title: CRISPR screens unveil signal hubs for nutrient licensing of T cell immunity [CRISPR screen]

status: Public on Mar 31 2022

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

country: USA

institute: St Jude Children's Research Hospital

summary: Integrative system approaches uncover a three-tier system for the regulatory modules of nutrient signaling-dependent mTORC1 activation in primary T cells

overall_design: Genome-wide CRISPR screen of pS6hi and pS6lo in iTreg cells upon TCR stimulation

first: Lingyun

last: Long

first: Jun

last: Wei

first: Hao

last: Shi


title: Examination of the effect of exosome in FBS on myogenic differentiation

city: Toyoake

first: Takahiko

last: Sato

state: Aichi

address: 1-98, Dengakugakubo, Kutsukakecho

country: Japan

institute: Fujita Health University

type: Expression profiling by high throughput sequencing

summary: we performed Next-generation sequencing analyses with C2C12 cells in growing conditions with 10% of FBS, or in differentiating conditions with 0.2% of FBS or 2% of horse serum with or without added exosomes

overall_design: Examination of the treatment with exosomes in differentiating C2C12 cells.


title: Genome wide CRISPR/Cas9 screen identifies the coagulation factor IX (F9) as a regulator of senescence

city: London

first: Ana

last: O'Loghlen

address: 4 Newark St

country: United Kingdom

institute: Queen Mary University of London

summary: During this last decade the development of pro-senescence therapies has become an attractive strategy as cellular senescence acts as a barrier against tumour progression. In this context, CDK4/6 inhibitors induce senescence and reduce tumour growth in breast cancer patients. However, even though cancer cells are arrested after CDK4/6 inhibitor treatment, genes regulating senescence in this context are still unknown limiting their anti-tumour activity. Here, using a functional genome wide CRISPR/Cas9 genetic screen we found several genes that participate in the proliferation arrest induced by CDK4/6 inhibitors. We find that downregulation of the coagulation factor IX (F9) using sgRNA and shRNA prevents the cell cycle arrest and senescent-like phenotype induced in MCF7 breast tumour cells upon Palbociclib treatment. These results were confirmed using another breast cancer cell line, T47D, and with an alternative CDK4/6 inhibitor, Abemaciclib, and further tested in a panel of 22 cancer cells. While F9 knockout prevents the induction of senescence, treatment with a recombinant F9 protein was sufficient to induce a cell cycle arrest and senescence-like state in MCF7 tumour cells. Besides, endogenous F9 is upregulated in different human primary cells cultures undergoing senescence. Importantly, bioinformatics analysis of cancer datasets suggest a role for F9 in human tumours. Altogether, these data collectively propose key genes involved in CDK4/6 inhibitor response that will be useful to design new therapeutic strategies in personalized medicine in order to increase their efficiency, stratify patients and avoid drug resistance.

overall_design: CRISPR/Cas9 sscreen to identidy genes whose loss overcome the cellular senescent arrest induced by the CDK4/6 inhibitor, Palbociclib or PD-0332991 (Palbo)

first: Michela

last: Borghesan


title: RNA-seq analysis of hormone receptor positive breast cancer cell line T47D with 24h hormone treatment

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

institute: University of Colorado Denver Anschutz Medical Campus

summary: T47D cells treated with hormones 24h

overall_design: Triplicates of OH (vehicle), E2, R5020, E2+R5020

first: Kiran

middle: V

last: Paul

first: Ashley

last: Ward

first: Peter

last: Kabos

first: Carol

middle: A

last: Sartorius


title: CRISRP screens reveal determinants of PARP inhibitor response in prostate cancer

city: Boston

first: Li

last: Jia

state: Massachusetts

address: 20 Shattuck Street, Thorn 1529

department: Surgery

institute: Brigham and Women's Hospital

summary: Gene expression profilings for prostate cancer cells after olaparib treatment

overall_design: Two cell lines with two treatments.

first: Takuya

last: Tsujino

first: Tomoaki

last: Takai


title: Genome-wide Analysis Reflects Novel 5-Hydroxymethylcytosines Implicated in Diabetic Nephropathy

city: Chicago

first: Wei

last: Zhang

state: IL

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

type: Methylation profiling by high throughput sequencing

summary: Background:  Long-term complications of type 2 diabetes (T2D) are the major causes for T2D-related disability and mortality. Notably, diabetic nephropathy (DN) has become the most frequent cause of end-stage renal disease (ESRD) in most countries. Understanding epigenetic contributors to DN can provide novel insights into this complex disorder and lay the foundation for more effective monitoring tools and preventive interventions, critical for achieving the ultimate goal of improving patient care and reducing healthcare burden.

overall_design: The 5hmC-Seal, a selective chemical labeling technique was used to profile genome-wide 5-hydroxymethylcytosines (5hmC), an emerging class of cytosine modifications, in patient-derived circulating cell-free DNA (cfDNA). Differentially modified 5hmC genes were identified across T2D patients with DN (n = 12), T2D patients with non-DN vascular complications (non-DN) (n = 29), and T2D patients with no complications (controls) (n = 14).

first: Songmei

last: Liu

first: Chuan

last: He

first: Ying

last: Yang

first: Zhou

first: Chang

last: Zeng


title: Genome-wide mapping of the histone modification H3K4me3 in bovine early embryos [ChIP-seq]

city: Hangzhou

first: Kun

address: 866 Yuhangtang Rd

country: China

institute: Zhejiang University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Reprogramming of histone modification regulates gene expression and mammal preimplantation development. Trimethylation of lysine 4 on histone 3 (H3K4me3) has unique landscape in mouse oocytes and early embryos. However, the dynamics and function of H3K4me3 in livestock embryos remain unclear. To address how it is reprogrammed in domestic animals, we profiled changes of H3K4me3 during bovine early embryo development. Notably, the overall signal of H3K4me3 decreased during embryonic genome activation (EGA). By utilizing ultra-low-input native ChIP-seq (ULI-NChIP-seq) technology, we observed widespread broad H3K4me3 domains in oocytes and embryos. The signal of broad H3K4me3 began to decrease after fertilization and was lowest after EGA. Along with the removal of broad H3K4me3, deposition of H3K4me3 at promoter regions enhanced gradually. Besides, the transcriptional activity and signal of promoter H3K4me3 showed positive correlation after the erasure of broad H3K4me3 at 16-cell stage. Moreover, knocking down of demethylases KDM5A, KDM5B and KDM5C caused EGA delay and blastocyst formation failure. RNA-seq analysis revealed 47.8% down-regulated genes in knockdown embryos at 8/16-cell stage were EGA genes, and 63.1% of up-regulated genes were maternal transcripts. Particularly, the positive correlation between transcriptional activity and promoter H3K4me3 during EGA was restrained when knocking down of KDM5A, KDM5B and KDM5C. Overall, our work initiatively mapped the genomic reprogramming of H3K4me3 during bovine preimplantation development, and KDM5A/B/C played roles in modulating oocyte-to-embryonic transition (OET) through timely erasure of broad H3K4me3 domains far away from promoters.

overall_design: Examination of  H3K4me3 genomic distribution by ULI-NChIP-seq in bovine embryos

first: Yanna

last: Dang


title: Identification of circular RNAs expression pattern in caprine fetal fibroblast cells exposed to a chronic noncytotoxic dose of graphene oxide-silver nanoparticle nanocomposites

city: Yangzhou

first: LiLing

last: Li

address: 中国江苏省扬州市双桥街道扬州大学文汇路校区

institute: Yangzhou University

type: Non-coding RNA profiling by high throughput sequencing

summary: circRNA sequencing for 6 samples.The increasing use of graphene oxide-silver nanoparticle nanocomposites (GO-AgNPs) in biomedical sciences and research also increases the chances of human and animal exposure to its chronic non-toxic doses. However, the available information is truly little for profound understanding of the effect of low-dose chronic exposure to GO-AgNPs on the epigenetic modification of the organism. In this research, we have investigated the impact of non-toxic doses of GO-AgNPs (0.5 µg/mL for 10 weeks, this dose does not interfere cell viability and ROS level) on the differential expression of circular RNAs (circRNAs) in caprine fetal fibroblast cells (CFFCs). In addition, using bioinformatics tools we have predicted the functions of those differentially expressed circRNAs on CFFCs. Furthermore, we have validated the expression of ten circRNAs using qRT-PCR to ensure the reliability of the sequencing data. The results showed that the differentially expressed circRNAs potentially regulates the GO-AgNPs induced epigenetic toxicity through a regulatory network consisted of circRNAs, miRNAs and mRNAs. Therefore, the inclusion of epigenetics approaches is essential to assess the biosafety level of GO-AgNPs nanomaterials.

overall_design: Examing 2 conditions, each with 3 replicates

first: Yu-Guo

last: Yuan

first: Song-Zi


title: Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2 [Hi-C]

city: Ottawa

first: Lynn

last: Megeney

state: Ontario

address: 501 Smyth Road

department: Regenerative Medicine Program

country: Canada

institute: Ottawa Hospital Research Institute

summary: Induction of lineage-specific gene programs are strongly influenced by alterations in local chromatin architecture. However, key players that impact this genome reorganization remain largely unknown. Here, we report that removal of special AT-rich binding protein 2 (SATB2), a nuclear protein known to bind matrix attachment regions, is a key event in initiating myogenic differentiation. Deletion of myoblast SATB2 in vitro initiates chromatin remodeling and accelerates differentiation, while in vivo ablation depletes the muscle progenitor pool. Genome wide analysis indicates that SATB2 binding influences both chromatin loop and sub-TAD domain formation. These chromatin changes are both repressive and inductive, as loss of SATB2 leads to expression of differentiation regulatory factors and inhibition of genes that impair this process. Finally, we noted that the differentiation-specific decline in SATB2 protein is dependent on a caspase 7-mediated cleavage event. Taken together, this study demonstrates that temporal control of SATB2 protein is critical for shaping the chromatin environment and coordinating the myogenic differentiation program

overall_design: Hi-C of siControl and siSatb2 proliferating C2C12 cells (2 replicates)

first: Ryan

last: Bell

first: Hina

last: Bandukwala


title: Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2

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

overall_design: Refer to individual Series


title: Next generation RNAseq from human hepatic sinusoidal endothelial cells (EC) and mouse sinusoidal EC plated on soft vs hard gels

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

summary: next generation RNAseq data from human hepatic sinusoidal endothelial cells and primary mouse sinusoidal endothelial cells plated on soft vs hard gels reveals the chemokine CXCL1 being among the top up-regulated genes from granulocyte and agranulocyte migration/diapedesis pathway.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: next generation RNAsequencing from human hepatic sinusoidal endothelial cells (EC) and mouse sinusoidal EC plated on soft vs hard gels.

first: Vijay

middle: H

last: Shah

first: Usman

last: Yaqoob


title: RNA-seq of HNRNPAB morpholino in zebrafish

city: Beijing

first: Shuyan

address: 2# Yabao Road

institute: Children's Hospital of Capital Institute of Pediatrics

summary: To investigate the transcriptomic alterations following 24hpf knockdown of the gene HNRNPAB in zebrafish, we injected HNRNPAB morpholino with 3ng and 6ng into 1-cell  zebrafish embryos separately, and the 24hpf embryos were collected for RNA-seq.

