title: Brain Gene Expression Differences Related to Ethanol Preference in the Collaborative Cross Founder Strains

status: Public on Aug 27 2022

city: Portland

first: Justin

last: Anderson

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Behavorial Neuroscience

country: USA

institute: Oregon Health & Science University

summary: The collaborative cross (CC) founder strains include five classical inbred laboratory strains (129S1/SvlmJ, A/J, C57BL/6J (B6), NOD/ShiLtJ, and NZO/HILtJ) and three wild-derived strains (CAST/EiJ, PWK/PhJ (PWK) and WSB/EiJ) The strains encompass 89% of the genetic diversity available in Mus musculus and about 10 to 20 times more genetic diversity than found in Homo sapiens. For more than 60 years the B6 strain has been used as the model strain for high ethanol preference/high consumption. However, another one of the CC founder strains, PWK, was identified as a high ethanol preference/high consumption strain. The current study determined how the transcriptomes of the B6 and PWK strains differed from the 6 low preference CC strains across 3 nodes of the brain addiction circuit. RNA-Seq data were collected from the central nucleus of the amygdala, the nucleus accumbens core and the prelimbic cortex. Differential expression (DE) analysis was performed in each of these brain regions for all 28 possible pairwise comparisons of the CC founder strains. Unique genes for each strain were identified by selecting for genes that differed significantly (false discovery rate (FDR) < 0.05) from all other strains in the same direction. B6 was identified as the most distinct inbred laboratory strain, having the highest number of total differently expressed genes (DEGs) and DEGs with high log fold change, and unique genes compared to other CC strains. Less than 50 unique DEGs were identified in common between B6 and PWK within all three brain regions, indicating the strains potentially represent two distinct genetic signatures for risk for high ethanol-preference. 238 DEGs were found to be commonly different between B6, PWK and the average expression of the remaining CC strains within all three regions. The commonly different up-expressed genes were significantly enriched (FDR < 0.001) among genes associated with neuroimmune function. These data compliment the observation that neuroimmune signaling is key to understanding alcohol use disorder and and support use of these 8 strains and the highly heterogeneous mouse populations derived from them to identify alcohol-related brain mechanisms and treatment targets.

overall_design: Mice were obtained from Jackson Laboratory at 5 weeks of age and allowed to habituate at the VAPORHCS VMU facility for three weeks. At 8 weeks of age, naive mice were euthanized by cervical location and brains removed and immediately frozen on dry ice. Brain regions of interest were dissected from frozen brains using biopsy punch methods and atlas landmarks. The brain regions are the prelimbic cortex (Prl), the nucleus accumbens core (NacC), and the central nucleus of the amygdala (CeA). The eight strains of mice used are: C57BL/6J (B6), A/J (A), 129S1/SvImJ (129), NOD/LtJ (NOD), NZO/HILtJ (NZO), CAST/EiJ (CAST), PWK/PhJ (PWK) and WSB/EiJ (WSB). From each strain of mice, three males and three females were used, for a total of 48 animals and 144 samples. Dissected brain tissue was submitted to the GPSR at OHSU for RNA isolation using QIASymphony robot and standard Qiagen kits/reagents. A total of 144 libraries were multiplexed 2 per lane, balanced for sex, family and strain, yielding between 12 and 41 million total paired-end reads per sample. Sequence alignment was based on the mm10 version of the mouse genome (Ensembl_Mouse_GRCm39_GCA_000001635.9). FastQC (Andrews, 2010) was used for quality checks on the raw sequence data and revealed one batch with significantly lower read counts. This batch was re-sequenced for quality control, bringing the mean counts up to the numbers found in the other two batches. Sequenced data were aligned using the STAR aligner (Dobin et al., 2013), allowing for a maximum of three mismatches per 100 bp read. On average, around 80% of the reads were uniquely aligned. Read counts were also obtained through the STAR aligner. Reads were aligned to the Mus_musculus.GRCm39.105 mouse annotation to generate counts at the gene level. Gene expression data were imported into the R application environment.

first: Priscila

last: Darakjian

first: Robert

last: Hitzemann

first: Denesa

last: Lockwood

first: Tamara

middle: J

last: Phillips

first: Angela

last: Ozburn


title: SETD4 Cells Contribute to Brain Development and Maintain Adult Stem Cell Reservoir for Neurogenesis

status: Public on Aug 25 2022

city: Hangzhou

first: sunli

last: cai

address: 866 Yuhangtang Rd

country: China

institute: Zhejiang University

type: Expression profiling by high throughput sequencing

summary: Cellular quiescence facilitates maintenance of neural stem cells (NSCs) and their subsequent regenerative functions in response to brain injury and aging. However, the specification and maintenance of NSCs in quiescence from embryo to adulthood remains largely unclear. Here, using Set domain-containing protein 4 (SETD4), an epigenetic determinant of cellular quiescence, we mark a small but long-lived NSC population in deep quiescence in the subventricular zone of adult murine brain. Genetic lineage tracing shows that SETD4+ cells appear before neuroectoderm formation and contribute to brain development. In the adult, conditional knock-out of SETD4 resulted in quiescence exit of NSCs, generating newborn neurons in the olfactory bulb and contributing to damage repair. However, long period deletion of SETD4 lead to exhaustion of NSC reservoir or SETD4 overexpression caused quiescence entry of NSCs, leading to suppressed neurogenesis. This study reveals the existence of long-lived deep quiescent NSCs and their neurogenetic capacities beyond activation.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of subventricular zone neural stem cells with ADV-GFP (control) or ADV-SETD4-GFP (SETD4 OE) infection.

first: Sunli

last: Cai

first: Yaoshun

last: Yang


title: Longitudinal characterization of circulating neutrophils uncovers phenotypes associated with severity in hospitalized COVID-19 patients

status: Public on Aug 28 2022

city: Cambridge

first: Thomas

middle: James

last: LaSalle

state: MA

address: 415 Main Street

institute: Broad Institute

summary: Mechanisms of neutrophil involvement in severe COVID-19 remain incompletely understood. Here we collect longitudinal blood samples from 306 hospitalized COVID-19+ patients and 86 controls, and perform bulk RNA-sequencing of enriched neutrophils, plasma proteomics, and high-throughput antibody profiling to investigate relationships between neutrophil states and disease severity. We identify dynamic switches between 6 distinct neutrophil subtypes. At days 3 and 7 post-hospitalization, patients with severe disease display a granulocytic myeloid-derived suppressor cell-like gene expression signature, while patients with resolving disease show a neutrophil progenitor-like signature. Humoral responses are identified as potential drivers of neutrophil effector functions, with elevated SARS-CoV-2-specific IgG1-to-IgA1 ratios in plasma of severe patients who survived. In vitro experiments confirm that while patient-derived IgG antibodies induce  phagocytosis in healthy donor neutrophils, IgA antibodies predominantly induce neutrophil cell death. Overall, our study demonstrates a dysregulated myelopoietic response in severe COVID-19 and a potential role for IgA-dominant responses contributing to mortality.

overall_design:
Neutrophil Bulk RNA-seq: Longitudinal gene expression profiling analysis using bulk RNA-seq data of neutrophils enriched from fresh whole blood of 306 hospitalized COVID-19+ patients, 78 symptomatic controls, and 8 healthy controls for a total of 781 samples. Blood samples were drawn on D0, D3, and D7 (days post-hospitalization) if the patient remained hospitalized, and some patients had an event-driven draw (DE) which corresponds to a change in patient status (e.g. intubation, removal from ventilator).

Please  note that 'COVID-19 status'  simply refers to whether the patient is COVID+ or COVID-. COVID- includes both negative symptomatic controls and healthy controls. The healthy controls have an H in their sample name, and also in the time point, and the disease severity characteristics. Any other sample which is COVID- is a symptomatic control.

NOTE:
The data for the study were collected at the very beginning of the COVID-19 pandemic, and as such, a waiver of informed consent was approved by the governing institutional review board at Massachusetts General Hospital, in compliance with the Code of Federal Regulation (45CFR 46, 2018 Common Rule). To protect the identity of individual subjects, public posting of raw sequencing data from the patients has not been approved; Therefore, raw data is not provided.

first: Anna

middle: L

last: Gonye

first: Samuel

middle: S

last: Freeman

first: Paulina

last: Kaplonek

first: Nir

last: Hacohen

first: Moshe

last: Sade-Feldman


title: Opposing Roles of Hepatic Stellate Cell Subpopulations in Hepatocarcinogenesis

status: Public on Aug 26 2022

city: NEW YORK

middle: F

last: Schwabe

state: NY

address: 1130 ST NICHOLAS AVE - ROOM 916B

department: Medicine

institute: Columbia University

summary:
Hepatocellular carcinoma (HCC), the fourth leading cause of cancer mortality, develops almost exclusively in patients with chronic liver disease (CLD) and advanced fibrosis. Here we interrogated functions of hepatic stellate cells (HSC), the main source of liver fibroblasts, during hepatocarcinogenPesis. Genetic depletion, activation or inhibition established HSC as tumour-promoting in mouse models of HCC. HSC were enriched in the preneoplastic environment, where they closely interacted with hepatocytes and modulated hepatocarcinogenesis by regulating hepatocyte proliferation and death. Analysis of mouse and human HSC subpopulations and their associated mediators by single cell RNA-sequencing in conjunction with genetic ablation revealed dual functions of HSC in hepatocarcinogenesis. Hepatocyte growth factor, enriched in quiescent and cytokine-producing HSC (cyHSC), protected from hepatocyte death and HCC development. In contrast, type I collagen, enriched in activated myofibroblastic HSC (myHSC), promoted proliferation and tumour development via increased stiffness and TAZ activation in pretumoural hepatocytes and via activation of discoidin domain receptor 1 in established tumours. An increasing HSC dysbalance between cyHSC and myHSC during liver disease progression was associated with elevated HCC risk in patients. In summary, the dynamic shift of HSC subpopulations and their mediators during CLD is associated with a switch from HCC protection to HCC promotion.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Refer to individual Series:

