title: Bulk RNAseq analysis of butyrate and/or secondary bile acid treatment of T84 cell line

status: Public on Aug 06 2022

city: Worcester

first: Beth

last: McCormick

state: MA

address: 368 Plantation Street

institute: University of Massachusetts Chan Medical School

summary: P-glycoprotein is a key component of the intestinal epithelium playing a pivotal role not only in the removal of toxins but also in the efflux of endocannabinoids to prevent excessive inflammation and sustain a homeostatic tone within the intestine.  Previous studies have shown short-chain fatty acids and secondary bile acids produced by the intestinal microbiota potentiate induction of P-glycoprotein expression, yet the mechanism remains to be elucidated.  Here, we employ RNA sequencing to evaluate the transcriptome signature triggered by each metabolite alone, and unique pathways activated by the metabolite combination.  We show butyrate regulates NRF2 signaling and pathways related to chromatin modifications, while bile acids activate nuclear receptor pathways including vitamin D receptor and pregnane X receptor.  In combination these metabolites activate a unique transcriptional program involving multiple pathways including transcription factors and kinases that converge on P-glycoprotein induction.

overall_design: T84 cells were seeded from six separate flasks for six biological replicates.  Cells were treated with 5mM butyrate, 50µM each of three secondary bile acids together (lithochoilc acid, deoxycholic acid, ursodeoxycholic acid) or a combination of all four metabolites at the listed concentrations.  DMSO vehicle group served as a control.  24 samples of 4 conditions with 6 biological replicates each.

middle: A

first: Sage

last: Foley


title: RNA-seq of FAC sorted leaf palisade cells

status: Public on Aug 11 2022

city: La Jolla

first: Carl

last: Procko

state: CA

address: 10010 N Torrey Pines Rd

country: USA

institute: Salk Institute for Biological Studies

type: Expression profiling by high throughput sequencing

summary: Arabidopsis leaf protoplasts were sorted to generate palisade cell and non-palisade photosynthetic reference cell populations. Treatments include with and without transcription inhibitors, and high light.

overall_design: RNA-seq of paired leaf protoplast populations were compared.

first: Travis

last: Lee

first: Joe

last: Ecker

first: Joanne

last: Chory


title: Transcriptomic analysis of BNC2 regulated genes in LX2 cells

status: Public on Aug 07 2022

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: CNRS

summary: Human myofibroblastic LX2 cells were transfected using a siRNA directed against BNC2 (siBNC2) or a control siRNA (siCTRL) and RNA were processed for microarray analyses.

overall_design: Transfection of siRNA (used at 20 nM) into LX2 cells was performed using JetPrime (Polyplus transfection). siBNC2 (Thermo Fisher Scientific, Cat# 4392420 s29452) and Silencer select negative control (Thermo Fisher Scientific Cat# 4390844) were used. 48h after transfection,  RNA was purified and processed for analysis using Affymetrix GeneChip arrays (HTA 2.0) according to standard procedures.

first: Marie

last: Bobowski-Gerard

first: Celine

last: Gheeraert

first: Jerome


title: snRNAseq study of adrenal cortex adjacent to aldosterone-producing adenoma

status: Public on Aug 05 2022

city: Paris

first: Maria-Christina

last: Zennaro

address: 56 rue Leblanc

institute: Inserm

summary: To investigate the development of aldosterone-producing adenoma, we profiled cells of different areas of the adjacent adrenal cortex by snRNAseq to obtain possible trajectories towards adenoma formation.

overall_design: Gene expression profiling at single cell level of adrenal cortex adjacent to aldosterone-producing adenoma.

first: Maria

middle: C

first: Fabio

middle: F

last: Rosa

first: Sheerazed

last: Boulkroun

first: Kelly

last: De Sousa


title: BNC2 cistrome and epigenome in myofibroblastic LX2 cells

type: Genome binding/occupancy profiling by high throughput sequencing

summary: LX2 cells were used for BNC2 and H3K27ac ChIP-seq as well as for CoP-seq

overall_design: LX2 cells were cross-linked, chromatin was sonicated and used for chromatin immunoprecipitation or CoP (Column Purified chromatin) assays followed by high-throughput sequencing

first: Boulet

last: Clemence

last: Gerard


title: Sex differences in susceptibility to influenza A virus infection depend on host genotype

status: Public on Aug 13 2022

city: Burlington

first: SABIKUNNAHAR

last: SABIKUNNAHAR

state: Vermont

address: 318 Rowell, 106 Carrigan Dr

department: Biomedical and Health Sciences

institute: The University of Vermont

summary:
Using influenza A virus (IAV)  infection in a mouse model of  naturally selected genetic diversity, namely C57BL6/J (B6) mice carrying chromosomes (Chr) derived from the wild-derived and genetically divergent PWD/PhJ (PWD) mouse strain (B6.ChrPWD consomic mice), we examined the effects of genotype and sex on severity of IAV-induced disease
To determine the role of genetic variation of host during IAV infection on gene expression, we performed RNAseq analysis on whole lung RNA isolated from two different mice.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for male and female B6 and B6.ChrX.3PWD mice on on day 6 post-infection with IAV

Please note that each processed file contains mouse genotype comparison within each sex with the normalized count values for all samples (instead of only 8 samples that were being compared).

first: Bristy

last: Sabikunnahar

first: Karolyn

middle: G

last: Lahue

first: Loredana

last: Asarian

first: Qian

last: Fang

first: Mahalia

middle: M

last: McGill

first: Laura

last: Haynes

first: Cory

last: Teuscher

first: Dimitry

middle: N

last: Krementsov


title: Transcriptome profiling of TNFa-stimulated urothelial cells

city: Ljubljana

first: Tadeja

last: Kuret

state: Slovenia

address: Vrazov trg 2

department: Faculty of Medicine

country: Slovenia

institute: University of Ljubljana

summary: In this study, we aimed to determine the overall effect of TNFα on transcriptomic profile of urothelial cells using RNA sequencing. Our study represents a reference database that could lead to a better understanding of the role of urothelial cells in IC/BPS pathology and more importantly, sets grounds for future studies exploring potential biomarkers and therapeutic targets for IC/PBS diagnosis and treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RT4 urothelial cancer cells (untreated vs TNFa-treated, three independent experiments).

first: Dominika

last: Peskar

first: Mateja

middle: E

last: Kreft

first: Andreja

last: Erman

first: Peter

last: Veranič


title: Gene expression of CD4+CD8+ Tfh cells in lesions of IgG4-related disease and CD4+CD8+ Tfh in tonsil.

status: Public on Aug 10 2022

city: Sapporo

first: Ippei

last: Ikegami

state: Hokkaido

address: S1 W17, Chuo-ku

department: Department of Human Immunology

country: Japan

institute: Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine

summary: To further know features of CD4+CD8+ Double positive (DP)-Tfh cells in respective lymphoid tissues, we subsequently investigated transcriptomes of DP-Tfh cells in submandibular gland lesions of IgG4-RD in comparison to those of DP-Tfh cells in tonsils. Results showed that DP-Tfh cells of IgG4-RD lesions were more apt to present CTL-related genes such as Eomes and granzymes than DP-Tfh cells in tonsils. It was also noted that the level of CD70 in DP-Tfh cells of IgG4-RD lesions was higher than that of tonsillar DP-Tfh cells. Genes related to Tfh cell function were seemed to be presented in DP-Tfh cells of tonsils compared to DP-Tfh cells of IgG4-RD lesions.

overall_design: T follicular helper (Tfh) cells shape humoral immunity by helping B cell responses at initial and recall phases. Recent studies indicate a possible involvement of Tfh cells in the process of chronic inflammation; however, the functional role of Tfh cells in persistent immune settings still unclear. Here we report a unique capacity of CD4+CD8+ (double positive, DP: CD3+CD4+CD8+PD-1hiCXCR5hi) Tfh cells, which abundantly resided in the fibroinflammatory lesions of IgG4-related disease (IgG4-RD). According to transcriptome analyses, DP-Tfh cells in the lesions of IgG4-RD preferentially expressed the signature genes identifying cytotoxic CD8+ T cells. These findings may illustrate a potential feedback loop for immune tolerance operated by such Tfh cell species in chronic inflammatory conditions.

first: Kosuke

last: Murayama

first: Shingo

last: Ichimiya


title: Transcriptomic analysis of the livers of Bnc2 heterozygous or wild-type mice fed with a pro-fibrogenic NASH diet

first: Jérôme

last: Eeckhoute

summary: The Ayu21-18 mouse line (B6;CBA-Bnc2Gt(pU21)18Imeg/Orl; Infrafrontier EM-05043) was used to generate mice with heterozygous inactivation of Bnc2,which were compared to their wild-type (WT) littermates. Mice were fed a pro-fibrogenic NASH diet for 7.5 weeks and livers were used used to prepare RNA.

overall_design: Adult male mice were fed with a CDAA-HFSC diet consisting of ad libitum feeding with a choline-deficient, L-amino acid-defined (CDAA) diet supplemented with 35% sucrose, 21% fat and 2% cholesterol. Control mice were fed with a chow diet containing 12% sucrose and 7% fat (Ssniff, custom diets). Livers were used to prepare RNA which was then processed for analysis using MoGene-2_0-st Affymetrix microarrays according to standard procedures.

first: Marie

last: Bobowski-Gerard

first: Celine

last: Gheeraert

first: Jerome


title: Toosendanin suppresses African swine fever virus replication through upregulating IRF1 in porcine alveolar macrophage cultures

status: Public on Aug 08 2022

city: Guangzhou

first: Xinheng

last: Zhang

address: No.483, Wushan Road, Tianhe District

country: China

institute: South China Agricultural University

summary: African swine fever virus (ASFV) is a highly infectious and lethal swine pathogen that causes severe socio-economic consequences in affected countries. Unfortunately, effective vaccine for combating ASF is unavailable so far, and the prevention and control strategies for ASFV are still very limited. Toosendanin (TSN), a triterpenoid saponin extracted from the medicinal herb Melia toosendan Sieb. Et Zucc, has been demonstrated to possess analgesic, anti-inflammatory, anti-botulism and anti-microbial activities, and was used clinically as an anthelmintic, while the antiviral effect of TSN on ASFV has not been reported. In this study, we revealed that TSN exhibited a potent inhibitory effect on ASFV GD955-38 strain in porcine alveolar macrophages (PAMs) (EC50=0.085 μM, SI = 365) in a dose-dependent manner. TSN showed robust antiviral activity in different doses of ASFV infection and reduced the transcription and translation levels of ASFV p30 protein, viral genomic DNA quantity as well as viral titer at 24 and 48 hours post-infection. In addition, TSN did not affect virion attachment and release but intervened in its internalization in PAMs. Further investigations disclosed that TSN played its antiviral role by upregulating the host IFN-stimulated gene (ISG) IRF1 rather than by directly inactivating the virus particles. Overall, our results suggest that TSN is an effective antiviral agent against ASFV replication in vitro and may have the potential for clinical use.

