title: Transcriptomic analysis of gnotobiotic Aedes aegypti mosquitoes

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: We compare the transcriptome of gnotobiotic Ae. aegypti generated by contaminating axenic (bacteria-free) larvae with bacterial isolates found in natural mosquito breeding sites. We focused on four bacterial isolates (Lysobacter, Flavobacterium, Paenibacillus and Enterobacteriaceae)  and found that different gnotobiotic treatments resulted in massive transcriptomic changes throughout the mosquito development.

overall_design: 48 samples, 3 mosquito stages (larval, pupal and adult stages), 5 conditions, 3 replicates of each type of sample. The non-axenic samples were the reference sample at each stage.

first: Emilie

last: Giraud

first: Odile

last: Sismeiro

first: Hugo

last: Varet

first: Louis

last: Lambrechts


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes Mechanism for Autophagy Inhibition Enhanced Salt Stress Sensitivity of Wheat Seedling

status: Public on Dec 15 2021

city: Tianjin

first: Jieyu

last: Yue

state: Tianjin

address: Road Binshuixidao NO.393

country: China

institute: Tianjin Normal University

type: Expression profiling by high throughput sequencing

summary:
Purpose: To characterize the functional implication of autophagy in the wheat response to stress, the key genes contributing in mediated salt tolerance of wheat seedlings through 3-MA were identified in normal or salt stress conditions in the presence or absence of added 3-MA by the transcriptome profiles.
Methods: Four days after NaCl and 3-MA treatment, the roots and the third leaves were collected respectively with every 10 of them being mixed as one biological replicate for each treatment. Every treatment had four biological replicates. The wheat root and leaves mRNA profiles were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: The RNA-Seq data had high quality and reliable results were obtained from the transcriptome assembly. A high correlation between biological replicates was observed for all treatments, which indicated that the four biological replicates were reliable in this study. Based on the principal component analysis (PCA), a clear separation between the NaCl-treated group and controls could be observed. The Q30 percentage (sequences with sequencing error rate lower than 0.1%) was over 94%, and the average GC content of the RNA-seq reads was 55.46%. After removing the adaptor and low-quality sequence, each library received 68310810-83844286 clean reads. These clean reads were mapped to the reference genome with match ratios in the range of 93.6%-95.9%, and 120744 genes predicted from the genome were found to be expressed (with FPKM > 0), including 25180 annotated genes in wheat genome. 3-MA treatment shifted the transcriptome a salt-stressed wheat seedling. The up-regulated DEGs and DEMs were increased, and the down-regulated DEGs and DEMs were decreased in 3-MA-added plants under NaCl stress condition. The study may help us understand the mechanism for 3-MA mediated salt tolerance and provide a theoretical basis for autophagy regulated salt response in wheat seedlings.
Conclusions: 3-MA treatment shifted the transcriptome a salt-stressed wheat seedling. The up-regulated DEGs and DEMs were increased, and the down-regulated DEGs and DEMs were decreased in 3-MA-added plants under NaCl stress condition. The study may help us understand the mechanism for 3-MA mediated salt tolerance and provide a theoretical basis for autophagy regulated salt response in wheat seedlings.

overall_design: Four days after NaCl and 3-MA treatment, the mRNA profiles of the roots and the third leaves.

first: Yingjie

last: Wang


title: Inhibition of IGF1R/IR and autophagy as an intervention in PDAC

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

country: USA

institute: UNC

summary:
To determine whether suppression of IGF-1 signaling in was synergistic with inhibition of autophagy in PDAC, and to identify transcriptional response illicited
mice were injeced with KPC MT4 cells s.c. and treated with vector BMS754807 or hydroxychloroquine alone or incombination. RNA was isolated from median tumors from each group and transcriptomics conducted

overall_design: 4 groups (n=6/group), Control, BMS754807 only, hydroxychloroquine only, BMS754807+hydroxychloroquine

first: Clint

middle: A

last: Stalnecker

first: Kajal

middle: R

last: Grover

first: Cole

last: Edwards

first: Michael

middle: F

last: Coleman

first: Runying

last: Yang

first: Bjoern

last: Papke

first: Mariaelena

last: Pierobon

first: Emanuel

last: Petricoin

first: Adrienne

middle: D

last: Cox

first: Channing

middle: J

last: Der

first: Stephen

last: Hursting

first: Kirsten

middle: L

last: Bryant


title: Mitochondrial transcription factor A (TFAM) represses the expression of interferon signaling genes in human lung epithelial cells

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Mitochondrial transcription factor A (TFAM) is associated with a number of neurodegenerative diseases and also with asthma. TFAM deficiency-induced mitochondrial DNA stress primes the antiviral innate immune response in mouse embryonic fibroblasts. In this study, we overexpressed TFAM in human lung epithelial cells (A549), then obtained and analyzed the TFAM-regulated transcriptome by Illumina-sequencing technology. We found that TFAM overexpression down-regulated and up-regulated the expression 642 and 169 genes (DEGs), respectively. The TFAM-repressed genes were highly enriched in cytokine-mediated signaling pathway, type I interferon- and INFmediated signaling pathways, and viral response pathways. We also revealed that 2563 alternative splicing events in 1796 genes (ASG) were de-regulated upon TFAM overexpression. These TFAM-responding ASGs were strongly enriched in DNA repair, nerve growth factor receptor signaling pathway, and also transcription regulation. Further analysis revealed that the promoters of TFAM-repressed DEGs were enriched by DNA binding motifs of transcription factors whose alternative splicing regulated by TFAM. These findings suggested that TFAM regulates not only immune response gene expression in human lung epithelial cells, but also alternative splicing which may play a role in mediating transcriptional regulation. This TFAM-centered gene regulation network could be targeted in developing therapies against various diseases.

overall_design: Detecting the expression level of differential genes and alternative splicing after TFAM overexpression in A549 cells by RNA-seq

first: Jinsong

last: Luo

first: Hong

last: Liu

first: Jun

last: Li

first: Bin

last: Song


title: Transcriptome analysis using Quant-RNAseq after NPM1 or HIF-1α silencing under normoxia or Hypoxia

city: Larissa

first: Antonis

last: Giakountis

address: Biopolis

department: Biochemistry and Biotechnology

country: Greece

institute: University of Thessaly

summary: Hypoxia inducible factor-1 (HIF-1) is a central transcriptional regulator of genes associated with adaptive responses to hypoxia. NPM1 is a histone chaperone found to associate with HIF-1α in a phosphorylation dependent manner and increase its activty. The aim of this study was to find if HIF-1α and NPM1 regualate gene expression under hypoxia. Transcriptome analysis using Quant-RNA-seq after HIF-1α or NPM1 silencing under hypoxia reveals a significant number of genes, the hypoxic expression of which depends on both proteins.

overall_design: Examinaton of genes expressed after silencing with siRNA NPM1 or HIF-1α in HeLa cells and subsequent incubaton in normaxia or hypoxia.

first: Kreon

last: Koukoulas

first: George

last: Simos

first: Ilias

last: Mylonis


title: Epigenetically defined therapeutic targeting in H3G34R/V high-grade gliomas [RNA-Seq]

city: Ann Arbor

first: Sriram

last: Venneti

state: MI

address: 1150 W. Medical Center Drive

department: Department of Pathology

institute: University of Michigan

summary: H3.3G34R/V hemispheric gliomas carrya dismal prognosisas current treatments including radio/chemotherapy are not curative. We undertook a systematic and comprehensive epigenetic approach to define therapeutic dependenciesin H3.3G34R/V gliomas.

overall_design: Three biological replicates were analyzed for each of 3 conditions

first: Stefan

last: Sweha


title: Epigenetically defined therapeutic targeting in H3G34R/V high-grade gliomas

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Epigenetically defined therapeutic targeting in H3G34R/V high-grade gliomas [ChIP-Seq]

summary: H3.3G34R/V hemispheric gliomas carry a dismal prognosis as current treatments including radio/chemotherapy are not curative. We undertook a systematic and comprehensive epigenetic approach to define therapeutic dependencies in H3.3G34R/V gliomas.


title: A pulmonary vascular model from endothelialized whole organ scaffolds

status: Public on Dec 14 2021

city: New Haven

first: Micha Sam

middle: Brickman

last: Raredon

state: Connecticut

address: 10 Amistad Street

department: Biomedical Engineering

institute: Yale University

summary: We introduce a novel in vitro platform that could simulate key native pulmonary vascular phenotypes and functions, and shows the potential of using the bioengineered whole organ as a platform for disease modeling. Since it is becoming clear that vascular endothelium and the coagulation cascade are adversely affected in some COVID19 patients, such an engineered organ system may play an important role in dissecting disease mechanisms and treatments.

overall_design: Single-cell RNA sequencing data was generated from native pulmonary endothelium, primary pulmonary endothelium cultured on tissue flasks, primary pulmonary endothelium cultured in acellular lung scaffolds, induced pluripotent stem cell-derived endothelium cultured on tissue flasks, and induced pluripotent stem cell-derived endothelium cultured in acellular lung scaffolds

first: Yifan

last: Yuan

first: Micha

middle: B


title: Human Tongue Fungiform Papilla Transcriptome and Proteome Reveal Sex Differences in Long Intergenic Noncoding RNA, Immune Response and Metabolism Genes [array]

city: Baltimore

first: Josephine

middle: M.

last: Egan

state: MD

address: BRC Suite 100, 251 Bayview Boulevard

department: Laboratory of Clinical Investigation

institute: National Institute on Aging - NIH

summary: Fungiform papillae (FP) are visible protrusions on the anterior tongue surface that contain taste buds, their nerves, and capillaries, epithelial cells, stromal cells, and immune-surveilling cells. As FP are easily biopsied in a minimally invasive procedure and have been shown to regrow, we compared three different mechanical methods of FP protein extraction and found that mechanical disruption of FP under liquid nitrogen or bead beating were more efficient than mincing in terms of yield and proteomic profile. A successful protocol to extract RNA from individual FP using bead beating was employed for transcriptomic analysis by RNA sequencing and microarray. Relative to female FP, male FP proteomes and transcriptomes showed predominant expression of Y chromosome-encoded Y antigens, such as EIF1AY, DDX3Y, SMCY, NLGN4Y, UTY, and PCDH11Y, validating our findings. We further found significantly higher levels of Human Leucocyte Antigen (HLA)-associated transcripts and HLA-A protein levels in males than in females. Several long intergenic non-coding (LINC) RNAs exhibit sex-specific expression, in particular LIN02888 with unknown function is more highly expressed in female relative to male FP. Transcripts in the interferon response pathway a key element of the innate immune system's defense against pathogens exhibits differential regulation between the sexes. This indicates that FP biopsy is a minimally invasive method to obtain human tissue in order to study, for example, age-related and sex specific changes of interest, while allowing for dynamic investigation of interindividual differences over time in the context of both health and disease.

overall_design: Gene expression microarray study of human tongue fungiform papillae comparing young males (N=4) and females (N=4).

first: Gayan

middle: C

last: Premaratne

first: Hasitha

middle: U

last: Premathilake

first: Ceereena

last: Ubaida-Mohien

first: Alexey

last: Lyashkov

first: Elin

last: Lehrmann

first: Qing

first: Yongqing

last: Zhang

first: Ashley

last: Appleton

first: Chee

last: Chia

middle: M

first: Máire

middle: E

last: Doyle


title: Epigenome analysis of muscle tissue samples from male participants of the Hertfordshire Sarcopenia Study (HSS) and Hertfordshire Sarcopenia Study extension (HSSe)

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

country: United Kingdom

institute: University of Oxford

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of muscle tissue genomic DNA. The Illumina Infinium MethylationEPIC array was used to obtain DNA methylation profiles across approximately 850,000 CpGs. Samples were male, taken from both the Hertfordshire Sarcopenia Study (HSS, n=34) and the Hertfordshire Sarcoepnia Study exension (HSSe, n=44), to determine DNA methylation associations with measures of muscle mass and function. We further aimed to test whether differences in the muscle methylome are associated with sarcopenia in older individuals. We found significant associations between DNA methylation in the muscle tissue and sarcopenia, as well as individual measures of muscle mass and function, enriched around EZH2 binding sites.

overall_design: Bisulphite converted DNA from the 78 samples were hybridised to the Illumina Human Infinium MethylationEPIC array


title: RNA-sequencing data analysis of PC9 cell lines

city: Shanghai

first: Fang

last: Hu

address: 241 Huaihai West Road, Xuhui District

institute: Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiaotong University

summary: The function of tsRNA-5001a on the growth of tumor cells was studied by cell function experiment. RT-qPCR was used to detect the expression of tsRNA-5001a in paired samples of lung adenocarcinoma. Cell localization of tsRNA-5001a was performed by nuclear-cytoplasmic separation assay. Transcriptome sequencing was used to screen the molecules involved in the regulatory network of tsRNA-5001a.

overall_design: We use three samples for knockdown tsRNA-5001a, and the other three samples for control.

first: F

first: Y

last: Niu

first: L

middle: Y

last: Jiang


title: Lens epithelial cell transcriptome reprogramming at 24 hours post cataract surgery (PCS) in wild type (WT) and β8 integrin Conditional Knockout (β8ITGcKO) mice.

