title: Histone Deacetylase 6 inhibition restores leptin sensitivity and reduces obesity

city: Nashville

first: Masoud

last: Ghamari-Langroudi

state: TN

address: 8435 MRB #IV, 2215 Garland ave

institute: Vanderbilt University

summary:
Introduction: Obesity and overweight affect more than one third of the world population, and are significant risk factors for type II diabetes, cardiovascular disease and cancer. Common obesity is usually accompanied by hyperleptinemia and leptin resistance.
Purpose: Here, we investigate the molecular pathways underlying the effects of HDAC6 inhibition in reversing diet-induced obesity and interrogate potential pathways that link HDAC6 with leptin receptor signaling by conducting whole transcriptome analysis in white adipose tissues of the diet-induced obese mice that were treated with tubastatin A (an HDAC6-specific inhibitor) and in fat-specific HDAC6 knockout mice.
Methods: Male 4-5 week-old C57B/6J wild type mice were fed with high fat diet for 16-20 weeks to generate diet-induced obese (DIO) mice. Around 28 weeks of age, mice were treated with daily ip injections of either tubastatin A-HCl (TubA, 25 mg/kg) or vehicle for four days. We probed the whole transcriptome in epididymal white adipose tissue (eWAT), and inguinal white adipose tissue (iWAT) following vehicle or TubA administration (eWAT.Veh, eWAT.TubA, iWAT.Veh, iWAT.TubA groups). In a separate cohort, DIO HDAC6 global knockout mice were treated with vehicle (Veh group) or TubA (TubA group). eWAT was excised for RNA extraction. In the third cohort, adipose tissue specific HDAC6 knockout mice were generated crossing adiponectin-Cre mice with HDAC6-floxed mice. These fat specific HDAC6 KO mice (AdKO) and their adiponectin-Cre controls (AdCre) were treated with vehicle for five weeks. eWAT was excised for RNA extraction.Total RNA samples from each tissue were extracted using Trizol. RNA Sequencing for the wild-type iWAT and eWAT samples from vehicle or TubA-treated mice was performed by the University of Michigan Sequencing Core, using the Illumina Hi-Seq 4000 platform. RNA sequencing for the other samples were conducted by Novogene, NovaSeq 6000 PE150,  HiSeq SE50 platform.  The following bioinformatics analysis have been conducted by Novogene: 1. Data Quality Control: filtering reads containing adapter or with low quality. 2. Statistics Analysis of Data Production and Quality. 3. Mapping Reads to Reference Genome. 4. Gene Expression Quantification. 5. Correlation analysis (For biological replicates only). 6. Differential Expression Analysis (two or more groups of samples). 7. GO Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples). 8. KEGG Pathway Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples). 9. GSEA Enrichment Analysis of Expressed Genes (two or more groups of samples). 10. Protein Protein Interaction Analysis. 11. Reactome Pathway Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples and only for mouse samples). 12. Oncogene Functional Annotation analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples and only for mouse sample).
Results: Inhibitors of the cytosolic enzyme histone deacetylase 6 (HDAC6) act as potent anti-obesity agents, and leptin sensitizers. HDAC6 inhibitor TubA suppresses food intake and reduce obesity, in an HDAC6-dependent manner, resulting in up to fifty percent decrease in fat mass in DIO mice accompanied by significantly reduced hepatic steatosis and improved systemic glucose homeostasis.
Conclusions: Mechanistically, peripheral -but not central- inhibition of HDAC6 confers central leptin sensitivity, and the anti-obesity effect of TubA is significantly attenuated in animals defective in the central leptin-melanocortin circuitry, including the db/db and MCR4 KO mice.

overall_design: Transcriptome profiles in epididymal and inguinal white adipose tissues of Tubastatin A or vehicle-treated about 28-week-old diet induced obese male mice.

first: Isin

last: Cakirr

first: Colleen

last: Hadley

first: Pauline

last: Lining Pan

first: Roger

middle: D

last: Cone


title: circRNA expression profile of HBV-positive liver cancer cells

status: Public on Dec 05 2021

city: Shanghai

first: Xiaojin

last: Yang

address: No. 128 Ruili Road

department: Department of infectious diseases

country: China

institute: Shanghai Fifth People's Hospital, Fudan University

summary: A large part of liver cancer is caused by hepatitis B virus (HBV) infection. In recent years, more and more reports have proved that circular RNAs (circRNAs) has a regulatory effect on the development of cancers, but the role of circRNAs in HBV-positive liver cancer needs to be further studied. In this study, the abnormally expressed circRNAs in two HBV-positive liver cancer cells compared to another two HBV-negative liver cancer cell lines were identified through microarray analysis. This study provides a comprehensively circRNA expression profiling in HBV-positive liver cancer cells, which is meaning for the mechanism study of circRNAs in HBV-related liver cancer.

overall_design: Sino Human ceRNA array V3.0. was used to identify dysregulated RNA in two HBV-positive liver cancer cells (HepG2.2.15 and Hep3B) and two HBV-negative liver cancer cell lines (HepG2 and Huh7). Subsequently, RNA was labeled and hybridized. Agilent Feature Extraction software was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software package. Abnormally expressed RNAs were screened under the threshold of fold change absolute: FC (abs) ≥2. Finally, circRNA data was extracted from all the data.

first: Yinghua

last: Yuan

first: Desheng

last: Xie


title: RNA sequencing of hippocampus of Prnp+/+ and PrnpZH3/ZH3 animals

city: Barcelona

first: Arnau

last: Hervera

address: Baldiri Reixac 15-21

country: Spain

institute: IBEC

type: Expression profiling by high throughput sequencing

summary: Purpose: Gain insight into the gene expression patterns altered in the PrnpZH3/ZH3 mice, that correleate with their neurobehavioural impaiments. Results: Around 700 genes showed alterations in their expression profile (323 upregulated and 390 downregulated in PrnpZH3/ZH3 compared to Prnp+/+).

overall_design: Methods: Hippocampal mRNA profiles of 17-20-week-old wild-type (WT) or PRNP ZH3 knock out mice (PRNP(ZH3/ZH3)) mice were generated by deep sequencing, 8 replicates per group.

first: Andreu

last: Matamoros-Angles

first: Jordi

last: Soriano

first: Eulalia

last: Marti

first: Patricia

last: Carulla

first: Fran

last: Llorens

first: Mario

last: Nuvolone

first: Adriano

last: Aguzzi

first: Isidre

last: Ferrer

first: Agnes

last: Gruart

first: Jose

middle: M

last: Delgado-Garcia

middle: A

last: Del Rio


title: The RNA methyltransferase METTL8 installs m3C32 in mitochondrial tRNAsThr/Ser(UCN) to optimise tRNA structure and mitochondrial translation

status: Public on Dec 04 2021

city: Goettingen

first: Markus

middle: T.

last: Bohnsack

address: Humboldtallee 23

department: Institute for Molecular Biology

country: Germany

institute: Goettingen University

summary: Modified nucleotides in tRNAs are important determinants of folding, structure and function. Here, we identify METTL8 as a mitochondrial matrix protein and active RNA methyltransferase responsible for installing m3C32 in the human mitochondrial (mt-)tRNAThr and mt-tRNASer(UCN). METTL8 crosslinks to the anticodon stem loop (ASL) of many mt-tRNAs in cells, raising the question of how methylation target specificity is achieved. Dissection of mt-tRNA recognition elements revealed U34G35 and t6A37/(ms2)i6A37, present concomitantly only in the ASLs of the two substrate mt-tRNAs, as key determinations for METTL8-mediated methylation of C32. Several lines of evidence demonstrate the influence of U34, G35, and the m3C32 and t6A37/(ms2)i6A37 modifications in mt-tRNAThr/Ser(UCN) on the structure of these mt-tRNAs. Although mt-tRNAThr/Ser(UCN) lacking METTL8-mediated m3C32 are efficiently aminoacylated and associate with mitochondrial ribosomes, mitochondrial translation is mildly impaired by lack of METTL8. Together these results define the cellular targets of METTL8 and shed new light on the role of m3C32 within mt-tRNAs.

overall_design: RNA-seq analysis was performed on rRNA-depleted total RNA from HEK293 Flp-In T-Rex cells

first: Nicole

last: Kleiber

first: Nicolas

last: Lemus-Diaz

first: Carina

last: Stiller

first: Marleen

last: Heinrichs

first: Mandy

last: Mai

first: Philipp

last: Hackert

first: Ricarda

last: Richter-Dennerlein

first: Claudia

last: Höbartner

first: Katherine

middle: E

middle: T


title: Analysis of gene expression of hESCs upon genetic modification with EBNA and S/MAR episomal vectors

city: Heidelberg

first: Alicia

last: Roig Merino

address: Im Neuenheimer Feld 242

institute: DKFZ

summary:
Analysis of the episomal backbone's influence on gene expression.
The first hypothesis tested in the present study is that the episomal EBNA vectors, which rely on the EBNA-1 oncoprotein for episomal maintenance, have a greater influence on the cells' expression profiles than S/MAR vectors. The second hypothesis tested was that when bacterial sequences are removed from the episomal vector backbone, the gene disturbance is minimal.

overall_design: Total RNA obtained from hESCs nucleofected with EBNA-GFP, pSMAR-GFP or nSMAR-GFP episomal vectors.

last: Roig-Merino

first: Richard

middle: P

last: Harbottle


title: An adipose lncRAP2 - Igf2bp2 complex enhances adipogenesis and energy expenditure by stabilizing target mRNAs [RNA-seq]

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

country: USA

institute: Harvard University

summary: lncRAP2 is a conserved cytoplasmic lncRNA enriched in adipose tissue and required for adipogenesis. Using purification and in vivo interactome analyses, we show that lncRAP2 forms complexes with proteins that stabilize mRNAs and modulate translation, among them Igf2bp2. Surveying transcriptome-wide Igf2bp2 client mRNAs in white adipocytes reveals selective binding to mRNAs encoding adipogenic regulators and energy expenditure effectors, including Adiponectin. These same target proteins are downregulated when either Igf2bp2 or lncRAP2 is downregulated, hindering adipocyte lipolysis. Proteomics and ribosome profiling show this occurs predominantly through mRNA accumulation, as lncRAP2-Igf2bp2 complex binding does not impact translation efficiency. Phenome-wide association studies reveal specific associations of genetic variants within both lncRAP2 and Igf2bp2 with body mass and type 2 diabetes, and both lncRAP2 and Igf2bp2 are suppressed in adipose depots of obese and diabetic individuals. Thus, the lncRAP2-Igf2bp2 complex potentiates adipose development and energy expenditure and is associated with susceptibility to obesity-linked diabetes.

overall_design: RNA-seq of adipocytes differentiated in culture from directional cDNA libraries generated from poly(A)+ RNA and sequenced on an Illumina NextSeq instrument.


overall_design: Flp-In T-Rex HEK293 cell lines expressing METTL8-His6-Prescission protease cleavage site-2xFLAG (His6-2xFLAG) or the His6-2xFLAG tag alone were crosslinked using UV light at 254 nm and analyzed by the crosslinking and analysis of cDNA (CRAC) approach.


title: Albinism Family Array CGH Data

status: Public on Dec 03 2021

city: Mumbai

first: Jitendra

middle: Vasudeo

last: Suralkar

state: Maharashtra

address: 13th floor, NMS Building, KEM Hospital Campus, Parel

department: Cytogenetics

country: India

institute: ICMR - National Institute of Immunohaematology

summary:
The study was carried out to identify copy number variations using array-CGH in family having three children affected with albinism (OCA1B) and the males were affected with ID. Agilent’s SureScan microarray scanner with SurePrint G3 Human CGH, 8x60K array platform was used for the study.
The probes used for the experiment was approximately 60000 oligonucleotide, allowing detection of deletions above 200 Kb and duplication above 500 kb in entire human genome. CytoGenomics software used to carryout data analysis revealed CNVs in participants.