overall_design: Effects of TSN on the mRNA Expression Level of Host Genes in PAMs by RNA Sequencing

first: Yuanjia

last: Liu

first: Zexin

first: Li

last: Huang


title: Anti YTHDF1 and YTHDF2 RIP-seq to identify target mRNAs in mouse cortex and retina

city: Shenzhen

first: Fugui

last: Niu

state: Guangdong

address: 1088 Xueyuan Avenue

department: Biology

institute: Southern University of Science and Technology

summary: To identify the target mRNAs of the m6A reader proteins YTHDF1 and YTHDF2, we carried out anti-YTHDF1 and anti-YTHDF2 RNA Immunoprecipitation (RIP) followed by RNA-sequencing. Using EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from E12.5 wild-type mouse cortices and P0 wild-type mouse retinas was pulled down by rabbit polyclonal anti-YTHDF1 (proteintech) and rabbit polyclonal anti-YTHDF2 (proteintech), and then sequenced on Illumina HiSeq3000 platform. The filtered reads were mapped to the mouse reference genome (GRCm38) using STAR v2.5 with default parameters. The resulting bam files were fed to the HTSeq tool to count the number of RNA-seq reads, which was further normalized to calculate FPKM. To determine which gene is enriched, we computed the FPKM from RIP elute to input, and any fold change greater than 2 was considered enriched.   From the embryonic cortex, we identified 986 and 1860 mRNAs by anti-YTHDF1 and anti-YTHDF2 RIP-seq, respectively. Anti-YTHDF1 and anti-YTHDF2 RIP-seq in mouse retina identified 2969 and 1638 mRNAs, respectively. This study provides the gene lists which show mRNAs binding with YTHDF1 and YTHDF2 in the mouse cortex and retina.

overall_design: 2 replicates, each containing input and IP samples

first: Sheng-Jian

last: Ji

first: Lixin

last: Yang


title: Transcriptomic analysis of BNC2 regulated genes in mouse EMS404 cells

summary: Mouse myofibroblastic EMS404 cells were transfected using a siRNA directed against BNC2 (siBNC2) or a control siRNA (siCTRL) and RNA were processed for microarray analyses.

overall_design: Transfection of siRNA (used at 20 nM) into EMS404 cells was performed using lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA). siBNC2 (Cat# 4390771 s109765) and Silencer select negative control (Thermo Fisher Scientific Cat# 4390844) were used. 48h after transfection,  RNA was purified and processed for analysis using Affymetrix GeneChip arrays (MoGene2.0st) according to standard procedures.


title: Confined Migration Induces Heterochromatin Formation and Alters Chromatin Accessibility

city: Ithaca

first: Chieh-Ren

last: Hsia

state: New York (NY)

address: 526 Campus Road

department: Molecular Biology and Genetics

institute: Cornell University

summary: We show that confined migration results in predominantly decreased chromatin accessibility, consistent with the increased heterochromatin marks staining. A small fraction of ATAC-seq peaks shows increased accessibility at gene promoters of diverse pathways, such as chromatin silencing, tumor invasion, and DNA damage response; whereas the majority shows decreased accessibility at intergenic regions near centromeres or telomeres, suggesting possible heterochromatin spreading.

overall_design: ATAC-seq of HT1080 cells migrating in high (1.7 mg/mL), medium (1.0 mg/mL) and low (0.3 mg/mL) concentration rat tail type-I collagen matrices for 48 hours

first: Julius

last: Judd


title: RNA-Seq analysis in human trophoblast stem cells (CT27) upon depletion of Hippo signaling Component TAZ (WWTR1)

city: Kansas City

first: Soumen

last: Paul

state: KS

address: Hemenway Building 3901 Rainbow Boulevard

department: Department of Pathology & Laboratory Medicine

institute: University of Kansas Medical Center

summary: The hippo signaling cofactor TAZ (Also known as WWTR1) regulates expression of genes upon interaction with TEAD transcription factors. Among the TEAD transcription factors, TEAD4 is implicated in regulation of the self-renewal process of human trophoblast stem cells. However, we have a poor understanding about the contribution of TAZ, a co-factor of TEAD4, in that process. Thus, the goal of this study is to define the importance of TAZ in orchestrating global gene expression program in human trophoblast stem cells. Using a RNA interference strategy (RNAi), we depleted TAZ expression in human trophoblast stem cells and compared global gene expression patterns via RNA sequencing (RNA-seq).   Three individual experiments were performed. The submitted files contain the data (raw fastq files, count data and deseq2 output) from  those experiments.

overall_design: TAZ expression was depleted in CT27 human TSC lines via RNA interference using  shRNA. Global gene expressions were monitored by culturing control and TAZ-depleted cells in stem state culture condition.

first: Rajnish

last: Kumar


title: Interleukin-1 contributes to clonal expansion and progression of bone marrow fibrosis in JAK2V617F-induced myeloproliferative neoplasm

city: Charlottesville

first: Golam

last: Mohi

state: Virginia

address: 1340 Jefferson Park Ave

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: The somatic JAK2V617F mutation is found in a majority of patients with myeloproliferative neoplasms (MPN). Chronic inflammation is often associated with MPN, but the role of inflammation in the pathogenesis of MPN remains elusive. Expression of interleukin-1 (IL-1), a key regulator of inflammation, is found elevated in MPN. Here, we show that increased IL-1β enhances myeloid cell expansion and promotes the development of bone marrow (BM) fibrosis in heterozygous Jak2V617F mouse model of MPN. Genetic deletion of IL-1 receptor 1 (IL-1R1) preferentially inhibited the expansion of Jak2 mutant hematopoietic stem/progenitor cells. Furthermore, IL-1R1 deletion or blockade with anti-IL-1R1 antibody significantly reduced leukocytosis and splenomegaly, and markedly inhibited BM fibrosis in homozygous Jak2V617F mutant mice. Collectively, our results suggest that IL-1 signaling plays an important role in progression to BM fibrosis in MPN, and targeting of IL-1R1 could be a useful strategy for the treatment of myelofibrosis.

overall_design: RNA-sequencing on sorted LSK and LK cells from heterozygous Jak2V617F knock-in mice treated with vehicle (PBS) and IL-1β. RNA-seq analysis on bone marrow (BM) mesenchymal stromal cells (MSC) stimulated with vehicle (PBS) and IL-1β.

first: Mohammad Ferdous-Ur

last: Rahman

first: Yue

first: Bao

middle: T

last: Le


title: Role of human fetal membranes in xenobiotic metabolism and nutrient transport

city: Manila

first: Ryan

last: Lintao

address: 547 Pedro Gil Street

department: College of Medicine

country: Philippines

institute: University of the Philippines Manila

summary:
This study characterized CYP450 and nutrient transport expression in human fetal membranes.
RNA sequencing (RNA-Seq) of RNA derived from human placental and fetal membrane tissues and cells was done.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human placental and fetal membrane tissues and cells from term not in labor women

first: Ananth

middle: K

last: Kammala

first: Kamil

last: Khanipov

first: George

last: Golovko

first: Ramkumar

last: Menon


title: Midkine expression by stem-like tumor cells drives persistence to mTOR inhibition and rewires the microenvironment toward an immune-suppressive state

city: Boston

first: Yan

last: Tang

address: 20 Shattuck street

institute: Brigham and Women's Hospital

summary: mTORC1 regulates cell metabolism to enable cell proliferation, and is hyperactive in multiple cancer types1,2. Here, we performed integrative analysis of single cell transcriptomic profiling, paired T cell receptor (TCR) sequencing, and spatial transcriptomic profiling on Tuberous Sclerosis Complex (TSC) associated tumors with mTORC1 hyperactivity, and identified a stem-like tumor cell state (SLS) linked to T cell dysfunction via tumor-modulated immunosuppressive macrophages. Rapamycin and its derivatives (rapalogs) are the primary treatments for TSC tumors, and the stem-like tumor cells showed rapamycin resistance in vitro, reminiscent of the cytostatic effects of these drugs in patients. The pro-angiogenic factor midkine (MDK) was highly expressed by the SLS population, and associated with enrichment of endothelial cells in SLS-dominant samples. Inhibition of MDK showed synergistic benefit with rapamycin in reducing the growth of TSC cell lines in vitro and in vivo. In aggregate, this study suggests an autocrine rapamycin resistance mechanism and a paracrine tumor survival mechanism via immune suppression adopted by the stem-like state tumor cells with mTORC1 hyperactivity. We also provide a comprehensive resource to advance the understanding of TSC and potentially other mTORC1-hyperactive tumors.

overall_design: scRNA-seq data of 5 AML tumors, 4 matched adjacent normal kidneys, and 4 LAM specimen

first: David

middle: J

last: Kwiatkowski

first: Elizabeth

middle: P

last: Henske


title: A Notch-dependent transcriptional mechanism controls expression of temporal patterning factors in Drosophila medulla

city: Urbana

first: Xin

last: Li

state: IL

address: 601 S. Goodwin Avenue, B107 CLSL

department: CDB

institute: University of Illinois Urbana-Champaign

summary: In this work, we show that the expression of one temporal transcription factor(TTF), Sloppy-paired (Slp),  in the Drosophila medulla TTF cascade, is regulated directly by two other TTFs and the Notch signaling pathway. We show that the previous TTF, Eyeless, another TTF Scro and Su(H)/NICD regulate the transcription of Slp through binding to two cis-regulatory elements in the slp locus. Slp expression is delayed when Notch signaling is lost or when cell cycle progression is blocked, which also cause loss of Notch signaling. Furthermore, we show that supplying Notch signaling can rescue the delayed Slp expression in cell-cycle arrested neuroblasts. Thus our work demonstrates that Notch signaling cooperates with TTFs to promote the progression of the TTF transcriptional cascade.

overall_design: Dam-ID sequencing to profile the binding sites of Su(H) and Ey

first: Alokananda

last: Ray


title: Midkine expression by stem-like tumor cells drives persistence to mTOR inhibition and rewires the microenvironment toward an immune-suppressive state [scTCR-seq, spatial transcriptomics]

summary: mTORC1 regulates cell metabolism to enable cell proliferation, and is hyperactive in multiple cancer types. Here, we performed integrative analysis of single cell transcriptomic profiling, paired T cell receptor (TCR) sequencing, and spatial transcriptomic profiling on Tuberous Sclerosis Complex (TSC) associated tumors with mTORC1 hyperactivity, and identified a stem-like tumor cell state (SLS) linked to T cell dysfunction via tumor-modulated immunosuppressive macrophages. Rapamycin and its derivatives (rapalogs) are the primary treatments for TSC tumors, and the stem-like tumor cells showed rapamycin resistance in vitro, reminiscent of the cytostatic effects of these drugs in patients. The pro-angiogenic factor midkine (MDK) was highly expressed by the SLS population, and associated with enrichment of endothelial cells in SLS-dominant samples. Inhibition of MDK showed synergistic benefit with rapamycin in reducing the growth of TSC cell lines in vitro and in vivo. In aggregate, this study suggests an autocrine rapamycin resistance mechanism and a paracrine tumor survival mechanism via immune suppression adopted by the stem-like state tumor cells with mTORC1 hyperactivity. We also provide a comprehensive resource to advance the understanding of TSC and potentially other mTORC1-hyperactive tumors.

overall_design: scTCR-seq data of 4 AML tumors, spatial transcriptomics


title: Custom Nanostring nCounter Pig (Sus scrofa) Cognitive Development Panel

city: Palmerston North

first: Ankita

last: Jena

state: MANAWATU-WANGANUI

address: Massey University Manawatu (Turitea), Tennent Drive

country: New Zealand

institute: Riddet institute, Massey university

summary: The objective of this study was to determine whether different milk treatments affected the genes related to cognitive function in the piglet's brain

overall_design: Brain samples from three regions (hippocampus, striatum and prefrontal cortex) from 24 piglets that were fed with three different types of milk (8 piglets per milk treatment) were analysed for expression of 77 genes related with brain cellular process (synaptogenesis, myelination, neurotrophins, and synaptic vesicle cycle), neurotransmission (neurotransmitter receptor, transporter, and enzymes involved in neurotransmitter synthesis). M1 - Bovine, M2 - Caprine, M3 - Ovine.