1) GSE206409: scRNAseq samples of HSC from fibrotic livers; bulk RNAseq of HSC from fibrotic livers,bulk RNAseq of normal; NT and tumor tissues induced by DEN+CCl4 after HSC inhibition
2) GSE212039: scRNAseq of liver cells (n=2) and Col1a1+ liver cells from Mdr2KO mouse (n=1)
3) GSE212042: bulk RNAseq of HSC YAP wt of YAP ko
4) GSE212045: microarray of HSC Lhx2 wt or Lhx2 ko
5) GSE212046: snRNAseq  from liver explants (NT cirrhotic: n=2 and HCC n=2)


title: Single cell sequencing of human primary LCs

status: Public on Aug 30 2022

city: Southampton

first: James

middle: David

last: Davies

state: Hampshire

address: LE57, Lab and Pathology block, Tremona Road

department: Clinical and Experimental Sciences

country: United Kingdom

institute: University of Southampton

summary: Langerhans cells (LC) coordinate immune homeostasis at the human epidermis, proficent in initiating tolerogenic immune responses. To investigate the transcriptomic mediators of human LC tolerogenic immune responses, we performed single cell RNA-sequencing of steady state LC extracted via Liberase TM digestion and migratory LCs extracted from epidermal sheets.

overall_design: Steady state and Migrated human LC were subjected to single cell RNA-sequencing following encapsulation with Drop-seq. Following digest with dispase overnight at +4C, Steady state LC were extracted from epidermis by 90 minute Liberase TM digestion +37C and Migrated LC were extracted from 48 hour culture of epidermis sheets.

first: Marta

middle: E

last: Polak

first: Sofia

last: Sirvent

first: Andres

last: Vallejo


title: Bacteria modulate tamoxifen-induced death via host fatty acid metabolism

status: Public on Aug 23 2022

city: Worcester

first: Hefei

last: Zhang

state: Massachusetts

address: 4 Miles Ave

department: Department of Systems Biology

institute: University of Massachusetts Chan Medical School

summary: Our microbiota affects numerous processes involved in development, health, and the response to chemotherapeutic drugs. Tamoxifen is a selective estrogen receptor (ER) modulator that is used to treat ER positive breast cancer, but that at high doses kills both ER positive and ER-negative breast cancer cells. We recapitulate this off-target effect in Caenorhabditis elegans, which does not have an ER ortholog. We find that different bacteria dramatically modulate tamoxifen toxicity in C. elegans, with a three-order of magnitude difference between animals fed Escherichia coli, Comamonas aquatica, and Bacillus subtilis. Remarkably, host fatty acid (FA) biosynthesis mitigates tamoxifen toxicity, and different bacteria provide the animal with different FAs, resulting in distinct FA profiles. Surprisingly these bacteria modulate tamoxifen toxicity by different death mechanisms, some of which are modulated by FA supplementation and others by antioxidants. Together, this work reveals a complex interplay between bacteria, FA metabolism and tamoxifen toxicity that may provide a blueprint for similar studies in more complex mammals.

overall_design: C. elegans RNA-sequencing of three experiments. Animals were treated with 400 µM citrate or 400 µM tamoxifen for 48 hours in biological triplicate.

first: Cédric

last: Diot

first: Albertha

last: Walhout


title: Transcriptomic plasticity of the hypothalamic osmoregulatory control centre of the Arabian dromedary camel

city: Bristol

first: Panjiao

last: Lin

address: Dorothy Hodgkin Building, Whitson Street

department: Bristol Medical School

institute: University of Bristol

summary: To investigate the central control of water homeostasis in the dromedary camel, we have performed transcriptomic studies on the supraoptic nucleus samples from camels under control (water ad libitum) and dehydrated (water deprivation for 20 days) conditions by RNA sequencing. We have identified genes that change in expression in response to hyperosmotic challenge and transcriptomic response networks that might be essential for adaptations of camel to live and thrive in aird desert environment.

overall_design: Unilateral supraoptic nucleus samples were isolated from hypothalamus of male dromedary camels under control (water ad libitum) and dehydrated (water deprivation for 20 days) conditions (n=5 per group). Total RNA was extracted using a Direct-zol™ RNA MiniPrep kit (Zymo research, R2052) following the manufacturer’s instructions. Average RNA Integrity Number (RIN) of samples processed for sequecing (n=10) was 6.27. Ribosomal depleted sequencing libraries were produced using TruSeq® Stranded Total RNA library preparation kit (illumina). Libraries were sequenced on Illumina NextSeq500 platform using NextSeq 500 High Output v2.5 (2 x 75 bp run) Kit (Illumina; 20367064).

first: David

last: Murphy

first: Michael

middle: P

last: Greenwood


title: Negative supcoils pattern meiotic crossovers

status: Public on Aug 24 2022

city: Jinan

first: liangran

last: zhang

state: Shandong

address: Jingshi Street

department: State Key Laboratory of Microbial Technology

institute: Shandong University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Interference exists ubiquitously in many biological processes. Crossover interference patterns meiotic crossovers, which are required for faithful chromosome segregation and evolutionary adaption. However, what the interference signal is and how it is generated and regulated are unknown. We show that yeast top2 alleles cannot bind or cleave DNA accumulate a higher level of negative supercoils and show weaker interference. However, top2 alleles cannot religate the cleaved DNA or release the religated DNA accumulate less negative supercoils and show stronger interference. Moreover, the level of negative supercoils is negatively correlated with crossover interference strength in various strains. Furthermore, negative supercoils preferentially enrich at crossover-associated Zip3 regions before the formation of meiotic DNA double-strand breaks, and regions with more negative supercoils tend to have more Zip3. Additionally, the strength of crossover interference and homeostasis change coordinately in mutants. These findings suggest that the accumulation and relief of negative supercoils pattern meiotic crossovers.

overall_design: ChIP-seq analysis of binding of TMP(marker of negative supercoils) in S. cerevisiae during meiosis. Total 36 samples were analyzed. ChIP: 3 time point(3, 4 and 5h in SPM) from WT, spo11-Y135F, pCLB2-TOP2, top2-L475A and fragmental DNA of WT (negative control; 4h in SPM) . Input: 4h in SPM from  WT, spo11-Y135F, pCLB2-TOP2, top2-L475A and fragmental DNA of WT(negative control; 4h in SPM). Each sample was with two biological repeats.

first: Taicong

last: Tan

first: Yingjin

first: Ying

last: Wang

first: Liangran


title: Gene expression changes following latency reversal agents screening in a cellular model of HIV-1 latency

city: Badalona

first: IFEANYI

middle: JUDE

last: EZEONWUMELU

state: Barcelona

address: C. Canyet s/n

department: Virus Host interactions team

country: Spain

institute: AIDS Research Institute - IrsiCaixa  Hospital Germans Trias i Pujol

summary: To delineate the mechanism driving JAK2 inhibitors´ induced effects on HIV-1 latency, whole transcriptome profiling was performed in the HIV-1 latency model HL-HIG, treated with the LRA fedratinib, the LPA pacritinib, the pan-JAKi ruxolitinib and PMA as a positive control of latency reactivation and immune activation.

overall_design: Gene expression changes after treatment of HL-HIG with JAK inhibitors (Fedratinib, Ruxolitnib and Pacritinib) and PMA. Drugs were used at concentrations previously shown to be effective at reversing or promoting latency in our model systems.

first: Ifeanyi

last: Ezeonwumelu

first: Edurne

last: Garcia-Vidal

first: Bruna

last: Oriol-Tordera

last: Ruiz-Riol

first: Andre

last: Gohr

first: Eva

last: Riveira-Muñoz

first: Ester

last: Ballana


title: Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

type: Methylation profiling by high throughput sequencing

summary: Maternal obesity during pregnancy is associated with neurodevelopmental disorder (NDD) risk. We utilized integrative multi-omics to examine maternal obesity effects on offspring neurodevelopment in rhesus macaques by comparison to lean controls and two interventions. Differentially methylated regions (DMRs) from longitudinal maternal blood-derived cell-free fetal DNA (cffDNA) significantly overlapped with DMRs from infant brain. The DMRs were enriched for neurodevelopmental functions, methylation-sensitive developmental transcription factor motifs, and human NDD DMRs identified from brain and placenta. Brain and cffDNA methylation levels from a large region overlapping mir-663 correlated with maternal obesity, metabolic and immune markers, and infant behavior. A DUX4 hippocampal co-methylation network correlated with maternal obesity, infant behavior, infant hippocampal lipidomic and metabolomic profiles, and maternal blood measurements of DUX4 cffDNA methylation, cytokines, and metabolites. We conclude that in this model, maternal obesity was associated with changes in the infant brain and behavior, and these differences were detectable in pregnancy through integrative analyses of cffDNA methylation with immune and metabolic factors.

overall_design: Rhesus macaque dams with confirmed male pregnancies were divided into four groups: obese, obese with caloric restriction, obese with pravastatin, and lean matched controls. From a total of 25 pregnancies, low-pass whole genome bisulfite sequencing (WGBS) was utilized to assay cell-free fetal DNA (cffDNA) across 4 timepoints representing all three trimesters of pregnancy (GD45, GD90, GD120, and GD150) and three brain regions (hippocampus, hypothalamus, and prefrontal cortex) from 6-month-old infants.


title: Transcriptional abnormalities in iPSC-derived oligodendrocytes of individuals with primary progressive multiple sclerosis

city: Stanford

first: Melanie

last: Plastini

state: CA

address: 290 Campus Drive

institute: Stanford University

summary: Multiple sclerosis (MS) is the most common neurological disorder in young adults and is classically defined as a chronic inflammatory demyelinating disease of the central nervous system (CNS). Although MS affects millions of people worldwide, its underlying cause remains unknown making discovery of effective treatments challenging. Whether intrinsic or extrinsic factors contribute to MS initiation and progression is still unclear. This is especially true for primary progressive MS (PPMS), the rarest form of the disease, in which progressive and irreversible loss of neurological function is often observed in the absence of an overt immune-inflammatory response. To test the hypothesis that intrinsic dysfunction in oligodendrocytes (OLs), the primary targets of damage in MS, may contribute to PPMS etiopathology, we differentiated human induced pluripotent stem cell (hiPSC) lines derived from PPMS and healthy individuals into mature OLs to compare their transcriptional profile. PPMS derived OLs displayed hundreds of differentially expressed genes compared to control OLs, many associated with cell adhesion, apoptosis and inflammation, including the inflammasome component Nlrp2, which was highly upregulated. NLRP2 immunoreactivity in OLs was confirmed in post-mortem PPMS brain tissues, with higher expression than in control tissues. Altogether, our findings suggest that mature OLs in PPMS affected individuals carry intrinsic abnormalities that could contribute, at least in part, to the pathophysiology of this form of the disease.

