title: Single cell RNA-seq of ileal biopsies from IBD patients

city: Southampton

first: James

middle: David

last: Davies

state: Hampshire

address: LE57, Lab and Pathology block, Tremona Road

department: Clinical and Experimental Sciences

institute: University of Southampton

summary: Crohn’s disease arises through host-environment interaction, with abnormal gene expression resulting from disturbed pathway activation or response to bacteria. Single cell RNA-sequencing of ileal tissue from 2 paediatric Crohn’s disease patients was performed, identifying populations of CD8+ effector memory T cells (CD8+ Tem), memory B-cells, monocytes, epithelial cells and plasma cells within the ileal tissue. Specialised epithelial cells driving differential expression of S100A8 and S100A9 and associated with defence to bacterium were identified, as well as IL17-signalling associated pathways in monocyte and epithelial cell populations.

overall_design: IBD patient ileal biopsies were collected and digested with liberase TM (90 minutes, +37C), within 30 minutes from biopsy. Single cell suspensions of whole ileal tissue was then processed through the Drop-seq in which cells were co-encapsulated with genetically barcoded beads. 1000 STAMPS (beads exposed to a single cell) for each biopsy were taken further for library preparation. Prepared libraries were run on an Illumina NextSeq (1 × 105 reads/cell). Read filtering, barcode and UMI counting were performed using bcl2fasq software from Illumina and alignment to the Hg_19 human reference genome was performed using STAR. Data analyses were run using the python-based Scanpy with R (3.6.0). Genes (detected <10 cells) and cells (20% or more counts contributed by mitochondrial genes) were filtered. Data was normalised using Scran. A single-cell neighbourhood graph, with data integrated from separate tissue samples, was computed using BBKNN. Data were visualised using Uniform Manifold Approximation and Projection (UMAP), with Leiden algorithm cell clustering. Cell type annotation was performed using SingleR (database: BlueprintEncodeData) and enrichment analysis (ToppGene and EnRICHR) using the top 50 cluster marker genes.

first: Andres

last: Vallejo-Pullido

first: Marta

middle: E

last: Polak

last: Ashton


title: Dorsal-ventral inversion in the air-filled organ (lungs, gas bladder) of vertebrates: RNA-sequencing of laser capture microdissected embryonic tissue

status: Public on May 12 2021

city: Ithaca

first: Emily

middle: C

last: Funk

state: NY

address: 215 Tower Rd

department: Ecology and Evolutionary Biology

country: USA

institute: Cornell University

type: Expression profiling by high throughput sequencing

summary: How modification of gene expression generates novel traits is key to understanding the evolutionary process.  Here we investigated the genetic basis for the origin of the piscine gas bladder from lungs of ancestral bony vertebrates.  Distinguishing these homologous organs is the direction of budding from the foregut during development; lungs bud ventrally and the gas bladder buds dorsally.   We investigated whether this morphological inversion is associated with the molecular inversion of conserved genes regulating lung and gas bladder development. Using laser-capture microdissection and RNA-seq, we assayed transcript abundance and compared expression patterns between dorsal and ventral foregut tissues at three developmental stages spanning gasbladder development.  Our focal taxon, bowfin (Amia calva), representing the sistergroup to teleosts, is an early diverging ray-finned fish with a gas bladder. We discovered a number of genes with unknown function during lung development that are differentially expressed during gas bladder development and annotated to functions relevant for organ budding. We also identified several known lung-regulatory genes that exhibit inverted dorsoventral expression during gasbladder development relative to lung development. In particular, we found Tbx5 is strongly expressed in the dorsal mesoderm surrounding the gas bladder during bowfin development, and several interacting genes are co-expressed dorsally with Tbx5. In contrast, in mouse and bichir (Polypterus senegalus), the only ray-finned fish that have lungs, Tbx5 is expressed in the ventral lung mesoderm during lung development. Our data demonstrating dorsoventral inversion of conserved genes suggest that these genes may have contributed to the evolutionary transition between ventral lungs and a dorsal gas bladder in ray-finned fishes.

overall_design: mRNA profiles of dorsal and ventral regions of the foregut and gas bladder at three stages of bowfin, Amia calva, development

first: Ezra

middle: S

last: Lencer

first: Amy

middle: R

last: McCune


title: Transcriptomic analysis of airway macrophages from preschool wheeze

city: London

first: Clare

middle: Margaret

last: Lloyd

address: Inflammation, Repair and Development, National Heart and Lung Institute, Sir Alexander Fleming Building

department: National Heart and Lung Institute

country: United Kingdom

institute: Imperial College London

summary: Preschool wheeze is an early life bronchoconstriction disorder with an increased risk of progression to chilhood asthma. Preschool wheeze is typically triggered by respiratory infection, but airway inflammatory phenotypes, including the phenotype of airway macrophages (AMs), in preschool wheeze is not fully understood. In this study, AMs were sorted from preschool wheeze patients and non-wheezing paediatric controls under clinical investigation for chronic cough and gene expression assessed by Illumina mRNA sequencing (110 base pair, paired end reads). A number of differentially expressed genes were observed in AMs from preschool wheeze compared to those from controls, including genes encoding pro-inflammatory chemokines and genes associated with a more immature and inflammatory AM phenotype. These findings suggest that AMs contribute to an altered airway immune landscape in preschool wheeze.

overall_design: CD206+ AMs were bead sorted from bronchoalveolar lavage of children under clinical investigation for preschool wheeze (N=3) or chronic cough without wheeze (N=5). RNA was extracted and converted to mRNA libraries before performing Illumina paired end sequencing. Reads were aligned to the Hg38 genome using COBWeb. Transcripts were quantified from aligned reads using DESeq. Low abundance transcripts were filtered (< 5 reads in < 3 of the samples) and differential expression analysis performed with DESeq2, using the Wald method with Benjamini-Hochberg false discovery rate correction.

last: Cook

first: William

middle: J

last: Branchett

first: Anne

last: O'Garra

first: Sejal

last: Saglani

middle: M


title: Enhancing single-cell cellular state inference by incorporating molecular network features

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

country: China

institute: Peking University

summary: Although small intestine epithelium has been studied widely in murine, a comprehensive expression landscape in human is still lacking. To explore the cellular diversity of human small intestine epithelium, we sampled the ileal crypts from two patients suffered from right-sided colon cancer while their ilea were relatively normal. scRNA-seq libraries were generated using the 10X v3 Kit, which could guarantee both throughput and quality

overall_design: Using 10X Genomics v3 Kit, we generated a human adult ileal scRNA-seq dataset, where identified several novel stem/progenitor clusters, including a Cripto-1+ cluster. Moreover, two distinct groups of goblet cells were identified and only one of them tended to secrete mucus. Besides, we found that the recently identified BEST4+OTOP2+ microfold cells also highly expressed CFTR, which is different from their colonic counterparts.

first: Peijie

last: Zhou

first: Yichong

last: Wu

first: Wendong

last: Wang

first: Yidong

last: Chen

first: Xin

first: Wei

last: Fu

first: Tiejun

last: Li

first: Fuchou

last: Tang


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and disinfectants stressed Acinetobacter baylyi ADP1 Transcriptomes

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

summary: The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of wild-type A.baylyi ADP1, and its mRNA response under the exposure of two disinfectants, chloramine and free chlorine. The concentrations 10 mg/L. The group without dosing disinfectants was the control group. Each concentration was conducted in triplicate. By comparing the mRNA profiles of experimental groups and control group, the effects of these two disinfectants on transcriptional levels can be revealed. Illumina HiSeq 2500 was applied. The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the A.baylyi ADP1 reference genome (NC_005966.1), using SeqAlto (version 0.5). Cufflinks (version 2.2.1) to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R. (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

overall_design: Bacterial mRNA profiles of wild-type A.baylyi ADP1, in response to 10 mg/L disinfectants, i.e., chloramine or free chlorine, for 2 hours, bacteria without dosing disinfectants are the control group, in triplicate, using Illumina HiSeq 2500

first: Shuai

last: Zhang

first: Yue

first: Likai

last: Mao


title: Comprehensive analysis of the complexity and heterogeneity of the lncRNAs transcriptome in multiple myeloma

city: Pamplona

first: Teresa

last: Ezponda

state: Navarra

address: Pio XII 55

department: Hematology/Oncology

country: Spain

institute: Center for Applied Medical Research

summary: RNA-seq analysis comparing the transcriptional landscape of LINC-SMILO silenced cells versus control cells in KMS-11 multiple myeloma cell line.

overall_design: KMS-11 multiple myeloma cell line was transduced in duplicate with pLKO.1-puro vector containing a scramble or a shRNA expressing lentiviral system targeting LINC-SMILO gene. Samples were harvested after 4 days of shRNA infection.

first: Felipe

last: Prosper

first: Xabier

last: Agirre

first: Arantxa

last: Carrasco-Leon


title: Temporal transcriptional response from primary human chronic lymphocytic leukemia (CLL)-cells after B-cell receptor stimulation.

city: Strasbourg

first: Laurent

last: Vallat

address: 1, avenue Molière

department: Hematology

country: France

institute: Strasbourg University Hospital

summary: The B-cell receptor (BCR) signaling is crucial for the pathophysiology of most leukemias and lymphomas  originated from mature B lymphocytes and has emerged as a new therapeutic target, especially for chronic lymphocytic leukemia (CLL). However, the precise mechanisms by which BCR signaling controls neoplastic B-cell proliferation are ill characterized.   This work was performed using primary leukemic cells of untreated patients at initial stage of CLL (Binet stage A / Rai 0) presenting biological characteristics of aggressive form of the disease (unmutated IGHV genes and ZAP70 protein expression). In order to mimic the primary leukemogenic step occurring in vivo, this study focused on the BCR-dependent proliferation of CLL cells induced ex vivo using anti-IgM, together with mandatory co-stimulating factors (CD40L, IL-4 and IL-21) (Schleiss, Sci Rep, 2019). Cell proliferation was objectivized by the emergence of proliferative clusters and the presence of more than 25% of CLL cells that did undergo division within the cell culture at day 6. To capture the specific actors of the proliferative response in these samples, we also included non-proliferating control CLL samples. Gene expression was analyzed by RNA-seq before stimulation (T0) and at the time points 1h, 1h30, 3h30, 6h30, 12h, 24h, 48h and 96h after cell stimulation (n=54 data points), the latest time points corresponding to the emergence of the proliferation clusters.

overall_design: Temporal transcriptional response (T0 + 8 time points) of primary chronic lymphocytic leukemia (CLL) cells after BCR engagement ex vivo (anti-IgM, IL-4, CD40Ligand and IL-21) of 3 Proliferating (P1, P2, P3) and 3 Non Proliferating samples (NP1, NP2, NP3).

first: Cedric

last: Schleiss

first: Raphael

last: Carapito


title: Gene expression data from BM1 (1833) tumors that are wild type or overexpressing RKIP in a xenograft mouse model

city: Chicago

first: Ali

middle: Ekrem

last: Yesilkanal

state: IL

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: The University of Chicago

summary: RKIP is a metastasis suppressor that is lost or silenced in most metastatic cancers. Here we reintroduce RKIP exogenously into BM1 cells (bone-tropic derivative of MDA-MB-231 cells, also known as 1833) that lack RKIP expression, in order to study transcriptomic changes that lead to metastasis in vivo and identify actionable targets to be used in anti-metastatic treatment strategies.

