title: Comprehensive Analysis of Transcriptome‐wide M6A Methylation for Hepatic Ischemia Reperfusion Injury in Mice

status: Public on May 12 2023

city: Haerbin

first: Yongliang

last: Hua

state: Heilongjiang

address: Department of Pediatric Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Harbin, Heilongjiang, China

institute: 哈医大一院

summary:
Background: Hepatic ischemia reperfusion injury (IRI) is a complex clinical complication during surgery and often leads to cell damage and dysfunction. N6-Methyladenosine (m6A) is an emerging epigenetic modification that plays key roles in the regulation of biological functions and cellular mechanisms in IR injury in different organs. However, the understanding of m6A-modified mRNAs in hepatic IRI is limited.
Methods: Methylated RNA immunoprecipitation with high-throughput sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were used to profile the transcriptome-wide distribution of m6A methylation for hepatic IRI in mice.
Results: In this study, there were 2061 nonoverlapping m6A peaks within 22471 coding gene transcripts (mRNAs) in the sham group and 2669 nonoverlapping m6A peaks within 22766 coding gene transcripts in the hepatic IR group. The distribution of m6A peaks was especially enriched in the coding sequence (CDS) and 3'UTR. Moreover, functional enrichment analysis demonstrated that the significantly enriched terms of genes with upmethylated m6A sites were the mRNA surveillance pathway, purine metabolism and metabolic pathways, and the significantly enriched terms of genes with downmethylated m6A sites were the Rap1 signaling pathway, sphingolipid signaling pathway, platelet activation, Wnt signaling pathway, chemokine signaling pathway and focal adhesion. Furthermore, we identified a relationship between differentially methylated genes and differentially expressed genes to obtain the three overlapping predicted target genes (Fnip2, Phldb2, and Pcf11).
Conclusions: Our study first identified a transcriptome-wide map of m6A mRNAs in hepatic IRI. An in-depth analysis according to methylation modifications will provide effective treatment strategies and a theoretical basis for future research in terms of molecular mechanisms.

overall_design: The mRNA profiles of m6A methylation for hepatic IR group and the sham group in mice

first: Yong


title: Gene expression profile at single cell level of thalamus

status: Public on May 10 2023

city: Yangzhou

first: Tianfeng

last: Huang

address: 98 Nantong West Road

country: China

institute: Northern Jiangsu People's Hospital

type: Expression profiling by high throughput sequencing

summary: Knowledge of the full repertoire of thalamus cells and their gene expression profiles is a fundamental first step in this endeavor. Here, using single-nuclei RNA sequencing (snRNA-seq), we sequenced the transcriptomes of 32332 single brain cells, revealing a total of four major cell types within the four thalamus sample from mice.

first: Yinggang

last: Xiao

first: Ju

last: Gao

first: Yang

last: Zhang


title: Co-cultures of colon cancer cells and cancer-associated fibroblasts recapitulate the aggressive features of mesenchymal-like colon cancer

status: Public on May 11 2023

city: Rotterdam

first: Mathijs

last: Verhagen

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

overall_design: In order to sort single cells from the co- and mono-culture conditions, single cell suspensions were made. In brief, on day 8 of the experiment droplets were scooped out of the well and resuspended in Liberase to dissolve the co-culture matrix. Cell clusters and organoids were digested into single cells through incubation and resuspension with TrypLE. Viable single cells were sorted in 384-well cell capture plates using the BD FACSAria II. Plates were shipped on dry ice to Single Cell Discoveries, where single-cell RNA sequencing was performed according to an adapted version of the SORT-seq protocol. Cells were heat-lysed at 65° C followed by cDNA synthesis. After second-strand cDNA synthesis, all the barcoded material from one plate was pooled into one library and amplified using in vitro transcription (IVT). Following amplification, library preparation was done following the CEL-Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers (Illumina). The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit.

first: Esther

middle: A

last: Strating

middle: P

first: Sjoerd

middle: G

last: Elias

first: Onno

middle: W

last: Kranenburg


title: Single Cell Transcriptomics Reveals TGF-Beta and HMGA1 as Global Markers of Transcriptional Diversity in Cellular Senescence

status: Public on May 04 2023

city: newberry

first: Shane

last: Evans

state: Florida

address: 22806 West Newberry Road

department: Bio Med

country: USA

institute: Brown University

summary: Here, through single-cell transcriptional profiling of genetically homogenous clonal cell lines, we analyzed subpopulations in all three major forms of senescence, namely Oncogene Induced Senescence (OIS), Replicative Senescence (RS), and DNA Damage Induced Senescence (DDIS).

overall_design: Single cell RNA-seq using 10x chromium conducted on Proliferating, RS, OIS, and DDIS human diploid lung fibroblasts. All cell populations were derived from clonal cell lines that possessed a 4-OHT inducible HRAS:G12V construct.

first: Yee

middle: V

last: Teo

first: Kelly

last: Clark

first: Takahiro

last: Ito

first: John

middle: M

last: Sedivy

first: Nicola

last: Neretti


title: Gene expression of human angiosarcoma

status: Public on May 03 2023

city: Singapore

first: Jason

middle: Yongsheng

last: Chan

address: 30 Hospital Blvd

country: Singapore

institute: National Cancer Centre Singapore

summary: Gene expression profiling of human angiosarcoma samples was performed using the NanoString Human nCounter PanCancer IO 360 Panel

overall_design: A series of human angiosarcomas was profiled using the NanoString PanCancer IO 360 panel


title: Control of cell identity and early neuronal fate commitment by the enhancer module of Integrator [scRNA-Seq]

status: Public on May 02 2023

city: Philadelphia

first: Alessandro

last: Gardini

state: PA

address: 3601 Spruce St, Room 230

institute: The Wistar Institute

summary: Cell fate specification occurs via coordinated transcriptional changes in pluripotent cells, resulting in progressive commitment towards distinct lineages. Lineage-specific transcription factors (TFs), through their intrinsic DNA-binding ability, operate as master orchestrators of early and late developmental processes by turning on select cis-regulatory enhancers and proximal promoter elements. TF binding ultimately drives recruitment of the basal transcriptional machinery that comprises RNA Polymerase II (RNAPII) and a host of polymerase-associated multiprotein complexes, including the metazoan-specific Integrator complex. Integrator is primarily known to modulate RNAPII processivity and to surveil RNA integrity. Here we show that a set of Integrator subunits (enhancer module) plays a direct role in cell fate specification by promoting epigenetic changes and TF binding at enhancer elements that drive neurogenesis and maintain neuronal cell identity. Depletion of a single Integrator subunit (INTS10) results in loss of molecular and morphological neuronal features, while diverting progenitor cells towards mesenchymal identity. Commissioning of developmental enhancers rely on Integrator’s enhancer module, which stabilizes SOX2 binding at chromatin upon exit from pluripotency. Integrator therefore operates as a functional bridge between enhancers and target promoters and is a driver of early developmental processes, providing new insight into a growing family of neurodevelopmental syndromes.

overall_design: scRNA-seq was done in WT and INTS10heterzyogote NPCs.

first: Connor

last: Hill


title: Control of cell identity and early neuronal fate commitment by the enhancer module of Integrator [ChIP-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: INTS10/11/13, RNAPII, H3K27ac, H3K4me1 was ChIPed in WT and INTS10heterzyogote iPSCs/NPCs and WT Neurons. H3K27me3 was ChIPed in WT and INTS10heterzyogote NPCs. INTS10/11/13 and RNAPII were ChIP in WT SHSY5Y cells.


title: Control of cell identity and early neuronal fate commitment by the enhancer module of Integrator [RNA-Seq]

overall_design: 3' - mRNA Seq was done in WT and INTS10heterzyogote iPSCs/NPCs/Neurons/ReN cells and WT and INTS10KO SHSY5Y cells.


title: Control of cell identity and early neuronal fate commitment by the enhancer module of Integrator [ATAC-Seq]

overall_design: Omni-ATAC-seq was done in WT and INTS10heterzyogote NPCs and WT iPSCs.


title: Single-nuclei paired multiomic analysis of young, aged, and Parkinson’s disease human midbrain reveals age-associated glial changes and their contribution to Parkinson’s disease

status: Public on Apr 27 2023

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

summary: Age is the primary risk factor for Parkinson’s disease (PD), but how aging changes the expression and regulatory landscape of the brain remains unclear. Here, we present a single-nuclei multiomic study profiling shared gene expression and chromatin accessibility of young, aged and PD post-mortem midbrain samples. Combined multiomic analysis of midbrain nuclei along a pseudopathogenesis trajectory reveals all glial cell types are affected by age, but microglia and oligodendrocytes are further altered in PD. We present evidence for a novel age-associated oligodendrocyte subtype that appears during normal aging, characterized by elevated protein folding and chaperone-mediated autophagy pathways. Differential gene and protein-protein interaction analyses show that these functions are significantly compromised in PD. Peak-gene association from our paired data identifies differential cis-elements linked to regulation of differentially expressed genes between PD patients and neurologically healthy controls. Our study suggests a previously undescribed role for oligodendrocytes in aging and PD pathogenesis.

overall_design:
Single-nuclei Multiome sequencing data were generated by deep sequencing
*** Raw data for these human patients will be submitted for controlled access ***

first: Levi

last: Adams

first: Min

middle: K

last: Song

first: Yoon-seong

last: Kim


title: Amorphous calcium phosphate-coated surfaces as a model for bone microenvironment in prostate cancer.

status: Public on Apr 26 2023

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 309 Mossman Bldg. 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

summary: To develop a model for bioavailable calcium, usable for bone metastasis studies. The present study focuses on the effect of a calcium-rich surface on prostate cancer.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data from non tumorogenic prostate epithelial cells (RWPE), early adenocarcinoma model cells (LNCaP) and Bone metastatic cells (VCaP, MDAPCa2a), cultured on calcium and normal plastic
culture surfaces, in both the presence and absence of testosterone

first: Rebeca

last: San Martin

first: Prijoyit

last: Das

first: Tianchun

last: Xue

first: Morgan

middle: R

last: Brown

first: Michael

last: Essington

first: Adrian

last: Gonzalez


title: Control of cell identity and early neuronal fate commitment by the enhancer module of Integrator

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

overall_design: Refer to individual Series


title: Control of cell identity and early neuronal fate commitment by the enhancer module of Integrator [Hi-C]

overall_design: Hi-C was done in WT and INTS10heterzyogote NPCs.