overall_design: High quality genomic DNA of participants was used to perform the assay.

first: Anjali

last: Shah

middle: V

first: Somprakash

last: Dhangar

first: Purvi

last: Panchal

first: Babu

last: Rao Vundinti


title: Single-cell transcriptomes combining with consecutive genomics reveal clonal evolution and gene regulatory networks in relapsed and refractory multiple myeloma

first: Jiadai

last: Xu

state: Shanghai

address: Fenglin Road 180, Shanghai, China

department: Hematology

institute: Zhongshan Hospital, Fudan University

summary: In the end-stage of MM (PD9), malignant PCs appeared in the patient's peripheral blood (PB), the proportion of which reached 10%. Her PB mononuclear cells (PBMC) were used for scRNA-seq.

overall_design: One PBMC sample from a RRMM patient.


title: NuA4 and H2A.Z control environmental responses and autotrophic growth in Arabidopsis

status: Public on Dec 02 2021

city: Poznan

first: Piotr

last: Ziolkowski

address: Uniwersytetu Poznanskiego 6

department: Institute of Molecular Biology and Biotechnology

country: Poland

institute: Adam Mickiewicz University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The nucleosomal acetyltransferase of H4 (NuA4) is an essential transcriptional coactivator in eukaryotes, though it remains poorly characterized in plants. Here, we describe Arabidopsis homologues of the NuA4 scaffold proteins Enhancer of Polycomb-Like1 (EPL1) and Esa1-Associated Factor1 (EAF1). Loss of AtEAF1 results in inhibition of growth and chloroplast development. These effects are stronger in the Atepl1 mutant and are further enhanced by loss of Golden2-Like (GLK) transcription factors suggesting that NuA4 activates nuclear plastidic genes alongside GLK. We demonstrate that AtEPL1 is necessary for nucleosomal acetylation of histones H4 and H2A.Z by NuA4 in vitro. These chromatin marks are diminished in Atepl1 genome-wide while another active chromatin mark H3K9ac is locally enhanced. Many chloroplast-related genes depend on NuA4 as they are downregulated with loss of H4ac and H2A.Z alone. Finally, we demonstrate that NuA4 promotes deposition of H2A.Z and by doing so prevents spurious activation of stress response genes.

overall_design: RNA-Seq transcriptome analysis of of A. thaliana wild type, Atepl1-2,  Ateaf1-1, glk leaves, and ChIP-Seq profiling of wild type and Atepl1-2 for H3K9ac, H4K5ac, H2A.Zac and H2A.Z

first: Tomasz

last: Bieluszewski

first: Weronika

last: Sura

first: Wojciech

last: Dziegielewski

first: Anna

last: Bieluszewska

first: Catherine

last: Lachance

first: Michał

last: Kabza

first: Maja

last: Szymanska-Lejman

first: Mateusz

last: Abram

last: Wlodzimierz

first: Nancy

last: De Winne

first: Geert

last: De Jaeger

first: Jacques

last: Côté

first: Jan

last: Sadowski


title: Comparative transcriptomic analysis of the proximal tibial growth plates of 14-day old Longshanks and wildtype mice

status: Public on Dec 01 2021

city: Calgary

first: Matthew

last: Workentine

state: Alberta

address: 3280 Hospital Drive NW

country: Canada

institute: University of Calgary

summary: This study was undertaken to uncover the molecular pathways that underlie differences among individuals in rates of longitudinal growth and mature length of the long bones in a rodent model. To do so, the transcriptomic profiles of the proximal epiphyses of 14-day old CD-1 wildtype mice and the Longshanks mice were compared. The Longshanks mouse was selectively bred for longer tibiae in relation to body mass (see Marchini et al 2014 – BMC Evol Biol 14:258). Over 13 generations, Longshanks tibiae were 11-12% longer compared to random-bred wildtype mice (hereafter Controls) from the same  genetic background (ICR or CD-1), but body mass was unchanged. By comparing the transcriptomes of samples of Control and Longshanks proximal tibiae, we sought to identify differentially expressed genes that were associated with the faster growth and longer tibia of the Longshanks mouse, as a window into the pathways that may underlie intra- and interspecific differences in limb bone size and shape. Results were further validated using qPCR and cell and tissue culture assays.

overall_design: Three Longshanks mice (line LS1, biological replicates) and three Control mice (biological replicates) from different families in generation F13 were used for RNA sequencing at 14 days old. The two tibial proximal epiphyses from each mouse were pooled for total RNA extraction, sequencing and differential gene expression analyses as described in the protocols.

first: Marta

last: Marchini

first: Rolian

last: Campbell


title: miRNA-seq in healthy human iPSC-derived cardiomyocytes

city: Munich

first: Dena

last: Esfandyari

state: Bavaria

address: Haus 607, Biedersteiner Str. 29, IPT

department: Institute of Pharmacology and Toxicology

institute: Technical University of Munich

type: Non-coding RNA profiling by high throughput sequencing

summary: Abnormalities of ventricular action potential (AP) cause malignant cardiac arrhythmias and sudden cardiac death. Here, we sought to identify microRNAs (miRNAs) that regulate the human cardiac AP and asked whether their manipulation allows for therapeutic modulation of AP abnormalities. Quantitative analysis of the miRNA targetomes in human cardiac myocytes identified miR-365 as a primary miRNA to regulate repolarizing ion channels. AP recordings in patient-specific induced pluripotent stem cell-derived cardiac myocytes (iPSC-CMs) showed that elevation of miR-365 level significantly prolonged AP duration in hiPSC-CMs derived from a Short-QT syndrome (SQTS) patient, whereas specific inhibition of miR-365 normalized pathologically prolonged AP in Long-QT syndrome (LQTS) iPSC-CMs. Transcriptome analyses in human iPSC-CMs at bulk and single-cell level corroborated the key cardiac repolarizing channels as direct targets of miR-365, together with functionally synergistic regulation of additional AP-regulating genes by this miRNA. Whole-cell patch clamp experiments revealed miR-365-based regulation of repolarizing ionic currents. Finally, refractory period measurements in human myocardial slices substantiated the prolonging effect of miR-365 on AP duration also in adult human myocardial tissue. Our results delineate miR-365 to regulate human cardiac AP duration by targeting key factors of cardiac repolarization.

overall_design: small RNA-seq of 2 healthy hiPSC-CMs at day 60

first: Stefan

last: Engelhardt


title: single cell RNA-seq in healthy and LQT1 hiPSC-CMs upon manipulation of miR-365

overall_design: healthy hiPSC-CMs treated with mimic-365 and antimiR-365 were subjected to single cell RNA-seq. Untreated, antimiR-Ctrl and antimiR-365-treated LQT1-specific hiPSC-CMs were labeled with cell hashing oligos (HTO), multiplexed and subjected to single cell RNA-seq (10x Genomics).


title: Biomaterials direct functional B cell response in a material specific manner

city: Baltimore

first: Christopher

last: Cherry

state: MD

address: 1800 Orleans St

institute: Johns Hopkins University

summary: B cells are an adaptive immune target of biomaterials development in vaccine research but despite their role in wound healing have not been studied tissue engineering and regenerative medicine. We evaluated the B cell response to biomaterial scaffold materials implanted in a muscle wound; a biological extracellular matrix (ECM) and synthetic polyester polycaprolactone. In the local muscle tissue, small numbers of B cells are recruited in response to tissue injury and biomaterial implantation. ECM materials induced plasmablasts in lymph nodes and antigen presentation in the spleen while the synthetic PCL implants delayed B cell migration and induced an antigen presenting phenotype. In muMt- mice lacking B cells, the fibrotic response to the synthetic biomaterials decreased. Immunofluorescence confirmed antigen presenting B cells in fibrotic tissue surrounding silicone breast implants. In sum, the adaptive B cell immune response to biomaterial depends on composition and induces local, regional and systemic immunological changes.

overall_design: Murine tissue samples (quadriceps femoris muscle and inguinal lymph nodes) were obtained for single cell flow cytometry and/or fluorescence activated cell-sorting. Quad tissue samples were finely diced and digested with 1.67 Wünsch U/mL Liberase TL (Roche Diagnostics) and deoxyribonuclease I (0.2 mg/ml; Roche Diagnostics) in RPMI-1640 medium (Gibco) for 45 min at 37°C. The digested quad tissues were ground through 70-µm cell strainers (Thermo Fisher Scientific), rinsed with RPMI-1640 + 5% fetal bovine serum. Percoll (GE Healthcare) density gradient centrifugation was used to remove debris from quad digestions and enrich the leukocyte fraction. Inguinal lymph node samples were ground through 70-µm cell strainers with excess RPMI-1640 + 10 mM HEPES buffer solution. The enriched single-cell suspensions were washed and stained following antibody panels, respective to the intended application. No differences in single-cell isolation from different material environments were observed.

first: Jennifer

middle: H

last: Elisseeff


title: Effects of the sex chromosome complement, XX, XO or XY, on the transcriptome and development of mouse oocytes during follicular growth.

city: Montreal

first: Dunarel

last: Badescu

address: 740 Dr Penfield Ave

department: Human Genetics

institute: McGill University

summary:
Purpose: To understand how sex chromosome complement, XX, XO and XY, influences the transcriptome in the oocytes of grwoth phase.
Methods: Oocytes of 50 and 60 µm in diameter were isolated from mouse ovaries at 18 dpp and subject to RNA-sequencing.
Results: (1) Many X-linked genes are subject to X chromosome dosage dependent expression. (2) Many genes are expressed from both short and long arms of the Y chromosome. (3) The transcriptome landscape in XY oocytes is closer to XX oocytes than XO oocytes. (4) About 10 genes are differentially expressed in XY oocytes compared to XX or XO oocytes.
Conclusions: The differences in XY oocytes became exacerbated to differ from XX or XO oocytes near the end of growth phase.

overall_design: Transcription of XX,XO and XY mouse oocytes during follicular growth

first: Wataru

last: Yamazaki

first: Seang

middle: L

last: Tan

first: Jiannis

last: Ragoussis

first: Teruko

last: Taketo


title: Transcriptomic profiling of mouse substantia nigra tissue by RNA-seq

city: Seoul

first: Dong-Wook

last: Kim

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Physiol.

country: South Korea

institute: Yonsei University College of Medicine

summary: Transcriptomic profiling of substantia nigra of wild type (WT) and Tpbg knockout (KO) mice (RNA-seq)

overall_design: Substantia nigral RNA profiles of WT and Tpbg knockout (KO) mice at 14 months old

first: Sanghuyn

last: Park

first: Dae-Sung


title: SO018 visceral adipose tissue gene expression

city: clermont ferrand

first: frederic

last: capel

address: 28 place henri dunant

department: alimentation humaine

country: France

institute: INRA

summary:
identification of the effect of transgenerationnal supplementation with omega 3 fatty acids on the resistance to a diet induced obesity challenge
identification of the effect of transgenerationnal supplementation with omega 3 fatty acids on the resistance to a diet induced obesity challenge

overall_design: 3 groups of mice were included n=8 per group, a control low fat diet group, a hifh fat-control lineage group and a high fat-omega 3 lineage group.