overall_design: Total RNA was collected from n=7 control BM1 tumors and n=5 RKIP-expressing tumors grown orthotopically in athymic nude mice. All samples were run in a single lane on a Illumina Hiseq 4000 in order to identify differentially expressed genes by RKIP in xenograft tumors.

first: Marsha

last: Rosner


title: Circulating plasma MicroRNA in patients with active acromegaly

status: Public on May 11 2021

city: Moscow

first: Alex

last: Nik

address: Orekhoviy bulvar, 28

country: Russia

institute: FSCC

summary: Plasma microRNAs were quantified by next-generation sequencing (NGS) to evaluate the difference in circulating microRNAs (miRNAs) associated with chronic growth hormone overproduction in adults

overall_design: A cross-sectional case-control study was conducted at a tertiary medical center. 12 patients with acromegaly and 12 healthy controls were included in the discovery phase of the study. Validation phase cohorts included 47 patients with acromegaly and 28 healthy controls.

first: Alexander

last: Lutsenko

first: Zhanna

last: Belaya

first: Alexey

last: Nikitin

first: Philipp

last: Koshkin


title: Senescent cells suppress innate VSMC repair functions in atherosclerosis

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: Background & Aims: To determine the effects of senolysis on VSMC populations in atherosclerosis.

overall_design: Control Ldlr-/- mice were treated with ABT263 or vehicle for one week under LFD-feeding conditions.

first: Jan

last: van Deursen


title: Bach2 attenuates IL-2R signalling to control Treg homeostasis and Tfr development

city: Shanghai

first: Heng

last: Zhang

address: No.227 Sounth Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Differentiation and homeostasis of Foxp3 + regulatory T cells (Tregs) are tightly controlled by the interleukin-2 receptor (IL-2R) signaling, yet the mechanisms  governing these processes are incompletely understood. Here we report that transcription factor Bach2 attenuates IL-2R signaling to coordinate Treg differentiation  and homeostasis by directly repressed CD25 (IL-2Rα). Thus, Bach2 balances IL-2R signaling to orchestrate development and homeostasis of various Treg subsets.

overall_design: Fresh Tregs (CD4+B220 CD25+YFP+) were first sorted from the spleens of 7 weeks old Bach2 sufficient and deficient mice using a FACSAria Ⅲ cell sorter (BD Biosciences) and then stimulated by anti-CD3 and anti-CD28 for 24h. Total RNA were isolated with TRIzol (Invitrogen) and subjected to RNA sequencing. The library for mRNA sequencing was generated using Illumnia TruSeq Preparation Kit  (RS-122-2001) and sequenced using Illumnia Illumina Novaseq6000 sequencer.

first: Chuanxin

last: Huang


title: The role of ESRG in human pluripotency

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

summary: Human pluripotent stem cells (PSCs) express human endogenous retroviruses type-H (HERV-Hs), which exist more than a thousand copies on the human genome and frequently produce chimeric transcripts as long-non-coding RNAs (lncRNAs) fused with downstream neighbor genes. Previous studies showed that HERV-H expression is required for the maintenance of PSC identity, and the aberrant HERV-H expression attenuated neural differentiation potentials, but little is known what their roles are. In this study, therefore, we focused on ESRG, which is known as a PSC-related HERV-H-driven lncRNA. The global transcriptome data of various tissues and cell lines and quantitative expression analysis showed that ESRG expression is much higher than other HERV-Hs and tightly silenced after differentiation, letting us hypothesize its crucial role in human pluripotency. However, the loss of function by the complete excision of the entire ESRG gene body using a CRISPR/Cas9 platform revealed that ESRG is dispensable for the maintenance of primed and naïve pluripotent states. The loss of ESRG hardly affects the global gene expression of PSCs and differentiation potentials toward trilineage. Differentiated cells derived from ESRG knockout PSCs retained the potential to be reprogrammed into induced PSC (iPSC) by the forced expression of OCT3/4, SOX2, and KLF4. In conclusion, ESRG is dispensable for the maintenance and the recapturing of human pluripotency.

overall_design: Human pluripotent stem cell line in primed condition, N=6  Human pluripotent stem cell line in naive condition, N=6  Human pluripotent stem cell-derived embryoid body, N=12

first: K

first: M

last: Narita


title: The role of ESRG in human pluripotency II

overall_design: Pluripotent stem cell line, N=5  Cancer cell line, N=4  Somatic cell line, N=10  Adult tissue, N=24  Fetal tissue, N=5


title: Gene Expression Analysis of RBM5 KO in Brain

city: Pittsburgh

first: Travis

middle: C.

last: Jackson

state: Pennsylvania

address: 3550 Terrace Street

department: Critical Care Medicine

institute: University of Pittsburgh

summary:
This study analyzed the effect of RBM5 gene deletion in cortical brain tissue on differential gene expression/splicing changes 48h after a traumatic brain injury (TBI). TBI was induced in WT vs. KO mice by controlled cortical impact (CCI) injury.  The four grouops included: (1) Sham-WT, (2) CCI-WT, (3) Sham-KO, and (4) CCI-KO.
The objective of this study was to test if RBM5 KO decreased the expression of cell death mediators in the contused brain 48h post-injury.

overall_design: A total of 28 brain tissues were isolated from 12-15wk old mice for microarray analysis. Seven animals were compared per group (n=7/group). Each group contained a mix of female and male mice as indicated for each sample in the list below. Injured mice recieved a craniotomy over the left parietal cortex via a dental drill, and subjected to a CCI injury (6m/s; 1.2mm depth). Control (sham) mice received anesthesia but did not get a craniotomy. 48h after the injury mice were euthanized and cortical tissues collected for total RNA extraction. Extracted RNA was hybridized to microarray chips (MTA 1.0).


title: Functional Diversification, Redundancy and Epistasis among Paralogs of the Drosophila melanogaster Obp50a-d Gene Cluster

city: Greenwood

first: Vijay

last: Shankar

state: South Carolina

address: 115 Milford Pines Drive

institute: Clemson University

summary: Large multigene families, such as the insect odorant binding proteins (OBPs), are thought to arise through functional diversification after repeated gene duplications. Whereas many OBPs function in chemoreception, members of this family are also expressed in tissues outside chemosensory organs. Paralogs of the Obp50 gene cluster are expressed in metabolic and male reproductive tissues, but their functions and interrelationships remain unknown. Here, we report the genetic dissection of four members of the Obp50 cluster, which are in close physical proximity without intervening genes. We used CRISPR technology to excise the entire cluster while introducing a PhiC31 re-integration site to reinsert constructs in which different combinations of the constituent Obp genes were either intact or rendered inactive. We performed whole transcriptome sequencing and assessed sexually dimorphic changes in transcript abundances (“transcriptional niches”) associated with each gene-edited genotype. Using this approach, we were able to estimate redundancy, additivity, diversification, and epistasis among Obp50 paralogs. We analyzed the effects of gene editing of this cluster on organismal phenotypes and found a significant skewing of sex ratios attributable to Obp50a, and sex-specific effects on starvation stress resistance attributable to Obp50d. Thus there is functional diversification within the Obp50 cluster with Obp50a contributing to development and Obp50d to stress resistance. The deletion-reinsertion approach we applied to the Obp50 cluster provides a general paradigm for the genetic dissection of paralogs of multigene families.

overall_design: RNA sequencing on 14 transgenic Drosophila melanogaster lines, separately by sex, with two biological replicates per line (56 samples total). Lines are grouped into eight genotypes which differ in their mutations in the four Obp50a-d genes. Four genotypes ("Obp50a," "Obp50b," "Obp50c," and "Obp50d") have premature termination codon (PTC) mutations in all but one of the four Obp50a-d genes (each of these genotypes consists of two lines, except for the genotype with no PTCs in Obp50d, which consists of a single line). One genotype ("Obp50Neg") has PTCs in all four Obp50a-d genes (two lines). One genotype ("Obp50Pos") has no PTCs in any of the four Obp50a-d genes (one line).  One genotype ("Obp50NegBCD") has missense mutations in Obp50b and PTCs in Obp50a, Obp50c, and Obp50d (two lines). One genotype ("Obp50cBCD") has missense mutations in Obp50b and PTCs in Obp50a and Obp50d (two lines).

first: Joel

middle: A

last: Johnstun

first: Sneha

last: Mokashi

first: Lakshmi

middle: T

last: Sunkara

first: Ugonna

last: Ihearahu

first: Roberta

middle: L

last: Lyman

first: Trudy

middle: F

last: Mackay

first: Robert

last: Anholt


title: RNA sequencing of the lung pre-metastatic niche in a syngeneic mouse model of rhabdomyosarcoma

city: Bethesda

first: Rosandra

middle: N

last: Kaplan

state: Maryland

address: 10 Center Drive

department: Pediatric Oncology Branch

institute: National Institute of Health

summary: The objective of this study was to profile the transcriptional landscape in the pre-metastatic lungs of mice with and without IL12-GEMy treatment.

overall_design: RNA was isolated from the lungs of naive and tumor-bearing mice, with and without IL12-GEMy treatment.

first: Sabina

last: Kaczanowska


title: Cold-induction of Afadin in Brown Fat supports its thermogenic capacity

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Transcriptomic analysis of brown fat from fat-specific Afadin depleted mice either at thermoneutrality or after 6 houts of cold exposure (5 degree celsius)

overall_design: Fat-specific Afadin KO and control littermates incubated at termoneutrality or exposed to cold for 6 hrs. RNA-seq on isolated BAT. N=5-7

first: Morten

last: Lundh

last: Altıntaş

first: Marco

last: Tozzi

first: Odile

last: Fabre

first: Tao

last: Ma

first: Farnaz

last: Shamsi

first: Zachary

last: Gerhart-Hines

first: Romain

last: Barrès

first: Yu-Hua

last: Tseng

first: Brice

last: Emanuelli


title: Effects of estradiol supplementation on the brain transcriptome of old rhesus macaques maintained on an obesogenic diet.