title: DNA methylation profiling of Arboleda-Tham syndrome in primary human fibroblasts

status: Public on Aug 04 2022

city: Los Angeles

first: Valerie

last: Arboleda

address: 615 Charles E. Young Drive South

department: Department of Pathology and Laboratory Medicine

institute: UCLA

type: Methylation profiling by genome tiling array

summary: Arboleda-Tham Syndrome is a rare disease caused by de novo mutations in the KAT6A gene. Epigenetic changes to the genome resulting from pathogenic mutations were investigated by DNAme profiling.

overall_design: Genome wide DNA methylation profiling of fibroblast cell cultures from skin punch biopsies of control and arboleda-tham syndrome affected individuals. The Illumina MethylationEPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs. Samples include 12 unique healthy controls and 8 unique affected individuals and 5 replicated samples.


title: Gene expression profiling of adipocyte and stromal vascular cells from adipose tissue in lean, obese and formerly obese mice

first: Olivia

last: Osborn

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

summary: To investigate the transcriptional profiles of adipocytes and stromal vascular cells from mouse visceral adipose tissue(vWAT) in lean (Low fat diet, LFD fed), obese (high fat diet, HFD fed) and formerly obese (diet switch (SW) from 9 weeks HFD, to 3 weeks LFD) to induce weight loss.

overall_design: Male wild type C57BL/6J mice (Jackson Laboratories) were group housed in standard cages and fed either a 10% (LFD, D12450, Research Diets, New Brunswick, NJ) or 60% fat diet (HFD, D12492) from 9-10 weeks of age. After 9 weeks of HFD feeding, half of the HFD-fed mice where switched to the LFD (SWD) for 3 weeks to induce ~10% weight loss which is sufficient to normalize glucose tolerance and insulin sensitivity to equivalent levels in observed in lean, normal chow fed mice

first: Rizaldy

last: Zapata


title: Molecular and pathological subtypes related to prostate cancer disparities and disease outcomes in African American and European American patients

city: Tuskegee

first: Honghe

last: Wang

state: AL

address: 1200 W Montgomery Rd

institute: Tuskegee Universitry

summary:
To investigate genetic and molecular differences that may exist between prostate cancers of African American and European American origin.
Gene expression profile analysis was performed comparing RNA seq data of African American prostate cancer cell lines (inhouse) and European American prostate cancer cell lines (public repository)

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for African American cell lines (RC77T, RC43T, and RC165T [inhouse], and MDA Pca 2b [public repository]) and European American cell lines (LNCaP, VCaP, and RWPE-2)

Please note that the MDA PCa2b, LNCaP, VCaP, and RWPE-2 data sets are already available to the public:
SRR8615579: MDA PCa 2b, LNCaP, and VCaP
SRR10575173: RWPE-2


title: Analysis of a neuroblastoma cell line transcriptome by polyA+ RNA sequencing under silencing of RNA helicases DDX5 and DDX17

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

summary:
DEAD-box RNA helicases DDX5 and DDX17 regulate gene expression at different levels such as transcription and splicing, but the underlying mechanisms are not fully understood. A transcriptome analysis of DDX5/DDX17-depleted human cells confirmed was carried out to further characterize the widespread deregulation of alternative splicing. This study also revealed a deregulation of 3’ end processing leading to transcriptional read-through.
Univ Lyon, ENS de Lyon, CNRS UMR 5239, INSERM U1293, Laboratory of Biology and Modelling of the Cell, 46 Allée d'Italie, F-69007, Lyon, France.
Corresponding author: cyril.bourgeois@inserm.fr

overall_design: mRNA profiles of DDX5/17-depleted neuroblastoma cell line were generated by sequencing, in triplicate

first: Cyril

last: BOURGEOIS

first: Sophie

last: TERRONE

first: Jessica

last: VALAT

last: POLVECHE


title: Microglial aryl hydrocarbon receptor enhances phagocytic function and promotes remyelination in a model of multiple sclerosis

status: Public on Aug 03 2022

city: shanghai

first: yumeng

last: wang

address: dongan road 130

institute: Fudan University

summary: We employed a cuprizone-induced demyelinating model to identify the role of AhR in remyelination with microglial AhR-deficient mice and wild type mice. RNA-seq was performed to compare gene transcriptional profile in wild type mice and microglial AhR-deficient mice of cuprizone model to gain insight into the effects of AhR on microglia function.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the corpus callosum of wild type mice and microglial AhR-deficient mice in cuprizone model

first: Yumeng

first: Jingxian

last: Sun

first: Jun

first: Yanqing


title: Inhibiting tumor cell-intrinsic UBA6 by inosine augments tumor immunogenicity

city: Shanghai

first: LEI

last: ZHANG

address: No. 650 Songjiang Road

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine,

summary: Metabolic alteration influences cancer immunity. However, the role and mechanism of metabolic adaption on immune checkpoint blockade (ICB) responses remains ill-defined. Here, metabolomic profiling in mouse tumor models and cancer patients treated with ICB was performed. We found that metabolite inosine was associated with ICB sensitivity in mice and humans, and overcame ICB resistance in several mouse tumor models. Notably, inosine sensitized tumor cells to T cell-mediated cytotoxicity by amplifying tumor-intrinsic immunogenicity. Chemical proteomics further identified that inosine directly bound and inhibited ubiquitin-activating enzyme UBA6. Tumor intrinsic UBA6 loss augmented tumor immunogenicity and substituted the synergistic effect of inosine in combination with ICB. Clinically, tumor UBA6 expression negatively correlated with ICB response in cancer patients. Thus, we reveal an unappreciated function of inosine on tumor-intrinsic immunogenicity and UBA6 as a candidate target for immunotherapy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wildtype and UBA6 knockout 4T1 breast cancer cells.

first: Lei

last: Zhang

first: Li

last: Jiang

first: Liang

last: Yu

first: Baokun

last: He


title: Methamphetamine induces transcriptional changes in cultured HIV-infected mature monocytes that may contribute to HIV neuropathogenesis

city: Bronx

first: Joan

middle: W

last: Berman

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: We performed RNA sequencing to characterize the effects of methamphetamine on HIV-infected mature monocytes. In vitro cultured HIV-infected mature (CD14+ CD16+) monocytes were treated with and without methamphetamine for 6h. RNA was extracted, sequenced, and analyzed for differential gene expression.

overall_design: We compared gene expression profiles between in vitro cultured HIV infected mature monocytes  treated with or without methamphetamine for 6 hours (n=3 independent biological samples).

first: Vanessa

last: Chilunda

last: Weiselberg

first: Samuel

last: Martinez-Meza

first: Lwidiko

last: Mhamilawa

first: Laura

last: Cheney


title: Nucleotide Excision Repair Removes Thymidine Analog 5-Ethynyl-2’-deoxyuridine From the Human Genome

status: Public on Aug 02 2022

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

summary: 5-Ethynyl-2’-deoxyuridine (EdU) is one of the several thymidine analogs that are used in labeling DNA in cells and in DNA combing (DNA fiber analysis) to study DNA replication1-5. We wished to use these analogs to investigate the repair complex (DNA-protein) of nucleotide excision repair. UV irradiated human cell lines were incubated with EdU, BrdU, IdU, CldU, F-ara-EdU or AmdU to incorporate these analogs into the 26-27 nucleotide long excision repair products. Unexpectedly, we found that EdU even in the absence of DNA damage was released in the form of 26-27nt-long oligomers. We conclude that EdU is incorporated into replicating DNA and is recognized as damage by the nucleotide excision repair system and removed from the genome followed by repair synthesis and re-incorporation into DNA, thus creating futile cycle that leads to cell death. This property of EdU, which was not seen with any of the other thymidine analogs, may be taken advantage of in treating cancer, in particular brain cancers because EdU crosses blood-brain barrier.

overall_design: XR-seq experiment was done as previously reported  with modifications. In brief, Hela cells were treated with 10 μM EdU and harvested after 6h, 12h and 24h. Cell pellets from two 150 mm culture plates were suspended and lysed in 1mL cold buffer A ((25 mM HEPES at pH7.9, 100 mM KCl, 12 mM MgCl2, 0.5 mM EDTA, 2 mM DTT, 12.5% glycerol, 0.5% NP-40). The primary EdU excision products were isolated by immunoprecipitation with TFIIH antibody followed by ligation of 5′ and 3′ adapters. After adaptor ligation, excision oligomers containing EdU were further purified by immunoprecipitation with anti-BrdU antibody that also reacts with EdU. Purified EdU excision oligomers were directly subjected to PCR amplification using 50- and 63-nt-long primers that introduce specific barcodes compatible with the Illumina TruSeq small RNA kit, without damage reversal step as this is done with CPD or (6-4)PP photoproducts. The PCR products containing excised oligonucleotides were ∼145 base pairs (bp) in length and resolved on 10% sequencing gel. EdU excision oligomers from different time point were gel purified, pooled and sequenced on the NextSeq-P3 platform at the University of North Carolina–Chapel Hill High-Throughput Sequencing Facility.

last: Wang

first: Xuemei

last: Cao

first: Consu

last: Kose

first: Hiroaki

last: Kawara

last: Lindsey-Boltz

first: Christopher

last: Selby

first: Aziz

last: Sancar


title: Age dependent gene and transposon expression in male wildtype (wDAH) and FOXO deletion (wDAH ∆94) fly strains.

status: Public on Aug 01 2022

city: Waltham

first: Michael

middle: Thomas

last: Marr

state: Massachusetts

address: 415 South street

institute: Brandeis University

summary: Transposable elements (TE) are mobile sequences of DNA that can become transcriptionally active as an animal ages. Activation of the stress response transcription factor FOXO can increase longevity in flies and worms. Research into the subject has centered on metabolism as the driver of aging. Whether TE activity is a byproduct of heterochromatin breakdown or can contribute towards the aging process is not known. Neither is the potential effect of FOXO on TE expression during aging. Here we examine dFOXO’s effect on TE expression during aging by using bulk RNAseq of whole male flies.

overall_design: Comparative gene expression analysis of RNA-seq data from male wildtype (wDAH) and dFOXO deletion (wDAH ∆94) whole flies at 5 days-old and 30 days-old. 3 biological replicates were analyzed per timepoint.

first: Joyce

last: Rigal


title: Molecular convergence between Down syndrome and Fragile X syndrome identified using human pluripotent stem cell models

first: VICTOR

last: BARRERA BURGOS

address: Landmark 401 Park Drive 3 East

department: Biostatistics

institute: Harvard School of Public Health

summary: The goal of this study was to define molecular overlap between Down syndrome and Fragile X syndrome using human pluripotent stem cells (hPSCs) and in vitro derived glutamatergic neurons.

overall_design: RNA-seq was performed in FMR1y/+ ad FMR1y/- hPSCs and neurons as well as trisomy 21 and euploid control iPSCs and neurons, each with 5 biological replicates.

first: Lindy

last: Barrett

first: Sara

last: Susco

first: Victor

last: Barrera


title: ScRNA-seq analysis and functional characterization of myeloid lincRNAs differentially expressed during COVID-19