overall_design: The differentiation of 3 control induced pluripotent stem cell (iPSC) lines and 2 primary progressive multiple sclerosis iPSC lines into oligodendrocytes to examine transcriptional changes. Differentiations were duplicated for a total of 6 control samples and 4 PPMS samples

first: Haritha

last: Desu

first: Maureen

middle: C

last: Ascona

first: Anna

last: Lang

first: Mario

middle: A

last: Saporta

first: Roberta

last: Brambilla


title: Endothelial Cell Cycle State Determines Propensity for Arterial-Venous Fate

status: Public on Aug 22 2022

city: Charlottesville

first: Nicholas

middle: W

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

summary: Formation and maturation of a functional blood vascular system is required for the development and maintenance of all tissues in the body. During the process of blood vessel development, primordial endothelial cells are formed and become specified toward arterial or venous fates to generate a circulatory network that provides nutrients and oxygen to, and removes metabolic waste from, all tissues. Specification of arterial and venous endothelial cells occurs in conjunction with suppression of endothelial cell cycle progression, and endothelial cell hyperproliferation is associated with potentially lethal arterial-venous malformations. However, the mechanistic role that cell cycle state plays in arterial-venous specification is unknown. Herein, studying vascular development in Cdh5-CreERT2;R26FUCCI2aR reporter mice, we find that venous and arterial endothelial cells exhibit a propensity for different cell cycle states during development and in adulthood. That is, venous endothelial cells are predominantly FUCCI-Negative, while arterial endothelial cells are enriched for the FUCCI-Red reporter. Single cell RNA sequencing analysis of developing retinal endothelial cells reveals that venous endothelial cells are enriched for the FUCCI-Negative state and BMP signaling, while arterial endothelial cells are enriched for the FUCCI-Red state and TGF-b signaling. Further transcriptional analyses and live imaging of cultured endothelial cells expressing the FUCCI reporter show that reporter-negative corresponds to an early G1 state and reporter-red corresponds to late G1 state. We find the early G1 state is essential for BMP4-induced venous gene expression, whereas late G1 state is essential for TGF-b1-induced arterial gene expression. In a mouse model of endothelial cell hyperproliferation and disrupted arterial-venous specification, pharmacological inhibition of endothelial cell cycle prevents the vascular defects. Collectively, our results show that endothelial cell cycle control plays a key role in arterial-venous network formation, and distinct cell cycle states provide distinct windows of opportunity for the molecular induction of arterial vs. venous specification.

overall_design: Endothelial cells from retinal tissue of P6 R26FUCCI2aR mice of three separate litters were isolated by digesting and FACS purification. Single cell suspensions of endothelial cells were separated by FACS into FUCCI-Green S/G2/M, FUCCI-Negative and FUCCI-Red G1 populations by gating on mCherry and mVenus channels. RNA from HUVEC-FUCCI sorted into different cell cycle states (n = 3 biological replicates) was isolated and purified.

first: Karen

middle: K

last: Hirschi


title: Effect of depletion of MDMX (aka MDM4) on gene expression in uveal melanoma cell line MEL202

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

summary:
To investigate the effect of MDMX depletion on the transcriptome of MEL202 cells we established 5 derivatives either containing a doxycyline- inducible Contrl shRNA or with 4 distinct MDMX -targeting shRNAs
In thee biological replicates the cells were treated with doxycycline for 48 hrs after which RNA was isolated

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MEL202/i-shCtrl compared to MEL202/i-shMDMX).

first: Aart

middle: G

last: Jochemsen

first: Szynion

middle: M

last: Kielbasa


title: Hepatic Stellate Cells activation induced by Lhx2 deletion

first: Robert

last: Schwabe

summary: Gene expression in isolated mouse Hepatic Stellate Cells (HSC) Lhx2 ko compared to HSC Lhx2 floxed.

overall_design:
Affymetrix Mouse 1.0ST  gene expression measurements were used to characterize the transcriptomic of HSC under the following conditions:
1) HSC from  Lhx2 floxed mice (without Mx1Cre) treated with 3xpoly(I:C)
2) HSC Lhx2 ko induced by 3xpoly(I:C) in Mx1Cre+ Lhx2 floxed mice.

first: Aveline

last: Filliol

first: Richard

last: Friedman


title: Impact of dietary cholesterol on Macrophages during non-alcoholic steatohepatitis progression

city: Los Angeles

first: Ana

last: Maretti-Mira

address: 1450 Biggy Street, NRT 3514

institute: USC

summary: Inflammation, mediated by liver-resident Kupffer cells (KCs) and recruited infiltrating macrophages (IMs), plays a critical role in NAFLD pathogenesis. Cholesterol induces pro-inflammatory cytokine production by macrophages and has been identified as a key factor involved in progression from simple steatosis to NASH. In this study, using the fructose, palmitate, cholesterol & trans-fat (FPC) diet model which recapitulates human NAFLD, we aimed to determine the impact of cholesterol manipulation on NAFLD progression/regression and macrophage phenotype in vivo.The transcriptomic evaluation of hepatic macrophages from mice fed with FPC diet contained the highest concentration of cholesterol (1.25%) suggest these cells might contribute to liver inflammation, steatohepatitis, and hepatocarcinoma pathways during the progression phase.

overall_design: In our NASH model, we fed C57BL/6J mice with the Fructose, Palmitate, Cholesterol, and Trans-Fat (FPC) diet containing different concentrations of cholesterol: 1.25%, 0.2%, and 0.05% (control) for 20 weeks (progression phase). Then, we reduced the cholesterol in the FPC diet, keeping it at 0.05% for additional ten weeks (regression phase). At the end of each phase, we euthanized the animals. We harvested the hepatic non-parenchymal cells and sorted the hepatic macrophages for RNAseq analysis.

first: Lucy

last: Golden-Mason

first: Matthew

last: Salomon


title: Identification of Differentially Expressed Genes in Human Gingival and Periodontal Derived Stromal Cells Compared with Human Dermal Fibroblasts

city: Okayama

first: Kiyofumi

last: Takabakake

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Oral Pathology and Medicine Graduate school of Medicine, Dentistry and Pharmaceutical Science

country: Japan

institute: Okayama University

summary: The normal epithelium derived stromal cells included ECM, normal fibroblast, mesenchymal stromal cells and osteoblast also plays a significant role in the progress of cancers but poorly investigated in the progress of OSCC. In this study, the stromal cells derived from gingival and periodontal tissues were extracted and human dermal fibroblasts were selected as control group. The differentially expressed genes in Gingival derived stromal cells and Periodontal derived stromal cells were identified by microarray. Furthermore, the biological process, cellular component, molecular function and cell pathways of differentially expressed genes in gingival derived stromal cells and periodontal derived stromal cells were analyzed by GO enrichment analysis and KEGG enrichment analysis respectively. All of these findings could provide potential genes in gingival derived stromal cells and periodontal derived stromal cells that influences the progress of OSCC.

overall_design: the cells were digested and collected after the HDF and stromal cells extracted from gingival and periodontal tissues covered the dish. Adjusted the cell density at 5×10^5 to 3×10^6 and the RNA were extracted to conduct the microarray.

last: Takabatake

first: Hotaka

last: Kawai

first: Haruka

last: Omori

first: Shan

last: Qiusheng

first: Keisuke

last: Nakano


title: A defect in cell wall recycling confers antibiotic resistance and sensitivity in Staphylococcus aureus.

city: Toronto

first: Stephanie

last: Tan

state: ON

address: 661 University Ave

country: Canada

institute: University of Toronto

summary: WalKR is a two-component system that is essential for viability in Gram-positive bacteria that regulates the all-important autolysins. Here we show a T101M mutation in walR confers a defect in autolysis, a thickened cell wall and decreased sensitivity to antibiotics that target the lipid II cycle, a phenotype that is reminiscent of the clinical resistance form known as vancomycin intermediate-resistant Staphylococcus aureus. Importantly, this is accompanied by dramatic sensitization to tunicamycin. We demonstrate that this phenotype is due to partial collapse of a pathway consisting of autolysins, AtlA and Sle1, a transmembrane sugar permease, MurP, and GlcNAc recycling enzymes, MupG and MurQ. We suggest that this causes a shortage of substrate for MraY causing it to be hypersensitive to competitive inhibition by tunicamycin. This constitutes a new molecular model for antibiotic sensitivity in S. aureus and a promising new route for antibiotic discovery.

overall_design: Comparative gene expression profiling analysis of RNA-seq data Staphylococcus aureus ATCC 29213 (wild type), walR1  and walR1-walK(tun)

first: Kelvin

last: Cho

first: Justin

middle: R

last: Nodwell


title: Single cell RNA sequencing of P6 and P15 retinal endothelial cells

first: Nicholas

last: Chavkin

summary: Formation and maturation of a functional blood vascular system is required for the development and maintenance of all tissues in the body. During the process of blood vessel development, primordial endothelial cells are formed and become specified toward arterial or venous fates to generate a circulatory network that provides nutrients and oxygen to, and removes metabolic waste from, all tissues. Specification of arterial and venous endothelial cells occurs in conjunction with suppression of endothelial cell cycle progression, and endothelial cell hyperproliferation is associated with potentially lethal arterial-venous malformations. However, the mechanistic role that cell cycle state plays in arterial-venous specification is unknown. Herein, studying retinal vascular development in Cdh5-CreERT2;R26FUCCI2aR reporter mice, we found that venous and arterial endothelial cells are in distinct cell cycle states during development and in adulthood. That is, venous endothelial cells reside in early G1 state, while arterial endothelial cells reside in late G1 state. Single cell RNA sequencing of developing retinal endothelial cells revealed that BMP signaling and early G1 state are enriched in venous endothelial cells, while TGF-b signaling and late G1 state are enriched in arterial endothelial cells. Cultured endothelial cells in early vs. late G1 exhibited significant differences in gene expression and activity, especially among BMP/TGF-b signaling components. The early G1 state was found to be essential for BMP4-induced venous gene expression, whereas late G1 state is essential for TGF-b1-induced arterial gene expression. In a mouse model of endothelial cell hyperproliferation and disrupted arterial-venous specification, pharmacological inhibition of endothelial cell cycle prevented the vascular defects. Collectively, our results show that endothelial cell cycle control plays a key role in arterial-venous network formation, and distinct cell cycle states provide distinct windows of opportunity for the molecular induction of arterial vs. venous specification.