first: Frederic

last: Capel

first: Alexandre

last: Pinel

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Targeting MyD88 Downregulates Inflammatory Mediators and Pathogenic Processes in PBMC From DMARDs-Naïve Rheumatoid Arthritis Patients

status: Public on Nov 30 2021

city: Atlanta

first: Sergio

last: Ramirez-Perez

state: Georgia

address: 615 Michael St NE

department: Orthopaedics

institute: Emory University

summary:
Purpose: We analyzed RNA-seq from peripheral blood mononuclear cells (PBMC) in DMARDs-naïve RA patients and healthy subjects. Our goal was to evaluate the transcriptional profiles of ST2825-treated PBMC to identify its therapeutic potential.
Methods: We analyzed bulk RNA-seq from peripheral blood mononuclear cells (PBMC) in DMARDs-naïve RA patients after stimulation with LPS and IL-1β, PBMC were treated with the MyD88 chemical inhibitor, ST2825. Collection of RNA was performed after 24 h of treatment and samples were sequenced to determine transcriptional changes and regulated processes in treated PBMC.
Results: paired-end reads were mapped to the hg19 human genome assembly. RNA levels were normalized using DESeq. We identified 796 differentially expressed (DE) genes by 2-fold change (p<0.05) between RA patients and healthy subjects. Our analysis revealed 631 DE genes between DMARDs-naïve RA patients before and after ST2825 treatment. We identified 471 DE genes between LPS-stimulated RA PBMC and LPS-stimulated RA PBMC treated with ST2825.
Conclusion: Our study provides comprehensive evidence supporting the potential application of the MyD88 inhibitor, ST2825, as a modulator of gene expression signtaures involved in pathogenic processes in PBMC from DMARDs-naïve RA patients. Our indepth analysis of RNA-seq data will serve as a valuable resource containing the inflammatory gene expression signatures by MyD88.

overall_design: Identification of the potential effect of ST2825 as an inhibitor of MyD88-dependent gene expression signatures to modulate inflammatory processes in RA patients.

first: Pallavi

last: Bhattaram


title: Cigarette Smoking-Associated Isoform Switching and 3’ UTR Lengthening Via Alternative Polyadenylation

city: Boston

first: Peter

last: Castaldi

address: 181 Longwood Ave

institute: Harvard Medical School

summary: Cigarette smoking accounts for approximately one in five deaths in the United States. Previous genomic studies have primarily focused on gene level differential expression to identify related molecular signatures and pathways, but the genome-wide effects of smoking on alternative isoform regulation and posttranscriptional modulation have not yet been described. We attempted to fill this void by identifying smoking-associated isoform switches and their responsible splicing events and consequences using RNA-seq.

overall_design:
RNA-seq data were generated from whole blood samples from 454 current and 767 former smokers enrolled in the COPDGene Study. Raw read data are submitted to dbGaP.
NOTE from submitter: RAW DATA will be uploaded to dbGAP

first: Zhonghui

last: Xu


title: MicroRNA profiling of Gingival tissue from chronically SIV infected rhesus macaques

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

summary: The study describes miRNA expression in Gingival tissue of chronically SIV-infected rhesus macaques. HIV/SIV-associated periodontal disease (gingivitis/periodontitis) (PD) represents a major comorbidity affecting HIV patients on anti-retroviral therapy. Employing a systems biology approach, we report molecular changes underlying PD and its modulation by phytocannabinoids [delta-9-tetrahydrocannabinol (9-THC)] in uninfected and SIV-infected rhesus macaques (RMs) untreated (VEH-untreated/SIV) or treated with vehicle (VEH/SIV) or 9-THC (THC/SIV).  VEH- untreated/SIV but not THC/SIV RMs showed significant enrichment of genes linked to anti-viral defense, interferon-beta, NFkB, RIG-1, and JAK-STAT signaling. We focused on the anti-microbial DUOX1 and immune activation marker IDO1 that were reciprocally regulated in gingiva of VEH-untreated/SIV RMs. Both proteins localized to the gingival epithelium and CD163+ macrophages, and showed differential expression in the gingiva of THC/SIV and VEH/SIV RMs. Additionally, inflammation-associated miR-21, miR-142-3p, miR-223, and miR-125a-5p showed significantly higher expression in the gingiva of VEH/SIV RMs. In human primary gingival epithelial cells, miR-125a-5p post-transcriptionally downregulated DUOX1  These findings strongly support a role for differential miRNA expression associated with HIV/SIV induced gingival mucosal dysfunction.

overall_design: Thirteen age and weight matched male Indian rhesus macaques were randomly divided into 3 groups. Group 1 (n=4) remained uninfected. Group 2 (VEH/SIV, n=6) animals were infected intravenously with 100TCID50 of SIVmac251. Group 3 (THC/SIV, n=3) were treated with delta-9-tetrahydrocannabinol and infected intravenously with 100TCID50 SIVmac251. Gingival tissue was collected at necropsy, ~180 days post SIV infection. ~100 ng of total RNA was first reverse transcribed and preamplified according to the manufacturer’s recommendation. MicroRNA expression profiling was performed using TaqMan ®OpenArray® Human microRNA panels. Data analysis was performed using ExpressionSuite® software, which utilizes the comparative Cτ (ΔΔCτ) method to rapidly and accurately quantify relative miRNA expression across many genes and samples. miRNA expression data were normalized using global normalization method.  Comparisons were made between uninfected and VEH/SIV and THC/SIV and VEH/SIV rhesus macaques.

first: M


title: Transcriptomic analysis of Wild type M.tb H37Rv, HigB KO M.tb H37Rv and complemented Hig B KO M.tb H37Rv

city: New Delhi

first: Amita

last: Gupta

state: Delhi

address: University of Delhi south campus

department: Department of Biochemistry and CIIDRET

institute: University of Delhi

summary:
Gene expression microarray was performed using early log phase culture at 37 degree and 200 rpm followed by RNA extraction from M.tb H37Rv, HigB KO M.tb H37Rv and complemented Hig B KO M.tb H37Rv
For gene expression profiling, total RNA was isolated from wild type H37Rv, higB KO mutant strain and complemented strains. The bacterial pellets for M.tb H37Rv wild type, M.tb H37Rv HigB KO mutant strain and complemented strain were resuspended in 1.0 ml TRIzol (Invitrogen Corporation, Carlsbad, CA); mRNA was extracted as per standard protocols and cleaned using RNAeasy columns (Qiagen GmbH, Hilden, Germany). Extracted mRNA (1 μg) was treated with DNase I using the Ambion DNA-free kit (Invitrogen Corporation, Carlsbad, CA) to remove genomic DNA contamination and quantified using    Nanodrop 2000c spectrophotometer (Thermo Scientific, USA). The purity and integrity of RNA samples were assessed Agilent 2100 Bio analyzer (Agilent TechnologiesInc., USA). Further, 25ng of RNA was amplified and labeled using Low input Quick Amp WT Labeling kit (Agilent Technologies, USA). The labeled cRNA was purified using RNAeasy columns (Qiagen, USA) and total yields were quantified using Nanodrop 2000c spectrophotometer.

overall_design: Wild type M.tb H37Rv, HigB KO M.tb H37Rv and complemented Hig B KO M.tb H37Rv were grown till early log phase at 37 degree and 200rpm. Two independent experiments were done for Wild type M.tb H37Rv and three independent experiments were done for each of HigB KO M.tb H37Rv and complemented HigB KO M.tb H37Rv.


title: One-pot universal NicE-seq: All enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics

city: Ipswich

first: Sriharsa

last: Pradhan

address: 240 County Road

institute: New England Biolabs

summary: Accessible chromatin landscape allows remodeling of transcription factors and enhancers during development and molecular subtypes of cancer in patient samples. One-tube universal NicE-seq (OuNicE-seq) is an improved accessible chromatin profiling method that negate DNA purification and incorporate sonication free enzymatic fragmentation before library preparation and is suited to a variety of mammalian cells. OuNicE-seq is versatile, capable of profiling 4% formaldehyde fixed chromatin in 25 fixed cells and opens the possibility for automation. Accessible chromatin profile is more efficient on formaldehyde fixed cells using OuNicE-seq compare to Tn5 transposon mediated methods, demonstrating its versatility.

overall_design: HCT116, HeLa, HEK293 and GM12878 cells were grown according to ATCC ‘s recommendations. DNA damage detection and chromatin labeling efficiency studies were performed in HCT116 with 0.2%, 1% and 4% formaldehyde fixation. OuNicE-seq for low cell numbers were performed in HCT116, HeLa, HEK293 and GM12878 cells fixed with 4% formaldehyde. Accessible chromatin labeling was done based on UniNicE-seq protocol and library for sequencing was generated based on OuNicE-seq protocol.

first: Udayakumar

middle: S

last: Vishnu

first: Pierre

middle: O

last: Esteve


title: Comparative profiling of hippocampal gene expression in AppNL-G-F knock-in mouse model of Alzheimer's disease.

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

summary:
To identify molecular pathological alterations in Alzheimer’s disease (AD) brains, we had previously performed comparative gene expression profiling with human gene array using RNAs prepared from postmortem human brains donated for the Hisayama study. The hippocampi from AD brains showed the most significant alteration in gene expression profile (PMID: 23595620). In the present study, in order to obtain a comprehensive view of gene expression profiles in AD hippocampus, we applied human transcriptome array and deep RNA-sequencing to the same samples and reanalyzed the gene array data, and performed integrative analysis of all 3 methods.  We also applied gene array to hippocampus of 6-month-old App[NL-G-F/NL-G-F] knock-in AD model mice, and at last we performed the interspecies comparison.
IPA analysis of the top significantly altered genes derived from integrative analysis of all 3 methods in human AD hippocampus revealed that neurotransmission, synaptic transmission and development of neurons are the top significantly decreased functions. In hippocampi of App[NL-G-F/NL-G-F] mice which exhibit significant amyloidosis but not neuronal degeneration, we found that expression of Gfap (astrocyte marker) and Cd68 (microglia marker) genes are significantly upregulated together with genes categorized in the immune response of cells. Comparing the human and mouse data, we found major common genes are related to recruitment of inflammatory cells. Amyloid-beta accumulation is the major hallmark of AD at 6 month-old App[NL-G-F/NL-G-F] mice, therefore our data suggests that amyloid-beta accumulation increases the recruitment of inflammatory cells in early stage of AD brain, prior to neuronal degeneration.

overall_design: Six month-old female wild-type and App[NL-G-F/NL-G-F] mice harboring three pathogenic App-knock-in mutations, that promote aggressive amyloidosis by increasing total Aβ production (Swedish mutation KM670/671NL) and increasing the Aβ42 aggregation (Arctic mutation E693G) and increasing the Aβ42/Aβ40 ratio (Iberian mutation I716F) under the control of the endogenous APP promoter were used for hippocampal gene expression profiling with the Affymetrix Genechip Mouse Gene 2.0 ST Array. Array data was processed by Affymetrix Transcriptome Analysis Console (TAC) software 4.0.

first: Nona

last: Abolhassani


title: Fms-like tyrosine kinase 3 (Flt3) contributes to a receptor tyrosine kinase signature regulating the cardiac side population