title: Deep learning for explainable prediction of HPV-status in head and neck cancer using transcriptome data organized as pathway treemaps

status: Public on Apr 24 2023

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

summary: We propose a convolutional neural network (CNN) model predicting HPV-status in head and neck cancer from transcriptome data allowing identification of molecular pathways driving individual classifier decisions.  The CNN was trained on transcriptome data from 264 (13% HPV-positive) and tested on 85 (25% HPV-positive) patients after transformation into 2D-treemaps representing molecular pathways. Model stability was assessed by shuffling pathways within 2D-images. Grad-CAM saliency was used to quantify pathways contribution to CNN decisions. For comparison, a logistic regression model was generated.  The CNN achieved ROC-AUC/PR-AUC of 0.96/0.90 for all treemap variants. Saliency heatmaps consistently found KRAS-, spermatogenesis-, bile acid metabolism- and inflammatory-signaling as most informative for classification of HPV-positive-, and MYC-targets-, epithelial-mesenchymal transition and protein-secretion pathways for HPV-negative patients. The regression-based 18-gene model achieved a ROC-AUC/PR-AUC of 0.97/0.97.  We present a high-performance explainable CNN-model from transcriptome data of a typically sized oncological cohort providing molecular pathway information at the individual level.

overall_design: the gene expression profiles from HPV-associated and HPV-negative head and neck squamous cell carcinoma were transformed into 2D-tremap images and subjected to a convolutional neural network in order to explainably predict HPV-status.

first: Julia

last: Hess

first: Claus

middle: B

last: Belka

first: Guillaume

last: Landry


title: Control of cell identity and early neuronal fate commitment by the enhancer module of Integrator [CUT&TAG]

first: Alessandro

last: Gardini

overall_design: CUT&TAG for H3K27ac, H3K4me1, H3K27me3  was done in WT and INTS10knockout SHSY5Y cells. CUT&TAG for H3K27ac and H3K4me1  was done in shLUC and shSOX2 NPCs.


title: Gene expression analysis in zebrafish adult and livers with and without arsenic exposure with and with out as3mt mutation

status: Public on May 01 2023

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: This SuperSeries is composed of the SubSeries listed below. Zebrafish adults or larvae which are WT or as3mt MUTANT (Allele B); some are from 5 dpf whole embryo after 0 or 1 mM iAs from 6-120 hpf others are untreated.

overall_design: Refer to individual Series.

first: Patrice

last: Delaney


title: Translatome analysis of brain endothelial cells in the acute epileptic mouse model

city: Daegu

first: Sehyun

last: Chae

address: 61, Cheomdan-ro

department: Neurovascular Unit Research Group

country: South Korea

institute: Korea Brain Research Institute

summary: In this study, we provide the translatome data in the brain endothelial cells (BECs) of the adult cortex in response to acute neuronal activation by using translating ribosome affinity purification (TRAP) combined with high-throughput RNA sequencing analysis in Tie2-Cre:Ribo-Tag mice, which are designed for expressing hemagglutinin A (HA)-tagged RPL22, a ribosomal protein in endothelial cells depending on CRE recombinase. To increase neural activity rapidly, we adopted an acute epilepsy induction model in which pentylenetetrazol (PTZ), a GABAA receptor antagonist was injected and observed significant upregulation of c-fos-positive cells in the cortex. To obtain a high-quality BEC pool, we modified the TRAP method by adding the capillary isolation process before the immunoprecipitation step and finally verified BEC-specific translating mRNA purification using RT-PCR.  We then analyzed RNA-seq data obtained from the BECs of cortex of adult mice injected with phosphate buffered saline (PBS) or PTZ and identified brain endothelial cell genes that are changed dynamically due to neuronal activation. This information will be useful for researchers to study neurovascular interaction or to identify biomarkers in epilepsy.

overall_design: RNA profiles of brain endothelial cells obtained from cortex of adult mice injected with PBS or PTZ.

first: Won-Jong

last: Oh

first: Nam-Suk


title: A single-cell RNA sequencing atlas of circulating leukocytes from healthy and osteosarcoma affected dogs

status: Public on Apr 25 2023

city: Fort Collins

first: Dylan

middle: T

last: Ammons

state: CO

address: 200 W Lake St

department: MIP

institute: Colorado State University

summary: We used single-cell RNA sequencing to characterize the heterogeneity of circulating leukocytes in dogs, then employed the dataset to investigate how primary osteosarcoma (OS) tumors impacted circulating leukocytes.

overall_design: The complete dataset consists of circulating leukocytes from 7 healthy dogs and 10 OS affected dogs. The final processed Seurat objects are provided as 'final_dataSet_H.rds' (Healthy only) and 'final_dataSet_HvO.rds' (Healthy and osteosarcoma PBMCs). Each major immune cell type subset is provided where 'cytotoxic.rds' = CD8/NK cell, 'helper.rds' = CD4 T cells, 'myeloid.rds' = Myeloid, and 'bcell.rds' = B cells. All R code used to complete the analysis can be found at: https://github.com/dyammons/Canine_Leukocyte_scRNA.

first: Steven

last: Dow


title: mRNA expression profile in HeLa cells that subject to pitavastatin treantment.

status: Public on Mar 29 2023

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: mRNA expression profiles were compared between treatment of pitavastatin or not in the presence or absence of a Sendai virus infection.

overall_design: HeLa cells were cultured in a 24-well plate, and were then subjected to treatment of pitavastatin (2µM) or DMSO (0.1%) for 24 hours.  Next, the cells were infected with or without Sendai virus for 24 hr.

first: H

last: Oshiumi

first: T

last: Kouwaki


title: The F-box protein Fbx23 regulates the development of Penicillium oxalicum fungi and the expression of cellulolytic genes

status: Public on Apr 03 2023

city: Qingdao

first: zhongjiao

last: liu

state: Shandong

address: Aoshanwei

institute: Shandong University

summary: The goals of this study are to compare different gene expressions for Penicillium oxalicum wild type strain (WT), Fbx23 deletion strain (Δfbx23), and Fbx23 ecover strain (Refbx23) under conditions of 2% glucose or 1% bran + 1% microcrystalline cellulose as carbon source. The results of correlation analysis between each sample showed that the gene expression level of Δfbx23 was significantly different from that of the WT strain. The deletion of Fbx23 significantly down-regulates the expression levels of sporulation process genes. And the absence of Fbx23 can broadly up-regulate the expression level of cellulase-encoding genes, indicating that Fbx23 can cause a decrease in cellulase synthesis by affecting the expression of cellulase-encoding genes.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain, Fbx23 deletion mutant strains and Fbx23 recover strain in 18h in modifeid Mendal’s medium with 2% glucose or 1% bran + 1% microcrystalline cellulose as carbon sources. Three replicates were included for each samples.

first: Yuqi

last: Qin


title: Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish

status: Public on Apr 20 2023

city: Boston

first: Scott

last: Freeburg

state: MA

address: 77 Ave Louis Pasteur, New Research Building #458

institute: Brigham and Women's Hospital

summary: Vitamin D deficiency and mutations in Vitamin D Receptor (VDR) are associated with liver disease and obesity, but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates, this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue-specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth.

overall_design: Comparative gene expression profiling analysis of RNA-seq data following hepatocyte-specific Vdr modulation in larval and adult zebrafish. fabp10a:dn-vdra and fabp10a:ca-vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation, respectively. Larval experiments were performed on sorted hepatocytes at 96 hours post fertilization (hpf) and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 months post fertilization (mpf) and are composed of 3 livers per sample. wild-type controls are included for each experiment. For larval fabp10a:dn-vdra, N = 4 wt, 4 dn-vdra. For fabp10a:ca-vdra, N = 4 wt, 3 ca-vdra. For adult fabp10a:dn-vdra, N = 4 wt, 4 dn-vdra.

middle: H

first: Wolfram

last: Goessling


title: GATA4 regionalizes intestinal metabolism and commensal bacterial colonization to prevent immunopathology

city: Chicago

first: Joseph

middle: Joy

last: Sifakis

state: IL

address: 900 East 57th Street

department: Chemistry

institute: The University of Chicago

summary: Different regions of the gastrointestinal tract have distinct digestive and absorptive functions, which may be locally disrupted by infection or autoimmune disease. Yet, the mechanisms underlying intestinal regionalization and its dysregulation in disease are not well understood. Here, we used mouse models, transcriptomics, and immune profiling to show that regional epithelial expression of the transcription factor GATA4 prevented adherent bacterial colonization and inflammation in the proximal small intestine by regulating retinol metabolism and luminal IgA. Loss of epithelial GATA4 expression increased mortality in mice infected with Citrobacter rodentium which was dependent on commensal microbiota induced immunopathology. In active celiac patients with villous atrophy, low GATA4 expression was associated with metabolic alterations, mucosal Actinobacillus, and increased IL-17 immunity. This study reveals broad impacts of GATA4-regulated intestinal regionalization and highlights an elaborate interdependence of intestinal metabolism, immunity, and microbiota in homeostasis and disease.

overall_design: RNA from whole tissue or sorted 100,000 CD45- EPCAM+ intestinal epithelial cells from the jejunum and ileum of littermate control WT and GATA4ΔIEC mice were sequenced

first: Zachary

last: Earley

first: Wioletta

last: Lisicka

middle: J

first: Raúl

last: Aguirre-Gamboa

first: Anita

last: Kowalczyk

first: Jacob

last: Barlow

first: Dustin

last: Shaw

first: Valentina

last: Discepolo

first: Ineke

middle: L

last: Tan

first: Saideep

last: Gona

first: Jordan

middle: D

last: Ernest

first: Polly

last: Matzinger

first: Luis

last: Barreiro

first: Andrey

last: Morgun

first: Albert

last: Bendelac

first: Rustem

middle: F

last: Ismagilov

first: Natalia

last: Shulzhenko

first: Samantha

last: Riesenfeld

first: Bana

last: Jabri


title: Transcriptome analysis of BV-2 microglial cells displaying a CRISPR/Cas9-induced knockout of peroxisomal genes (Abcd1, Abcd2, Abcd1/Abcd2, Acox1)

status: Public on Mar 28 2023

city: Dijon

first: Stéphane

last: Savary

address: 6 Bd Gabriel

country: France

institute: University of Bourgogne

summary:
Here, we report the characterization and the comparison of the transcriptomes of BV-2 murine microglial mutant cell lines (CRISPR/Cas9-edited mutations in peroxisomal genes) by RNA-sequencing.
Microglia is  suspected to play a major role in the neurodegenerative processes observed in peroxisomal leukodystrophies. From CRISPR/Cas9-edited BV-2 microglial cell lines, we aimed at exploring the transcriptomic consequences of a defect of peroxisomal beta-oxidation.

overall_design: Five genotypes were included in the study: WT BV-2 cells and 4 mutant BV-2 cells (Abcd1-deficient, Abcd2 deficient, Abcd1/Abcd2 double-deficient, Acox1-deficient. See Raas et al. 2019, PMID: 30769094 and PMID: 30312667 for the description of the mutant cell lines.