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

summary: Obesity during menopause contributes risk for mood disorders, dementia and Alzheimer’s disease (AD). Given the high prevalence of obesity among postmenopausal women there is an urgent need to evaluate the efficacy of hormone therapy (HT) administered immediately (vs delayed) at menopause in different brain regions involved in memory and cognition. Here, and to more closely replicate the endocrine environment of obese postmenopausal women, either on or off HT, middle-aged female rhesus macaques were ovariectomized/hysterectomized (OvH) and maintained on a high-fat, high-sugar, obesogenic Western-style diet (WSD) for 30 months; half of the animals received HT immediately after OvH and half served as placebo controls.  RNAseq of the occipital (OC) and prefrontal cortex (PFC), hippocampus (HIP) and amygdala (AMG), identified 293, 379, 505 and 4,993 differentially expressed genes (DEGs), respectively. Pathway enrichment analysis, identified an activation of neuroinflammation in OC and HIP, but an inhibition in the AMG with HT. Synaptogenesis, circadian rhythm, mitochondrial dysfunction, mTOR, glutamate, serotonin, GABA, dopamine, noradrenaline/adrenaline, glucocorticoid receptor signaling. neuronal NOS and amyloid processing were exclusively enriched in AMG. As compared to the placebo control group, most of these signaling pathways are downregulated after HT, suggesting a protective effect of HT in OvH females under a WSD. Overall, our results suggest that a chronic obesogenic diet may induce a wide range of alterations in multiple signaling pathways that are linked to age-associated brain pathology and dementia. In these individuals, HT seems to have a protective effect against neuroinflammation, amyloid beta depositions and tau tangles formation.

overall_design: Fourteen old (range = 19.4 - 23.2 years) female rhesus macaques (Macaca mulatta) were socially housed indoors in pens (3–4 animals per pen). Daily meals at ~08:00 h and ~15:00 h were supplemented with fresh fruits or vegetables; fresh drinking water was available ad libitum. At Month 0, the animals’ diet (Monkey Diet, LabDiet, Inc., St Louis, MO, USA) was replaced with unlimited access to a typical American diet or WSD (TAD Primate Diet; LabDiet, Inc.), which provided calories with 36% fat, 44% carbohydrates (includes 18.5% sugars) and 18% protein. In comparison, regular monkey chow provides calories with 13% fat, 69% complex carbohydrates (includes 6% sugars) and 18% protein. Approximately 6 weeks after the start of the WSD, all of the animals were OvH. Half of the females (n = 7, OvH-HT) were immediately started on hormone replacement therapy (HT) in the form of estradiol (E) E-containing elastomer capsules, which achieved serum E concentrations of 82.1 ± 0.9pg/ mL; the other half (n = 7) received empty capsules (placebo), which achieved serum E concentrations of 6.6 ± 0.2pg/mL on average 32 months. Serum E was measured every 2 months and the capsule replaced or its size adjusted as deemed appropriate [43]. Details on the average of serum E concentrations (high physiological) have been previously published, as well as the transient attenuation in body weight gain and improved insulin sensitivity by HT. After the 30-month duration of the study, a detailed necropsy protocol previously used in our laboratory was used to systematically collect brain tissues from all subjects.

first: Rita

last: Cervera-Juanes

first: Megan

last: Ball

first: Steven

middle: G

last: Kohama

first: Henryk

last: Urbanski


title: miR-146a regulates many lncRNAs in RAS induced senescence [Anti-146a]

city: Montreal

first: Gerardo

last: Ferbeyre

state: Qc

address: 2900 Boul. Édouard-Montpetit

department: Biochimie

country: Canada

institute: Université de Montréal

summary: miR-146a is a known anti-inflammatory miRNA. Intringuigly, it is overexpressed in RAS-induced senescent cells which is accompanied with a rich pro-inflammatoy secretpry phenotype. We aim to study possible sponges for miR-146a.

overall_design: Examination of differentially expressed lncRNAs in IMR90 RAS sensecent cells expressing an antagomir against miR-146a or a control antagomir.

first: Lian

last: Mignacca

first: Emmanuelle

last: Saint-Germain

first: Rami

last: Shukr

first: Tony

last: Buffard


title: Next Generation Sequencing  Quantitative Analysis of TEAD Palmitoylation Inhibitor MGH-CP1 in Breast Cancer Cell Line

city: Charlestown

first: Yang

last: Sun

state: MA

address: 149 13th Street, CBRC 3050E

department: CBRC

institute: Massachusetts General Hospital

summary:
Purpose: The goal of this study is to understand the signaling pathway alteration in cancer cell line treated with TEAD palmitoylation inhibitor MGH-CP1,  and to further validate TEAD inhibitor for specifity in TEAD-YAP interuption.
Methods:Breast cancer cell line MDA-MB-231 was chosen to be treated with TEAD palmitoylation inhibitor MGH-CP1 at 10μM for 24 hours. Total RNA was isolated for the analysis. RNA samples were sent to Novogen for library construction, RNA sequencing and raw data process.
Results: MGH-CP1 specifically blocks TEAD transcriptional activity compared with YAP/TAZ siRNA in MDA-MB-231 cells.
Conclusions: Our study privides gene expression profiling evidence to validate our TEAD palmitoylation inhibitor MGH-CP1 as specific small molecule to block TEAD transcriptional activity.
We report the application of next generation sequencing technology for high-throughput profiling of TEAD palmitoylation inhibitor MGH-CP1 in breast cancer cells.

overall_design:
Examination of vehicle control and MGH-CP1 in one breast cancer cell line.
*** Submitter has indicated raw files are no longer available.

first: Xu

last: Wu


title: ChIP-seq analysis of wild-type and K885A SETDB1 in 3T3-L1 preadipocytes

city: Akita

first: Yoshihiro

last: Matsumura

state: Akita

address: Hondo 1-1-1

department: Biochemistry and Metabolic Science

institute: Akita University Graduate School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The lysine methyltransferase SETDB1, an enzyme responsible for methylation of histone H3 at lysine 9, plays a key role in H3K9 tri-methylation dependent silencing of endogenous retroviruses and developmental genes. Recent studies have shown that ubiquitination of human SETDB1 complements its catalytic activity and the silencing of endogenous retroviruses in human embryonic stem cells. However, it is not known whether SETDB1 ubiquitination is essential for its other major role in epigenetic silencing of developmental gene programs. We previously showed that SETDB1 contributes to the formation of H3K4/H3K9me3 bivalent chromatin domains that keep adipogenic Cebpa and Pparg genes in a poised state for activation and restricts the differentiation potential of pre-adipocytes. Here, we show that ubiquitin resistant K885A mutant of SETDB1 represses adipogenic genes and inhibits preadipocyte differentiation similar to wild-type SETDB1. We show this was due to a compensation mechanism for H3K9me3 chromatin modifications on the Cebpa locus by other H3K9 methyltransferases Suv39H1 and Suv39H2. In contrast, the K885A mutant did not repress other SETDB1 target genes such as Tril and Gas6 suggesting SETDB1 represses its target genes by two mechanisms; one that requires its ubiquitination and another that still requires SETDB1 but not its enzyme activity.

overall_design: Retroviral expression of FLAG-tagged wild-type and K885A mutant mSETDB1 in 3T3-L1 preadipocytes. ChIP using anti-FLAG antibody followed by next-generation sequencing.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Manganese (II) or LPS treated Wild Type BMDC Transcriptomes

city: Beijing

first: Zhengfan

last: Jiang

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary:
Purpose: The goals of this study are to compare the different functions of manganese (II) and LPS on the activation and maturation of antigen presenting cells-BMDCs.
Methods: BMDCs were generated by culturing bone marrow cells with 20 ng/ml of IL-4 (Genscript) and 20 ng/ml of GM-CSF (Genscript) at 37°C and 5% CO2 for 7 days.Then BMDCs were treated with MnCl2 (200 μM) or LPS (100 ng/ml) for 20 h. Then mRNAs were purified, sequenced and analyzed.
Results: Using an optimized data analysis workflow, we compared 20339 transcripts in BMDCs. Manganese (II) induced 1677 transcripts expression with a fold change ≥1.5 and LPS induced 1555 transcripts expression with a fold change ≥1.5.
Conclusion: Manganese (II) activates the production of type I IFNs and the maturation of BMDCs. But there are also some differences between functions of manganese (II) and LPS on BMDCs.

overall_design: mRNA profiles of control, Manganese (II) or LPS treated BMDCs were generated by deep sequencing, in triplicate, using Illumina Hiseq2500.

first: Rui

last: Zhang

first: Chengguang

last: Wang


title: Transcriptome Analysis of Non-Human Primate Induced Pluripotent Stem Cell-Derived Cardiomyocytes in 2D Monolayer Culture versus 3D Engineered Heart Tissue

city: Stanford

first: Joseph

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

summary: In this study, we utilized both monolayer culture (2D) and engineered heart tissue (EHT) (3D) with NHP iPSC-CMs, which served as surrogates of direct cell injection and cell patch in vivo during exposure to hypoxic conditions, and the outcomes were compared at the transcriptome level. We found the 3D EHT model was more sensitive to ischemic conditions and similar to the native in vivo myocardium in terms of cell-extracellular matrix/cell-cell interactions, energy metabolism, and paracrine signaling.

overall_design: 6 samples for both monolayer culture (2D) and engineered heart tissue (EHT) (3D) with NHP iPSC-CMs, and 3 samples in each conditions were treated with exposure to hypoxic conditions or not.

first: Huaxiao

last: Yang

first: Ning-Yi

last: Shao


title: The role of ESRG in human pluripotency IV

first: Kazutoshi

last: Takahashi

overall_design: Human pluripotent stem cell line in primed condition, N=18  Human pluripotent stem cell line in naive condition, N=18

first: K

first: C

last: Okubo


title: Senescent cells suppress innate vascular smooth muscle cell repair functions

first: Hu

last: Li

summary: Treatment of LDLr-/- mice with the senolytic ABT263 enhances VSMC phenotypic switching to promote formation, maintenance, and restoration of the fibrous cap in atherosclerotic lesions of all stages.

overall_design: Low-density lipoprotein receptor knockout mice were fed high-fat diet (TD88137) for 12 weeks and then switched to LFD for 3 weeks prior to sacrifice. On week 1 one of LFD feeding, mice were treated 1xdaily with 100 mg/kg ABT263 by IP injection.  Three vehicle-treated and three ABT263-treated replicates are included.

first: Jan

last: van Deursen


title: miR-146a regulates many lncRNAs in RAS induced senescence [miR-CLIP

first: Gerardo

last: Ferbeyre

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

overall_design: Refer to individual Series


title: The role of ESRG in human pluripotency III

overall_design: Pluripotent stem cell line, N=12 (3 replicates each of: SB-U6-NC-CNKH-transduced, SB-U6-shHERVH1-CNKH-transduced, SB-U6-shHERVH2-CNKH-transduced, SB-U6-shHERVH3-CNKH-transduced)

first: M

last: Narita


title: Leukocyte - endothelial cell interaction in infections: the role of IL1, TNF and IFN pathways

city: Groningen

first: Xiaojing

last: Chu

state: Groningen

address: Antonius Deusinglaan 1

department: Genetics

country: Netherlands

institute: University medical center Groningen

summary: Here we comprehensively characterized the transcriptomic responses of human leukocytes (PBMC) and EC to Gram negative-bacteria, Gram positive-bacteria, and fungi by RNAseq. We showed that the common response of leukocytes to various pathogens converges on EC activation. By exposing EC to leukocyte-released mediators, with or without the presence of IL1RA and TNFα antibody, we identified specific roles for IL1 and TNFα in driving the majority of, but not exclusively, endothelial activation. Furthermore, interferon pathways are strongly induced in EC by leukocyte-released mediators, but independently from IL1 and TNFα. Our study, therefore reveals a role for IFN, together with IL1 and TNFα signaling, in mediating leukocyte-endothelial interaction in infections

overall_design: We first constructed RNAseq from PBMCs from 8 individuals with 5 types of pathogens at 2 timepoints (4h and 24h). Following the transcriptome analysis in which the pathogenic impacts on PBMCs coverge on Endothelial cells, we construcuted RNAseq data on HUVECs. We investigated direct stimulation effect on HUVECs by stimulating HUVECs with IL1alpha, TNF alpha, LPS and RPMI (As a control) for 6 hours. Besides, we also obtained RNAseq from HUVECS stimulated with supernatants  collected from 24h-stimulated PBMCs (with LPS, S.pneumoniae and C.albicans).  Furthermore, we also add IL-1 receptor antagonist and TNF-a Ab to neutralize IL1 and TNF effect in the supernatant before exposure to HUVECs.