overall_design: Single Cell RNA Sequencing: Endothelial cells from P6 and P15 wild-type mice were isolated, and single cell suspensions of endothelial cells were selected through FACS of CD31+CD45- immunostaining. Single cell RNA sequencing was then performed by the Yale Center for Genomic Analysis, which used around 12,000 cells per sample through the 10x Genomics Drop-Seq platform to generate single cell barcoded cDNA libraries. Next-generation sequencing of single cell barcoded cDNA libraries was performed in collaboration with WuXi NextCODE (Boston, MA and Shanghai, China). Single cell RNA sequencing datasets were analyzed by Seurat v3.0 to filter out cells by high mitochondrial gene expression, low or high gene numbers, and contaminating cell types (Hbb.bt, Neurod1, Cd63). P6 and P15 datasets were integrated by IntegrateData function using SCT normalization.

first: Karen

last: Hirschi


title: CD169 is a marker of IFN-γ-stimulated inflammatory macrophages in brain tumor

city: Daejeon

first: Heung Kyu

last: Lee

address: 291 Daehak-ro, Yuseong-gu

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

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

overall_design: Refer to individual Series


title: Alternative splicing changes are associated with pre-birth adaptation during mouse lung development

city: Lisboa

first: Francisca

middle: Ferreira

last: Vasconcelos

state: Lisboa

address: Av. Prof. Egas Moniz, Edificio Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular João Lobo Antunes

summary: Analysis of gene expression and alternative splicing changes in mouse lungs at different developmental time-points (E15.5, E18.5, P5, P8) was performed through RNAseq. We performed 101 nt paired-end RNAseq using HiSeq 4000 on triplicate samples. We obtained an average of 59.8 million reads per sample.   The sequence reads that passed quality filters were analyzed at the transcript and at the alternative splicing events level using using D  For gene expression analysis, the ~56.8 M raw reads generated per sample were uniquely mapped to the mm10 assembly and annotated to the Gencode vM14 transcriptome using TopHat2, with Bowtie2. Gene expression levels were quantified with HTSeq-count (version 0.10.0). After applying quality filters, we obtained 16,152 expressed genes for downstream analysis.   For AS event-level analysis, raw reads were mapped to previously annotated AS events for the mouse reference assembly (mm10 vastdb.mm2.23.06.20) from VastDB (VastDB v2 released). Abundance of AS events in Percent spliced in (PSI) values was estimated using VAST-TOOLS.  We found that most of the AS changes during alveologenesis occur at the perinatal period in genes associated with blood vessel and epithelial cell development. In particular, we found that Vegfa undergoes AS in lungs at the transition from embryonic to post-natal life, starting at the end of the embryonic period. Our results suggest provide a framework for understanding how AS changes impact on lung development during the critical period of transition to the postnatal life.

overall_design: RNAseq data sets of bulk mouse lung tissue collected at E15.5, E18.5, P5 and P8. Samples were collected in triplicates.

first: Claudio

last: Franco

first: Marta

last: Fidalgo

first: Catarina

last: Fonseca

first: Alexandre

last: Raposo

first: Tania

last: Balboni


title: RNA-Seq of Hrip1-treated rice leaves

status: Public on Aug 21 2022

city: Beijing

first: Zeng

last: Hongmei

state: Beijing

address: Chinese Academy of Agricultural Sciences, 12 Zhongguancun,, Haidian district, Building 39, International Students Dorm

department: Biological Control

summary:
Hrip1 was isolated from Alternaria tenuissima and was found to induce systematic acquired resistance in tobacco. In rice plants, it was found to confer immunity against rice blast fungi. To understand the genomic signature of Hrip1-induced immunity, rice seedlings were treated with 30 nm Hrip1 protein and triplicate leaf samples were subjected to sequencing on the BIGSEQ500 platform.
Two groups of rice seedlings were grown to the three-leaf stage. The experiment group was treated with 30nm Hrip1 protein while the control plants were treated with Tris-HCl buffer. Triplicate samples from both setups were taken at 6, 12, 24, and 48 hr after treatment. Total RNA was extracted and reverse transcribed in first strand cDNA as input material.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Hrip1-treated samples (HT) and control samples (CB) (Treatment versus control).

first: Vincent

last: Ninkuu

first: Jianpei

last: Yan

first: Lin

last: Zhang

first: Zhenchao

last: Fu

first: Tengfeng

last: Yang

first: Shupeng

last: Li

first: Beibei

first: Jiaqi

last: Duan

first: Jie

last: Ren

first: Guangyue

first: Xiufen

first: Hongmei

last: Zeng


title: The transcriptome alteration in tumoral NK cells in response to  dual or monotherapy of STING agonist and IL-35 blocking antibodies

city: chapel hill

first: Jenny

last: Ting

state: North Carolina

address: 450 West Drive

department: LCCC

institute: UNC-CH

summary:
To investigate the role of STING agonist and IL-35 blocking antibodies in the regulation of NK cell function, tumor-infiltrated NK cells were flow cytometrically separated from control (IgG), cGAMP, anti-IL-35, or combination treated groups
We performed gene expression profiling analysis using data obtained from RNA-seq of tumor-infiltrated NK cells sorted from four groups.

overall_design: We constructed mouse pancreatic tumor models and treated the tumor bearing mice with i.v injections of STING agonist and i.p injections of IL-35 blocking antibodies. On day 21, we sorted out tumor-infiltrated NK cells from control (IgG), cGAMP, anti-IL-35, or combination treated groups

first: Li

last: Sirui

first: Mirlekar

last: Bhalchandra

first: Tan

last: Xianming


title: Analysis of gonadal fat from male control and adipocyte-specific LAMA4 knockout mice

city: Baton Rouge

first: Carrie

last: Elks

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

summary: To determine the transcriptomic effects of LAMA4 loss on adipose tissue structure and gene expression in two dietary paradigms, we assessed gonadal white adipose tissue of male control and adipocyte-specific LAMA4 knockout mice using a Quant-Seq strategy.

overall_design: Epididymal fat pads were dissected from a) 6 male wild-type and 6 male adipocyte-specific LAMA4 knockout mice following 20 weeks of regular diet feeding,  and b)  6 male wild-type and 6 male adipocyte-specific LAMA4 knockout mice following 20 weeks of 45% fat diet feeding,  followed by isolation of total RNA and messenger RNA quantification via Quant-Seq.

first: Jennifer

last: Bailey


title: Single cell sequencing of de-differentiated adipocytes induced by breast tumor

status: Public on Sep 02 2022

city: Dallas

first: Philipp

last: Scherer

state: TX

address: 5323 Harry Hines Boulevard

department: Touchstone Diabetes Center, Internal Medicine

institute: UT Southwestern Medical Center

summary: Purpose: The goals of this study are to determine adipocyte de-differentiation and the fate of these de-differentiated cells in breast tumor.  Methods: Library prepared followed by 10X Genomics standard protocol. Transcriptome was generated by high throughput sequencing.

overall_design: We previously described a doxycycline-inducible (Tet-On) ‘pulse-labeling’ adipocyte-tracer system, the ‘inAd-Chaser-mTmG mice’ (Adiponectin-rtTA; TRE-Cre; Rosa26RmT/mG). Prior to doxycycline treatment, all cells express membrane tdTomato from Rosa26 locus; whereas upon doxycycline treatment, Cre recombinase excises the loxp-flanked tdTomato cassette and it thus constitutively activates membrane EGFP expression specifically in adipocytes. Thus, it allows us not only to label adipocytes with EGFP, but also cells subsequently derived from these adipocytes. We hypothesized that adipocytes undergo de-differentiation during breast tumor progression. To this end, we induced breast tumor in the Ad-Chaser-mTmG mice, either by crossing to PyMT-mice or by implanting EO771 breast cancer cells into the mammary gland. After the ‘pulse labeling’, we isolated the tumor fibroblasts either from the PyMT-tumor or allograft-tumor and sorted the EGFP+/ tdTomato- cells by FACS, respectively. These EGFP+/ tdTomato- cells were then used for single-cell sequencing.

first: Qingzhang

last: Zhu

first: Qianbin


title: Modeling human telencephalic development and autism-associated SHANK3 deficiency using organoids generated from single neural rosettes [bulk RNA-seq2]

city: Salt Lake City

first: Yueqi

last: Wang

state: Utah

address: 20 South 2030 East

institute: University of Utah

summary: Human telencephalon is an evolutionary advanced brain structure associated with many uniquely human behaviors and disorders. However, cell lineages and molecular pathways implicated in human telencephalic development remains largely unknown. We generated human telencephalic organoids from stem cell-derived single neural rosettes (SNRs) and investigated telencephalic development under normal and pathological conditions. SNR-derived organoids contained pallial and subpallial neural progenitors (NPs), excitatory and inhibitory neurons, as well as macroglial and periendothelial cells, and demonstrated predictable organization and cytoarchitecture. We comprehensively characterized the properties of neurons in SNR-derived organoids and identified transcriptional programs associated with the specification of excitatory and inhibitory lineages from a common pool of NPs early in telencephalic development. We also demonstrated that neurons in organoids with a hemizygous deletion of an autism- and intellectual disability associated gene SHANK3 exhibit intrinsic and excitatory synaptic deficits associated with impaired expression of clustered protocadherins. Collectively, this study validates SNR-derived organoids as a reliable new model for studying human telencephalic development and identifies novel molecular pathways disrupted by SHANK3 hemizygosity in human telencephalic tissue.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data for ESC(H9, EYQ)-derived 5-months-old telencephalic organoids.

