title: Iron-bound lipocalin-2 protects renal cell carcinoma from ferroptosis

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

institute: Goethe University Frankfurt

summary: While the importance of the iron-load of lipocalin-2 (Lcn-2) in promoting tumor progression is widely appreciated, underlying molecular mechanisms largely remain elusive. Considering its role as an iron-transporter, we aimed at clarifying iron-loaded, holo-Lcn-2 (hLcn-2)-dependent signaling pathways in affecting renal cancer cell viability. Applying RNA sequencing analysis in renal CAKI1 tumor cells to explore highly upregulated molecular signatures in response to hLcn-2, we identified a cluster of genes (SLC7A11, GCLM, GLS), which are implicated in regulating ferroptosis. Indeed, hLcn-2-stimulated cells are protected from erastin-induced ferroptosis. We also noticed a rapid increase in reactive oxygen species (ROS) with subsequent activation of the antioxidant Nrf2 pathway. However, knocking down Nrf2 by siRNA was not sufficient to induce erastin-dependent ferroptotic cell death in hLcn-2-stimulated tumor cells. In contrast, preventing oxidative stress through N-acetyl-L-cysteine (NAC) supple-mentation was still able to induce erastin-dependent ferroptotic cell death in hLcn-2-stimulated tumor cells. Besides an oxidative stress response, we noticed activation of the integrated stress response (ISR), shown by enhanced phosphorylation of eIF-2α and induction of ATF4 after hLcn-2 addition. ATF4 knockdown as well as inhibition of the ISR sensitized hLcn-2-treated renal tumor cells to ferroptosis, thus linking the ISR to pro-tumor characteristics of hLcn-2. Our study provides mechanistic details to better understand tumor pro-survival pathways initi-ated by iron-loaded Lcn-2.

overall_design: mRNA-seq of CAKI1 cells after 24h stimulation with 5µg/ml holo Lcn-2, and an unstimulated control.

first: Julia

middle: K

last: Meier

first: Michaela

last: Jung


title: High-fat diet activated fatty acid oxidation mediates intestinal stemness and tumorigenicity

status: Public on Jun 01 2021

city: Cambridge

first: Constantine

middle: Nicholas

last: Tzouanas

state: MA

address: 45 Carleton St

department: Harvard-MIT Health Sciences and Technology

country: USA

institute: Massachusetts Institute of Technology

type: Expression profiling by high throughput sequencing

summary: We apply scRNA-seq to identify shared patterns of gene expression related to fatty acid oxidation, across stem cells from the proximal small intestine, distal small intestine, and colon

overall_design: scRNA-seq of 6month old mice, fed either a high fat diet (n = 3) or control diet (n = 2)

first: Miyeko

last: Mana

middle: N

first: Alex

last: Shalek

first: Omer

last: Yilmaz


title: Analysis of differentially expressed lncRNA, circRNA and mRNA between FaDu and cisplatin-resistant FaDu cell

status: Public on Jun 02 2021

city: Changsha

first: Wei

last: LI

state: Hunan

address: Tongzipo Road

department: Department of Otorhinolaryngology-head and neck surgery

country: China

institute: Third Xiangya hospital of Central South University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Cisplatin is a common chemotherapeutic drug for hypopharyngeal cancer. But cisplatin-resistance of hypopharyngeal cancer is rarely explored. We cultured hypopharyngeal cancer cell (FaDu) and induced its cisplatin-resistant cell (FaDu/DDP4). The resistance index (RI) of FaDu/DDP4 was 2.828. Then we tested the differentially expressed genes (DEGs) between FaDu and FaDu/DDP4. DEGs contain 2388 lncRNAs, 1932 circRNAs, 745 mRNAs and 202 miRNAs. We used Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyzed the DEGs. The differentially expressed 745 mRNAs were classified into 3 domains and 47 secondary GO terms. In KEGG pathway enrichment, “TNF signaling pathway”, “IL-17 signaling pathway” and “JAK-STAT signaling pathway” have greater enrich factors. And we drew the ceRNA networks of DEGs. 52 lncRNAs, 148 circRNAs, 155 mRNAs and 18 miRNAs were selected to draw the network. We noticed several potential targets (as miR-197-5p, miR-6808-5p, APOE, MMP1, S100A9 and CYP24A1). At last, we chose 8 miRNAs and 6 mRNAs for qRT-PCR to verify our microarray. In them, miR-197-5p, miR-6808-5p, APOE, MMP1, S100A9 and CYP24A1 might be potential genes inducing resistance.

overall_design: Detect the expression of lncRNA, circRNA and mRNA in FaDu and its cisplatin-resistant cell, FaDu/DDP4. Each cell strain was detected only once.

last: Li

first: Gehou

last: Zhang

first: Guolin

last: Tan


title: mRNA-seq in siNC and siCNN3 C2C12 cells

city: Guangzhou

first: Rui

last: Chen

address: 466 Xin Gang Zhong Road

department: Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute

institute: Guangdong Second Provincial General Hospital

summary: We evaluate the effects of CNN3 on myogenesis and further explored its potential molecular mechanisms. C2C12 cells were transfected with siRNA CNN3 and its NC control siRNA. Total mRNA was extracted from cells using TRIZOL reagent in accordance with the manufacturer’ protocol. And transcriptomes of CNN3 gene silenced C2C12 cells was detected by RNA-Seq.

overall_design: Examination of mRNA-seq in siNC and siCNN3 C2C12 cells

first: Yanling

last: She


title: Heterogeneity in human iPSC-derived alveolar epithelial type II cells revealed with ABCA3/SFTPC reporters

city: Boston

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

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

overall_design: Refer to individual Series


title: Global transcriptomic analyses of pluripotent stem cell-derived type II alveolar epithelial-like cells identified by ABCA3:GFP and SFTPCtdTomato bi-fluorescent reporters

summary: We performed transcriptomic profiling of cells derived from human pluripotent stem cells (PSCs) using distal lung directed differentiation protocol previously described to generate alveolar type II epithelial-like cells (iAEC2s). We used the RUES2-STAG human embryonic stem cell line containing bi-fluorescently targeted ABCA3:GFP knock-in fusion reporter and SFTPCtdTomato knock-in reporter to potentially identify heterogenous iAEC2 populations and determine their gene expression profiles. On day 36 of differentiation, we sorted SFTPCtdTomato/ABCA3:GFP double positive (DP), ABCA3:GFP single positive (SP) and reporter double negative (DN) cells for transcriptomic analysis by bulk RNA sequencing. We found DN cells to be enriched in non-lung endodermal cells. Comparison between the reporter positive iAEC2 populations revealed high transcriptomic similarity with expression of canonical AEC2 transcripts in both the DP and SP cells. Analyses of differentially expressed transcript between the DP and SP cells revealed higher levels of surfactant and lamellar body-related transcripts in the DP cells. Moreover, we find enrichment of proliferative markers associated with cellular proliferation indicating the ABCA3:GFP single positive iAEC2s to potentially be a more proliferative subset of iAEC2s.

overall_design: Global transcriptomic analysis of day 36 PSC-derived cells comparing SFTPCtdTomato/ABCA3:GFP reporter double positive (DP), ABCA3:GFP reporter single positive (SP), and reporter double negative (DN)  cells in triplicate differentiations (n=3)

first: Yuliang

middle: L

last: Sun

first: Darrell

last: Kotton


title: TET2 inhibits PD-L1 gene expression in breast cancer cells through histone deacetylation

city: Shanghai

first: Yinghui

last: Shen

address: 131 Dongan Road

institute: Fudan University

summary: The mRNA expression profile was performed to study the downstream genes regulated by TET2 in human breast cancer cells. In MCF7 cells, CRISPR method was used to knock out TET2 and  shRNA was used for knocking down TET2.  Through the deep sequencing and analysis of wild-type and loss of TET2 MCF7 cells, we identified the negative regulation of PD-L1 gene transcription by TET2.

overall_design: Total RNA were extracted from MCF7 cells and performed by deep sequencing on Illumina platform

first: Li


title: Inhibitory effect of empagliflocin on IL1-β-mediated gene expression in human proximal tubular cells

city: Innsbruck

first: Johannes

last: Leierer

address: Anichstr. 35

department: Internal Medicine IV - Nephrology

country: Austria

institute: Medical University Innsbruck

summary: We aim at elucidating pathways involved in SGLT2i-mediated nephro-protection by using a systematic molecular approach in 2 independent human proximal tubular cell lines.

overall_design: Human proximal tubular cells (HK-2 and RPTEC/TERT1) were serum- and supplement-starved for 24 h and then - after an additional medium change - stimulated for 24 h with 10 ng/ml IL-1ß and 500 nM empagliflocin.   24 h with 10 ng/ml IL-1ß or 500 nM empagliflocin or left unstimulated for another 24h (control).

first: Markus

last: Pirklbauer

first: Gert

last: Mayer

first: Petra

last: Staudinger


title: Single-cell RNA-seq reveals fibroblast heterogeneity and increased mesenchymal fibroblasts in human skin fibrotic diseases (RNA-seq)

city: GuangZhou

first: Yongfei

last: Hu

state: GUangDong

address: Road LuJing

institute: Dermatology Hospital of Southern Medical University

summary: Skin fibrotic disease representsa major global healthcare burden, characterized by fibroblast hyperproliferation and excessive accumulation of extracellular matrix.Fibroblasts are found to be heterogeneous in multiple fibrotic diseases,but the fibroblast heterogeneity of skin fibrotic diseases remains unknown.In this study, we performed single-cell RNA-seq in keloid, a paradigm of skin fibrotic diseases, andnormal scardermis tissues.Our results indicate thatkeloid and normal scar fibroblasts could be divided into 4 subpopulations: secretory-papillary, secretory-reticular, mesenchymal and pro-inflammatory.The percentage of mesenchymal fibroblast subpopulationincreased significantly in keloid compared to normal scar. Interestingly, we also found increasing mesenchymal fibroblast subpopulation in scleroderma, another skin fibrotic disease.Function studies showed that the mesenchymal fibroblasts promoted collagen synthesis of the other fibroblasts in keloid partiallythrough secreting POSTN. These findings will help us understandskin fibroticpathogenesis in depth,and provided potential target cells for fibrotic diseases therapies.

overall_design: We just used dermis for scRNA-seq analysis because keloid represents a skin dermis fibrosis disease. After stringent quality control, we obtained transcriptomes of 40655 cells (Keloid(nsample=3): 21488; Normal scar(nsample=3):19167). For RNA-seq, We flow sorted keloid fibroblasts that were CD90+ and CD266+/CD9- or CD90+ other cells (other fibroblasts),performed RNA-seq to compare the gene expression of CD266+/CD9- fibroblasts and other fibroblasts.