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Fms-like tyrosine kinase 3 (Flt3) is a regulator of hematopoietic progenitor cells. It is a target of tyrosine kinase inhibitors (TKIs) used for acute myeloid leukemia treatment. Flt3 and its ligand (Flt3L) are expressed in the heart and cardiac side effects occur under Flt3-targeting TKIs. Whether Flt3/Flt3L also regulate cardiac progenitor cells (CPCs), however, is not known. The cardiac side population (SP) is a pool of heterogenous CPCs that can give rise to all cardiac lineages, hence contributing to cardiovascular homeostasis. Here we show that SP-CPCs produce and are responsive to Flt3L. Compared to wild-type, SP-CPCs from flt3L-/- mice are less abundant, with less contribution of CD45-CD34+ cells, and lower expression of gene sets related to epithelial-to-mesenchymal transition, cardiovascular development and stem cell differentiation. Upon culturing and compared to wild-type, flt3L-/- Sca1+CD31- SP-CPCs show increased proliferation and less vasculogenic commitment, but differentiation can be induced in the presence of receptor tyrosine kinase-activating growth factors. The observed differences are associated with decreased microvascularisation and global systolic function of flt3L-/- hearts. Thus, Flt3 contributes to a receptor tyrosine kinase signature necessary for the maintenance and functionality of SP-CPCs. These findings have potential implications regarding cardiovascular side effects observed under TKI therapy.

overall_design: Comparison of gene expression in freshly isolated wt and flt3L-/- SP-CPCs.

first: Julien

last: Roux

first: Giacomo

last: Verde

first: Gabriela

last: Kuster


title: Transcriptome profiling of Gingival tissue from chronically SIV infected rhesus macaques

summary: HIV/SIV-associated periodontal disease (gingivitis/periodontitis) (PD) represents a major comorbidity affecting HIV patients on anti-retroviral therapy. Employing a systems biology approach, we report molecular changes underlying PD and its modulation by phytocannabinoids [delta-9-tetrahydrocannabinol (THC)] in uninfected and SIV-infected rhesus macaques (RMs) treated with vehicle (VEH/SIV) or THC (THC/SIV).  VEH/SIV but not THC/SIV RMs showed significant enrichment of genes linked to anti-viral defense, interferon-beta, NFkB, RIG-1, and JAK-STAT signaling. We focused on the anti-microbial DUOX1 and immune activation marker IDO1 that were reciprocally regulated in gingiva of VEH/SIV RMs. Both proteins localized to the gingival epithelium and CD163+ macrophages, and showed differential expression in the gingiva of THC/SIV and VEH/SIV RMs. Additionally, inflammation-associated miR-21, miR-142-3p, miR-223, and miR-125a-5p showed significantly higher expression in the gingiva of VEH/SIV RMs. In human primary gingival epithelial cells, miR-125a-5p post-transcriptionally downregulated DUOX1 and THC inhibited IDO1 protein expression through a cannabinoid receptor-2 mediated mechanism. Interestingly, THC/SIV RMs showed relatively reduced plasma levels of kynurenine, kynurenate, and the neurotoxic quinolinate compared to VEH/SIV RMs. Most importantly, THC blocked HIV/SIV-induced depletion of Firmicutes and Bacteroidetes, and reduced Gammaproteobacteria abundance in saliva. Reduced IDO1 protein expression was associated with significantly (p<0.05) higher abundance of Prevotella, Lactobacillus (L. salivarius, L. buchneri, L. fermentum, L. paracasei, L. rhamnosus, L. johnsonii) and Bifidobacteria and reduced abundance of the pathogenic Porphyromonas cangingivalis and Porphyromonas macacae. These translational findings suggest that phytocannabinoids could help reduce gingival/systemic inflammation and salivary dysbiosis in ART naïve and treated HIV individuals.

overall_design: Gingival tissue mRNA profiles of uninfected control (n=5) and chronically SIV-infected rhesus macaques that were treated with vehicle (n=7) or delta-9-tetrahydrocannabinol (THC) (n=3) were generated by deep sequencing using Illumina.


title: Disruption of the Nα-acetyltransferase NatB causes sensitivity to reductive stress in Arabidopsis thaliana

status: Public on Nov 29 2021

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: In Arabidopsis thaliana the evolutionary conserved N-terminal acetyltransferase (Nat) complexes NatA and NatB co-translationally acetylate 60% of the proteome. Both have recently been implicated in the regulation of plant stress responses. While NatA mediates drought tolerance, NatB is required for pathogen resistance and the adaptation to high salinity and high osmolarity. Salt and osmotic stress impair protein folding and result in the accumulation of misfolded proteins in the endoplasmic reticulum (ER). The ER-membrane resident E3 ubiquitin ligase DOA10 targets misfolded proteins for degradation during ER stress and is conserved among eukaryotes. In yeast, DOA10 recognizes conditional degradation signals (Ac/N-degrons) created by NatA and NatB. Assuming that this mechanism is preserved in plants, the lack of Ac/N-degrons required for efficient removal of misfolded proteins might explain the sensitivity of NatB mutants to protein harming conditions. In this study, we investigate the response of NatB mutants to dithiothreitol (DTT) and tunicamycin (TM) induced ER stress. We report that NatB mutants are hypersensitive to DTT but not TM, suggesting that the DTT hypersensitivity is caused by an over-reduction of the cytosol rather than an accumulation of unfolded proteins in the ER. In line with this hypothesis, the cytosol of NatB depleted plants is constitutively over-reduced and a global transcriptome analysis reveals that their reductive stress response is permanently activated. Moreover, we demonstrate that doa10 mutants are susceptible to neither DTT nor TM, ruling out a substantial role of DOA10 in ER-associated protein degradation (ERAD) in plants. Contrary to previous findings in yeast, our data indicates that N-terminal acetylation (NTA) does not inhibit ER targeting of a substantial amount of proteins in plants. In summary, we provide further evidence that NatB-mediated imprinting of the proteome is vital for the response to protein-harming stress and rule out DOA10 as the sole recognin for substrates in the plant ERAD pathway.

overall_design: Comparison of the wild-type Arabidopsis thaliana accession Col-0 (N=3) with the naa20-1 mutant (N=3) that is depleted of the catalytically active subunit of the Nat B complex under DTT-induced reductive stress.

last: Wirtz

last: Huber


title: Profiling of H3K4me3 and H3K27me3 and their roles in regulating gene transcription in allotetraploid cotton (ChIP-Seq)

city: Xuzhou

first: Cen

middle: Ai

last: Zhang

state: Jiangsu

address: No.2 Kunpeng

institute: Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District

summary: Cotton is an excellent model for studying heterosis, crop domestication and bioengineering improvement. Chromatin profiling helps to reveal how histone modifications are involved in controlling differential gene expression between A and D subgenome in allotetraploid cotton. However, the detailed profiling and functional characterization of H3K27me3 and H3K4me3/H3K27me3 bivalent mark are still understudied in cotton.   In this study, we conducted H3K4me3 and H3K27me3-related ChIP-seq followed by comprehensively characterizing their roles in regulating gene transcription in cotton. We found that H3K4me3 and H3K27me3 exhibited active and repressive roles in regulating expression of genes between A and D subgenome, respectively. Expression of H3K4me3-H3K27me3 bivalent genes was regulated by combinatorial actions of both marks and may be dominantly controlled by H3K4me3. More importantly, H3K4me3 exhibited enrichment levels, positioning and distance-related effects on expression levels of related genes. In addition, H3K4me3, H3K27me3 and bivalent mark can indirectly influence gene expression through TF-mediated regulatory networks. Thus, our study provides insights in functions of H3K4me3 and H3K27me3 in regulating differential gene expression between A and D subgenome in cotton.

overall_design: RNA-seq, ChIP-seq

first: A

first: Y

last: Wei

last: Shi

first: X

last: Deng

first: J

last: Gao

last: Feng

first: D

last: Zheng

last: Cheng

first: Z

last: Li

first: T

last: Wang

first: K

first: F

last: Liu

first: R

last: Peng

first: W


title: Development of human iPSC-derived quiescent hepatic stellate cell-like cells for drug discovery and in vitro disease modeling

city: Bunkyo-ku

first: Yuta

last: Koui

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

institute: The University of Tokyo

summary: Hepatic stellate cells (HSCs) play a central role in the progression of liver fibrosis by producing extracellular matrices. The development of drugs to suppress liver fibrosis has been hampered by the lack of human quiescent HSCs (qHSCs) and an appropriate in vitro model that faithfully recapitulates HSC activation. In the present study, we developed a culture system to generate qHSC-like cells from human-induced pluripotent stem cells (hiPSCs) that can be converted into activated HSCs in culture. To monitor the activation process, a red fluorescent protein (RFP) gene was inserted in hiPSCs downstream of the activation marker gene actin alpha 2 smooth muscle (ACTA2). Using qHSC-like cells derived from RFP-reporter iPSCs, we screened a repurposing chemical library and identified therapeutic candidates that prevent liver fibrosis. Hence, hiPSC-derived qHSC-like cells will be a useful tool to study the mechanism of HSC activation and to identify therapeutic agents.

overall_design: Human iPSC-derived qHSC-like cells were prepared from two iPS cell lines (4M: TkDN4-M and FF: FF-1, n=3, 3). Human iPSC-derived aHSCs were prepared by culturing 4M and FF iPSC-derived qHSC-like cells (n=3, 3) for 5 days. Total 12 samples were analyzed.

first: Yusuke

last: Mori

first: Taketomo

last: Kido


title: Ultradian Molecular Rhythms Emerge in the Absence of a Circadian Clock

status: Public on Nov 28 2021

city: Rehovot

first: Gal

last: Manella

state: Israel

address: 234 Herzel St.

country: Israel

institute: Weizmann Institute of Science

summary: In the chronobiology field, a fundamental dichotomy exists to explain daily rhythmicity of biological processes: these can be elicited in response to cyclic extrinsic/environmental signals such as light, or driven endogenously by the circadian clock. In mammals, the circadian clock ticks in almost every cell of the body, and functions based on a network of transcription-translation feedback loops. The PI3K-AKT signaling pathway relays environmental information of nutritional/metabolic state to regulate cell size and proliferation. AKT, a Serine/Threonine protein kinase, is activated by phosphorylation, where phospho-serine 473 (pAKT) serves as a hallmark for its activation. Following activation, it proceeds to phosphorylate dozens of target proteins that convey the signal to regulate gene expression and other key cellular functions. Overall, this pathway is widely known to be activated in response to feeding related signals, and previous studies in mice found elevated pAKT levels in correspondence with food ingestion. However, it is still unknown whether this can (also) be driven through intrinsic mechanisms, such as the circadian clock. Here, we inspected daily activation of AKT both in cultured cells and animal models. Unexpectedly, we found, that neither environmental cues nor the circadian clock were necessary for pAKT rhythms, which exhibited ultradian, rather than circadian, cycles of phosphorylation. In addition, hepatic gene expression also exhibited short rhythms in clock disrupted mice, corresponding with AKT related genes/functions. Reciprocally, inhibition of AKT phosphorylation did not affect the rhythmicity of the circadian clock. Overall, our findings uncover temporal regulation of AKT activation and reveal ultradian molecular rhythmicity that cycles independently of the canonical circadian clock.

overall_design: RNA-sequencing on either wild type (WT) or Per1/2-/- (PerDKO) mice, kept in constant Darkness. RNA was extracted from livers collected over a two-day time course, in 4h intervals.