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

summary: This trancriptome analysis reveals the first detailed analysis on how the remnant lens epithelial cells (LECs) greatly reprogram their transcriptome by 24 hours post cataract surgery (PCS) and the dependence of this phenomenom on endogenous β8 integrin gene expression.

overall_design: Living mice of both WT and β8ITGcKO were subjected to lens fiber cell removal leaving behind the lens epithelium and capsule to model human cataract surgery. NovaSeq 6000, S2 100PE transcriptome profiling was performed in biological triplicate on remnant LECs isolated either immediately after surgery or 24 hours later in order to ascertain the response of lens epithelial cells to cataract suregery with the goal of understanding the role of αVβ8 integrin in posterior capsular opacification (PCO) pathogenesis.

first: Shihan

middle: H

last: Mahbubul

first: Duncan

middle: K

last: Melinda


title: The DNMT1 inhibitor GSK-3484862 mediates global demethylation in murine embryonic stem cells

city: Montreal

first: William

middle: A.

last: Pastor

state: Quebec

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

type: Methylation profiling by high throughput sequencing

summary: We generated WGBS datasets from mESCs treated with the novel drug GSK-3484862 attained from two different commercial sources or the conventional DNMT1 inhitibitor 5-azacytidine.  To assess efficacy, datasets were generated from mESCs treated with GSK-3484862 at two concentrations and after treatment for 6 days and 14 days each. Additionally, for comparison purposes, we generated WGBS datasets from Dnmt1/3a/3b deficient mESCs which have very low levels of DNA methylation and WT mESCs treated with DMSO which retain high levels of DNA methylation.

overall_design: Examination of global DNA methylation levels in Dnmt1/3a/3b deficient mESCs and WT mESCs treated with DMSO, 5-azaycytidine or GSK-3484862. GSK-3484862 treatments lasted for 6 days or 14 days at 2μM and 10μM, before collection. GSK-3484862  from two commercial suppliers - ChemieTek and MedChemExpress - were tested simultaneously. 5-azacytdine treatments were done at 100nM or 300nM for 48 hours, after which cells were allowed to recover for 46 hours before collection for sequencing.

middle: A


title: Single nucleus RNA-seq atlas of mouse mediobasal hypothalamus

first: Martin

middle: G

last: Myers Jr

address: 1000 Wall St

summary: To uncover the cellular identifies of the mouse mediobasal hypothalamic cells, we used single nucleus RNA-seq (snRNA-seq).

overall_design: Wild-type mice were maintained on ad libitum chow prior and treated with either saline or insulin prior to microdissection of the hypothalamus. We then isolated nuclei and subjected these nuclei to snRNA-seq using the 10x Genomics 3’ gene expression platform.

first: Alan

last: Rupp

last: Myers


title: Leptin-mediated control of body weight by a conserved population of Glp1r-expressing neurons

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: Single nucleus RNA-seq atlas of mouse Lepr-expressing hypothalamic cells

summary: To uncover the cellular identifies of the mouse hypothalamic Lepr cells, we used single nucleus RNA-seq (snRNA-seq) from enriched hypothalamic Lepr cells.

overall_design: Lepr-Cre;R26-LSL-Sun1-sfGFP mice were maintained on ad libitum chow prior to microdissection of the hypothalamus. We then isolated nuclei, FACS sorted for GFP-positive nuclei, and subjected these nuclei to snRNA-seq using the 10x Genomics 3’ gene expression platform.


title: Capturing tumor heterogeneity in pre- and post-chemotherapy colorectal cancer ascites-derived cells using single-cell RNA-sequencing

city: Ratchathewi

first: Varodom

last: Charoensawan

state: Bangkok

address: 272 Thanon Rama VI

country: Thailand

institute: Faculty of Science, Mahidol University

summary:
Purpose: Malignant ascites is an abnormal accumulation of fluid within the peritoneal cavity, caused by metastasis of several cancer types including colorectal cancer. Cancer cells in ascites reflect poor prognosis and can be a source of recurrence. They also represent a good source of specimens for the study of tumor heterogeneity. Single-cell RNA-sequencing (scRNA-seq) has recently emerged as a powerful tool for exploring and characterizing cellular heterogeneity in both normal tissues and cancers. However, molecular profiles of malignant ascites cells in response to treatment are still poorly understood.
Materials and Methods: We have performed scRNA-seq of ascites-derived cells from a colorectal cancer patient to profile and characterize the cellular heterogeneity and different expression hallmarks within the cell populations before and after a chemotherapy treatment. The effect of different single cell preparation protocols, namely, manual and enzymatic methods, on cell viability and gene expression were also assessed.
Results: Unbiased clustering of 19,653 cells in total reveals 12 sub-clusters with unique transcriptomic patterns from four major cell types: epithelial cells, myeloid cells, fibroblast, and lymphocytes. Interestingly, the percentages of cells recovered from different cell types appeared to be influenced by the preparation protocols; enzymatic and mechanical separations, with more than 90% reduction in myeloid cell number when enzymatic method was used. Subcluster analysis of epithelial cell populations before and after chemotherapy treatment identified distinct cell clusters with unique transcriptomic profiles. Moreover, there were only three out of 11 epithelial subclones with more than 50% reduction in tumor cell number after treatment. This finding indicated that most clones were resistant to the treatment, which reflected the poor treatment outcome observed in our patient.
Conclusions: Overall, our study underscores cellular heterogeneity within malignant ascites and uncovers the gene expression profile of colorectal cancer ascites-derived cells in single-cell resolution. Our findings emphasize the potential benefit of using scRNA-Seq to monitor real-time treatment response in cancer patients.

overall_design: single-cell RNA-seq of ascites-derived cells before and after chemotherapy using either mechanical or enzymatic dissociation for cell preparation

first: Tiraput

last: Poonpanichakul

first: Ekaphop

last: Sirachainan

first: Natini

last: Jinawath


title: Single nucleus RNA-seq atlas of rat mediobasal hypothalamus

summary: To uncover the cellular identifies of the rat mediobasal hypothalamic cells, we used single nucleus RNA-seq (snRNA-seq).

overall_design: Wild-type rats were maintained on ad libitum chow prior to microdissection of the hypothalamus. We then isolated nuclei and subjected these nuclei to snRNA-seq using the 10x Genomics 3’ gene expression platform. A mouse mediobasal hypothalamus tissue sample was processed and sequenced simultaneously in one sample.


title: scRNA-seq of total mouse aortic cells with CITE-seq and cell Hashing

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

summary: We performed single-cell RNA-seq analysis with CITE-seq and cell hashing of total viable aortic cells from Ldlr-/- mice fed a high fat diet for 13 weeks

overall_design: Aortas were collected from Ldlr-/- mice fed a HFD (Altromin, 15% milk fat, 1.25% cholesterol) for 13 weeks and treated with an irrelevant isotype control antibody (100 µg rat IgG2b anti-Phyt1, clone AFRC Mac51, i.p. twice weekly) for 4 weeks before sacrifice. 2 aortas were pooled to generate each sample, and n=5 pools were analyzed. To exclude circulating leukocytes from analysis, mice were injected with 2.5µg anti-CD45.2 APC (clone 104, BioLegend) intravenously 5 minutes before sacrifice to label blood borne immune cells. Aortas were enzymatically digested in RPMI medium containing 450U/ml collagenase I (Sigma-Aldrich C0130), 125U/ml collagenase XI (Sigma-Aldrich C7657), 60U/ml Hyaluronidase (Sigma-Aldrich H3506) for 1 hour at 37°C with agitation, washed in PBS/1% FCS and passed through a 70µm cell strainer. Cells were labeled for 20 minutes at 37°C with CalceinViolet-AM (BioLegend 425203) according to the manufacturer’s instructions. Cells were washed and resuspended in PBS 1% FCS, plated in round bottom 96 well plates, and incubated for 10 minutes on ice with anti-CD16/32 (Biolegend, Clone 93, 10µg/ml) to block unspecific binding of antibodies to Fc receptor. Cells were subsequently labeled in a final volume of 100µl for 15 minutes at 4°C with anti-CD45.2 Alexa488 (2.5µg/ml, clone 104, BioLegend), anti-Ter119 PE-Cy7 (1µg/ml, clone TER119, BioLegend), 1:1000 Fixable Viability Dye, CITE-seq antibodies (see table), and hashtag antibodies. Each sample was labeled with a specific Hashtag antibody (Hashtag 1 to 5, final concentration 1:200, BioLegend). Cells were washed twice and all the sample were pooled. Viable Ter119negCD45.2-APC(i.v.)negCalceinAM+ cells were sorted using a BD FACS Aria III with a 100µm nozzle. The amount of sorted cells was adjusted so that ~50% of the total cells represent leukocytes (CD45-Alexa488+). Cells were sorted in PBS supplemented with 0.04% BSA, washed and counted in Trypan blue to assess viability (>85%). 18,000 cells were loaded at a concentration of 600 cells/µl in the 10x Genomics Chromium (Single Cell 3’ v3 reagents, 10x Genomics) and scRNA-seq ADT and HTO libraries were prepared.

first: Sarah

last: Schäfer

first: Alma

last: Zernecke

first: Panagiota

last: Arampatzi

first: Clément

last: Cochain


title: microRNA profiling in the aqueous humor of highly myopic eyes by next generation sequencing

first: Jibo

last: Zhou

state: Shanghai

address: 639 Zhizaoju Road, Shanghai, 200011, China

department: Department of Ophthalmology, Shanghai Ninth People's Hospital

institute: Shanghai Jiao Tong University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: To characterize microRNAs (miRNAs) and their possible roles in high myopia by using next generation sequencing
Methods: Aqueous humor samples were obtained from 15 highly myopic eyes and 15 cataract eyes at the onset of surgery. miRNA next generation sequencing and bioinformatics analyses were performed using RNA extracted from aqueous humor samples.
Results: A total of 341 miRNAs were detected in the aqueous humor samples of highly myopic eyes; 201 miRNAs were detected in the aqueous humor samples of cataractous control eyes. A total of 249 mature miRNAs and 17 novel miRNAs were differentially expressed during myopia. Possible pathways regulated by these aberrantly expressed miRNAs included the TNF, MAPK, PI3K-Akt, and HIF-1 signaling pathways.
Conclusions: The current study provided an overall view of miRNA profiling in the aqueous humor of highly myopic eyes. These profiles may be associated with myopia pathogenesis, and are potential biomarkers.