first: Cheng-Cheng

last: Deng

first: Ding-Heng

last: Zhu


title: The assessment of differential expression in the hypothalamus following MMS

city: Edinburgh

first: Eamon

last: Fitzgerald

state: Midlothian

address: 47 Little France Cres

country: United Kingdom

institute: University of Edinburgh

summary: The hypothalamus was extracted from MMS and control groups immeadiately at the end of the paradigm on P6, RNA extraction done using Qiagen RNA/DNA extraction kits.

overall_design: 3' RNA sequencing was carried out on 6 samples per group

first: Amanda

middle: J

last: Drake


title: Generation of ABCA3:GFP expressing type II alveolar epithelial-like cells from human pluripotent stem cells

summary: We perform transcriptomic profiling of cells derived from human induced pluripotent stem cells (iPSCs) using distal lung directed differentiation protocol previously described to generate alveolar type II epithelial-like cells (iAEC2s). We use the BU3 ABCA3:GFP iPSC line containing a GFP knock-in fluorescent reporter for the canonical AEC2 gene, ABCA3, to sort out pure populations of GFP positive and negative cells on day 31 of distal lung differentiation for bulk RNA sequencing analysis. We find canonical AEC2s transcripts as well as lamellar body-associated transcripts to be enriched in the ABCA3:GFP positive population suggestive of enrichment of AEC2 program. In contrast, we find non-lung endodermal lineages to be enriched in the ABCA3:GFP negative cells. Combined, these findings indicate the reliability of the ABCA3:GFP reporter in enriching iAEC2s in our in vitro distal lung directed differentiation protocol.

overall_design: Global transcriptomic analysis of day 31 PSC-derived cells comparing ABCA3:GFP reporter positive vs ABCA3:GFP reporter negative cells in triplicate differentiations (n=3)


title: DNA methylation immunoprecipitation of hypothalamic DNA following modified maternal separation (MMS)

type: Methylation profiling by high throughput sequencing

summary: This study was designed to investigate the effect of a novel model of early life stress (MMS) on DNA methylation within the hypothalamus

overall_design: 3 control samples, 3 MMS samples, 1 control input, 1 MMS input, 1 IgG

first: Matthew

last: Sinton


title: Genome-wide identification of target genes for the transcription factor Sox10 in the Msc80 Schwann cell line.

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

country: Germany

summary: To identify target genes of the Sox10 transcription factor in peripheral glia in a genome-wide and unbiased approach, we performed CRISPR/Cas9-dependent genome editing of the mouse Sox10 gene in the Msc80 Schwann cell line, followed by RNA-Seq studies on Sox10-expressing control Msc80 cells and Sox10-negative genome edited cell clones. Among others we detected substantial changes in the expression of genes associated with Schwann cell adhesion and the formation of the node of Ranvier.

overall_design: We generated mRNA profiles of Msc80 cells (ctrl) and Sox10-negative Msc80 cells (Sox10ko) using the Illumina HiSeq 2500 platform.

first: Franziska

last: Fröb


title: Neurogenesis Potential Evaluation and Transcriptome Analysis of Fetal Hypothalamic Neural Stem/Progenitor Cells With Prenatal High Estradiol Exposure

first: Huihui

last: Wang

state: Shanghai

address: No. 845, Lingshan Road, Pudong New District, Shanghai

department: Center for Reproductive Medicine

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

type: Non-coding RNA profiling by high throughput sequencing

summary: High maternal estradiol is reported to induce metabolic disorders by modulating hypothalamic gene expression in offspring. Since neurogenesis plays a crucial role during hypothalamus development, we explored whether prenatal high estradiol exposure (HE) affects proliferation and differentiation of fetal hypothalamic neural stem/progenitor cells (NSC/NPCs) in mice and performed RNA sequencing to identify the critical genes involved. NSC/NPCs in HE mice presented attenuated cell proliferation but increased neuronal differentiation in vitro compared with control (NC) cells. Gene set enrichment analysis of mRNA profiles indicated that genes downregulated in HE NSC/NPCs were enriched in neurogenesis-related Gene Ontology (GO) terms, while genes upregulated in HE NSC/NPCs were enriched in response to estradiol. Protein-protein interaction analysis of genes with core enrichment in GO terms of neurogenesis and response to estradiol identified 10 Hub mRNAs, among which three were potentially correlated with six differentially expressed (DE) lncRNAs based on lncRNA profiling and co-expression analysis. These findings offer important insights into developmental modifications in hypothalamic NSC/NPCs and may provide new clues for further investigation on maternal environment programmed neural development disorders.

overall_design: Fetal hypothalamic NSC/NPC mRNA and lncRNA profiles of E14.5 HE and NC mice

first: Chengliang

last: Zhou

first: Min

last: Hou

first: Hefeng

last: Huang

first: Yun


city: Shenzhen,Guangdong Province,China

first: Yayan

last: Feng

state: --- Select a state ---

address: No. 7 pengfei road, dapeng new district, shenzhen

institute: Chinese Academy of Agricultural Sciences

summary:
As the most studied type of epigenetic modifications found in many taxa, DNA methylation has been confirmed to play a crucial role in transposon silencing, transcriptional regulation and thus phenotypic variation, as well as rapid adaption to changing environments. To fully understand the methylome variation in Trichinella, here, we report 12 single-base resolution methylomes of three life stages using WGBS. By comparative epigenomics, we observe that the methylome variation in Trichinella is significantly divergent and host-related.
By comparative epigenomics, we observe that the methylome variation in Trichinella is significantly divergent and host-related. By comparing DNA methylation patterns between different host classes of species, we found a fraction of parasitism-related genes under epigenetic regulation, such as G-protein-coupled receptor, DNaseII and ligand-gated chloride channel. Moreover, we also reveal associations between methylation divergence and genetic basis, including nucleotide variant and structural variation.

sample_organism:
Trichinella spiralis
Trichinella nativa
Trichinella nelsoni
Trichinella pseudospiralis
Trichinella britovi
Trichinella sp. T6
Trichinella sp. T8
Trichinella murrelli
Trichinella sp. T9
Trichinella papuae
Trichinella zimbabwensis
Trichinella patagoniensis

overall_design: We report 12 single-base resolution methylomes of three life stages using WGBS

first: Fei

last: Gao


title: Transcriptome profiling of human non-alcoholic fatty liver disease

status: Public on May 31 2021

city: Suita

first: Takahiro

last: Kodama

state: Osaka

address: 2-2 Yamadaoka

department: Department of Gastroenterology and Hepatology

country: Japan

institute: Osaka university, Graduate School of Medicine

summary:
Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide. Nonalcoholic steatohepatitis (NASH), the progressive form of NAFLD, and advanced fibrosis are associated with poor outcomes but their molecular pathogenesis is not fully elucidated.
Global RNA sequencing of snap frozen liver tissue from 98 patients with biopsy-proven NAFLD was performed.
Unsupervised hierarchical clustering well-distinguished NASH from NAFL, and NASH patients exhibited molecular abnormalities reflecting their pathological features. Transcriptomic analysis identified multiple secreted proteins upregulated in NASH and/or advanced fibrosis

first: Hiroki

last: Murai

first: Tetsuo

last: Takehara

first: Daisuke

last: Motooka

first: Yasuteru

last: Kondo


summary:
As DNA methylation can modulate gene expression, we then focused our analysis on changes of methylation at the host taxonomic level, that is between encapsulated and non-encapsulated clade, and within non-encapsulated clade, to reveal epigenetic regulation on transcriptomes from Ad and ML stages.
By comparing DNA methylation patterns between different host classes of species, we found a fraction of parasitism-related genes under epigenetic regulation, such as G-protein-coupled receptor, DNaseII and ligand-gated chloride channel.

platform_organism:
Trichinella spiralis
Trichinella nativa
Trichinella nelsoni
Trichinella pseudospiralis
Trichinella britovi
Trichinella sp. T6
Trichinella sp. T8
Trichinella murrelli
Trichinella sp. T9
Trichinella papuae
Trichinella zimbabwensis
Trichinella patagoniensis

overall_design: We report 12 transcriptomes of three life stages using RNA-Seq


title: Three life stages


title: Continuous inflammatory stimulation leads via metabolic plasticity to a pro-metastatic phenotype in triple-negative breast cancer cells

status: Public on May 30 2021

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University


title: Profiling cell-type-specific transcriptional changes and DNA break sites in response to contextual fear learning

first: Li-Huei

last: Tsai

address: 43 Vassar St

department: Brain and Cognitive Sciences

institute: MIT

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Neuronal activity generates DNA double-strand breaks (DSBs) in vitro and in vivo, and these breaks facilitate the rapid transcriptional induction of immediate early genes (IEGs). Yet the locations of these DSBs in vivo and their relation to brain function remains unclear. Here, following contextual fear conditioning in mice, we profiled the locations of DSBs genome-wide along with transcriptomic changes in neurons and glia in two brain regions.
Interestingly, while DSB-susceptible genes induced by fear learning in neurons are predominately involved in synaptic processes, we also observe increased DNA breaks at genes upregulated in glia. Both activity-regulated and proteostasis-related transcription factors appear to govern these gene expression changes across cell types. Finally, we find that glia but not neurons have a robust transcriptional response to glucocorticoids, and these are sites of DSBs. Overall, our data show that fear learning rapidly induces transcriptional changes at genes important for brain function, including stress-responsive genes in glia, and this correlates with hotspots of DSBs.

overall_design: gH2AX foci and total RNA profiling in neurons and glia of the hippocampus and medial prefrontal cortex

first: R

last: Stott

first: L


title: Continuous inflammatory stimulation leads via metabolic plasticity to a pro-metastatic phenotype in triple-negative breast cancer cells I

summary: Chronic inflammation promotes cancer progression by affecting the tumor cells and their microenvironment. Here, we demonstrate that the continuous stimulation (6 weeks) of triple-negative breast tumor cells (TNBC) by the potent pro-inflammatory cytokines tumor necrosis factor α (TNFα) and interleukin 1β (IL-1β) had a robust effect on gene expression, demonstrating that the cancer cells have been skewed to strong pro-inflammatory phenotype. Moreover, continuous TNFα + IL-1β stimulation has reduced cell-to-cell contacts in the cancer cells and has induced metabolic plasticity in TNBC cells: this was exemplified by increase in active mitochondria area and elevations in the glycolytic as well as mitochondrial respiratory potential of the cancer cells (OXPHOS). Glycolysis has induced p65 activation and has led to increased transcription and expression of pro-metastatic chemokines such as CXCL8, CXCL1 and CCL2 and sICAM-1; agreeing with the ability of these chemokines to induce the recruitment of deleterious myeloid cells to tumors, mainly inhibition of glycolysis has given rise to reduced monocytic cell migration, in vitro and in vivo, in response to cancer cell supernatants obtained following continuous TNFα + IL-1β stimulation. Such inflammation-induced metabolic plasticity, which promotes metastatic cascades in TNBC, may have important clinical implications in the treatment of TNBC patients

overall_design: To explore this important aspect of inflammation-driven effects on breast tumor cells, we chose to study the most aggressive subtype of breast cancer, namely triple-negative breast cancer (TNBC). The TNBC subtype account for 15-20% of breast cancer cases, demonstrating high degree of recurrence and poor survival [19-21]. In view of the large versatility of pro-metastatic functions demonstrated by TNBC cells, it was of major interest to determine if a continuous stimulation by TNFα + IL-1β will further potentiate some of these activities or even lead to acquisition of novel pro-metastatic capabilities by TNBC cells.