first: Rona

last: Aviram

first: Gad

last: Asher

first: Marina

last: Golik


title: RNA-seq in healthy and SQT1 hiPSC-CMs upon manipulation of miR-365

first: Dena

last: Esfandyari

summary: Abnormalities of ventricular action potential (AP) cause malignant cardiac arrhythmias and sudden cardiac death. Here, we sought to identify microRNAs (miRNAs) that regulate the human cardiac AP and asked whether their manipulation allows for therapeutic modulation of AP abnormalities. Quantitative analysis of the miRNA targetomes in human cardiac myocytes identified miR-365 as a primary miRNA to regulate repolarizing ion channels. AP recordings in patient-specific induced pluripotent stem cell-derived cardiac myocytes (iPSC-CMs) showed that elevation of miR-365 level significantly prolonged AP duration in hiPSC-CMs derived from a Short-QT syndrome (SQTS) patient, whereas specific inhibition of miR-365 normalized pathologically prolonged AP in Long-QT syndrome (LQTS) iPSC-CMs. Transcriptome analyses in human iPSC-CMs at bulk and single-cell level corroborated the key cardiac repolarizing channels as direct targets of miR-365, together with functionally synergistic regulation of additional AP-regulating genes by this miRNA. Whole-cell patch clamp experiments revealed miR-365-based regulation of repolarizing ionic currents. Finally, refractory period measurements in human myocardial slices substantiated the prolonging effect of miR-365 on AP duration also in adult human myocardial tissue. Our results delineate miR-365 to regulate human cardiac AP duration by targeting key factors of cardiac repolarization.

overall_design: hiPSC-CMs from a healthy individual were assigned to 5 treatment groups: untreated, mimic-Ctrl, mimic-365, antimiR-Ctrl and antimiR-365, and hiPSC-CMs from a short QT syndrome type 1 patient were treated with mimic-Ctrl or mimic-365 (n=3 replicates per each condition).

first: Stefan

last: Engelhardt


title: Knockout of circRNAs by base editing back-splice sites of circularized exons

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: Subcellular RNA-seq datasets are used for genome-wide analysis of circRNAs in 293FT cells. Here we knocked out circRNAs by base editor (BE)-mediated nucleotide changes.

overall_design: Poly(A)+, poly(A)- and RNaseR-treated RNAs of 293FT cells are extracted and sequenced for downstream circRNA analysis.

first: Ling-Ling

last: Chen

first: Xiang

last: Gao

first: Xu-Kai

last: Ma

first: Guo-Wei

first: Chu-Xiao

first: Jun

last: Zhang

first: Ying

first: Jia

last: Wei


title: Genome-wide distribution of Tus-GFP in KRX E. coli

city: Douglas

first: Patrick

last: Schaeffer

state: QLD

address: 1 James Cook Drive

department: CPHMVS

country: Australia

institute: James Cook University

summary: We examined the chromosomal distribution of GFP-tagged Tus (Tus-GFP) in exponentially growing E. coli (KRX) using chromosome immunoprecipitation (ChIP)-Seq. Our ChIP-seq allowed delineation of a refined minimal replication fork trap within E. coli comprising two clusters of three Ter sites

overall_design: Three biological replicates of immunoprecipitated DNA (ChIP) are shown each consisting of 2-3 technical replicates. Input DNA (Pre-Immunoprecipitated sample) was subjected to the same protocol and used as a control

first: Morgane

last: Moreau

first: Casey

last: Toft


title: scRNA-seq experiments on human foreskin fibroblasts, foreskin fibroblasts induced directly to retina pigment epithelium, and induced pluripotent stem cell derived retina pigment epithelium.

city: Kobe

first: Cody

last: Kime

state: Hyogo

address: Minatojima Minamimachi, 2-2-3

department: Center for Biosystems Dynamics Research

institute: RIKEN

summary: Regenerative medicine relies on basic research to find safe and useful outcomes that are only practical when cost-effective. The human eyeball requires the retinal pigment epithelium (RPE) for support and maintenance that interfaces the neural retina and the choroid at large. Nearly 200 million people suffer from age-related macular degeneration (AMD), a blinding multifactor genetic disease among other retinal pathologies related to RPE degradation. Recently, autologous pluripotent stem cell-derived RPE cells were prohibitively expensive due to time, therefore we developed a new simplified cell reprogramming system. We stably induced RPE-like cells (iRPE) from human fibroblasts by conditional overexpression of broad plasticity and lineage-specific pioneering transcription factors and treated some with nicotinamide and chetomin (iRPENC). iRPE cells showed features of modern RPE benchmarks and significant in-vivo integration in transplanted chimeric hosts. Herein, we provide the single-cell RNA (scRNA) sequencing profiling of the foreskin fibroblasts, iRPE, iRPENC, and model iPSC.RPE cells.

overall_design:
Cell culture samples were prepared as approximately 3,000 single cells and then sampled for scRNA-seq 10x Genomics 5' (v1.0 Chemistry) VDJ kit library construction with standard protocol for 5' Gene Expressoin libraries that skips Steps 4&5. Libraries were sequenced with paired-end reads on Illumina HiSeq X at one library per lane and then mapped to a custom reference human genome (hg38) using Cell Ranger (Version 3.1).
related study: https://doi.org/10.1101/2020.07.27.215103

first: Ivo

last: Ngundu Woogeng

first: Yoshiki

last: Sahara

first: Imad

last: Abugessaisa

first: Akira

last: Hasegawa


title: Phased gene expression and chromatin accessibility during progressive EMT and MET linked to dynamic CTCF engagement (ATAC-Seq)

city: Waco

first: Joe

last: Taube

address: One Bear Place #97388

institute: Baylor University

summary: We report the chromatin accessibility alterations and gene expression changes in TGFB-induced and -withdrawn reversible EMT in MCF10A mammary epithelial cells

overall_design: MCF10A cells were treated and withdrawn from TGFB for various durations and subjected to ATAC- and RNA-seq

first: Kelsey

last: Johnson

first: Joseph


title: The identification of small RNAs differentially expressed in apple buds reveals a potential role of the miR159-MYB regulatory module during dormancy

city: Montpellier

first: Gautier

last: Sarah

address: Place Pierre Viala

institute: INRAE

summary: Winter dormancy is an adaptative mechanism that temperate and boreal trees have developed to protect their meristems against low temperatures. In apple trees (Malus domestica), cold temperatures induce bud dormancy at the end of summer/beginning of the fall. Apple buds stay dormant during winter until they are exposed to a period of cold, after which they can resume growth (budbreak) and initiate flowering in response to warm temperatures in spring. It is well-known that small RNAs modulate temperature responses in many plant species, but however, how small RNAs are involved in genetic networks of temperature-mediated dormancy control in fruit tree species remains unclear. Here, we have made use of a recently developed ARGONAUTE (AGO)-purification technique to isolate small RNAs from apple buds. A small RNA-seq experiment resulted in the identification of small RNAs that change their pattern of expression in apple buds during dormancy.

overall_design: small RNAs expression during dormancy in apple. Four stages with three replicates for each

first: Julio

last: Garighan

first: Etienne

last: Dvorak

first: Joan

last: Estevan

first: Karine

last: Loridon

first: Bruno

last: Huettel

first: Isabelle

last: Farrera

first: Julie

last: Leclercq

first: Priscila

last: Grynberg

first: Roberto

middle: C

last: Togawa

first: Marcos

last: do Carmo Costa

first: Evelyne

last: Costes

first: Fernando

last: Andrés


title: circRNA  maps in  AhR antagonist treated K1 cells

city: Changchun

first: Feng

last: Guan

state: China

address: Department of Nuclear Medicine, The First Hospital of Jilin University

institute: The First Hospital of Jilin University

summary: High-throughput data analysis was performed to identify the differentially expressed circRNAs in K1 control cell and AhR antagonist treated K1 cells. In total, 45 differentially expressed circRNAs were found.


title: Unravelling the role of PAX2 mutation in human Focal Segmental Glomerulosclerosis

city: Bergamo

first: Susanna

last: Tomasoni

state: BG

address: Via Stezzano 87

department: Molecular Medicine

country: Italy

institute: Istituto di Ricerche Farmacologiche Mario Negri IRCCS

summary: We performed a genomewide differential gene expression analysis by Ion AmpliSeqTM Transcriptome sequencing that targets more than 20,000 human genes to gain insights into the genes and pathways involved in the onset of familial steroid-resistant Focal Segmental Glomerulosclerosis (FSGS) driven by the presence of a heterozygous mutation in the PAX2 gene (PAX2G189R/+). Using a stepwise protocol, we differentiated control and PAX2G189R/+ induced pluripotent stem cells into podocytes and we performed whole-transcriptomic analysis on control and patient cells on days 6, 13 and 18 of differentiation. Our data indicated that the PAX2 mutation mainly affects the focal adhesion pathway and the expression of IGF1, a PAX2 target, in adult podocytes that are more susceptible to cell death by environmental triggers.

overall_design: Gene expression profiles of CTR and patient cells on days 6, 13 and 18 of differentiation  towards podocytes  were generated by Ion AmpliSeq Transcriptome sequencing, in duplicate, using Ion Proton Sequencer.

first: Lorena

last: Longaretti

first: Piera

last: Trionfini

first: Caterina

last: Mele

first: Matteo

last: Breno


title: Expression data of Gyc76C mutant larvae

status: Public on Nov 25 2021

city: Sendai

first: Naoyuki

last: Fuse

state: Miyagi

address: Aoba 6-3, Aramaki, Aoba-ku

department: Graduate School of Pharmaceutical Sciences

institute: Tohoku University

summary:
We identified Gyc76C as a novel regulator in Drosophila innate immunity
We used microarray to examine gene expression in Gyc76C mutant lines.

overall_design: RNAs were extracted from larvae before and after bacteria infection, and the labeled probes were hybridized with Drosophila genome array.

first: Takayuki

last: Kuraishi

first: Shoichiro

last: Kurata


title: The regulatory role of miR-365 in human iPSC-derived cardiac myocytes

city: Munich

first: Dena

last: Esfandyari

address: Haus 607, Biedersteiner Str. 29, IPT

institute: Technical University of Munich

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

overall_design: Refer to individual Series


title: β-catenin, Tcf7l1, and Esrrb mediate seeding density-dependent gene regulation during mouse embryonic stem cell differentiation

status: Public on Nov 24 2021

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

summary: Cell density affects numerous biological processes, including gene expression and cell fate specification. However, mechanistic understanding of how changes in cell density alter the transcriptome is lacking. Here, we reveal that the expression of thousands of genes in mouse embryonic stem cells is affected by cell density. Furthermore, we find that low cell density enhances the efficiency of differentiation. Mechanistically, β-catenin is localized primarily to adherens junctions during conditions of high cell-cell contact. At low seeding density during differentiation, we observe that β-catenin translocates to the nucleus and co-activates target genes in concert with Tcf7l1, leading to the induction of lineage markers. Meanwhile, Esrrb sustains the expression of high density-specific, pluripotency-associated genes, but low seeding density differentiation reduces its occupancy on its target loci. Our demonstration of factors that transcriptionally regulate genes responsive to cell density contributes to our understanding of gene regulation in stem cells and has implications for reproducibility, as density can vary between substantially labs and experimental protocols.

overall_design: Expression and transcription factor occupancy in mouse embryonic stem cells at high and low cell seeding density.