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

country: Germany

institute: Philipps-Universität Marburg

summary: Myeloid cell differentiation and immune-activation is controlled by numerous regulators, keeping the activity of the immune system within tight physiological limits. The transcriptional circuitries governing human myeloid immunity during COVID-19, however, remain incompletely understood. Recently, long non-coding RNAs were found to play important roles in immune gene regulation. Here, we studied human myeloid lineage specific lncRNAs by bulk and single cell RNA-seq and identified PIRAT (a.k.a. LINC00211) as a nuclear regulator of human monocyte immunity during COVID-19. Loss- and gain-of-function studies using CRISPR/Cas9 and lentiviral transgene expression revealed PIRAT as a negative feedback regulator of PU.1 transcription factor activity, controlling the expression of the major alarmins S100A8 and A9. Both alarmins critically contribute to the immunopathologies observed in patients with severe COVID-19. Mechanistically, ChIRP-seq revealed PIRAT as a decoy RNA, fostering PU.1 binding to pseudogenes and inhibiting PU.1 binding to alarmin promoters. Down-regulation of PIRAT during COVID-19 thus releases a break on alarmin expression. Additionaly, we found the lncRNA LUCAT1 to promote alarmin expression during COVID-19, by promoting NFkB-target gene expression at the cost of the JAK/STAT pathway. Taken together, our data suggest that RNA-based gene expression control in the human myeloid immune cell lineage plays a critical role in human host defence against SARS-CoV-2 infection and in the development of severe COVID-19.

overall_design: Single cell RNA-seq analysis of control and COVID patient PBMCs was performed using a BD Rhapsdy system and a targeted immune- and lncRNA-panel. Furthermore, stranded mRNA-Seq analyis of different PIRAT knockout and overexpression cell lines and LUCAT1 deficient cells lines was performed. For over-expression studies, THP1 cells were transduced with an empty lentiviral (SparQ) backbone or an lncRNA expressing backbone. For loss-of-function analysis THP1 wild-type single cell clones or PIRAT promoter-deficient clones were raised using empty or guideRNA-containing pX458 CRISPR vector constructs. LUCAT1 deficient cells were generated using a lentiviral CRISPR-interference system. PIRAT ChIRP-seq analysis was performed using primary human blood-derived CD14+ monocytes.


title: Combined protein and transcript single cell RNA sequencing in human peripheral blood mononuclear cells

city: La Jolla

first: Vasantika

last: Suryawanshi

state: CALIFORNIA

address: 9420 Athena Circle

institute: La Jolla Institute of Immunology

summary: We utilized CITESeq to investigate changes in immune cell frequencies and their transcriptomic signatures in between PBMCs obtained from healthy women and matched subjects living with HIV or cardiovascular disease from the WIHS cardiovascular sub-study

overall_design: To show differences between healthy and matched individuals living with HIV with and without cardiovascular disease.

first: Klaus

last: Ley

first: Robert

last: Kaplan

first: Catherine

last: Hedrick

first: Lewis

middle: L

last: Lanier

first: Coleen

last: McNamara


title: Effect of deletion of Irf3, Irf7 or Irf9 on gene expression in sgScd2 Th1 cells.

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

institute: KAZUSA DNA Research Institute

summary:
To investigate the role of the IRF family in the regulation of interferon stimulated genes, we conducted CRISPR/Cas9 mediated genome editing of Irf3, Irf7 or Irf9 in sgScd2 Th1 cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq of control, sgScd2, sgScd2/sgIrf3, sgScd2/sgIrf7 or sgScd2/sgIrf9 Th1 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Th1 cells and its KO derivatives (sgScd2, sgScd2/sgIrf3, sgScd2/sgIrf7 and sgScd2/sgIrf9 Th1 cells).

first: Keisuke

last: Miyako

first: Takahiro

last: Nakajima

first: Satoru

last: Yokoyama

first: Shigemi

last: Sasamoto

first: Hikari

last: Asou

first: Osamu

last: Ohara

first: Toshinori

last: Nakayama

first: Yusuke

last: Endo


title: Investigation of genome wide binding profile of IRF9 in I-IFN treated or sgScd2 Th1 cells

summary: To investigate the role of IRF9 in the transcriptional regulation of interferon stimulated genes in sgScd2 Th1 cells, we assessed the genome-wide binding pattern of IRF9 by chromatin immunoprecipitation DNA-sequencing (ChIP-seq).

overall_design: Functions of IRF9, a family of interferon regulatory family, are assessed by ChIP-seq. To more accurately evaluate the IRF9 binding profiles, we prepared IRF9-deficient Th1 cells as a negative control.


title: Transcriptional Dynamics of Motor Neuron Maturation in vivo and in vitro

city: Piscataway

first: Tulsi

last: Patel

state: New Jersey

address: 683 Hoes Lane West

department: Neuroscience and Cell Biology

institute: Rutgers University

summary: Mouse spinal motor neurons are specified in the embryo on embrynic day 9.5 (E9.5), but motor function doesn't fully mature till the third week of postnatal life (P14-P21) and the degenerative disease Amyotrophic Lateral Sclerosis only affects motor neurons in adulthood (age of onset differs between models). In order to better understand motor neuron maturation, we have generated a temporal map of motor neuron transcriptional states at E10.5, E13.5, P4, P13, P21, P56, 2yr. In addition we have also profiled stem cell derived motor neurons that were co-cultured with astrocytes at DIV0, DIV7, DIV28.

overall_design: We performed RNA-seq and ATAC-seq on motor neurons or motor neuron nuclei at all in vivo and in vitro timepoints. In vivo mouse motor neurons were purified at E10.5 from HB9-GFP mice by dissociating and FACs sorting for GFP+ motor neuorns. At E13.5-2yr, motor neuron nuclei were purified from Chat-Cre;SUN1-gfp-myc mice. For in vitro experiments, embryonic stem cells were derived from Chat-Cre;SUN1-gfp-myc mice, differentiated into motor neurons and co-cultured with astrocytes. Nuclei were purified at DIV0 (before co-culture), DIV7, and DIV28. In addition, to understand the role of activity in controlling gene expression, motor neurons were co-cultured with astrocytes for 28 days in the presence of TTX.

first: Hynek

last: Wichterle


title: Integrative and comparative single-cell analysis reveals the transcriptomic difference between tumefactive demyelinating lesion and glioma

status: Public on Jul 28 2022

city: Fuzhou

first: Xiaoyong

last: Chen

address: Taijiang district

institute: The First Affiliated Hospital of Fujian Medical University

summary: Tumefactive demyelinating lesion (TDL) is an immune-mediated disease which could appear like glioma. Here, we perform integrative and comparative single-cell RNA sequencing (ScRNA-seq) transcriptomic analysis on TDL and glioma lesions.

overall_design: Integrative and comparative single-cell RNA sequencing (ScRNA-seq) transcriptomic analysis on Tumefactive demyelinating lesion and glioma lesions.

first: Xiao-Yong

first: Yue

first: De-Zhi

last: Kang

first: Chen-Yu

last: Ding


title: Developmentally informed large-scale production and cryopreservation of human induced pluripotent stem cell-derived microglia

status: Public on Aug 22 2022

city: Bonn

first: Harald

last: Neumann

address: Venusberg-Campus 1

institute: University Hospital of Bonn

summary:
Purpose: mRNA expression profiles of iPSC-derived microglia (iPSdMiG) generated with a new cutting-edge protocol were compared to human primary microglia and cortex samples, iPSC-derived microglia-like cells (iMGL), THP1 macrophages, and parental iPSCs.
Methods: Library preparation was performed using the Quantseq 3’mRNA-Seq kit (Lexogen, USA). Reads were generated on a HiSeq 2500 V4 sequencer (Illumina, USA) and quality as well as adapter trimming were performed using BBDuk from BBMap. Reads were aligned to hg38 with the ensemble gene annotation version 97 using STAR and read counts were generated using featureCounts ignoring multimapping reads. Unwanted variance due to differences in library preparation and sequencing were removed using RUVSeq and subsequent differential gene expression analysis was performed with DESeq2. Transcription factor enrichment analysis was performed with ChEA3 and co-expression analysis was performed using WGCNA.
Results: Overall, our iPSdMiG highly resemble human primary microglia. They have a similar expression of lineage-specific genes and cluster in close proximity in PCA. Our iPSdMiG and human primary microglia share key transcription factors driving cellular identity and co-express genes belonging to a immunity-related gene module.

overall_design: Examination of mRNA profiles of iPSC-derived microglia (iPSdMiG), parental iPSC lines and THP1 macrophages.  Third-party-reanalysis:  In silico comparison with human primary microglia and cortex samples from GSE99074 and iPSC-derived microglia-like cells (iMGL) from GSE89189.

first: Mona

last: Mathews

first: Jannis

last: Wißfeld

first: Lea

last: Flitsch

first: Anahita

last: Shahraz

first: Vesselina

last: Semkova

first: Yannik

last: Breitkreuz

first: Oliver

last: Brüstle


title: Analysis of the genome-wide distribution of RNA Pol II in a neuroblastoma cell line under silencing of RNA helicases DDX5 and DDX17

first: Hélène

last: Polvèche

summary:
DEAD-box RNA helicases DDX5 and DDX17 regulate gene expression at different levels such as transcription and splicing, but the underlying mechanisms are not fully understood. A calibrated ChIP-seq analysis of total RNA Polymerase II was carried out in DDX5/DDX17-depleted SH-SY5Y cells to analyse the contribution of DDX5/DDX17 to RNAPII distribution.
Univ Lyon, ENS de Lyon, CNRS UMR 5239, INSERM U1293, Laboratory of Biology and Modelling of the Cell, 46 Allée d'Italie, F-69007, Lyon, France.
Corresponding author: cyril.bourgeois@inserm.fr

overall_design: For each of the 3 replicates of calibrated RNAPII ChIP-seq, we pooled 4 independent IP, each of them performed on 40 µg of chromatin supplemented with 32 ng of Drosophila spike-in chromatin (Active Motif #53083), with 4 µg of mouse anti-Pol II F-12 antibody (F-12, sc55492, Santa Cruz) and 2 µg of spike-in antibody (Active Motif #61686).

first: Jessica

last: VALAT

last: POLVECHE

first: Cyril

last: BOURGEOIS


title: Circ_0047339 promotes the activation of fibroblasts and affects the development of urethral stricture by targeting the miR-4691-5p/TSP-1 axis

status: Public on Jul 30 2022

city: Changsha

first: Bin

last: Ye

address: Renmin Middle Road

institute: Second Xiangya Hospital, Central South University

summary:
Background: Urethral stricture is related to scar tissue fibrosis, but its pathogenesis is still unclear. This study aims to explore the mechanism of circular RNA (circRNA) in the occurrence and development of urethral stricture.

Methods: CircRNA microarray was employed to analyze circRNA expression profiles between human urethral scar tissue and normal urethral tissue. The first nine circRNA differentially expressed were selected for RT-qPCR detection. Urethral scar fibroblasts were isolated from human urethral scar tissue and cultured in vitro. The cells were transfected with si-circ_0047339, LV-circ_0047339, and miR-4691-5p mimic and their corresponding negative controls. Related gene and protein expression was measured by RT-qPCR, Western Blot and immunofluorescence staining, and the cell function was detected by CCK-8 and EDU assay. The targeting relationship between miR-4691-5p and circ_0047339 or TSP-1 was analyzed by dual-luciferase reporter assay.

