal muscle using the Affymetrix GeneChip™ miRNA 4.0 micoarrays.
In this dataset, we include the expression of 1218 rat miRNAs at early postmortem interval.

overall_design: A total of five rat skeletal muscle samples were obtained from a post-mortem interval rat model which was previously established in our laboratory [17]. The muscle samples correspond to Wistar rats that had 24 h of PMI. As a control group, we analyzed four skeletal muscle samples of rats that correspond to the 0 h of PMI, that were taken im-mediately after euthanasia. The miRNome in the skeletal muscle samples, we used the Affymetrix GeneChip miRNA 4.0 Array (Affymetrix, Santa Clara, CA, USA). The Affymetrix GeneChip miRNA 4.0 Array. The CEL files were analyzed with the Affymetrix Transcriptome Analysis Console (TAC) Software. With this software, the probes intensities of the miRNAs were nor-malized, and the miRNA gene expression was calculated with the Robust Multi-chip Analysis (RMA), setting the value of Detected Above Background (DABG) to 0.05. The changes of gene expression were expressed as Fold Change (FC), considering miRNAs over or down expressed with a threshold above >2 or below <2, respectively. Significant dysregulated miRNAs were those with p-value less than 0.01 and a False Discovery Rate value less than 0.05.


title: Characterization and MicroRNA Levels of Serum-Derived Extracellular Vesicles in Hepatitis B Virus-Related diseases

city: changsha

first: min

last: liu

address: Xiangya Road, Kaifu District

institute: central south university

summary: Serum samples were collected from patients with CHB, DeCi and normal controls. We separated EVs from serum and identified them. MiRNAs from EVs were sequenced by NGS and analyzed to obtain differentially expressed miRNAs. Then we detected the expression level of candidate miRNAs from every single sample by qRT-PCR. The differences of serum EVs in patients with liver disease and 4 miRNAs with significantly different expression levels in EVs were determined. These serum EVs and miRNAs in EVs may be candidates for diagnosing and monitoring liver disease, or important therapeutic targets for the treatment of liver disease.

overall_design: We collected Serum samples from patients with CHB, DeCi and normal controls. Every 5 samples of the same group are randomly mixed into a pool. EVs RNAs were extracted from 5 pooled CHB serum samples, 5 pooled DeCi serum samples and 5 pooled healthy serum samples. MiRNAs were sequenced by NGS and analyzed to obtain differentially expressed miRNAs.

first: Xionghao

last: Liu

first: Wenlong

last: Wang

first: Mujun

first: Min


title: Transit-amplifying lineage states convey the susceptibility of PTEN and P53 loss to gliomagenesis [PPO2_Bulk_RNA-seq]

summary:
To investigate the glioma mouse model by knocking out Pten and Trp53 in embryonal Olig2 positive cells in glioma pathogenesis.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 PPO2 tumor tissue with 2 Control cortex tissue.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PPO2 glioma and wild type control cortex.


title: An epigenetic switch controls the expression of an alternative NR2F2 isoform that unleashes a pro-metastatic program in melanoma.

status: Public on Dec 31 2022

city: Badalona

first: IJC

last: Bioinformatics

state: Catalonia

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute


title: Diversity of arterial cell and phenotypic heterogeneity induced by high-fat and high-cholesterol diet

city: Shenzhen

first: Rongsong

last: Ling

state: Guangdong

address: 3688 Nanhai Avenue, Nanshan District

institute: Shenzhen University

summary:
Objective: Disturbed blood flow characterized by low and oscillatory shear stress and complex microenvironment is one of the causes of the atherosclerosis progression. During the development, endothelial cells generally develop into a dysfunction state, so do other cells. To further analyze the heterogeneity of different cell types, single-cell RNA sequencing was used to provide detailed transcriptomic information.

Approach and results: Transcriptional analysis of single cells from aortic arch of 16-week Apoe-/- mice under normal and atherosclerotic condition was carried out using single-cell RNA sequencing. By unsupervised clustering, 10 types of cells were identified: endothelial cells, immune cells, fibroblasts, erythroids, smooth muscle cells, cycling basal cells, clara cells, mesothelial cells, adipocytes and neurons. Among these cells, endothelial cells and immune cells exhibited great heterogeneity especially between normal and atherosclerotic group. Gene expression profile of later screened cells identified ten subpopulations of endothelial cells of different functions. Distribution of these cells in the control group and HFD group varies. Immune cells consist of macrophages, foam cells, B cells, T cells, neutrophils and NK cells mainly. During the data processing, the cell sorting is done by recognition with specific markers and rules.