overall_design: miRNA profiles in aqueous humor of highly myopic patients (15 eyes of 15 patients),  aqueous humor of cataract patients as control (15 eyes of 15 patients) , aquous humor from 3 eyes mixed as 1 sample, detected in quintuplicate, using Illumina Hiseq4000

first: Yi

last: Zhu

first: Weiran

last: Li

first: Dongqing


title: Rescue of chloride and bicarbonate transport by elexacaftor-ivacaftor-tezacaftor in organoid-derived CF intestinal and cholangiocyte monolayers

city: Rotterdam

first: Henk

middle: P.

last: Roest

state: Choose State

address: Doctor Molewaterplein 40

department: Surgery

country: Netherlands

institute: Erasmus MC

summary: In cystic fibrosis (CF), loss of CF transmembrane conductance regulator (CFTR)-dependent bicarbonate secretion precipitates the accumulation of viscous mucus in the lumen of respiratory and gastrointestinal epithelial tissues. We investigated whether the combination of elexacaftor (ELX), ivacaftor (IVA) and tezacaftor (TEZ), apart from its well-documented effect on Phe508del-CFTR-mediated chloride transport, also restores bicarbonate transport.

overall_design: Epithelial monolayers were cultured from intestinal and intra-hepatic bile duct organoids of homozygous Phe508del-CFTR patients and controls. Transcriptome sequencing was performed, and bicarbonate and chloride transport were assessed in the presence or absence of ELX/IVA/TEZ, using the intestinal current measurement technique.

first: Marcel

last: Bijvelds

first: Floris

last: Roos

first: Kelly

middle: F

last: Meijsen

middle: P

first: Monique

last: Verstegen

first: Hetty

last: Janssens

first: Luc

last: van der Laan

first: Hugo

middle: R

last: de Jonge


title: Regulation of translation under mitoprotein-induced stress in Saccharomyces cerevisiae

city: Stanford

first: Felix

middle: Christian

last: Boos

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

summary: Proteotoxic stress triggers adaptive cellular responses, including changes in gene expression on the levels of transcription and translation. In this study, we analyzed the translational response of yeast cells to impaired protein import into mitochondria, a condition under which mitochondrial precursor proteins accumulate in the cytosol and impose proteotoxic stress. We analyzed changes in translational efficiency as well as more subtle changes in the distribution of ribosomes along transcripts, with a special focus on translation initiation sites.

overall_design: Ribosome footprints from clogger-expressing and control cells after 4.5 h of clogger induction were isolated and sequenced in 3 biological replicates. Cells in replicate 1 were treated with cycloheximide before cell lysis to enrich translation initiation sites. Replicates 2 and 3 were not in contact with cycloheximide before cell lysis.

first: Kevin

last: Stein

first: Judith

last: Frydman


title: Differences in gene expression of liver tissues between MAFLD patients and controls.

city: Changsha

first: Yongqiang

last: Ma

address: 139 Renmin Road

institute: Department of Liver Transplant, Second Xiangya Hospital, Central South University

summary: Transcriptomic analysis was applied to liver tissues of seven patients with MAFLD and nine normal controls,then, differential genes were identified by comparative analysis of sequencing results, and target genes that may be related to the pathogenesis of MAFLD were further studied.This study may provide new ideas for understanding the pathogenesis of MAFLD and thus provide new targets for the treatment of MAFLD.

overall_design: RNAseq data of liver tissues of 7 MAFLD patients and 9 controls

first: Jiequn


title: Comparison of brown adipose tissue (BAT) gene expression between Letmd1 KO and wild-type control mice housed at 30˚C or 7˚C for 3 weeks.

city: Seoul

first: Kyung-Mi

last: Choi

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: We identified Letm1 domain containing 1 (Letmd1) as a candidate regulator of BAT thermogenesis. We generated Letmd1 KO mice, raised at thermoneutral or cold conditions, and performed RNA-sequencing in BAT.

overall_design: Transcriptome profiles of BAT of adult Letmd1 KO and wild-type mice housed at 30˚C or 7˚C for 3 weeks.

first: Jung Hak

last: Kim

first: John

last: Yoon


title: Gene expression based profiling of pleomorphic xanthoastrocytoma highlights two prognostic subgroups

city: New Delhi

first: Vaishali

last: Suri

state: Delhi

address: Sri Aurobindo Marg, Ansari Nagar, Ansari Nagar East

department: Pathology

country: India

institute: AIIMS

summary: First comprehensive analysis highlighting distinct molecular subgroups of PXA. The DEGs between two clusters may potentially be used for developing histology independent classification scheme, prognostication and suggest prospective   therapeutic targets

overall_design: Genome-wide expression profiling of 14 PXA and 6 APXAs was performed by microarray. Amongst differentially expressed genes ( DEGs), Cyclin Dependent Kinase 14 (CDK 14)  and Mitochondrial Fission Process 1  (MTFP 1) were validated by qRT-PCR.

first: Jyotsna

last: Singh

first: Prerana

last: Jha

first: Iman

last: Dandpath

first: Nidhi

last: Shukla

first: Rahul

last: Gupta

first: Amit

last: Katiyar

first: Vikas

last: Sharma

first: Swati

last: Mahajan

first: Sujata

last: Chaturvedi

first: Arvind

last: Ahuja

first: Meenakshi

last: Bhardwaj

first: Ravindra

last: Saran

first: Ajay

last: Garg

first: Mehar

first: Niveditha

last: Manjunath

first: Ashish

first: Ritu

last: Kulshreshtha

first: Chitra

last: sarkar


title: The distinct effects of MEK and GSK3 inhibition upon the DNA methylome and transcriptome of mouse embryonic stem cells

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Mouse embryonic stem cells (mESCs) were first cultured in vitro in serum-containing medium with leukaemia inhibitory factor, in which they exhibit heterogeneous expression of both pluripotency and some early differentiation markers. Over the last decade, however, it has become commonplace to grow mESCs with inhibitors of MEK and GSK3 signalling, which together elicit a more homogeneously ‘naive’ state of pluripotency. Whilst 2i/L-cultured mESCs have been shown to be globally hypomethylated, a comprehensive understanding of the distinct effects of these signalling inhibitors upon the DNA methylome is still lacking. Here we carried out whole genome bisulphite and RNA sequencing of mESCs grown with MEK or GSK3 inhibition alone, including different time points and concentrations of MEK inhibitor treatment. This demonstrated that MEK inhibition causes a dose-dependent impairment of maintenance methylation via loss of UHRF1 protein, as well as rapid impairment of de novo methylation. In contrast, GSK3 inhibition triggers impairment of de novo methylation alone, and consequent hypomethylation is enriched at enhancers with a 2i/L-specific chromatin signature and coincides with upregulation of nearby genes. Our study provides detailed insights into the epigenetic and transcriptional impacts of inhibiting MEK or GSK3 signalling in mouse pluripotent cells.

overall_design: Biological duplicate whole genome bisulphite sequencing of mouse embryonic stem cells cultured under different conditions, and RNA sequencing of biological triplicate samples from the same experiments.

first: Julia

last: Spindel

first: Christel

first: Wolf

last: Reik


title: A comparison of the transcriptional profiles of DP CD24highCD44lowNK1.1-CD1d-tet+TCRa+ cells (i.e. very immature NKT cells) with those of more mature NKT cell subsets

city: Townsville

first: Margaret

middle: Agnes

last: Jordan

state: QLD

address: The Science Place, James Cook Dr

department: Molecular & Cell Biology

country: Australia

institute: James Cook University

summary:
Type 1 NKT cells play a critical role in controlling the strength and character of adaptive and innate immune responses. Their functional characteristics are distinct from conventional T cells, and are induced by a transcriptional program initiated by positive selection on CD4+CD8+ (double positive, DP) thymocytes. Here we examined transcriptional events in four immature thymic NKT cell subsets in a novel Vα14 TCR transgenic strain bearing greatly expanded numbers of CD24+CD44- NKT cells.
We used a  transcriptional regulatory network approach to map TCR validation to the transition from DP T to DP NKT cells, and positive selection and lineage commitment to the transition from DP NKT to CD4 NKT

overall_design: Thymocytes from NOD.Va14tg mice, a strain with greatly increased numbers of NKT cells with the characteristics of pre-selection and Stage 0 NKT cells, were subjected to FACS sorting to isolate four subsets: DPhighCD24highNK1.1-CD1d-tet-TCRa+ cells (immature DP conventional T cells), DP CD24highCD44lowNK1.1-CD1d-tet+TCRa+ cells (DP NKT cells), CD4+CD8-CD24high NK1.1-CD1d-tet+TCRa+ cells (CD4 NKT cells) and CD4-CD8-CD24 highNK1.1-CD1d-tet+TCRa+ cells (DN NKT cells). RNA was isolated and Affymetrix Mouse Gene_1.0ST arrays utilised to compare gene expression levels of the sorted T and NKT cell subsets (7 samples/group) in order to allow us to dissect the transcriptional programs involved in NKT cell positive selection and lineage commitment.


title: Real-time quantitative PCR analysis of human serum

city: Madrid

first: ELISA

last: CONDE MORENO

address: Carretera de Colmenar KM9.100

country: Spain

institute: Instituto Ramón y Cajal de Investigación Sanitaria, IRYCIS

summary: open-label single-arm pilot phase II clinical trial of Regorafenib as a single agent in Frail Patients With Metastatic Colorectal Cancer. Blood samples for determination of serum miRNAs were taken on entry into the study and at the time of disease progression.

overall_design: qPCR miRNA expression profiling. 200 ul of Serum samples from six patients per group (Favorable/Non favorable) were used for quantitative PCR Array screening of 752 miRNAs using the miRCURY LNA miRNA miRNome PCR Panels I+II (YAHS-312 YG-8, Qiagen)

first: Elisa

middle: C

last: Moreno

first: Laura

last: Bermejo


title: Single-cell RNA sequencing of mouse and human cochlea

city: San Francisco

first: Aaron

last: Tward

address: 505 Parnassus AVE

institute: UCSF

summary: Developmental time course data of isolated mouse and human cochleas

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA sequencing of E12.5, E14.5, E16.5, E18.5, P2, Adult mouse cochleas and week 15, 17 and 23 embryonic human fetal cochlea.