Results: The results of circRNA microarray showed that there were 268 differential genes between urethral scar tissue and normal urethral tissue (circRNA expression difference multiple ≥2 and p value≤0.05). The enrichment analysis of KEGG (Kyoto encyclopedia of genes and genomes) showed that these circRNAs were significantly correlated with ECM-receptor interaction. The first nine differentially expressed circRNA were selected to predict the circRNA-miRNA network. RT-qPCR results showed that circ_0047339 was upregulated considerably in urethral scar tissue. After silencing circ_0047339, the proliferation of urethral scar cells decreased significantly, and the expression of collagen 1 (COL-1) and α-smooth muscle actin (α-SMA) also reduced. Circ_0047339 as a competing endogenous RNA (ceRNA) could increase the expression of TSP-1 by competitively binding miR-4691-5p. In addition, miR-4691-5p mimic transfection could inhibit the proliferation of urethral scar fibroblasts and the presentation of thrombospondin-1 (TSP-1), α-SMA and COL-1, while circ_0047339 overexpression eliminated this inhibition.

Conclusion: Our results showed that the dysfunctional circ_0047339 might promote the growth and fibrosis of urethral scar fibroblasts through the ceRNA mechanism, thus promoting the development of urethral stricture via miR-4691-5p/TSP-1 axis.

first: Ke

first: Daoyuan

last: Li

first: Rui

last: Zhang

first: Meilin

last: Zuo


title: Expression data from the hippocampus of epileptic mice carrying two different pathogenic de novo mutations in the hyperpolarization-activated, cyclic nucleotide-gated, non-selective cation channel gene Hcn1 in comparison to wildtype controls

city: Cologne

first: Andrea

last: Merseburg

state: North Rhine-Westphalia

address: Kerpener Str. 62

department: Institute for Molecular and Behavioral Neuroscience

institute: German Center for Neurodegenerative Diseases (DZNE), Bonn, and University of Cologne, Cologne, Germany

summary:
Expression data from the hippocampus of epileptic mice carrying two different pathogenic de novo mutations in the hyperpolarization-activated, cyclic nucleotide-gated, non-selective cation channel gene Hcn1 (p.G391D in human corresponding to G380D in mouse; p.M153I in human corresponding to M142I in mice) in comparison to wildtype controls.

De novo mutations in voltage- and ligand-gated channels have been associated with an increasing number of cases of developmental and epileptic encephalopathies, which often fail to respond to classic antiseizure medications. Here, we examine two knock-in mouse models replicating de novo mutations in the HCN1 voltage-gated channel gene, p.G391D and p.M153I (Hcn1G380D/+ and Hcn1M142I/+ in mouse), associated with severe drug-resistant neonatal- and childhood-onset epilepsy, respectively. Heterozygous mice from both lines displayed spontaneous generalized tonic-clonic seizures. Animals replicating the p.G391D variant had an overall more severe phenotype, with pronounced alterations in the levels and distribution of HCN1 protein, including disrupted targeting to the axon terminals of basket cell interneurons. In line with clinical reports from patients with pathogenic HCN1 sequence variations, administration of the antiepileptic Na+ channel antagonists lamotrigine and phenytoin resulted in the paradoxical induction of seizures in both mouse lines, consistent with an effect to further impair inhibitory neuron function. We also show that these variants can render HCN1 channels unresponsive to classic antagonists, indicating the need to screen mutated channels to identify novel compounds with diverse mechanism of action. Our results underscore the need to tailor effective therapies for specific channel gene variants, and how strongly validated animal models may provide an invaluable tool towards reaching this objective.
This dataset contains a comparison of the gene expression profile of the hippocampus of epileptic mice carrying either the pathogenic G380D (GD) variant (Hcn1GD/+ mice), or the M142I (MI) variant (Hcn1MI/+ mice) in Hcn1 in comparison to wildtype (WT) controls (Hcn1+/+ mice).

overall_design: Four WT controls, four heterozygous mutant Hcn1GD/+ males, and four heterozygous mutant Hcn1MI/+ male mice of the same age were selected for RNA extraction from both hippocampi and hybridization on Clariom™ S Mouse arrays.

first: Bina

last: Santoro

first: Dirk

last: Isbrandt

first: Malte

last: Stockebrand


title: Single cell atlas of spinal cord injury in mice reveals a pro-regenerative signature in spinocerebellar neurons

city: Bethesda

first: Kaya

last: Matson

state: MD

address: 35 Convent Drive

department: NINDS

institute: NIH

summary: After spinal cord injury, tissue distal to the lesion contains undamaged cells that could support or augment recovery. Targeting these cells requires a clearer understanding of their injury responses and capacity for repair. Here, we use single nucleus RNA sequencing to profile how each cell type in the lumbar spinal cord changes after a thoracic injury in mice. We present an atlas of these dynamic responses across dozens of cell types in the acute, subacute, and chronically injured spinal cord. Using this resource, we find rare spinal neurons that express a signature of regeneration in response to injury, including a major population that represent spinocerebellar projection neurons. We characterize these cells anatomically and observed axonal sparing, outgrowth, and remodeling in the spinal cord and cerebellum. Together, this work provides a key resource for studying cellular responses to injury and uncovers the spontaneous plasticity of spinocerebellar neurons, uncovering a potential candidate for targeted therapy.

overall_design: 5 conditions (uninjured, 1 day post injury, 1 week post injury, 3 weeks post injury and 6 weeks post injury) with 3 biological replicates each, totaling 15 lumbar spinal cords that were taken through snRNAseq and downstream analysis.

first: Daniel

last: Russ

first: Claudia

last: Kathe

first: Isabelle

last: Hua

first: Dragan

last: Maric

first: Yi

last: Ding

first: Jonathan

last: Krynitsky

first: Randall

last: Pursley

first: Anupama

last: Sathyamurthy

first: Jordan

last: Squair

first: Boaz

last: Levi

first: Gregoire

last: Courtine

first: Ariel

last: Levine


title: The Plasmodium falciparum Nuclear Protein Phosphatase NIF4 is Required for Efficient Merozoite Invasion and Regulates Artemisinin Sensitivity

status: Public on Jul 27 2022

city: Shenyang

first: Xiaotong

last: Zhu

state: Liaoning

address: No. 77 Puhe Road Shenyang North NEW AREA

department: Department of Immunology

institute: China Medical University

summary: Artemisinin resistance in Plasmodium falciparum has been associated with a mutation in the NLI-interacting factor-like phosphatase PfNIF4, in addition to the mutations in the Kelch13 protein as the major determinant. We found that PfNIF4 was predominantly expressed at the schizont stage and localized in the nuclei of the parasite. To elucidate the functions of PfNIF4 in P. falciparum, we performed PfNIF4 knockdown (KD) using the inducible ribozyme system. PfNIF4 KD attenuated merozoite invasion and affected gametocytogenesis. PfNIF4 KD parasites also showed significantly increased in vitro susceptibility to artemisinins. Transcriptomic and proteomic analysis revealed that PfNIF4 KD led to the down-regulation of gene categories involved in invasion and artemisinin resistance (e.g., mitochondrial function, membrane, and Kelch13 interactome) at the trophozoite and/or schizont stage. Consistent with PfNIF4 being a protein phosphatase, PfNIF4 KD resulted in an overall up-regulation of the phosphoproteome of infected erythrocytes. Quantitative phosphoproteomic profiling identified a set of PfNIF4-regulated phosphoproteins with functional similarity to FCP1 substrates, particularly proteins involved in chromatin organization and transcriptional regulation. Specifically, we observed increased phosphorylation of Ser2/5 of the tandem repeats in the C-terminal domain (CTD) of RNA polymerase II (RNAPII) upon PfNIF4 KD. Furthermore, using the TurboID-based proteomic approach, we identified that PfNIF4 interacted with the RNAPII components, AP2-domain transcription factors, and chromatin-modifiers and binders. These findings suggest that PfNIF4 may act as the RNAPII CTD phosphatase, regulating the expression of general and parasite-specific cellular pathways during the blood-stage development.

overall_design: Expression analysis of genes in WT and PfNIF4 knockdown (KD) lines across various stages (three biological replicates per condition).

first: Siqi

last: Li

first: Chengqi

last: Wang

first: Yuanchao

last: Yu

first: Jingjing

first: Lu

last: He

first: Faiza

last: Siddiqui

first: Lumeng

last: Chen

first: Liying

first: Dan

last: Zhou

first: Junling

last: Qin

first: Jun

last: Miao

first: Liwang

last: Cui

first: Yaming

last: Cao


title: Early B Cell Factor 4 modulates FAS-mediated apoptosis and promotes cytotoxic function in human immune cells.

first: Michael

last: Lenardo

address: 9000 Rockville Pike, 10/11D14

department: NIAID

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

overall_design: Refer to individual Series


title: Early B Cell Factor 4 modulates FAS-mediated apoptosis and promotes cytotoxic function in human immune cells [RNA-seq]

summary: Apoptosis is a genetically regulated program of cell death that plays a key role in immune disease processes. We identified EBF4, a little-studied member of the early B cell factor (EBF) family of transcription factors, in a whole-genome CRISPR screen for regulators of Fas/APO-1/CD95-mediated T cell death. Loss of EBF4 increases the half-life of the c-FLIP protein and its presence in the Fas signaling complex impairs caspase-8 cleavage and apoptosis. Transcriptome analysis revealed that EBF4 regulates molecules such as TBX21, EOMES, granzyme, and perforin that are important for human natural killer (NK) and CD8+ T cell functions. Bio-ID - mass spectrometry analyses showed EBF4 binding to STAT3, STAT5, and MAP kinase 3, and a strong pathway relationship to IL-2 regulated genes which are known to govern cytotoxicity pathways. ChIP-seq analysis defined a canonical EBF4 binding motif 5’-CCCNNGG/AG-3’ closely related to the EBF1 binding site and using a luciferase-based reporter, we found a dose-dependent transcriptional response of this motif to EBF4. We also conducted ATAC-seq in EBF4 overexpressing cells and found increased chromatin accessibility upstream of granzyme and perforin and in topologically associated domains in human lymphocytes. Finally, we discovered that the EBF4 has basal expression in human but not mouse NK cells and CD8+ T cells and vanishes following activating stimulation. Together our data reveal key features of a previously unknown transcriptional regulator of human cytotoxic immune function.

overall_design: Total RNA-seq libraries were sequenced in triplicate of the following conditions: EBF4 knock out vs non-target guide RNA treated and Lentiviral transduction of EBF4 vs empty vector.

first: Tovah

last: Markowitz

first: Satoshi

last: Kubo


title: Early B Cell Factor 4 modulates FAS-mediated apoptosis and promotes cytotoxic function in human immune cells [ATAC-seq]

overall_design: ATAC-seq libraries in triplicate in Jurkat T cells with overexpressed EBF4 and matched empty vector controls.