first: Dina

last: Morein

first: Linor

last: Rubinstein-Achiasaf

first: Hadar

last: Brayer

first: Orly

last: Dorot

first: Edward

last: Pichinuk

first: Hagar

last: Ben-Yaakov

first: Tsipi

last: Meshel

first: Adit

last: Ben-Baruch


title: The effect of homocysteine on Human Aortic Endothelial Cells [RNA]

status: Public on May 29 2021

city: Philadelphia

first: Hong

last: Wang

state: PA

address: 3500 N Broad St. MERB1060

department: CMDR

institute: Temple University Lewis Katz School of Medicine

summary: Hyperhomocysteinemia (HHcy) is an established and potent independent risk factor for degenerative diseases, including cardiovascular disease (CVD), Alzheimer disease, type II diabetes mellitus, and chronic kidney disease. HHcy has been shown to inhibit proliferation and promote inflammatory responses in endothelial cells (EC), and impair endothelial function, a hallmark for vascular injury. However, metabolic processes and molecular mechanisms mediating HHcy-induced endothelial injury remains to be elucidated. This study examined the effects of HHcy on the expression of mRNA and microRNA (miRNA) in human aortic endothelial cells treated with a pathophysiologically relevant concentration of homocysteine (Hcy 500 μM).  This is the first study to consider the effects of HHcy on both global mRNA and miRNA expression changes for mechanism identification. Molecular axes and biochemical processes identified in this study are useful not only for the understanding of mechanisms underlying HHcy-induced endothelial injury, but also for discovering therapeutic targets for CVD in general.

overall_design: RNA was extracted from three biological replicates for each treatment group using the miRNeasy Mini Kit (Qiagen, Valencia, CA). RNA quality was assessed using the Nanodrop 2000 Spectrophotometer (Thermo Scientific). mRNA microarrays were performed using Affymetrix GeneChip® Human Gene 1.0 ST Arrays and miRNA microarrays were performed using Affymetrix GeneChip® miRNA 1.0 Arrays (Affymetrix, Santa Clara, CA).

first: Michael

last: Jan

first: Ramon

last: Cueto

first: Xiaohua

last: Jiang

first: Liu

last: Lu

first: Jason

last: Sardy

first: Xinyu

last: Xiong

first: Justine

middle: E

last: Yu

first: Hung

last: Pham

first: Mohsin

last: Khan

first: Xuebing

last: Qin

first: Yong

last: Ji

first: Xiao-Feng

last: Yang


title: The effect of homocysteine on Human Aortic Endothelial Cells [miRNA]


title: LRRC8A-containing chloride channel is crucial for cell volume recovery and survival under hypertonic conditions

city: Barcelona

first: Francesc

last: Posas

address: Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

summary: Regulation of cell volume is essential for tissue homeostasis and cell viability. In response to hypertonic stress, cells need rapid electrolyte influx to compensate water loss and to prevent cell death in a process known as regulatory volume increase (RVI). However, the molecular component able to trigger such process was unknown to date. Using a genome wide CRISPR/Cas9 screen, we identified LRRC8A, which encodes a chloride channel subunit, as the gene most associated with cell survival under hypertonic conditions. Hypertonicity activates the p38 stress-activated protein kinase pathway and its downstream MSK1 kinase, which phosphorylates and activates LRRC8A. LRRC8A-mediated Cl efflux facilitates activation of the with-no-lysine (WNK) kinase pathway, which in turn, promotes electrolyte influx via Na+ /K+ /2Cl cotransporter (NKCC) and RVI under hypertonic stress. LRRC8A-S217A mutation impairs channel activation by MSK1, resulting in reduced RVI and cell survival. In summary, LRRC8A is key to bidirectional osmotic stress responses and cell survival under hypertonic conditions.

overall_design: sgRNA counts from HeLa hCas9 cells infected with two lentiviral gRNA libraries (TKO-1 and TKO-2) challenged with hypertonic stress (150 mM NaCl) or kept in regular medium.

first: Eulalia

last: de Nadal


title: RNA sequencing of Streptococcus equi subsp. equi collected from carrier and acute cases

status: Public on May 28 2021

city: College Station

first: Ellen Ruth

middle: Alexander

last: Morris

state: Texas

address: TAMU 4475

institute: Texas A&M University

summary: Streptococcus equi subsp. equi (SEE) is a host-restricted bacterium that causes the common infectious upper respiratory disease known as strangles in horses.  Perpetuation of SEE infection appears attributable to inapparent carrier horses because it does not persist long-term in the environment, infect other host mammals or vectors, and result in short-lived immunity.  Whether pathogen factors enable SEE to remain in horses without causing clinical signs remains poorly understood.  Thus, our objective was to use next-generation sequencing technologies to characterize the transcriptome of isolates of SEE from horses with acute clinical strangles and inapparent carrier horses to assess pathogen-associated changes that might reflect adaptions of SEE to the host contributing to inapparent carriage.  RNA sequencing of SEE isolates from Pennsylvania demonstrated no genes that were differentially expressed between acute clinical and inapparent carrier isolates of SEE.

overall_design: Examination of transcripts from Streptococcus equi subsp. equi isolate collected from inapparent carrier cases and from acute clinical cases.

first: Ellen

middle: R


title: Arf6 regulation of glycolytic metabolism and effector functions in neutrophils

city: Quebec

first: Ezequiel

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

summary: Arf6 is a small GTPase regulating many cellular processes including cytoskeletal remodeling, receptor endocytosis, and phagocytosis of pathogens. Arf6 knockdown in neutrophil (PMN)-like cells was reported to inhibit chemotactic peptide-mediated activation of phospholipase D, the oxidative burst, and 2 integrin-dependent adhesion. In mice, the migration of PMNs knock out for Arf6 to the site of inflammation was diminished and associated with reduced cell surface expression of 2 integrins. Conditional knockout mice lacking Arf6 in PMNs were used to assess the impact of Arf6 depletion on the functions and gene expression profile of PMNs isolated from the mouse air pouch injected with lipopolysaccharide (LPS). The expression of several genes was modulated in PMNs-Arf6 cKO with Lpar6 and Lacc-1 being the most up-regulated and down-regulated genes, respectively. Decreased expressed of Lacc-1 was validated at the protein level in PMN-Arf6 cKO, and silencing of Arf6 in THP-1 monocytic cells delayed LPS-mediated Lacc-1 expression. Here we report that fMLP or zymosan-induced glycolysis and oxygen consumption rate were decreased in air pouch PMNs but not in BM PMNs of Arf6 cKO mice when compared to control floxed cells. Reduced oxygen consumption correlated with decreased production of superoxide and ROS. Depletion of Arf6 in mouse PMNs also reduced phagocytosis and interfered apoptosis. The data suggest that Arf6 regulates energy metabolism, which may contribute to impaired phagocytosis, ROS production, and apoptosis in PMN-Arf6 cKO. This study provides new information on the functions and the inflammatory pathways influenced by Arf6 in PMNs.

overall_design: Leucocytes that have migrated into the mouse air pouches injected with LPS were collected from the Arf6 cKO and the control groups (homozygous Cre+/+ and flox+/+Cre-/- mice, respectively). For each mouse genotype, three independent groups of 5 mice were used. Air pouch PMNs were pooled and purified by negative selection as described above. The cell suspensions were 98% Ly6G positive as estimated by flow cytometry (Supplemental Fig. 1). Mouse PMNs were lysed in TRIzol reagent for total mRNA extraction. RNA extraction and quality check of all RNA samples before the Affymetrix’s GeneChip arrays were performed at the CRCHU of Québec-Laval University Genomics Platform (CHU de Québec-Université Laval Research Center, Québec, QC, Canada). Briefly, 100 ng of total RNA was labeled using FlashTag Biotin HSR (Genisphere, Hatfield, PA) and hybridized on mouse Gene 2.0 ST-Pico Kit (Affymetrix, Santa Clara, CA). Total RNA was used as the input fraction. Arrays were scanned on a GeneChip scanner 3000 G7 (Affymetrix, Santa Clara, CA), . The image data were analyzed by using the Affymetrix Expression Console Software to perform the quality control, the background subtraction and the normalization of probe set intensities with the method of Robust Multiarray Analysis (RMA). Microarray analyses were performed by the CHU de Québec Research Center (CHUL) Gene Expression Platform, Quebec, Canada.

first: Sylvain

middle: G

last: Bourgoin

first: Andrew

middle: Z

last: Leong

first: Chenqi

last: Zhao

first: Emmanuelle

last: Rollet-Labelle

first: Fawzi

last: Aoudji

first: Hiroshi

last: Hasegawa

first: Jouda

last: Gamara

first: Lynn

last: Davis

first: Martin

last: Pelletier

first: Nathalie

last: Pagé

first: Tsunaki

last: Hongu

first: Yasunori

last: Kanaho


title: Glucocorticoid receptor axis in lung cancer

city: Utrecht

first: Stefan

last: Prekovic

address: Universiteitsweg 100

department: CMM

country: Netherlands

institute: UMC Utrecht

summary: To study mechanisms underlying growth arrest by glucocorticoids we performed mRNA sequencing, GR-ChIP sequencing, and 4C.

overall_design: Examination of lung cancer cell transcriptome, GR-chromatin binding, and looping at CDKN1C locus and CERES enhancer following treatment with glucocorticoids.

first: Wilbert

last: Zwart


title: Epigenetic reprogramming mediated by maternal diet rich in omega-3 fatty acids protects from breast cancer development in F1 offspring

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

summary: Diets rich in omega-3 fatty acids have been associated with lowered risks of developing certain types of cancers. We earlier reported that in transgenic mice prone to develop breast cancer (BCa), a diet supplemented with canola oil, rich in omega-3-rich fatty acids (FA) (as opposed to an omega-6-rich diet containing corn oil), reduced the risk of developing BCa, and also significantly reduced the incidence of BCa in F1 offspring. To investigate the underlying mechanisms of the cancer protective effect of canola oil in the F1 generation, we designed and performed the present study with the same diets using BALB/c mice to remove any possible effect of the transgene. First, we observed epigenetic changes at the genome-wide scale in F1 offspring of mothers fed diets containing omega-3 FAs, including a significant increase in acetylation of H3K18 histone mark and a decrease in H3K4me2 mark on nucleosomes around transcription start sites. These epigenetic modifications contribute to differential gene expressions associated with various pathways and molecular mechanisms involved in preventing cancer development, including p53 pathway, G2M checkpoint, DNA repair, inflammatory response, and apoptosis. When offspring mice were exposed to 7,12-Dimethylbenz[a)anthracene (DMBA), the group of mice exposed to a canola oil (with omega 3 FAs)-rich maternal diet showed delayed mortality, increased survival, reduced lateral tumor growth, and smaller tumor size. Remarkably, various genes, including BRCA genes, appear to be epigenetically re-programmed to poise genes to be ready for a rapid transcriptional activation due to the canola oil-rich maternal diet. This ability to respond rapidly due to epigenetic potentiation appeared to contribute to and promote protection against breast cancer after carcinogen exposure.