first: Simone

last: Chiola

first: Guang

first: Chad

last: Russell

first: Celeste

middle: J

last: Armstrong

first: Yuanyuan

last: Wu

first: Jay

last: Spampanato

first: Paisley

last: Tarboton

first: H

last: Ullah

first: Nicolas

middle: U

last: Edgar

first: Amelia

middle: N

last: Chang

first: David

last: Harmin

first: Vittoria

last: Dickinson Bocchi

first: Elena

last: Vezzoli

first: Dario

last: Besusso

first: Jun

last: Cui

last: Cattaneo

first: Jan

last: Kubanek

first: Aleksandr

last: Shcheglovitov


title: Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

institute: Netherlands Cancer Institute (NKI)

summary: Here, we uncovered the expression of thousands of previously unnoticed 5’-Uncapped and Polyadenylated Transcripts (5’UPTs). We show that 5’UPTs appear downstream of APA points that occur within the coding and intronic regions of their host genes. Furthermore, 5’UPTs are marked with N6-methyladenosine (m6A) at their 5’ termini, and this modification is linked to their expression. We also demonstrate that 5’UPTs are strongly enriched in polysomal RNA fractions, suggesting protein production capacity. In addition, we examined the expression of 5’UPTs in the biological context of T cell activation, known to induce APA usage. In line with a causal link between APA and 5’UPTs, T cell activation induced 5’UPTs expression and their incorporation into heavy polysomal fractions. Our findings indicate that APA does not only generates shorter upstream mRNA isoforms, but is also responsible for the generation of downstream uncapped and polyadenylated transcripts that possess potential translational capacity.

overall_design: Examination of mRNA levels and cleavage across CDS within transcripts in U2OS, 293, HeLa cells and mouse T-cells (2/3 replicates each).

first: Yuval

last: Malka

first: Ferhat

last: Alkan

first: Shinyeong

last: Ju

first: Pierre-René

first: Abhijeet

last: Pataskar

first: Eldad

last: Shulman

first: Fabricio

last: Loayza-Puch

first: Julien

last: Champagne

first: Casper

last: Wenzel

first: William

last: Faller

first: Ran

last: Elkon

first: Cheolju

last: Lee

first: Reuven

last: Agami


title: Transcriptome Analysis of 3-nitropropanoic acid Effects on COV434 cell lines

city: Wuhan

first: Wenpei

last: Xiang

address: Institute of Reproductive Health, Tongji Medical College, No.13 Hangkong Road

institute: Huazhong University of Science and Technology

summary: Oxidative stress (OS) is regarded as one of the culprits of ovarian dysfunction. OS causes damage to various types of ovarian cells including granulosa cells (GCs), jeopardizing the ovarian microenvironment, disturbing follicular development and participating in various female reproductive disorder. However, the specific molecular pathological mechanisms underlying this process have not been fully elucidated. Therefore, in this study, human ovarian granulosa cell lines COV434 were treated with 3-nitropropanoic acid, a mitochondrial toxin inducing OS by irreversibly inhibiting the succinate dehydrogenase enzyme in the complex II of electron transport chain, to explore the transcriptome changes upon OS exposure.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the control (ctr, in duplicate) group and the 3-nitropropanoic acid (3np, in triplicate) group of COV434 cells.

first: Hongbei

last: Mu

first: Huiying

last: Li

first: Wenpai


title: CD169 is a marker of IFN-γ-stimulated inflammatory macrophages in brain tumor [EGFRviii]

first: Heung Kyu

summary: Therapies against glioblastoma multiforme (GBM) have been largely ineffective due to the infiltration of immunosuppressive tumor-associated macrophages (TAMs). Recent studies demonstrated that TAMs can also be immune-activating. However, markers differentiating these heterogeneous macrophage populations have not been established. In this study, we identified a subset of macrophages expressing CD169 that promote an anti-tumoral microenvironment in GBM. Using single-cell transcriptome analysis, we found that CD169+ macrophages in human and mouse gliomas produced proinflammatory chemokines, leading to the accumulation of T cells and NK cells. Depletion of CD169+ macrophages shortened the survival of mice with gliomas and reduced the function of antitumor lymphocytes. We show that IFN-γ produced by NK cells was critical for the accumulation of CD169+ macrophages into gliomas. Additionally, CD169 expression on macrophages increased the phagocytosis of apoptotic glioma cells. Our finding suggests that the CD169+ subset of TAMs promotes antitumor immune responses against GBM.

overall_design: We analyzed glioma infiltrated immune cells by single cell RNA sequencing (scRNAseq) with 10X genomics. For genetically engineered GBM samples, deletion of PTEN and TP53, and overexpression of EGFRviii were induced in mouse brain ventricle. 16 weeks later, immune cells (CD45+) were sorted from brain tumor and normal brain and analyzed.

first: Hyun-Jin

last: Kim


title: Constitutive Piezo 1 knock out in mouse brain development

status: Public on Aug 20 2022

city: Irvine

first: Jamison

last: Nourse

address: 845 Health Sciences Rd.

department: Physiology and Biophysics

institute: University of California, Irvine

summary: E10.5 whole brain were isolated from WT and Piezo1-KO mice (C57BL/6J strain backgound) described in Ranade et al 2014.  https://doi.org/10.1073/pnas.1409233111

overall_design: six wild type control and nine Piezo1 knock out E10.5 brains

first: Medha

last: Pathak

middle: L

first: Hamid

last: Abuwarda


title: SARS-CoV-2 Variant Delta Potently Suppresses Innate Immune Response and Evades Interferon-Activated Antiviral Responses in Human Colon Epithelial Cells

city: Hyderabad

first: Nitesh

middle: Kumar

last: Singh

state: Telangana

address: Habsiguda

department: Bioinformatics

country: India

institute: Center for Cellular and Molecular Biology

summary: Here we report differential regulation of innate immune response by SARS-CoV-2 variants and immune antagonism by Alpha and Delta variant.

overall_design: Caco-2 cells were infected with four different variant isolates of SARS-CoV-2 for 24-, 48- and 72 hrs and the differential host gene expression was performed by RNA deep sequencing.

first: Dixit

last: Tandel

first: Vishal

last: Sah

first: Sai

last: Poojitha

first: Divya

middle: T

last: Sowpati

first: Krishnan

middle: H

last: Harshan


title: Graphdiyne oxide nanosheets display anti-leukemia efficacy specifically against DNMT3A-mutant AML cells [RNA-Seq]

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

institute: Zhejiang University

summary: Acute myeloid leukemia (AML) is a fatal hematological malignancy for most patients, and DNA methyltransferase 3A (DNMT3A) mutations occur in about 30-35% of AML patients. We show graphdiyne oxide (GDYO), a member of two-dimensional carbon nanomaterials3, demonstrates an anti-leukemia effect in vitro and in vivo against AML cells with DNMT3A mutation specifically. Here, we used RNA-seq to depict transcriptome of AML cells with or without GDYO treatment.

overall_design: Transcriptome profiles of OCI-AML3 cells with or without GDYO treatment.

first: Qiwei

last: Wang

first: Penglei

last: Jiang

first: Pengxu

last: Qian


title: Graphdiyne oxide nanosheets display anti-leukemia efficacy specifically against DNMT3A-mutant AML cells


title: Genome wide mapping of RBP95-HTP binding sites in yeast by CRAC

city: PARIS

first: Simon

last: Lebaron

address: 4 avenue de l'observatoire

country: France

institute: Université Paris Descartes

summary: We report the application of the Cross-Linking and cDNA (CRAC) technique to identify binding sites of RBP95, ribosome assembly factors, on RNAs in vivo. Once sequenced, Rnas associated have been aligned to the yeast genomes and enrichment of specific RNAs has been studied in more details. Specifically apparition of Mutation/deletion in the reads are of interesdt since they mostly corresponds to prceise site of cross-link between bait protein and target RNA. Here RBP95-HTP is mostly bound to 25S rRNA at one partiuclar site and to several snoRNAs, including SNR37, SNR30, SNR190, SNR86 and SNR128.

overall_design: We compare sequences enrichement of RNAs associated to Nap1_HTP or to a mock (un-tagged) control after protein/RNA cross-link in vivo.

first: Anthony

last: Henras


title: Transcriptional adaptations of HUVECs exposed to high and low fluid shear stress

status: Public on Aug 19 2022

city: Berlin

first: Petra

last: Knaus

state: Berlin

address: Thielallee 63

department: Department of Chemistry and Biochemistry

country: Germany

institute: Freie Universität Berlin

summary: The goal of this study was to identify gene signatures in HUVECs exposed to atheroprone low laminar shear stress (LSS) or atheroprotective high laminar shear stress (HSS). The obtained data was used to verify that HSS and LSS application induces gene expression patterns similar to more complex pulsatile and oscillatory flow, respectively.

overall_design: 3 biological replicates of HUVEC monolayers were subjected to HSS (30 dyne/cm^2) or LSS (1 dyne/cm^2). Cells cultured under static conditions were used as a control.

first: Paul-Lennard

last: Mendez

first: Jerome

last: Jatzlau

first: Verena

last: Stangl


title: Single cell transcriptomics reveals critical molecular programming of progenitors for motor neurons and oligodendrocytes in zebrafish

city: Nantong City

first: lingyan

last: xing

email: xlyan011@163.com, xlyan@ntu.edu.cn

address: Xincheng Bridge Street

institute: Nantong University

summary: pmn progenitors and their offspring in spinal cords are isolated for sc-RNAseq

overall_design: olig2+ cells were isolated from the trunks of Tg(olig2:dsred) by FACS and underwent scRNA-seq

first: Lingyan

last: Xing

first: Rui

last: Chai

first: Jiaqi

first: Gang

last: Chen


title: Expression data from human iTS-L cells: induced tissue-specific stem cells from liver

city: Kyoto

first: Yoshiki

last: Nakashima

state: Kyoto

address: Kyoto Research Park KISTIC Building Room 501, 5th floor, KISTIC building,  134 Chudoji Minami-cho, Shimogyo-ku

department: Research and Development Center

institute: Kyoto University Center for iPS Cell Research and Application Foundation (CiRA Foundation)

overall_design: 4 Total samples were analyzed. We performed a microarray analysis to compare the global gene-expression profiles of human iPSCs (201B7), iTS-L cells (No. 33), and hepatocytes from two different donors. Unsupervised hierarchical clustering of gene expression profiles of iPSCs (201B7), iTS-L cells (No. 33), and hepatocytes showed that iTS-L cells markedly differed from iPSCs and hepatocytes and that iTS-L cells (No. 33) clustered more closely with iPSCs (201B7) than hepatocytes from two different donors.