middle: D

first: Kevin

middle: S

last: Yu

first: Stacey

last: Frumm


title: Analysis of transcriptional changes associated to proteasome inhibition in HCT-116 human colorectal cancer cells

city: Mexico City

first: Luis

middle: Alonso

last: Herrera Montalvo

state: Mexico City

address: Periferico Sur 4809, Arenal Tepepan, Tlalpan

department: Unidad de Investigacion Biomedica en Cancer

country: Mexico

institute: Instituto Nacional de Cancerología / Instituto Nacional de Medicina Genómica

summary: The proteasome is a central player in several cellular aspects, such as homeostasis, cell cycle progression, and even transcription. Recent work has shown that proteasome inhibition promotes pervasive epigenetic changes in the human genome. However, the impact of proteasome inhibitors on ncRNAs is poorly understood. We treated control (asynchronous) or G2-synchronized HCT-116 human colon cancer cells with the proteasome inhibitors MG132 and bortezomib and performed total RNA-seq. We also included cells treated simultaneously with MG132 and the RNA-pol II inhibitor α-amanitin to determine the transcriptional changes mediated by such RNA polymerase. We report that MG132 and bortezomib impact similar regions of the genome. A remarkable transcriptional activation was observed in centromeres and pericentromers, especially in α-satellite repeats. RNAs emanating from these regions are known to participate in chromosome segregation. Our results suggest that the proteasome can regulate mitotic progression, not only by participating in protein turnover, but also by regulating ncRNAs.

overall_design: Total RNA-seq in 20 HCT-116 human cell line samples: Untreated (control), G2-synchronized, G2-synchronized + MG132 treated, G2-synchronized + MG132 and α-amanitin treated, and G2-synchronized + bortezomib treated (4 replicates each; rRNA-depleted)

first: Rodrigo

middle: E

last: Cáceres Gutiérrez

first: Marco

last: Andonegui

first: Diego

last: Oliva

last: González-Barrios

first: Fernando

last: Luna

first: Nicolas

last: Alcaraz

first: Erick

middle: I

last: Navarro

first: Cristian

last: Arriaga-Canon

first: Bao

last: Tran

first: Jyoti

last: Shetty

first: Yongmei

last: Zhao

last: Herrera


title: Streptococcus pneumoniae strain D39V were grown in six different conditions, mimicking the host niches

city: Groningen

first: Rieza

last: Aprianto

state: Groningen

address: Nijenborg 7

department: Molecular Genetics Department

institute: University of Groningen

first: Jan-Willem

middle: W

last: Veening

first: Michel

middle: M

last: Peren

first: Christian

last: Kemmer


title: Transcriptomic analysis of wild-type and amos mutant D. melanogaster third-instar larval antennal discs and adult antennae

status: Public on Dec 13 2021

city: Lausanne

first: Karolina

last: Bojkowska

address: Unil, Genopode

country: Switzerland

institute: University of Lausanne

summary: Comparative transcriptomic analysis of Drosophila melanogaster third-instar larval antennal discs and adult antennae from wild-type animals and amos mutant animals.

overall_design: Triplicate samples of developing olfactory tissue (third-instar larval antennal discs) and mature olfactory tissue (adult antennae) were collected from control wild-type animals and amos mutants, which lack the Or olfactory subsystem.

first: Jan

last: Armida

first: Richard

last: Benton


title: Silenced LINC01963 enhanced the chemosensitivity of prostate cancer cells to docetaxel by sponging miR-216b-5p to inhibit TrkB protein level

city: Hainan

first: Zengshu

last: Xing

address: No.43, Renmin Road, Meilan District, Haikou 570208, Hainan Prov., P.R. China.

institute: Affiliated Haikou Hospital of Xiangya Medical College, Central South University

summary: Long noncoding RNAs (lncRNAs) affect docetaxel chemosensitivity. However, the biological role and regulatory mechanisms of lncRNAs in docetaxel-resistant prostate cancer remain unclear. Differences in lncRNAs were evaluated by lncRNA sequencing and evaluated using quantitative real-time polymerase chain reaction, and TrkB expression was measured through Western blot analysis. Proliferation was measured using the MTS, while apoptosis and cell cycle were measured using flow cytometry. Additionally, migration and invasion were measured using transwell assays. Forty-eight female BALB/c nude mice were used for subcutaneous tumorigenicity and lung metastasis assays. We found that LINC01963 was overexpressed in the PC3-DR cells. LINC01963 silencing enhanced the chemosensitivity of PC3-DR to docetaxel and inhibited tumorigenicity and lung metastasis, while LINC01963 overexpression enhanced the chemoresistance of PC3 cells to docetaxel. It was found that LINC01963 sponges miR-216b-5p. The miR-216b-5p inhibitor reversed the suppressive effect of sh-LINC01963 on PC3-DR cell proliferation, migration, and invasion. Furthermore, miR-216b-5p can bind to the 3’-UTR of NTRK2 and inhibit TrkB protein levels. TrkB enhances docetaxel resistance in prostate cancer and reverses the effects of LINC01963 silencing and miR-216b-5p overexpression. In conclusion, silencing LINC01963 enhanced the chemosensitivity of PC3-DR to docetaxel by sponging miR-216b-5p to inhibit TrkB protein levels.

overall_design: Examination of 2 different PC3 cells, of which was PC3 and docetaxel-resistance PC3.

first: Gang

last: Yu

first: Guoren

last: Wang


title: Developmental arrest in response to reduced protein synthesis in C. elegans

city: Los Angeles

first: Sean

last: Curran

address: 3715 McClintock Ave

department: Davis School of Gerontology

institute: University of Southern California

summary: Reducing overall biosynthetic capacity is one avenue for increasing health and lifespan; however, animals must be post-developmental in order to reap these benefits. When protein synthesis is reduced in newly hatched C. elegans, worms enter a temporary arrest state that promotes stress resistance and increases lipid stores. In order to determine the genetic underpinnings to this developmental arrest, we used RNA-seq to determine the transcriptional profile of animals arrested for 48hrs and 120hrs as L2 animals (via egl-45/EIF3A and rps-11/RPS11 RNAi) versus 24hr Control RNAi non-arrested animals. The gene expression differences provide insights into the arrested state and allow for comparison to gene expression changes in adult animals in order to determine if they are activating similar pathways. Better understanding these gene expression changes will allow future research into activating the positive benefits of these pathways independently from any negative consequences of reducing biosynthetic capacity.

overall_design: Transcriptional profiles of animals arrested for 48hrs and 120hrs as L2 animals (via egl-45/EIF3A and rps-11/RPS11 RNAi) versus 24hr Control RNAi non-arrested animals.

first: Hans

last: Dalton


title: Gene expression in HTR-8/SVneo cells exposed to hypoxia or treated with sodium L-lactate

city: Bengbu

first: Xiang

last: Li

state: Anhui

address: First Affiliated Hospital of Bengbu Medical College, 287 Changhuai Road, Bengbu, China.

summary: Chronical hypoxia is a common occurrence following reduced uteroplacental blood flow resulting from incomplete trophoblast invasion and abnormal vascular remodeling of the spiral arteries in PE. Hypoxia can lead to active glycolysis, which increases the production of lactate, a substrate for histone lactylation. To screen for genes that may be regulated by histone lactylation in PE placentas, we performed RNA-seq in HTR-8/SVneo cells under hypoxia or treated with sodium L-lactate. The results showed that 3578 genes were upregulated in the HTR-8/SVneo cells under hypoxia compared to those under normoxia, and 355 genes were upregulated in HTR-8/SVneo cells treated with sodium L-lactate compared to the control cells. 152 upregulated genes in the HTR-8/SVneo cells under hypoxia and those treated with sodium L-lactate overlapping.

overall_design: The HTR-8/SVneo cells were incubated in 1% O2 (n=3) or treated with 25 mM sodium L-lactate (n=3) for 24 h. HTR-8/SVneo cells were incubated in 21% O2 for the control group (n=3).

first: Nana

last: Yang

first: Biao

last: Ding


title: Differential effect of SARS-CoV-2 spike glycoprotein 1 on human bronchial and alveolar lung mucosa models: Implications on pathogenicity.

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: The SARS-CoV-2 spike protein mediates attachment of the virus to host cell receptor and fusion between the virus and cell membrane. The S1 subunit of the spike glycoprotein (S1 protein) contains the angiotensin converting enzyme 2 (ACE2) receptor binding domain. The SARS-CoV-2 variants of concern contain mutations in the S1 subunit. The spike protein is the primary target of neutralizing antibodies generated following infection and constitutes the viral component of mRNA based COVID-19 vaccines. Therefore, in this work we assessed the effect of exposure (24 hours) of 10 nM SARS-CoV-2 recombinant S1 protein on physiologically relevant human bronchial (bro) and alveolar (alv) lung mucosa models cultured at air-liquid interface (ALI) (n=6/experimental group). Corresponding sham exposed samples served as control. The bro-ALI model was developed using primary bronchial epithelial cells and the alv-ALI model using representative type II pneumocytes. Exposure of S1 protein induced the surface expression of ACE2, toll like receptor (TLR) 2, and TLR4 in both bro-ALI and alv-ALI models. Transcript expression analysis identified 117 (bro-ALI) and 97 (alv-ALI) differentially regulated genes (p< 0.01). Pathway analysis revealed enriched terms as specific as COVID-19, interferon (IFN) signaling, influenza, Corona virus, anti-viral response in the bro-ALI. Secreted levels of Interleukin (IL) 4 and IL12 were significantly (p<0.05; non-parametric) increased whereas IL6 decreased in the bro-ALI. In case of alv-ALI, enriched terms involving p53, APRIL, tight junction, integrin kinase, IL1 signaling were identified. These terms are associated with lung fibrosis. Further, significantly (p<0.05; non-parametric) increased levels of secreted pro-inflammatory cytokines IFNγ, IL1ꞵ, IL2, IL4, IL6, IL8, IL10, IL12, IL13, and tumor necrosis factor alpha were detected in alv-ALI. Altered levels of these cytokines are also associated with lung fibrotic response. Taken together, we observed a typical anti-viral response in the bronchial model whereas a pro-fibrotic response in the alveolar model. Therefore the bro-ALI and alv-ALI models may serve as an easy and robust platform for assessing the pathogenicity of variants of concern at different lung regions.

overall_design: Human bronchial and alveolar lung mucosa models cultured at air-liquid interface were treated with SARS-CoV-2 recombinant S1 protein or controls

first: Mizanur

last: Rahman

first: Martin

last: Irmler

first: Sandeep

last: Keshavan

first: Micol

last: Introna

first: Lena

last: Palmberg

first: Gunnar

last: Johanson

first: Koustav

last: Ganguly

first: Swapna

last: Upadhyay


title: Transcriptome profiling of gingival epithelial cells response to IRF1 silencing using RNA-seq

city: Louisville

first: Richard

last: Lamont

state: Kentucky

address: 501 S. Preston St

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

summary: Understanding the role of IRF1 on gingival epithelial cell (GEC) responses using RNA-seq

overall_design: In order to understand the role of IRF1 on GECs responses, telomerase immortalized gingival keratinocytes were  transfected with either siRNA against IRF1 transcript (siIRF1) or scramble siRNA (SCR). Furthermore, TIGKs were stimulated with HSV60, followed by RNA-seq. There were four groups: SCR NI, SCR HSV, siIRF1 NI and siIRF1 HSV. Within each group there were 4-5 separate replicates. Total RNA was purified from the TIGKs and differential expression analysis was performed to compare and profile the transcriptome.

first: Carlos

middle: J

last: Rodriguez

first: Kevin

last: Sokoloski

first: Kendall

last: Stoke

first: Himabindu

last: Dukka

first: Shunying

last: Jin

first: Melissa

last: Metzler

first: Konstantin

last: Zaitsev

first: Boris

last: Shpak

first: Daonan

last: Shen

first: Daniel

last: Miller

first: Maxim

middle: N

last: Artymov

first: Juhi

last: Bagaitkar


title: Variant noncoding region regulates Prrx1 and predisposes to atrial arrhythmias