first: Lucy

last: LeBlanc

first: Mijeong


title: Profiling of H3K4me3 and H3K27me3 and their roles in regulating gene transcription in allotetraploid cotton

first: Cen

last: Zhang


title: Profiling of H3K4me3 and H3K27me3 and their roles in regulating gene transcription in allotetraploid cotton (RNA-Seq)

overall_design: RNA-seq,ChIP-seq

first: A

first: Y

last: Wei

first: J

last: Gao

first: X

last: Deng

last: Shi

last: Feng

first: D

last: Zheng

last: Cheng

first: F

last: Liu

first: R

last: Peng

first: W


title: BBS7 -SHH signaling activity regulates primary cilia for periodontal homeostasis

status: Public on Nov 23 2021

city: Seoul

first: PI EN

last: CHANG

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Department of Orthodontics

institute: Yonsei University College of Dentistry

summary:
Purpose : This study was performed to investigate the changes in gene expression in periodontal ligament (PDL) cells between normal occlusal function and hypofunction through RNA sequencing and elucidate the related role in maintaining the PDL homeostasis.
Method : Premolars extracted for orthodontic treatment were used. The teeth with occlusal contact for control group (n=17), teeth without occlusal contact for experienment group (n=17). After the PDL cells were isolated from the extracted teeth, differentially expressed gene (DEG) analysis, and real-time PCR were performed to compare the two groups.  The effect of Bardet-Biedl syndrome 7 (BBS7) knockdown was evaluated by RT-qPCR, Wound healing assay, and Tubule formation assay.
Result : We detected that the expression of BBS7 was downregulated in occlusal hypofunctional PDL through RNA-sequencing. Sonic Hedgehog signaling (Shh) activity was closely associated with BBS7 expression in periodontal ligament cells. In addition, the cell migration and angiogenesis were also suppressed by BBS7 knockdown in vitro.
Conclusion : We suggest that BBS7 plays an essential role in maintaining Shh signaling activity for PDL homeostasis.

overall_design: Examination of the gene expression between normal occlusal function and hypofuntion in huMAN premolar PDL

first: Pi

last: Chang

first: Shjin

last: Li

first: Hyun-Yi

first: Dong-Joon

last: Lee

first: Euiseong

first: Yoon

middle: J

last: Choi

first: Han-Sung

last: Jung


title: Effect of TET deletion on the global DNA methylation status of osteoclasts

city: Kyotanabe

first: Keizo

last: Nishikawa

state: Kyoto

address: 1-3, Tatara Miyakodani

department: Medical Life Systems

institute: Graduate School of Life and Medical Sciences

type: Methylation profiling by high throughput sequencing


title: Effect of TET deletion on the global DNA methylation status of osteoclasts (RNA-Seq)

summary: Epigenetic regulation is a fundamental mechanism mediating various cellular processes. However, epigenetic mechanisms in osteoclastogenesis remain incompletely understood. We performed RNA-seq analysis to investigate gene expression in osteoclasts derived from wild-type and Tet2Rank–/–; Tet3aRank+/–  mice.

overall_design: Examination of RNA expression in 2 cell types.


title: Vascular Damage, Thromboinflammation, Plasmablast Activation, T-Cell Dysregulation and Pathological Histiocytic Response in Pulmonary Draining Lymph Nodes of COVID-19

city: Basel

first: Jasmin

last: Haslbauer

address: Schönbeinstrasse 40

department: Institute of Medical Genetics and Pathology

institute: University of Basel

summary: This study aims to characterize pathophysiological changes in lethal COVID-19 lymph nodes. 22 lethal COVID-19 cases and 28 controls were enrolled in this study. Pulmonary draining lymph nodes (mediastinal, tracheal, peribronchial) were collected at autopsy. Control lymph nodes were selected from a range of histomorphological sequelae [unremarkable histology, infectious mononucleosis, follicular hyperplasia, non-SARS related HLH, extrafollicular plasmablast activation, non-SARS related diffuse alveolar damage (DAD), pneumonia]. Gene expression profiling was performed using the HTG EdgeSeq Immune Response Panel. Characteristic patterns of a dysregulated immune response were detected: 1. An accumulation of extrafollicular plasmablasts with a relative paucity or depletion of germinal centers. 2. Evidence of T-cell dysregulation demonstrated by immunohistochemical paucity of FOXP3+, T-Bet+ and LEF1+ positive T-cells and a downregulation of key genes responsible for T-cell crosstalk, maturation and migration as well as a reactivation of herpes viruses in 6/21 COVID-19 lymph nodes (EBV, HSV). 3. Macrophage activation by a proinflammatory, CD163+ phenotype and increased incidence of hemophagocytic activity. 4. Microvascular dysfunction, evidenced by an upregulation of hemostatic (CD36, PROCR, VWF) and proangiogenic (FLT1, TEK) genes and an increase of fibrin microthrombi and CD105+ microvessels. Taken together, these findings imply widespread dysregulation of both innate and adoptive pathways with concordant microvascular dysfunction in severe COVID-19.

overall_design:
Examination of autopsy lymph node tissue of lethal COVID-19 cases versus controls by gene expression profiling
Please note that the  'VLP00581_AI_Plate1_09JAN2021_Parsed-forReveal_QualityControlled.xlsx' processed data file contains 78 data columns, while 50 samples (used for the final manuscript of the study) are included in the records. The extra data columns refer to either universal RNA samples used for correlations tests by HTG Molecular, which are labelled uRNA on the second sheet ‘QC_Raw' of the count matrix excel file, -or- samples which failed the internal quality controls of HTG Molecular, such as poor quality of sample (Q0), insufficient read depth (Q1) or expression variability (Q2),  marked on the third sheet ‘QC_summary’.  Further samples were excluded as described in the forthcoming manuscript, such as inadequate patient data.

middle: D

first: Carl

last: Zinner

first: Anna

last: Stalder

first: Jan

last: Schneeberger

first: Thomas

last: Menter

first: Stefano

last: Bassetti

first: Kirsten

last: Mertz

first: Philip

last: Went

first: Matthias

last: Matter

first: Alexandar

last: Tzankov


title: Effect of TET deletion on the global DNA methylation status of osteoclasts (MeDIP-Seq)

summary: Epigenetic regulation is a fundamental mechanism mediating various cellular processes. However, epigenetic mechanisms in osteoclastogenesis remain incompletely understood. We performed MeDIP-seq analysis to investigate DNA methylation in osteoclasts derived from wild-type and Tet2Rank–/–; Tet3aRank+/–  mice.

overall_design: Examination of DNA methylation in 2 cell types.


title: Multiple tolerance checkpoints restrain affinity maturation of B cells expressing the germline precursor of a lupus patient-derived anti-dsDNA antibody in knock-in mice

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Anti-dsDNA antibodies are a hallmark of systemic lupus erythematosus and are highly associated with its exacerbation. Cumulative evidence has suggested that somatic hypermutation contributes to the high-affinity reactivity of anti-dsDNA antibodies. Our previous study demonstrated that these antibodies are generated from germline precursors with low-affinity ssDNA reactivity through affinity maturation and clonal expansion in patients with acute lupus. This raised the question of whether such precursors could be subject to immune tolerance. To address this, we generated a site-directed knock-in (KI) mouse line, G9gl, which carries germline-reverted sequences of the VH–DH–JH and Vκ–Jκ regions of patient-derived, high-affinity anti-dsDNA antibodies. G9gl heterozygous mice had a reduced number of peripheral B cells, only 27% of which expressed G9gl B cell receptor (BCR). The remaining B cells harbored non-KI allele-derived immunoglobulin heavy (IgH) chains or fusion products of upstream mouse VH and the KI gene, suggesting that receptor editing through VH replacement occurred in a large proportion of B cells in the KI mice. G9gl BCR-expressing B cells responded to ssDNA but not dsDNA, and exhibited several anergic phenotypes, including reduced surface BCR and shortened life span. Further, G9gl B cells were excluded from germinal centers (GCs) induced by several conditions. In particular, following immunization with methylated bovine serum albumin-conjugated bacterial DNA, G9gl B cells occurred at a high frequency in memory B cells but not GC B cells or plasmablasts. Thus, multiple tolerance checkpoints prevented low-affinity precursors of pathogenic anti-dsDNA B cells from undergoing clonal expansion and affinity maturation in GCs.

overall_design: To gain insight into the unique anergic phenotype of G9gl B cells, we compared global gene expression in Fo B cells isolated from WT and G9gl HL homozygous mice

last: Motooka

first: Shuhei

last: Sakakibara


title: Quantifying RNA Synthesis at Rate-Limiting Steps of Transcription Using Nascent RNA-sequencing Data

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH Royal Institute of Technology

summary: Precision Run-On sequencing (PRO-seq) data from human K562 cells, mapped to hg38.

overall_design: The raw PRO-seq data was generated in human K562 cells (Vihervaara et al., 2021, Mol Cell; GSE127844). Here, the PRO-seq data derived from unstressed K562 cells was remapped to the hg38 genome.


title: SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes

city: New Haven

first: Paulina

last: Pawlica

state: CT

address: 295 Congress Avenue, BCMM Room 131

department: MBB

institute: Yale University

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19), continues to be a pressing health concern. In this study, we investigated the impact of SARS-CoV-2 infection on host microRNA (miRNA) populations in three human lung-derived cell lines, as well as in nasopharyngeal swabs from SARS-CoV-2–infected individuals. We did not detect any major and consistent differences in host miRNA levels after SARS-CoV-2 infection. However, we unexpectedly discovered a viral miRNA-like small RNA, named CoV2-miR-O7a (for SARS-CoV-2 miRNA-like ORF7a-derived small RNA). Its abundance ranges from low to moderate as compared to host miRNAs and it associates with Argonaute proteins—core components of the RNA interference pathway. We identify putative targets for CoV2-miR-O7a, including Basic Leucine Zipper ATF-Like Transcription Factor 2 (BATF2), which participates in interferon signaling. We demonstrate that CoV2-miR-O7a production relies on cellular machinery, yet is independent of Drosha protein, and is enhanced by the presence of a strong and evolutionarily conserved hairpin formed within the ORF7a sequence.

overall_design: Calu-3, PC-9 and A459-hACE2 cells were infected with SARS-CoV-2 at different MOIs and time points, and small RNA sequencing was performed. In addition, anti-Ago immunoprecipitation followed by small RNA sequencing was performed on extracts from SARS-CoV-2 infected cells.

first: Therese

last: Yario

first: Sylvia

last: White

first: Jianhui

last: Wang

first: Walter

middle: N

last: Moss

first: Pei

last: Hui

first: Joseph

middle: M

last: Vinetz

first: Joan

last: Steitz


title: Transcriptomic and Single-Cell Analysis Reveals Regulatory Networks and Cellular Heterogeneity in Mouse Sjögren’s Syndrome Salivary Glands

city: Buffalo

first: Jonathan

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

institute: University at Buffalo

summary: Our scRNA-seq and bulk RNA-seq studies have revealed key pathways, mediators, new biomarkers, and have uncovered the complex nature of the cellular populations in the SMG that are likely to drive the progression of SS.

overall_design: 10x scRNA-Seq and bulk-RNA-seq of salivary gland of a Sjogren Syndrome mouse model.

first: Erich

last: Horeth

first: Akinsola

last: Oyelakin

first: Eun

last: Song

first: Monika

last: Che

first: Sangwon

last: Min

first: Jeremy

last: Kiripolsky

first: Jill

last: Kramer

first: Satrajit

last: Sinha

first: Rose

middle: A

last: Romano


title: Anakinra restores cellular proteostasis by coupling mitochondrial redox balance to autophagy

status: Public on Nov 27 2021

city: Perugia

first: Luigina

last: Romani

address: P.le Lucio Severi 1

institute: University of Perugia

summary: Autophagy selectively degrades aggregation-prone misfolded proteins caused by defective cellular proteostasis. However, the complexity of autophagy may prevent the full appreciation of how its modulation could be used as a therapeutic strategy in disease management. Here we define a molecular pathway through which recombinant interleukin-1 receptor antagonist (IL-1Ra, anakinra) affects cellular proteostasis independently from the IL-1 receptor (IL-1R1). Anakinra promoted H2O2-driven autophagy through a xenobiotic sensing pathway involving the aryl hydrocarbon receptor that, activated through the indoleamine 2,3-dioxygenase 1-kynurenine pathway, transcriptionally activates NADPH Oxidase 4 independent of the IL-1R1. By coupling the mitochondrial redox balance to autophagy, anakinra improved the dysregulated proteostasis network in murine and human cystic fibrosis. We anticipate that anakinra may represent a therapeutic option in addition to its IL-1R1 dependent anti-inflammatory properties by acting at the intersection of mitochondrial oxidative stress and autophagy with the capacity to restore conditions in which defective proteostasis leads to human disease.