title: Liver ILC2s suppress gluconeogenesis and limit blood glucose elevation through IL-13 signaling [scRNA-seq_ILC2]

city: Boston

first: Masanori

last: Fujimoto

state: MA

address: Center for Life Sciences 3 Blackfan Circle, Room CLS730

department: Division of Endocrinology

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

summary: The liver stores glycogen and releases blood glucose and is therefore essential for glucose metabolism. Group 2 innate lymphoid cells (ILC2s) in adipose and pancreatic tissues are involved in glucose homeostasis, but the metabolic contribution of liver ILC2s remains unclear. Herein, we show that interleukin (IL)-33 treatment induced IL-13 production in liver ILC2s, which consequently reduced blood glucose levels. IL-13 also directly suppressed gluconeogenesis in primary hepatocytes. Single-cell RNA sequencing (scRNA-seq) and cell-cell interaction analysis in liver ILC2s and hepatocytes demonstrated that IL-33 administration suppressed gluconeogenesis in a specific Hnf4a/G6pchigh-hepatocyte cluster involving expression of Stat3, which significantly interacted with liver ILC2s via IL-13/IL-13 receptor signaling. To address the regulatory mechanism underlying IL-13 production in liver ILC2s, we performed GATA3 transcriptional complex analysis, and GATA3-ChIP-seq, ATAC-seq, and scRNA-seq trajectory analyses, focusing on GATA3-interacting proteins that were functionally specific in ILC2s. AP-1 family members were found to suppress the induction of IL-13 in liver ILC2s. Thus, our study revealed a novel role for liver ILC2s in glucose homeostasis.

overall_design: Gene expression levels of liver and lung ILC2s from PBS-treated or IL-33 treated mice were evaluted using single cell RNA-seq.

first: Murata

last: Kazutaka

first: Tomoaki

last: Tanaka


title: Liver ILC2s suppress gluconeogenesis and limit blood glucose elevation through IL-13 signaling [scRNA-seq_Hepatocyte]

overall_design: Gene expression levels of primary hepatocyte from PBS-treated or IL-33 treated mice were evaluted using single cell RNA-seq.

first: Lee

last: Eunyoung

first: Ryo

last: Hatano

first: Takashi

last: Miki


title: Liver ILC2s suppress gluconeogenesis and limit blood glucose elevation through IL-13 signaling


title: Liver ILC2s suppress gluconeogenesis and limit blood glucose elevation through IL-13 signaling [ATAC-Seq]

overall_design: ATAC-seq in liver ILC2s and lung ILC2s. Change of open chromatin region of liver ILC2s responding to IL-33 were observed. And also, Open-chromatin regions both in IL-33 treated liver and lung ILC2s were narrowed by GATA3-binding peaks using GATA3-ChIP-seq data.

first: Atsushi

last: Onodera

last: Kaneda


title: Early B Cell Factor 4 modulates FAS-mediated apoptosis and promotes cytotoxic function in human immune cells [ChIP-seq]

summary: Apoptosis is a genetically regulated program of cell death that plays a key role in immune disease processes. We identified EBF4, a little-studied member of the early B cell factor (EBF) family of transcription factors, in a whole-genome CRISPR screen for regulators of Fas/APO-1/CD95-mediated T cell death. Loss of EBF4 increases the half-life of the c-FLIP protein and its presence in the Fas signaling complex impairs caspase-8 cleavage and apoptosis. Transcriptome analysis revealed that EBF4 regulates molecules such as TBX21, EOMES, granzyme, and perforin that are important for human natural killer (NK) and CD8+ T cell functions Bio-ID - mass spectrometry analyses showed EBF4 binding to STAT3, STAT5, and MAP kinase 3, and a strong pathway relationship to IL-2 regulated genes which are known to govern cytotoxicity pathways ChIP-seq analysis defined a canonical EBF4 binding motif 5'-CCCNNGG/AG-3' closely related to the EBF1 binding site and using a luciferase-based reporter, we found a dose-dependent transcriptional response of this motif to EBF4. We also conducted ATAC-seq in EBF4 overexpressing cells and found increased chromatin accessibility upstream of granzyme and perforin and in topologically associated domains in human lymphocytes. Finally, we discovered that the EBF4 has basal expression in human but not mouse NK cells and CD8+ T cells and vanishes following activating stimulation. Together our data reveal key features of a previously unknown transcriptional regulator of human cytotoxic immune function.

overall_design: Two biological replicates of EBF4-FLAG Jurkat T cells were immunoprecipitated using an anti-FLAG antibody. A matching input sample was created as a control.


title: Liver ILC2s suppress gluconeogenesis and limit blood glucose elevation through IL-13 signaling [bulkRNA-seq_Hepatocyte]

overall_design: Primary hepatocyte were isolated from wild type mouse, then cultured and stimulated with cAMP or glucagon, in the presence or absence of IL-13. Then RNA of each sample was extracted and subjected to RNA-seq to evaluted metabolism related genes including gluconeogenic enzyme.

first: Oshima

last: Motohiko

first: Iwama

last: Atsushi


title: Liver ILC2s suppress gluconeogenesis and limit blood glucose elevation through IL-13 signaling [ChIP-Seq]

first: Hiroyuki

last: Hosokawa


title: Tofacitinib blocks interferon-regulated biomarker genes in dermal and adventitial skin fibroblasts in early systemic sclerosis

status: Public on Jul 26 2022

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: Systemic sclerosis (SSc) is an autoimmune, connective tissue disease characterized by vasculopathy and fibrosis of the skin and internal organs. Trends in efficacy outcome measures favored tofacitnib. Baseline gene expression in fibroblast and keratinocyte subpopulations indicates interferon (IFN) activated gene expression.

overall_design: We randomized 15 participants with early diffuse cutaneous SSc to tofacitinib 5 mg twice a day or matching placebo in a Phase I/II double-blind, placebo-controlled trial.

first: Dinesh

last: Khanna

first: Robert

last: Lafyatis


title: USP13 Promotes Deubiquitination of ZHX2 and Tumorigenesis in Kidney Cancer

first: Austin

last: Hepperla

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Clear cell renal cell carcinoma (ccRCC) is characterized by loss of tumor suppressor Von Hippel Lindau (VHL) function. VHL is the component of E3 ligase complex that promotes the ubiquitination and degradation of hypoxia inducible factor alpha (including HIF1alpha and HIF2alpha) and Zinc Fingers And Homeoboxes 2 (ZHX2). Our recent research showed that ZHX2 contributed to ccRCC tumorigenesis in a HIF independent manner. However, it remains unknown whether ZHX2 can be regulated through deubiquitination. Here we performed a deubiquitinase (DUB) cDNA library binding screen and identified USP13 as a novel DUB that bound ZHX2 and promoted ZHX2 deubiquitination. As a result, USP13 promoted ZHX2 protein stability in an enzymatically dependent manner and depletion of USP13 led to ZHX2 downregulation in ccRCC. Functionally, USP13 depletion led to decreased cell proliferation measured by 2-D colony formation and 3-D anchorage independent growth. USP was a critical effector on maintaining kidney tumorigenesis in an orthotopic xenograft model and its depletion led to both decreased primary kidney tumorigenesis and spontaneous lung metastasis. Our results suggest that USP13 is a potential new therapeutic target in ccRCC.

overall_design: RNA-seq in 786-O cells after knockdown of ZHX2 or USP13 with two different shRNAs

first: Haibiao

last: Xie

first: Jin

last: Zhou

first: Yawei

last: Xu

first: Xijuan

last: Liu

first: Jeremy

last: Simon

first: Chengheng

last: Liao

first: Albert

middle: S

last: Baldwin

first: Kan

last: Gong

first: Qing

last: Zhang


title: Chloroquine enhances the effectiveness of 5 Fluorouracil in esophageal squamous cell carcinoma via activation of p53 signaling

status: Public on Jul 25 2022

city: Philadelphia

first: Kelly

last: Whelan

state: PA

address: 3307 N Broad St. PAHB Rm 203

department: Fels Institute

institute: Temple University

summary: To investigate the molecular mechanisms of chloroquine, 5 Fluorouracil, and their combination in ESCC cell line TE11

overall_design: We have treated ESCC cell line TE11 with 10 µM of chloroquine, 25 µM of 5 Fluorouracil, and their combination for 48 hours. Then we performed RNA sequencing.

first: Mohammad

last: Kabir

first: Adam

last: Karami


title: Interferon Regulatory Factor 5 represses mitochondrial matrix protein GHITM to limit macrophage oxidative capacity in early response to obesity [atm]

city: Paris

first: Nicolas

last: Venteclef

address: 156 rue de Vaugirard

institute: Institut Necker Enfants Malades, INSERM U1151

summary: To investigate the involvement of IRF5 in macrophages during obesity-related inflammation, we analyzed adipose-tissue macrophages (ATM) from mice with a myeloid-specific deletion of IRF5 or their wild-type littermates, fed with high fat diet.

overall_design: RNA-seq analysis from adipose tissue macrophages from mice following a short-term or long-term high-fat diet. Studies were carried out on mice with a myeloid-specific deletion of IRF5 or their wild-type littermates.

first: L

last: Orliaguet

first: T

last: Ejlalmanesh

first: R

last: Ballaire

first: M

last: Diedisheim

first: J

last: Charbit

first: P

last: Legoix

first: S

last: Lameiras

first: LG

last: Baudrin

last: Baulande

first: N

first: F

last: Alzaid


title: Interferon Regulatory Factor 5 represses mitochondrial matrix protein GHITM to limit macrophage oxidative capacity in early response to obesity [bmdm]

summary: To investigate the involvement of IRF5 in macrophages during obesity-related inflammation, we analyzed bone marrow-derived macrophages stimulated for 2 or 24 hours with Lipopolysaccharide (LPS), Palmitate or carrier (bovine serum albumin), from mice with a myeloid-specific deletion of IRF5 or their wild-type littermates.

overall_design: RNA-seq analysis from bone marrow-derived macrophages stimulated for 2 or 24 hours with LPS or with Palmitate. Studies were carried out on mice with a myeloid-specific deletion of IRF5 or their wild-type littermates.


title: CPEB1-4 RIP-Seq in S.VI Xenopus laevis oocytes [RIP-seq]

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

summary: The aim of this experiment was to investigate the binding profiles of the CPEB-family of RNA-binding proteins. To attain comparable results, all IPs were performed against the HA-tagged CPEBs.

overall_design: RNA-immunoprecipitation sequencing of CPEB1, CPEB2, CPEB3 and CPEB4 associated mRNAs in Xenoups laevis oocytes.

first: Berta

last: Duran Arqué

first: Manuel

last: Cañete Ríos


title: CroR-regulated genes in Enterococcus faecalis OG1

city: MILWAUKEE

first: CHRIS

last: KRISTICH

state: WI

address: 8701 WATERTOWN PLANK RD

institute: MCW

summary: The goal was to identify genes that are regulated by cell wall stress (bacitracin treatment) in wild-type cells but not in mutant cells lacking CroR, thereby revealing genes of the CroR regulon. Cells of a mutant lacking CroR or its otherwise isogenic wild-type E. faecalis OG1 were cultured in Mueller-Hinton broth and treated (or not) with bacitracin for 15 min. Total RNA was purified, depleted for rRNA, and subjected to preparation of TruSeq stranded mRNA libraries before sequencing on a NextSeq 550 (76-bp single read run).

overall_design: Four replicates per condition (wild-type untreated, wild-type treated, CroR mutant untreated, CroR mutant treated). Cells cultured at 37 C until exponential phase, then treated or not with bacitracin at 128 ug/ml for 15 min before RNA extraction.