overall_design: Whole mRNA profiles of 24 hour post fertilization of  control morpholino (con) and HNRNPAB morpholino (3ng and 6ng)

last: yang

first: Qin

last: zhang

first: Ting


title: RNA sequencing of MEX3A knockdown by siRNA in ovarian cancer cells

city: Jinan

first: Chen

last: Zhao

state: China

address: 107 Wenhua Xi Road

department: Department of Obstetrics and Gynecology

institute: Qilu Hospital, Shandong University

summary: RNA-binding proteins can serve as novel potential targets for cancer therapy. We used bioinformatics analysis to screen and identify the key RBPs in ovarian cancer (OC), from which we found that Mex-3 RNA Binding Family Member A (MEX3A) was intimately associated with the clinical prognosis of OC. High expression of MEX3A was involved in the malignant proliferation and aggressiveness of ovarian cancer.

overall_design: The assay was performed on three experimental triplictes of MEX3A knockdown and control ovarian cancer cells.

first: Fangfang

first: Yingwei


title: RNA-seq analysis of hormone receptor positive breast cancer cell line UCD4 with 24h hormone treatment

first: Jessica

last: Finlay-Schultz

summary: UCD4 cells treated with hormones 24h

first: Kiran

last: Paul

first: Ashley

last: Ward

first: Peter

last: Kabos

first: Carol

last: Sartorius


title: Genome-wide mapping and gene expression of the histone modification H3K4me3 in bovine early embryos

first: Kun

last: Zhang


title: Type 1 calreticulin mutations activate the IRE1α-XBP1 pathway of the unfolded protein response to drive MPN

first: Harrison

middle: Shea

last: Greenbaum

state: Illinois

address: GCIS W325, 929 E. 57th Street

institute: Ben May Department for Cancer Research

summary: Experimental data indicates unique activation of the unfolded response in calreticulin (CALR) mutant myeloproliferative neoplasms (MPN). To dissect UPR activation in an MPN, calreticulin-mutant context at the transcriptional level, RNA-seq was performed. Cell lines were generated with the addition of a plasmid containing the thrombopoietin receptor (MPL) in addition to a CALR variant: either wild-type calreticulin, calreticulin with a deletion of fifty-two base pairs/type I mutant, or calreticulin with an insertion of five base pairs/type II mutant. Cells were cultured in growth media containing 10% FBS RPMI with penicillin/streptomycin addition in a 5% CO2 incubator. Cells were washed three times with PBS followed by media replacement using growth media with or without IL3 addition. In unstarved conditions, cells were supplied with the cytokine IL3 at a 1:10,000 dilution for a final concentration of 2 ng/mL; in starved conditions, cells were depleted of the IL3 cytokine addition for twenty-four hours. RNA-seq was performed on both unstarved and starved cells in triplicates for each genotype. Additionally, for preliminary data purposes, a cell line was generated with MPL plasmid transduction and with the transduction of a plasmid containing the JAK2 kinase with the V617F mutation to examine MPN activation in a JAK2 mutant, MPN context; these samples (unstarved and starved) were not sequenced in triplicates but with one sample each.

overall_design: Triplicates for each calreticulin genotype in conditions of cytokine addition of IL3 (unstarved) or following cytokine absence for 24 hours (starved); only one unstarved and one starved sample of the JAK2VF-MPL cell line was conducted. RNA sample quality check, library construction, and sequencing were performed by the University of Chicago Genomics Facility following standard protocols. All samples were sequenced in two runs by a NovaSeq 6000 sequencer to generate paired-end 100bp reads. For each sample, the raw FASTQ files from two flow cells were combined before downstream processing. RNA-seq data were processed using a local Galaxy 20.05 instance for the following steps. Quality and adapter trimming were performed on the raw sequencing reads using Trim Galore! 0.6.3. The reads were mapped to both the mouse genome (GRCm38.p4 with GENCODE annotation) using RNA STAR 2.7.5b. The resulting mapped reads from each sample were counted by featureCounts 1.6.4 for per gene read counts.

first: Quinn

last: Smith

middle: S

first: Shannon

middle: E

last: Elf


title: Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2 [RNA-seq]

first: Lynn

last: Megeney

overall_design: Compared the transcriptomes of 24 h differentiated siControl and siSatb2 C2C12 cells (3 replicates).

first: Mohammad

last: Al-Khalaf

first: Alphonse

last: Chu


title: RIP- seq identified the interacted RNAs of SAFA with or without VSV infection

first: Lili

last: Cao

address: datun Road

institute: Chinese Academy of Sciences

summary: THP-1 cells were infected with VSV for 6 hours or 24 hours, RiP-seq was did with SAFA antibody.

overall_design: THP-1 cells were infected with 0.1MOI VSV for 6 hours or 24 hours. Then cells were collected, and RiP-seq was did with SAFA antibody.

first: Yunfei

last: Li


title: Mismatch hpRNA prevents intrinsic self-silencing and enhances RNAi stability

city: Acton

first: Ian

middle: K

last: Greaves

state: act

address: clunies ross street

country: Australia

institute: csiro

summary: Hairpin RNA (hpRNA) transgenes, with a perfect inverted-repeat (IR) DNA, have been the most successful RNA interference (RNAi) method in plants. Here we show that hpRNA transgenes were invariably methylated in the IR DNA and the adjacent promoter, causing transcriptional self-silencing and preventing the full potential of RNAi. Nucleotide substitutions in the sense sequence, which disrupts the perfect IR DNA structure, were sufficient to prevent the intrinsic DNA methylation resulting in more uniform and persistent RNAi. Substituting all cytosine (C) with thymine (T) nucleotides, in a G:U hpRNA design, prevented DNA methylation and self-silencing but still allowed for the formation of perfect hpRNA due to G:U wobble base-pairing. The G:U design induces effective RNAi in 90-96% of transgenic lines, compared to 57-65% for the traditional hpRNA design. Furthermore, while a traditional hpRNA transgene showed increasing DNA methylation and self-silencing from cotyledons to true leaves, the G:U transgenes avoided this developmental progression of self-silencing and induced RNAi throughout plant growth. The G:U and traditional hpRNA transgenes generated small interfering RNA (siRNA) with different 5’ phosphorylation, which resembled the endogenous tasiRNA and miRNA, respectively. Furthermore, our results suggest that siRNAs from the two transgene designs function differently to induce target DNA methylation, one (from traditional hpRNA) through the canonical RdDM pathway and the other (G:U hpRNA) a non-canonical pathway. Our study not only revealed a methylation-resistant RNAi transgene design but also provided new mechanistic insights into small RNA biogenesis and function in plants

overall_design: sRNA sequencing to compare different hpRNA structures for small RNA processing.

first: Ming-Bo

last: Wang

first: Daai

first: Chengcheng

last: Zhong

first: Neil

first: Rob

last: Defeyter

first: Steve

last: Swain

first: Ren


title: Genome-wide mapping of the histone modification H3K4me3 in bovine early embryos [RNA-seq]

first: Kun

overall_design: PolyA RNA profiles of bovine embryos

first: Yanna

last: Dang


title: Identification of target genes of miR-31 in PTC cells by RNA sequencing

city: Tianjin

first: Peitao

address: Qixiangtai Road 22

institute: Tianjin Medical University

summary: The purposes of this study were to compare and analyze the expression differences of  papillary thyroid carcinoma (PTC) induced by BrafV600E after knockdown of miR-31 deletion. And in order to gain insights into global gene expression regulated by miR-31 in human PTC cells, RNA-Seq experiments were performed in K1 cells with knockdout of miR-31.

overall_design: mRNA profiles of K1-control and K1-miR-31 KO were generated by deep sequencing, in duplicate, using Illumina novaseq6000 .

first: Lizhao

last: Guan

first: Li

last: Zhao


title: RNP- seq in wild-type and SAFA knockout or mutated cells

summary: wild-type and safa-/- THP-1 cells, or Flag-SAFA and Flag-Del-RGG stable expressed SAFA-/- cells were infected with VSV for 24 hours, samples were collected and send for RNA-seq.

overall_design: Wild-type or SAFA-/- THP-1 cells, and  SAFA-/- THP-1 cells stablely expressed with Flag-tagged SAFA or Flag-tagged Del-RGG mutant were infected with 0.1MOI VSV for 24 hours. Then cells were collected, and RNA samples were collected for RNA-sequencing.

first: Shengde

last: Liu


title: Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [Ribo-Seq]

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: The coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Understanding the molecular functions of SARS-CoV-2 proteins is thus imperative to developing effective antiviral treatments. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs. SARS-CoV-2 proteins, NSP8 and NSP12, are found to specifically bind to untranslated regions of the RNA viral genome, with NSP12 additionally binding to all transcription regulatory sequences. This provides evidence for their central roles in replication and transcription. Moreover, we discovered a potential site of NSP12 mediated genome recombination, which could explain the genetic diversity found in coronaviruses. SARS-CoV-2 proteins exogenously expressed in human lung epithelial cells bind to 4,281 unique host RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 which upregulates mitochondrial electron transport and N-linked glycosylation proteins. Furthermore, siRNA knockdown of NSP12-targeted proteins in human lung organoid cells demonstrates substantial antiviral effects. Conversely, NSP9 inhibits host gene expression via blocking mRNA export and dampens antiviral inflammation response such as interleukin 1α (IL1α) production. Our extensive viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.

overall_design: Total mRNA and mRNA in the polysomal fraction of two biological replicates were sequenced from BEAS-2B cells overexpressing ORF9c and compared to cells transfected with an empty plasmid vector.

first: Joy

last: Xiang

first: Jasmine

last: Mueller

first: En

middle: C

last: Luo

first: Brian

last: Yee

first: Danielle

last: Schafer

first: Jonathan

last: Schmok

first: Frederick

last: Tan

first: Hsuan

middle: L

last: Her

first: Chun

middle: Y

last: Chen

first: Kristopher

last: Brannan

first: Krysten

last: Jones

first: Samuel

last: Park

first: Wenhao

last: Jin

first: Rachael

last: McVicar

first: Elizabeth

last: Kwong

first: Phuong

last: Le

first: Eric

last: Kofman

first: Anthony

last: Vu

first: Yan

first: Kevin

last: Dong

first: Alexandra

last: Tankka

last: Song

last: Van Nostrand

first: Sandra

last: Leibel

middle: W


title: Non-oxidative pentose phosphate pathway controls regulatory T cell function by integrating metabolism and epigenetics

city: shang hai

first: Qi

last: Liu

address: 280 S. Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Regulatory T cells (Tregs) are critical for maintaining immune homeostasis and preventing autoimmunity. Here, we show that the non-oxidative pentose phosphate pathway (PPP) regulates Treg function to prevent autoimmunity. Deletion of transketolase (TKT), an indispensable enzyme of non-oxidative PPP, in Tregs causes a fatal autoimmune disease in mice, with impaired Treg suppressive capability despite regular Treg numbers and normal Foxp3 expression levels. Mechanistically, reduced glycolysis and enhanced oxidative stress induced by TKT deficiency triggers excessive fatty acid and amino acid catabolism, resulting in uncontrolled oxidative phosphorylation and impaired mitochondrial fitness. Reduced -KG levels as a result of reductive TCA cycle activity leads to DNA hypermethylation, thereby limiting functional gene expression and suppressive activity of TKT-deficient Tregs. We also find that TKT levels are frequently downregulated in Tregs of patients with autoimmune disorders. Our study identifies the non-oxidative PPP as an integrator of metabolic and epigenetic processes that control Treg function.