first: Quentin

last: Raas

first: Catherine

last: Gondcaille

first: Céline

last: Keime

first: Romain

last: Kaiser


title: Orpinolide disrupts a leukemic dependency on cholesterol transport by inhibiting the oxysterol-binding protein OSBP

status: Public on Mar 15 2023

city: Vienna

first: Hana

last: Imrichova

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM, Vienna

summary: Metabolic alterations in cancer precipitate in associated dependencies that can be therapeutically exploited. To meet this goal, natural product inspired small molecules can provide a resource of invaluable chemotypes. Here, we identify orpinolide, a synthetic withanolide analog with pronounced anti-leukemic properties via orthogonal chemical screening. Through multi-omics profiling and genome-scale CRISPR/Cas9 screens, we identify that orpinolide disrupts Golgi homeostasis via a mechanism that requires active phosphatidylinositol 4-phosphate (PI4P) signaling at the endoplasmic reticulum (ER)-Golgi membrane interface. Thermal proteome profiling and genetic validation studies reveal the oxysterol-binding protein OSBP as the direct and phenotypically relevant target of orpinolide. Collectively, these data reaffirm sterol transport as a therapeutically actionable dependency in leukemia and motivate ensuing translational investigation via the probe-like compound orpinolide.


title: Transcript degradation profiling for Mycolicibacterium smegmatis in log phase, hypoxia, and RNase E knock down conditions.

status: Public on Mar 20 2023

city: Worcester

first: Scarlet

last: Shell

address: 60 Prescott Street

department: Biology & Biotechnology

institute: Worcester Polytechnic Institute

summary: We calculated transcriptome-wide mRNA half-life using RNAseq to characterize the mRNA stability in log phase and hypoxia, as well as the impact of RNase E on mRNA degradation.

overall_design: mRNA abundance were measured at multiple time points after rifampicin treatment using Mycolicibacterium smegmatis in log phase, hypoxia, and RNase E knockdown condition. Three RNAseq replicates were used for each time point.

middle: S

first: Ying

last: Zhou

first: Huaming

last: Sun

first: Diego

middle: A

last: Vargas-Blanco


title: Withanolide analogues disrupt a leukemic dependency on cholesterol transport by inhibiting the oxysterol-binding protein OSBP  [CRISPR screen]

summary: Metabolic alterations in cancers precipitate in associated dependencies that can be therapeutically exploited. To meet this goal, natural product inspired small molecules can provide a resource of underexplored chemotypes. Here, we identify W7, a synthetic withanolide analog with pronounced anti-leukemic properties via orthogonal chemical screening. Through multi-omics profiling and genome-scale CRISPR/Cas9 screens, we identify that W7 disrupts Golgi homeostasis via a mechanism that requires active PI4P signaling at the ER-Golgi membrane interface. Thermal proteome profiling and genetic validation studies reveal the oxysterol-binding protein OSBP as the direct and phenotypically relevant target of W7. Collectively, these data reaffirm sterol transport as a therapeutically actionable dependency in leukemia and motivate ensuing translational investigation via the probe-like compound W7.

overall_design: KBM7 cells (constitutively expressing Cas9) were continuously treated for 20 days with DMSO or W7 (2x EC50 starting concentration).

first: Marko

last: Cigler

first: Georg

last: Winter


title: Spatial transcriptomics reveal topological immune landscapes of Asian head and neck angiosarcoma

status: Public on Mar 19 2023

first: Abner

last: Lim

address: 30 Hospital Boulevard

department: Division of Medical Oncology

institute: National Cancer Center Singapore

summary: Angiosarcomas are rare malignant tumors of the endothelium, arising commonly from the head and neck region (AS-HN) and recently associated with ultraviolet (UV) exposure and human herpesvirus-7 (HHV-7) infection. We examined 81 cases of angiosarcomas, including 47 cases of AS-HN, integrating information from whole genome sequencing, gene expression profiling and spatial transcriptomics (10X Visium). In this dataset spatial transcriptomics revealed topological profiles of the tumor microenvironment, identifying dominant but tumor-excluded inflammatory signals in “immune-hot” cases and immune foci even in otherwise “cold” cases. In conclusion, spatial transcriptomics reveal the tumor immune landscape of angiosarcoma, and in combination with multi-omic information, may improve implementation of treatment strategies.

overall_design:
Spatial transcriptomics of 4 Asian Head and Neck Angiosarcoma
10X Genomics Visium

first: Yong-Sheng

last: Chan

first: Jui

middle: W

last: Loh


title: Withanolide analogues disrupt a leukemic dependency on cholesterol transport by inhibiting the oxysterol-binding protein OSBP [RNA-Seq]

overall_design: KBM7 cells treated for 6h with DMSO and W7 (4x EC50). Triplicates per condition.

first: Cristina

last: Mayor-Ruiz


title: Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [RNA-Seq]

first: Aleksandra

last: Kornienko

state: Vienna

address: Dr. Bohrgasse 3

institute: Gregor Mendel Institute

summary: Background  Long non-coding RNAs (lncRNAs) are under-studied and under-annotated in plants. In mammals, lncRNA expression has been shown to be reaching the extent of protein-coding expression and be highly variable between individuals of the same species. Using A. thaliana as a model plant organism, we aimed to understand the true scope of lncRNA transcription across plants from different regions, characterize lncRNA natural expression variability, and study the causes of this variability.  Results  Using RNA-seq data spanning 499 natural lines and 4 different developmental stages to create a more comprehensive annotation of lncRNAs in A. thaliana, we found over 10,000 novel loci — three times as many as in the current public annotation. We showed that, while lncRNA loci are ubiquitous in the genome, most appear to be actively silenced and their expression and repressive chromatin levels are extremely variable between natural lines. It was particularly prominent in intergenic lncRNAs, where TE-like sequences present in 50% of the loci are associated with increased silencing and variation and such lincRNAs tend to be targeted by TE silencing machinery.   Conclusion  lncRNAs are ubiquitous in the A. thaliana genome, but their expression is highly variable between different lines and tissues. This high expression variability is largely caused by high structural and epigenetic variability of non-coding loci, especially those containing pieces of transposable elements. We create the most comprehensive A. thaliana lncRNA annotation to date and improve our understanding of plant lncRNA biology.

overall_design: We performed this RNA-seq to map lncRNAs and study their inter- and intra-accession expression variation in Arabidopsis thaliana. Plants from 27 different A.thaliana natural accessions were grown at the growth chambers of GMI, Vienna, Austria. The growing conditions were 21 degrees Celcius, long-day (16-hour light, 8-hour dark). For the “9-leaf rosette” samples we collected the full rosette at the 9-leaf stage with one plant harvested per sample. Seedlings were collected at 7 days post sowing (~5 days post germination). The full seedling with the root was collected with approximately 10 individuals/seedlings harvested per sample. For the “flower” samples we collected flowers and flower buds from approximately 5 individuals per sample. Accessions 1741, 6024, 6244, 9075, 9543, 9638, 9728, 9764, 9888, 9905, 22003, 22004, 22005, 22006, 22007 were cold-treated by placing them into 10oC growth chambers (long-day conditions) for ~ 4 weeks to induce flowering. Pollen was collected using the method described in (Johnson-Brousseau and McCormick, 2004) that uses vacuum suction and a series of filters to harvest dry pollen from flowering plants. We used polyester mesh filters of 3 sizes - 150mm, 60mm and 10mm - for the collection. Collected pollen was snap-frozen in liquid nitrogen, stored at -70oC and ground for RNA-sequencing using ~0.5ml of 0.5mm glass beads (Scientific Industries, Inc.). Frozen tissue was ground with a Retsch machine using steel beads. RNA was isolated using an in-house RNA isolation kit (magnetic beads based) and DNAse treated with DNAse I (New England Biolabs). We did not manage to get accessions 6069 and 6124 to flower, so for these two accessions we only have rosette and seedling samples.

middle: E

first: Viktoria

last: Nizhynska

first: Almudena

last: Morales

first: Dejan

last: Dukic


title: Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [ChIP-Seq]

overall_design: We performed this ChIP-seq to analyze epignetic patterns and silencing of lncRNAs in Arabidopsis thaliana. plants from many different A.thaliana natural accessions (https://1001genomes.org/accessions.html) were grown at the growth chambers of GMI, Vienna, Austria. 14 accessions were used for ChIP-sequencing with replicates corresponding to different growing batches, or in the case of not enough material - pooling samples from two-three batches. The growing conditions were 21 degrees Celcius, long-day (16-hour light, 8-hour dark). Mature leaves (not the oldest and not the youngest) from 2-3 individual plants were collected for each accession and snap frozen in liquid nitrogen. Leaves were collected when the plants reached 14-16-leaf stage prior to the start of bolting. Frozen tissue was ground with a Retsch machine using steel beads. Chromatin immunoprecipitation was performed with a protocol adapted from [Yelagandula R et al, Cell 2014]. Briefly, 1-2 grams of ground frozen leaf tissue was fixated with formaldehyde at 4oC for 5 min, then nuclei were isolated and lysed, and chromatin was fragmented using Covaris E220 Focused-ultrasonicator. The input sample was then taken out and frozen at -20oC and 5 antibody reactions were processed together. The antibodies used were: H1 (Agrisera) - 3 microgram per reaction, H3K4me3 (Abcam) - 3 microgram per reaction , H3K9me2 (Abcam) - 4 microgram per reaction, H3K27me3 (Millipore) - 4 microgram per reaction, H3K36me3 (Abcam) - 4 microgram per reaction. The immunoprecipitation was performed using pre-washed Dynabeads Protein A magnetic beads (Invitrogen) and ran overnight. Afterwards the samples were washed, followed by elution, overnight reverse-crosslinking, RNAse A (Fermentas) treatment for 30 min at room temperature, and DNA isolation using Qiagen PCR purification kit Qiaquick with 0.3M Sodium Acetate. Next, ChIP-seq libraries were prepared from a half of the resulting sample (due to very low amounts we did not measure the DNA concentrations) with the NEBNext Ultra II DNA kit (New England Biolabs) according to the manufacturer’s protocol and sequenced with 100bp single-end read mode on Illumina NovaSeq 6000 machine.


title: Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [Bisulfite-seq]

type: Methylation profiling by high throughput sequencing

summary:
Background
Long non-coding RNAs (lncRNAs) are under-studied and under-annotated in plants. In mammals, lncRNA expression has been shown to be reaching the extent of protein-coding expression and be highly variable between individuals of the same species. Using A. thaliana as a model plant organism, we aimed to understand the true scope of lncRNA transcription across plants from different regions, characterize lncRNA natural expression variability, and study the causes of this variability.
Results
Using RNA-seq data spanning 499 natural lines and 4 different developmental stages to create a more comprehensive annotation of lncRNAs in A. thaliana, we found over 10,000 novel loci — three times as many as in the current public annotation. We showed that, while lncRNA loci are ubiquitous in the genome, most appear to be actively silenced and their expression and repressive chromatin levels are extremely variable between natural lines. It was particularly prominent in intergenic lncRNAs, where TE-like sequences present in 50% of the loci are associated with increased silencing and variation and such lincRNAs tend to be targeted by TE silencing machinery.
Conclusion
lncRNAs are ubiquitous in the A. thaliana genome, but their expression is highly variable between different lines and tissues. This high expression variability is largely caused by high structural and epigenetic variability of non-coding loci, especially those containing pieces of transposable elements. We create the most comprehensive A. thaliana lncRNA annotation to date and improve our understanding of plant lncRNA biology.