first: Hirofumi

last: Noguchi


title: Gene expression profiles at the single cell levels of murine tumor inflitrating PD-1 and PD-1 KO NK cells

city: Solna

first: Chris

middle: Andrew

last: Tibbitt

state: non-US

address: Biomedicum C7,, Tomtebodavägen 16

country: Sweden

institute: KI

summary: Here, we found by single cell RNA sequencing analysis that PD-1 can be expressed on MHC class I-deficient tumor-infiltrating NK cells in vivo. We also demonstrate distinct alterations in the phenotype of PD-1-deficient NK cells and a more mature phenotype which might reduce their capacity to migrate and kill in vivo.

overall_design: Using WT and PD-1-/- mice, we performed single cell RNA-sequencing (scRNA-SEQ) using the SMART-SEQ2 platformon tumor-infiltrating NK cells from mice inoculated with the MTAP1A tumor.

first: Christopher

first: Benedict

last: Chambers


title: DNA methylation underpins the epigenomic landscape regulating genome transcription in Arabidopsis

first: Qiangwei

last: Zhou

state: Hubei

address: Hongshan district, shizishan #1

institute: Huazhong Agricultural university

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

overall_design: Refer to individual Series


title: Spatiotemporal transcriptomes of orchid flowers

status: Public on Aug 18 2022

city: Shanghai

first: Ji

last: Qi

state: Shanghai

address: E401, Life Science Building, Jiangwan Campus, Fudan University, 2005 Songhu Rd.

department: School of Life Sciences

institute: Fudan University

summary: We performed spatial transcriptome sequencing of orchid to provide spatial cell atlas of floral organogenesis.

overall_design: Phalaenopsis Big Chili flowers at early developing stages sequenced on 10X Visium platform

first: Chang

last: Liu

first: Jing

last: Leng

first: Yonglong

last: Li

first: Tingting

last: Ge

first: Jinglong

first: Yamao

first: Chunce

last: Guo


title: DNA Methylation shapes histone modification landscape for transcription regulation in Arabidopsis [RNA-Seq]

summary: DNA methylation and histone modifications cooperate to shape the epigenetic landscape for transcription regulation, but their orchestration is not fully understood due to the lack of met1 drm1 drm2 cmt2 cmt3 mutants (mddcc), in which total DNA methylation were eliminated. This is the first time to generate mddcc that allow us to elucidate the roles of DNA methylation in the upheaval of histone modification landscape, transposon activity and gene expression. We found that DNA methylation elimination-triggered genome-wide transcriptional reprogramming is largely orchestrated by the redistribution and conversion of histone modifications. We also distinguished the contribution of CG and non-CG methylation to the histone modification landscape. Furthermore, we reveal histone modifications can serve as an independent regulatory system despite the influence of DNA methylation. Taken together, we provide comprehensive insights into the roles of DNA methylation in shaping epigenomic landscape for genome transcription, which deep understanding of epigenomic regulation.

overall_design: Here, we generated genome-wide profiling of six histone modifications and RNA polymerase II occupancy using an enhanced chromatin immunoprecipitation (eChIP) approach in wild-type (Col-0), ddcc (drm1 drm2 cmt2 cmt3), met1, and mddcc (met1 drm1 drm2 cmt2 cmt3). By integrating DNA methylation, and transcriptome datasets, we revealed the roles of DNA methylation in histone modification landscape and transcriptional regulation.

first: Lun

last: Zhao

first: Li

last: He

first: Guoliang

first: Jian-Kang

last: Zhu


title: DNA Methylation shapes histone modification landscape for transcription regulation in Arabidopsis [ChIP-Seq]


title: DNA Methylation shapes histone modification landscape for transcription regulation in Arabidopsis [WGBS]


title: HyperTRIBE uncovers MSI2 RNA binding activity and the effect of Ro, GSK-591 and combination in Z-138 cells

status: Public on Aug 17 2022

city: new york

first: Michael

last: Kharas

state: New York

address: 417 68th street

department: Molecular Pharmacology Program

institute: Mamorial Sloan Kettering Cancer Center

summary: Identifying MSI2 RNA-direct binding targets in B-cell lymphoma and evaluating how MSI2 binding activity can be affected by the inhibition of PRMT5 using GSK-591 and the MSI2 inhibitor, Ro and the combination of the two agents.

overall_design: Z-138 cells overexpressing MSI2-ADA or MIG (empty vector) were treated for with DMSO, Ro, GSK-591 and combination for 24h and harvested for RNA-seq to look for A-G editing events.

first: Tatiana

last: Erazo

first: Chiara

last: Evans

first: Karen

last: Chu


title: Characterizing DNA methylation signatures of retinoblastoma using the aqueous humor liquid biopsy: moving beyond genomics

city: Los Angeles

first: Gangning

last: Liang

address: 1441 Biggy street

department: Urology

institute: USC Keck school of medicine

summary: Identify DNA methylation change in retinoblastoma using aqueous humor cfDNA

overall_design: DNA methylation status of four regions were checked using targeted bisulfite sequencing.

first: Hong-Tao

first: Liya

last: Xu

first: Jesse

last: Berry


title: Graphdiyne oxide nanosheets display anti-leukemia efficacy specifically against DNMT3A-mutant AML cells  [Bisulfite-Seq]

first: Jiang

last: Penglei

summary: Acute myeloid leukemia (AML) is a fatal hematological malignancy for most patients, and DNA methyltransferase 3A (DNMT3A) mutations occur in about 30-35% of AML patients. We show graphdiyne oxide (GDYO), a member of two-dimensional carbon nanomaterials3, demonstrates an anti-leukemia effect in vitro and in vivo against AML cells with DNMT3A mutation specifically. Here, we used reduced representation bisulfite sequencing (RRBS) to depict DNA methylome of AML cells with or without GDYO treatment.

overall_design: DNA methylation profiles of OCI-AML3 cells with or without GDYO treatment.

first: Qiwei

last: Wang

first: Penglei

last: Jiang

first: Pengxu

last: Qian


title: RNA-seq datasets of Ro, GSK-591 and combination treatment in Z-138 cells

summary: Dual targeting of PRMT5 and MSI2 inhibited synergisticly B-cells proliferation. Thus, next-generation sequencing was performed to evaluate the effect of the inhibitors of PRMT5 and MSI2, GSK-591 and Ro, respectively, in the global transcriptome of the mantle cell lymphoma cell line, Z-138.

overall_design: Z-138 cells overexpressing MIG (empty vector) were treated for with DMSO, Ro, GSK-591 and combination for 24h and harvested for RNA-seq


title: DNA methylation analysis of the cell free DNA from Retinoblastoma

type: Methylation profiling by genome tiling array

summary: Retinoblastoma (RB) is a primary intraocular cancer in infants and toddlers. Direct biopsy is contraindicated in RB due to the risks of provoking extraocular tumor spread. In this study, we demonstrated that DNA methylation profile can be obtained from the tumor-derived cell-free DNA in aqueous humor (AH) and is highly concordance with that directly from RB primary tumors. It is the first time to identify unique DNA methylation pattern from RB tumor before surgically removing the eye. We provde the evidence that DNA methylation from AH could not only be used for RB diagnosis, but also for the prognostic prediction and potential therapeutic targets by personalized approach.

overall_design: The cell-free DNA was extracted from aqueous humor of RB patient and DNA methylation was detected by Infinium methylationEPIC array.

last: Li


title: RNA-sequencing: Black Death shaped the evolution of immune genes

city: Chicago

first: Tauras

last: Vilgalys

state: Illinois

address: 5801 S Ellis Ave

institute: University of Chicago

summary: Expression response of cells stimulated with Y. pestis, including genes which overlap candidates for postiive selection inferred using ancient genomes.

overall_design: RNA expression profiles of control (mock-infected) and Yersinia pestis-infected monocyte-derived macrophages from 33 individuals (n=66 samples).

first: Jennifer

last: Klunk

first: Hendrik

last: Poinar

first: Luis

last: Barreiro


title: Ro, GSK-591 and combination treatment in Z-138 cells

status: Public on Aug 16 2022


title: Heterogeneity and molecular programming of progenitors for motor neurons and oligodendrocytes

first: lingyan

last: xing

summary: The pMN domain is a restricted domain in the ventral spinal cords, defined by the expression of olig2 gene. The fate determination of pMN progenitors is highly temporally and spatially regulated, with motor neurons and oligodendrocyte progenitor cells (OPCs) developing sequentially. Insight into the heterogeneity and molecular programs of pMN progenitors is currently lacking. With the zebrafish model, we identified multiple states of neural progenitors using single-cell sequencing: proliferating progenitors, common progenitors for both motor neurons and OPCs, and restricted precursors for either motor neurons or OPCs. We found specific molecular programs for neural progenitor fate transition, and manipulations of representative genes in the motor neuron or OPC lineage confirmed their critical role in cell fate determination. Deciphering progenitor heterogeneity and molecular mechanisms for these transitions will elucidate the formation of complex neuron-glia networks in the central nervous system during development, and understand the basis of neurodevelopmental disorders.

first: Lingyan

last: Xing

first: Rui

last: Chai

first: Jiaqi

first: Gang

last: Chen


title: Integrative Analysis Reveals Histone Demethylase LSD1/KDM1A Regulates RNA Polymerase II Pausing

city: Camperdown

first: Pengyi

last: Yang

address: The University of Sydney

country: Australia

institute: The University of Sydney

summary: Lysine-specific demethylase 1 (LSD1) catalyzes the demethylation at H3K4 and H3K9 and is well- known for its role in decommissioning enhancers during mouse embryonic stem cell (ESC) differentiation. However, its role at gene promoters remains poorly understood in ESCs despite their widespread presence at these sites. Here, we report that LSD1 promotes RNA Polymerase II (RNAPII) pausing, a rate-limiting step in transcription regulation, in ESCs. We found that the knockdown of LSD1 preferentially affects genes with higher RNAPII pausing than those with lower pausing. We show that LSD1 knockdown leads to the global reduction in RNAPII pausing and most significantly on the genes bound by LSD1. Next, we demonstrate that the co-localization of LSD1 and MYC, a factor known to regulate pause-release, is associated with the enrichment of other RNAPII pausing factors. Finally, we found that genes co-occupied by LSD1 and MYC are significantly enriched for housekeeping genes that are involved in metabolic processes and depleted of transcription factors compared to those bound only by LSD1. Our integrative analysis reveals a pleiotropic role of LSD1 in promoting RNAPII pausing and in regulating housekeeping programs besides its known role in regulating cell identity programs.

overall_design: Investigating the role of LSD1/KDM1A in RNA Polymerase II Pausing

first: Hani

last: Kim

first: Pishun

first: Taiyun

first: Andrew

last: Oldfield

first: Xiaofeng

last: Zheng


title: Helicobacter pylori shows tropism to gastric differentiated pit cells dependent on urea chemotaxis.