overall_design: CD4+CD25+YFP+ Tregs were isolated from 7-week-old WT and cKO mice which were added DMαKG or vehicle in drinking (n=3 per group). Total RNA was isolated from Tregs and used for RNA sequencing analysis by the Illumina HiSeq X Ten platform. In detail, mRNA was first randomly interrupted using divalent cations in NEB Fragmentation Buffer, then used to prepare libraries with the NEBNext Ultra RNA Library Prep Kit (New England Biolabs, Ipswich, MA), and finally sequenced using the Illumina HiSeq X Ten platform.

first: Xuemei

last: Tong


title: Changes in DNA Methylation Hallmark Alterations In Chromatin Accessibility And Gene Expression For Eye Lens Differentiation [Bisulfite-seq]

city: Boca Raton

first: Marc

last: Kantorow

state: FL

address: 777 Glades Road

institute: Florida Atlantic University

summary: Methylation at cytosines (mCG) is a well-known regulator of gene expression but its requirements for cellular differentiation have yet to be fully elucidated. A well-studied cellular differentiation model system is the eye lens, consisting of a single anterior layer of epithelial cells that migrate laterally and differentiate into a core of fiber cells. Here, we explore the genome-wide relationships between mCG methylation, chromatin accessibility and gene expression during differentiation of eye lens epithelial cells into fiber cells.  Whole genome bisulfite sequencing identified 7621 genomic loci exhibiting significant differences in mCG levels between lens epithelial and fiber cells. Changes in mCG levels were inversely correlated with the differentiation state-specific expression of 1285 genes preferentially expressed in either lens fiber or lens epithelial cells (Pearson correlation r = -0.37, p < 1x10-42). mCG levels were inversely correlated with chromatin accessibility determined by Assay for transposase-accessible sequencing (ATAC-seq) (Pearson correlation r = -0.86, p < 1x10-300). Many of the genes exhibiting altered regions of DNA methylation, chromatin accessibility and gene expression levels in fiber cells relative to epithelial cells are associated with lens fiber cell structure, homeostasis and transparency. These include lens crystallins (CRYBA4, CRYBB1, CRYGN, CRYBB2), lens beaded filament proteins (BFSP1, BFSP2), transcription factors (HSF4, SOX2, HIF1A), and Notch signaling pathway members (NOTCH1, NOTCH2, HEY1, HES5). Analysis of regions exhibiting cell-type specific alterations in DNA methylation revealed an overrepresentation of consensus sequences of multiple transcription factors known to play key roles in lens cell differentiation including HIF1A, SOX2, and the MAF family of transcription factors. Collectively, these results link DNA methylation with control of chromatin accessibility and gene expression changes required for eye lens differentiation. The results also point to a role for DNA methylation in the regulation of transcription factors previously identified to be important for lens cell differentiation.

overall_design: Examination of differentially methylated mCG regions between 3 biological replicates of pooled lens epithelial cells and 3 biological replicates of pooled lens fiber cells obtained from embryonic day 13 chick lenses and correlating with differentially expressed genes.

first: Joshua

last: Disatham

first: Lisa

last: Brennan

first: Xiaodong

last: Jiao

first: Zhiwei

last: Ma

first: J

middle: F

last: Hejtmancik


title: Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2 [ChIP-seq]

first: Lynn

last: Megeney

overall_design: Identification of Genome-wide of Satb2 binding sites in C2C12 cells.

first: Mohammad

last: Al-Khalaf

first: Alphonse

last: Chu


title: Hormone treatment of ER+ breast cancer cell lines

first: Jessica

last: Finlay-Schultz


title: Control of regulatory T cell function by the non-oxidative pentose phosphate pathway [RNA-Seq]

summary: Non-oxidative pentose phosphate pathway (PPP) is a crucial gatekeeper of glucose catabolism in metabolic tissues. However, its role in regulatory T cells (Tregs) remains unknown. Here we report deleting transketolase (TKT), an indispensable enzyme of non-oxidative PPP, in Tregs caused a fatal auto-immune disease in mice. TKT deletion impaired suppressive capability without disturbing Treg cell number. Mechanistically, TKT deficiency caused Treg metabolic remodeling with decreased glucose catabolism, activated fatty acid and amino acid catabolism and uncontrolled oxidative phosphorylation. Moreover, excessive ammonia from deregulated amino acid catabolism impaired mitochondrial fitness while reduced α-ketoglutarate/succinate ratio led to DNA hypermethylation, limiting functional gene expression and suppressive activity of TKT-deficient Tregs. Therefore, our study identifies non-oxidative PPP as a new pathway for controlling Treg function.

overall_design: CD4+CD25+YFP+ Tregs were isolated from 7-week-old female chimeric WT and chimeric cKO mice (n=3 per group). Total RNA was isolated from Tregs and used for RNA sequencing analysis by the Illumina HiSeq X Ten platform. In detail, mRNA was first randomly interrupted using divalent cations in NEB Fragmentation Buffer, then used to prepare libraries with the NEBNext Ultra RNA Library Prep Kit (New England Biolabs, Ipswich, MA), and finally sequenced using the Illumina HiSeq X Ten platform.


title: Compartment-specific total RNA profile of Hippocampal and Cortical cells from Mesial Temporal Lobe Epilepsy tissue

city: Utrecht

first: Ronald

middle: Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: UMC Utrecht

summary: Mesial temporal lobe epilepsy (mTLE) is a chronic neurological disease characterized by recurrent seizures. The pathogenic mechanisms underlying TLE involve defects in post-transcriptional regulation of gene expression. So far, transcriptome profiles from epileptic tissue have been performed using whole cells, thereby lacking information on RNA localization and function at a subcellular level. In this project, we set out to understand the compartment-specific total RNA profile of human mTLE tissue samples. For this, we had established a protocol to isolate cytoplasmic and nuclear compartments from human hippocampal tissue. Subcellular RNA was isolated from resected hippocampal (HC) and neo-cortical (Cx) tissue from mTLE no hippocampal sclerosis (non-HS) and mTLE HS International League Against Epilepsy (ILAE) Type 1 or mTLE+HS patients and postmortem control tissue. Later, we used total RNA sequencing (RNA-seq) to profile for the distinct RNA localization in mTLE in comparison to postmortem control tissue and identified disease related pathways in individual cell compartments. Here we report the total RNAseq (coding and non-coding) data.

overall_design:
We established a protocol to isolate pure nuclear and cytoplasmic fractions from human tissue. After quality controlling for purity of the isolated cell compartments, we performed total RNA-sequencing (RNA-seq) using illumina platform on five HC mTLE non-HS and five HC postmortem controls. Similarly, neo-cortical (Cx) tissue samples from six mTLE non-HS and six mTLE+HS samples and six Cx postmortem controls. From the data obtained, differential gene expression analysis was performed to identify mTLE specific transcript changes among subcellular compartments.
Pleaes note that each processed data file was generated from multiple samples as indicated in the file name:
Cortex(Cx)_Cytoplasm(cyt)_Control(CTL) & mTLE non-HS(W0)
Cortex(Cx)_Cytoplasm(cyt)_Control(CTL) & mTLE+HS(W4)
Cortex(Cx)_Cytoplasm(cyt)_PREvsPOST
Cortex(Cx)_Hippocampus_Cytoplasm(cyt)_Control(CTL)_vs_mTLE_non-HS & mTLE+HS(W4)
Cortex(Cx)_Hippocampus_Cytoplasm(cyt)_Nucleus(Nuc)_Control(CTL)_vs_mTLE non-HS & mTLE+HS(W4)
Cortex(Cx)_Nucleus(nuc)_Control(CTL) & mTLE non-HS(W0)
Cortex(Cx)_Nucleus(nuc)_Control(CTL) & mTLE+HS(W4)
Cortex(Cx)_Nucleus(nuc)_PREvsPOST
Hippocampus(Hip)_Cytoplasm(cyt)_Control(CTL) & mTLE non-HS(W0)
Hippocampus(Hip)_Nucleus(nuc)_Control(CTL) & mTLE non-HS(W0)
Hippocampus(hip)_vs_Cortex(Cx)_cytoplasm(cyt)_circRNA_differentially_expressed(DE)
Hippocampus(hip)_vs_Cortex(Cx)_nucleus(nuc)_circRNA_differentially_expressed(DE)
mTLE+HS(W4)_vs_mTLE_non-HS(W0)_Cortex(Cx)_cytoplasm(cyt)_circRNA_differentially_expressed(DE)
mTLE+HS(W4)_vs_mTLE_non-HS(W0)_Cortex(Cx)_nucleus(nuc)_circRNA_differentially_expressed(DE)
nucleus(nuc)_vs_cytoplasm_Cortex(Cx)_circRNA_differentially_expressed(DE)
nucleus(nuc)_vs_cytoplasm_hippocampus(hip)_circRNA_differentially_expressed(DE)

first: Vamshidhar

middle: R

last: Vangoor

first: Giuliano

last: Giuliani

first: Morten

middle: T

last: Venø

first: Jørgen

last: Kjems

first: R

middle: J


title: Microbiome-dependent tryptophan metabolism suppresses inflammatory immunity in the pancreatic tumor microenvironment by activation of the aryl hydrocarbon receptor

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

overall_design: Refer to individual Series


title: Microbiome-dependent tryptophan metabolism suppresses inflammatory immunity in the pancreatic tumor microenvironment by activation of the aryl hydrocarbon receptor [RNA-seq]

summary: To explore the role of macrophages and AhR in PDAC, we used an orthotopic model employing mouse PDAC organoid lines derived from a primary tumor isolated from the KPC model of PDAC and performed RNA-sequencing on FACS-sorted TAM from 14-day tumors and compared them to the residential macrophages from normal pancreas.

overall_design: Gene expression profiling of sorted macrophages (i.e. resident Macrophages, n=4 mice) or PDAC tumors from control (n=3) or Lyz2-AhR cKO (n=3) mice 14 days after tumor implantation.

first: Kebria

last: Hezaveh

first: Rahul

last: Shinde

first: Tracy

last: McGaha


title: Microbiome-dependent tryptophan metabolism suppresses inflammatory immunity in the pancreatic tumor microenvironment by activation of the aryl hydrocarbon receptor [scRNA-seq]

summary: To analyze transcriptome changes in the tumor microenvironment caused by loss of macrophage AhR we performed scRNA sequencing analysis.

overall_design: 14 days after tumor implantation, tumors from three Ahrfl/fl or three LysM-CRE cKO mice were digested, pooled, and stained with DAPI. Live cells were FACS-sorted into buffer (PBS + 2% FBS), washed 2 times with PBS + 0.04% BSA, and then only 10x10^3 cells mixed with 10X Genomics Chromium single-cell RNA master mix.