overall_design: H3K18ac and H3K4me2 profiles of 50 days old BALB/c mice mammary tissues.

first: Philippe

last: Georgel


title: Single cell RNA sequencing of distal lund epithelial cells generated from human induced pluripotent stem cells

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

summary: We perform transcriptomic profiling of a directed differentiation protocol for generating distal lung epithelial cells and alveolar type II epithelial cells (AEC2s) from pluripotent stem cells (PSCs) using bi-fluorescently targeted iPSC cell line BU3-NGST. On day 33 of distal lung differentiation, we sorted SFTPCtdTomato/NKX2-1GFP double positive cells and NKX2-1GFP single positive cells for Fluidigm single cell RNA sequencing analysis. We find canonical AEC2s genes expressed in both sorted populations but at a higher level in the SFTPCtdTomato/NKX2-1GFP double positive population. We also find genes associated with cellular proliferation to be enriched in the NKX2-1GFP single positive population, suggestive of a less mature but more proliferative subset of PSC-derived AEC2s.

overall_design: Global single cell transcriptomic analysis of day 33 PSC-derived distal lung epithelial cell populations identified by NKX2-1GFP and SFTPCtdTomato reporters.

first: Yuliang

last: Sun

first: Darrell

last: Kotton


title: Next Generation Sequencing Facilitates Quantitative Analysis of young nand aged control and Acsl6-/- Transcriptomes

status: Public on May 27 2021

city: Greenville

first: Jessica

middle: M

last: Ellis

state: NC

address: 115 Heart Drive

institute: Department of Physiology at the Bro

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived cerebellar transcriptome profiling (RNA-seq) to determine age-relatined impact of acsl6 deficiency on brain transcriptome profiles.
Methods: Cerebellar mRNA profiles of 2-month and 18-month control and long-chain acyl-coa synthetase 6-knockout (Acsl6) mice were generated and sent to Genewiz for RNAseq analysis
Results: Using an optimized data analysis workflow, we mapped about  3,451,694,754 sequence reads total and ~25-45 million reads per sample of which ~98% were mapped to the mouse genome.
Conclusions: Our study represents the first detailed analysis of cerebellar transcriptomes of Acsl6 knockout mice, compated to controls, at young and old ages.

overall_design: Cerebelum poly-A mRNA profiles of 2-month and 18-month old control and Acsl6-/- mice.


title: The role of SIRT1 in regulation of transcription and splicing in mouse embryonic stem cells

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

summary: SIRT1 is a nuclear enzyme that removes acetyl-groups from target proteins by using NAD+ as a co-substrate. SIRT1 regulates many vital biological processes such as metabolism, stress response, development, and aging. We have previously shown that SIRT1 is critically involved in mouse embryonic stem cell (mESC) maintenance and differentiation in part through modulation of the acetylation status of key transcription factors and their mediated amino acid metabolism and cell signaling. Recent reports have shown that a number of alternative splicing factors are deacetylation substrates of SIRT1. In this study, we aim to understand the total RNA transcriptome, including splicing landscapes, of WT and SIRT1 KO mESCs.

overall_design: Total RNA was extracted from WT and SIRT1 KO mESCs cultured in ESGRO medium in triplicates. All RNA-seq libraries were prepared with the TruSeq Stranded/Ribo kit (Illumina, San Diego, CA) and sequenced using the pair-end 76bp protocol at about 520 million reads per library using the NovaSeq platform (Illumina) per the manufacturer’s protocol.

first: Wei

last: Fan

first: Xiaoling

last: Li


title: Continuous inflammatory stimulation leads via metabolic plasticity to a pro-metastatic phenotype in triple-negative breast cancer cells II

first: Metsada

last: Pasmanik-Chor

first: Dina

last: Morein

first: Linor

last: Rubinstein-Achiasaf

first: Hadar

last: Brayer

first: Orly

last: Dorot

first: Edward

last: Pichinuk

first: Hagar

last: Ben-Yaakov

first: Tsipi

last: Meshel

first: Adit

last: Ben-Baruch


title: GSAP regulates mitochondrial function through Mitochondria-associated ER membrane in the pathogenesis of Alzheimer’s disease

city: New York

first: Peng

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: Gamma-secretase activating protein (GSAP) plays an important role in regulating  gamma-secretase activity and specificity, which contributes to the pathogenesis of Alzheimer’s disease (AD) and Down syndrome. GSAP is expressed in a variety of cell types in the bain. To elucidate the molecular function of GSAP across different cell types in the brain, we performed single nuclei RNA sequencing (sn-RNAseq) on hippocampal tissues obtained from wildtype (WT) and GSAP knockout (GKO) mice. To further investigate the pathogenic function of GSAP in the AD progression, we also determined effects of GSAP gene deletion in the J20 AD mouse model through sn-RNAseq on hippocampal tissues obtained from J20;WT and J20;GKO mice.

overall_design: Single nuclei RNA sequencing was performed using hippocampal tissues from WT (7-month old; 3 mice), GKO (7-month old; 3 mice), J20;WT (6-month old; 1 mouse), and J20;GKO mice (6-month old; 1 mouse).

last: Wang


title: ChIP-Seq of human: SMARCA4 deficient /BRG1-inducible NSCLC isogenic cell lines

first: Antonio

last: Gomez

address: Pg Vall d'Hebron 119-129

department: Rheumatology research Group

institute: VHIR

summary: To study the genome-wide effects of wild type and mutant SMARCA4 and of SAHA on the dynamics of H3K27 modification, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) of SMARCA4, EZH2, H3K27ac and H3K27me3, in the H1299 cell model

first: Octavio

middle: A

last: Romero

first: Montse

last: Sanchez-Cespedes

last: Gomez-Moruno


title: Single Cell Transcriptional Sequencing of Epicardium-Derived Cells and Endothelial Cells During Cardiac Development

city: Rochester

first: Eric

last: Small

address: 601 Elmwood Avenue, Box CVRI

institute: University of Rochester

summary: The goal of this study was to perform transcriptional profiling of single epicardium-derived cells during early cardiac development. Epicardium enriched Wilms Tumor Gene 1 (Wt1) genetic lineage tracing mouse line (Wt1CreERT2/+; R26mTmG) was utilized to collect fluorescently labeled epicardial cells at embryonic day (E) 12.5 and following epicardial-to-mesenchymal transition at E16.5. Additionally, single cell transcriptional profiling was performed in endothelial cells that were collected from Wt1CreERT2/+ mice and Wt1CreERT2/+;MRTF-A-/-;MRTF-Bflox/flox to generate myocardin-related transcription factor A and B gene deletions in the epicardium and evaluate the impact of deleting a mechanosensitive gene program on coronary vasculature development at E14.5. This transcriptional data provides a resource to determine relative mRNA changes in epicardium-derived cells and endothelial cells during significant stages of cardiac development.

overall_design: Evaluation of the transcriptome of single epicardium-derived cells during epithelial-to-mesenchymal transition. Evaluation of single endothelial cells following deletion of a mechanosensitive gene program (MRTF-A and -B deletion) in the epicardium.

first: Pearl

last: Quijada

first: Jacqueline

last: Myers

first: Cameron

last: Baker


title: Disruption of Nipbl/Scc2 in Cornelia de Lange Syndrome provokes cohesin genome-wide redistribution with an impact in the transcriptome

city: Hospitalet de Llobregat

first: Ethel

last: Queralt

state: Barcelona

address: Avenida Gran Via de L'Hospitalet 199

institute: Instituto de Investigación Biomédica de Bellvitge (IDIBELL)

summary: Cornelia de Lange syndrome (CdLS) is a rare disease affecting multiple organs and systems during development. Mutations in the cohesin loader, Nipbl/Scc2 were first described and are the most frequent in clinically diagnosed CdLS patients. The molecular mechanism driving the CdLS phenotypes are not understood. Apart from its canonical role in sister chromatid cohesion, cohesin has also been involved in the regulation of the spatial organization of the genome. Here, we investigated the transcriptome of CdLS-derived primary fibroblasts (gene expression microarray data included in the manuscript as an excel file) and observed the downregulation of genes involved in development and system skeletal organization providing a link to the developmental alterations and limb abnormalities characteristics of the CdLS patients. Genome-wide distribution studies demonstrated a global reduction of Nipbl at the Nipbl-associated high GC content regions in CdLS-derived cells. In addition, cohesin accumulates at Nipbl-occupied sites at CpG islands probably due to reduced cohesin translocation along chromosomes and fewer cohesin peaks colocalize with CTCF.

overall_design: ChIP-seq from control and CdLS patients

first: Patricia

last: Garcia

first: Rita

last: Fernandez-Hernandez

first: Ana

last: Cuadrado

first: Ignacio

last: Coca

first: Jairo

last: Rodriguez

last: Losada


title: Discordant twin PTSD DNA methylation

city: Kelvin Grove

first: Divya

last: Mehta

state: Australia

address: 60 Musk Avenue

country: Australia

institute: Queensland University Of Technology

summary: MZ twins DNA methylation

overall_design: 6 pairs of monozygotic (MZ) twins discordant for PTSD


title: Ribosomal mistranslation activates an age-dependent program of dystrophic muscle wasting

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

summary: Random errors in protein synthesis are prevalent and ubiquitous, yet their effect on organismal health has remained enigmatic for over five decades. We investigated the impact of translation errors by studying whether mice carrying the ribosomal ambiguity (ram) mutation Rps2-A226Y, recently shown to increase the inborn error rate of translation, if at all viable, presented any specific, possibly aging-related phenotype. We introduced Rps2-A226Y using a Cre/loxP strategy. Resulting transgenic mice were mosaic, with tissue-dependent expression of Rps2-A226Y in 5-30% of cells. We observed a muscle-related phenotype with reduced grip strength and body weight. Analysis of gene expression in skeletal muscle using RNA-Seq revealed changes characteristic of muscle dystrophy occurring in an age-dependent manner, involving an interplay of PGC1α, FOXO3, mTOR, and glucocorticoids as key signalling pathways for muscle function and mitochondrial biogenesis. Our results highlight the relevance of translation accuracy, and show how disturbances thereof can contribute to age-related pathologies.

overall_design: mRNA expression profiles of skeletal muscle from Rps2-A226Y mutant mice, expressed under a cre-lox system, and wild type (WT) ubiquitous Cre recombinase expressing mice, at 9 and 15 months of age.