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: The human gastric epithelium forms highly organized gland structures with different subtypes of cells. The carcinogenic bacterium Helicobacter pylori can attach to gastric cells and subsequently translocate its virulence factor CagA, but the possible host cell tropism of H. pylori is currently unknown. Here, we report that H. pylori preferentially attaches to differentiated cells in the pit region of gastric units. Single-cell RNA-seq shows that organoid-derived monolayers recapitulate the pit region, while organoids capture the gland region of the gastric units. Using these models, we show that H. pylori preferentially attaches to highly differentiated pit cells, marked by high levels of GKN1, GKN2 and PSCA. Directed differentiation of host cells enable enrichment of the target cell population and confirm H. pylori preferential attachment and CagA translocation into these cells. Attachment is independent of MUC5AC or PSCA expression, and instead relies on bacterial TlpB-dependent chemotaxis towards host cell-released urea, which scales with host cell size.

overall_design: mRNA profiles from ex vivo human gastric units, 3D human gastric organoids, and 2D human gastric organoid-derived monolayers (naïve, bystander and H. pylori infected).

first: Carmen

last: Aguilar

first: Mindaugas

last: Pauzuolis

first: Malvika

last: Pompaiah

first: Ehsan

last: Vafadarnejad

first: Panagiota

last: Arampatzi

first: Mara

last: Fischer

first: Dominik

last: Narres

first: Mastura

last: Neyazi

first: Özge

last: Kayisoglu

first: Thomas

last: Sell

first: Nils

last: Blüthgen

first: Markus

last: Morkel

first: Armin

last: Wiegering

first: Christoph-Thomas

last: Germer

first: Stefan

last: Kircher

first: Andreas

last: Rosenwald

first: Sina

last: Bartfeld


title: Tracking ex vivo hematopoietic stem cell function using Fgd5 and EPCR reveals molecular regulators of expansion.

city: Cambridge

first: Daniel

last: Bode

email: db704@cam.ac.uk, 1danielbode@gmail.com

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus

department: Cambridge Stem Cell Institute

institute: University of Cambridge

summary: Hematopoietic stem cells (HSCs) cultured outside the body are the fundamental component of a wide range of cellular and gene therapies. Recent efforts have achieved more than 200-fold expansion of functional HSCs, but their molecular characterization has not been possible due to the substantial majority of cells in these cultures being non-HSCs and the fact that single cell-initiated cultures display substantial clone-to-clone variability. Using the Fgd5 reporter mouse in combination with EPCR, we have identified an in vitro reporter strategy capable of exclusively identifying HSC-containing clones and prospectively separating HSCs from non-HSCs. Linking single clone functional transplantation data with single clone gene expression profiling, we also reveal the molecular profile of expanded HSCs which is more similar to actively cycling fetal liver HSCs than quiescent adult bone marrow HSCs from which they were derived. A gene expression signature derived from the molecular profiling identifies core molecular components of HSCs, including Prdm16, Fstl1 and Palld, that can further predict the functional outcome in transplantation assays. Taken together, this system represents a new tool to be used for a wide-range of functional screening and molecular experiments previously not possible to carry out due to limited HSC numbers

overall_design: We performed bulk RNA-sequencing on expanded clones, derived from single murine LT-HSCs. For each clone, the stem cell population (EPCR+Lin-Sca1+cKit+ [ELSK]) and all remaining cells (nonELSK) were separated by flow sorting and sequenced. In total, we collected and sequenced 11 ELSK and 12 nonELSK samples. Both ELSK and nonELSK groups are further divided by their repopulation outcome - repopulating ELSK (PosELSK), repopulating nonELSK (PosNonELSK), non-repopulating ELSK (NegELSK) and non-repopulating nonELSK (NegNonELSK). We also performed scRNA-seq on hibernating HSCs (n=36) and fetal liver HSCs (n=54).

first: James

last: Che

first: Iwo

last: Kucinski

first: Alyssa

last: Cull

first: Fiona

last: Bain

first: Melania

last: Barile

first: Grace

last: Boyd

first: Miriam

last: Belmonte

first: Juan

last: Rubio-Lara

first: Mairi

last: Shepherd

first: Anna

last: Clay

first: Adam

last: Wilkinson

first: Satoshi

last: Yamazaki

first: Berthold

last: Göttgens

first: David

last: Kent


title: Development of a platform to investigate long term potentiation in human iPSC-derived neuronal networks

city: La Jolla

first: Anne

last: Bang

state: CA

address: 10901 North Torrey Pines Road

department: Prebys Center

institute: Sanford Burnham Prebys Medical Discovery Insititute

summary: Although impairment of long-term potentiation (LTP) is a common feature of many neurological disorders, studies in humans are limited by inaccessibility of the brain. Human induced pluripotent stem cells (hiPSC) provide a unique opportunity to study LTP, especially in disease specific genetic backgrounds. We describe a multi-electrode array (MEA)-based assay to investigate chemically induced LTP (cLTP) in networks of hiPSC-derived midbrain dopaminergic (DA) and cortical neuronal populations. We demonstrate potentiation of activity that lasts for days, allowing for studies of the late phases of LTP. We show that cLTP on midbrain DA neuronal networks is largely independent of the N-methyl-D-aspartate receptor (NMDAR), and demonstrate partial dependence on brain derived neurotrophic factor (BDNF), as well as other factors released into the medium. Finally, we describe activity-regulated gene expression induced by cLTP. In summary, this cLTP-MEA assay platform will enable phenotype discovery and higher throughput analyses of synaptic plasticity on hiPSC-derived neurons.

overall_design: Study of activity regulated gene expression induced by chemical long term potentiation (cLTP), mediated by forskolin and rolipram (FSK/ROL) treatment, on human induced pluripotent stem cell  (hiPSC) derived midbrain dopaminargic neuronal cell population co-cultured with hIPSC derived astrocytes, five hours post washout of FSK/ROL.


title: Characterizing DNA methylation signatures of retinoblastoma using the aqueous humor liquid biopsy

first: Gangning

last: Liang


title: The alterations of gene expression profiling induced by LINC00857 knockdown in HCT116 cells

status: Public on Aug 15 2022

city: Weifang City

first: Jiaqiu

last: Li

state: 省/直辖市

address: No. 2428, Yuhe Road, Kuiwen District

institute: weifang medical university

summary: Long noncoding RNAs (lncRNAs) have been identified to play increasingly important roles in tumorigenesis, and they may serve as novel biomarkers for cancer therapy. Recently, LINC00857 was found to play an oncogenic role in in several cancers. Here we report gene expression profiles of HCT116 cells treated with LINC00857 siRNA. This study reveals a novel role of LINC00857 in downstream gene regulation and provides a new explanation of LINC00857’ s function in colorectal cancer.

overall_design: RNA-seq after knockdown of LINC00857 in HCT116 cells.


title: EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma

city: Columbus

first: Iftekhar

middle: Ahmed

last: Showpnil

state: OH

address: 700 Childrens Drive

department: CCCBD

institute: Nationwide Children's Hospital


title: EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (4C)

summary: Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or highly related fusions. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma.  We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. EWS/FLI binding is primarily associated with compartment activation, establishment of topologically-associated domain (TAD) boundaries, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation.  Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines.  These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators through three-dimensional reprogramming of chromatin.

overall_design: Circular chormatin conformation capture (4C) experiment performed using a GGAA-microsatellite as the viewpoint in A673 EF-Endo, EF-KD and EF-Rescue and in TC71 EF-Endo, EF-KD and EF-Rescue Ewing sarcoma cells.

first: Stephen

last: Lessnick


title: Scaling of cellular gene expression with ploidy

city: Kaiserslautern

first: Zuzana

last: Storchova

state: Rhineland Palatinate

address: Paul Ehrlich Straße 24

department: Molecular Genetics

institute: Technical University Kaiserslautern

summary:
Whereas most eukaryotic cells are diploid, carrying two chromosome sets, variances in ploidy are common. Despite the relative prevalence of ploidy changes and their relevance for pathology and evolution, the consequences of altered ploidy for cellular gene expression remain poorly understood. We quantified changes in the transcriptome and proteome of the yeast Saccharomyces cerevisiae with different ploidy, from the haploid to the tetraploid state. We found that the abundance of proteins increases with ploidy, but does not scale proportionally with increasing DNA content, suggesting a compensatory, cellular response to increases in ploidy.
We further found that pathways related to cytoplasmic ribosomes and translation are differentially regulated. With increasing ploidy the cells reduced the rRNA and ribosomal protein abundance, although they maintained a constant translational output. These adaptations stem from an active process that involves the kinases Tor1 and Sch9 and the transcriptional corepressor of rDNA transcription, Tup1. Consistent with our results in yeast, human tetraploid cells show reduced mTORC1 activity and downregulated their ribosome content via the Tup1 homolog Tle1, demonstrating that the proteome remodeling pathway discovered here constitutes a conserved response pathway to increased ploidy.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

first: G

last: Yahya

first: P

last: Menges

first: D

last: Ngandiri

last: Schulz

first: A

last: Wallek

first: N

last: Kulak

first: M

last: Mann

last: Cramer

first: V

last: Savage

last: Raeschle

first: Z


title: EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (CUT&Tag II)

overall_design: EWS/FLI knock-down with RNAi followed by rescue of EWS/FLI expression with a 3XFLAG tagged EWS/FLI cDNA construct


title: Differential expression of miRNAs and mRNAs in Moritella viscosa challenge Atlantic salmon

status: Public on Aug 14 2022

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Moritella viscosa is a bacterial pathogen causing winter-ulcer disease in Atlantic salmon. The lesions on affected fish lead to increased mortality, decreased fish welfare, and inferior meat quality in farmed salmon. MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional regulation by guiding the miRNA induced silencing complex to specific mRNA transcripts (target genes). The goal of this study was to identify miRNAs responding to Moritella viscosa in salmon by investigating miRNA expression in head-kidney and the muscle/skin from lesion sites caused by the pathogen. Protein coding gene expression was investigated by microarray analysis in the same materials.