overall_design: We performed this bisulfite-seq to analyze epignetic patterns and silencing of lncRNAs in Arabidopsis thaliana. plants from 32 different A.thaliana natural accessions (https://1001genomes.org/accessions.html) were grown at the growth chambers of GMI, Vienna, Austria. The growing conditions were 21 degrees Celcius, long-day (16-hour light, 8-hour dark). Mature leaves (not the oldest and not the youngest) from 2-3 individual plants were collected for each accession and snap frozen in liquid nitrogen. Leaves were collected when the plants reached 14-16-leaf stage prior to the start of bolting. Frozen tissue was ground with a Retsch machine using steel beads. DNA was isolated using Nuclear Mag Plant kit (Machery-Nagel) and the bisulfate libraries were prepared using a tagmentation method described in (Wang et al Nature Protocols 2013) using an in-house Tn5 transposase (IMBA-IMP-GMI Molecular Biology Services) and EZ-96 DNA Methylation-Gold Mag Prep kit (Zymo Research) for bisulfite conversion. The sowing, growing and sample collection was performed 2 to 4 times and this corresponds to 2 to 4 replicates per accession.


title: Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [smallRNAseq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: The smallRNA-seq data was obtained to investigate determinants of expression variation in natural accessions of A.thaliana and TE-like silencing of lncRNAs. Plants from 14 different A.thaliana natural accessions (https://1001genomes.org/accessions.html) were grown at the growth chambers of GMI, Vienna, Austria. The growing conditions were 21 degrees Celcius, long-day (16-hour light, 8-hour dark). Accessions 1741, 6024, 6244, 9888 and 9905 were cold-treated at 10 degrees for ~ 4 weeks to induce flowering. Flowers and flower buds from 5-10 individual plants were collected for each accession and snap frozen in liquid nitrogen. Frozen tissue was ground with a Retsch machine using 2 steel beads. RNA was isolated from the whole sample using NucleoSpin miRNA kit from Macherey-Nagel following the manufacturer's protocol.

last: Molla Morales


title: Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [lncRNA]

overall_design: We performed this RNA-seq to map lncRNAs and study their inter- and intra-individual expression variation in Arabidopsis thaliana. Plants from 28 different A.thaliana natural accessions (https://1001genomes.org/accessions.html) were grown at the growth chambers of GMI, Vienna, Austria. The growing conditions were 21 degrees Celsius, long-day (16-hour light, 8-hour dark). Leaves from 2-3 individual plants were collected for each accession and snap frozen in liquid nitrogen. Around 8 mature leaves, not the youngest and not the oldest, were collected when the plants reached 14-16-leaf stage prior to the start of bolting. Frozen tissue was ground with a Retsch machine using steel beads. RNA was isolated using an in-house RNA isolation kit (magnetic beads based) and DNAse treated with DNAse I (New England Biolabs). The sowing, growing and sample collection was performed 4 times.


title: Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing

overall_design: Refer to individual Series


title: Impact of 5-azacytidine on DNA methylation and gene expression in ACC cell lines

status: Public on Feb 19 2023

city: Paris

first: Gwenneg

middle: Vincent

last: Kerdivel

address: 24 rue du faubourg saint jacques

institute: Institut Cochin

summary: Adrenocortical carcinomas (ACCs) are rare and aggressive endocrine cancers of the adrenal gland. Recently, a subtype of ACC characterized by a CpG island methylator phenotype (CIMP), associated with especially poor diagnosis, has been discovered. The purpose of this study is to investigate the role of DNA methylation and the impact on demethylating agent 5-azacytidine in ACC tumors aggressiveness. To this aim, we generated RRBS and RNAseq data from two ACC and one non-tumour cell lines treated or not with 5-azacytidine. We showed that CIMP has a direct impact on the aggressiveness of tumors through two main mechanisms; (1) by increasing survival and proliferation and (2) by favoring the tumor immune escape. These two mechanisms could at least partially be reversed upon 5-azacytidine treatment. Overall, our results show that strongly suggest that the co-treatment with demethylating agents to enhance the efficacy of immunotherapy could be beneficial for patients with high CIMP ACC.

overall_design: Examination of DNA methylation by RRBS and transcriptome by RNA-seq in the two ACC cell lines, H295R and MUC-1, and the non tumor cell line HUVEC, treated or not with 5µM 5-azacytidine

first: Valentina

last: Boeva


title: Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Plant leaf intercellular space provides a nutrient-rich and heterogeneous niche for microbes that have a critical impact on plant health. However, how individual plant cells respond to heterogeneous microbial colonization remains largely elusive. Here, by time-resolved simultaneous single-cell transcriptome and epigenome profiling of plants (Arabidopsis thaliana) infected by virulent and avirulent bacterial pathogens (Pseudomonas syringae), we present an atlas of gene regulatory logic involving transcription factors, potential cis-regulatory elements, and target genes associated with disease and immunity. We also identify previously uncharacterized cell populations with distinct immune gene expression within major developmental cell types. Furthermore, we employ time-resolved spatial transcriptomics to reveal spatial heterogeneity of plant immune responses linked to pathogen distribution. Integration of our single-cell multiomics and spatial omics data enables spatiotemporal mapping of defense gene regulatory logic. Overall, this study provides a molecularly-defined spatiotemporal map of plant-microbe interaction at the single-cell resolution.

overall_design: Arabidopsis thaliana Col-0 were grown in a chamber at 22°C with a 12-h light period and 60-70% relative humidity for 30-31 days. Bacterial stains were cultured in the King’s B liquid medium with antibiotics (Rifampicin and Tetracyclin) at 28°C. Three bacterial strains–Pseudomonas syringae pv tomato DC3000 (Pto DC3000) carrying empty vector (pLAFR3), avrRpt2 (pLAFR3), and avrRpm1 (pLAFR3)–were described previously (Whalen et al. 1991; Kunkel et al. 1993). Bacteria were harvested by centrifugation and resuspended in sterile water to an OD600 of 0.001 (approximately 5 x 105 CFU ml-1). In total, 20 A. thaliana leaves (four fully-expanded leaves per plant) were syringe-inoculated with bacterial suspensions using a needleless syringe. For each strain, four time points (4, 6, 9, and 24 h) were sampled at the same time by infiltrating bacteria at different times. The 20 infected leaves were harvested with forceps and immediately processed for nuclei extraction. For the mock condition, water-infiltrated leaves were harvested after 9 h.

first: Tatsuya

last: Nobori


title: Viral RNA-binding protein KSHV ORF57 and host transcriptome

status: Public on Feb 13 2023

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

summary: Kaposi's sarcoma-associated herpesvirus (KSHV) encodes a viral RNA-binding protein ORF57 that plays an essential role in posttranscriptional regulation of viral gene expression. Ectopice expression of KSHV ORF57 in HEK293T cells was evaluated on its effect on host gene expression in the study, with the cells transfected with an empty vector serving as a control.

overall_design: A differential expression analysis of host transcritome in HEK293T cells ORF57 expressing vector (pVM7) or empty vector (pCMV5.1-FLAG).

first: Beatriz

last: Alvarado Hernandez

first: Vladimir

last: Majerciak


title: Transcriptional readthrough as a conserved mechanism for piRNA cluster expression in mosquitoes

status: Public on Feb 05 2023

city: Nijmegen

first: Jieqiong

last: Qu

address: Geert Grooteplein Zuid 28

department: Department of Medical Microbiology

institute: Radboud Institute for Molecular Life Sciences, Radboud University Medical Center

summary: We performed combined transcriptional and chromatin state analyses and showed that these core piRNA clusters in Aedes mosquitoes do not have their own independent promoters, but depend on readthrough transcription from upstream genes for piRNA biogenesis. We further showed core piRNA clusters biogenesis depends on key factors, the mRNA exporter Nxf1, three Tudor proteins, Veneno, Tejas, Yb, and an evolutionarily conserved cochaperone Shutdown.

overall_design: In Aedes aegypti Aag2 cells, we performed ChIP-seq of four histone marks, including H3K27ac, H3K4me3, H3K36me3, H3K9me3. Besides, we generated a series of RNA pol II ChIP-seq,  RNA pol II Ser5P ChIP-seq,  RNA pol II Ser2P ChIP-seq. In addition, we performed ATAC-seq to assay open chromatin regions. Such a comprehensive chromatin profiling data provides precise insights into transcriptional regulation and chromatin states of Aedes mosquitoes. We further explored key factors involoved in piRNA cluster biogenesis. We performed knockdown of the nuclear exporter Nxf1, UAP56 which plays an important role in piRNA cluster export and three Tudor proteins that were among the top enriched hits from Piwi5-IP experiment, Vreteno (AAEL020359), Tejas (AAEL022773), and Yb (AAEL001939). We also included Shutdown (AAEL011632), which is required for the biogenesis of all piRNA populations in D. melanogaster. After knockdown of target genes, RNA was isolated and prepared for small RNA-seq sequencing. dsLuc-1-3 serve as control knockdown for Nxf1 and UAP56, whereas dsLuc4-5 serve as control for knockdown of Vreteno, Tejas, Yb, and Shutdown.

first: Valerie

last: Betting

first: Ronald

last: van Rij


title: Distinct cervical tissue-adherent and luminal microbiome communities correlate with mucosal host gene expression and protein levels in Kenyan sex workers

status: Public on Feb 10 2023

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet

summary: Background: While the luminal microbiome composition in the human cervicovaginal tract has been defined, the presence and impact of tissue-adherent ectocervical microbiota remain incompletely understood. Studies of luminal and tissue-associated bacteria in the gastrointestinal tract suggest that they may have distinct roles in health and disease. Here, we performed a multi-omics characterization of paired luminal and tissue samples collected from a clinically well-characterized cohort of Kenyan women.      Results: We identified a tissue-adherent bacterial microbiome, with a higher alpha diversity than the luminal microbiome, in which dominant genera overall included Gardnerella and Lactobacillus, followed by Prevotella, Atopobium, and Sneathia. About half of the L. iners dominated luminal samples had a corresponding Gardnerella dominated tissue microbiome. Broadly, the tissue-adherent microbiome was associated with fewer differentially expressed host genes than the luminal microbiome. Gene set enrichment analysis revealed that L. crispatus-dominated tissue-adherent communities were associated with protein translation and antimicrobial activity, whereas a highly diverse microbiome was associated with epithelial remodeling and pro-inflammatory pathways. Communities dominated by L. iners and Gardnerella were associated with low host transcriptional activity. Tissue-adherent microbiomes dominated by Lactobacillus and Gardnerella correlated with host protein profiles associated with epithelial barrier stability, and with a more pro-inflammatory profile for the Gardnerella-dominated microbiome group. Tissue samples with a highly diverse composition had a protein profile representing cell proliferation and pro-inflammatory activity.      Conclusion: We identified ectocervical tissue-adherent bacterial communities in all study participants. These communities were distinct from cervicovaginal luminal microbiota in a significant proportion of individuals. This difference could possibly explain that L. iners dominant luminal communities have a high probability of transitioning to high diverse bacterial communities including high abundance of Gardnerella. By performing integrative multi-omics analyses we further revealed that bacterial communities at both sites correlated with distinct host gene expression and protein levels. The tissue-adherent bacterial community is similar to vaginal biofilms that significantly impact women’s reproductive and sexual health.

overall_design:
In this study we look at ectocervical gene transcription (n=108), and cervicovaginal protein profiles (n= 84) stratified by luminal and tissue-adherent microbiome profiles. Paired cervicovaginal (luminal, n=108) and ectocervical tissue adherent (n=93) microbiome profiles were characterized from a clinically well-characterized cohort of 108 Kenyan women.