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

institute: Amsterdam UMC

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

overall_design: Refer to individual Series


title: Variant noncoding region regulates Prrx1 and predisposes to atrial arrhythmias [RNA-seq]

summary: Right and left atrial cardiomyocyte RNA-seq of Prrx1(R1A)-/- and control adult mice (n=3)

overall_design: PCM1 RNA-seq of Prrx1(R1A)-/- RA and LA

first: Fernanda

last: Bosada

first: Karel

last: van Duijvenboden


title: Mouse primary hippocampal neural progenitor cell scRNA-seq from wild type and a Kmt2d-haploinsufficient model of Kabuki syndrome

city: Baltimore

first: Loyal

middle: A

last: Goff

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

summary: 10x v3 single cell RNA-Seq of cultured primary hippocampal neural stem/progenitor cells (NPCs) (isolated by microdissection from E17 day embryos) from wild type or Kmt2d+/B-Geo mice (a haploinsufficiency model of Kabuki Syndrome). Cells are either undifferentiated (day0) or differentiated via growth factor withdrawl for 2, 4, or 8 days.

overall_design: n=1 sample for each of two genotypes (C57Bl/6J wildtype or Kmt2d+/βgeo) at four different timepoints of in vitro differentiation. Day0 is a control 'undifferentiated' state for both genotypes.

first: Giovanni

last: Carosso

first: Gloria

last: Shin

first: Shijie

last: Zheng

first: Genevieve

last: Stein-O'Brien

first: Jonathan

last: Augustin

first: Jared

last: Slosberg

first: Briana

last: Winer

first: Hans

middle: T

last: Bjornsson

first: Kasper

last: Hansen


title: DNA methylome analysis of esophageal squamous cell carcinoma

city: Lyon

first: Fazlur

middle: Rahman

last: Talukdar

state: Rhone Alps

address: 150 Cours Albert Thomas

department: Epigenetics

institute: International Agency for Research on Cancer

summary: Genome wide DNA methylation profiling of esophageal squamous cell carcinoma (ESCC) tumor and adjacent normal samples using the Illumina Infinium MethylationEPIC array to obtain DNA methylation profiles across approximately 850,000 CpGs. Data included pathologically confirmed 108 tumor and 51 normal samples

overall_design: Bisulphite converted DNA from the 159 samples were hybridized to the Illumina Infinium MethylationEPIC array

first: Zdenko

last: Herceg


title: Leukotriene B4 receptor 1 antagonist in combination with kinase MST1/2 inhibitor has potential for treatment of myocardial infarction

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

summary: Timely inhibition of inflammation and initiation of resolution are important for the repair of injured tissues. Pharmacological inhibition of mammalian STE20-like protein kinase 1/2 (MST1/2) with XMU-MP-1 might augment tissue regeneration and repair by suppressing apoptosis and increasing cell proliferation. However, MST1 has anti-inflammatory activity, inhibition of which may result in therapy failure. Here, we identified an approach with the potential to overcome this limitation by protecting against cardiac inflammation resulting from inhibition of MST1 in macrophages. We found exacerbation of cardiac dysfunction in LysMCre-mediated Mst1/2-deficient mice after myocardial infarction (MI). This effect was attributed to a shift of macrophage subtypes from those expressing Cxcl2 and Cd163 toward those with Ccl2 and Ccl4 expression. Mass spectrometry identified leukotriene B4 (LTB4) as the lipid mediator that was upregulated in the absence of MST1. We found that MST1 phosphorylated 5-lipoxygenase (5-LOX) at its T218 residue, disrupting the interaction between 5-LOX and 5-LOX-activating protein, and resulting in reduction of LTB4 production. By contrast, a 5-LOXT218A variant showed no response to MST1. Moreover, treatment of peritoneal macrophages with LTB4 or with medium conditioned by Mst1-deficient macrophages resulted in high Ccl2 and Ccl4 expression and low Cxcl2 and Cd163 expression, except when the cells were co-treated with the LTB4 receptor 1 (BLT1) antagonist CP105696. Furthermore, CP105696 ameliorated cardiac dysfunction in LysMCre-mediated Mst1/2-deficient mice and enhanced cardiac repair in wild-type mice treated with XMU-MP-1 after MI. The combination of an MST1/2 inhibitor and a BLT1 antagonist represents a promising strategy for combatting the effects of MI.

overall_design: Single cell RNA-Seq of mouse hearts

first: Ding

last: Ai

first: Fang

last: Yao


title: Variant noncoding region regulates Prrx1 and predisposes to atrial arrhythmias [ATAC-seq]

first: Vincent

last: Christoffels

summary: Atrial cardiomyocyte nucleus ATAC-seq of Prrx1(R1A)-/- and control adult mice (n=4)

overall_design: ATAC-seq of Prrx1(R1A)-/- atria

first: Fernanda

last: Bosada


title: Transcriptome analysis of CMT64 cells following TGF-β and/or TNF-α treatment.

city: Bunkyo-ku

first: NAOYA

last: MIYASHITA

state: Tokyo

department: Respiratory Medicine

country: Japan

institute: The University of Tokyo

summary: We have previously demonstrated that TNF-α, a proinflammatory cytokine, enhances TGF-β-mediated EMT in A549 human lung cancer cells. RNA-sequencing analysis on CMT64 cells following TGF-β and/or TNF-α treatment revealed a subset of genes possibly regulated by TGF-β and/or TNF-α.

overall_design: CMT64 cells were stimulated with 5 ng/ml of TGF-β and/or 10 ng/ml of TNF-α, and RNA-sequencing was performed ugsing Illumina HiSeq.

first: Naoya

last: Miyashita

first: Takayoshi

last: Enokido

first: Masafumi

last: Horie

first: Akira

last: Saito

first: Takahide

last: Nagase


title: Transcriptome analysis of CMT64 cells transduced with Ascl1

summary: Ascl1 is a master transcription factor for neuroendocrine differentiation. RNA-sequencing analysis on CMT64 cells transduced with Ascl1 revealed a subset of genes possibly regulated by Ascl1.

overall_design: CMT64 cells transduced with Ascl1, and RNA-sequencing was performed ugsing Illumina HiSeq.


title: RNA-seq analysis about Hira/Ubn1/Ubn2 knocked down samples

status: Public on Dec 12 2021

city: Tianjin

first: Xiao

last: Feng

address: No.38 Tongyan Road, Haihe Education Park, Jinnan District

department: State Key Laboratory of Medicinal Chemical Biology

institute: College of Pharmacy, Nankai University

summary: Histone chaperones are responsible for the deposition and removal of histones in chromatin and critical to prevent the abnormal activation of retrotransposable elements, which can be harmful to genome stability. One of the important histone chaperones is HIRA complex, which consists of Hira, Ubn1/Ubn2, and Cabin1 and mediates the installment of H3.3-H4 to nucleosome. We studied the function of members of HIRA complex in suppressing ERVs and found that histone H3.3 are enriched on all three classes of ERVs. Different HIRA members act distinctly in silencing ERVs. Ubn2 represses Class III ERVs including MERVL and Hira mainly silences Class I and Class II ERVs. Hira is enriched on Class I and II ERVs whereas its depletion affects the recruitment of H3.3. In contrast, Ubn2 is enriched on Class III ERVs, while its depletion influences H3.3 deposition and H3K9 methylation. This study extends our understandings of the mechanism by novel factors regulates ERVs.

overall_design: we knocked down Hira/Ubn1/Ubn2 in E14 by shRNA. We performed RNA-seq analysis in order to exam the transcriptome after Hira/Ubn1/Ubn2 knockdown.

first: Xinyi

last: Lu

first: Miao

last: Zhang

last: Hu


title: Transcriptome of Zebrafish Intestine under Fe'i and Cavendish Banana Diet

city: Bandung

first: Indra

last: Wibowo

state: West Java

address: Jl. Ganesha No. 10

department: School of Life Sciences and Technology

country: Indonesia

institute: Institut Teknologi Bandung

summary: Fe'i banana (Musa troglodytarum) fruit is carotenoid-rich and has been proposed to be utilized as a functional food. We report the first transcriptome of zebrafish (Danio rerio) intestine that were subjected to 8 weeks of Fe'i banana and Cavendish (Musa acuminata) diet. We found that Fe'i consumption in zebrafish modulated genes related to innate immunity.

overall_design: Adult healthy zebrafish were divided into 3 diet groups: commercial feed (CO), Cavendish (CV), and Fe'i banana (FE). Zebrafish in commercial feed diet group was used as control and fed Tetramin (Tetra, Germany). Ripe Cavendish and Fe'i fruit pulp were mixed with commercial feed into 50% banana-containing granule by lyophilization. Treatment lasted for 8 weeks. At day 56, total RNA of intestine from each diet group were sequenced. Transcriptome assembly were done using Tophat-Cufflink pipeline.

first: Nasya

last: Cheryl

first: Putri

last: Wardhiny

first: Fenny

last: Dwivany

first: Husna

last: Nugrahapraja


title: Novel non-integrating DNA Nano-S/MAR vectors restore gene function in patient-derived pancreatic tumour models II

city: Heidelberg

first: Matthias

last: Bozza

address: Im Neuenheimer Feld 242

institute: DKFZ Heidelberg

summary: Non-integrating minimally sized Nano-S/MAR DNA vectors can be used to genetically modify dividing cells in place of integrating vectors such as lentivirus and sleeping beauty. They represent a unique genetic tool, which avoids vector-mediated genetic damage cells and the activation of innate immune responses. Previous work has shown that DNA vectors comprising the mammalian scaffold/matrix attachment region (S/MAR) element can provide persistent mitotic stability over hundreds of cell divisions, resisting epigenetic silencing and thereby allowing sustained transgene expression. The composition of the original S/MAR vectors does present some inherent limitations which reduce their stability and can provoke cellular toxicity. Here, we present a new system, the Nano-S/MAR, which drives higher transgene expression and has improved efficiency of establishment, due to their minimal impact on cellular processes and perturbation of the endogenous transcriptome. We show that these features enable the hitherto challenging genetic modification of patient-derived cells by using Nano-S/MARs to stably restore the tumour suppressor gene SMAD4 to a patient-derived SMAD4 knockout pancreatic cancer line. Nano-S/MAR modification does not alter the molecular or phenotypic integrity of the patient-derived cells in cell culture and xenograft mouse models.   In conclusion, we show that this class of DNA vector can be used to persistently modify a wide range of cells, providing sustained high levels of transgene expression while avoiding the risks of insertional mutagenesis and other vector-mediated toxicity.

overall_design: Parental unmodified Capan-1 transcriptome is compared to Capan-1 cells genetically engineered with a S/MAR episomal vector harbouring in one case the expression of the reporter gene Luciferase and in the other the expression of Luciferase coupled with the tumour suppressor gene SMAD4

first: Richard

last: Harbottle


title: RNA sequencing of bone marrow macrophages from non-Hodgkin lymphoma Raji cell engrafted mice

city: Duarte

first: Xu

last: Cao

address: 1500 E Duarte Rd

institute: City of Hope Comprehensive Cancer Center

summary: Purpose: The study aimed to characterize the molecular phenotype of bone marrow macrophages in NHL with RNA sequencing analysis.   Methods:RNA of sorted femur macrophages (CD11b+F4/80+) were extracted with an RNA extraction kit (Qiagen). The samples were submitted to Novogene Inc. for library preparation and subsequent RNA sequencing. RNA was used for cDNA library construction using an NEBNext® Ultra RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer’s protocol. The resulting 250-350 bp insert libraries were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific) and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Qualified libraries were sequenced on an Illumina HiSeq 4000 Platform (Illumina) using a paired-end 150 run (2×150 bases). Reads containing adapter or poly-N and those of low quality were trimmed, after which gene counts were obtained though mapping the clean reads to reference genome mm10 using STAR 2.5.3a.