first: Dimitri

last: Shcherbakov

first: Erik

middle: C

last: Böttger


title: The effect of homocysteine on Human Aortic Endothelial Cells

first: Hong

last: Wang

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Multiple cellular compartments engagement in Nicotiana benthamiana-peanut stunt virus-satRNA interactions revealed by systems biology approach

city: Poznań

first: Aleksandra

last: Obrepalska-Steplowska

address: 20 Władysława Węgorka

country: Poland

institute: Institute of Plant Protection - National Research Institute

summary: Virus infection is a process resulting in numerous molecular, cellular, and physiological changes, a wide range of which can be analyzed due to development of many high-throughput techniques. Plant RNA viruses are known to replicate in the cytoplasm; however, the roles of chloroplasts and other cellular structures in the viral replication cycle and in plant antiviral defense have been recently emphasized. Therefore, the aim of this study was to analyze the small RNAs, transcripts, proteins, and phosphoproteins affected during peanut stunt virus strain P (PSV-P)–Nicotiana benthamiana interactions with or without satellite RNA (satRNA) in the context of their cellular localization or functional connections with particular cellular compartments to elucidate the compartments most affected during pathogenesis at the early stages of infection. Moreover, the processes associated with particular cell compartments were determined. The ‘omic’ results were subjected to comparative data analyses. Transcriptomic and small RNA (sRNA)–seq data were obtained to provide new insights into PSV-P–satRNA–plant interactions, whereas previously obtained proteomic and phosphoproteomic data were used to broaden the analysis to terms associated with cellular compartments affected by virus infection. Based on the collected results, infection with PSV-P contributed to changes in the abundance of transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and the cytosol, and the most affected processes were photosynthesis, translation, transcription, and mRNA splicing. Furthermore, sRNA-seq and phosphoproteomic analyses indicated that kinase regulation resulted in decreases in phosphorylation levels. The kinases were associated with the membrane, cytoplasm, and nucleus components.

overall_design: Small RNA analysis concerned 4 samples for control, PSV-P, and PSV-P+satRNA treatments each.

first: Barbara

last: Wrzesinska


title: Single-cell RNA-Seq of mouse thyroid organoid

status: Public on May 26 2021

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

summary: The thyroid gland regulates metabolism and growth via secretion of thyroid hormone by thyroid follicular cells (TFCs). Loss of TFCs, by cellular dysfunction, autoimmune destruction or surgical resection, underlies hypothyroidism. Recovery of thyroid hormone levels by transplantation of mature TFCs derived from stem cells in vitro holds great therapeutic promise. However, the utilization of in vitro derived tissue for regenerative medicine is restricted by the efficiency of differentiation protocols to generate mature organoids. Here, to improve the differentiation efficiency for thyroid organoids, we utilized single-cell RNA-Seq to chart the molecular steps undertaken by individual cells during the in vitro transformation of mouse embryonic stem cells to TFCs. Our single-cell atlas of mouse organoid systematically and comprehensively identifies, for the first time, the cell-types generated during production of thyroid organoids. Using pseudotime analysis, we identify molecular pathways that regulate thyroid maturation in vitro. Our study highlights the potential of single-cell molecular characterization in understanding and improving thyroid maturation, and paves the way for identification of therapeutic targets against thyroid disorders.

overall_design:
One sample, containing a mixture of four different stages of differentiation protocol, was profiled using 10x Chromium pipeline and sequenced to a depth of 100 million reads. Cells from all stages were mixed in a single run and cannot be de-multiplexed.
The mixed cells are separated in silico using known markers of the corresponding stages. This is part of the downstream analysis and will be provided with the manuscript.

middle: P

first: Sabine

last: Costagliola


title: Transcriptome-scale analysis for RNAs of medium length, designated as melRNA-seq

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

summary: More than one million copies of short interspersed elements (SINEs), a class of retrotransposons, are present in the mammalian genomes, particularly within gene-rich genomic regions. Evidence has accumulated that ancient SINE sequences have acquired new binding sites for transcription factors (TFs) through multiple mutations following retrotransposition, and as a result have rewired the host regulatory network during the course of evolution. However, it remains unclear whether currently active SINEs contribute to the expansion of TF binding sites. To study the mobility, expression, and function of SINE copies, we first identified about 2,000 insertional polymorphisms of SINE B1 and B2 families within Mus musculus. Using a novel RNA sequencing method developed here, we detected the expression of SINEs in male germ cells at both the subfamily and genomic copy levels: the vast majority of B1 RNAs originated from evolutionarily young subfamilies, whereas B2 RNAs originated from both young and old subfamilies. DNA methylation and chromatin immunoprecipitation-sequencing (ChIP-seq) analyses in liver revealed that polymorphic B2 insertions served as a chromatin boundary element inhibiting the expansion of DNA hypomethylated and histone hyperacetylated regions, and decreased the expression of neighboring genes. Moreover, genomic B2 copies were enriched at the boundary of ChIP-seq peaks of various histone modifications. A total of > 100 polymorphic B2 insertions, together with >10,000 non-polymorphic B2 copies, were bound by CTCF, a well-known chromatin boundary protein. These results suggest that the currently active B2 copies are mobile chromatin boundary elements that can modulate gene expression level, and are likely involved in epigenomic and phenotypic diversification of the mouse species.

overall_design: This novel sequencing method has been designed for expression analysis of medium length (50-300 bp) RNAs, including those of short interspersed elements (SINEs), a class of retrotransposons. After converting the 5' end of transcribed RNAs into a ligatable end, libraries were prepared by a protocol almost same as that for small RNA sequencing. Single-end 300 bp sequencing yielded sequences of the whole length of RNAs.


title: Terminal uridyltransferase 7 regulates TLR4-triggered inflammation by controlling Regnase-1 mRNA uridylation and degradation [TAIL-Seq]

city: Taipei

first: Li-Chung

last: Hsu

address: No.7, ChungShan S. Rd., ZhongZheng Dist.

department: Graduate institute of Molecular Medicine

country: Taiwan

institute: National Taiwan University

summary: We revealed that the transcriptome of the mammalian cells under inflammatory status using TAIL-Seq. The reads from wild-type and Tut7-/- BMDMs were mapped to RefSeq mm10 using HISAT2 and trimmed illumina adapter sequences. Finally, using the specific sequences, including Zc3h12a and Il6 to filter out the sequences, and  linker-1 to extract the sequences we interested.

overall_design: LPS-induced BMDMs mRNA profiles of 7-week-old wild type and Tut7-/- mice were generated by deep sequencing, in duplicate, using Illumina Illumina Hiseq 2000 PE2*150

first: Chia-Ching

last: Lin


title: Dosage-dependent differential transcriptomic changes in the prefrontal cortex of heterozygous and homozygous Shank2-mutant mice

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

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

country: South Korea

institute: IBS/KAIST

summary: Shank2 is an abundant postsynaptic scaffolding protein known to regulate excitatory synaptic assembly and function and is implicated in autism spectrum disorders (ASD). Whereas patient Shank2 mutations in autistic individuals are heterozygous, Shank2 functions studied in mice have mainly relied on the results from homozygous mutant mice, largely because of relatively strong synaptic and behavioral phenotypes. Moreover, although synaptic changes at juvenile and adult Shank2-mutant mice seem to be largely similar, it remains unclear whether there are any age-dependent changes across these stages at the molecular level. To address these questions, we attempted RNA-Seq analyses of the transcriptomes in the prefrontal cortex of both heterozygous and homozygous Shank2-mutant mice lacking exons 6 and 7 at juvenile and adult stages. The results indicate that heterozygous, but not homozygous, juvenile Shank2-mutant mice show strong transcriptomic changes that promote excitatory synaptic transmission and suppress ASD-related gene expressions. In contrast, adult Shank2-mutant mice show largely similar and dosage-dependent transcriptomic changes.

overall_design: Transcriptome analysis of Shank2 heterozygote and homozygous mutant and wild-type mice at ages of 3 week and 12 week

first: Eunee

last: Lee

first: Seungjoon

first: Hyojin

last: Kang


title: Single Cell RNA-Seq of the embryonic day 14.5 genital tubercle

city: Gainesville

first: Martin

last: Cohn

state: Fl

address: 2033 Mowry rd

department: Molecular Genetics and Microbiology

institute: Univerisity of Florida

summary: Characterize the cellular diversity of the embryonic genital tubercle before sexual dimorphic morphogenesis in male and female mice.

overall_design: Genital tubercles were harvested from pregnant female mice on embryonic day 14.5.  Embryos were dissected out in ice-cold Dulbecco’s phosphate-buffered saline and a small amount of tissue was taken for genotyping. The embryo was placed into RPMI 1640 medium (Thermo Fisher Scientific, 11875093) on ice for 2 hours while the genotyping for sex took place. After genotyping results were finished three male and three female embryos were chosen from 2 litters and pooled by sex. The genital tubercles were then dissected from the body and placed into 1.3mg/ml collagenase XI (Sigma-Aldrich, C7657-25MG) on ice. Collagenase XI was made by first dissolving 13mg into 1ml TESCA buffer at 37°C for 5 minutes and then further diluting to 1.3mg/ml in 10% inactivated fetal bovine serum/ Dulbecco’s phosphate-buffered saline. The genital tubercles were chopped into small pieces using forceps while in 500μl collagenase XI on ice. The entire 500μl of collagenase XI and tissue was collected and placed into a 1.5ml microcentrifuge tube for remainder of digestion.  Cells were agitated at 37°C for 30 mins and tritrated with a glass pipettes every 5 mins. After digestion, cells were centrifuged at 500rpm for 5 minutes at 4°C, then were was resuspended in 100ul of magnesium and calcium free 1xPBS with 0.04% bovine serum albumin, filtered through a 40μm strainer (Flowmi Bel-Art H13680-0040), and placed on ice.  Male and female samples were loaded separately for encapsulation, synthesis and amplification of barcoded cDNAs (10X Next GEM Single Cell 3’ Gel Bead Kit v3.1). After QC, Illumina libraries (Next GEM SC 3’ Library Kit v3.1) were sequenced on an Illumina NexSeq 500/550 using 2x150bp paired-end reads at a targeted depth of 25K reads per cell.    Libraries were prepared using Chromium Single Cell Library kit V3 (10x Genomics) following standard protocol and sequenced on an Illumina NextSeq using 150 bp paired-end sequencing.


title: Metabolic control of Tfh and humoral immunity by phosphatidylethanolamine

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: Cytidine diphosphate (CDP)-ethanolamine pathway of phospholipid metabolism coordinates metabolic programming of Tfh cell responses and humoral immunity.