Please note that total 112 transcriptomics samples that were considered for inclusion. Of these, 108 samples had corresponding 16S lavage samples, and 93 also had corresponding 16S from a second tissue biopsy (published in the European Nucleotide Archive).
All GSE183513 (except two samples, GSM5558554 GSM5558564, thus total 94 sample) and GSE194276 (16 samples) samples were included in the analysis.

**Raw data not provided due to patient privacy concerns.***


title: Differential expression analysis of intra- and peritumoral immune-related gene in murine hepatocellular carcinoma

status: Public on Dec 31 2022

city: Guangzhou

first: Shi-Ting

last: Feng

state: Guangdong

address: The Second Zhongshan Road

institute: The first affiliated hospital of Sun Yat-sen University

summary: As immunotherapy plays an increasingly important role in the treatment of hepatocellular carcinoma, the immune infiltration heterogeneity of the tumor provides an important reference for immunotherapy decisions. In this study, a mouse hepatocellular carcinoma model was established, and the intra-tumor and peritumor tissues were sampled and analyzed by RNA sequencing, respectively, to explore the heterogeneity of immune-related gene expression in intra- and peritumor regions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for intra-tumor and peritumor tissues.

first: Mengqi

last: Huang

first: Chenyu

last: Song


title: TLR-dependent transcriptional reprogramming of LXRα cistrome in bone marrow-derived macrophages

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

summary: The Liver X receptors (LXRα and LXRβ) are members of the nuclear receptor superfamily of transcription factors, and play key roles in the coordination of both metabolic and immune responses in macrophages. Both LXRs are expressed in macrophages and they share a high degree of sequence homology but their individual roles in different models of macrophage cultures, particularly in response to inflammation, have not been characterized. Previous studies have shown that ligand pre-treated LXRs repress the induction of pro-inflammatory cytokines in macrophages. Here, we show evidence that the expression of LXRα (but not LXRβ) is transcriptionally regulated at late phases of an LPS-induced inflammatory response in bone marrow-derived macrophages (BMDMs). Regulation of LXRα expression is controlled at the transcriptional levels by inflammatory signaling networks. Transcriptional profiling studies and ChIP-seq data identified a number of innate immune pathways whose expression is substantially controlled by LXRα in BMDMs. In summary, our data shows that LXRα plays a previously unrecognized role in innate immunity by transcriptional regulation of a battery of inflammatory genes through TLR and Type-I IFN-dependent signaling in macrophages.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for nuclear receptor LXR-alpha, p65 subunit of transcription factor NF-kB, and the histone modification H3K27ac in BMDM cells.

first: Antonio

last: Castrillo

first: Juan

middle: V

last: de la Rosa Medina


title: mRNA-seq of worms who raised on control RNAi or prp-19 RNAi were untreated or treated with atp-2 RNAi

city: Beijing

first: Xia

last: Peixue

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: Mitochondria are the central hub of energy and metabolism of the cell,acting as one of the most important organelles of living cells.Under mitochondrial stresses, cells will trigger mitochondrial unfolded protein response (UPRmt) to maintain mitochondrial homeostasis.We have verified that splicing facotrs are required for the activation of UPRmt.Knocking down of splicing fator prp-19 could   supresse UPRmt activation.We analysis the differencial alternative splicing of worms on L4440 RNAi or prp-19 RNAi and untreated or treated with atp-2 RNAi, we found that inhibition of prp-19 interrupts splicing homeostasis of c.elegans.

overall_design: Examination of differiencial alternative splicing and mRNA profile of worms. Worms grown on L4440 RNAi or prp-19 RNAi were untreated or treated with atp-2 RNAi.

first: Peixue

last: Xia

first: Jialiang

last: Guan

first: Wanqiu

last: Ding


title: CD8+ CD226high T cells in liver metastases dictate the prognosis of colorectal cancer patients treated with chemotherapy and radical surgery

status: Public on Dec 01 2022

city: Besancon

first: Julien

last: Viot

address: 3 boulevard alexandre fleming

institute: CHU besancon

summary: In this study, we aimed to assess the prognostic value of CD226 on tumor-infiltrating lymphocytes derived from liver metastases of colorectal cancer (CRC) patients treated with chemotherapy and radical surgery.  CD226high expression was associated with a potent immune infiltrate in RNAseq from primary colorectal cancer and liver metastases. CD226 expression contributes to defining the immune contexture of CRC liver metastases and primary tumors. In liver metastases, CD226 expression on CD8 T cells was not specifically co-expressed with other immune checkpoints such as PD1, TIGIT and TIM3. Multivariate Cox regression analysis revealed that CD226 expression on CD8 T cells was an independent prognostic factor (p=0.003) along with CD3 density at invasion margins (p=0.003) and TIGIT expression on CD4 T cells (p=0.019). CD155 was not associated with CD226 prognostic value. Gene expression analysis in a validation dataset confirmed the prognostic value of CD226 selectively in liver metastases but not in primary tumors. Down regulation of CD226 on CD8+ infiltrating lymphocytes in liver microenvironment might be restored by IL-15 treatment.   CD226 expression on liver metastases-infiltrating CD8+ contributes selectively to the immune surveillance of liver metastases from CRC and displays a prognostic value for patients undergoing radical surgery.

overall_design: Liver metastases and paired primary (when available) from 28 patients, treated with chemotherapy, and 10 treatment naïve patients were analyzed with RNAseq

first: Evan

last: Seffar

first: Angelique

last: Vienot

first: Christophe

last: Borg


title: Massively parallel reporter assays with multi-layer annotation identified cell-type-specific functional variants and genes associated with melanoma (MPRA)

status: Public on Nov 28 2022

city: Rockville

first: Jiyeon

last: Choi

address: 9615 Medical Center Drive, Rm 3116

institute: NCI

summary: The most recent genome-wide association study (GWAS) of cutaneous melanoma identified 54 risk-associated loci, but functional variants and their target genes for most have not been established. Here, we performed massively parallel reporter assays (MPRA) using malignant melanoma and normal melanocyte cells and further integrated multi-layer annotation to systematically prioritize functional variants and susceptibility genes from these GWAS loci. Of 1,992 risk-associated variants tested in MPRA, we identified 285 from 42 loci (78% of the known loci) displaying significant allelic transcriptional activities in either cell type (FDR < 1%). We further characterized MPRA-significant variants by motif prediction, epigenomic annotation, and statistical/functional fine-mapping to create integrative variant scores, which prioritized one to six plausible candidate variants per locus for the 42 loci and nominated a single variant for 43% of these loci. Overlaying the MPRA-significant variants with genome-wide significant expression or methylation quantitative trait loci (QTLs) from melanocytes or melanomas identified candidate susceptibility genes for 60% of variants (172 of 285 variants). CRISPRi of top-scoring variants validated their cis-regulatory effect on the eQTL target genes, MAFF (22q13.1) and GPRC5A (12p13.1). Finally, we identified 36 melanoma-specific and 45 melanocyte-specific MPRA-significant variants, a subset of which are linked to cell-type-specific target genes. Analyses of transcription factor availability in MPRA datasets and variant-transcription factor interaction in eQTL datasets highlighted the roles of transcription factors in cell-type-specific variant functionality. In conclusion, MPRA along with variant scoring effectively prioritized plausible candidates for most melanoma GWAS loci and highlighted cellular contexts where the susceptibility variants are functional.

overall_design: Targeted amplicon RNA-sequencing of ectopic luciferase constructs with sequence tags transfected into UACC903 human melanoma cell lines (n = 8 biological replicates) and C283T human immortalized normal melanocytes (n = 5 biological replicates) together with amplicon DNA sequncing of input luciferase constructs for normalization control (n = 3 biological replicates)

first: Erping

last: Long

first: Jinhu

last: Yin

first: Karen

middle: M

last: Funderburk

first: Kevin

last: Brown


title: Modeling maternal cholesterol exposure reveals a reduction of neural progenitor proliferation using human cerebral organoids

city: Nanjing

first: Yan

last: Liu

state: JiangSu

address: 101Longmian Avenue

department: Institute for Stem Cell and Neural Regeneration

institute: Nanjing Medical University

summary: Maternal obesity raises the risk of high-cholesterol exposure for their offspring. Studies in cohorts and animal models report that maternal obesity could increase the risk of neurodevelopmental disorders (NDDs) in offspring including intellectual disabilities and autism spectrum disorders (ASD). However, whether exposure to high cholesterol is responsible for brain developmental defects, as well as its underlying mechanism, is still unclear. Here, we constructed a cholesterol exposure model utilizing hiPSC-derived cerebral organoids by exogenously adding cholesterol into the culture system.  We preformed scRNA sequence analysis to explore the gene expression changes in brain organoids under additional cholesterol exposure.

overall_design: one sample from brain organoids under additional cholesterol treatment.

first: Pan

last: Fan

first: Kaiqin

last: Lu

first: Yuanhao

last: Wang

first: Min

last: Xu

first: Yuan

last: Hong

first: Xiao

last: Han


title: Massively parallel reporter assays with multi-layer annotation identified cell-type-specific functional variants and genes associated with melanoma (RNA-Seq)

overall_design: Whole transcriptome RNA-sequencing of UACC903 human melanoma cell lines (n = 3 biological replicates) and C283T human immortalized normal melanocytes (n = 3 biological replicates)


title: Massively parallel reporter assays with multi-layer annotation identified cell-type-specific functional variants and genes associated with melanoma