overall_design: RNA sequencing of bone marrow macrophages from Raji engrafted mice (Day 0, Day 4 and Day 18 after tumor engraftment through intravenous injection.)

first: Mingye


title: RNA-seq of human lens with cataracts, alopecia, & microdontia

city: Sewickley

first: Bharesh

middle: Kumar

last: Chauhan

state: PA

address: 400 45th St., Faculty Pavilion, Suite 5111

department: Ophthalmology

institute: University of Pittsburgh

summary:
The genetic daignosis of a pediatric patient with primary symptoms bilateral cataracts, alopecia and microdontia could not be obtained through standard genetic tests.
We sought to obtain the diagnosis of this rare syndrome through RNA-seq of the cataract lens against an age-matched donor lens.

overall_design: Lens transcriptome of pediatric patient was generated by RNA-seq technology using Illumina HiSeq 2500.

middle: K


title: Novel non-integrating DNA Nano-S/MAR vectors restore gene function in patient-derived pancreatic tumour models I


title: Astrogenesis in the murine dentate gyrus – a life-long and plastic process mediated by proliferation of neural stem cells and local astrocytes

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

summary: Astrocytes are highly abundant cells in the mammalian brain and their numerous functions are of vital importance for all aspects of development, adaption and aging of the central nervous system (CNS). Mounting evidence indicates the astrocytes’s cardinal contribution to a wide range of neuropathies, still, our understanding of astrocyte development significantly lags behind those of other CNS cells. Using the dentate gyrus (DG) as a model system, we here combine genetic fate-mapping, behavioral paradigms, single cell transcriptomics and in vivo two-photon imaging, to assess the generation and proliferation of astrocytes across the lifespan of a mouse in great detail. Astrogenesis in the DG is initiated by perinatal radial glia-like neural stem cells (rNSCs) giving rise to locally dividing astrocytes that enlarge the astrocyte compartment in an outside-in-pattern. This process occurs simultaneously to neurogenesis and likewise continues life-long. In the adult DG, rNSCs occasionally give rise to newborn astrocytes, but the vast majority of astrogenesis is mediated through proliferation of local astrocytes. Interestingly, locally dividing astrocytes revealed an unexpected plasticity and were able to adapt their proliferation to environmental and behavioural stimuli. Our study thus establishes astrocytes as enduring plastic elements in DG circuits, implicating a vital contribution of astrocyte dynamic to hippocampal plasticity.

overall_design: Single-cell RNA sequencing of the dentate gyrus of adult WT mice. Adult animals (8-week-old) held under standard conditions served as controls, and were compared to littermates that had access to a running wheel for 12 days as well as to 14-month-old hGFAPeGFP animals (non-running conditions).

first: Julia

last: Schneider

first: Marie-Theres

last: Wittmann

first: Julian

last: Karpf

first: Arif

middle: B

last: Ekici

first: André

last: Reis

first: Ruth

last: Beckervordersandforth


title: scRNA-seq profiling of vascular cells isolated from disease-free human breast based on the expression of CD36 and/or CD31

status: Public on Dec 11 2021

city: San Francisco

first: Thea

last: Tlsty

address: 513 Parnassus Avenue

institute: University of California, San Francisco

summary: To identify markers preferentially expressed by capillary ECs (highly expressing CD36) in the disease-free human breast and gain insights into their biology, we used single cell RNA sequencing (scRNA-seq). For this analysis, dissociated cells from disease-free tissues were barcoded using the MULTI-seq protocol and pooled prior to FACS-based isolation of CD36+ and/or CD31+ cells. The droplet-based 10x Genomics Chromium platform was used to encapsulate single cells and construct cDNA libraries. Populations of fibroblasts, perivascular, lymphatic and vascular endothelial ECs where identified in this analysis.

overall_design:
CD36 and/or CD31 expressing cells (labled with unique lipid-modified oligonucleotides barcodes) were isolated from Human breast tissue (14 donors) by FACS and subjected to scRNAseq using the 10X Genomics Single Cell V2 platform.
NOTE from submitter: the human tissues were collected under an approved protocol that has not been updated to consent the publication of raw sequencing data.

first: Joseph

last: Caruso


title: Reduced expression of mitochondrial complex I subunit Ndufs2 does not impact healthspan in mice

city: Chicago

first: Navdeep

last: Chandel

state: IL

address: 303 E Superior St, SQ5

department: Pulmonary and Critical Care

institute: Northwestern University

summary: Aging in mammals leads to reduction in genes encoding the 45-subunit mitochondrial electron transport chain (ETC) complex I.  It has been hypothesized that normal aging and age-related diseases such as Parkinson’s disease are in part due to modest decrease in expression of mitochondrial complex I subunits.  By contrast, diminishing expression of mitochondrial complex I genes in lower organisms increases lifespan. Furthermore, metformin, a putative complex I inhibitor increases healthspan in mice and humans.  In the present study, we investigated whether loss of one allele of Ndufs2, the catalytic subunit of mitochondrial complex I, impacts healthspan and lifespan in mice. Our results indicate that Ndufs2 hemizygous mice (Ndufs2+/-) show no overt impairment in motor function, learning, tissue histology, organismal metabolism, or sensitivity to metformin in a C57B6/J background. However, there are detectable changes at the level of gene expression in individual cell types and tissues due to loss of one allele of Ndufs2. Our data indicate that modest decline in expression of mitochondrial complex I subunit Ndufs2 is not detrimental to healthspan.

overall_design: RNA sequencing of mouse tissues (liver, kidney) and cell types (alveolar type II cells, alveolar macrophages, CD4 T cells, CD8 Tcells, Regulatory T cells) including analysis of young (<6 months) vs old (>18 months) male and female mice and comparison of tissues with and without treatment with metformin.

first: Gregory

last: McElroy


title: Nuclear ßArrestin1 Regulates Androgen Receptor Function in Castration Resistant Prostate Cancer

city: Gainesville

first: HAMSA

last: THAYELE PURAYIL

state: Florida

address: 2033 Mowry Road

department: ANATOMY AND CELL BIOLOGY

institute: UNIVERSITY OF FLORIDA

summary:
We report that ßArrestin1 depletion inhibits androgen receptor function in canstration resistant prostate cancer cells.
We used shcontrol and shßArr1 C4-2 cells for sequencing and analysed for androgen receptor regulated gene expression

overall_design: Two groups of cells 1) shcontrol cells and 2) shßArr1 cells

first: Hamsa

last: Thayele Purayil

first: Yehia

last: Daaka


title: Genome wide mRNA profiling of AGS, gastric cancer cell line upon treatment with 5µM of PD98059

city: Madurai

first: Kumaresan

last: Ganesan

state: Tamil Nadu

address: School of Biological Sciences,

department: Genetics

institute: Madurai Kamaraj University

summary: ERK/MAPK pathway is one of the highly activated and a crucial player in gastric cancer proliferation and progression. To delineate the complex transcription program associated with ERK/MAPK pathway, PD98059 a known ERK/MAPK inhibitor was treated in AGS, one of the ERK/MAPK signaling pathway over expressed gastric cancer cell line. The resultant changes in genome-wide mRNA expression pattern between control and PD98059 treated was profiled using Human Gene 1.0 ST arrays.

overall_design: Total RNA was isolated from AGS gastric cancer cell line treated with 5µM of PD98059 and DMSO as a control and profiled using Affymetrix Human Gene 1.0 ST Array (HuGene-1_0-st).

first: Jaishree

last: Pandian


title: Transcriptome profiling of gingival epithelial cells response to IFN stimulation using RNA-seq

first: Richard

last: Lamont

summary: Understanding the difference between Type I and Type III IFN stimulation on gingivalepithelial cell (GEC) responses using RNA-seq.

overall_design: In order to understand the difference between Type I and Type III IFN stimulation on GECs responses, telomerase immortalized gingival keratinocytes were stimulated with IFN-β or IFN-λ, followed by RNA-seq. There were three groups: untreated, IFN-β and IFN-λ. Within each group there were 3 separaate replicates. Total RNA was purified from the TIGKs and differential expression analysis was performed to compare and profile the transcriptome.

first: Carlos

last: Rodriguez

first: Kevin

last: Sokoloski

first: Kendall

last: Stoke

first: Himabindu

last: Dukka

first: Shunying

last: Jin

first: Melissa

last: Metzler

first: Konstantin

last: Zaitsev

first: Boris

last: Shpak

first: Daonan

last: Shen

first: Daniel

middle: P

last: Miller

first: Maxim

last: Artymov

first: Juhi

last: Bagaitkar


title: Homozygous iMycCα transgenic mice as a model of plasma B-cell lymphomas

city: Limoges

last: Ferrad

address: rue Pr. Descottes

department: UMR CNRS 7276, INSERM U1262, Equipe Labellisée LIGUE 2018, Université de Limoges

country: France

institute: Université de Limoges

summary:
in order to document molllecular signature of iMycCα B-cell lymphomas, RNA sequecing of CD138+ and CD138-B-cell lymphomas was performed and normalized expression data was obtained for all protein-coding genes
Methods: B220+IgM+IgD+CD138+ and B220+IgM+IgD+CD138- B-cell lymphomas were investigated in the iMycCα mice. Total RNA from lymphoma cells (purified with B220-coupled beads from Miltenyi Biotech) was extracted and analysed by microarray (Génome et Transcriptome, GenoToul, Toulouse, France; get.genotoul.fr). RNA-seq paired-end libraries were prepared according to the Illumina protocol with some adjustments, using the TruSeq Stranded Total RNA Gold library prep Kit (Illumina, San Diego, USA). Libraries were quantified by qPCR using the KAPA Library Quantification Kit (Roche, Basel, Switzerland). Libraries quality was assessed by the HS NGS kit on the Fragment Analyzer (Agilent Technologies, Santa Clara, USA). Libraries were equimolarly pooled and RNA sequencing was then performed on one S4 lane of the Illumina NovaSeq 6000 instrument (Illumina, San Diego, USA), using the NovaSeq 6000 S4 v1.5 Reagent Kit (300 cycles), and a paired-end 2 x 150 pb strategy
Results: Bioinformatic analysis defined CD138+ and CD138- B-cell lymphomas as two groups with a different transcriptome signature ( 2522 genes differentially expressed)  driving various arrays of the immune responses and expressing different signaling/metabolic pathways. Enrichment of previously established human Burkitt lymphoma (BL) and multiple myeloma signatures was tested in our CD138+ B-cell lymphomas. In contrast to BL, myeloma up and down signatures were significantly enriched, emphasizing the molecular similarity of mouse CD138+ B-cell lymphomas to human multiple myeloma cells  and the relevance of our mice as pertinent model of plasma B-cell lymphomas.
Conclusions: Our mouse model carrying a homozygous insertion of c-myc into the IgH locus develops B-cell lymphoma with a large part of CD138+ plasma cell neoplasms. Its interesting and large transcriptome similarities with human myelomas make this mouse model an accurate, reliable experimental myeloma model.