Conclusions: Our data provide a comprehensive description of all kinds of cells in aortic arch and the heterogeneity brought by western diet. These findings open a new sight into the transcriptional development of atherosclerosis.

overall_design: Single cell suspension of the two aortas from each group was pooled together as one sample. Single cell RNA sequencing, library construction and quality control were executed using the illumina-HiSeq3000 platform by Genergy Bio-technology (Shanghai) Co., Ltd. Dying cells with mitochondrial RNA above 30% and cells lacking information with UMI<200 were eliminated during the quality control and 8155 dissociated cells, with 5416 cells from control group and 2739 from HFD one, were filtered out then. The median reads per cell were 3955 for control group and 3421 for HFD group, transcripts detected per cell in the two groups were 1364 and 1069 respectively.

first: Jieqi

last: Wen

first: Ruiyue

last: Chen

first: Siyan

last: Zhang

first: Yarong

last: Dai

first: Tingtao

first: Fanyu

last: Guo

first: Qingxin

first: Guixin

first: Yizhou

last: Jiang


title: An epigenetic switch controls the expression of an alternative NR2F2 isoform that unleashes a pro-metastatic program in melanoma [EPIC]

summary: Metastatic melanoma develops once transformed melanocytic cells begin to de-differentiate into migratory and invasive melanoma cells with neural crest cell (NCC)-like and epithelial-to mesenchymal transition (EMT)-like features. However, it is still unclear how transformed melanocytes assume a metastatic melanoma cell state. Here, we define DNA-methylation changes that accompany metastatic progression in melanoma patients and discover Nuclear Receptor Subfamily 2 Group F, Member 2 – isoform 2 (NR2F2-Iso2) as an epigenetically regulated metastasis driver. NR2F2-Iso2 is transcribed from an alternative transcriptional start site (TSS) and it is truncated at the N-terminal end which encodes the NR2F2 DNA-binding domain. We find that NR2F2-Iso2 expression is turned off by DNA methylation when NCCs differentiate into melanocytes. Conversely, this process is reversed during metastatic melanoma progression, when NR2F2-Iso2 becomes increasingly hypomethylated and re-expressed. Our functional and molecular studies suggest that NR2F2-Iso2 drives metastatic melanoma progression by modulating the activity of full-length NR2F2 (Isoform 1) over EMT- and NCC associated target genes. Our findings indicate that DNA-methylation changes play a crucial role during metastatic melanoma progression, and their control of NR2F2 activity allows transformed melanocytes to acquire NCC-like and EMT-like features. This epigenetically regulated transcriptional plasticity facilitates cell state transitions and metastatic spread.

overall_design: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium Human Methylation EPIC BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner.

first: Veronica

last: Davalos

first: Manel

last: Esteller


title: An epigenetic switch controls the expression of an alternative NR2F2 isoform that unleashes a pro-metastatic program in melanoma [450K]

overall_design: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner.


title: Rio1 downregulates centromeric RNA levels to promote the timely assembly of structurally fit kinetochores.

city: Trento

first: Peter

last: De Wulf

state: TN

address: via Sommarive, 9

department: Department of Cellular, Computational and Integrative Biology

institute: University of Trento

summary: RNA-Seq analysis of S. cerevisiae to study the biology of centromere and pericentromere transcripts.

overall_design: RNA-Seq analysis of wild-type yeast and a trf4∆ mutant.

first: Ksenia

last: Smurova


title: OKseqHMM: a genome-wide replication fork directionality analysis toolkit

city: Paris

first: Chunlong

address: 26 rue d’Ulm

country: France

institute: Institut Curie

summary: During each cell division, tens of thousands of DNA replication origins are coordinately activated to ensure the complete duplication of the entire human genome. However, the progression of replication forks can be challenged by numerous factors. One such factor is transcription-replication conflict (TRC), which can either be co-directional or head-on and the latter has been revealed as more dangerous for genome integrity. In order to study the direction of replication fork movement and TRC, we developed a bioinformatics tool, called OKseqHMM, to direct measure the replication fork directionality (RFD) as well as replication initiation and termination, along human genome obtained by sequencing of Okazaki fragments (OK-Seq) and related techniques. We have gathered and analyzed OK-seq data from a large number of organisms including yeast, mouse and human, to generate high-quality RFD profiles and determine initiation zones and termination zones by using Hidden Markov Model (HMM) algorithm (all tools and data are available at https://github.com/CL-CHEN-Lab/OK-Seq). In addition, we have extended our analysis to data obtained by related techniques, such as eSPAN and TrAEL-seq, which also contain RFD information. Our works, therefore, provide an important tool and resource for the community to further study TRC and genome instability, in a wide range of cell line models and growth conditions, which is of prime importance for human health.

overall_design: OK-seq experimetant of HeLa S3 was performed as previous described, and OK-seq data were proceeded by the R_based pipeline OKseqHMM to generate the replication fork directionnality (RFD) profile and to detect the replication initiation and termination zones.

first: Yaqun

first: Xia

last: Wu

first: Yves

last: D'aubenton-Carafa

first: Claude

last: Thermes

first: Chun-Long


title: An epigenetic switch controls the expression of an alternative NR2F2 isoform that unleashes a pro-metastatic program in melanoma

first: IJC

type: Methylation profiling by genome tiling array

overall_design: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2011.2) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.