title: IL-25 participates in keratinocyte-driven dermal matrix turnover and is reduced in Systemic Sclerosis epidermis

city: Geneva

first: Barbara

last: Russo

address: Rue Michel Servet 1

department: DEPARTEMENT DE MEDECINE (DEMED)

country: Switzerland

institute: Centre Medical Universitaire

summary: Aberrant deposition of extracellular matrix (ECM) resulting in dermal fibrosis is a hallmark of systemic sclerosis (SSc). Evidence suggests that dysfunctional SSc keratinocytes may contribute to fibrosis by altering dermal homeostasis. Whether interleukin-25 (IL-25), an IL-17 family member involved in epithelial/mesenchymal/immune cell interplay takes part in skin fibrosis is unknown. Here we address the role of IL-25 in SSc skin fibrosis.   Compared to healthy donor (HD), in SSc and scleroderma-like disorders the epidermis expressed significantly lower levels of IL-25. In epidermal equivalents, IL-25 regulated several molecular pathways related to wound healing and ECM remodeling. Compared to control conditioned medium (CM), the CM from IL-25-primed keratinocytes enhanced the production by fibroblasts of matrix metalloproteinase-1 (MMP-1), IL-6, IL-8 (p< 0.05), but not of type-I collagen (Col-I ) nor fibronectin. However, IL- 25 significantly reduced the production of Col-I when applied directly to fibroblasts. The activation of keratinocytes by IL-25 was receptor-dependent and evident after a very short incubation time (10 min), largely mediated by IL-1, suggesting enhanced and specific release of preformed mediators.  These results show that IL-25 participates to skin homeostasis and its decreased expression in SSc may contribute to skin fibrosis by favoring ECM deposition over degradation.

overall_design: mRNA profile of IL-25 treated epidermal equivalent reconstituted from 3 different primary human adult keratinocytes were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000 sequencer.

first: B

first: C

last: Chiizzolini


title: Reduction N6AMT1-mediated 6mA DNA modification promotes tumor progression [RNA-seq]

first: Ping

last: Wang

address: No22.Qixiangtai Rd.,Heping Dist

summary: Background: DNA N6-methyladenosine (6mA) as a novel epigenetic signaling modification in humans and has been implicated in progression and tumorigenesis of several cancers. However, the function and mechanisms of 6mA in breast cancer (BC), the most common cancer among women, are unclear. Methods: The clinical role of 6mA was investigated by immunohistochemical (IHC) staining and Kaplan-Meier analysis of BC and their normal tissues. 6mA immunoprecipitation (IP) sequencing, mRNA sequencing and bioinformatics analysis were used to screen and validate the direct targets of 6mA. Results: Decreases in N6AMT1 correlated with the extent of 6mA in BC tissues and predicted a worse overall survival of BC patients. Knockdown N6AMT1 markedly reduced 6mA in DNA and promoted the proliferation and migration of BC in vivo and in vitro, whereas overexpression of N6AMT1 had the opposite effect, indicating N6AMT1 is a functional methyltransferase for DNA 6mA and relates with gene transcription. Critical negative regulators of the cell cycle, such as RB1, P21, REST and TP53 were identified as targets of N6AMT1 in BC. Conclusion: These results suggest N6AMT1 enhances DNA 6mA levels to repress tumor progression via transcriptional regulation of cell cycle inhibitors.

overall_design: Global mRNA profiles of MDA-MB-453 cells by transfected with siRNAs for N6AMT1 (n=3) or Controls (n=3).

first: Jiongyu

last: Chen

first: Yixuan

last: Zhuang

first: Jinfeng

last: Ning

first: Wei

last: Liu

first: Yiteng

last: Huang

first: Xueqiong

last: Lin

first: Lin

last: Peng

first: Donghong

last: Zhang


title: Regulation of flowering by AaTFL1 in Arabis alpina

city: Köln

first: Maria

last: Albani

address: Carl-von-Linné-Weg 10

department: Botanical institute

institute: University of Cologne

summary: AaTOE2 regulates flowering in various pathway

overall_design: Arabis alpina eop089 mutants plants were grown under control condition, their shoot apex and leaf were dissected and analyzed for mRNA abundances using RNA-sequencing.

first: Yanhao

last: Zhou

first: Natanael

last: Viñegra de la Torre


title: MicroRNA 3'-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position [1]

city: Cambridge

first: Sean

middle: E.

last: McGeary

state: MA

address: 455 Main St.

department: Biology

institute: Whitehead Institute / MIT

summary: MicroRNAs (miRNAs), in association with Argonaute (AGO) proteins, direct repression by pairing to sites within mRNAs. Compared to pairing preferences of the miRNA seed region (nucleotides 2–8), preferences of the miRNA 3′ region are poorly understood, due to the sparsity of measured affinities for the many pairing possibilities. We used RNA bind-n-seq with purified AGO2–miRNA complexes to measure relative affinities of >1,000 3′-pairing architectures for each miRNA. In some cases, optimal 3′ pairing increased affinity by >500-fold. Some miRNAs had two high-affinity 3′-pairing modes—one of which included additional nucleotides bridging seed and 3′ pairing to enable high-affinity pairing to miRNA nucleotide 11. The affinity of binding and the position of optimal pairing both tracked with the occurrence of G or oligo(G/C) nucleotides within the miRNA. These and other results advance understanding of miRNA targeting, providing insight into how optimal 3′ pairing is determined for each miRNA.

overall_design: small RNA sequencing of AGO-RBNS binding reactions and input libraries. This study comprises 56 samples spanning three naturally occuring and four artificial miRNA sequences. The let-7a experiment was performed in replicate, using two different purifcations of both the AGO–miRNA complex and the programmed library.

first: Namita

last: Bisaria

first: David

middle: P

last: Bartel


title: Transcriptome profiling of olive flounder responses under acute and chronic heat stress

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

country: South Korea

institute: Chungbuk National University

summary: To screen for altered gene expression during heat stress,  flounder tissues under acute and chronic heat stress were subjected to gene expression profiling.

overall_design: Transcriptome profiles of acute and chronic heat-treated flounder tissues were generated by deep sequencing, in duplicate, using BGISEQ-500.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Seed Development of Easy Dehulling Tartary Buckwheat Transcriptomes

city: Shanghai

first: Moyang

address: dongchuan road 800

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

summary: We generated 78.41 Gb of high-quality sequencing data (~8.71 Gb per sample) and catalogued the expression profiles of 9,765 annotated Tartary buckwheat genes in each sample. The analysis showed differences of transcriptomes during the development of easy dehulling buckwheat seed. We identified numerous differentially expressed genes that exhibited distinct expression patterns. These genes have known or potential roles in development of easy dehulling buckwheat seed. Therefore, we are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to easy dehulling character.

overall_design: buckwheat seeds mRNA profiles of the development were generated by deep sequencing, in  triplicate, using Illumina HiSeq4000.


title: RNPS1 inhibits excessive TNF/TNFR signaling to support hematopoiesis in mice

city: Dallas

first: Sara

last: Hildebrand

state: TX

address: 5323 Harry Hines blvd

department: Center for the Genetics of Host Defense

institute: UT Southwestern Medical Center

summary: Null mutations of spliceosome components or cofactors are homozygous lethal in eukaryotes, but viable hypomorphic mutations provide an opportunity to understand the physiological impact of individual splicing proteins. We describe a viable missense allele of Rnps1, encoding an essential regulator of splicing and nonsense-mediated decay, identified in a mouse genetic screen for altered immune cell development. Homozygous mice displayed a stem cell-intrinsic defect in hematopoiesis of all lineages due to excessive apoptosis induced by TNF-dependent death signaling. Numerous splicing variants were observed in Rnps1 mutant splenic CD8+ T and HSC cells, potentially driven by dysregulated splicing, characterized by magnification of both intron retention and exon skipping. Strikingly, Tnf knockout rescued all hematopoietic cells to normal or near-normal levels in Rnps1 mutant mice. Thus, RNPS1 is necessary for accurate splicing, without which disinhibited TNF signaling triggers hematopoietic cell death.

overall_design: Examination of transcript abundance and splicing variants in Rnps1+/+;Tnf+/+, Rnps1+/+;Tnf-/-, Rnps1F181I/F181I;Tnf+/+, or Rnps1F181I/F181I;Tnf-/- splenic CD8+ T and HSC cells

first: Xue

last: Zhong


title: Regulation of flowering by TOE2 in Arabidopsis thaliana and Arabis alpina

overall_design: Arabis alpina pep1-1 and eop055 mutants plants were grown under control condition, their shoot apex and leaf were dissected and analyzed for mRNA abundances using RNA-sequencing.


title: circRAB3IP modulates cell proliferation by reorganizing gene expression and mRNA processing in a paracrine manner [HUVEC_KD]

status: Public on Mar 30 2022

city: Goettingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str 40

department: Department of Pathology

institute: University Medical Center Goettingen

summary: Circular RNAs are endogenous long-lived and abundant non-coding species. Despite their prevalence, only few circRNAs have been dissected mechanistically as regards their function to date. Here, we catalogued nascent RNA-enriched circRNAs from primary human cells and focus on circRAB3IP to assign to it a role in sustaining cellular homeostasis. We combine “omics” and functional experiments to show how circRAB3IP depletion deregulates hundreds of genes, suppress cell cycle progression, and brings about senescence-like gene expression changes. Conversely, excess circRAB3IP delivered to endothelial cells via exosomes suffices for accelerating their cell division. We attribute these effects to widespread changes in isoform usage that stem from the interplay between circRAB3IP and the general splicing factor SF3B1. Together, our findings link the maintenance of cell homeostasis to the tightly regulated titers of a single circRNA.

overall_design: HUVEC cells pulled from three donors were treated with NTC or circRAB3IP or circCAMSAP1 siRNA.

first: Natasa

last: Josipovic


title: circRAB3IP modulates cell proliferation by reorganizing gene expression and mRNA processing in a paracrine manner [HUVEC_EVs_OE]

overall_design: circRAB3IP-piggyBAC HEK293 cells were grown in exosome-depleted medium and induced and selected with additionally induced with 3 μg/ml of doxycycline (DOX, Sigma) and 400 μg/ml of G418 (Sigma). After 48h, the medium was used for purification of extracellular vesicles which were used to treat normal grown HUVEC cells for 24h. HUVECs were then collected for RNA extraction and RNA sequencing.


title: circRAB3IP modulates cell proliferation by reorganizing gene expression and mRNA processing in a paracrine manner [HEK293_KD]

overall_design: HEK293 cells were treated with NTC or circRAB3IP or circCAMSAP1 siRNA.

first: Anne

last: Zirkel


title: RNA-Seq of Arabidopsis thaliana growth promotion by Priestie megaterium YCR-R4

city: Oeiras

first: Juan

middle: Ignacio

last: Vilchez

state: Lisbon

address: Avenida da Republica, -

department: Plant Division

country: Portugal

institute: ITQB - NOVA

summary:
Plant growth promoting test in A. thaliana by using biostimulant strain P. megaterium YC4-R4 in liquid inoculant
A. thaliana mRNA profiles of 13-day old wild type (WT) mock and WT treated (inoculated with P. megaterium YC4-R4)

overall_design: Sample was taken 7 days after treatment and compared to mock set of samples. Phenotypes were evident after 14 day of treatment

middle: I

first: Huiming


title: Transcriptome analysis of mutations in plant novel nuclear basket protein GBPL3 pnet2_abc mutants

city: Berkeley

first: yangnan

last: Gu

address: 371 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

summary:
Purpose: To understand the molecular mechanism underlying the phenotype caused by mutation in the plant novel nuclear basket protein GBPL3, we performed the whole genome transcriptome analysis on 7-day-old seedlings of WT, gbpl3 mutant using RNA-seq.
Conclusions: PNET2 negatively regulates immune response and positively regulates auxin signal and microtuble activity.