overall_design: mRNA of 9 B220+IgM+IgD+CD138+ and 3 B220+IgM+IgD+CD138-  B-cell lymphomas developed by iMycCα

first: Nour

last: Ghazzaui

first: Hussein

last: Issaoui

first: Emilie

last: Drouineau

first: Christelle

last: Oblet

first: Tiffany

last: Marchiol

first: Jeanne

last: Cook-Moreau

first: Yves

last: Denizot


title: Dose-Dependent Stage-Specific Effects of a small moleculeon Follicular Maturation IVF

city: Jinan

first: Lianbao

last: Cao

state: shandong province

address: Wenhuaxi road

department: Medical department

country: China

institute: Shandong Univerisity

summary: Dual roles of a small molecule on fertility

overall_design: We report the application of a small molecular in IVM and IVF in mammalian oocyte and embryo. By single cell RNA-seq

first: Gang

last: Lu


title: Transcriptome profiling of THP-1 cells treated with chemicals

city: Seoul

first: Hailian

last: Quan

address: 103 Daehak-ro, Jongno-gu,

department: Department of Microbiology and Immunology, and Institute of Endemic Disease

institute: Seoul, South Korea

summary: We profiled the transcriptome of Dexamethasone-, Tofacitinib-, Tacrolimus-, Prednisolone-, sodium lauryl sulfate (SLS)-, Aciclovir-, Benzoic acid-, Genistein-, Ribavirin-, Mercuric chloride-, Cyclosporine- and LPS-treated monocytes and without chemical-treated (basal, vehicle) monocytes. A Bioconductor software package in R called edgeR was used to conduct the differential expression analysis. Lowly expressed genes were filtered out by keeping only genes with worthwhile counts in a minimum number of samples. The default normalization method in edgeR, trimmed mean of M-values (TMM) normalization was performed, and dispersion estimates (common and tagwise dispersions) were obtained to proceed with differential expression determination. Differentially expressed genes were determined by conducting pairwise comparisons between each type of immunosuppressor or non-immunosuppressor and vehicle or control by applying fold-change and p-value cutoffs (|fold-change| > 1.5 and p-value < 0.05). Each immunosuppressor, excluding sodium lauryl sulfate, was compared with the vehicle group. Immunosuppressor sodium lauryl sulfate and non-immunosuppressor lipopolysaccharide were compared with the basal group. Non-immunosuppressors genistein and ribavirin were compared with the vehicle group.

overall_design: Total RNA profiles of THP-1 cells were used for the differential expression analysis, hierarchical clustering, and gene ontology analysis using the Bioconductor software package in R (edgeR), MeV software, and DAVID bioinformatics resources 6.8.

first: Seung

middle: H

last: Seok

first: Yi

middle: R


title: DNA methylation characterization in mesenchymal stromal cells (MSCs) of MDS (myelodysplastic syndromes), AML (acute myeloid leukemia) and healthy donors (HD)

city: Tours

first: Benjamin

last: Roux

address: 2 boulevard Tonnelle

institute: CHRU Tours

summary: Genome wide DNA methylation profiling of normal and pathologic mesenchymal stromal cells (MSCs). The Illumina Infinium 850k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs total DNA from in vitro-amplified MSCs. Samples included 11 normal MSCs, 11 MSCs from MDS patients, and 10 MSCs from AML patients.

overall_design: Bisulphite converted DNA from the 32 samples were hybridised to the Illumina Infinium MethylationEPIC (850K) Beadchip

first: Frédéric

last: Picou

first: Christine

last: Vignon

last: Debeissat

first: Nathalie

last: Gallay

first: Myriam

last: Koubi

first: Pierre

last: Hirsch

first: Elfi

last: Ducrocq

first: Amélie

last: Foucault

first: Noémie

last: Ravalet

first: Marie-Christine

last: Bene

last: Mazurier

first: Florence

last: Rouleux-Bonnin

first: Fabrice

last: Gouilleux

first: Michel

last: Maigre

first: Mathilde

last: Hunault

first: Jean

last: Mosser

first: Amandine

last: Etcheverry

first: Louis-Romée

last: Le Nail

first: Emmanuel

last: Gyan

first: Jorge

last: Domenech

first: Olivier

last: Herault


title: C/D box snoRNA SNORD113-6 guides 2´-O-methylation and directs fragmentation of tRNALeu(TAA) in human arterial fibroblasts

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

institute: Leiden University Medical Center

summary: C/D box small nucleolar RNAs (snoRNAs) transcribed from the DLK1-DIO3 locus are associated with vascular remodelling and cardiovascular disease. None of these snoRNAs has any known targets yet, except for one, AF357425 in mice and SNORD113-6 in humans. We previously showed that this snoRNA targets mRNAs of the integrin signalling pathway and affects arterial fibroblast function. Here, we aimed to identify whether AF357425/SNORD113-6 can also target small RNAs. We overexpressed or inhibited AF357425 in murine fibroblasts and performed small RNA sequencing. Expression of tRNA fragments (tRFs) was predominantly regulated. Compared to overexpression, AF357425 knockdown led to an overall decrease in tRFs, but with an enrichment in smaller tRFs (<30 nucleotides). We focused on tRNA Leucine anti-codon TAA (tRNALeu(TAA)), that has a conserved predicted binding site for AF357425/SNORD113-6. Adjacent to this site, the tRNA is cleaved to form tRFLeu 47-64, in both primary murine fibroblasts and human arterial fibroblasts. We show that AF357425/SNORD113-6 methylates tRNALeu(TAA) and thereby prevents the formation of tRFLeu 47-64. Exposing fibroblasts to oxidative or hypoxic stress, increased AF357425/SNORD113-6 and tRNALeu(TAA) expression, but AF357425/SNORD113-6 knockdown did not lead to an additional formation of tRFLeu 47-64. Thus, independent of cellular stress, AF357425/SNORD113-6 directs site-specific fragmentation of tRNALeu(TAA) via 2’O-ribose-methylation.

overall_design: Small RNA-seq on whole cell lysates of primary murine ear cells with AF357425 overexpression (AF357425-High) or inhibition (AF357425-Low)

first: Eva

last: van Ingen

first: Pleun

last: Engbers

first: M

middle: L

last: van der Bent

first: Johann

last: Wojta

first: Paul

last: Quax

first: A

middle: Y

last: Nossent


title: Diverse mammalian retinal ganglion cell types revealed by single cell transcriptome profiling

city: Guangzhou

first: Kangxin

last: Jin

state: Guangdong Province

address: 7 Jinsui Rd

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: By single-cell RNA-sequencing (scRNA-seq) analysis, we classify adult mouse RGCs into 28 types, which can be distinguished by distinct sets of characteristic genes or even by single gene markers.

overall_design: Single-cell RNA-seq of 3-month mouse RGCS (Retinal ganglion cells) that were enriched by FACS sorting of Brn3b::GFP reporter.

first: Mengqing

last: Xiang

first: Youjin

last: Hu

first: Wen

last: Wei

first: Rong

last: Zhang

first: Qiannan

last: Lei

first: Shuting

last: Liu

first: Xintong

last: Zheng

first: Yanan

last: Guo

first: Jiawei

last: Zhong

first: Pinhong

last: Rao

first: Lin

last: Cheng


title: Comprehensive analysis of RNA expression profiling in patients with multi- vs single-vessel coronary artery disease

city: Beijing

first: Mengliang

address: 8 Xishiku St, Xicheng District

department: Department of Geriatrics

institute: Peking University First Hospital

summary: Patients with multi-vessel coronary artery disease (MV-CAD) often exhibit poor clinical outcomes compared to single-vessel coronary artery disease (SV-CAD). Increasing evidence suggests that microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) may play a critical role in cardiovascular diseases, however their impact on various vessel lesions, is largely unknown. Here, six patients were selected for the SV-CAD group and 13 for the MV-CAD group by the number of diseased coronary branches. Total RNAs were extracted from peripheral blood of the patients, and the expression profiling was conducted by RNA sequencing (RNASeq). Differentially expressed mRNAs, miRNAs and lncRNAs were identified with p<0.05 and |log2 FC|>1. The GO and KEGG pathway enrichment analysis indicated that differentially expressed mRNAs were mainly enriched in Wnt, Ras and ErbB signaling pathways; miRNAs in mTOR and ErbB signaling pathways; lncRNAs in ErbB signaling pathway, fatty acid metabolism and platelet activation. In addition, we established the ceRNA network and revealed that lncRNA ENST00000501122 may competitively combine with miR-6724-5, regulating the expression of its target mRNAs. Lastly, the most significantly differentially expressed miRNAs, let-7b-5p, let-7e-5p and miR-190a-5p, were selected to evaluate their effects on lipid metabolism and inflammation in cell lines. Overall, our study provides a comprehensive analysis of the transcriptome between MV-CAD and SV-CAD, which will not only help us better understand the mechanisms of different CADs, but also provide a theoretical basis for the prevention and treatment of cardiovascular disease.

first: Meilin


title: TCR affinity defines tumor-specific CD8 T cell differentiation and dysfunction [RNA-seq]

city: New York

first: Andrea

last: Schietinger

state: NY

address: 1275 York Avenue

department: Immunology

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-seq analysis of tumor-specific CD8 T cells encountering tumor antigens with varying TCR/pMHC affinity.

overall_design: Transgenic antigen-specific CD8 T cells were adoptively transferred into tumor-bearing mice, isolated and flow-sorted from tumor draining lymph nodes and tumors at distinct time points post transfer for subsequent RNA-seq analysis. MCA 205 tumor cell lines were generated to express a defined tumor-specific model antigen, SV40 large T antigen epitope-I (TAG), as altered peptide ligands (APL), recognized by antigen-specific TCR SV40-I CD8 T cells with varying affinities (high-affinity N4, intermediate affinity F6, and low affinity D4 APL). TAG-specific effector CD8 T cells isolated during acute Listeria infection were used as controls.

first: Mojdeh

last: Shakiba

first: Doron

last: Betel

last: Zumbo

first: Friedericke

last: Dündar


title: Transcriptome analysis of human placental samples

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

overall_design: Human Plancental villi from normal and miscarriage sample (below 8 weeks) was isolated. Whole placental villi were used to prepare RNA using Qiagen RNeasy Mini Kit with on column DNase digestion. RNA-seq analysis were performed using a illumina HiSeq2000 platform.

first: Paul

last: Soumen

first: Ganguly

last: Avishek

first: Bhattacharya

last: Bhaswati

first: Home

last: Pratik

first: Gunewardena

last: Sumedha


title: TCR affinity defines tumor-specific CD8 T cell differentiation and dysfunction [ATAC-seq]

summary: ATACseq analysis of tumor-infiltrating CD8 T cells encountering high (F6) or low (D4) affinity tumor antigen.

overall_design: Transgenic antigen-specific CD8 T cells were adoptively transferred into tumor-bearing mice, isolated and flow-sorted from tumors 14 days post-transfer for subsequent ATAC-seq analysis. MCA 205 tumor cell lines were generated to express a defined tumor-specific model antigen, SV40 large T antigen epitope-I (TAG), as altered peptide ligands (APL), recognized by antigen-specific TCR SV40-I CD8 T cells with varying affinities (high/intermediate affinity F6, and low affinity D4). Naive antigen-specific TCR SV40-I CD8 T cells were used as controls.

first: Friederike


title: Global gene expression profile of TE7 cells (control cells and cells overexpressing human CDH26)

city: Cincinnati

first: Marc

middle: E

last: Rothenberg

state: OH

address: 3333 Burnet Ave. MLC-7028

department: Allergy

institute: Cincinnati Children's Hospital Medical Center

summary: Currently, no studies exist that identify the function of human CDH26 protein. We aimed to understand the impact of high levels of CDH26 expression on esophageal epithelial gene expression.

overall_design: RNA was isolated from TE7 cell clones transduced with a control construct (pMIRNA1-puro-control) (n=2) or with a CDH26 expression construct (pMIRNA1-puro-CDH26) (n=3) followed by hybridization on Affymetrix microarrays.