overall_design: mRNA profiles of alveolar macrophages purified from C57BL/6 and Il1r1-/- mice treated or not with Anakinra


title: Codon-dependent transcriptional changes in response to tryptophan limitation in the tryptophan auxotrophic pathogens Chlamydia trachomatis and Streptococcus pyogenes

city: Omaha

first: Scot

last: Ouellette

state: NE

address: 985900 Nebraska Medical Center

department: Pathology, Microbiology, and Immunology

institute: University of Nebraska Medical Center

summary: RNAseq analysis was performed for C. trachomatis serovar L2 and S. pyogenes NZ131 in the presence and absence of tryptophan to monitor transcriptional changes.

sample_organism:
Homo sapiens
Streptococcus pyogenes NZ131

overall_design: RNA was collected from C. trachomatis L2 infected cells at 10, 14, and 24h post-infection. At 10hpi, tryptophan or leucine starvation was induced with Indolmycin or AN3365, respectively, or cells were treated with IFN-gamma. Treatment samples were collected at 14 and 24hpi. Comparisons were made over the timecourse series and comparing treatments to untreated at 10hpi. For S. pyogenes NZ131, the bacteria were cultured in the presence or absence of tryptophan for 1hr prior to RNA collection in the presence or absence of rifampicin (Rif) to determine transcript half-life. All data were compared to the amino acid content of the encoded protein for a given gene.

first: Nathan

last: Hatch

first: Nicholas

last: Wood

first: Andrea

last: Herrera

first: Michael

last: Chaussee


title: Gene Expression Profiling of HEMGN-/- and WT HSPCs sorted from primary recipients 6h after transplantation (early homing cells)

status: Public on Nov 22 2021

city: Beijing

first: Xian

last: Liu

address: 38 Life Science Park Street

institute: Beijing Institute of Life Omics

summary: To clarify the mechanism through which HEMGN (also known as EDAG in human) controls the survival and functions of hematopoietic stem and progenitor cells (HSPCs) under transplantation stress, we compared the transcriptome of Hemgn-/- and WT HSPCs isolated from primary recipients 6h after transplantation by RNA sequencing (RNA-Seq).

overall_design: 2×10^7 bone marrow cells from Hemgn-/- or WT (CD45.2+) mice were injected intravenously via the tail vein into recipients mice (CD45.1+) previously irradiated with a split dose of 9Gy (4.5Gy+4.5Gy). At 6h after transplantation, donor HSPCs (CD45.2+Lin-Sca-1+c-Kit+) were isolated and total RNA was isolated using the QIAGEN RNeasy Micro Kit (QIAGEN). Each group contain three replicates. Smart-Seq2 method was used to produce cDNA. The cDNA production was checked by Qubit® 3.0 Flurometer and Agilent 2100 Bioanalyzer to ensure the expected production with length around 1~2kbp. Then the cDNA was sheared randomly by ultrasonic waves for Illumina library preparation protocol including DNA fragmentation, end repair, 3’ ends A-tailing, adapter ligation, PCR amplification and library validation. After library preparation, PerkinElmer LabChip® GX Touch and Step OnePlus™ Real-Time PCR System were introduced for library quality inspection. Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing at the ANNOROAD GENOME Co., Ltd. (Beijing, CN) following the vendor's recommended protocol.

first: Ke

last: Zhao

first: Jinfang

last: liu

first: Changyan

last: Li

first: Xiaoming

last: Yang


title: Intermittent PI3Kα/β/δ Inhibitor Treatment Alleviates Immunosuppressive Environment in PTEN-null prostate Cancer and facilitate Anti-PD-1 Therapy

first: Zihan

last: Xu

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: Examination of gene expression level in tumor tissue or CD8T cell in vehicle,  BAY1082439 (Single dose), BAY1082439 daily/intermittent treatment, BAY1082439 treatment release drug treatment group. Examination of gene expression level in CAP2 CAP8 PC3 and LNCaP cell line in vehicle or BAY1082439 treatment. Examination of gene expression level in spleen CD8T cell in vehicle or intermittent BAY1082439 treatment.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Examination of gene expression levels using RNA-seq.

The Supplementary_data_1.xlsx was added to the records on Jan 10, 2022.

first: Zhi

last: Qi


title: RNA-seq gene expression of flow cytometry sorted breast cancer stem cell populations

status: Public on Nov 21 2021

city: Cincinnati

last: Haas

state: OH

address: 3125 Eden Ave Vontz 3442

institute: University of Cincinnati

summary: MMTV-PyMT transgenic FVBN mice spontaneously developed breast tumors. Two tumors were collected as replicate samples, and cells from the dissociated tissue were sorted into 2 cancer stem cell (CSC) populations, along with the remaining non-CSCs. The samples were submitted for RNAseq to generate differential gene expression profiles of the breast tumor CSC populations.

overall_design: Gene expression profile of ALDH positive and CD29 hi, CD61 positive CSC populations compared to non-CSC from mouse breast tumor.

first: Syn

middle: K

last: Yeo

first: Jun-Lin

last: Guan


title: Liraglutide inhibits osteoclastogenesis and improves bone loss by down-regulating Trem2 in female type 1 diabetic mice: findings from transcriptomics

first: Jie

last: Yu

address: Shuaifuyuan No.1,Dongcheng District

department: Department of Endocrinology

institute: Peking Union Medical College Hospital, Chinese Academy of Medical Science

summary: Aims:We aimed to explore possible mechanisms of bone loss in T1D and clarify whether liraglutide have effects on bone quality of T1D mice using transcriptomics, .  Methods:Female streptozotocin-induced diabetic C57BL/6J mice were randomly divided into 4 groups and received the following treatments daily for 8 weeks: saline as controls; insulin; liraglutide; liraglutide combined with insulin. These groups were also compared to non-STZ-treated normal glucose tolerance (NGT) group. Trunk blood and bone tissues were collected for analysis. Three tibia from each of the NGT, saline treated and liraglutide treated group were randomly selected for transcriptomics.  Results:Compared with NGT mice,saline treated T1D mice manifested markedly hyperglycemia and weight loss, and micro-CT revealed significantly lower bone mineral density(BMD) and deficient microarchitectures in tibias.8 weeks’ treatment with liraglutide alone or combined with insulin rescued the decreased BMD and partly corrected compromised trabecular microarchitectures. Transcriptomics analysis showed there were 789 differentially expressed genes mainly mapped to osteoclastogenesis and inflammation pathways.RT-qPCR verified gene expression of Trem2, Nfatc1, Trap and Ctsk were significantly increased in tibia of T1D compared to that in NGT group. Liraglutide treatment alone or combined with insulin could effectively suppress osteoclastogenesis by down-regulating gene expression of Trem2, Nfatc1, Ctsk and Trap.

overall_design: Three tibia from each of the NGT, saline treated and liraglutide treated T1D group were randomly selected for transcriptomics.

first: Lingling

first: Yuxiu


title: NFAT5/TonEBP controls metabolic adaption and tone of pulmonary vascular smooth muscle cells in the hypoxic lung [SMC]

status: Public on Nov 26 2021

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary: Hypoxia provokes adaptive responses of cells, which ensure their energy supply including the adjustment of the transcriptome to match their metabolism. In this context, we explored the transcriptional impact of nuclear factor of activated T-cells 5 (NFAT5) on the function of vascular smooth muscle cells (VSMC) in the hypoxic lung.  Exposure to hypoxia induced a rapid nuclear translocation of NFAT5 in cultured murine VSMCs. SMC-specific ablation of Nfat5 (Nfat5(SMC-/-)) increases the systolic pressure in the right ventricle (RVSP) of the mouse heart and impairs its function upon exposure to hypoxia for 7 and 21 days. Analyses of the transcriptome of the lung revealed a robust increase in the expression genes attributed to mitochondrial respiration. Further analyses of hypoxia-exposed pulmonary artery VSMCs revealed that loss of Nfat5 stimulates the expression of multiple mitochondria-related genes encoding cytochrome oxidases while decreasing the expression of lactate dehydrogenase A (Ldha) and phosphofructokinase 3 (Pfkfb3). Both, inhibition of LDHA or PFKFB3 activity and loss of Nfat5 stimulated the mitochondrial production of reactive oxygen species (ROS) in hypoxic pulmonary artery VSMCs while scavenging of ROS normalized the RVSP values in hypoxia-exposed Nfat5(SMC-/-) mice.  In summary, our findings suggest a crucial role for NFAT5 in adjusting the transcriptome of hypoxia-exposed pulmonary artery VSMCs to support an adequate glycolysis-centered metabolism. Loss of Nfat5 impairs this response thereby fueling the mitochondrial respiration and ROS production that amplifies the hypoxia-mediated constriction of pulmonary arteries.

overall_design: Nfatfl/fl (control) mice or Nfat5(SMC)-/- (KO) mice were exposed to hypoxia (n=3, 10% oxygen) for 7 days

first: Thomas

last: Korff


title: Effect of salivary exosomal miR-25-3p on periodontitis with insulin resistance

status: Public on Nov 20 2021

city: Daejeon

first: Ho Yeop

last: Lee

address: 266, Munhwa-ro, Jung-gu

institute: Chungnam national university

summary: Salivary exsomal miRNAs may play important role in the pathogenesis of chronic inflammatory disease, such as periodontitis. There are many studies which suggested the connection between periodontitis and systemic disease, however, the role of specific miRNA as a intersection of periontitis and diabetes are not elucidated. We suggested miR-25-3p as possible common mediator in the pathogenesis of periodontitis and diabetes.

overall_design: Salivary exosomal miRNA profiles of Control and Type2 Diabetes patients

first: Jinseok

last: Byun

first: Soyeon

last: Bae


title: Mutation and selection explain why eukaryotic centromeric DNA is often A+T rich

city: Nottingham

first: WILLIAM

middle: RA

last: BROWN

state: NOTTS

address: Life Sciences Department, Queens Medical Centre

department: Life Sciences

country: United Kingdom

institute: Nottingham University

summary: The reasons why centromeric DNA is often A+T rich are not understood. We have used chromosome engineering to replace native centromeric DNA with different test sequences at native centromeres in two different strains of the fission yeast Schizosaccharomyces pombe and have discovered that A+T rich DNA, whether synthetic or of bacterial origin, will function as a centromere and that the functionality of the A+T rich DNA does not differ substantially from that of native centromeric DNA. Using genome size as a surrogate for the inverse of effective population size (Ne) we also show that the relative A+T content of centromeric DNA scales with Ne across 45 eukaryotic species. This suggests that in most eukaryotes the A+T content of the centromeric DNA is adaptive and that the A+T content of centromeric DNA is determined by a balance between selection and mutation.  Combing the experimental results and the evolutionary analyses allows us to conclude that A+T rich DNA of almost any sequence will function as a centromere in most eukaryotes. The fact that many G/C to A/T substitutions are unlikely to be selected against may contribute to the rapid evolution of centromeric DNA.  We also show that neo-centromeres are not simply weak versions of native centromeres but that their establishment or inheritance may require factors in addition to those required by native centromeres.

overall_design: ChIP~seq analysis of GFP-labelled centromeric histone CENP-ACnp1 in different strains of S. pombe that have been modified by genome engineering techniques to investigate the sequence requirments for centromere function.