overall_design: Microarray analysis of 6 Samples; Pcyt2KO treated with LCMV for 3 days (n =3) and Non Targerting control treated with LCVM for 3 days (n = 3)

first: Guotong

last: Fu

first: Yogesh

last: Dhungana

first: Hao

last: Shi


title: RNA sequencing in ovarian cancer cell line HEYA8 in terms of ECM1 silencing and reintroduction of ECM1 subtypes ECM1a and ECM1b

city: Shanghai

first: Gong

last: Yang

address: Dong'an Rd

institute: Fudan Univesity Shanghai Cancer Center

summary: Extracellular Matrix Protein-1 (ECM1) promotes tumorigenesis in multiple organs, but the mechanisms associated with the functions and putative receptors of ECM1 subtypes have yet to be systematically clarified. We found in this study that secretory ECM1a functions as an oncoprotein to induce tumorigenesis through binding of the Gly-Pro-Arg (GPR) motif to integrin aXb2 and activation of AKT/FAK/Rho/cytoskeletal signaling. Nonsecretory ECM1b binds to myosin to block myosin phosphorylation, thus preventing cytoskeletal signaling activation and tumorigenesis. Based on RNA sequencing, we further found that the heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) protein induced by ECM1a favors the alternative mRNA splicing of ECM1a to control ECM1-associated signaling and tumorigenesis. ATP binding cassette subfamily G member 1 (ABCG1) transduces ECM1a-integrin aXb2 interactive signaling to facilitate the phosphorylation of AKT/FAK/Rho/cytoskeletal molecules and to confer cisplatin resistance in cancer cells through upregulation of CD326-mediated cell stemness.

overall_design: Alteration of mRNA profiles by silencing of ECM1 and reintroduction of ECM1a and ECM1b

first: Yang

last: Gong

first: Ren

last: Chunxia

first: Yin

last: Huijing

first: Wang

last: Jingshu

first: Li

last: Hui

first: Yu

last: Jinjue


title: Analysis of the oxidative stress regulon identifies soxS as a genetic target for resistance reversal in multi-drug resistant Klebsiella pneumoniae

city: Columbia

first: Sathesh

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

summary: In bacteria the defence system to counter oxidative stress is orchestrated by three transcriptional factors – SoxS, SoxR and OxyR. Although the transcriptional regulon of these factors are known in many bacteria, similar data is not available for K. pneumoniae. To address this data gap, oxidative stress was induced in K. pneumoniae MGH 78578 using paraquat and the corresponding regulon was identified using RNA-seq. Since soxS was significantly induced , a soxS mutant was constructed to decipher this regulon in K. pneumoniae MGH75878. The ‘oxidative SoxS regulon’, comprising common genes differentially regulated genes in oxidative and soxS regulon was identified from both regulons – characterised a stringent group of genes which were regulated by SoxS during oxidative stress. Efflux pump encoding genes like acrAB-tolC, acrE along with marRABwere identified in the oxidative SoxS regulon. The phenotypic effect of the observed efflux pump regulation was confirmed in the soxS mutant that exhibited  an 2 fold reduction in the minimum bactericidal concentration (MBC) against tetracycline compared to that of the isogenic wild type. Impaired efflux activity, allowing tetracycline to be accumulated in the cytoplasm to bactericidal levels, was further confirmed using tetraphenylphosphonium (TPP+) ion accumulation assay. The susceptibility of the soxS mutant against tetracycline was also apparent in vivo, in the zebrafish embryo model. We conclude that the soxS gene could be considered as a genetic target against which an inhibitor could be developed and be used in combinatorial therapy with tetracycline to combat infections associated with multi-drug resistant K. pneumoniae.

overall_design: Bacterial transcriptomic profile generated by inducing oxidative stress by exposing the culture to Paraquat, deep sequencing, in duplicates, using Illumina HiSeq2500.

first: João

last: Anes

first: Katherine

last: Dever

first: Athmanya

last: Eshwar

first: Scott

last: Nguyen

last: Cao

first: Sandra

last: Sakalauskaitė

first: Angelika

last: Lehner

first: Stephanie

last: Devineau

first: Rimantas

last: Daugelavičius

first: Séamus

last: Fanning

first: Shabarinath

last: Srikumar


title: Distinct Lineage Derived Chondrocytes From Isogenic Human Peripheral Blood Induced Pluripotent Stem Cells For Articular Cartilage Regeneration

city: Madison

first: Ming-Song

last: Lee

state: WI

address: 2715 Marshall CT., Apt 319

institute: UW-Madison

summary: We report the application of next-generation sequencing (NGS) to analysis the gene expression profile among three different cells:iPSC-MC-Ch, iPSC-NCC-Ch and primary chondrocyte. Our results shown that iPSC-MC-Chs were more similar to iPSC-NCC-Chs than primary chondrocytes.

overall_design: To define which lineage derived chondrocyte is the best for generating hyaline cartilage, human iPSCs were differentiated into mesodermal and ectodermal lineage cells and further induced to chondrocytes.

first: Wan-Ju

last: Li

first: Mark

last: Berres


title: Genome-scale CRISPR-Cas9 screen of Wnt/β-catenin signalling identifies therapeutic targets for Colorectal Cancer (ChIP-seq)

city: Clayton

first: Ron

last: Firestein

state: VIC

address: 21 Wright street

department: CCR

institute: Hudson Institute of Medical Research

summary: Using genome-scale CRISPR-Cas9 screening, our study revealed KMT2A as a critical regulator of β-catenin-driven CRC progression. To determine the role of KMT2A in β-catenin-mediated transcription, control and KMT2A-ablated DLD1 and SW480 colorectal cancer (CRC) cells were subjected to CHIP-seq analysis using anti-β-catenin and anti-H3K4me3 antibodies. Data obtained from the CHIP-seq experiments indicated a key role of KMT2A in β-catenin binding on active promoters.

overall_design: Examine the impact of KMT2A knockout on β-catenin binding and H3K4me3 modification.

first: Sylvia

last: Mahara

first: Chunhua

last: Wan

first: Claire

middle: X

last: Sun


title: Genome-scale CRISPR-Cas9 screen of Wnt/β-catenin signalling identifies therapeutic targets for Colorectal Cancer (RNA-seq)

summary: To identify novel regulators and therapeutic targets of β-catenin-driven colorectal cancer development, genome-scale CRISPR-cas9 screens of Wnt/β-catenin were conducted and identified KMT2A as a key player of β-catenin-driven CRC progression. RNA-seq data was integrated with CHIP-seq and other experiments to assess the effect of KMT2A knockout on the transcriptomic profiling of CRC cells.

overall_design: 1) RNA samples from triplicates of NTC sgRNA-targeting DLD1 cells; 2) RNA samples from triplicates of two different KMT2A sgRNA-targeting DLD1 cells


title: Gene expression profiles in BMDM cells of Trex1-KO and wild-type mice after treatment of STING antagonists

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: Mounting evidence demonstrates that cGAS-STING signaling is the major pathway in sensing cytosolic DNAs. However, aberrant accumulation of self DNA molecules in Trex1 (a 3'-to-5' DNA exonuclease) deficient cells usually causes over-activation of cGAS-STING signaling, which is associated with the pathology of several autoimmune diseases. Here, we investigated gene expression changes in BMDM cells of Trex1 knockout mice after manipulating cGAS-STING signaling activity via treatment of two STING antagonists (SN-011 and H151) .

overall_design: Total RNA in BMDM cells of Trex1-KO and wild-type mice after treatment of STING antagonists was isolated and sequenced by deep sequencing using Illumina HiSeq 2500

first: Ze

last: Hong

first: Jiahao

last: Mei


title: Mechanical Strain Drives Myeloid Cell Differentiation Toward Pro-Inflammatory Subpopulations

status: Public on May 25 2021

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

summary: We quantify the effects of mechanical strain on three-dimensional (3D) cultured mouse myeloid cells at the cellular and transcriptomic level using single cell RNA-sequencing. We demonstrate that mechanical stress induces pro-inflammatory fates.

overall_design: scRNA-seq was performed on mouse myeloid cells from 5 mice in physiologically relevant, 3-dimensional, in vitro, collagen scar systems

first: Dominic

last: Henn

first: Geoffrey

last: Gurtner


title: Loss of TARBP2 Drives the Progression of Hepatocellular Carcinoma via miR-145-SERPINE1 Axis

city: Chicago

first: Issam

last: Awad

state: IL

address: 5841 S. Maryland Avenue

department: Department of Neurology

institute: The University of Chicago

summary: The clinical outcomes of hepatocellular carcinoma (HCC) remain dismal. Elucidating the molecular mechanisms for the progression of aggressive HCC holds the promise for developing novel intervention strategies. The transactivation response element RNA-binding protein (TRBP/TARBP2), a key component of microRNA (miRNA) processing and maturation machinery has exhibited to play conflicting roles in tumor development and progression. We sought to investigate the expression of TARBP2 in HCC using well-characterized HCC cell lines, patient-derived tissues and blood samples. Additionally, the potential prognostic and diagnostic value of TARBP2 in HCC were analyzed using Kaplan-Meier plots and ROC curve. Cell counting kit‐8 (CCK‐8), wound healing and transwell assays examined the ability of TARBP2 to induce cell proliferation, migration, and invasion in HCC cell lines. RNA sequencing was applied to identify the downstream elements of TARBP2. The interaction of potential targets of TARBP2, miR‐145 and serpin family E member 1 (SERPINE1), was assessed using luciferase reporter assay. TARBP2 expression was down-regulated in HCC cell lines relative to normal hepatocyte cells, with a similar pattern further confirmed in tissue and blood samples. Notably, the loss of TARBP2 was demonstrated to promote proliferation, migration, and invasion in HCC cell lines. Interestingly, the reduction of TARBP2 was shown to result in the upregulation of SERPINE1, also known as plasminogen activator inhibitor (PAI-1), which is a vital gene of the HIF-1 signaling pathway. Knockdown of SERPINE1 rescued the TARBP2-lost phenotype. Moreover, TARBP2 depletion induced the upregulation of SERPINE1 through reducing the processing of miR-145, which directly targets SERPINE1. Finally, overexpression of miR-145 repressed SERPINE1 and rescued the functions in sh-TARBP2 HCC cells. Our findings underscore a linear TARBP2-miR-145-SERPINE1 pathway that drives HCC progression, with the potential as a novel intervention target for aggressive HCC.

overall_design: The purpose of this study is to investigate whether TARBP2 was dysregulated in HCC patients and correlated with progosis. We utilized RNA-Seq to identify potential downstream gene players and their functional relevance.

first: Wei

last: Zhang

first: Chang

first: Liman

first: Songmei

last: Liu


title: Terminal uridyltransferase 7 regulates TLR4-triggered inflammation by controlling Regnase-1 mRNA uridylation and degradation

first: Li-Chung

last: Hsu

summary: We revealed that the transcriptome of the mammalian cells under inflammatory status using RNA Sequencing (RNA-Seq). The transcriptome of BMDMs from wild-type and Tut7-/- was compared to baseline. The fold-change was presented by the logarithm of p-values to the base 2 and the significance was presented by the negative logarithm of that to the base 10.  log2FC > +0.2 and log2FC < -0.2 indicate the increase of transcript levels by >20% and decreased by >20%, respectively. Among the 352 genes, 111 of them involving in innate immune response were downregulated in Tut7-/- cells.