overall_design: mRNA profiles of 7-day-old seedlings of wild type (Col-0), gbpl3 mutant were generated by deep sequencing, in triplicate, using Illumina HiSeq PE-150.

first: Yangnan

first: Yu

last: Tang


title: Next Generation Sequencing for Identification of Transcriptomes from  Serum Exosomes

first: Peng

last: Chen

address: 88 ChongQing South Road

institute: Shanghai Jiao Tong University of medicine

summary:
Purpose:  The purpose of this study is to apply RNA-Seq to identify diffeerentially expressed RNA in hepatocellular-derived serum exosomes compared with non hepatocellular carcinoma derived serum exosomes to evaluate prognosis-related and tumorigenesis-related potential biomarkers.
Methods: Genome profiles of  serum exosomes isolated from liver cirrohosis subjects, early-stage HCC subjects amd advanced stage HCC subjects respectively were generated by deep sequencing,  using Illumina. The sequence reads that passed quality filters were aligned and analyzed  using HISAT2 and STRINGTIE. The constructed transcriptome profiles were conveyed to further analysis.
Results: With the help of RNA-Seq technology, 58,243 genes and 200,478 transcripts were aligned, and genome and transcriptome RNA-Seq archives were constructed, showcasing the abundance and depth of our sequencing. Then we systematically screened the RNA type, and selected long non-coding RNA (lncRNA) expression profiles. We used DESeq2 algorithm and set  |log2 (fold-change)|>1 and P-value <0.05  as criteria. Finally we discovered 2,070 genes, 6,543 transcripts, 942 lncRNAs were differentially expressed in group advanced stage HCC compared with group liver cirrohosis. 1,600 genes, 6,904 transcripts,  1,067 lncRNAs were differentially expressed  in group early stage HCC compared with group liver cirrohosis.
Conclusions: Our study creatively represented the detailed analysis of serum exosomes genomes and transcriptomes, which were generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that compared with liver cirrohosis serum exosome samples, the early-stage and advanced stage hepatocellular carcinoma groups detected some unique differential mRNAs and miRNAs, which can be potential biomarkers.

overall_design: Serum exosome total RNA genome and transcriptome profiles of 8 included subjects, which passed quality control, 3 liver cirhosis, 3 early stage HCC, and 2 advanced stage HCC, respectively.

first: Tao

last: Li


title: Gene expression in D4 WT and P38α KO uteri

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

summary: Differential expression genes were normalized to fragments per kilobase of exon model per million mapped reads (RPKM) using EdgeR package in R with the criteria of fold change significantly greater than 2 or less than 0.5 and P<0.05.

overall_design: Total RNAs from D4 uteri were extracted by TRIzol and purified by ploy-A before subjected to RNA-Seq. The expression of level of each gene is normalized to RPKM.


title: Transcriptomic stress response in Streptococcus mutans following treatment with a sublethal concentration of chlorhexidine digluconate

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

institute: Quantitative Biology Center (QBiC)

summary:
Despite the widespread use of antiseptics such as chlorhexidine digluconate (CHX) in dental practice and oral care, the risks of potential resistance toward antiseptics in oral bacteria have only been highlighted very recently. Since the molecular mechanisms behind antiseptic resistance or adaptation are not entirely clear yet and the bacterial stress response has not been investigated systematically so far, the aim of the present study was to investigate the transcriptomic stress response in Streptococcus mutans after treatment with CHX using RNA sequencing.
Planktonic cultures of stationary phase S. mutans were treated with a sublethal dose of CHX (125 µg/mL) for 5 min. After treatment, RNA was extracted, and RNA sequencing was performed on the Illumina NextSeq 500. Differential expressed genes were analyzed and validated by qRT-PCR.
The analysis of the differential gene expression following pathway analysis revealed a considerable number of genes and pathways significantly regulated in S. mutans after sublethal treatment with CHX. In summary, expression of 423 genes was up-regulated and 295 genes down-regulated after CHX treatment. Analysis of differentially expressed genes and significantly regulated pathways showed regulation of genes involved in purine nucleotide synthesis, biofilm formation, transport systems and stress responses.
In conclusion, these results show an overview of the transcriptomic stress response in S. mutans upon exposure to CHX and give an insight in potential mechanisms that may result in development of resistances.

overall_design: Streptococcus mutans treated with a sublethal concentration of chlorhexidine digluconate.

first: Fabian

last: Cieplik

first: Denise

last: Muehler


title: ALA_PDT promotes the ferroptosis-like death of Mycobacterium abscessus and antibiotic sterilization via oxidative stress

city: Chongqing

first: Xiaoyu

last: Wang

address: Shabei street

institute: Key Laboratory of Biorheological Science and Technology, Ministry of Education

summary: Mycobacterium abscessus is one of the common clinical non-tuberculous mycobacteria (NTM) which can cause severe skin infections. 5-Aminolevulinic acid photodynamic therapy (ALA_PDT) is an emerming effective antimicrobial medication. To explore whether ALA_PDT can treat M. abscessus infections, we found that ALA_PDT can kill M. abscesses via colony forming unit method. ALA_PDT promoted ferroptosis-like death of M. abscesses, and the antioxidant N-Acetyl-L-cysteine (NAC) and ferroptosis inhibitor Ferrostatin-1(Fer-1) can mitigate the ALA_PDT-mediated sterilization. Furthermore, ALA_PDT significantly up-regulated the transcription of heme oxygenase MAB_4773, increased the intracellular Fe2+ concentration, altering the transcription of M. abscessus iron metabolism genes. ALA_PDT disrupted the integrity of the cell membrane and enhanced the permeability of the cell membrane, as evidenced by the boosted sterilization effect of antibiotics. In summary, ALA_PDT can kill M. abscesses via promoting the ferroptosis-like death and antibiotic sterilization through oxidative stress. This new mechanism of ALA_PDT against M. abscessus might underlie its clinical efficacy.

overall_design: The Ctrl, PDT1 and PDT2 bacteria were harvested for RNA preparation.RNA-seq is measured by Zhongke New Life (Shang Hai).(Ctrl: 0µg/mL ALA+0J/cm2 light, PDT1: 100µg/mL ALA+80J/cm2 light , PDT2: 100µg/mL ALA+160J/cm2 light)

first: Jianping

last: Xie

first: Li

first: Xia

last: Lei


title: TIGIT Blockade Exerts Synergistic Effects on Microwave Ablation against Cancer

city: changzhou

first: yaping

last: chen

address: 185 juqian street

institute: soochow university

summary: Combination immunotherapy based on immune checkpoint inhibitors (ICIs) has shown great success in the treatment of many types of cancers and has become the mainstream in the comprehensive treatment of cancers. Ablation in combination with immunotherapy has achieved tremendous efficacy in some preclinical and clinical studies. To date, our team proved that ablation in combination with ICIs was a promising antitumor therapeutic strategy for the liver metastasis of colorectal cancer (CRC). Moreover, we found that the expression of T cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT) expression was up-regulated after microwave ablation (MWA), indicating that TIGIT was involved in immunosuppression, and the combination of MWA and TIGIT blockade represented a potential clinical treatment strategy. In this study, we analyzed the single-cell RNA sequencing (scRNA-seq) data from the MWA and MWA plus anti-TIGIT groups. We found that  TIGIT blockade in combination with MWA significantly promoted the expansion and functions of CD8+ TILs and reshaped myeloid cells in the tumor microenvironment (TME). In conclusion, TIGIT blockade in combination with MWA was a novel treatment strategy for the liver metastasis of CRC, and this combination therapy could reprogram the TME toward an antitumor environment.

overall_design: MC38 tumor cells were subcutaneously inoculated into the bilateral flanks of C57BL/6 mice. MWA was only carried out on the tumor on the right flank when the tumor volume reached approximately 300 mm3. TIGIT blockade was administered intraperitoneally three times every 3 days starting 1 day after MWA. On day 8 after MWA treatment, tumor on the left side were isolated, digested and isolated CD45+ cells. Libraries were constructed using 10x Genomics.

first: Yaping

first: Changping

last: Wu


title: Transcriptome sequence of hTERT-HPNE and PANC-1 cells upon hydrogen peroxide treatment

city: Guangzhou

first: Shihua

last: Liu

state: Guangdong

address: 651 Dongfeng East Road

department: Collaborative Innovation Center for Cancer Medicine

institute: Sun Yat-sen University Cancer Center

summary: To explore the whole transcriptional regulation of lncRNA and mRNA expression in hydrogen peroxide (H2O2) signaling, we used human pancreatic normal epithelial cell line hTERT-HPNE and pancreatic cancer cell line PANC-1 for H2O2 treatment and utilized transcriptome sequence to analyze the change of lncRNA and mRNA transcripts. Then we predicted the potential transcription factor for these significantly changed transcripts.

overall_design: hTERT-HPNE cells with or without 0.3 mM H2O2 treatment for 12h, PANC-1 cells with or without 1.0 mM H2O2 treatment for 12h

last: Huang

first: Ya

last: Qiu

first: Rong

last: Xiang


title: Early Predicting COVID-19 Severity Value with Extracellular Vesicles and Extracellular RNAs

city: San Francisco

first: Tsukasa

last: Kadota

address: 513 Parnassus Ave.

department: Medicine

institute: UCSF

summary: The SARS-CoV-2 outbreak started on December 2019 in China and rapidly spread worldwide. Clinical manifestations of Coronavirus-disease 2019 (COVID-19) vary broadly, ranging from asymptomatic infection to acute respiratory failure and death, yet the underlying mechanisms and predictive biomarkers for this high variability are still unknown. Emerging evidence has shown that circulating extracellular vesicles (EVs) and extracellular RNAs (exRNAs) are functionally involved in a number of physiologic and pathologic processes. To test the hypothesis that these extracellular components are a key determinant of severity in COVID-19, we collected 31 serum samples from mild COVID-19 patients at admission in single center. After standard therapy without corticosteroids, 9 of 31 patients became severe COVID-19. We analyzed exRNA profiles from the 31 serums and 10 healthy controls for predicting COVID-19 severity value.

overall_design: Total RNA was extracted from aliquots (200 μL) of the serum samples using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol.  The QIAseq miRNA-seq  analysis was performed using  the extracted miRNA.

first: Yu

last: Fujita

first: Tokio

last: Hoshina

first: Juntaro

last: Matsuzaki

first: Shota

last: Fujimoto

first: Hironori

last: Kawamoto

first: Naoaki

last: Watanabe

first: Kenji

last: Sawaki

first: Yohei

last: Sakamoto

first: Makiko

last: Miyajima

first: Kwanyole

last: Lee

first: Kazuhiko

last: Nakaharai

first: Tetsuya

last: Horino

first: Ryo

last: Nakagawa

first: Jun

last: Araya

first: Masaki

last: Yoshida

first: Kazuyoshi

last: Kuwano

first: Takahiro

last: Ochiya


title: circRAB3IP modulates cell proliferation by reorganizing gene expression and mRNA processing in a paracrine manner

first: Argyris

last: Papantonis

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

overall_design: Refer to individual Series


title: RNA Sequencing Analysis between Control and CGA knockdown Multi-drug resistant Cells

city: Xi'an

first: Xiaodi

last: Zhao

address: No.127 Changle West Road

department: Xijing Hospital of Digestive Diseases

institute: Xijing Hospital of Fourth Military Medical University

summary: The aim of this study is to compare the CGA Knockdown multi-drug resistant (MDR) cells (SGC7901/ADR and SGC7901/VCR) to the control cells. The total RNA of the indicated cells were extracted using Qiagen RNA Extraction Kit and RNA sequencing was performed. Significant differences in genes and signaling pathways were found between CGA knockdown and control MDR cells. This study provides a basis for applying RNA sequencing techniques to characterize targets in MDR cells.