first: Vinod

last: Kumar

first: Jill

last: Moser


title: Next Generation Sequencing Facilitates Quantitative Analysis of three groups from mouse liver Transcriptomes

city: chengdou

first: ji

middle: hong

last: jie

address: 37 Guoxue Road, Chengdu, China

institute: West China Hospital

summary: Liver mRNA profiles of WT liver(WT1-WT3) and Alb-Cre:Hdac3−/− liver (0d(Ha-Hc), 7d(Hd-Hg), 21d(Hh-Hk), 50d(Hl-Hn)) receiving successive PH(sPH),  Alb-Cre:Hdac3−/− tumor tissues(HCC1-HCC3) and adjacent non-tumor tissues(N1-N3), spontaneous liver cancers of Alb-Cre:Hdac3-/- mice (HCC1-HCC3) and liver tumor of recipient Fah-/- mice (HCCa-HCCc) were generated by deep sequencing.

overall_design: mRNA profiles of  spontaneous liver cancers of Alb-Cre:Hdac3-/- mice (HCC1-HCC3) and liver tumor of recipient Fah-/- mice (HCCa-HCCc) were used to analyze the Pearson correlation coefficient; liver mRNA profiles of WT liver and Alb-Cre:Hdac3−/− liver  (0d(Ha-Hc), 7d(Hd-Hg), 21d(Hh-Hk), 50d(Hl-Hn))  receiving successive PH(sPH),  Alb-Cre:Hdac3−/− tumor tissues (HCC1-HCC3) and adjacent non-tumor tissues (N1-N3)were used to  analyze the volcano plot, heatmap etc.

first: Yujun

last: Shi

first: Hongjie

last: Ji


title: Analysis of gene expression signatures for RAB27A knockdown

status: Public on May 10 2021

city: Suita

first: Aasa

last: Shimizu

state: Osaka

address: 2-2, Yamadaoka

institute: Osaka University

summary: To comprehensively detect differential gene expression between the two ovarian cancer cell lines (ES-2 and SKOV3ip1) transfected with control shRNA or shRAB27A, total RNA was extracted and cDNA microarray analyses were performed.

overall_design: Ovarian cancer cell lines (ES-2 and SKOV3ip1) transfected with control shRNA or shRAB27A. One experiment was performed at each sample.

first: Kenjiro

last: Sawada


title: scRNAseq of Antigen Presenting Cells in severe COVID-19 patients

city: Paris

first: Melissa

last: Saichi

address: 1 avenue Claude Vellefaux

institute: Human Immunology Pathophysiology Immunotherapy (HIPI)- Inserm

summary: We isolated PBMC from healthy, moderate ( Oxygen supply < 10L/min), and severe (Oxygen supply >= 10L/min) COVID-19 patients after their admission to Intensive Care Units (ICU), at two timepoints (Day-1 and Day-4); and performed both CD14+ Monocyte enrichment followed by a Pan-DC kit to retrieve all Antigen Presenting Cell (APC) subsets from these age-matched patients. We performed single cell RNA sequencing using 10X technology on the single cell suspensions and constracted a high-resolution map of 81,643 Antigen Presenting Cells (APC) from the three COVID-19 severity groups. We were able to retrieve all the known six APC subsets and deciphered the altered pathways and ati-viral mechanisms, correlated with the disease severity.

overall_design: After FICOLL (GE Healthcare and Lymphoprep StemCell) gradient centrifugation, total PBMC were enriched in CD14 monocytes using the human CD14 microbeads (Miltenyi Biotec) for positive magnetic selection according to the manufacturer’s instructions. The negative fraction remaining after the positive selection of CD14 cells was used for pan-DC enrichment employing the EasySep human  pan-DC enrichment kit (StemCell Technologies). Total pan-DC were resuspended with 20,000 CD14 cells and sent for sequencing. Cell suspensions were subjected to Gel Bead Emulsion using Chromium 10x Genomics controller according to manufacturer guidelines. Both library preparation and sequencing were performed accroding to manufacturer guidelines.

first: Maha

last: Zohra Ladjemi

first: Sarantis

last: Korniotis


title: Next Generation Sequencing Analysis of PRMT5 inhibitor-treated MYC-driven liver tumors

first: Yuhong

last: Luo

state: MD

address: 37 Convent Dr

department: NCI

institute: NATIONAL INSTITUTES OF HEALTH

summary: Liver cancer is one of the leading causes of cancer-related deaths worldwide. Hepatocellular carcinoma (HCC) is the most common liver cancer, and limited therapeutic options are available. Here we discovered that urinary dimethylarginine, especially symmetric dimethylarginine (SDMA), was found to be increased in HCC in a MYC-dependent manner. Mechanistically, protein arginine methyltransferase 5 (Prmt5), which was highly induced in HCC, is a direct MYC target gene. Moreover, administration of GSK3326595, a PRMT5 inhibitor, to human MYC-overexpressing transgenic mice that spontaneously develop HCC, suppressed the growth of liver tumors. GSK3326595 exhibited anti-proliferative activity and enhanced anti-tumor immune response. Collectively, this study suggest that PRMT5 could be a new drug target for HCC treatment.

overall_design: Bulk RNA-seq of RNA isolated from liver tumors of vehicle or GSK3326595-administrated LAP-tTA-tetO-MYC mice.

first: Frank

last: Gonzalez


title: 10X Genomics Single Cell RNAseq of wild-type Ciona robusta embryos at 12 hours post fertilization (hpf)

city: New York

first: wei

last: wang

address: 100 washington square east

department: Biology

institute: New York University

summary: We used 10X Genomics Chromium system to profile single cells from a pool of Wild-type Ciona robusta embyros at 12 hours post fertilization (hpf)

overall_design: A few hundred wild-type Ciona intestinalis embryos were collected at 12 hours post fertilization (hpf). Embryos were dissociated and loaded into 10X Chromium cell controller, single-cell library was prepared using Chromium Single Cell 3' v2 Reagent kit following the manufacturer's manual.

first: Wei

last: Wang

first: Yelena

last: Bernadskaya


title: miR-146a regulates many lncRNAs in RAS induced senescence [miR-CLIP]

first: Gerardo

last: Ferbeyre

overall_design: Examination of miR-146a interactome using a technique called miR-CLIP.

first: Lian

last: Mignacca

first: Emmanuelle

last: Saint-Germain

first: Rami

last: Shukr

first: Tony

last: Buffard


title: Genome-wide maps of Qki-5, Srebp2, and Pol II in oligodendrocytes

city: Shanghai

first: Chenxi

last: He

address: 131 Dong'an Rd, Mingdao Bldg, Rm 512

institute: Fudan University

summary: We found the genome-wide co-localization of Qki-5 and Srebp2. Notably, the genomic distribution analysis revealed that Qki-5 and Srebp2 highly co-occupied the regions of the promoter/transcription start site (TSS), where active transcription was taken place in a oligodendrocyte-specific manner, which was indicated by Pol II binding events. GO analysis of the genes whose promoters were co-bound by Qki-5, Srebp2, and Pol II showed a significant enrichment of the Srebp2-mediated cholesterol biosynthesis pathway, and Qki depletion led to reduced recruitment of Srebp2 and Pol II on the promoters of the genes involved in cholesterol biosynthesis. These data suggest Qki-5 as a potential transcription co-activator of Srebp2-mediated cholesterol biosynthesis in oligodendrocytes.

overall_design: Examination of genome-wide maps Qki-5, Srebp2, and Pol II in WT and Qki KO oligodendrocytes which are differentiated from neural stem cells.

first: Xin

last: Zhou

first: Seula

last: Shin

first: Jian

last: Hu

first: Fei

last: Lan


title: A survey of the mouse hindbrain in the fed and fasted state using single-nucleus RNA sequencing.

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary:
Objective: The area postrema (AP) and the nucleus tractus solitaris (NTS), located in the hindbrain, are key nuclei that sense and integrate peripheral nutritional signals and, consequently, regulate feeding behaviour. While single cell transcriptomics have been used in mice to reveal the gene expression profile and heterogeneity of key hypothalamic populations, similar in-depth studies have not yet been performed in the hindbrain.
Methods: Using single-nucleus RNA sequencing, we provide a detailed survey of 16,034 cells within the AP and NTS of the mouse, in the fed and fasted state.
Results: Of these, 8910 are neurons that group into 30 clusters, with 4289 coming from mice fed ad libitum and 4621 from overnight fasted mice. 7124 nuclei are from non-neuronal cells, including oligodendrocytes, astrocytes and microglia. Interestingly, we identified that the oligodendrocyte population was particularly transcriptionally sensitive to an overnight fast.  The receptors GLP1R, GIPR, GFRAL and CALCR, which bind GLP1, GIP, GDF15 and amylin respectively, are all expressed in the hindbrain and are major targets for anti-obesity therapeutics. We characterise the transcriptomes of these four populations and show that their gene expression profiles are not dramatically altered by an overnight fast. Notably, we find that roughly half of cells that express GIPR are oligodendrocytes. Additionally, we profile POMC expressing neurons within the hindbrain and demonstrate that 84% of POMC neurons express either PCSK1, PSCK2 or both, implying that melanocortin peptides are likely produced by these neurons.
Conclusion: We provide a detailed single-cell level characterisation of AP and NTS cells expressing receptors for key anti-obesity drugs that are either already approved for human use or are in clinical trials. This resource will help delineate the mechanisms underlying the effectiveness of these compounds, and also prove useful in the continued search for other novel therapeutic targets.

overall_design: Single-nucleus RNA sequencing data from 6 mice fed ad libitum and 6 mice fasted overnight, aged 6-8 weeks.

first: Georgina

middle: K

last: Dowsett

middle: Y

first: Giles

last: Yeo


title: GATA2 deficiency phenotype associated with tandem duplication of the GATA2 locus linked to a common structural variant

city: Newcastle upon Tyne

first: Anastasia

last: Resteu

address: M3.127, 3rd Floor Leech Building, Framlington Place

institute: Newcastle University

summary: Typical features of GATA2 deficiency were observed in a individual with wild-type GATA2 sequence. The patient had a de novo tandem duplication of 187Kb spanning GATA2 and RPN1 containing a deletion of 25Kb 5’ of RPN1, inherited from the mother. The deletion is a copy number variant present in about 4% of Europeans (GRCh37: esv2725896 and nsv513733; GRCh38: esv3597711) and removes an alternative 5’ start site of RPN1 at 128,400Kb, associated with CTCF and H3K27ac binding peaks. A second copy of GATA2 is translocated to this region by the tandem duplication. RNA-Seq was underatken in order to identify any gene fussion events resulting from the mutation and to inverstigate differences in gene expression between the patient and controls.

overall_design: Patient-derived PBMC and fibroblasts were sequnced alongside their control-derived counterparts, each derived from two biologial replicates.

first: Preeti

last: Singh

first: Matthew

last: Collin


title: Chromatin accessibility governs the differential response of cancer and T-cells to arginine starvation (Illumina HumanHT-12 V4.0 beadchip)

city: Oxford

first: Thomas

last: Milne

address: John Radcliffe Hospital, Headington

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Depleting the microenvironment of important nutrients such as arginine is a key strategy for immune evasion by cancer cells. Many tumors overexpress arginase but it is unclear how these cancers, but not T-cells, tolerate arginine depletion. Here, we show that tumor cells synthesize arginine from citrulline by upregulating argininosuccinate synthetase 1 (ASS1). Under arginine starvation, ASS1 transcription is induced by ATF4 and CEBPbeta binding to a previously uncharacterized enhancer within ASS1. T-cells cannot induce ASS1, despite the presence of active ATF4 and CEBPbeta, as the gene is repressed. Arginine starvation drives global chromatin compaction and repressive histone methylation which disrupts ATF4/CEBPbeta binding and target gene transcription. We find that T-cell activation is impaired in arginine-depleted conditions, with significant metabolic perturbation linked to incomplete chromatin remodeling and misregulation of key genes. Our results highlight a T-cell behavior mediated by nutritional stress, exploited by cancer cells to enable pathological immune evasion.