first: William

last: Brown


title: NFAT5/TonEBP controls metabolic adaption and tone of pulmonary vascular smooth muscle cells in the hypoxic lung [normoxia vs hypoxia]

overall_design: Nfatfl/fl mice were exposed to normoxia (n=4) and hypoxia (n=4, 10% oxygen) for 7 days,


title: Knockout of NFAT5 in endothelial cells

summary: Endothelial cell-specific genetic ablation of Nfat5 was induced in adult mice. These anmials and control mice were exposed to hypoxia (10% oxygen) for 7 days. The lungs were processed for RNA exptraction and further analyses of the transcriptome

overall_design: 3 samples of each experimental group were analyzed


title: Postmortem high-dimensional immune profiling of severe COVID-19 patients reveals distinct patterns of immunosuppression and immunoactivation [RNA-seq]

city: Hefei

first: Cheng

last: Sun

state: Anhui

address: 17, Lujiang Road

department: the First Affiliated Hospital of USTC

institute: University of Science and Technology of China

summary: To delineate the in situ immune responses to SARS-CoV-2 viral infection, we performed comprehensive immune profiling in COVID-19 decedents. In this study, we described the immune microenvironment of COVID-19 patients through transcriptome sequencing.

overall_design: This dataset contains expression from SARS-CoV-2 infected patients and healthy control, various tissues.

first: Peiqi

last: He


title: Postmortem high-dimensional immune profiling of severe COVID-19 patients reveals distinct patterns of immunosuppression and immunoactivation [NanoString GeoMx]

overall_design: This dataset contains expression from localized sampling within 8 SARS-CoV-2 infected patient FFPE samples collected during rapid autopsy. Up to 12 segments were collected within each patient sample. RNA Scope on serial sections was used to guide ROI selection, and ROI ISH staining by RNA Scope is noted in the sample annotations.


title: Alternative Polyadenylation by Sequential Activation of Distal and Proximal PolyA Sites

city: Wuhan

first: Yu

last: Zhou

state: Hubei

address: Luojia Hill

department: College of Life Sciences

institute: Wuhan University

summary: Analogous to alternative splicing, alternative polyadenylation (APA) has long been thought to result from competition between proximal and distal polyA sites. By Fractionation-seq, we unexpectedly identified several hundred APA genes where their distal polyA isoforms are retained in chromatin/nuclear matrix and proximal polyA isoforms released into the cytoplasm. Global metabolic PAS-seq and Nanopore long-read RNA-seq provided further evidence that the strong distal polyA sites are first processed and the resulting transcripts are anchored in chromatin/nuclear matrix for further processing at proximal polyA sites and removal of certain slowly spliced introns. By engineering an autocleavable ribozyme between the proximal and distal polyA sites, we demonstrated that the distal polyA isoform is indeed the precursor to the proximal polyA isoform. Therefore, unlike alternative splicing, APA sites are recognized independently, rather than competitively, and in many cases, in a sequential manner. This provides a versatile strategy to regulate gene expression in mammalian cells.

overall_design: Examination of long and short 3'UTR isoform distribution by Cellular fractionation coupled with NGS RNA-seq and Nanopore RNA-seq.  Examination of proximal and distal polyA site usage by SLAM PAS-seq. Detection of 3′ intermediates from sequential polyadenylation with Cleave-seq.

first: Peng

last: Tang

first: Yang


title: NFAT5/TonEBP controls metabolic adaption and tone of pulmonary vascular smooth muscle cells in the hypoxic lung

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

overall_design: Refer to individual Series


title: Expression data of Gyc76C mutant adults

city: Sendai

first: Naoyuki

last: Fuse

address: Aoba 6-3, Aramaki, Aoba-ku

institute: Tohoku University

summary:
We identified Gyc76C as a novel regulator in Drosophila innate immunity
We used microarray to examine gene expression in Gyc76C mutant adult.

overall_design: RNAs were extracted from adult flies, and the labeled probes were hybridized with Drosophila genome array.

first: Akira

last: Goto

first: Shoichiro

last: Kurata


title: TCR variable regions transcripts of CT26-shppp2r1a and CT26-scr samples

city: Taichung

first: Yu-Ting

last: Yen

address: No.91, Hsueh-Shih Road

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: China Medical University

summary: TCR variable regions transcripts of three CT26-shppp2r1a samples and three CT26-scr samples

first: Shih-Chieh

last: Hung

first: May

last: Chien


title: MCPH1 inhibits condensin II during interphase by regulating its SMC2-kleisin interface

status: Public on Nov 19 2021

city: Houston

first: Muhammad

middle: Saad

last: Shamim

state: Texas

address: 6100 Main Street

department: Bioengineering

institute: Rice University

summary: The dramatic change in morphology of chromosomal DNAs between interphase and mitosis is one of the defining features of the eukaryotic cell cycle. Two types of enzymes, namely cohesin and condensin confer the topology of chromosomal DNA by extruding DNA loops. While condensin normally configures chromosomes exclusively during mitosis, cohesin does so during interphase. The processivity of cohesin’s loop extrusion during interphase is limited by a regulatory factor called WAPL, which induces cohesin to dissociate from chromosomes via a mechanism that requires dissociation of its kleisin from the neck of SMC3. We show here that a related mechanism may be responsible for blocking condensin II from acting during interphase. Cells derived from patients affected by microcephaly caused by mutations in the MCPH1 gene undergo premature chromosome condensation but it has never been established for certain whether MCPH1 regulates condensin II directly.  We show that deletion of Mcph1 in mouse embryonic stem cells unleashes an activity of condensin II that triggers formation of compact chromosomes in G1 and G2 phases, which is accompanied by enhanced mixing of A and B chromatin compartments, and that this occurs even in the absence of CDK1 activity.  Crucially, inhibition of condensin II by MCPH1 depends on the binding of a short linear motif within MCPH1 to condensin II’s NCAPG2 subunit.  We show that the activities of both Cohesin and Condensin II may be restricted during interphase by similar types of mechanisms as MCPH1’s ability to block condensin II’s association with chromatin is abrogated by the fusion of SMC2 with NCAPH2. Remarkably, in the absence of both WAPL and MCPH1, cohesin and condensin II transform chromosomal DNAs of G2 cells into chromosomes with a solenoidal axis showing that both cohesin and condensin must be tightly regulated to adjust the structure of chromatids for their successful segregation.

overall_design: Analysis of the impact of Mcph1 deletion on genome architecture

first: Martin

last: Houlard

first: Erin

middle: E

last: Cutts

first: Jonathan

last: Godwin

first: David

last: Weisz

first: Lothar

last: Schermelleh

first: Aviva

middle: P

last: Aiden

first: Erez

first: Alessandro

last: Vannini

first: Kim

last: Nasmyth


title: The regulatory role of lncRNA AC093797.1 in the Hepatocellular carcinoma cell line HCCLM3 in nude mice.

city: Luzhou

first: Cunliang

last: Deng

state: Sichuan

address: Taiping street No.25

department: Department of infectious diseases

country: China

institute: The affiliated hospital of southwest medical university

summary:
Purpose: The clinical significance, biological function of AC093797.1 are still unexplored in HCC or any other malignant tumor. In this study, we aimed to investigate the biological function of AC093797.1 in HCC and screen the candidate hub genes and pathways related to hepatocarcinogenesis via RNA-sequencing.
Methods: The effects of AC093797.1 on tumor growth in vivo was clarified by nude mice tumor formation experiments. The 5-weeks old female BALB/c nude mice weighing 15-20g were maintained under specific-pathogen-free conditions and randomly divided into OE-AC093797 group and negative control (NC) group (n=5 per group). Then the HCCLM3 cells stably transfected with control vector pcDNA3.1 or the overexpression vector OE-AC093797.1 (5×10^7cells in 100μl) were subcutaneously injected into nude mice. Calculate the volume of the tumors by the following formula: Vtumor= length × width2×π/6. When the tumor grows to about 2000 mm3, the mice were sacrificed after anesthesia and their tumor tissues were isolate. Three mice of each group were used to RNA-sequencing and bioinformatics analysis based on subcutaneous tumor tissue.
Results: The “DESeq2” package of R software was used to filtered the differential expressed genes between the OE-AC093797 group and the NC group. The cut-off criteria of differential expressed genes was |log2FoldChange|>1.5 and adj. p value (FDR)<0.05. 710 differentially expressed genes (243 up-regulated genes and 467 down-regulated genes) were screened between groups, which mainly enriched in amino acid metabolism，extracellular matrix structure constituent, cell adhesion molecules cams，signaling to Ras, and signaling to ERKs, etc. via gene ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and gene set enrichment analysis (GSEA).
Conclusion: AC093797.1 can inhibits tumor group might via reprogram cell metabolism or Extracellular matrix dynamics in HCC.

overall_design: mRNA profiles of tumors in the  OE-AC093797 and NC group

first: Qing

last: Yang


title: Transcriptomic analysis of the follicle associated epithelium of Peyer's Patches, intestinal villous epithelium and ileum from young and aged mice

city: Lancaster

first: Barbara

middle: Bo-Ju

last: Shih

address: Bailrigg

department: Biomedical and Life Sciences

institute: Lancaster University

summary: We have previously shown that aging affects the functional maturation of M cells in the follcile associated epithelium (FAE) of Peyer's patches in the small intestine.  To further characterise how aging affects the FAE, mRNA-seq was performed on micro-dissected FAE and villous epithelial sheets as well as whole ileum from young (4 month old) and aged (26-28 month old) mice

overall_design: mRNA profiles of follicle associated epithelium of Peyer's Patches (n=3 mice), intestinal villous epithelium (n=4-6 mice) and ileum (n=4 mice) from young and aged mice.

last: Donaldson

first: Neil

last: Mabbott


title: Expression data of Gyc76C overexpressing larvae

first: Naoyuki

last: Fuse

department: Graduate School of Pharmaceutical Sciences

summary:
We identified Gyc76C as a novel regulator in Drosophila innate immunity
We used microarray to examine gene expression in Gyc76C overexpressed lines.

overall_design: RNAs were extracted from larvae, and the labeled probes were hybridized with Drosophila genome array.

first: Shinzo

last: Iwashita

first: Akira

last: Goto

first: Shoichiro

last: Kurata


title: The transcription factor EGR2 is indispensable for tissue-specific imprinting of alveolar macrophages in health and tissue repair

city: Edinburgh

first: Calum

last: Bain

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh


title: The transcription factor EGR2 is indispensable for tissue-specific imprinting of alveolar macrophages in health and tissue repair [Alveolar macrophages]

summary: We compare the transcriptional profile of Egr2-sufficient or Egr2-deficient airway macrophages obtained from Lyz2-Cre-Egr2-floxed mice

overall_design: Alveolar macrophages were purified by FACS from enzymatically digested lung tissue, RNA isolated and analysed by ultra-low input bulk RNA-seq

first: Jack

last: McCowan

first: Frederic

last: Fercoq

first: Phoebe

last: Kirkwood

first: Wouter

last: T'Jonck

first: Connar

last: Mwaer

first: Richard

last: Cunningham

first: Ananda

last: Mirchandani

first: Anna

last: Hoy

first: Gareth-Rhys

last: Jones

first: Carsten

middle: G

last: Hansen

first: Nik

last: Hirani

first: Stephen

last: Jenkins

first: Sandrine

last: Henri

first: Bernard

last: Malissen

first: Sarah

middle: R

last: Walmsley

middle: H

last: Dockrell

first: Philippa

middle: T

last: Saunders

first: Leo

last: Carlin