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


title: mRNA, lncRNA, and circRNA expression profiles in a new aortic dissection murine modelinduced by hypoxia and Ang II

status: Public on Nov 16 2022

city: WuHan

first: shuai

last: mei

address: 1095# Jiefang Ave

summary: Background and aims: Aortic dissection (AD) is a cardiovascular emergency with degeneration of the aortic media. Mounting evidence indicates obstructive sleep apnea (OSA) as an independent risk factor for AD development with unknown mechanisms. This study aims to establish a stable murine model of OSA-related AD (OSA-AD) and uncover the potential changes in gene transcripts in OSA-AD. Materials and methods: ApoE-/- mice were exposed to the chronic intermittent hypoxia (CIH) system combined with Ang II administration to establish the OSA-AD model. Pathological staining was performed to exhibit the physiological structure of the mouse aorta. The SBC mouse ceRNA microarray was used to identify significantly differentially expressed (DE) mRNAs, DE long-non-coding RNAs (DElncRNAs), and DE circular RNAs (DEcircRNAs) in OSA-AD tissues. Subsequently, bioinformatics analysis, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genome (KEGG), and protein–protein interaction (PPI) analyses, was performed to evaluate the function of the significantly differentially expressed transcripts (DETs). The hub genes were confirmed using quantitative real-time polymerase chain reaction (qRT-PCR). Results: ApoE-/- mice exposed to CIH and Ang II showed a high ratio of aortic accident (73.33%) and significant aortic diameter dilatation (1.96 ± 0.175 mm). A total of 1,742 mRNAs, 2,625 lncRNAs, and 537 circRNAs were identified as DETs (LogFC ≥ 1.5 or ≤ –1.5, P < 0.05). GO and KEGG analyses demonstrated that the differentially expressed mRNAs (DEmRNAs) were most enriched in cell proliferation, migration, apoptosis, inflammation, and hypoxia-related terms, which are closely related to aortic structural homeostasis. The PPI network contained 609 nodes and 934 connections, the hub genes were highlighted with the CytoHubba plugin and confirmed by qRT-PCR in AD tissues. KEGG pathway analysis revealed that the cis-regulated genes of DElncRNAs and circRNAs-host genes were enriched in aortic structural homeostasis-related pathways. Conclusion: Our findings help establish a de novo OSA-AD animal model using ApoE-/- mice. Many DEmRNAs, DElncRNAs, and DEcircRNAs were screened for the first time in OSA-AD tissues. Our findings provide useful bioinformatics data for understanding the molecular mechanism of OSA-AD and developing potential therapeutic strategies for OSA-AD.

overall_design: the ApoE-/- mice were attributed to two groups randomly, and then the mice of one group were exposed to the chronic intermittent hypoxia (CIH) system combined with Ang II administration to establish the OSA-AD model. The other group were treated by normal saline and normoxia as the control.

first: Dating

last: Sun

first: Jiangtao

last: Yan


title: Raw data of testicular small RNA-Seq in Hezuo pigs and Landrace pigs at two different ages

status: Public on Nov 18 2022

city: Lanzhou

first: Bo

last: Zhang

address: No. 1 Yingmen village, Anning District

institute: Gansu Agricultural University

summary: Hezuo pigs are known in China for early sexual maturity. In this study, we obtained small RNA-Seq data from testicular tissues of 30-day-old and 120-day-old Hezuo and Landrace pigs. Through comparative analysis of their differences, we searched for some miRNAs related to the regulation of precocious sexual traits in male cooperating pigs and revealed their molecular regulatory mechanisms, which can then provide references for the diagnosis and treatment of precocious sexual diseases in humans and for accelerating the breeding of high-fertility animals.

overall_design: Testicular tissues of 30 and 120 days old Hezuo and Landrace pigs, 3 biological replicates each, 12 samples in total.

first: Zunqiang

first: Shuangbao

last: Gun


title: Alterations in MAPK Signaling in Alveolar Bronchiolar Carcinomas from B6C3F1/N Mice Exposed to Antimony Trioxide by Inhalation for 2 Years

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary:
To identify transcripts differentially expressed between control samples and spontaneous tumors, or control samples and antimony treated lung tumors, we collected RNA from male and female B6C3F1 mice from a 2-year inhalation NTP bioassay exposed to 0 to 30 mg/m3 antimony trioxide.  These samples were interrogated with the Affymetrix Mouse Genome 430 2.0 GeneChip Array.
A total of 9941 gene transcripts were differentially expressed between control samples and spontaneous tumors, and 12441 gene transcripts were differentially expressed between control samples and treated antimony tumors (false discovery rate (FDR) < 0.05).

overall_design: There were 3 groups and 6x replication for each group, for 18 total samples. The groups were (1) vehicle control, (2) spontaneous tumors, (3) tumors present with antimony treatment. We compared vehicle control vs spontaneous tumor and control vs treated tumor using ORIOGEN software. The permutation based p-values for each test were significant for FDR≤5%.

first: Arun

last: Pandiri


title: Multiplatform Analysis of Primary and Metastatic Breast Tumors from the AURORA US Network identifies microenvironment and epigenetics differences as drivers of metastasis

status: Public on Jan 03 2023

city: Chapel Hill

first: Charles

middle: M.

last: Perou

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary:
The goal of this dataset is to compare the gene expression patterns between primary and metastatic tumors
Metastatic cancer patients typically have short survival times and their successful treatment represents one of most challenging aspects of patient care. This poor prognostic behavior is likely due to many factors, including increased clonal heterogeneity, multiple drug resistance mechanisms, and the role of the tumor microenvironment. The AURORA US Metastasis Project was established to collect and molecularly characterize specimens from 55 breast cancer (BC) patients representing 51 primary cancers and 102 metastases. The 153 unique tumors were assayed using RNAseq, tumor/germline DNA exomes and low pass whole genome sequencing, and global DNA methylation microarrays. We found intrinsic molecular subtype differences between primary tumors and their matched metastases to be rare in triple negative breast cancer (TNBC)/Basal-like subtype tumors. Conversely, tumor subtype changes were relatively frequent in estrogen receptor positive (ER+) cancers where ~30% of Luminal A cases switched to Luminal B or HER2-enriched (HER2E) subtype. Clonal evolution studies identified changes in expression subtype coincident with DNA clonality shifts, especially involving HER2 amplification and/or the HER2E expression subtype. Microenvironment differences varied according to tumor subtype where ER+/Luminal metastases had lower fibroblast and endothelial cell content, while TNBC/Basal-like metastases showed a dramatic decrease in adaptive immunity. In 17% of metastatic tumors, we identified DNA methylation and/or focal DNA deletions near HLA-A that were associated with its  significantly reduced expression, and with lower immune cell infiltrates. We also identified low immune cell features in brain and liver metastases when compared to other metastatic sites, even within the same patient. These findings have direct implications for the treatment of metastatic breast cancer patients with immune- and HER2-targeting therapies and suggest potential novel therapeutic avenues for the improvement of outcomes for some MBC patients.

first: Susana

middle: G

last: Recio


title: Single-cell analysis of human iPSC-derived multi-lineage mini-cardiac organoid reveals molecular pathways to promote cardiomyocyte maturation and heart repair

status: Public on Feb 09 2023

first: Jie

address: 30 Shuangqing Rd, Haidian District, Beijing, China

department: School of Medicine

institute: Tsinghua University

summary: Human induced pluripotent stem cell (hiPSC)-derived cardiovascular cells are promising cell source for cell therapy to repair the heart. Cardiac microtissue consisted of cardiomyocytes and fibroblast cells exhibited much better physiological functions. How different cardiovascular cell types interact and evolve in 3D microenvironment is unknown. In this study, we performed single-cell transcriptome profiling of hiPSC-derived mini-cardiac organoid consisted of cardiomyocytes, endothelial cells and smooth muscle cells. Our analysis showed that cardiac fibroblasts emerged spontaneously in 3D microenvironment which in turn facilitated the maturation of cardiomyocytes. HiPSC-derived cardiomyocytes, endothelial cells and smooth muscle cells assembled into mini-cardiac organoid in collagen-matrigel after 2 weeks. Single-cell study uncovered significant cell fate shift and improvement in cardiomyocyte maturation status upon-multilineage co-culture. Ligand-receptor analysis identified DLK1-Notch signaling to be one of the most upregulated pathways in the fibroblast population. Modulate the activity of DLK1-Notch signaling affected the assembly of the mini-cardiac organoid and the expression of immune regulatory genes. Interestingly, transplantation of trilineage mini-cardiac organoid into a rat model of myocardial infarction leads to significant improvement of cardiac function. Collectively, our single-cell analysis of mini-cardiac organoid provided rich information about cell fate dynamics and multilineage cross-talks occurred in the 3D microenvironment, which bring new insight on the molecular mechanism that promotes cardiomyocyte maturation and heart repair.

overall_design: single cell RNA-seq of hiPSC-derived human cardiomyocytes, endothelial cells, smooth muscle cells and mini-cardiac organoid

first: Fengzhi

first: Hui

last: Qiu

first: Changyong


title: Bioprinted 3D Outer Retina Barrier Uncovers RPE-dependent Choroidal Phenotype in Advanced Macular Degeneration

status: Public on Oct 21 2022

city: Bethesda

first: David

last: McGaughey

state: MD

address: 10 Center Dr

department: NEI

institute: NIH

summary:
We engineered a native-like 3D-oBRB tissue by bioprinting endothelial cells, pericytes, and fibroblasts on the basal side of a biodegradable scaffold and establishing an RPE monolayer on top.
To investigate the communication between endothelial cells, fibroblasts, pericytes and retinal pigment epithelial cells, we grew them as either 2D cell cultures or as 3D bioprinted outer blood retinal barrier tissues and harvested cells for single-cell RNAseq after 6 weeks of maturation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary and iPSC-derived endothelial cells, fibroblasts, pericytes and retinal pigment epithelial cells in either 2D culture, 3D-bioprinted outer blood-retinal barrier tissues, and 3D-bioprinted outer blood-retinal barrier tissues without RPE.

first: Min

last: Song

first: Russell

last: Quinn

first: Eric

last: Nguyen

first: Christopher

last: Hampton

first: Ruchi

last: Sharma

first: Tea

last: Park

first: Céline

last: Koster

first: Ty

last: Voss

first: Carlos

last: Tristan

first: Claire

last: Malley

first: Anju

last: Singh

first: Roba

last: Dejene

first: Devika

last: Bose

first: Yu-Chi

last: Chen

first: Paige

last: Derr

first: Kristy

first: Sam

last: Michael

first: Francesca

last: Barone

first: Guibin

first: Manfred

last: Boehm

first: Arvydas

last: Maminishkis

first: Ilyas

last: Singec

first: Marc

last: Ferrer

first: Kapil

last: Bharti


title: m6A MeRIP-Seq of interscapular brown adipose tissue (iBAT) in Wtapflox/flox and BAT-specific Wtap knockout (BKO) mice

status: Public on Oct 19 2022

city: Harbin

first: Zheng

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary:
Purpose: Through mRNA m6A-profiling, we aim to characterize the mRNA m6A changes in iBAT obtained from Wtapflox/flox and Wtap-BKO mice.
Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from iBAT of Wtap flox/flox and Wtap-BKO mice at 8 weeks old. Each sample (300 μg total RNA) was pooled from 8 mice for each group. Poly(A)+ RNA was purified using Dynabeads™ mRNA Purification Kit (Invitrogen) following the manufacturer’s instructions. Fragmented mRNA was incubated with m6A antibody (Synaptic System, 202003) for immunoprecipitation. Then, immunoprecipitated mRNAs or Input was used for library construction with NEBNext ultra RNA library prepare kit for Illumina (New England Biolabs).The library preparations were sequenced on an Illumina Novaseq 6000 platform with a paired-end read length of 150 bp according to the standard protocols. The m6A peaks were detected by exomePeak R package (version 2.16.0). The motif search was detected by HOMER(version 4.9.1).
Conclusion: The iBAT mRNA m6A profiles in Wtapflox/flox and BKO mice were characterized.