first: Samantha

last: Atkinson

first: Jaime

last: Little

first: Christopher

last: Kristich


title: Transcriptome and translatome analyses of mouse and human oocytes

city: beijing

first: Wenqi

last: Hu

state: beijing

address: Room D110, Medical Science Building, School of Medicine, Tsinghua University

institute: Tsinghua University

summary:
Translatomes are more accurate than transcriptomes as indicators of gene expression profiles in cells, especially in cellular processes that cease transcriptional expression and rely on translational control, such as oocytes. Here, we developed a dual omics methodology to simultaneously examine gene expression using the transcriptomes and translatomes of single oocytes or embryos and identified a protein that can promote human oocyte maturation. First, we developed a transcriptome and translatome sequencing (T&T seq) strategy using single mouse oocytes and extended this method to human oocytes and early embryos. Many genes that are differentially expressed through translational control at different developmental stages and between two species were identified using this method. Overall, our dual omics methodology opens a new avenue for simultaneously assessing the transcriptome and translatome of a cell.
We developed a dual omics methodology to simultaneously examine gene expression using the transcriptomes and translatomes of single oocytes or embryos and identified a protein that can promote human oocyte maturation. First, we developed a transcriptome and translatome sequencing (T&T seq) strategy using single mouse oocytes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of the transcriptome and translatome of human and mouse oocytes

first: Kehkooi

last: Kee

first: Xiaoyan

last: Liang


title: 6-Gingerol attenuates subarachnoid hemorrhage-induced early brain injury via GBP2/PI3K/AKT pathway in the rat model

city: Nanchong

first: Hui

last: Tang

state: Sichuan

address: No.97, South Renmin Road, Shunqing District

institute: Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College

summary: Numerous studies have elucidated the neuroprotective effect of 6-gingerol in central nervous system diseases. However, the potential role and mechanism of 6-gingerol on early brain injury (EBI) after subarachnoid hemorrhage (SAH) remains poorly understood. Here, we report that 6-gingerol exerts a neuroprotective effect on SAH-induced EBI through the GBP2/PI3K/AKT pathway. A SAH rat model was established by injecting femoral artery blood into the cisterna magna. 6-gingerol or vehicle was injected intraperitoneally one hour post-SAH induction. We found that the neurological function score and brain edema of SAH rats were significantly improved after 6-gingerol treatment, as well as neuronal apoptosis was attenuated in SAH rats by Nissl staining assay and TUNEL assay. To further explore potential molecular mechanisms associated with 6-gingerol, RNA sequencing was implemented to investigate the differences in transcriptomes between SAH rats with and without 6-gingerol treatment; and found that the expression of guanylate-binding protein 2 (GBP2) evidently was suppressed with 6-gingerol treatment compared to vehicle group. In addition, dual immunofluorescence was also employed to investigate changes in neurons, astrocytes, and microglia after 6-gingerol treatment. The results showed that GBP2 was expressed in neurons but not astrocytes or microglia. Western blotting analysis results demonstrated that the PI3K/AKT pathway was activated in the SAH rats treated with 6-gingerol. Furthermore, recombinant GBP2 protein and LY294002 (PI3K inhibitor) treatment reversed the effects of 6-gingerol treatment in SAH rats. These results indicate that 6-gingerol suppressed the expression of GBP2 to activate the PI3K/AKT pathway, improve neurologic outcomes, reduce brain edema and neuronal apoptosis. In summary, our findings suggest that 6-gingerol could attenuate EBI post-SAH in rats, and 6-gingerol may serve as a novel candidate neuroprotective drug for SAH-induced EBI.

overall_design: To test the effect of 6-Gingerol on the gene expression, SAH rats were treated with PBS or 6-Gingerol. SAH rats treated with 6-Gingerol were compared to control rats.

first: Chuan

last: Shao

first: Xiaoya

last: Wang

first: Yi

last: Cao

first: Zhou

last: Li

first: Xiaoquan

last: Luo

first: Xiang

last: Yang

first: Yuekang

last: Zhang


title: Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning

status: Public on Jul 22 2022

city: Solna

first: Hong

state: Stockholm

address: Tomtebodavägen 23A

department: Systems Biology

country: Sweden

institute: KTH Royal Institute of Technology/Science For Life Laboratory

summary: Background & Aims  Non-alcoholic fatty liver disease (NAFLD) encompasses a wide spectrum of liver pathologies. However, not medical treatment has been approved for the disease so far. In our previous study, we found PKLR could be a potential target for treatment of NALFD. Here the aim is to investigate the effect of PKLR in in vivo model and reposition a drug which could be used for treatment of NAFLD.   Results  The Pklr KO reversed the increased hepatic triglyceride level in mice fed with high sucrose diet and partly recovered the transcriptomic changes in liver as well as other three tissues. Both liver and white adipose tissues exhibited dysregulated circadian transcriptomic profiles, and these dysregulations were reversed by hepatic knockout of Pklr. In addition, 10 small molecule drugs were identified as potential inhibitor of PKLR by the drug repositioning pipeline, and two of them significantly inhibited both the PKLR expression and triglyceride level in in vitro model. Finally, the two selected small molecule drugs were evaluated in in vivo rat models and it was demonstrated that these drugs attenuated hepatic steatosis without side effect on other tissues.  Conclusion: In conclusion, our study provided biological insights about the critical role of PKLR in NAFLD progression and proposed a treatment strategy for NAFLD patients, which could be validated in further clinical trials.

overall_design: Eight male C57BL/6J mice wild-type mice and eight Pklr-/- mutant mice were fed a standard mouse chow diet and housed in a 12‐h light–dark cycle. From the age of 8 weeks, both the wild-type and mutant mice were then divided into two groups of 4 mice fed with chow diet, high-sucrose diet for another 8 weeks, respectively. At the age of 16 weeks, all mice are sacrificed and necropsies from liver, muscle, WAT and heart tissue were taken for RNA sequencing and lipid quantification.

first: Cheng

first: Mengnan

last: Shi

first: Woonghee

last: Kim

first: Muhammad

last: Arif

first: Martina

last: Klevstig

first: Xiangyu

first: Cemil

last: Bayram

first: Ismail

last: Bolat

first: Özlem

middle: O

last: Tozlu

first: Ahmet

last: Hacımuftuoglu

first: Serkan

last: Yıldırım

first: Yongjun

last: Wei

first: Xiaojing

first: Jens

last: Nielsen

first: Hasan

last: Turkez

first: Mathias

last: Uhlen

first: Jan

last: Boren

first: Adil

last: Mardinoglu


title: Exercise Training Ameliorates Myocardial Phenotypes in Heart Failure with Preserved Ejection Fraction by Changing N6-methyladenosine Modification in Mice Mode

status: Public on Jul 21 2022

first: wenhao

last: ju

state: chaoyang

address: yabaolu

institute: shouduerkeyanjiusuo

summary: Heart failure with preserved ejection fraction (HFpEF) shows complicated and not clearly defined etiology and pathogenesis. Although no pharmacotherapeutics have improved the survival rate in HFpEF, exercise training has become an efficient intervention to improve functional outcomes. Here, we investigated N6-methyladenosine (m6A) RNA methylation modification in a “two-hit” mouse model with HFpEF and HFpEF with exercise (HFpEF + EXT). The manner of m6A in HFpEF and HFpEF + EXT hearts were explored via m6A-specific methylated RNA immunoprecipitation followed by high-throughput and RNA sequencing methods. A total amount of 3 992 novel m6A peaks were spotted in HFpEF+EXT, and 426 differently methylated sites, including 371 hypermethylated and 55 hypomethylated m6A sites, were singled out for further analysis (fold change >2, p < 0.05). Totally, m6A which is a significant alternation of epitranscriptomic processes, is a potentially meaningful therapeutic target.


title: Prefrontal cortex transcriptome of Arid1b heterozygote mutantation mice and drug treated-mice age of postnatal day 120

city: Daejeon

first: Eunjoon

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

summary: Arid1b is a chromatin remodeler implicated in neurodevelopmental disorders. Arid1b mutant mice with haploinsufficiency (Arid1b HT) displayed persistent excitatory synaptic dysfunction from juvenile to adult stage, decreased synaptic density and transmission. Moreover, they showed autistic-like behaviors in both of early and adult stages, decreased sociability in pup USV calling and adult social interaction, and adult repetitive grooming. We found that early chronic fluoxetine treatment could carry out long-lasting restoration in electrophysiological and behavioral deficits in Arid1b HT mice. Prefrontal cortex specific transcriptomic analysis with mice at postnatal day 120 which underwent chronic fluoxetine treatment from postnatal day 3 to postnatal day 21 via mammillary milk was done to investigate transcriptomic reprogramming which contributes to this restoration.

first: Hyosang

first: Hyojin

last: Kang


title: Transcriptome analysis of the broad-host range pathogen Pythium myriotylum during infection of ginger (Zingiberis officinale) leaves.

city: Nanjing

first: Paul

last: Daly

state: Jiangsu

address: 50 Zhongling St

institute: Jiangsu Academy of Agricultural Sciences

summary: Oomycetes, such as the broad host-range necrotrophic plant pathogen Pythium myriotylum, cause devastating crop losses. We have previously identified P. myriotylum as the major pathogen infecting ginger (Zingiber officinale) rhizomes in China with symptoms of Pythium soft rot (PSR) disease. Ginger is an important crop with global production estimated at approximately three million metric tonnes with about 20% of this production in China.  To better understand how P. myriotylum infects ginger, transcriptomic analysis was performed on two P. myriotylum isolates (SWQ7 and SL2) infecting ginger leaves. From both of the isolates, there was a clear separation between the transcriptome replicates from the mycelial control condition and those from the infection of the ginger leaf. In SWQ7 and SL2, there were 2,110 and 2,513 genes upregulated during infection of ginger, respectively. Of the putative effectors, a subset of the NEP1-like toxin protein (NLP) effectors were highly induced during the infection of ginger leaves. Insights from the transcriptome highlight the important role of a subset of plant cell wall degrading enzymes (PCWDEs) and effectors in the pathogenicity of P. myriotylum towards ginger. The surprisingly large numbers of P. myriotylum PCWDEs and effectors within the genome may be due to the broad host-range of P. myriotylum whereby particular subsets of the PCWDEs and effectors are required for pathogenicity towards particular hosts.

overall_design: 12 RNA samples in total were analyzed from two isolates from two conditions in triplicate (mycelial control and infection of ginger leaf).

first: Dongmei

last: Zhou

first: Danyu

last: Shen

first: Qimeng

last: Zhang

first: Lihui


title: BNC2 regulated genes in myofibroblasts and liver fibrosis

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

institute: CNRS

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

overall_design: Refer to individual Series


title: RNA-seq sample preparation kits strongly affect transcriptome profiles of a gas-fermenting bacterium

status: Public on Jul 20 2022

city: Tartu

first: Kaspar

last: Valgepea

state: Tartu

address: Nooruse 1, room 520

department: Institute of Technology

country: Estonia

institute: University of Tartu

summary: Transcriptome analysis via RNA sequencing (RNA-seq) has become a standard technique employed across a variety of biological fields of study. This rapid adoption of the RNA-seq approach has been mediated, in part, by the development of various commercial RNA-seq library preparation kits compatible with common next-generation sequencing (NGS) platforms. Generally, the essential steps of library preparation such as rRNA depletion and first-strand cDNA synthesis are tailored to a certain group of organisms (e.g. eukaryotes versus prokaryotes) or genomic GC content. Therefore, selection of appropriate commercial products is of crucial importance to capture the transcriptome of interest as closely to the native state as possible without introduction of technical bias. However, researchers rarely have the resources and time to test various commercial RNA-seq kits for their samples. In this work, we report a side-by-side comparison of RNA-seq data from the same Clostridium autoethanogenum input samples obtained using three commercial rRNA removal and strand-specific library construction products by NuGEN Technologies, Qiagen, and Zymo Research, and compare their performance with published data. While all three vendors advertise their products as suitable for prokaryotes, we found significant differences in their performance in terms of rRNA removal, strand-specificity, and, most importantly, transcript abundance distribution profiles. Notably, RNA-seq data obtained with Qiagen products were most similar to published data and delivered the best results in terms of library strandedness and transcript abundance distribution range. Our results highlight the importance of finding appropriate organism-specific workflows and library preparation products for RNA-seq studies.