overall_design: LPS-induced BMDMs mRNA profiles of 7-week-old wild type and Tut7-/- mice were generated by deep sequencing, in duplicate, using Illumina HiSeq PE150

first: Chia-Ching

last: Lin


title: Transcriptome profiling of cytomegalovirus-infected guinea pig placenta.

city: Minneapolis

first: Craig

middle: John

last: Bierle

state: Minnesota

address: 2001 6th Street SE

department: Pediatrics

institute: University of Minnesota

summary: We report the transcriptomes of gunea pig cytomegalovirus (GPCMV)- and mock-infected placentas.

overall_design: Time-mated guinea pigs were either infected with 2E5 PFU of GPCMV or injected with PBS. After animals were euthanized at 21 days post-infection, samples of placenta were stored in RNAlater until RNA extraction and next-generation sequencing.

first: Zachary

middle: W

last: Berkebile

first: Dira

middle: S

last: Putri

first: Juan

last: Abrahante


title: Tumor-associated hematopoietic stem and progenitor cells positively linked to glioblastoma progression

city: Essen

first: Sied

last: Kebir

address: Hufelandstr. 55

institute: DKFZ-Division Translational Neurooncology at the West German Cancer Center (WTZ)

summary: Brain tumors are typically immunosuppressive and refractory to immunotherapies for reasons that remain poorly understood. The unbiased profiling of immune cell types in the tumor microenvironment may reveal immunologic networks affecting therapy and course of disease. Here we identify and validate the presence of hematopoietic stem and progenitor cells (HSPCs) within tumor tissues that are positively linked to glioblastoma malignancy. In contrast to the medullary hematopoietic compartment, tumor-associated HSPCs are comprised of a majority of CD38- immature cells, such as hematopoietic stem cells and multipotent progenitors, express genes related to glioblastoma progression and display patterns of accelerated cell cycle. When cultured ex vivo, tumor-associated HSPCs form prevalently myeloid colonies, suggesting potential in situ myelopoiesis. In experimental models, HSPCs promote tumor cell proliferation, expression of the immune checkpoint PD-L1 and secretion of tumor promoting cytokines such as IL-6, IL-8 and CCL2, indicating concomitant support of both malignancy and immunosuppression. Additionally, the frequency of tumor-associated HSPCs is prognostic for patient survival and correlate with immunosuppressive phenotypes. These findings identify a new element in the complex landscape of glioblastoma that may serve as an independent prognostic factor or target for brain tumor immunotherapies.

overall_design: Examination of single-cell transcriptomics from tumor-associated HSPCs and canonical HSPC

first: Igor

last: Cima

first: Celia

last: Dobersalske


title: Single cell RNA sequencing of mock and RV1A infected human airway epithelial organoids

city: New Haven

first: Ellen

middle: F

last: Foxman

state: Connecticut

address: 333 Cedar Street

department: Department of Laboratory Medicine

institute: Yale University

summary: We used single cell RNA sequencing to retrieve transcriptomics of different cell types in human airway epithelial organoids following RV1A infection. By aligning the raw reads to the viral genome,  we also quantified viral RNA copies in each cell. The sequencing obtained transcription profile of 6260 cells with 53153 mean reads per cell in the mock sample, and 5727 cells with 61652 mean reads in the RV1A infected sample, before filtering in downstream analysis. We found that RV1A copies is only detected in a small proportion of the entire cell population, however, nearly all cells regardless of cell types showed ISG induction when comparing the mock and RV1A infected sample. We also characterized the expression profile genes related to viral entry: RV1A receptors of LDLR family are ubiquitously expressed in the culture.

overall_design: Single cell transcriptomics in mock and RV1A infected sample 5 day post infection

first: Valia

last: Mihaylova

first: Guilin

last: Wang

first: Bao


title: KRT18 regulates the alternative splicing of cell proliferation and apoptosis genes via splicing factors in gastric cancer cells and clinical samples

city: Wuhan

first: Dong

last: Chen

state: Hubei

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

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: We knocked down KRT18 in AGS cells using siRNAs to study KRT18-regulated genes using RNA-seq technology, followed by analysis of KRT18-regulated splicing factors in transcription and posttranscriptional level.

overall_design: Transcriptional analysis of KRT18 knockdown and control in AGS cells.

first: Biao

first: Ximing

last: Xu

first: Dan-dan

first: Xin

first: Yang-tao

first: Wei-guo

last: Dong


title: An unbiased machine learning exploration reveals gene sets predictive of allograft tolerance after kidney transplantation

status: Public on Jun 04 2021

city: Boston

first: Qiang

last: Fu

state: Massachusetts

address: 55 Fruit St.

institute: Massachusetts General Hospital

type:
Expression profiling by array
Third-party reanalysis

summary: Efforts at finding potential biomarkers of tolerance after kidney transplantation have been hindered by limited sample size, as well as the complicated mechanisms underlying tolerance and the potential risk of rejection after immunosuppressant withdrawal. In this work, three different publicly available genome-wide expression data sets of peripheral blood lymphocyte (PBL) from 63 tolerant patients were used to compare 14 different machine learning models for their ability to predict spontaneous kidney graft tolerance. We found that the Best Subset Selection (BSS) regression approach was the most powerful with a sensitivity of 91.7% and a specificity of 93.8% in the test group, and a specificity of 86.1% and a sensitivity of 80% in the validation group. A feature set with five genes (HLA-DOA, TCL1A, EBF1, CD79B, and PNOC) was identified using the BSS model. EBF1 downregulation was also an independent factor predictive of graft rejection and graft loss. An AUC value of 84.4% was achieved using the two-gene signature (EBF1 and HLA-DOA) as an input to our classifier. Overall, our systematic machine learning exploration suggests novel biological targets that might affect tolerance to renal allografts, and provides clinical insights that can potentially guide patient selection for immunosuppressant withdrawal.

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overall_design: Total of 31 Tolerant (TOL) participants, 39 Standard Immunotherapy (SI) participants, and 24 Healthy Controls (HC)

first: Divyansh

last: Agarwal

first: Kevin

last: Deng

first: Rudy

last: Matheson

first: Liang

last: Wei

first: Qing

last: Ran

first: Hongji

last: Yang

first: Shaoping

first: James

last: Markmann


title: Loss of BAF complex in developing cortex perturbs radial neuronal migration in a WNT signaling-dependent manner

status: Public on May 23 2021

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: We performed RNA-Seq from postnatal cortical tissue at stage P1 from controls and BAF double knock-out (dcKO) mice.

overall_design: Postnatal cortical tissue at stage P1 from controls and BAF double knock-out (dcKO) mice

first: Cemil

last: Kerimoglu


title: Single-cell microRNA sequencing method comparison and profiling of cell lines and circulating lung tumor cells

city: Saarbrücken

first: Tobias

last: Fehlmann

address: Campus E2 1

institute: Saarland University

summary: In a stepwise approach, we evaluated available protocols before performing an analysis on circulating tumor cells of small cell lung cancer patients. We first compared 19 protocols on single MCF7 cells spiked miRExplore. Second, we analyzed MCF7 single cell equivalents of the eight best protocols. Third, we carried out single cell small RNA sequencing using the best performing protocol on 8 cell lines and 67 circulating tumor cells from seven small cell lung cancer patients.

overall_design: Single cell miRNA-Seq /w 19 protocols, miRExplore spike-in, single cell equivalents, 8 cell lines and 67 circulating tumor cells

first: Sarah

last: Hücker

first: Andreas

last: Keller

first: Stefan

last: Kirsch


title: Loss of histone methyltransferase ASH1L in the developing mouse brain causes autistic-like behaviors

city: East Lansing

first: Jin

last: He

state: Michigan

address: 603 Wilson Road, Biochem Bldg. Rm. 410

institute: Michigan State Univeristy

summary: Autism spectrum disorder (ASD) is a neurodevelopmental disease associated with various gene mutations. Recent genetic and clinical studies report that mutations of the epigenetic gene ASH1L are highly associated with human ASD and intellectual disability (ID). However, the causality and underlying molecular mechanisms linking ASH1L mutations to genesis of ASD/ID remains undetermined.  Here we show loss of ASH1L in the developing mouse brain is sufficient to cause multiple developmental defects, core autistic-like behaviors, and impaired cognitive memory. Gene expression analyses uncover critical roles of ASH1L in regulating gene expression during neural cell development. Thus, our study establishes a new ASD/ID mouse model revealing the critical function of an epigenetic factor ASH1L in normal brain development, a causality between Ash1L mutations and ASD/ID-like behaviors in mice, and potential molecular mechanisms linking Ash1L mutations to brain functional abnormalities.

overall_design: Examine the differential gene expression between wild-type and Ash1L-KO neural pregenitor cells during induced differentiation in vitro


title: Single-cell RNA-seq reveals fibroblast heterogeneity and increased mesenchymalfibroblastsin human skin fibrotic diseases

city: GuangZhou

first: Hobart

last: Hu

state: GUangDong

address: Road LuJing

institute: Dermatology Hospital of Southern Medical University

summary: Skin fibrotic disease representsa major global healthcare burden, characterized by fibroblast hyperproliferation and excessive accumulation of extracellular matrix.Fibroblasts are found to be heterogeneous in multiple fibrotic diseases,but the fibroblast heterogeneity of skin fibrotic diseases remains unknown.In this study, we performed single-cell RNA-seq in keloid, a paradigm of skin fibrotic diseases, andnormal scardermis tissues.Our results indicate that keloid and normal scar fibroblasts could be divided into 4 subpopulations: secretory-papillary, secretory-reticular, mesenchymal and pro-inflammatory.The percentage of mesenchymal fibroblast subpopulationincreased significantly in keloid compared to normal scar. Interestingly, we also found increasing mesenchymal fibroblast subpopulation in scleroderma, another skin fibrotic disease.Function studies showed that the mesenchymal fibroblasts promoted collagen synthesis of the other fibroblasts in keloid partiallythrough secreting POSTN. These findings will help us understandskin fibroticpathogenesis in depth,and provided potential target cells for fibrotic diseases therapies.

overall_design: We just used dermis for scRNA-seq analysis because keloid represents a skin dermis fibrosis disease. After stringent quality control, we obtained transcriptomes of 40655 cells (Keloid(nsample=3): 21488; Normal scar(nsample=3):19167).

first: Cheng-Cheng

first: Yongfei

first: Ding-Heng

last: Zhu


title: The impacts of microbiome and microbiota-derived sodium butyrate on Drosophila transcriptome and metabolome revealed by multi-omics analysis

status: Public on May 24 2021

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Drosophila melanogaster was used to investigate the influence of microbiota-derived intestinal flora and its metabolites on host transcriptional regulation by adding sodium butyrate to a sterile diet for constructing a sterile Drosophila model. In order to further investigate the effects of sodium butyrate on Drosophila melanogaster at the molecular mechanism level, we detected the abundance and composition of midgut microbial colonies based on 16S rRNA gene sequences, and analyzed the overall structure and metabolic activities of host transcriptional networks by combining transcriptome and non-target metabolomics data.