overall_design: To map the mRNA m6A modification caused by WTAP in iBAT, MeRIP-seq was performed in iBAT obtained from Wtapflox/flox and BKO mice.

first: Yuqin

last: Wang


title: Elevated methionine flux drives pyroptosis evasion in persister cancer cells

status: Public on Dec 02 2022

city: Tampa

first: Asmaa

last: Elkenawi

state: Fl

address: 12902 Magnolia Drive

department: Radiation Oncology

institute: Moffitt Cancer Center

summary: Induction of cell death represents a primary goal of most anti-cancer treatments. Despite the efficacy of such approaches, a small population of “persisters” develop evasion strategies to therapy-induced cell death. While previous studies have identified mechanisms of resistance to apoptosis, the mechanisms by which persisters dampen other forms of cell death, such as pyroptosis, remain to be elucidated. Pyroptosis is a form of inflammatory cell death that involves formation of membrane pores, ion gradient imbalance, water inflow and membrane rupture. Herein, we investigate mechanisms by which cancer persisters resist pyroptosis, survive, then proliferate in the presence of tyrosine kinase inhibitors (TKI). Lung, prostate and esophageal cancer persister cells remaining after treatments exhibited several hallmarks indicative of pyroptosis resistance. The inflammatory attributes of persisters included chronic activation of inflammasome, STING, and type I interferons. Comprehensive metabolomic characterization uncovered that TKI-induced pyroptotic persisters display high methionine consumption and excessive taurine production. Elevated methionine flux or exogenous taurine maintained plasma membrane integrity via osmolyte-mediated effects. Increased dependency on methionine flux decreased the level of one carbon metabolism intermediate S-(5'-adenosyl)-L-homocysteine, a determinant of cell methylation capacity. The consequent increase in methylation potential induced DNA hypermethylation of genes regulating metal ion balance and intrinsic immune response. This enabled thwarting TKI resistance by using the hypomethylating agent decitabine. In summary, the evolution of resistance to pyroptosis can occur via a stepwise process of physical acclimation and epigenetic changes without existing or recurrent mutations.

overall_design: PC9 Cells were treated in 4 96 well plates with 2μM Erlotinib for 3, 19, 27, 75 days (one plate for each time point).  Cells were monitored by Incucyte live-cell imaging to identify early expanding clones (EEs or named Lauria’s clones), Persisters (P) in plates 2-3, and descendant of persisters (DPs) in plate 4.  We then collected one plate at each time point.  We then processed untreated, early expanding clones (EEs), Persisters (P), and descendant of persisters (DPs) for RNA seq profiling. Control PC9 cells were left untreated and were collected on day 3 (plate 1).

first: Yonghong

last: Zhang

last: El-Kenawi


title: Single-nucleus transcriptome analysis of interscapular brown adipose tissue (iBAT) in Wtapflox/flox and BAT-specific Wtap knockout (BKO) mice

status: Public on Oct 20 2022

summary:
Purpose: Through Single-nucleus transcriptome analysis, we aim to characterize the changes of cell heterogeneity in iBAT obtained from Wtap-BKO mice compared with that in Wtapflox/flox mice.
Methods: Nuclei were isolated from iBAT of Wtap flox/flox and Wtap-BKO mice at 8 weeks old. Each sample was pooled from 4 mice for each group.
Conclusion: The Single-nucleus transcriptomes of iBAT in Wtapflox/flox and BKO mice were characterized.

overall_design: Nuclei were isolated from iBAT of Wtap flox/flox and Wtap-BKO mice at 8 weeks old and analyzed using single-nucleus RNA-seq.


title: The effects of WTAP on BAT function

summary:
Purpose: The goal of this study is to compare transcriptome profilings of interscapular brown adipose tissue (iBAT) from BAT-specific WTAP knockout and control mice
Methods: iBATs were collected from WTAP BKO and f/f mice at 8 weeks old (n=3 for each group), and total RNA was isolated using TriPure.  RNA-seq was performed by using Illumina NovaSeq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome (Ensemble_grcm38_p6) with TopHat (version 2.0.12), and the aligned reads were used to quantify mRNA expression by using HTSeq-count (version 0.6.1).
Conclusion:Our study represents the first detailed analysis of iBAT transcriptomes from WTAP BKO and f/f mice, generated by RNA-seq technology. The RNA-seq analysis showed that 894 genes were down-regulated and 1410 genes were up-regulated in the iBAT of WTAP BKO mice. GO analysis showed that the down-regulated genes were primarily related to related to generation of precursor metabolites and energy, cellular respiration, energy derivation by oxidation of organic compounds, electron transport chain, nucleotide metabolic process and purine ribonucleotide metabolic process.

overall_design: RNA samples were isolated from iBATs of WTAP BKO and f/f mice at 8 weeks old (n=3 for each group). mRNA profiles of WTAP BKO and f/f iBATs were generated by deep sequencing using Illumina NovaSeq 6000 platform.


title: WGBS from motor neuron (ENCSR734EFX)

status: Public on Oct 16 2022

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: Control PGP - iPSC

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Testing the usage of divalent metal cations and nucleases during NET-seq for Pol I

status: Public on Oct 27 2022

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

institute: University of Alabama at Birmingham

summary: The goal of this study was to determine the effects of commonly used nuclease treatments and their divalent metal cation cofactors on Pol I occupancy during NET-seq. Other groups have previously used micrococcal nuclease (MNase) + CaCl2 and deoxyribonuclease I (DNase I) + MnCl2 in NET-seq protocols probing for Pol II occupancy. However, the effect of these treatments on polymerase occupancy has not been fully explored. Therefore, we tested the impact of these treatments (CaCl2, CaCl2 + MNase, MnCl2, and MnCl2 + DNase I) on Pol I occupancy in vivo. We found that the exposure of Pol I to either CaCl2 or MnCl2 caused a significant reduction in occupancy on the rDNA template. Nuclease treatment (with either MNase or DNase I) did not cause an additional significant effect on Pol I occupancy in vivo beyond that of either CaCl2 or MnCl2. Finally, we found that MnCl2 treatment caused a more significant reduction in Pol I occupancy as compared to CaCl2, suggesting that perhaps MnCl2 stimulates the intrinsic cleavage activity of Pol I more robustly vs. CaCl2 in vivo. Altogether, these findings indicate that the inclusion of these treatments (especially that of divalent metal cations) in NET-seq protocols for Pol I cause a significant change in the polymerase occupancy.

overall_design: NET-seq was performed in triplicate with a WT yeast strain across five different treatment conditions: (1) Untreated Control, (2) CaCl2 Treated, (3) CaCl2 + MNase Treated, (4) MnCl2 Treated, and (5) MnCl2 + DNase I Treated.

middle: K

first: David

last: Schneider


title: WGBS from motor neuron (ENCSR509LMK)

summary:
Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: Control CS14 - iPSC

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: WGBS from motor neuron (ENCSR978LOX)

summary:
Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: Control SMA - iPSC

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Transcriptomic evolution across bilaterian tissues

status: Public on Oct 12 2022

city: Barcelona

first: Federica

last: Mantica

address: Dr. Aiguader 88

institute: CRG

summary: We investigate tissue transcriptomic evolution across bilaterian animals by analyzing RNA-seq data from eight different tissues across twenty species.

sample_organism:
Blattella germanica
Tribolium castaneum
Bombyx mori
Aedes aegypti
Drosophila melanogaster
Strongylocentrotus purpuratus
Branchiostoma lanceolatum
Callorhinchus milii
Danio rerio
Xenopus tropicalis
Monodelphis domestica
Octopus bimaculoides
Strigamia maritima
Cloeon dipterum
Episyrphus balteatus

overall_design: Characterization of ancestral and novel tissue gene expression patterns throughout bilaterian evolution.

first: Manuel

last: Irimia

first: Antonio

last: Torres-Mendez

first: Caroline

last: Albertin

last: Martin

first: Fernando

last: Noriega

first: Hector

last: Escriva

first: Isabel

last: Almudi

first: Karl

last: Wotton

first: Michael

last: Akam

first: Stephanie

last: Bertrand

first: Toby

last: Doyle


title: An atlas of healthy and injured cell states and niches in the human kidney [scCv3]

status: Public on Oct 10 2022

city: La Jolla

first: Kun

last: Zhang

state: California

address: 9500 Gilman Drive

institute: UCSD

summary: Understanding kidney disease relies upon defining the complexity of cell types and states, their associated molecular profiles, and interactions within tissue neighborhoods. We applied multiple single-cell or -nucleus assays (>400,000 nuclei/cells) and spatial imaging technologies to a broad spectrum of healthy reference (45 donors) and diseased (48 patients) kidneys. This has provided a high resolution cellular atlas of 51 main cell types that include rare and novel cell populations. The multi-omic approach provides detailed transcriptomic profiles, epigenomic regulatory factors, and spatial localizations spanning the entire kidney. We further define 28 cellular states across nephron segments and interstitium that were altered in kidney injury, encompassing cycling, adaptive or maladaptive repair, transitioning and degenerative states. Molecular signatures permitted localization of these states within injury neighborhoods using spatial transcriptomics, while large-scale 3D imaging analysis (~1.2 million neighborhoods) provided corresponding linkages to active immune responses. These analyses defined biological pathways relevant to injury time-course and niches, including signatures underlying epithelial repair that predicted maladaptive states associated with a decline in kidney function. This integrated multimodal spatial cell atlas of healthy and diseased human kidneys represents the most comprehensive benchmark of cellular states, neighborhoods, outcome-associated signatures, and publicly available interactive visualizations.