overall_design: Total RNA isolated from THP1 cells or stimulated human CD4 T-cells cultured in full RPMI or RPMI lacking arginine

first: Nicholas

last: Crump

first: Andreas

middle: V

last: Hadjinicolaou

first: Lars

last: Olsen

first: Stephen

last: Taylor

first: Vincenzo

last: Cerundolo


title: Differential expression profile of liver tissue in rats with hepatic fibrosis

status: Public on May 09 2021

city: Tangshan

first: zhang

last: ronghua

address: 21 Bohai Road, Caofeidian

institute: North China University of Science and Technology

summary: Liver fibrosis is a common pathological complication of end-stage liver disease, which is usually associated with chronic liver inflammation and injury. Liver fibrosis was induced by bile duct ligation (BDL) in rats. The differentially expressed genes in liver tissue of BDL rats were identified by microarray technique.

overall_design: In this study, the rat model of hepatic fibrosis was induced by bile duct ligation (BDL). Compared with the control group, the daily growth rate of the BDL group was significantly lower, whereas the ratio of liver wet weight to body mass of BDL group was significantly higher, respectively. The serum levels of ALT, AST, TBA and TBIL in the BDL group were significantly higher compared with those of the control group. The levels of deposition of collagen Ⅰ was assessed using Sirius red staining and the number of collagen fibers were assessed using Masson trichrome staining. The results showed that the rat model of hepatic fibrosis was successfully constructed. Then 3 liver fibrosis model rats and 3 normal rats were selected for microarray analysis,and differential gene expression in liver tissue of hepatic fibrosis was compared with that in normal liver tissue.

first: Guangling

last: Zhang

first: Ronghua


title: Single cell transcriptomics reveal disrupted kidney filter cell-cell interactions after early and selective podocyte injury

first: Abbe

middle: R

last: Clark

state: Massachusetts

address: 415 M St

institute: Broad Institute

summary: We recently demonstrated that podocyte ablation via doxycycline-inducible deletion of an essential endogenous molecule, CTCF (iCTCFpod-/-), is sufficient to drive progressive CKD. However, the earliest events connecting podocyte injury to disrupted intercellular communication within the kidney filter remain unclear. Here we performed single-cell RNA sequencing of kidney tissue from iCTCFpod-/- mice after one week of doxycycline induction to generate a map of the earliest transcriptional effects of podocyte injury on cell-cell interactions at single cell resolution

overall_design: Doxycycline was administered via drinking water (50g/L) to four animals of each genotype, WT and iCTCFpod-/- (KO), for one week. After one week, kidneys were harvest and glomeruli isolated for single-cell RNA sequencing.  Some samples were submitted with technical replicates to maximize the number of cells that were sequenced per sample without overloading the 10X chip.

first: Anna

last: Greka


title: Chromatin accessibility governs the differential response of cancer and T-cells to arginine starvation


title: Comparative Evaluation of Expression Patterns and Cellular Functions for the Three ZBTB Methyl-CpG Binding Proteins in Prostate Cancer

city: Salt Lake City

first: Aneesa

last: Al-Soodani

state: UT

department: Chemistry

institute: University of Utah

summary: To date, prostate cancer (PCa) remains the most frequently diagnosed cancer in men. While some genetic mutations have been correlated with prostate tumorigenesis, many PCa presentations do not harbor a clear genetic mutation driver. In many cancers, including PCa, aberrant alterations in DNA methylation patterns has been correlated with cancer promotion and progression. The ZBTB methyl-CpG binding proteins (MBPs), consisting of ZBTB33 (Kaiso), ZBTB4 and ZBTB38, constitute a family of transcription factors that selectively recognize mCpG-containing sites. Upon DNA recognition, these MBPs recruit enzyme complexes that act to remodel chromatin and alter transcriptional outcomes. Given the role of these proteins in eliciting epigenetic-based transcription, we sought to comparably analyze protein levels and cellular distribution patterns for all three ZBTB MBPs within 123 cases of prostate adenocarcinomas exhibiting variable Gleason scores. It was generally observed that relative to benign, nuclear and/or cytoplasmic levels of all three ZBTB MBPs increased in prostate tumors, though the expression and predominant localization trends varied between family members and Gleason score. These tumor observations were generally recapitulated in multiple PCa cell line models, prompting comparative analysis of phenotypic and transcriptome alterations after systematic depletion of each ZBTB MBP. While functional overlap between family members was evident, each ZBTB MBP was also found to modulate distinct disease relevant transcription, including at gene targets known to be hyper-methylated in PCa tumors. Collectively, these findings represent the first comparative analysis of all three ZBTB MBP family members within the same disease context and suggest these proteins may be epigenetic-drivers of aberrant transcription in PCa.

overall_design: Determination of cellular and transcriptional consequences for ZBTB33, ZBTB4 or ZBTB38 depletion in PC3 cells. Three replicates of PC3 cells were transfected with either ZBTB33, ZBTB38, or ZBTB4 specific  (si1 or si2) or control (Scr) siRNAs.

first: Bethany

last: Buck-Koehntop


title: PHAROH lncRNA regulates c-Myc translation in hepatocellular carcinoma via sequestering TIAR

city: Cold Spring Harbor

first: Allen

middle: Tingjun

last: Yu

state: NY

address: 1 Bungtown Road

institute: CSHL

summary: Hepatocellular carcinoma, the most common type of liver malignancy, is one of the most lethal forms of cancer. We identified a long non-coding RNA, Gm19705, that is over-expressed in hepatocellular carcinoma and mouse embryonic stem cells. We named this RNA Pluripotency and Hepatocyte Associated RNA Overexpressed in HCC, or PHAROH. Depletion of PHAROH impacts cell proliferation and migration, which can be rescued by ectopic expression of PHAROH. RNA-seq analysis of PHAROH knockouts revealed that a large number of genes with decreased expression contain a c-Myc motif in their promoter. C-MYC is decreased at the protein level, but not the mRNA level. RNA-antisense pulldown identified nucleolysin TIAR, a translational repressor, to bind to a 71-nt hairpin within PHAROH, sequestration of which increases c-MYC translation. In summary, our data suggest that PHAROH regulates c-MYC translation by sequestering TIAR and as such represents a potentially exciting diagnostic or therapeutic target in hepatocellular carcinoma.

overall_design: RNA-seq: Transcriptome profiles of sgRenilla control and PHAROH KO cells

first: A

first: D

last: Spector


title: Chromatin accessibility governs the differential response of cancer and T-cells to arginine starvation (ChIP-seq)

overall_design: ChIP-seq (33 samples)

first: I-Jun

last: Lau

first: Laura

last: Godfrey


title: Coordination of microbe-host homeostasis via a crosstalk with plant innate immunity

city: Köln

first: Yulong

last: Niu

state: Nordrhein-Westfalen

address: Carl-von-Linne-Weg 10

department: Plant Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

summary: Asymptomatic plants grown in natural soil are colonized by phylogenetically structured communities of microbes known as the microbiota. Individual microbes can activate microbe-associated molecular pattern (MAMP)-triggered immunity (MTI), which limits pathogen proliferation but curtails plant growth, a phenomenon known as the growth-defense trade-off. We report that in mono-associations, 41% (62/151) of taxonomically diverse root bacteria commensals suppress Arabidopsis thaliana root growth inhibition (RGI) triggered by immune-stimulating MAMPs or damage-associated molecular patterns. Amplicon sequencing of bacteria 16S rRNA genes reveal that immune activation alters the profile of synthetic communities (SynComs) comprised of RGI-non-suppressive strains, while the presence of RGI-suppressive strains attenuates this effect. Root colonization by SynComs with different complexities and RGI-suppressive activities alters the expression of 174 core host genes with functions related to root development and nutrient transport. Further, RGI-suppressive SynComs specifically downregulate a subset of immune-related genes. Mutation of one commensal-downregulated transcription factor, MYB15, or pre-colonization with RGI-suppressive SynComs render plants more susceptible to opportunistic Pseudomonas pathogens. Our results suggest that RGI-non-suppressive and suppressive root commensals modulate host susceptibility to pathogens by either eliciting or dampening MTI responses, respectively. This interplay buffers the plant immune system against pathogen perturbation and defense-associated growth inhibition, ultimately leading to commensal-host homeostasis.

overall_design: Arabidopsis thaliana plants were germinated with the synthetic communities (SynComs) in the presence or absence of 1 µM flg22 and incubated for 14 days before harvesting. For pWER::FLS2-GFP plants, single-end RNA-Seq experiments were conducted for 4 conditions (3 biological replicates for each condition). For Col-0 plants, pair-end RNA-Seq experiments were conducted for 10 conditions (4 biological replicates for each condition).

first: Ka-Wai

last: Ma


title: RNA-seq WT vs TLE3KO ( treated with AR inhibitor)

status: Public on May 08 2021

city: Amsterdam

first: Sander

last: Palit

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

summary: Transcriptome analysis of LNCaP control and TLE3 KO cells treated with AR inhibitor

overall_design: LNCaP control and TLE3KO cells were cultured in presence of 10uM enzalutamide for 5 days

first: Daniel

last: Vis

first: Cor

last: Lieftink


title: Equine Cervical Remodelling during Prepartum Period and Placentitis: A Transcriptomic Approach (Stroma)

city: Lexington

first: Barry

middle: A.

last: Ball

state: Kentucky

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

institute: University of Kentucky

summary: Placentitis was induced in five mares at approximately 290d of gestation (placentitis group), four mares with gestationally age-matched (290 d) pregnancies did not receive any treatment (control group), and the remaining three mares were maintained until approximately 330 d of gestation (prepartum group). For induction of placentitis in the former group, Streptococcus equi subsp. zooepidemicus was introduced intracervically.

overall_design: Cervical stroma samples were collected from mares with experimentally induced placentitis (290 d GA, n =5), normal pregnant mares (290 d GA, n=4), and prepartum mares (330d GA, n=3). Total RNA was isolated from all  samples using RNeasy Mini Kit (#74104; Qiagen), and DNA digestion was performed on-column using RNase-free DNase I (#79254: Qiagen), followed by cleanup procedures.  Paired-end reads with 150 nucleotides in length were produced. A TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA) was used to prepare libraries for mRNA sequencing. Libraries were loaded onto an Agilent DNA 1000 chip and validated on an Agilent 2100 Bioanalyzer (Agilent). Quantitation was performed with the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems. Libraries were run on a NextSeq 500 v2 (Illumina) 300cycles High Output kit in a 2x150 base pairs with paired-end reads. The Fastq files were evaluated for read quality using FastQC 0.11.4. Subsequently, Trim Galore 0.4.1 was used for the adapter and read quality trimming (Phred score threshold of 30). Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using the software STAR 2.5.3a, then annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1. Fragments per kilobase per million (FPKM) was used to determine the expression level of genes. Lastly, we used Cuffdiff 2.2.1 to calculate differentially expressed genes (DEG) between samples from the control and urea groups. The significance level was set at the FDR-adjusted p-value of the test statistic < 0.05 using the Benjamini-Hochberg correction.