overall_design: Transcriptomic profiling between CGA siRNAs transfected SGC7901/ADR (or SGC7901/VCR) cells and scrambled control siRNA transfected SGC7901/ADR (or SGC7901/VCR) cells.

first: Tianyu

last: Cao


title: Inspecting VWF gene deep intronic region and in-depth study of the endothelial colony-forming cells to identify an underlying pathogenic molecular mechanism in a type 3 VWD patient

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

institute: University Clinic Bonn

summary: A type 3 von Willebrand disease (VWD) index patient (IP) remains mutation-negative after completion of conventional diagnostic analysis, including multiplex ligation-dependent probe amplification and sequencing of the promotor, exons, and flanking intronic regions of VWF gene (VWF). In this study, we intended to elucidate causitive genetic defect through screening of the whole VWF (including complete intronic region), mRNA analysis, and study of the patient-derived endothelial colony-forming cells (ECFCs). The entire VWF was analyzed by next-generation sequencing (NGS) on an Illumina platform. The NGS revealed a novel variant in VWF intron 8 (997+118 T>G). The subsequent assessments using bioinformatics tools (e.g. SpliceAl) predicted this variant creates a new donor splice site (ss) in intron 8, which could outcompete the consensus 5’ donor ss at exon/intron 8 junction. This leads to an aberrant mRNA which contains a premature stop codon, targeting it to nonsense-mediated mRNA decay. The VWF mRNA from whole blood and isolated ECFCs were quantified using the TaqMan assay on an ABI 7500 real-time PCR system. The quantitative analysis confirmed the virtual absence of VWF mRNA. Additionally, the level of secreted VWF from IP ECFCs was considerably reduced (~6% of healthy donors).

overall_design: 6 samples

first: Hamideh

last: Yadegari

first: Muhammad

last: Ahmer Jamil


title: Effect of miR-200c-3p overexpression on primary human macrophages

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

institute: Goethe University Frankfurt

summary: Macrophages constitute a major part of the tumor-infiltrating immune cells and within the tumor microenvironment acquire an alternatively activated, tumor-supporting phenotype. Factors released by tumor cells are crucial for the recruitment of tumor-associated macrophages. In the present project, we aimed to understand the role of miR-200c in the interplay between tumor cells and macrophages. To this end, we employed a coculture system of MCF7 breast tumor cells and primary human macrophages and observed a substantial transfer of miR-200c from apoptotic tumor cells to macrophages, which required intact CD36 receptor in macrophages. We further comprehensively determined miR-200c targets in macrophages by mRNA-sequencing and found numerous migration-associated mRNAs to be downregulated by miR-200c. Consequently, miR-200c attenuated macrophage infiltration into 3-dimensional tumor spheroids. The miR-200c-mediated reduction of infiltration further correlated well with a miR-200c migration signature comprised of four miR-200c-repressed targets (PPM1F, RAB11FIB2, RDX, MSN).

overall_design: mRNA-seq of primary human macrophages transfected with miR-200c-3p mimic or control harvested 72 h after transfection (n = 4).

first: Rebecca

last: Raue

first: Shahzad

middle: N

last: Syed


title: mRNA expression in RNase deletion mutants of Thermus thermophilus HB8

city: Toyonaka

first: Yota

last: Iio

state: Osaka

address: 1-1 Machikaneyama-cho

department: science

institute: Osaka university

summary: We analyzed the expression profile of protein kinase and protein phosphatase deletion strains of Thermus thermophils HB8. Keywords: cell type comparison

overall_design: The T. thermophilus HB8 wild-type strain and disruptants were cultured in TT medium at 70°C until the cells reached to OD600 of 0.8 (log phase) or to stationary phase.  The cultures were added to an equal volume of 100% ethanol and stored at -80°C.  Total RNA was extracted from these frozen cells by following the same procedure as described previously (Shinkai et al. 2007) with the exception that the RNA was resuspended in 20 μL of water after ethanol precipitation.  The cDNA was synthesized with SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA) in the presence of the RNase inhibitor SUPERase (Ambion, Austin, TX) and 6-base random primers (Invitrogen).  The cDNA was fragmented with 35 units of DNase I (GE Healthcare, Amersham, UK) at 37°C for 10 min; after inactivation at 98°C for 10 min, the cDNA fragments were labeled with the GeneChip DNA labeling reagent (Affymetrix, Santa Clara, CA), using terminal transferase, according to the manufacturer's instructions (Affymetrix). The 3'-terminally labeled cDNA (2 μg) was hybridized to a TTHB8401a520105F GeneChip (Affymetrix), which contained probe sets of 25-mer oligonucleotides representing 2238 ORFs and 1096 intergenic regions.  The procedure was basically the same as that described previously with the exception that 20 μg of herring sperm DNA (Promega) was added to the hybridization mixture (Shinkai et al. 2007).  The array was automatically washed and stained with streptavidin-phycoerythrin (Invitrogen) using a GeneChip Fluidics Station 450XP (Affymetrix).  The probe array was then scanned with a GeneChip Scanner 3000 (Affymetrix).  To determine the mRNA expression level in disruptants relative to that in wild-type, the image data for the three samples in each disruptant and growth phase were processed. The expression intensity of each of the 2238 ORFs for the three wild-type strains was evaluated using image data and scaled by means of the one-step Tukey's biweight algorithm using GeneChip Operating Software version 1.0 (Affymetrix).  Scaled probe value was calculated as Sc = 500 according to Statistical Algorithms Description Document (Affymetrix).

first: Y

first: K

last: Fukui

last: Agari

first: A

last: Shinkai

first: N

first: R

last: Masui

first: S

last: Kuramitsu


title: RNA-seq of total RNA from Staphylococcus aureus culture infected with Staphlococcus phage SAM1

city: Cork

first: Colin

last: Buttimer

state: Cork

address: College Road

department: APC Microbiome Ireland

country: Ireland

institute: University College Cork

summary: We examined the transcriptional regulation of the genes of Staphlococcus phage SAM1 during infection of its bacterial host

overall_design: Examination of mRNA at three different time points during Staphylococcus phage SAM1 infection of its host

first: Sara

last: Arroyo-Moreno

first: Aidan

last: Coffey


title: Altiratinib blocks Toxoplasma gondii and Plasmodium falciparum development by selectively targeting   a kinase critical for splicing

city: La Tronche

first: Alexandre

last: Bougdour

state: Isère

address: Domaine de la Merci, Campus santé

department: Prevention and Therapy of Chronic diseases

country: France

institute: Centre de Recherche Inserm U1209 / CNRS UMR5309 / UGA

summary: Purpose: To shed light on the parasiticidal mechanisms of Altiratinib, we have adapted a workflow which combines a forward genetic approach based on transcriptome sequencing, computational mutation discovery and CRISPR/Cas9 genome editing in Toxoplasma gondii. Drug-resistant parasites were generated by chemical random mutagenesis. Multiple independent resistant lines were isolated. Single nucleotide variations (SNVs) were identified based on NGS transcriptomic analysis. By focusing on mutations present in coding sequences, we identified a single gene, TgPRP4K, that harbored SNVs leading to amino acid substitutions in 5 out of the 6 drug-resistant lines that were not present in the parental strain. Finally, using CRISPR/Cas9 genome editing we confirmed that the mutations identified confer resistance against Altiratinib.

overall_design: Methods: RNA profiles were generated from HFF cells infected by RH wild-type or Altiratinib-resistant T. gondii strains. Total RNAs were extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Plus Mini Kit (Qiagen). RNA-sequencing was performed by GENEWIZ (South Plainfield, NJ, USA). The RNA quality was assessed using TapeStation System (Agilent Technologies, Palo Alto, California, USA).  Illumina TruSEQ RNA library prep of selected polyA RNAs and sequencing reagents were used following the manufacturer's recommendations (Illumina, San Diego, CA, USA). The samples were paired-end multiplex sequenced (2 × 150 bp) on the Illumina Hiseq platform and generated at least 40 million reads for each sample.

first: Christopher

last: Swale

first: Valeria

last: Bellini

first: Matthew

last: Bowler

first: Nardella

last: Flore

first: Marie-Pierre

last: Brenier-Pinchart

first: Dominique

last: Cannella

first: Lucid

last: Belmudes

first: Caroline

last: Mas

first: Yohann

last: Couté

first: Fabrice

last: Laurent

first: Artur

last: Scherf

first: Mohamed-Ali

last: Hakimi


title: RNA-Seq analysis of human granulosa cell after COS and mild ovarian stimulation

first: Xiaoping

last: Liu

address: Shougouling Road

institute: The Sixth Affliated Hospital of Sun Yat-sen University

summary: To explore the differences  on the granulosa cells between the COS and mild ovarian stimulation

overall_design: Total 10 samples were analysed

first: Rui

last: Huang


title: Construction of lux-based promoter-reporter platforms in Mycobacterium bovis BCG for screening of drug repurposing small-molecule compounds as new anti-tuberculosis drugs

city: Hong Kong

first: Wing Tung

last: Lee

address: Room Y934, 9/F, Lee Shau Kee Building, The Hong Kong Polytechnic University, Hung Hom, Kowloon

department: Department of Health Technology and Informatics

country: Hong Kong

institute: The Hong Kong Polytechnic University (PolyU)

summary: This study aimed to construct a rapid screening system to identify novel anti-TB agents from a library of small-molecule compounds.

sample_organism: Mycobacterium tuberculosis variant bovis BCG

overall_design: RNA-sequencing (RNA-seq) was conducted to determine the drug mechanisms of the selected compounds as novel antibiotics or anti-virulent agents against the M. tuberculosis complex.

first: Gilman

last: Siu

first: Annie

last: Wing-Tung Lee

first: Li

last: Zhu


title: Next Generation Sequencing Facilitates Quantitative Analysis of HHSteCs, HHSteCs treated with Myoglobin (MB), HHSteCs treated with Neuroglobin (NGB)

city: Osaka

first: Hieu

middle: Ngoc

last: Vu

address: 1-4-3 Asahimachi, Abeno-ku

department: Department of Hepatology

institute: Osaka City University

summary:
Purpose: Hepatic stellate cells (HSCs) plays an important role in liver fibrosis. MB and NGB can inhibit the activation of HSCs. The goal of this study is to investigate the MB and NGB targeted signalling pathways regulating the activation of HSCs.
Method: mRNA profiles of HHSteCs control, HHSteCs treated with MB (4 µM, for 48 hour), and HHSteCs treated with NGB (4 µM, for 48 hour) were generated by deep sequencing.
Results: The RNA-seq data  confirmed that extracellular matrix-encoding genes and fibrosis-related genes  were down-regulated by the MB and NGB treatment.

overall_design: mRNA profiles of HHSteCs with or without MB, and NGB treatment

first: Norifumi

last: Kawada

first: Le

last: Thuy

first: Vu

last: Hieu


title: The function of the GIGANTEA gene StGI.04 in potato: Uncovering a new function affecting the anthocyanin content of tuber skin

city: Gödöllő

first: Zsófia

last: Bánfalvi

address: Szent-Györgyi Albert u. 4.