overall_design:
Single Cell RNA-Seq performed on kidney tissues from 15 Chronic Kidney Disease (CKD), 12 Acute Kidney Disease (AKI) and 20 healthy reference (Ref) individuals. This research was performed as part of the Kidney Precision Medicine Project (KPMP) and the Chan Zuckerberg Initiative (CZI) and Human Cell Atlas (HCA).
>>> Submitter declares that the raw data are deposited in KPMP due to patient privacy concerns. <<<

first: Rajasree

last: Menon

first: Edgar

last: Otto

first: Abhijit

last: Naik

first: Jeffrey

middle: B

last: Hodgin

first: Matthias

last: Kretzler


title: A Gas-only Bioreactor System Maintains Stable Culture Environments and Reveals that Moderate pH deviations Trigger Transcriptome-wide Responses in Human Cells Cultured in Physioxia and Physiological Buffers

status: Public on Oct 06 2022

city: THUWAL

first: Samhan

last: Alsolami

address: Thuwal 23955

department: BESE

country: Saudi Arabia

institute: KAUST

summary: We report RNAseq data derived from GM12878 cell line exposed to defined pH treatments using enhanced gasses based bioreactor system

overall_design: Examining 4 different pH treatments influence on GM12878 transcrioptomics

first: Silvia

last: Arossa

first: Shannon

last: Klein

first: Alexandra

last: Steckbauer

first: Anieka

last: Parry

first: Yingzi

first: Gerardo

last: Ramos Mandujano

first: Juan

middle: C

last: Iizpiasua-Belmonte

first: Carlos

last: Duarte

first: Mo

last: Li


title: Memory-induced transcriptome in Huntington's disease (HD) mice [RNA-seq]

city: strasbourg

first: Charles

last: DECRAENE

address: 12 rue Goethe

department: UMR 7364 CNRS

institute: CNRS

summary: Evaluation of the effect of procedural  memory using the double-H maze (DH) on striatal and hippocampal transcriptome in HD R6/1 mice

overall_design: RNAseq data were generated using the striatum of WT and HD mice in resting condition (home cage, HC), during memory formation (after 2 days of training in the double H maze, DH-2d) and during memory consolidation/recall (after the probe test performed after 4 days of training, DH-5d)

first: Karine

last: Merienne

first: Rafael

last: Alcala-Vida

first: Caroline

last: Lotz

first: Jonathan

last: Seguin


title: An atlas of healthy and injured cell states and niches in the human kidney

first: Kun

last: Zhang

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

overall_design: Refer to individual Series


title: RNA expression of mechanically stretched human induced pluripotent stem cell-dervied cardiomyocytes

status: Public on Nov 14 2022

city: Helsinki

first: Lotta

last: Pohjolainen

address: Viikinkaari 5 E

country: Finland

institute: University of Helsinki

summary: The effect of cyclic mechanical stretch (0.5 Hz, 10-21% elongation) on gene expression of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) was studied using RNA sequencing.

overall_design: RNA sequencing was carried out from 24-h, 48-h and 72-h stretched and unstretched control samples. One hour before stretching, the cells were treated with 30 µM of experimental compound 1262 (only at 72-h time point) or vehicle (0.3% DMSO). At each time point, there were 3-4 biological replicates, which were from individual cardiomyocyte differentations.

first: Heikki

last: Ruskoaho

first: Virpi

last: Talman


title: Conservation at the uterine-placental interface

status: Public on Sep 20 2022

city: Stillwater,

first: Khursheed

last: Iqbal

state: OK

address: 310 N Monroe St,

institute: Oklahoma state university

summary: The hemochorial placentation site is characterized by a dynamic interplay between trophoblast cells and maternal cells. These cells cooperate to establish an interface required for nutrient delivery to promote fetal growth. In the human, trophoblast cells penetrate deep into the uterus. This is not a consistent feature of hemochorial placentation and has hindered the establishment of suitable animal models. The rat represents an intriguing model for investigating hemochorial placentation with deep trophoblast cell invasion. In this study, we used single cell RNA sequencing to characterize the transcriptome of the invasive trophoblast cell lineage, as well as other cell populations within the rat uterine-placental interface during early (gestation day, gd, 15.5) and late (gd 19.5) stages of intrauterine trophoblast cell invasion. We identified a robust set of transcripts that define invasive trophoblast cells, as well as transcripts that distinguished endothelial, smooth muscle, natural killer, and macrophage cells. Invasive trophoblast, immune, and endothelial cell populations exhibited distinct spatial relationships within the uterine-placental interface. Furthermore, the maturation stage of invasive trophoblast cell development could be determined by assessing gestation-stage dependent changes in transcript expression. Finally, and most importantly, expression of a prominent subset of rat invasive trophoblast cell transcripts is conserved in the invasive extravillous trophoblast cell lineage of the human placenta. These findings provide foundational data to identify and interrogate key conserved regulatory mechanisms essential for development and function of an important compartment within the hemochorial placentation site that is essential for a healthy pregnancy.

overall_design: Rat uterine-placental interface (UPI) tissues were dissected on gd 15.5 and 19.5 . Dissected UPI compartments from wild type  placentation sites were minced and enzymatically digested into a single cell suspension. Samples were further processed for scRNA-seq by Chromium Single Cell RNA-seq (10X Genomics). Single cell suspensions were prepared by enzymatic digestion of the uterine-placental interface. Single cell libraries were then constructed using the 10X Genomics platform and sequenced with an Illumina NovaSeq 6000 system. Computational analysis with the Cell-Ranger pipeline led to the identification a number of unique cell clusters defined by their transcript profiles, samples were analyzed.

first: Regan

last: Scott

first: Michael

last: Soares

first: Geetu

last: Tuteja


title: Comprehensive methylome sequencing reveals prognostic epigenetic biomarkers for prostate cancer mortality

status: Public on Oct 03 2022

city: Darlinghurst

first: Ruth

last: Pidsley

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

summary: We profiled DNA from primary tumour RP tissue specimens from 15 patients (and adjacent normal tissue specimens from 4 patients) in a discovery cohort using whole-genome bisulphite sequencing (WGBS). We identified a set of differentially methylated regions in the primary tumour samples between patients who died ≤ 10 yrs post-RP and those still alive > 10 yrs post RP (median follow-up time: 19.5 years).

overall_design:
We used WGBS data to detect methylation differences in tumours from patients with lethal (n = 7) and non-lethal (n = 8) disease.

'GSE158927_BigTable.tsv.gz’ is a tsv file providing coverage and methylation data for each sample (columns) at each CpG site (rows).

In the column names, chr = chromosome, position = genomic position, then for each sample, C = count methylated and cov = total coverage

first: R


title: NOMeseq analysis of Etv2 induced MEF reprogramming

status: Public on Oct 04 2022

city: Minneapolis

first: Daniel

last: Garry

state: MN

address: 2231 6th Street SE, 4th Floor

department: Lillehei Heart Institute

institute: University of Minnesota

summary: The vasculature is an essential organ for the delivery of blood and oxygen to all tissues of the body and thus relevant to the treatment of ischemic diseases, injury-induced regeneration, and solid tumor growth. Therefore, the definition of pioneer factors and regulatory pathways that govern the specification and differentiation of endothelial progenitors will serve as a platform for targeted therapies to promote cardiovascular regeneration and treatment of solid organ tumors. Previously, we demonstrated that ETV2 was an essential transcription factor for the development of cardiac, endothelial and hematopoietic lineages.  Here, we report that ETV2 functions as a novel pioneer factor that relaxes closed chromatin and regulates endothelial development. By comparing engineered embryonic stem cell differentiation and reprogramming models with single cell RNA-seq, ATAC-seq and ChIP-seq techniques, we demonstrated that ETV2 was able to bind nucleosomal DNA and function as a pioneer factor independent of the cellular context. We determined that ETV2 executes a pioneering role by recruiting BRG1 to remodel chromatin around endothelial genes and help maintain an open configuration.  ETV2 chromatin binding also resulted in increased H3K27ac deposition.  Collectively, these results will serve as a platform for the development of therapeutic initiatives directed towards cardiovascular and oncological diseases.

overall_design: NOMe-seq was performed in duplicates using 250,000 cells from control and day 1 reprogrammed MEFs per sample following the protocol described in Lay et al.29 The reagents used in the studies are GpC Methyltransferase (M.CviPI) (NEB # M0227), Klenow Fragment (3'→5' exo-) (NEB # M0210S), EZ DNA Methylation™ Kit (VWR # 77001-534), End-It™ DNA End-Repair Kit (VWR # 75927-936), Rapid DNA Ligation Kit (ThermoFisher # K1422), xGen™ Methyl UDI-UMI Adapters, 1-16 (IDT # 10006644), xGen Library Amplification Primer Mix (IDT # 1077677), KAPA HiFi HotStart Uracil+ Kit (Roche # 07959052001). 200-500 bp size gel purified libraries were sequenced with the The NOVASeq S4 flow cell with 150 bp paired end reads.

first: Wuming

last: Gong

first: Nikita

last: Dsouza


title: Examining exosomes from blood taken from gastric cancer samples

status: Public on Sep 15 2022

city: shandong

first: zhaogang

last: dong

address: No.107 wenhua west road ,jinan ,shandong province

institute: qilu hospital of shandong university

overall_design: Examining 2 conditions in exosomes from blood, each with 3 replicates


title: Paternal obesity alters the sperm epigenome and and is associated with changes in the placental transcriptome and its cellular composition

status: Public on Sep 09 2022

city: Sainte-Anne-de-Bellevue

first: Anne-Sophie

last: Pépin

state: QC

address: 21111 Lakeshore road

department: Department of Pharmacology and Therapeutics

institute: McGill University


title: Paternal obesity alters the sperm epigenome and and is associated with changes in the placental transcriptome and its cellular composition [RNA-seq]

summary: Growing evidence point towards a strong contribution of paternal factors in placental health with implications in adult-onset complex disease risk. We have recently demonstrated that paternal diet-induced obesity alters sperm histone methylation and is associated with metabolic disturbances in the next generation. Diet-sensitive epigenetic regions in sperm were found at genes involved in trophectoderm and placental development, and corresponded to epigenetic and gene expression profiles in these tissues. We sought to investigate whether paternal diet-induced obesity before conception can alter the placental transcriptome, and whether differential gene expression corresponds with sperm obesity-associated epigenetic signatures. C57BL6/J males were fed either a control or high-fat diet for 10 weeks beginning at 6 weeks of age. They were then bred to control-fed C57BL6/J females to induce pregnancies and E14.5 placentas were collected. RNA-sequencing was performed (n=4 per group per sex) to detect sex-specific transcriptional changes associated with paternal diet. At necropsy, sperm was collected for chromatin immunoprecipitation followed by sequencing (ChIP-seq; n=3 per group) targeting histone H3 lysine 4 tri-methylation (H3K4me3) to detect obesity-induced changes in H3K4me3 enrichment. There were sex-specific differentially expressed genes in placentas with some overlapping with promoters showing obesity-associated sperm epimutations. A deconvolution analysis using single-cell RNA-seq data from mouse E14.5 placenta (Han et al., Cell, 2018) revealed significant differences in trophoblast subtype proportions in placentas derived from HFD sires. This study highlights a previously underappreciated role of the placenta at the origin of paternally-induced metabolic disturbances in offspring.

overall_design: Examination of sperm H3K4me3 in control or high-fat fed sires (n=3 per group), examination of E14.5 placenta total RNA derived from control or high-fat fed sires (n=4 per sex per group)

last: Pepin

first: Sarah

last: Kimmins