first: Hossam

last: El-Sheikh Ali

first: Kirsten

middle: E

last: Scoggin

first: Rebecca

last: Ruby

first: Alan

last: Loynachan

first: Yatta

last: Boakari

first: Claudia

last: Fernandes

first: Pouya

last: Dini

first: Carleigh

last: Fedorka

first: Shavahn

middle: C

last: Loux

first: Alejandro

last: Esteller-Vico


title: Analysis of microRNA expression profiles and prediction of target gene signaling pathways in familial hypertrophic cardiomyopathy with myosin-binding protein C3 (MYBPC3) gene mutations

city: fuzhou

first: XUEQUN

last: HU

state: fujian province

address: 134 East Street, Gulou District, Fuzhou

institute: Clinical Medical College of Fujian Provincial Hospital, Fujian Medical University,

type: Non-coding RNA profiling by high throughput sequencing

summary: We investigated the role of microRNA (miRNAs) in familial hypertrophic cardiomyopathy (FHCM) with MYBPC3 gene mutations. We investigated the miRNAs expression profile in three patients with FHCM with MYBPC3 gene mutations and compared the miRNA expression profiles with those of the normal control group by miRNA-seq. The significantly differentially expressed miRNAs was verified by real-time polymerase chain reaction (PCR). Target genes and signaling pathways of the identified differentially expressed miRNAs were predicted by bioinformatics analysis. The three probands were all hypertrophic obstructive cardiomyopathy with severe myocardial hypertrophy, and two of the families had a family history of sudden cardiac death, representing a “malignant” phenotype. A total of 33 significantly differentially expressed miRNAs were detected in the peripheral blood of the three probands, of which 28 were upregulated and 5 were downregulated. Real-time PCR confirmed that the expression of miR-208b-3p was consistent with the microarray results, and the difference was statistically significant (P＜0.05). Bioinformatics analysis showed that miR-208b-3p was mainly enriched in 79 target genes including Dally, Frizzled, Dvl, Nlk, Stbm and CaMKII, and gene ontology (GO) analysis of target genes showed that miR-208b was mainly involved in the processes of growth cone, phosphoprotein phosphatase activity, and postsynapse organization. Kyoto encyclopedia of genes and genomes (KEGG) analysis revealed that the target genes regulated by miR-208b-3p were mainly involved in Wnt signaling pathway. These findings show the existence of a specific expression profile of miRNAs in patients with FHCM with MYBPC3 gene mutations, in which miR-208b-3p is significantly elevated, and is implicated as a regulator of cardiac hypertrophy. In addition, our results indicate that miRNA-208b-3p activates the Wnt signaling pathway through its target gene to promote cardiac hypertrophy.

overall_design: In this study, we investigated the role of microRNA (miRNAs) in familial hypertrophic cardiomyopathy (FHCM) with MYBPC3 gene mutations. We investigated the miRNAs expression profile in three patients with FHCM with MYBPC3 gene mutations and compared the miRNA expression profiles with those of the normal control group by miRNA-seq. The significantly differentially expressed miRNAs was verified by real-time polymerase chain reaction (PCR). Target genes and signaling pathways of the identified differentially expressed miRNAs were predicted by bioinformatics analysis.

first: Lihong

last: Lu

first: Xuequn

last: Hu

first: Jiazhen

last: Dai

first: Ningning

last: Lin

first: Lirong

first: Rehua

last: Wang

first: Zhangxin

last: Xie

first: Xuemei

last: Chen


title: Non-coding RNAs Associated With Prader-Willi Syndrome Regulate Transcription Of Neurodevelopmental Genes In Human Induced Pluripotent Stem Cells

city: Birmingham

first: Monika

last: Sledziowska

address: School of Biosciences, University of Birmingham, Edgbaston B15 2TT

institute: University of Birmingham

summary: We generated knockdowns (KD) of long non-coding RNAs (lncRNAs) arising from locus 15q11-q13, deletions in which result in Prader-Willi syndrome, in induced pluripotent stem cells. We extracted chromatin-associated RNA (chRNA) and total RNA and sequenced those using Illumina platform. There were four conditions for chRNA: control, KD of sno-lncRNAs, KD of SPA-lncRNAs, KD of both sno/SPA-lncRNAs, in biological duplicate. There were only two conditions for the total RNA seq: control and sno/SPA-lncRNAs. We found differential expression of genes relating to neurodevelopment and cell death between control and sno/SPA-lncRNAs only in chRNA samples.

overall_design: Differential gene expression between KDs of lncRNAs in locus 15q11-q13 in induced pluripotent stem cells and controls

first: Matt

last: Jones

first: Ruba

last: Almaghrabi

first: Daniel

last: Hebenstreit

first: Paloma

last: Garcia

first: Pawel

last: Grzechnik


title: Ku70 and Ligase IV deficiencies reveal distinct alternative end-joining outcomes in G1-arrested progenitor B cells

city: Stanford

first: Marie

last: Le Bouteiller

state: CA

address: 269 campus drive

department: Radiation Oncology

institute: Stanford University

summary: Classical nonhomologous end-joining (C-NHEJ) repairs DNA double-stranded breaks (DSBs) throughout interphase but is thought to predominate in G1-phase when homologous recombination is unavailable. Complexes containing the Ku70/80 ("Ku") and XRCC4/Ligase IV (Lig4) core C-NHEJ factors are required, respectively, for sensing and joining DSBs. While such factors are exclusively required for joining RAG1/2-initiated DSBs during V(D)J recombination in G1-phase lymphocyte progenitors, cycling cells deficient for core C-NHEJ factors join chromosomal DSBs by alternative end-joining (A-EJ) pathways. Restriction of V(D)J recombination to C-NHEJ has been attributed to RAG-mediated exclusion of A-EJ; however, it remains unclear whether A-EJ is similarly excluded from more general DSBs in G1. Here, we report that Ku actively and robustly suppresses A-EJ of RAG1/2 and two classes of engineered endonuclease-mediated DSBs in G1-arrested progenitor B cell lines. Thus, while targeted DSBs remain as free broken ends in Lig4-deficient G1-arrested progenitor B cells, deletion of Ku70 in Lig4-deficient cells restores DSB rejoining and translocation to levels observed in Ku70-deficient counterparts. Correspondingly, while V(D)J recombination is abrogated in Ligase4-deficient lines, V(D)J-like joining occurs in Ku70-deficient and Ku70/Lig4 double-deficient lines through a translocation-based A-EJ mechanism. We conclude that in G1, Lig4-deficient progenitor B cells are functionally end-joining deficient due to a near complete Ku-dependent block in A-EJ. Thus, the differential impacts of Ku deficiency versus XRCC4/Ligase IV deficiency on V(D)J recombination, severity of neuronal apoptosis, and embryonic development, including Ku-deficiency rescuing Lig4-deficient embryonic lethality, may be explained by Ku-mediated inhibition of A-EJ in the G1 cell cycle phase.

overall_design:
We employed JoinT-seq, HTGTS-Rep-Rejoin and LAM-HTGTS to map genome-wide and rejoining repair outcome in G1-arrested murine pro-B cells and to elucidate the roles of Ku70 and Lig4 in repair pathway choice.
We performed GRO-seq to study the gene transcription activity in cycling and G1-arrested v-Abl transformed pro-B cells.

first: Zhuoyi

last: Liang

first: Vipul

last: Kumar

first: Jeffrey

last: Zurita

first: Josefin

last: Kenrick

first: Sherry

first: Jiangman

last: Lou

first: Jianqiao

first: Adam

last: Ye

first: Cristian

last: Boboila

first: Frederick

middle: W

last: Alt

first: Richard

last: Frock


title: Huntington’s disease mice and human brain tissue exhibit increased G3BP1 granules and TDP43 mislocalization

status: Public on May 07 2021

city: Irvine

first: Whitney

last: England

address: 2403 Natural Sciences I

department: Pharmaceutical Sciences

institute: University of California Irvine

summary: We identify cerebrospinal fluid extracellular vesicle miRNAs in Huntington’s Disease that are enriched for targeting G3BP1 and show aberrant G3BP1 granule dynamics in HD mice and human brain tissue.

overall_design: miRNA isolated from extracellular vesicles from the cerebrospinal fluid of 10 Huntington’s Disease patients and 10 control individuals

first: Isabella

middle: I

last: Sanchez

first: Thai

middle: B

last: Nguyen

first: Ryan

last: Lim

first: Anthony

middle: Q

last: Vu

first: Ricardo

last: Miramontes

first: Lauren

middle: M

last: Byrne

first: Sebastian

last: Markmiller

first: Alice

last: Lau

first: Iliana

last: Orellana

first: Maurice

middle: A

last: Curtis

last: Faull

first: Gene

last: Yeo

first: Christie

middle: D

last: Fowler

first: Jack

last: Reidling

first: Edward

middle: J

last: Wild

first: Robert

last: Spitale

first: Leslie

last: Thompson


title: Crosstalk between Auxin Signaling and Osmotic Stress Response in the Regulation of Leaf Growth of Arabidopsis thaliana

city: Antwerp

first: SHWETA

last: KALVE

state: ANTWERP

address: 171 Groenenborgerlaan

department: Department of Biology

country: Belgium

institute: University of Antwerp

summary: Genome-wide transcriptome analysis of Arabidopsis thaliana was performed to understand the role of auxin in the response of leaf growth to osmotic stress. We studied transcriptional changes in proliferating leaves of the seedlings grown in vitro on control medium, medium supplemented with 25mM mannitol, 0.1μM NAA and 0.1μM NAA + 25mM mannitol.

overall_design: Total mRNA was obtained from the first leaf pair of plants grown on medium containing 25mM mannitol, 0.1µM NAA and the combination of NAA and mannitol at 10 DAS (days after stratification) and compared with leaves of plants grown on control medium. Three biological replicates were used for each treatment (3 replicates x 4 treatments = 12 samples).

first: Shweta

last: Kalve

first: Marios

middle: N

last: Markakis

first: Céline

last: Helsmoortel

first: Frederik

last: Coppens

first: Geert

last: Vandeweyer

first: Kris

last: Laukens

first: Manou

last: Sommen

first: Stephan

last: Naulaers

last: Vissenberg

first: Els

last: Prinsen

first: Gerrit

middle: T

last: Beemster


title: RNA Sequencing Analysis of T Cell Receptor Alpha and Beta Chain in Thymic WT versus CIC-deficient CD4+ SP Non-Treg and Treg Cells.

city: Pohang

first: Soeun

last: Kim

address: 77, Cheongam-ro

country: South Korea

institute: POSTECH

summary:
Purpose : The goal of this study is to compare the repertoire of T cell receptor (TCR) alpha and beta chain between WT and CIC-deficient thymic CD4+ single positive (SP) T cells, in both non-Treg and Treg populations, to confirm the effect of CIC deficiency on T cell development in the aspect of TCR repertoire.
Methods : Treg (CD4+CD8-CD25+GFP+) and non-Treg (CD4+CD8-GFP-) cells from Foxp3-GFP;Cicf/f and Foxp3-GFP;Cicf/f;Vav1-Cre mice were sorted by MoFlo-XDP (Beckman Coulter). Total RNA was extracted using RiboEX (GeneAll) according to the manufacturer's instructions. RNA was then amplified using a commercially available multiplex primer mix covering the TCR alpha and beta chains in two separate PCR reactions. Reverse transcription and subsequent PCR amplification (RT-PCR1) were performed using the Qiagen OneStep RT PCR mix (Qiagen). The cDNA was selected and unused primers were removed by SPRIselect bead selection (Beckman Coulter) followed by a second round of amplification performed with a pair of primers specific for communal sites engineered onto the 5ʹ end of the C- and V- primers used during RT-PCR1. After library preparation, paired-end sequencing was performed using the Illumina Miseq v3 600-cycle Reagent Kit (Illumina).
Results : We observed increased frequency of TCRs with long CDR3 length in CIC-deficient non-Treg and Treg cells. We also found significant alterations in the TCR repertoire of TCR beta chain in CIC-deficient Treg cells compared to WT cells, including altered frequency of V and J chain usage.
Conclusions : Our study represents the first comparative analysis of TCR repertoire of thymic CD4 SP cells from WT and hematopoietic lineage cell-specific Cic deficient mice. We concluded that CIC deficiency leads to alterations in TCR repertoire of thymic Treg cells.