department: Genetics and Biotechnology Institute

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

summary: GIGANTEA (GI) is a plant-specific, circadian clock-regulated, nuclear protein with pleiotropic functions studied in many plant species. It is involved in flowering, circadian clock control, chloroplast biogenesis, carbohydrate metabolism, stress responses and synthesis of volatiles. In potato (Solanum tuberosum L.), however, only its role in tuber initiation is reported. Based on the findings in other plant species we hypothesized that the function of GI is not restricted to tuberization in potato. To test this hypothesis we repressed the expression of a GI gene, StGI.04 in the commercial potato cultivar ‘Désirée’ and investigated the effect of repression at morphological and transcriptome level. We found that, like GI in other plant species, StGI.04 influences the expression of the key genes of circadian clock, flowering, starch synthesis and stress responses. Furthermore, we detected a novel function of a GI gene in influencing the anthocyanin synthesis and skin colour of potato tubers.

overall_design: RNA-seq of leaves of a StGI.04-repressed (aGI) potato line compared to the non-transformed control 'Désirée' (DES)

first: Karsai-Rektenwald

last: Flóra

first: Khongorzul

last: Odgerel

first: Jeny

last: Jose


title: D-mannose suppressed γδ T cells and alleviated murine psoriasis.

city: Beijing

first: Mingyang

last: Li

address: 95 YongAn Road, Xicheng District

institute: Beijing Friendship Hospital, Capital Medical University

summary: Psoriasis is a chronic skin suffering with multiple comorbidities such as psoriatic arthritis and cardiovascular diseases. Increasing evidences have shown the γδ T cells as the sources of IL-17A play critical roles in the psoriatic syndrome. However, there is still lack an effective way to manipulate these pathogenic γδ T cells which were less studied relative to ab T cells. The present study aims to characterize the phenotype of γδ T cells and evaluate the impact of D-mannose (a C-2 epimer of glucose) on γδ T-mediated psoriasis. We found the psoriatic γδ T cells underwent robust proliferation and acquired an IL-17 producing phenotype. The transcriptomic profiles of these skin draining LN γδ T cells had elevated glycolytic features. Importantly, Treatment of D-mannose inhibited γδ T cells and successfully alleviated the local and systematic inflammations induced by imiquimod. The decreased AKT/mTOR/HIF-1a signaling and glycolytic ability may contribute to the suppression of γδ T cells achieved by mannose. Our study deepened the understandings of γδ T cells in psoriasis, meanwhile, promoted D-mannose utilization as a potent clinical application for γδ T cells driven autoimmune diseases.

overall_design: mRNA profiles of γδ T cells from skin draining LN and spleen of healthy and psoriatic mice.

first: Dong

last: Zhang


title: Decrease in Rnase HII and accumulation of lncRNAs/DNA hybrids: a causal implication in psoriasis?

city: Nice

first: Minoo

last: Rassoulzadegan

address: parc Valrose

department: Institut de Biologie Valrose: iBV

institute: Nice Sophia Antipolis

summary:
Long functional non-coding RNAs (lncRNAs) have been in the limelight in aging research because short telomeres are associated with higher levels of TERRA (Telomeric Repeat containing RNA). The genomic instability caused in Immune-mediated inflammatory diseases (IMID) especially in patients with psoriasis, which lead to short telomeres in psoriasis lesions, is a mechanism leading to cell aging. Research on the fraction of TERRA in hybrid with DNA offers avenues for new strategies. Skin samples were fractionated to obtain the RNA associated with DNA as a R-loop structure. TERRA analysis was performed by RT-qPCR and RNA-seq analysis. The higher amount of TERRA levels attached with each chromosome end was found with psoriasis patients. The increased levels of TERRA linked with telomeres correlate with the decrease in the RNase-HII transcript which means the unresolved DNA/RNA hybrids may ultimately facilitate the formation of skin lesions. LncRNAs have multiple molecular functions, including the regulation of heterochromatin, which controls genome stability and epigenome shaping and may be used as a trans-generational prognostic marker in patients with psoriasis.
The signal of the lncRNAs is higher as DNA/RNAs hybrid (R-Loop) in patients  with psoriasis in lesional tissues and above all, already in non-lesional tissues; -lncRNAs such as TERRA  are found at higher levels at the end of each chromosome in patients with psoriasis, resulting in  telomeres shortening; - and more importantly the idea that higher levels of lncRNAs attached to the  genome lead to phenotypic changes

overall_design: DNA-associated RNA molecules were purified form 7 skin biopsy samples (2 Lesional, 2 Non-lesional, and 3 Control). 10-100 ng of RNA after Dnase digestion were recovered and analyzed by high throughput sequencing on Illumina.

first: Ecmel

last: Mehmetbeyoglu

first: Leila

last: Kianmehr

first: Murat

last: Borlu

first: Zeynep

last: Yilmaz

first: Seyma

last: Başer Kılıç

first: Hassan

last: Rajabi-Maham

first: Serpil

last: Taheri


title: Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Txndc5

city: Zaragoza

first: Jesus

last: Osada

state: Spain

address: C/ Miguel Servet 177

department: Biochemistry and Molecular Biology

country: Spain

institute: Universidad de Zaragoza

summary:
Purpose: The goal of this study was to determine the hepatic transcriptomic´s difference in mice TXNDC5 KO
Method: Hepatic mRNA profile of C57Bl/6J wild-type vs TXNDC5 KO mice fed over 4 weeks with a purified chow diet was analysed by Transcriptome sequencing using BGISEQ-500 platform. Sequence reads that passed quality filters were mapped onto reference genome, followed by novel gene prediction, SNP & INDEL calling and gene-splicing detection.
Results: When using optimized Bioinformatics Workflow, mapping ratio for both tested groups was about 84,76%, 16,178 genes were identified in which 16,178 of them are known genes and 764 of them are novel genes. 5,419 novel transcipts were identified in which 4,115 of them are previously unknown splicing event for known genes, 764 of them are novel coding transcripts without any known features, and the remaining 540 are long noncoding RNA.
Conclusions: This study represents the first analysis of hepatic transcriptome in respond to TXNDC5 absence. Result data confirm that RNA-Sequencing is a sensitive and accurate tool that provides a framework for comparative investigations of known and novel DEGs.

overall_design: 3 pooles og hepatic wild-type RNA was compared versus 3 pooles of hepatic TXNDC5 KO RNA. Mice sustrate was C67BL/6J, were feed during 4 weeks over a purified chow diet and sacrified with a 16 hours fasting.

first: Javier

last: Sánchez-Marco

first: María

middle: A

last: Navarro

first: Roberto

last: Martínez-Beamonte

first: Joaquín

last: Surra


title: Differential expression of circRNAs in the three stages of heart failure in TAC mice

first: Xiang

address: 11 fengxin road, guangzhou science city

institute: Guangdong Laboratory Animals Monitoring Institute

summary: To identify the role of circRNA on the mouse heart during pressure overload induced heart failure, we have employed circRNA microarray expression profiling as a discovery platform to detect circRNA expression. Samples were collected from the sham group and the pressure overload groups (2, 4 and 8 weeks after TAC), with 2 samples per group. The candidate circRNA that may affect the process of heart failure was screened by comparing the pressure overload groups and the sham group.

overall_design: Arraystar mouse circular RNA array V2 was used to profile circRNA expression in murine hearts during cardiac remodeling progression. After isolation, the total RNAs were digested with RNase R to remove linear RNAs and enrich circular RNAs. The latter were further amplified and transcribed by random priming into fluorescent cRNA. The labeled cRNA concentration and activity in pmol Cy3/μg cRNA were measured. One microgram of each labeled cRNA was fragmented, heated, and assembled onto the Arraystar Mouse circular RNA Array V2 (8x15K; Agilent Technologies). The arrays were hybridized, washed, fixed, scanned with an Agilent scanner (No. G2505C; Agilent Technologies), and analyzed with Agilent feature extraction software v.11.0.1.1 (Agilent Technologies).

first: Weijiang

last: Tan

first: Feng

middle: H

last: Yang


title: Gene Expression of preterm and term human placenta

city: New Haven

first: Liza

last: Konnikova

state: CT

address: 375 Congress Ave LSOG 407

department: Pediatrics

institute: Yale University

summary: The goal of this study was to transcriptionally profile the three layers of the human placenta (decidua, fetal membrane and placental villi) from preterm and term human placentas

overall_design: Bulk mRNA extracted from three tissues isolated from matched placentas.

first: Tatiana

last: Silva


title: Differential expression of mRNAs in the three stages of heart failure in TAC mice

last: Li

summary: To identify the role of mRNA on the mouse heart during pressure overload induced heart failure, we have employed high-throughput sequencing to detect mRNA expression. Samples were collected from the sham group and the pressure overload groups (2, 4 and 8 weeks after TAC), with 2 samples per group. The candidate mRNA that may affect the process of heart failure was screened by comparing the pressure overload groups and the sham group.

overall_design: Total RNAs from the ventricular tissues of the sham group and the pressure overload groups (2, 4 and 8 weeks after TAC) were isolated using TRIzol® Reagent. Each group contains two independent samples. Subsequently, a total amount of 3 µg RNA per sample were used for high-throughput sequencing.

first: Shuang

last: Zheng


title: Whole trascriptome analysis of high-risk corneal grafts with CD80/86 antibodies

city: Bunkyo-ku

first: Takenori

last: Inomata

state: Tokyo

address: 3-1-3 Hongo

institute: Juntendo University Graduate School of Medicine

summary: To investigate the mRNA profiles of corneal grafts with CD80/86 antibodies injection.

overall_design: Corneal mRNA profiles of corneal grafts with CD80/86 antibodies injection 14 days after high-risk corneal transplantation

first: Jun

last: Zhu

first: Masahiro

last: Nakamura

first: Kenta

last: Fujio


title: Insight into late synovial joint development by single cell transcriptomics in murine

city: Baltimore

first: Qin

last: Bian

address: 733 N Broadway

institute: Johns Hopkins University

summary: we performed single cell RNA-Seq analysis of 2,267 cells from E17.5 murine knee joint. Using computational analytics and in situ hybridization, we identified five sub-populations contributing to joint constituents, and the underlying transcriptional networks, signaling, and core regulators involving in potential lineage transition during late joint developmental stage.

overall_design: We sampled Gdf5-lineage cells of the murine knee at embryonic time points e17.5 and subjected it to single cell RNAseq analysis via 10x.

first: Patrick

last: Cahan


title: mRNA Sequencing of CMT2A, CMT1A patients and Normal human fibroblasts

city: St. Louis

first: Xiawei

last: Dang

state: MO

address: 660 S Euclid Ave.

department: Internal Medicine

institute: Washington University in St. Louis

summary: We performed RNA sequencing on the 3 CMT2A-causing MFN2 mutations patient cell lines and 3 normal control lines, all cultured in galactose, we found striking transcriptional signature for CMT2A was present. And the CMT2A fibroblast transcriptional signature was >90% different from that of primary fibroblasts from a patient with CMT1 with a duplication mutation within the PMP22 gene.