overall_design: RNA-seq of Clostridium autoethanogenum using NuGEN, Qiagen and Zymo library construction kits.

first: Lorena

middle: A

last: Lima

first: Kristina

last: Reinmets

first: Lars

first: Esteban

last: Marcellin

first: Audrey

last: Harris

first: Michael

last: Köpke


title: Prefrontal cortex transcriptome of Arid1b heterozygote mutation mice age of postnatal day 10

last: Kim

summary: Arid1b is a chromatin remodeler implicated in neurodevelopmental disorders. Arid1b mutant mice with haploinsufficiency (Arid1b HT) displayed persistent excitatory synaptic dysfunction from juvenile to adult stage, decreased synaptic density and transmission. Moreover, they showed autistic-like behaviors in both of early and adult stages, decreased sociability in pup USV calling and adult social interaction, and adult repetitive grooming. To investigate early transcriptomic changes in Arid1b mutant mice, RNAseq analysis of prefrontal cortex from wild-type and Arid1b mutant mice at postnatal day 10 was done. Transcriptomic changes support these electrophysiological and behavioral deficits. Arid1b HT mice at postnatal day 10 showed alterations in genes implicated in synaptic functions and ASD.


title: Whole-brain transcriptome of Arid1b heterozygote mutation mice age of postnatal day 3

summary: Arid1b is a chromatin remodeler implicated in neurodevelopmental disorders. Arid1b mutant mice with haploinsufficiency (Arid1b HT) displayed persistent excitatory synaptic dysfunction from juvenile to adult stage, decreased synaptic density and transmission. Moreover, they showed autistic-like behaviors in both of early and adult stages, decreased sociability in pup USV calling and adult social interaction, and adult repetitive grooming. To investigate pup stage transcriptomic changes in Arid1b mutant mice, RNAseq analysis of whole brain from wild-type and Arid1b mutant mice at postnatal day 3 was done. Transcriptomic changes support these electrophysiological and behavioral deficits. Arid1b HT mice at postnatal day 3 showed alterations in genes implicated in synaptic functions and ASD.


title: Brain transcriptome analysis of Arid1b heterozygote mutation and long-lasting effects of early chronic fluoxetine treatment for mutant mice


title: Allergic sensitization and exposure to ambient air pollution beginning early in life leads to a COPD-like phenotype in young adult mice

city: Sao Paulo

first: Alexis Germán

last: Murillo Carrasco

email: agmurilloc@gmail.com, agmurilloc@usp.br

state: Sao Paulo

address: Av. Dr. Arnaldo 251, Sao Paulo

country: Brazil

institute: ICESP

summary: The perinatal period and early infancy are considered critical periods for lung development, and adversities during this period are believed to impact lung health in adulthood.The main factors affecting postnatal lung development and growth include environmental exposures, cigarette smoking, (viral) infections, allergic sensitization, and asthma.Therefore, we hypothesized that concomitant exposure in the early postnatal period in mice would cause more profound alterations in lung alveolarization and growth in adult life, quantified by stereology, and differently modulate lung inflammation and gene expression than either insult alone.Five-day-old male mice were immunized intraperitoneally (i.p.) with 10 µg of ovalbumin (OVA). This procedure was repeated at the 7th day of life, animals from the control group received i.p. injection of PBS only. Mice were exposed to either ambient PM2.5 or filtered air from the 5th to the 39th day of life, using an ambient particle concentrator developed at the Harvard School of Public Health (HAPC).Total RNA of lung samples (n=3 animals per group) was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany), according to manufacturer's instructions. The microarray analysis was performed using three RNA samples for each studied group (Control, OVA, PM2.5, OVA+PM2.5), totalizing 12 samples. One hundred nanograms of total RNA was ampliﬁed with the Ambion WT Expression Kit and hybridized onto the GeneChip Mouse Gene 2.0 ST Array (Thermo Scientific, Massachusetts, USA), following manufacturer’s protocol. The comparison between the control and OVA group exhibit 32 DEGs (28 up-regulated and 4 down-regulated), between the control and PM2.5 group had 6 DEGs (4 up and 2 down) and between the control and OVA+PM2.5 group had 5 DEGs (4 up and 1 down). The comparison between OVA and PM2.5 group showed 97 DEGS (22 up and 75 down) and between OVA and OVA+PM2.5 group had 7 DEGs (4 up and 3 down). Finally, the comparison between the PM2.5 and OVA+PM2.5 group exhibit 34 DEGs (2 up and 32 down).Our experimental data provide pathological support for the hypothesis that either allergic or environmental insults in early life have permanent adverse consequences to lung growth. In addition, combined insults were associated with the development of a COPD-like phenotype in young adult mice.

overall_design: This study analyzes data for four BALB-c mice groups: Control, OVA, PM2.5, OVA+PM2.5. Five-day-old male mice were immunized intraperitoneally (i.p.) with 10 µg of ovalbumin (OVA). This procedure was repeated on the 7th day of life. Animals from the control group received an i.p. injection of PBS only. Mice were exposed to either ambient PM2.5 or filtered air from the 5th to the 39th day of life, using an ambient particle concentrator developed at the Harvard School of Public Health (HAPC). Total RNA of lung samples (n=3 animals per group) was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer's instructions. The microarray analysis was performed using three RNA samples for each studied group (Control, OVA, PM2.5, OVA+PM2.5), totaling 12 samples.

first: Natália

last: de Souza Xavier Costa

first: Aila

last: Mirtes Teles

first: Jôse

last: de Brito

first: Renata

last: Calciolari

first: Fernanda

last: Magalhães Arantes Costa

first: Beatriz

last: Saraiva

first: Tatiane

last: Furuya

first: Alexis

first: Mariana

last: Matera Veras

first: Paulo

middle: H

last: Nascimento Saldiva

first: Roger

last: Chammas

first: Thais

last: Mauad


title: Brain transcriptome analysis of Arid1b heterozygote mutation and long-lasting effects of early chronic fluoxetine treatment for mutant mice [RNA-Seq]

first: Eunjoon

summary: Arid1b is a chromatin remodeler implicated in neurodevelopmental disorders. Arid1b mutant mice with haploinsufficiency (Arid1b HT) displayed persistent excitatory synaptic dysfunction from juvenile to adult stage, decreased synaptic density and transmission. Moreover, they showed autistic-like behaviors in both of early and adult stages, decreased sociability in pup USV calling and adult social interaction, and adult repetitive grooming. To investigate early transcriptomic changes in Arid1b mutant mice, RNAseq analysis of whole brain from wild-type and Arid1b mutant mice at postnatal day 10 was done. Transcriptomic changes support these electrophysiological and behavioral deficits. Arid1b HT mice at postnatal day 10 showed alterations in genes implicated in synaptic functions and ASD.  Next, we found that early chronic fluoxetine treatment could carry out long-lasting restoration in electrophysiological and behavioral deficits in Arid1b HT mice. Whole brain transcriptomic analysis with mice at postnatal day 120 which underwent chronic fluoxetine treatment from postnatal day 3 to postnatal day 21 via mammillary milk was done to figure out transcriptomic reprogramming which contributes to this restoration. Comparing fluoxetine treated Arid1b HT mice and vehicle group, fluoxetine treated mice showed upregulation of synapse-related genes and disease related gene sets with reverse-ASD directions.

overall_design: Whole-brain transcriptome of Arid1b heterozygote mutation mice age of postnatal day 10 & drug treated mutant mice of postnatal day 120

first: Hyosang

first: Hyojin

last: Kang


title: Comparative functional genomics identifies unique molecular features of EPSCs [ATAC-seq]

status: Public on Jul 19 2022

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: Extended pluripotent or expanded potential stem cells (EPSCs) possess the superior developmental potential to embryonic stem cells (ESCs). However, the molecular underpinning of their in vitro maintenance is not well defined. We comparatively studied transcriptome, chromatin accessibility, active histone modification chromatin marks and relative proteomes of ESCs and the two well-established EPSCs to probe the molecular foundation of their unique developmental potential. We found a great overlap in the transcriptomic and chromatin accessibility profiles and reliance on pluripotency factors Oct4, Sox2, and Nanog for self-renewal between ESCs and EPSCs. Importantly, we identified a subset of genomic, transcriptomic, and proteomic signatures that distinguish EPSCs from ESCs in transcriptional and translational regulation as well as epigenetic and metabolic control. We also identified molecular differences between the two well-established EPSCs. Our study provides a rich resource for dissecting the regulatory network underlying the developmental potency of EPSCs and exploring alternative states of totipotency.

overall_design: ATAC-seq analysis of mouse extended pluripotent or expanded potential stem cells (EPSCs) and embryonic stem cells (ESCs).

first: Xin

last: Huang

first: Ruge

last: Zang


title: Comparative functional genomics identifies unique molecular features of EPSCs [ChIP-seq]

overall_design: ChIP-seq analysis of mouse extended pluripotent or expanded potential stem cells (EPSCs) and embryonic stem cells (ESCs).


title: Specific methylation marks in promoter regions are associated to the pathogenic process of Chronic Chagas disease Cardiomyopathy by modifying transcription factor binding patterns  [RNA-Seq]

status: Public on Jul 18 2022

city: Marseille

first: Pauline

last: Brochet

address: 13288 MARSEILLE cedex 09

summary: Chagas disease, caused by Trypanosoma cruzi, is an endemic parasitical disease of Latin America, affecting 7 million people. Although most patients are asymptomatic, 30% develop complications, including Chronic Chagasic Cardiomyopathy (CCC), which ranges from moderate to severe stages depending on the cardiac ejection fraction. The pathogenic process remains poorly understood, although genetic and epigenetic factors have already been proposed. Based on bulk RNA-seq and EPIC methylation data, we investigated the genetic and epigenetic deregulations present in the moderate and severe stages of CCC. We identified 4 main biological processes associated with the pathology development, including immune response, ion transport, cardiac muscle processes and nervous system. An in-depth study of the transcription factors binding sites in the differentially methylated regions corroborated the importance of these processes. We also conducted a methylation study on blood to identify potential biomarkers for CCC. Our data revealed 198 differentially methylated positions (DMPs) that could serve as biomarkers of the disease, of which 61 are associated with disease severity.

overall_design: Heart tissue samples (20–30 mg) were cleared from pericardial fat, crushed with ceramic beads (CK14, diameter 1.4 mm, Bertin) in 350 µL of RLT lysis buffer supplemented with 3.5 µL of β-mercapto-ethanol. Total RNA was extracted from biopsies using the RNeasy Mini Kit adapted with Trizol. RNA quantity and quality were measured with a 2100 BioAnalyzer (Agilent). Ribosomal RNAs were depleted and samples were prepared for sequencing according to the Illumina TruSeq RNA Preparation Kit and subjected to pairwise sequencing (2x150bp) with an Illumina HiSeq sequencer. Sequencer results were obtained as raw fastq file format.

first: Chevillard

last: Christophe

first: Cunha-Neto

last: Edecio

first: Spinelli

last: Lionel

first: Brochet

last: Pauline