overall_design: TCR alpha and beta chain of Treg (CD4+CD8-CD25+GFP+) and non-Treg (CD4+CD8-GFP-) cells from Foxp3-GFP;Cicf/f and Foxp3-GFP;Cicf/f;Vav1-Cre mice were sequenced for TCR repertoire analysis.

first: Yoontae

last: Lee


title: Chromatin bindings of IRF4 in the bone marrow-derived conventional dendritic cell 2 (cDC2) cultured with Flt3L

city: Saint Louis

first: Sunkyung

state: MO

address: Clinical Science Research Building, 7th Floor, Room 7701A, Campus Box 8118

department: Department of Pathology and Immunology

institute: Washington University School of Medicine

summary: We performed ChIP-seq to analyze chromatin bindings of IRF4 transcription factor in cDC2.

overall_design: Bone marrow-derived conventional cDCs were differentiated with Flt3 ligand and CD11c+ MHC II+ CD24- CD172a+ BST2- CD45RA- cDC2s were sort-purified. IRF4 ChIP-seq was performed to analyze IRF4 transcription factor chromatin bindings in the cDC2.

first: Arifumi

last: Iwata

first: Kenneth

last: Murphy


title: RNA-seq for HCT116 and KO-CREB1 cells

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

summary: We report the gene expression differences in CREB1 wild-type and knockout HCT116 cells by RNA-seq analysis.

overall_design: CREB1 wild-type and knockout HCT116 cells were collected by using RNAzol. And the total RNA was subjected to strand specific RNA-seq for gene expression difference analysis.

first: Bin

last: Li

first: Jianhua

first: Lianghu

last: Qu


title: Drosophila lncRNA-NANPI enhances Toll signaling pathway by interacting with Dif/Dorsal to facilitate transcription of antibacterial peptides

city: Nanjing

first: Hongjian

last: Zhou

address: No.1 Wenyuan Road, Xianlin University Town, Nanjing

institute: Nanjing Normal University

summary: LncRNAs have important regulatory functions but their roles in Drosophila innate immunity are poorly understood. The Drosophila Toll signaling pathway responds to Gram-positive bacterial infection and is highly conserved with mammalian TLR signaling. Recent studies focused mainly on Toll signaling pathway regulation by protein-coding genes. In the present study, we found that lncRNA-CR33942 was upregulated after Micrococcus luteus infection. Gain-of-function and loss-of-function assays disclosed that lncRNA-CR33942 regulates the Toll signaling pathway and affects Drosophila survival. RNA-seq of infected CR33942-overexpressing flies was performed to explore the CR33942 mechanism. About 70% of all upregulated core enrichment genes in the Toll signaling pathway were antibacterial peptides and PGRPs transcribed by Dif/Dorsal. We also demonstrated CR33942 interactions with Dif/Dorsal and revealed that they induce antibacterial peptides. Hence, we renamed CR33942 as lncRNA-NANPI (NF-κB-associated non-coding RNA promotional immunology). The present study identified the novel Toll signaling pathway regulator NANPI, elucidated its mode of action, clarified the function of lncRNA, and expanded our understanding of the Toll signaling pathway.

overall_design: the infected M. luteus male adult CR33942-overexpressing and control flies were collected at 12 h post-infection for subsequently RNA-seq

first: Shengjie

first: Fei

last: Ma

first: Ping

last: Jin


title: Transcriptome of Nasonia vitripennis nymphal testes during development in control and heat-stressed conditions

city: Tours

first: Charlotte

last: Lécureuil

address: Parc de Grammont

institute: University Tours

summary: The aim of this study is to obtain mRNA profiles of Nasonia vitripennis's testes during development and to compare its development at 25°C and 36°C.

overall_design: mRNA profile of white nymphal testes reared at 25°C (t0), 10hours later at 25°C or 36°C (t10) or 24h later at 25°C and 36°C (t24)


title: Diet-induced obesity promotes infection by impairment of the innate antimicrobial defense function of dermal adipocyte progenitors

first: Maksim

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: We report the transcriptomes of single cells isolated from whole skin of wild type B6 male mice fed a standard or 60% high fat diet 48-hours after mock- or S. aureus-infection.

overall_design: Wild type B6 male mice fed a standard or 60% high fat diet ad libitum were mock- or S. aureus-infected. Two days post-infection whole skin samples were collected and processed for 3'-end single cell RNA-sequencing.

first: Christian

middle: F

last: Guerrero-Juarez

first: Ling-juan

last: Zhang

first: Richard

middle: L

last: Gallo


title: HDAC inhibitor PCI-24781 inhibits metastasis in breast cancer

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

summary: RNA-seq analysis was performed to identify key signaling responding to PCI-24781 in MDA-MB-231

overall_design: Four independent sample groups were exposed to PCI-24781 and controls were treated with DMSO for 24 h and 48 h (DMSO-treated groups: DMSO 24 h, DMSO 48 h; PCI-24781-treated groups: 100 nM 24 h; 100 nM 48 h; 200 nM 24 h; 200 nM 48 h) in MDA-MB-231 and were analyzed through RNA-seq.

first: Yan

last: Wang


title: RNA-sequencing analysis of aberrantly expressed long non-coding RNAs and mRNAs in a mouse model of ventilator-induced lung injury

city: Shanghai

first: Bo

last: Xu

state: Shanghai

address: 1665 Kongjiang Road

department: Department of Anesthesiology and SICU

institute: Xinhua Hospital, Shanghai Jiaotong University, School of Medicine

summary: Long non-coding RNAs  are closely associated with the regulation of various biological processes and are involved in the pathogenesis of numerous diseases. However, the role of lncRNAs in ventilator-induced lung injury (VILI) has yet to be evaluated. This study aims to evaluate the expression profile and role of lncRNAs and mRNAs in VILI.

overall_design: In the present study, high-throughput sequencing was applied to investigate differentially expressed lncRNAs and mRNAs (fold change >2; false discovery rate <0.05). Bioinformatics analysis was employed to predict the functions of differentially expressed lncRNAs.

first: Yizhou

first: Xiujuan

first: Yanfei

last: Mao

first: Xiaoming

last: Deng


title: RNA-seq Analysis of Injured vs Sham Aortic Valves in Mice 48 hours Post-Injury

city: Columbus

first: Emily

last: Nordquist

state: OH

address: 575 Children's Crossroad

department: Department of Cardiovascular Research

institute: Nationwide Children's Hospital

summary: In order to analyze molecular changes in response to endothelial injury, the aortic valve in wild type mice was injured by inserting a thin anigoplasty guidewire into the mouse carotid artery and advancing the wire through the aortic valve opening. This procedure produced damage to the layer of valve endothelial cells surroung the outer edge of the valve leaflet. Sham surgery consisted of the same wire insertion prcoedure but the wire was not advanced to the level of the valve. The surgical procedure was performed in young (3-4 month old) and aging (16-18 month old) mice. Individual sham and injured aortic valves were collected 48 hours after surgery and submitted for sequencing (one valve per biological replicate).

overall_design:
11 samples were analyzed: 3 replicates of young injured valve, 3 replicates of young sham valve, 2 replicates of aging injured valve, and 3 replicates of aging sham valve. Differential expression was ranked based on false discovery rate (<0.1) and fold change (>2).
[contributor]  Ocean Ridge Biosciences

first: Joy

last: Lincoln


title: RNA-seq in untreated and Cadherin-11 Knockdown Human Intestinal Myofibroblast cells (HIMF)

city: Cleveland

first: Jiannan

last: Li

address: 9500 Euclid Ave

institute: Cleveland Clinic

summary: The goal of this experiment was to identify if there are any genes differentially expressed in Cadherin-11 KD HIMF

overall_design: RNA was isolated, cDNA libraries (100 bp, paired-end) were made at the University of Chicago Genomics Facility, and sequenced on an Illumina NovaSeq6000, in triplicates, according to standard protocols.

first: Shuai

last: Zhao


title: Equine Cervical Remodelling during Prepartum Period and Placentitis: A Transcriptomic Approach (Mucosa)

first: Barry

last: Ball

overall_design: Cervical mucosa samples were collected from mares with experimentally induced placentitis (290 d GA, n =5), normal pregnant mares (290 d GA, n=4), and prepartum mares (330d GA, n=3). Total RNA was isolated from all  samples using RNeasy Mini Kit (#74104; Qiagen), and DNA digestion was performed on-column using RNase-free DNase I (#79254: Qiagen), followed by cleanup procedures.  Paired-end reads with 150 nucleotides in length were produced. A TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA) was used to prepare libraries for mRNA sequencing. Libraries were loaded onto an Agilent DNA 1000 chip and validated on an Agilent 2100 Bioanalyzer (Agilent). Quantitation was performed with the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems. Libraries were run on a NextSeq 500 v2 (Illumina) 300cycles High Output kit in a 2x150 base pairs with paired-end reads. The Fastq files were evaluated for read quality using FastQC 0.11.4. Subsequently, Trim Galore 0.4.1 was used for the adapter and read quality trimming (Phred score threshold of 30). Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using the software STAR 2.5.3a, then annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1. Fragments per kilobase per million (FPKM) was used to determine the expression level of genes. Lastly, we used Cuffdiff 2.2.1 to calculate differentially expressed genes (DEG) between samples from the control and urea groups. The significance level was set at the FDR-adjusted p-value of the test statistic < 0.05 using the Benjamini-Hochberg correction.

first: Hossam

last: El-Sheikh Ali

first: Kirsten

last: Scoggin

first: Rebecca

last: Ruby

first: Alan

last: Loynachan

first: Yatta

last: Boakari

first: Claudia

last: Fernandes

first: Pouya

last: Dini

first: Carleigh

last: Fedorka

first: Shavahn

last: Loux

first: Alejandro

last: Esteller-Vico


title: Generation of human blastocyst-like structures from pluripotent stem cells

city: THUWAL

first: Samhan

middle: M.

last: Alsolami

address: Thuwal 23955

department: BESE

country: Saudi Arabia

institute: KAUST

summary: Human blastocysts are comprised of the first three cell lineages of the embryo: trophectoderm, epiblast, and primitive endoderm, all of which are essential for early development and organ formation1,2. However, due to ethical concerns and restricted access to human blastocysts, we lack a comprehensive understanding of early human embryogenesis. To bridge this knowledge gap, we need a reliable model system that recapitulates early stages of human embryogenesis. Here we report a ∼three-dimensional (3D), two-step induction protocol for generating blastocyst-like structures (EPS-blastoids) from human extended pluripotent stem (EPS) cells. Morphological and single-cell transcriptomic analyses revealed that EPS-blastoids contain key cell lineages and are transcriptionally similar to human blastocysts. Furthermore, EPS-blastoids also exhibited the developmental potential to undergo post-implantation morphogenesis in vitro to form structures with a cellular composition and transcriptome signature similar to human embryos that had been cultured in vitro for 8 or 10 days. In conclusion, human EPS-blastoids provide a new experimental platform for studying early developmental stages of the human embryo.