overall_design: Comparison transcritional signature among CMT2A, CMT1A patients and Normal human fibroblasts

first: Gerald

last: Dorn II


title: Cardiac-dead mouse lungs may remain transplantable at 37ºC for 4 hours if gas exchange is preserved

city: Pittsburgh

first: XINGAN

last: WANG

state: Pennsylvania (PA)

address: 200 Lothrop Street, W1206A

institute: University of Pittsburgh

summary: Despite a potentially huge number, uncontrolled donation after circulatory death contributed little to alleviating donor lung shortage due to rapidly progressive warm ischemia. Many methods have been studied in animals, but the tolerable warm ischemic time (WIT) remains less than 90 minutes. Using a refined mouse model of pulmonary artery ligation (PAL), we firstly determined the maximum tolerable WIT. 4-hour PAL caused mild lung infiltration without dysfunction upon reperfusion, whereas 5-hour PAL triggered arterial endothelium injury and more significant infiltration with dysfunction. Transcriptional profiling showed a myeloid-dominant inflammation with mild injury in 4-hour PAL. The maximum WIT was then adapted in a clinically relevant scenario. Donor mice died of circulatory arrest without heparization and remained at 37ºC for 4 hours, followed by isogenic transplantation. As observed in 4-hour PAL, nonhypoxic warm ischemia-reperfusion hardly affected graft function and histology, no matter if warm ischemic lung preserved gas exchange by spontaneously breathing or by postmortem protective ventilation. If the dead donors were left untouched, however, the grafted lungs suffered severe hypoxic warm ischemia-reperfusion injury, varying from partially aerated totally lost. Taken together, the retrieval time can be extended to 4 hours at 37ºC by preventing cardiac-dead donor lung hypoxia.

overall_design: Transcriptional profiling were performed on three naïve lung samples and three left lung with warm ischemia-reperfusion injury induced by 4 hours of pulmonary artery ligation and 24 hours of reperfusion in adult wild type (WT) B6 mice

first: Xingan

last: Wang


title: Transcriptomic Profiling of the Telomerase Transformed Mesenchymal Stromal Cells Derived Adipocytes in Response to Rosiglitazone.

city: Sharjah

first: Amir

middle: Ali

last: Khan

address: Emirates of Sharjah

department: Department of Applied Biology

country: United Arab Emirates

institute: University of Sharjah

summary: In our earlier study, it was shown that Rosiglitazone enhances the brown adipogenesis of Immortalized Human Bone Marrow Mesenchymal Stromal Cells - hTERT (iMSC3). The current study compared the transcriptomics profiles of the different adipocytes derived from iMSC3 reported in our previous study. The complete transcriptomic profiles of iMSCs and adipocytes differentiated with and without Rosiglitazone treatment revealed a set of marker genes that warrant further investigation. The transcriptomics analysis revealed the upregulation and uniquely expression of genes due to Rosiglitazone treatment seems to have roles in brown adipogenesis.

overall_design: Total RNAs were isolated from iMSC3 and iMSC3‑derived adipocytes without and with Rosiglitazone treatment. The experminamtal groups were as following: (A) undifferentiaed iMSC3; adipocytes (B) derived with no Rosiglitazone treatment; adipocytes (C) derived with Rosiglitazone present in induction media only while adipocytes (D) derived with Rosiglatazone present in both induction and maintenance media. This was followed by library preparation for transcriptomic sequencing. The constructed libraries were subjected to high throughput mRNA sequencing using Illumina NovaSeq 6000. Differential gene expression analysis was performed using DESeq2 R package, followed by GO and KEGG enrichment analysis using clusterProfiler R package.

last: Ali Khan

first: Muhammad

last: Nasir Khan Khattak

first: Moza

last: Al-Ali


title: Meningioma methylation analysis

city: Toronto

first: Yasin

last: Mamatjan

state: Ontario

address: 610 University Ave.

institute: Princess Margaret Cancer Center

summary:
Methylation analysis of meningioma samples.
Genomic DNA isolated directly from fresh-frozen human meningioma specimens.

overall_design: Meningioma samples n = 121,  No technical replicates performed.

first: Nassiri

last: Farshad


title: Transcription Factors Involved in DNA Demethylation  During Human Cellular Development

city: Yokohama

first: Yurina

last: Miyajima

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

type: Methylation profiling by genome tiling array

summary: DNA methylation is an important epigenetic modification involved in the regulation of mammalian gene expression, with each type of cell developing a specific methylation profile during its differentiation. The enzymatic mechanisms of DNA methylation and demethylation are well understood; however, little is known about how cell-type-specific DNA methylation profiles are developed. Recently, a small subgroup of transcription factors (TFs) have been shown to promote DNA demethylation at their binding sites (e.g., RUNX1 reported by our group).

overall_design: Bisulphite converted DNA from the 50 samples were hybridised to the Illumina Infinium 850K Human Methylation Beadchip

first: Shuhei

last: Noguchi

first: Yuki

last: Tanaka

first: Jing-Ru

last: Li

first: Hajime

last: Nishimura

first: Mami

last: Kishima

first: Joanne

last: Lim

first: Erina

last: Furuhata

first: Takahiro

last: Suzuki

first: Takeya

last: Kasukawa

first: Harukazu


title: single-cell RNA sequencing of in vivo matured and maturation deficient human oocytes

city: beijing

first: jing

last: hang

address: No.49 huayuan north road

institute: peking university, third hospital

summary: Single cell transcriptomic composition of in vivo matured (IVO) MII oocytes and maturation deficient (MD) oocytes discloses the aberrant expression level of spliceosomal proteins, accompanying with differential alternative splicing (DAS) events.

overall_design: Using single-cell transcriptomic RNA sequencing (RNA-seq), differentially expressed genes (DEGs) between IVO and MD oocytes and enriched pathways were analyzed based on the polyadenylated transcripts abundance. Three MD oocytes and three normal IVO oocytes were derived from six individuals.

first: Jing

last: Hang


title: Gene expression data from Collaborative Cross mice treated with TAK-857

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

country: USA

institute: UNC Eshelman School of Pharmacy

summary:
Eight (8) male mice (4 matched pairs) from each of 45 Collaborative Cross lines were treated with a single oral (gavage) dose of either vehicle (methylcellulose) or TAK-875 (600 mg/kg) to facilitate the evaluation of very early liver events in the pathogenesis of IDILI and the identification of genetic risk factors that influence toxicity susceptibility at the hepatocyte level
Microarray profiling in the liver identified treatment-induced changes differing by strain and correlating with serum liver chemistries that were enriched in mitochondrial dysfunction, oxidative stress, bile acid homeostasis and immune response pathways suggesting multiple mechanisms contribute to TAK-875 toxicity.
Candidate risk factor genes were then identified using individual-transcript and pathway-based mapping of the expression data and further support the contribution of these mechanisms to TAK-875 toxicity.

overall_design: Eight (8) male mice (4 matched pairs) from each of 45 Collaborative Cross lines were treated with a single oral (gavage) dose of either vehicle (methylcellulose) or TAK-875 (600 mg/kg). Livers were harvested 24 h post dose for gene expression profiling.


title: Endothelial loss of Zeb2 distorts the hepatic angioarchitecture and aggravates liver fibrosis in mice

city: Rotterdam

first: Eskeatnaf

last: Mulugeta

address: Wytemaweg 80

department: Cell Biology

institute: Erasmus University Medical Center Rotterdam (Erasmus MC)

summary: Expression of the Zinc-Finger E-Box-binding Homeobox (Zeb)2 is enriched in Liver Sinusoidal Endothelial cells (LSECs), but its role in liver ECs remains unknown. We performed RNA sequencing on the main liver cell types from wild-type mice and mice lacking Zeb2 specifically in endothelial cells to identify cell-autonomous and non-autonomous RNA expression changes and to find pathways and GO-terms affected by genetic Zeb2 inactivation.

overall_design: Endothelial cells, Kupffer cells, hepatic stellate cells and hepatocytes (n=2) were isolated from livers of wild-type and endothelial-specific Zeb2 knock-out mice by density centrifugation and FACS. RNA was isolated using Reliaprep (Promega) and was sequenced according to the Smart-seq2 method.

first: Willeke

last: de Haan

first: Wouter

last: Dheedene

first: Leo

last: van Grunsven

first: Aernout

last: Luttun


title: Recombinant RANKL causes modulation of inflammatory signaling pathways in C2C12 myotubes

city: Indianapolis

first: Andrea

last: Bonetto

state: IN

address: 980 W. Walnut Street, R3-C522

institute: Indiana University School of Medicine

summary: Previous reports indicate that RANKL-RANK signaling participates in regulating muscle mass and strength in denervated animals, while RANKL inhibition by OPG-Fc peptide improves the muscle phenotype in dystrophic mdx mice. RANKL has also been shown to activate STAT3 to regulate osteoclastogenesis, although it is not known whether such interaction also plays a role in skeletal muscle. The objective of this aim is to clarify whether RANKL directly affects skeletal muscle.

overall_design: In order to determine the effects of RANKL on muscle fiber, after 5 days of differentiation C2C12 myotubes were exposed to 100 ng/ml recombinant mouse TRACE/RANK L/TNFSF11 protein for 72 hours.

first: Fabrizio

last: Pin

first: Ashok

last: Narasimhan

first: Teresa

last: Zimmers


title: Deficiency of myeloid PHD proteins aggravates atherogenesis via macrophage apoptosis and paracrine fibrotic signaling [bulk RNA-seq]

city: Heidelberg

first: Javier

last: Perales-Paton

state: Baden-Württemberg

address: Im Neuenheimer Feld 267

department: Faculty of Medicine

institute: Heidelberg University

summary: Atherosclerotic plaque hypoxia is detrimental for macrophage function. Prolyl hydroxylases (PHDs) initiate cellular responses to hypoxia and may therefore govern macrophage function in plaque hypoxia. PHD inhibitors are clinically investigated to treat anemia in patients with chronic kidney disease, but the consequences for cardiovascular disease are not clear. Hence, we studied the influence of myeloid specific PHD deficiency on atherosclerotic plaque development and stability.

overall_design: PHD mRNA and protein levels were expressed by human plaque macrophages, and murine bone-marrow-derived macrophages, thus myeloid specific PHD knockout (PHDko) mice were fed 0.25% cholesterol diet for 6-12 weeks to induce atherosclerosis. Aortic root plaque size was augmented 2.6fold in PHD2cko, and 1.4-fold in PHD3ko, but not in PHD1ko mice compared to controls, independent of plasma cholesterol levels. Macrophage apoptosis was promoted in PHD2cko and PHD3ko mice in vitro and in vivo via the HIF1α/BNIP3 axis as shown by pathway analysis of bulk and single cell RNA sequencing of murine bone-marrow-derived macrophages and plaque macrophages, respectively, and validated by siRNA silencing. Human plaque BNIP3 mRNA associated with carotid plaque necrotic core content, suggesting similar adverse effects in humans. Further, PHD2cko plaques -not PHD1 or PHD3ko- displayed enhanced fibrosis at two different disease stages, and across vascular beds, independent of macrophage function. We show PHD2cko bone-marrow-derived macrophages enhanced collagen secretion by fibroblasts in a paracrine manner, while smooth muscle cell function was unchanged. In silico analysis of macrophage-fibroblast communication predicted SPP1 signaling by PDH2cko macrophages to regulate the fibroblast transcriptome, in line with enhanced SPP1 protein content in plaques of PDH2cko mice

first: Judith

middle: C

last: Sluimer