title: RNA-seq analyses of gene expression in Helicobacter pylori CrdRS two-component system deletion strains

status: Public on Dec 24 2022

city: Williamsburg

first: Madison

last: Allen

address: 540 Landrum Dr

institute: William & Mary

summary: Next-generation sequencing (NGS) was used to analyze gene expression in H. pylori CrdRS two-component system deletion strains. The goal of this study was to examine the role that the CrdRS two-component system plays in H. pylori gene expression through identification of regulon differences

overall_design:
Analysis of transcriptional changes in H. pylori strains with CrdRS two-component system deletions compared to a control
A total of 6 independent samples were analyzed; 2 replicates of RNA preparations from H. pylori 26695/ΔrdxA for comparison to the 2 replicates of RNA preparations from H. pylori 26695/ΔrdxA/ΔcrdS and 2 replicates of RNA preparations from H. pylori 26695/ΔrdxA/ΔcrdR

first: Mark

last: Forsyth


title: Ribosome profiling in Drosophila ovary enriched for late-stage oocytes (late-ovary)

city: Princeton

first: Elizabeth

last: Gavis

state: NJ

address: 401 Schultz Lab

institute: Princeton University

summary: To investigate the distribution of ribosomes in late-stage oocyte to infer their translational status.

overall_design: Read patterns in Ribo_Seq libraries are used to infer local enrichment of ribosomes. Corresponding RNA_Seq libraries are used as control to filter out reads enrichment due to experimental artifact.

first: Yingshi

last: Peng

first: Zachary

last: Flamholz


title: A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth

status: Public on Dec 22 2022

city: Boston

first: Sizun

state: MA

address: 3 Blackfan Circle

institute: BIDMC/Harvard

summary: Epstein-Barr virus (EBV) immortalizes resting human B lymphocytes in vitro through expression of viral transcription factors (TFs). These viral TFs activate the expression of key oncogenes, many through long-range enhancer looping. Here we combined various chromatin conformation capture related methods (HiC, HiChIP, 4C-seq etc) to systematically evaluate the effect of EBV infection on host genome-wide 3D organization.

overall_design:
HiC was performed on resting B cells to recapticulate the 3D chromatin feature before EBV infection and transformation. A time-course RNA-seq was performed to track the dynamics of viral infection of resting B cells. Next, HiChIP was performed on conditional cells for the viral TF, EBNA3A, to understand how it rewires the host nucleus, particular enhancer-promoter interactions. In addition, HiChIP for RNA Polymerase II was also performed on primary B cells at Day 0 and Day 28 after EBV infection. Finally, 4C-seq was performed on conditional cells for the viral TF, EBNA3C, to understand how it modulates host chromatin interactions at the CDKN2A and AID loci.

Please note that the peak data (for GSM5456429-GSM5456440) are generated from both replicates and is linked to the corresponding *rep1 sample records.

first: Jun

last: Liang

first: Yohei

last: Narita

first: Chong

last: Wang

first: Mingxiang

last: Teng

first: Bo

last: Zhao


title: A manganese-independent aldolase enables Staphylococcus aureus to resist host-imposed metal starvation

status: Public on Dec 19 2022

city: Urbana

first: Thomas

last: Kehl-Fie

state: Il

address: 601 South Goodwin Avenue, MC-110

department: Microbiology

institute: University of Illinois at Urbana-Champaign

summary: The goal of this study was to determine gene expression in WT and arlRS KO bacteria when grown in the presence and absence of glucose.

overall_design: WT and arlRS KO S. aureus Newman were grown in TSB with and without glucose and gene expression was then determined by RNAseq.

first: Jana

middle: N

last: Radlin

first: Lindsay

last: Clark

first: Christopher

last: Fields


title: RNAs bound by the glucocorticoid receptor during dexamethasone treatment

status: Public on Dec 17 2022

city: Boulder

first: Nickolaus

middle: Charles

last: Lammer

state: Colorado

address: 3415 Colorado Ave

institute: University of Colorado, Boulder

summary: The RNA binding ability of the glucocorticoid receptor (GR) remains an understudied area of GR regulation. Through in vitro binding assays, we identified hairpin RNAs as GR's preferred binding motif. To study how GR-bound RNAs change with dexamethasone treatment, we first generated stable U2OS cells expressing wild-type GR-HaloTag. We then treated the cells with dexamethsone every hour over three hours, UV crosslinked, harvested, and pulled down GR using a specific and covalently-bound HaloTag ligand. GR-bound RNAs were then isolated, library prepped, and sequenced.

overall_design: RIP-seq with UV crosslinking and HaloTag pulldown to measure changes in the GR-bound RNA population in U2OS cells stably expressing GR-HaloTag over 3 hours of 100 nM dexamethasone treatment.

first: Mary

first: Deborah

middle: S

last: Wuttke

first: Robert

middle: T

last: Batey


title: Expression data from Tead1 beta cell KO

status: Public on Dec 14 2022

city: Pittsburgh

first: Vijay

middle: K.

last: Yechoor

state: PA

address: 200 Lothrop Street, BST 1058W

institute: University of Pittsburgh

summary: Tead1 is a transcription factor downstream of the hippo pathway. Gene expression is compared between whole islets from beta cell specific tead1 KO (using Rip-Cre) and Floxed control islets

overall_design: Islets from 3 Tead1 beta cell specific Ko islets and 3 flox mice were isolated, and total RNA extracted, labelled and hybridized to mouse Affy 430_2 arrays.

first: Jeongkyung

last: Lee