sample_organism:
Drosophila melanogaster
insect gut metagenome

overall_design: Drosophila were reared in bacteria and sterile environment, respectively, and sodium butyrate was added to diet. Drosophila RNA-seq and midgut 16S rDNA were performed to study the effects of intestinal microflora and its metabolites on host transcription and metabolic regulation.

first: Fan

last: Zhou

first: Biaodi

last: Liu

first: Guanzheng

last: Luo


title: A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes.

city: Oxford

first: Thomas

last: Milne

address: MRC MHU, WIMM, John Radcliffe Hospital

department: Radcliffe Department of Medicine

institute: University of Oxford

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

overall_design: Refer to individual Series


title: Common features of aging fail to occur in Drosophila raised without a bacterial microbiome

status: Public on May 22 2021

city: Bethesda

first: Edward

last: Giniger

state: MD

address: Bldg 35,Rm 1C-1002; 35 Convent Dr

department: NINDS

institute: NIH

summary: By comparing the transcriptomes of Drosophila raised either under conventional conditions or in the complete absence of bacteria, we find that 70% of the transcriptional changes that normally occur with age are actually adaptive responses to the microbiome, not unavoidable features of aging. In the germ-free state, these seemingly ‘age-dependent’ gene expression changes never happen.

overall_design: Total RNA was isolated from the heads of wild type Drosophila grown either under conventional conditions (3, 10, 30 and 45 days old) or in the presence of antibiotics (10, 30 and 45 days old). Genome-wide gene expression was assayed using Affymetrix DroGene 1.0 ST microarrays, and data was analyzed as described in the associated manusript.

first: Kory

last: Johnson


title: Trimethylamine oxide is a new plant signaling molecule that mediates abiotic stress tolerance

city: Madrid

first: Rafa

last: Catalá

address: C/Ramiro de Maeztu n9

department: Biotechnology

institute: Centro de Investigaciones Biologicas

summary: We report the identification of RCI5, an Arabidopsis cold inducible gene encoding a FMO. RCI5 seems to participate in the biosynthesis of TMAO, a new plant methabolite. We also demonstrate that TMAO positevely controls Arabidopsis tolerance to low temperature, high salt in the soil and drough stress, by promoting a wide transcriptomic reprograming of stress-relate genes. Finally, we found that diferent crops also contain TMAO in their tissues, and that exogenous applications of TMAO also increases tomato tolerance to abiotic stress.

overall_design: Transcriptomic profiling through RNAseq of Col-0 and FMO5-OE T1 plants under control conditions.

first: Rafael

first: Rosa

last: López-Cobollo

first: Julio

last: Salinas


title: Effects of Engineered Nanomaterials on Mouse Airways: Assessment of 28 Nanomaterials.

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: C57BL/6 mice were exposed by oropharyngeal aspiration to 28 nanomaterials including different surface functionalizations on 4 concecutive days with the dose of 10ug/day. Total RNA was collected  from the mice lung biopsies after sacrificing.

overall_design: DNA microarrays were utilised to study the transcriptional changes of the the mice lung biopsies exposed to nanomaterial. Phosphate buffered saline (PBS) without nanomaterial was used as negative control. Each condition was performed in triplicate.

first: Pia

last: Kinaret

first: Joseph

last: Ndika

first: Marit

last: Ilves

first: Henrik

last: Wolff

first: Gerard

last: Vales

first: Hannu

last: Norppa

first: Kai

last: Savolainen

first: Tiina

last: Skoog

first: Juha

last: Kere

first: Bengt

last: Fadeel

first: Piia

last: Karisola

first: Harri

last: Alenius


title: Immunological and pathological landscape of dengue serotypes 1-4 infections in immune-competent mice [liver]

city: Riverside

first: Juliet

last: Morrison

state: CA

address: 900 University Avenue

department: Microbiology and Plant Pathology

country: USA

institute: University of California, Riverside

summary:
In this study, we show that the host response to DENV1-4 infection in immunocompetent mice recapitulates transcriptional and immunological changes that have been described in human studies.
Dengue virus (DENV), a Flavivirus, causes a broad spectrum of disease in humans with key clinical signs including thrombocytopenia, vascular leakage and hemorrhaging. A major obstacle to understanding DENV immunity has been the lack of a validated immune-competent mouse model. Here, we report the infection profiles of human clinical isolates of DENV serotypes 1-4 in an immune-competent mouse model. We detected replicating DENV in the peritoneal cells, liver and the spleen that was generally resolved within 2 weeks. The DENV target cell types for infection were monocytes/macrophages, dendritic cells, endothelial cells, and we identified a novel DENV cellular target, fibroblast reticular cells of the spleen. We observed gross pathologies in the spleen and liver that are consistent with dengue disease, including hemorrhaging as well as transcriptional patterns suggesting that antiviral responses and tissue damage were induced. Key clinical blood parameters that define human DENV disease such as hemoconcentration, leukopenia and reduced number of platelets were also observed. Thus, immune-competent mice sustain replicating infection and experience signs, such as hemorrhaging, that define DENV disease in humans. This study thoroughly characterizes DENV1-4 infection in immune-competent mice and confirms the wild-type mouse model as a valid and reproducible system for investigating the mechanisms of DENV pathogenesis.

overall_design: Gene expression in liver and spleen were measured on days 1 and 3 post mock infection or infection with DENV1, 2, 3 or 4. Three mice were profiled for each treatment category and timepoint.

first: Ashley

middle: L


title: Immunological and pathological landscape of dengue serotypes 1-4 infections in immune-competent mice [spleen]


title: Structure, composition and evolution of the nonvital B chromosome of maize

first: Handong

last: Su

address: No.1,Shizishan Street · Hongshan District

country: China

institute: Huazhong Agricultural University

summary: To determine the centromere of the maize B chromosome, we used previously published anti-CENH3-ChIP-seq data from TB-9Sb, which contain a complete functional B centromere. Distribution of centromere-specific DNA repeats, including CentC, CRM element and B-repeat, were observed in the proximal end of the assembled maize B chromosome, and this region was shown to be associated with CENH3 nucleosomes. Furthermore, six small scaffolds with sizes ranging from 10 to 174 kilobase display CENH3 enrichment, also with the distribution of these repeat sequences. These results were consistent with previously cytogenetic observation. Therefore, approximately 520 kb centromeric regions were determined in the assembled maize B chromosome.

overall_design:
MNase-seq was carried out using material from young leaves of B73 +2B.
------------------------------
*This dataset consists of 1 control sample only

first: Fangpu

last: Han

first: James

last: Birchler


title: Genome-scale CRISPR-Cas9 screen of Wnt/β-catenin signalling identifies therapeutic targets for Colorectal Cancer

city: Clayton

first: Ron

last: Firestein

address: 21 Wright street

institute: Hudson Institute of Medical Research


title: Regulatory KIR+RA+ T cells accumulate with age and are highly activated during viral respiratory disease

status: Public on May 21 2021

city: Bilthovem

first: Rob

last: Mariman

address: Antonioe van Leeuwenhoeklaan 9

institute: RIVM

summary: Severe respiratory viral infectious diseases such as influenza and COVID- 19 espe-cially affect the older population. This is partly ascribed to diminished CD8+ T- cell re-sponses a result of aging. The phenotypical diversity of the CD8+ T- cell population has made it difficult to identify the impact of aging on CD8+ T- cell subsets associated with diminished CD8+ T- cell responses. Here we identify a novel human CD8+ T- cell subset characterized by expression of Killer- cell Immunoglobulin-l ike Receptors (KIR+) and CD45RA (RA+). These KIR+RA+ T cells accumulated with age in the blood of healthy individuals (20– 82 years of age, n = 50), expressed high levels of aging- related mark-ers of T- cell regulation, and were functionally capable of suppressing proliferation of other CD8+ T cells. Moreover, KIR+RA+ T cells were a major T- cell subset becoming activated in older adults suffering from an acute respiratory viral infection (n = 36), including coronavirus and influenza virus infection. In addition, older adults with influ-enza A infection showed that higher activation status of their KIR+RA+ T cells associ-ated with longer duration of respiratory symptoms. Together, our data indicate that KIR+RA+ T cells are a unique human T- cell subset with regulatory properties that may explain susceptibility to viral respiratory disease at old age.

overall_design: KIR+RA+, NKG2A+RA+, TNAIVE, and TEMRA cell subsets were sorted from healthy donor PBMCs (n = 6) and their gene expression profiles were analyzed by  Next-Generation Sequencing using the Illumina Nextseq

first: Teun

last: Guichelaar

first: Daan

last: Pieren


title: Multiplexed functional genomic analysis of somatic 5’ untranslated region mutations across the spectrum of human prostate cancer (Exome-Seq)

status: Public on May 20 2021

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: The functional consequences of cancer patient-derived genetic variants within the 5’ untranslated regions (UTRs) on a genome-wide scale and their effects on mRNA transcript and translation levels are poorly understood. To systematically interrogate the mutational landscape of 5’ UTRs across cancer patients with localized to metastatic disease, we analyzed the genomes of 226 prostate cancer patients and observed thousands of mutations, many of which impact known cis-regulatory elements. We developed a high-throughput multi-layer massively parallel sequencing-based method called PLUMAGE (Pooled full-length UTR Multiplex Assay on Gene Expression) to simultaneously quantify the effects of 545 5’ UTR somatic mutations across recurrently mutated or cancer-related genes from our patient cohort. Our method enabled unprecedented insights into how 5’ UTR mutations can control multiple levels of gene expression simultaneously. In particular, we identified 190 mutations that significantly altered 5’ UTR function, either by creating new DNA binding elements, disrupting known translation regulatory motifs, or simultaneously impacting both transcript levels and mRNA translation. Furthermore, we also determined that 5’ UTR mutations to the MAP kinase signaling pathway are significantly associated with early metastasis. This study is the first to comprehensively interrogate the functional 5’ UTR mutational landscape of a human cancer revealing the importance of untranslated regions in regulating multiple levels of oncogenic gene expression and provides a high-throughput functional genomics solution applicable to many genetically driven diseases.

overall_design:
We searched for somatic 5’ UTR single nucleotide variants in a cohort of five primary mCRPC patient-derived xenografts (PDX) belonging to the LuCaP series23, which encompass major genomic and phenotypic features of human prostate cancer, including adenocarcinoma (LuCaP 78, LuCaP 81, LuCaP 92), neuroendocrine prostate cancer (LuCaP 145.2), and a hypermutated prostate cancer (LuCaP 147). The five LuCaP series of prostate cancer xenografts used in this study (LuCaPs 78, 81, 92, 145.2  and 147) were obtained from the University of Washington Prostate Cancer Biorepository and generated from advanced prostate cancer patients
Processed data are produced for each matched pair of cancer tissue and matched normal sample. VCF files for the paired samples are included on the prostate cancer sample.

first: Yiting

last: Lim

first: Andrew

last: Hsieh