overall_design: The experiment was setup to investigate appropriate growth factors that enable trophectoderm differentiation from human extended pluripotent stem cells (EPS)

first: Yong

last: Fan

first: Zhe-Ying

last: Min


title: APOC2 increase PHF8 binding on chromatin

first: Jian

last: Chen

address: 507 Zhengmin Road

department: Department of thoracic Surgery

institute: Shanghai pulmonary Hospital

summary: We performed PHF8 ChIP-seq analysis of APOC2 overexpressed RKO cells and control cells to identify high-confident PHF8 regulated targets.

overall_design: Identification of PHF8 targets that regulated by APOC2

first: Zhihai

last: Peng


title: Heterogeneity of NKp46+ ILC in skin pre-cancerous lesions

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary:
The family of innate lymphoid cells (ILC) comprises the well-described conventional cytotoxic natural killer cells (NK cells) that patrol lymphoid and non-lymphoid organs to discriminate and eliminate stressed cells (i.e. infected and tumor cells) as well as other ILC subsets that are mainly located in epithelial tissue. How a tumor influences the phenotype and function of those ILC populations at different stages of carcinogenesis is of growing interest. We performed functional and transcriptomic analyses of purified NKp46+ innate lymphoid cells (ILC) from skins, cutaneous lesions and lymph nodes of mice subjected to chemically-induced skin carcinogenesis.
We showed that isolated papilloma-derived NKp46+ ILC showed the most divergent gene expression profile compared to their surrounding skin and tumor counterpart. our study indicates that NKp46+ ILC isolated at pre-cancerous stage were enriched in ILC1 subset with less cytotoxic potential than NKp46+ ILC from tumors. These findings revealed a so far unappreciated behavior of NKp46+ ILC at different stages of skin carcinogenesis.

overall_design: FVB/N mice were treated on their shaved-skin twice at week 1 (day 1) and week 7 (day 50) either with the carcinogen 7,12-dimethylbenz[a]anthracene (DMBA, 200nmol per application) diluted in acetone or with acetone alone (naive group). All the mice received the application of the tumor promoter phorbol 12-myristate 13-acetate (PMA, Sigma-Aldrich) diluted in acetone (5nmol per application) twice a week between week 2 and week 6 and between week 8 and 20. Group of mice received only PMA and not DMBA (control group). Cells were extrated from skin lesions, draining lymph nodes and skins and RNA isolation was then performed. Profiling of NKp46+ ILC from the various organs were performed using whole genome mouse microarrays.

first: C

last: Luci

first: A

last: Popa

first: F

last: Anjuere

first: P

last: Barbry

last: Bihl


title: Expression data  in Wheat TGMS line BS366 under fertile and sterile conditions

status: Public on May 06 2021

city: Beijing

first: Shiqing

last: Gao

address: Shuguang Garden Middle Street

department: Beijing Engineering Research Center for Hybrid Wheat

institute: Beijing Academy of Agriculture and Forestry Sciences

summary:
The male sterility of a wheat thermosensitive genic male sterile (TGMS) line is strictly controlled by temperature.
We used microarrays to identify genes that play pivotal roles in anthers during  cold-stress hypersensitivity.

overall_design: Anthers were selected at five developmental stages from BS366 under fertile and sterile conditions for hybridization  with the Affymetrix GeneChip Wheat  Genome Arrays

first: Changping

last: Zhao

first: Liping

last: Zhang


title: Identification of DAXX As A Restriction Factor Of SARS-CoV-2 Through A CRISPR/Cas9 Screen

city: PARIS 15

first: Artem

last: Baidaliuk

address: 25-28 rue Dr. Roux

institute: Institut Pasteur

summary: While the interferon response restricts SARS-CoV-2 replication in cell culture, only a handful of Interferon Stimulated Genes with antiviral activity against SARS-CoV-2 have been identified. Here, we describe a functional CRISPR/Cas9 screen aiming at identifying SARS-CoV-2 restriction factors.

overall_design: We performed a CRISPR/Cas9 screen specifically designed to identify restriction factors for SARS-CoV-2, assessing the ability of 1905 ISGs to modulate SARS-CoV-2 replication in human epithelial lung cells.

first: Alice

last: Mac Kain

first: Thomas

last: Vallet

first: Etienne

last: Simon-Loriere

first: Ferdinand

last: Roesch


title: Upregulation of selected HERVW loci in Multiple Sclerosis

city: Zaragoza

first: Alberto

last: Cebollada

state: Aragón

address: C/ San Juan Bosco, 13

institute: Instituto Aragonés de Ciencias de la Salud

summary: We undertook a Next Generation Sequencing (NGS)-based analysis of transcripts amplified from cDNA obtained from patients with CIS and samples from healthy controls.Reads were mapped to the human genome to determine the copies they were transcribed from.

overall_design: Examination of HERVW ENV copies in Clinical Isolated Syndrome (CIS)

first: Jon

last: Schoorlemmer

first: Mark

middle: H

last: PETRUS STRUNK

first: Sofía

last: Macías Redondo


title: Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

city: Boston

first: Hai-Tao

last: Wang

address: Center for Life Science Building,  Rm 3117.16, 3 Blackfan Circle

department: Department of Biological Chemistry and Molecular Pharmacology

institute: Boston Children’s Hospital

summary: Proper defense against microbial infection depends on the controlled activation of the immune system. This is particularly important for the innate immune receptors that recognize viral double-stranded RNA (dsRNA) and initiate antiviral immune responses with the potential of triggering systemic inflammation and immunopathology. How the functions of the dsRNA receptors and their downstream effector molecules are coordinately regulated to avoid excessive immune response is poorly understood. We here demonstrate that stress granules (SGs), biomolecular condensates that form in response to various stresses including viral dsRNA, play key roles in regulating dsRNA-triggered immune response. Upon dsRNA stimulation, SGs recruit many innate immune molecules, including RIG-I-like receptors (RLRs), protein kinase R (PKR) and oligoadenylate synthases (OASes), target these molecules and dsRNA for autophagy and limit their functions through sequestration. In the absence of SGs, dsRNA stimulation results in hyperactivation of inflammatory signaling pathways, global translational arrest and bulk RNA degradation, altogether compromising the cellular capacity to restore homeostasis and triggering cell death. In contrast to most dsRNA-induced immune signaling pathways that are hyperactivated in the absence of SGs, a sub-branch of the RLR pathway (IRF3-dependent type I interferon signaling) shows time-dependent changes, where the initial spike in signaling is followed by a significant drop due to increased caspase-dependent negative feedback regulation. This highlights the role of SGs in regulating the delicate balance between the type I interferon pathway and cell death. Altogether, our data suggest that cells utilize SGs as shock absorbers to moderate antiviral innate immune response, thereby allowing cells to guard against its own immune system as well as viruses.

overall_design: Two or three biological replicates were analyzed for U2OS and A549 cells both treated/untreated with dsRNA in different genotype and timepoints.

first: Cristhian

last: Cadena

first: Max

last: Paget

first: Sun

last: Hur


title: Characterization of the transcriptomic profile of Plagl1+/-pat retina

city: Lethbridge

first: Yaroslav

last: Ilnytskyy

state: AB

address: 4401, University Drive W

department: Biology

institute: University of Lethbridge

summary: Retinal damage triggers reactive gliosis in Müller glia across vertebrate species, but only in regenerative animals, such as teleost fish, do Müller glia initiate repair; proliferating and undergoing neurogenesis to replace lost cells. We found that Plagl1, a maternally imprinted gene, is dynamically regulated in reactive Müller glia post-insult, with transcript levels transiently increasing before stably declining. To study Plagl1 retinal function, we examined Plagl1+/-pat null mutants postnatally, revealing defects in retinal architecture, visual signal processing and a reactive gliotic phenotype. Plagl1+/-pat Müller glia proliferate ectopically and give rise to inner retinal neurons and photoreceptors. Transcriptomic and ATAC-seq profiles revealed similarities between Plagl1+/-pat retinas and neurodegenerative and injury models, including an upregulation of pro-gliogenic and pro-proliferative pathways, such as Notch, not observed in wild-type retinas Plagl1 is thus an essential component of the transcriptional regulatory networks that retain mammalian Müller glia in quiescence.

overall_design: Transcriptomic prolifing of post-natal (P)7 Plagl1 Knock-out (8 biological samples) and 4 wild-type (4 biological samples) retinas

first: Yacine

last: Touahri

first: Igor

last: Kovalchuk

first: Carol

last: Schuurmans


title: PIK3CA-dependent hepatocarcinogenesis. A microarray comparing PIK3CA E545K and H1047R injected mice compared to age matched controls.

city: Regensburg

first: Alexander

last: Scheiter

state: Bavaria

address: Franz-Josef-Strauss Allee 11

department: Institute of Pathology

institute: University of Regensburg

summary:
Gene expression microarray analyses of PIK3CA H1047R and E545K induced preneoplastic lesions and tumors compared to age matched controls.
Plasmids expressing oncogenic forms of PIK3CA (H1047R or E545K mutants) were delivered to the mouse liver by tail vein hydrodynamic injection combined with Sleeping Beauty–mediated somatic integration (SBT-HTVI). Resulting preneoplastic and neoplastic lesions were subjected to gene expression microarray analysis. The putative PIK3CA target gene Galectin1 (Gal1) was further characterized by in vitro studies. Transfection of either PIK3CA E545K or H1047R mutants via SBT-HTVI was sufficient to induce hepatocellular carcinomas in mice. A stepwise hepatocarcinogenesis from singular pericentral lipid-rich preneoplastic hepatocytes to clusters, expansive preneoplastic lesions, and HCCs was observed. In PIK3CA H1047R injected mice, HCCs were detected in the 12 months injection group, while PIK3CA E545K injections resulted in tumor occurrence as early as 3 months after SB-HTVI. Histologically, a predominant lipid-rich phenotype characterized all tumorigenesis stages, as confirmed by Sudan III staining and electron microscopy. Immunohistochemically, preneoplastic lesions and tumors displayed high levels of the lipid master regulators Fatty acid synthase and Stearoyl-CoA desaturase-1. Gal1 was commonly overexpressed in PIK3CA-driven preneoplastic and neoplastic liver lesions by gene expression microarray analysis compared with age-matched controls.

overall_design: 4 x PIK3CA H1047R preneoplasia 3 months vs 5 x empty vector control 3 months; 5 x PIK3CA E545K preneoplasia 3 months vs 5 x empty vector control 3 months; 5 x PIK3CA E545K tumor 5 months vs 5 x empty vector control 5 months; 5 x empty vector control 6 months versus 5 x empty vector control 3 months; 2 x PIK3CA H1047R 6 and 12 months versus 5 x empty vector control 6 months


title: Transcriptional characterization of cardiomyocyte nuclei from neonatal mice with volume overload

city: Amsterdam

first: Vincent

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

institute: Amsterdam UMC

summary: Expression analysis of cardiomyocytes from 12 day old mice with and without left ventricular volume overload

overall_design: RNA-seq on mouse cardiac tissue

first: Marie

last: Günthel

first: Karel

last: van Duijvenboden