first: Julie

last: Caldwell

first: Margaret

last: Collins

first: Katherine

last: Kemme

first: Joseph

middle: D

last: Sherrill

first: Ting

last: Wen

first: Mark

last: Rochman

first: Emily

last: Stucke

first: Lissa

last: Amin

first: Haitong

last: Tai

first: Philip

last: Putnam

first: Maximiliano

last: Dalmaroni

last: Wormald

first: Aleksey

last: Porollo

first: J

last: Abonia


title: M-CSF-responsive immortal macrophages are a new model for studying macrophage function

city: Brookings

first: Natalie

middle: W

last: Thiex

state: SD

address: 1390 College Ave

department: Biology & Microbiology

institute: South Dakota State University

summary: We generated non-senescent, macrophage colony stimulating factor (M-CSF) dependent macrophages from murine fetal livers. These fetal liver macrophages (FLM-M) resemble bone marrow macrophage (BMM) morphology and express similar macrophage surface markers as BMM. In comparison to granulocyte monocyte-colony stimulating factor (GM-CSF) derived FLM (FLM-G), FLM-M have higher surface expression of CD11b, CD68, CD14 and CD64, and lower expression of CD11c. BMM, FLM-M and FLM-G all produce TNFα and IL-6 in response to lipopolysaccharide activation. BMM and FLM-M cells have similar phagocytic properties with 99.3% of BMM and FLM-M actively phagocytosing opsonized sheep erythrocytes and a phagocytic efficiency of 0.9. The average number of internalized erythrocytes per cell was higher (13.1±10.0) in BMM than in FLM-M (7.6±2.9). FLM-G had fewer actively phagocytic cells (86%), lower phagocytic efficiency (0.7) and fewer internalized erythrocytes per macrophage (4.2±2.1) than BMM or FLM-M. Principal component analysis and hierarchical clustering demonstrated mRNA expression profiles were more similar between BMM and FLM-M cells than FLM-G. Transcriptome comparison to the ImmGen tissue atlas shows cultured BMM and FLM-M cluster with macrophage progenitors and bone marrow macrophages. In conclusion, FLM-M cell cultures share major morphological, phenotypic and functional properties of BMM except for senescence, and can be an effective substitute to BMM. These new cells will facilitate study of macrophage biology by enabling experiments requiring long-term culture or genetic modifications.

overall_design: Comparison of 3 different murine macrophage cell cultures.

first: Padmapriya

last: Swaminathan

first: Jason

last: Kerkvliet

first: Maxim

middle: I

last: Lebedev

first: H

middle: C

last: Eisenbeisz

first: Lisa

middle: M

last: Martinez

first: Xijin

last: Ge

first: Anne

last: Fennell

first: Adam

last: Hoppe


title: circRNA microarray for 6 mouse intestinal tissue samples

status: Public on Dec 10 2021

city: Dalian

first: Xiaofeng

last: Tian

address: Zhongshan Road NO.467

department: General Surgery

institute: The Second Hospital of Dalian Medical University

summary: We analyzed the expression profiles of 9,821circRNAs on intestine tissues from mice suffering from sham and intestinal I/R using microarray analysis. And find that 4 circRNAs are up-regulated and 58 are down-regulated significantly.

overall_design: In the study, we analyzed the expression profiles of circRNAs in 3 randomly selected samples from intestinal I/R and sham group using microarray analysis.

first: Deshun

last: Liu

first: Xuzi

last: Zhao

first: Zhecheng

last: Wang

first: Guangzhi

first: Zhao

last: Chen

first: Shili

last: Ning

first: Xin

last: Sun

first: Ruimin

first: Yan

first: Li

last: Lv

first: Jihong

last: Yao


title: Evolutionarily conserved bacterial effectors hijack abscisic acid signaling to induce an aqueous microenvironment in the apoplast

city: Sherbrooke

first: Peter

last: Moffett

state: Québec

address: 2500 boulevard de l'universite, Departement de Biologie

department: Biologie

institute: Universite de Sherbrooke

summary:
Purpose: The goal of this study is to compare NGS-derived Arabidopsis thaliana transcriptome profiling  (RNA-Seq) obtained from tissues infected with a variety of Pseudomonas syryingae effector mutants to better understand their impact on their host's transcriptional program.
We report the application of RNA-sequencing technology (Illumina Hi-Seq) for high-throughput profiling Arabidopsis thaliana transcriptomes upon infection with the model pathogen Pseudomonas syringae (wild-type and mutants).

overall_design: Examination of Arabidopsis thaliana ecotype Col-0 infected with Pseudomonas syringae pv. tomato DC3000 (wild-type, hopm1-, avre1- and hopm1-/avre1-).

first: Charles

last: Roussin-Léveillée


title: ZFP541 is indispensable for pachytene progression by interacting with KCTD19 and activates meiotic gene expression in mouse spermatogenesis

city: beijing

first: shuntai

last: yu

state: beijing

address: 7 Science Park Road ZGC Life Science Park, Beijing

department: transgenic animal center

institute: NIBS

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

overall_design: Refer to individual Series


title: SRSF5 enhances the splicing of M gene by directly binding  to  M mRNA.

city: Bei jing

first: zhimin

last: jiang

address: No.2 Yuanmingyuan West Road, Haidian District, Beijing

department: college of Veterinary medicine

institute: China agriculture university

summary: Influenza A viruses (IAVs) mRNA splicing represents an essential step in the viral life cycle.  Here, we show that induction of SRSF5 by IAVs promotes viral replication by enhancing M mRNA splicing. To determine the motif in the M pre-mRNA targeted by SRSF5 RRM2 domain, the RNA eluted from co-precipitation of SRSF5–Flag from IAV-infected srsf5−/− HEK293 cells was subjected to deep sequencing analysis.

overall_design: The RNA eluted from co-precipitation of SRSF5–Flag from IAV-infected srsf5−/− HEK293 cells was subjected to deep sequencing analysis.

first: Qiuchen

last: Li

first: Zhimin

last: Jiang


title: GFP CUT&Tag from P18 wild type and Zfp541-EGFP mouse testes

summary: To evaluate the chromatin binding of ZFP541 in mouse testes.

overall_design: To evaluate the chromatin occupancies of ZFP541 in testes. Two P18 WT testicular cell samples, and two P18 Zfp541-EGFP testicular cell samples.

first: Yushan

first: Shanze

first: Jiawen

first: Fengchao


title: Transcriptome analysis in the Zfp541 Het and Zfp541 KO testes

summary: Due to the DNA binding affinity and interacting ability with HDACs, we wonder if ZFP541 can regulate gene expression during meiotic prophase.

overall_design:
1. Differential expression analysis in the P14 testes, P18 testes and P18 spermatocytes of Zfp541Het and Zfp541 KO male mice.
2. Three biological replicates were prepared for mRNA profiles.

first: Bowen

last: Gu


title: Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios [Omni2.5]

city: Houston

first: Yuya

last: Sasaki

state: TX

address: 1515 Holcombe Blvd

institute: M.D. Anderson Cancer Center

type:
Genome variation profiling by array
SNP genotyping by SNP array

summary: Recurring genetic abnormalities have been identified in Philadelphia chromosome (Ph)-positive acute lymphoblastic leukemia (ALL). Among them, IKZF1 deletion was associated with poor prognosis in patients treated with imatinib-based or dasatinib-based regimens. However, the molecular determinants for clinical outcomes in ponatinib-treated patients remain unknown. We systematically analyzed genetic alterations in adults with Ph-positive ALL uniformly treated in clinical trials with dasatinib-based regimens or a ponatinib-based regimen and investigated the molecular determinants for treatment outcomes using pretreatment specimens collected from adults with Ph-positive ALL treated with Hyper-CVAD plus dasatinib or ponatinib. DNA sequencing and SNP microarray were performed and recurrent genetic abnormalities were found in 84% of the patients, among whom IKZF1 deletion was most frequently detected (60%). IKZF1 deletion frequently co-occurred with other copy-number abnormalities (IKZF1plus, 46%) and was significantly associated with unfavorable overall survival (OS) (false discovery rate < 0.1) and increased cumulative incidence of relapse (p = 0.01). In a multivariate analysis, dasatinib therapy, lack of achievement of 3-month complete molecular response, and the presence of IKZF1plus status were significantly associated with poor OS. The differential impact of IKZF1plus was largely restricted to patients given Hyper-CVAD plus ponatinib; dasatinib-based regimens had unfavorable outcomes regardless of the molecular abnormalities.

overall_design:
We report the results of SNP arrays using either IIllumina Infinium Omni-2.5 or Illumina Infinium CytoSNP-850K v1.2 BeadChip     (Agilent Technologies, Santa Clara, CA, USA) for 99 samples obtained from patients with Philadelphia chromosome (Ph)-positive acute lymphoblastic leukemia (ALL).
We re-analyzed 99 individual hybridizations conducted on IIllumina Infinium Omni-2.5 and Illumina Infinium CytoSNP-850K v1.2 BeadChip.This series includes the 80 samples obtained from patients with Ph-positive ALL on Illumina Infinium Omni-2.5 Exome-8 Kit and 19  samples obtained from patients with Ph-positive ALL on Illumina Infinium CytoSNP-850K v1.2 BeadChip. Samples were either bone marrow aspirate or peripheral blood obtained from previously untreated patients.
Genomic DNA extracted from leukemic cell was genotyped using IIllumina Infinium Omni-2.5 Kit.

first: Koichi

last: Takahashi

first: Hidetaka

last: Uryu


title: TP53 signature predicts survival outcome in triple-negative breast cancer with neoadjuvant chemotherapy

city: Bunkyo-ku

first: Mai

last: Onishi

department: Clinical oncology

institute: Juntendo university Graduated schoo;

summary: In the study presented here, a consecutively operated, well-defined cohort of 30 triple-negative breast cancer cases with neoadjuvant chemotherapy, followed up more than five years, was used to acquire TP53 signature composed  of a total of 33  genes. Combining the response to NAC and the TP53signature score in triple-negative breast cancer was able to predict an unfavorable prognosis.

overall_design: In the study presented here, a consecutively operated, well-defined cohort of 30 triple-negative breast cancer cases with neoadjuvant chemotherapy, followed up more than five years, was used to acquire expression profiles of a total of 33  genes,

first: Shigeo

last: Yamaguchi


title: Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios [CytoSNP]

overall_design:
We re-analyzed 99 individual hybridizations conducted on Infinium Omni-2.5 Kit (IIllumina) and Infinium CytoSNP-850K v1.1 BeadChip (Illumina).This series includes the 80 samples obtained from patients with Ph-positive ALL on Illumina Infinium Omni-2.5 Exome-8 Kit and 19  samples obtained from patients with Ph-positive ALL on Illumina Infinium CytoSNP-850K v1.1 BeadChip. Samples were either bone marrow aspirate or peripheral blood obtained from previously untreated patients.
Genomic DNA extracted from leukemic cell was genotyped using Illumina Infinium CytoSNP-850K v1.1 BeadChip.


title: TAVR patients

city: Bonn

first: Mohammed Rabiul

last: Hosen

state: NRW

address: Venusberg-Campus 1

department: Internal Medicine-II

institute: University of Bonn

summary: HUMAN TAVR-patient with robust LVEF improvement and no LVEF improvement

overall_design: qPCR gene expression profiling. Circulating plasma-EV RNA . Equal amount total RNA from each donor was pooled prior to gene expression analysis.