overall_design: Atlantic salmon was bath challenged with the pathogen. Head kidney and ulcers (skin and muscle) were sampled after 9, 23 and 34 days.

first: Ramberg

last: Sigmund

first: Andreassen

last: Rune

first: Krasnov

last: Aleksei


title: Application of the Illumina MethylationEPIC on small amount of fragmentized HCT116 genomic DNA

first: Gangning

last: Liang

summary: Cell-free DNA is generally in fragments around 200 bp. Genomic DNA from HCT116 cell is sonicated to around 200 bp to mimic cell-free DNA. This is a control assay to test the sensitivity of Infinium methylationEPIC array for low amount of fragmentized DNA.

overall_design: The genomic DNA was extracted from HCT116 cell and sonicated to fragment around 200 bp. DNA methylation was detected by Infinium methylationEPIC array.

first: Hong-Tao

last: Li


title: Expression profiling explores pathways involved in pterygium progression

status: Public on Aug 13 2022

city: Beijing

first: lvzhen

last: Huang

state: (State)

address: Xizhimen South Street 11, Xi Cheng District

institute: Peking university people‘s hospital

summary: Pterygium is an ocular surface disease that can cause visual impairment if it progressively invades the cornea. Although many pieces of research showed that ultraviolet radiation triggers pterygium pathological progress, the underlying mechanism in pterygium remains indistinct. In this study, we used microarray to evaluate the changes of transcripts between primary pterygium and adjacent normal conjunctiva samples in China, hoping to find underlying pathways involved in pterygium progression.

overall_design: Two nasal primary pterygium samples and two adjacent normal conjunctiva samples were obtained from participants through pterygium excision surgery.

first: Jiarui

first: Tianchang

last: Tao

first: Lvzhen


title: EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (RNA-Seq)

first: Iftekhar

last: Showpnil

overall_design: RNA-sequencing of A673 and TC71 Ewing sarcoma cells containing EWS/FLI or depleted of EWS/FLI using RNAi

first: Stephen

last: Lessnick


title: EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (CuT&Tag I)

overall_design: EWS/FLI and EWS/ERG CUT&Tag in A673, TC71, SK-N-MC, EWS-502 and TTC-466 Ewing sarcoma cells


title: Arteriovenous Fistulae in Chronic Kidney Disease and the Heart: Physiological, Histological, and Transcriptomic Characterization of a Novel Rat Model

city: Leuven

first: Jef

last: Van den Eynde

address: Herestraat 49

department: Department of Cardiovascular Sciences

country: Belgium

institute: KU Leuven

summary: Arteriovenous fistulae (AVF) are the gold standard for vascular access in those requiring hemodialysis, but may put an extra hemodynamic stress on the cardiovascular system. The complex interactions between the heart, kidney, and AVF remain incompletely understood. In this project, we characterized a novel rat model of 5/6th partial nephrectomy (NX) and AVF.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from heart (H) and kidney (K) samples of 3 groups of rats (Sprague-Dawley, 13 weeks old): (1) sham, (2) NX only, and (3) AVF+NX.

first: Xander

last: Jacquemyn

first: Nicolas

last: Cloet

first: Dries

last: Noé

first: Hilde

last: Gillijns

first: Marleen

last: Lox

first: Willy

last: Gsell

first: Uwe

last: Himmelreich

first: Aernout

last: Luttun

first: Keir

last: McCutcheon

first: Stefan

last: Janssens

first: Wouter

last: Oosterlinck


title: Effect of depletion of SOD1 on gene expression of organoid culture

status: Public on Aug 12 2022

first: Yingchao

last: Wang

address: 145 Middle Shandong Road

institute: Shanghai Institute of Digestive Disease

summary: To investigate the function of SOD1 in regulation of ISC growth, we established intestinal organoids from tamoxifen–inducible intestinal epithelial cell (IEC)–specific Sod1 knockout (Sod1f/f; Vil-creERT2) mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of Sod1f/f and Sod1f/f;Vil-creERT2 organoids after 3 days of tamoxifen treatment. Organoids were derived from three mice of each genotype.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and SOD1 knockout organoids

first: Ying-Chao

first: Xiao-Xu

last: Leng

first: Cheng-Bei

last: Zhou

first: Shi-Yuan

last: Lu


title: Mechanism of activation of porcine dendritic cells by an alpha-D-glucan nanoparticle adjuvant and nanoparticle/poly(I:C) combination adjuvant.

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

institute: Purdue University

summary: RNA sequencing was performed to identify immune-related genes that were differentially expressed in porcine monocyte-derived dendritic cells following stimulation with a novel phytoglycogen-based nanoparticle (Nano-11) and the TLR3 agonist poly(I:C).

overall_design: Comparative gene ontology and KEGG pathway enrichment analyses were performed to identify differentially expressed genes in porcine DCs induced by Nano-11 and the combination adjuvant.

first: Juan

middle: F

last: Hernandez-Franco

first: Jyothi

last: Thimmapuram

first: Darryl

last: Ragland

first: Harm

last: HogenEsch


title: Target genes of thyroid hormone (TH) in white adipose tissue (WAT) and striatum and their role during metabolic stressors

city: Lyon

first: Yanis

last: ZEKRI

address: 32-34 Avenue Tony Garnier

institute: IGFL-ENS

summary: We gathered in a single database available RNAseq and ChIPseq data to better characterize the target genes of the thyroid hormone receptors in several cell types. This database can serve as a resource to analyze the mode of action of the hormone. Also, it is an easy-handling convenient tool to obtain information on specific genes in regards to T3 regulation, or extract larger list of genes of interest based on the users’ criteria. Overall, this atlas is a unique compilation of recent sequencing data focusing on thyroid hormones, their receptors, mode of action, targets and roles which may profit researchers within the field. A preliminary analysis indicates extensive variations in the repertoire of target genes which transcription is upregulated by chromatin-bound nuclear receptor. Although it has a major influence, chromatin accessibility is not the only parameter that determines the cellular selectivity of hormonal response.

overall_design: We performed high-throughput gene expression profiling of striatum and white adipose tissue (WAT) in hypothyroid mice (treated with PTU) after thyroid hormone (TH) treatment

last: Zekri

first: Romain

last: Guyot

first: Frédéric

last: Flamant


title: EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (Cut&Tag III)

first: Iftekhar

last: Showpnil

relation:
Reanalysis of: GSM4292892
Reanalysis of: GSM4292893
Reanalysis of: GSM4292898
Reanalysis of: GSM4292899
Reanalysis of: GSM4292900
Reanalysis of: GSM4292901
Reanalysis of: GSM4292906
Reanalysis of: GSM4292907
Reanalysis of: GSM4292908
Reanalysis of: GSM4292909
Reanalysis of: GSM4292914
Reanalysis of: GSM4292915
SubSeries of: GSE185132

middle: A

first: Stephen

last: Lessnick


title: Mouse complete embryoid development within a yolk sac recapitulates gastrulation, neurulation and early organogenesis

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Embryo-like structures generated from stem cells can achieve varying developmental milestones, but none have been shown to progress through gastrulation, neurulation, and organogenesis. Here, we show that "ETiX" mouse embryoids, assembled from embryonic stem cells, trophoblast stem cells and inducible extraembryonic endoderm stem cells, can develop into gastrulating embryoids, and beyond to generate neurulating embryoids, which generate the progenitors needed to create the entire organism. The head-folds of ETiX neurulating embryoids show anterior expression of Otx2, defining forebrain and midbrain regions that resemble those of the natural mouse embryo. Neurulating embryoids also develop beating heart-like structures, trunks comprising a neural tube and somites, tail buds containing neuromesodermal progenitors and primordial germ cells, and gut tubes derived from definitive endoderm. Notably, neurulating embryoids also develop a yolk sac with blood islands. Overall, ETiX neurulating embryoid formation strongly resembles natural embryogenesis, advancing embryo-like development further than any other stem-cell derived model and within extra-embryonic membranes.

overall_design: We applied tiny sci-RNA-seq3 to profile 285,640 single cell transcriptomes from multiple individual ETiX mouse embryoids (day6 and day8) and natural mouse embryos (E7.5, E8, E8.5, E8.75. and E9), in one experiment.

first: Gianluca

last: Amadei

first: Charlotte

middle: E

last: Handford

first: Joachim

last: De Jonghe

first: Hannah

last: Greenfeld

first: Martin

last: Tran

first: Beth

last: Martin

first: Dong-Yuan

last: Chen

first: Alejandro

last: Aguilera-Castrejon

first: Jacob

last: Hanna

first: Michael

last: Elowitz

first: Florian

last: Hollfelder

first: Jay

last: Shendure

first: David

last: Glover

first: Magdalena

last: Zernicka-Goetz


title: Characterization of hepatic stellate cells (HSC) genes in the normal liver or diverse liver fibrotic models by scRNAseq and bulk RNAseq.

city: NEW YORK

first: Robert

last: Schwabe

state: NY

address: 1130 ST NICHOLAS AVE - ROOM 916B

department: Medicine

institute: Columbia University

summary: Hepatocellular carcinoma (HCC), the fourth leading cause of cancer mortality, develops almost exclusively in patients with chronic liver disease (CLD) and advanced fibrosis. Here we interrogated functions of hepatic stellate cells (HSC), the main source of liver fibroblasts, during hepatocarcinogenPesis. Genetic depletion, activation or inhibition established HSC as tumour-promoting in mouse models of HCC. HSC were enriched in the preneoplastic environment, where they closely interacted with hepatocytes and modulated hepatocarcinogenesis by regulating hepatocyte proliferation and death. Analysis of mouse and human HSC subpopulations and their associated mediators by single cell RNA-sequencing in conjunction with genetic ablation revealed dual functions of HSC in hepatocarcinogenesis. Hepatocyte growth factor, enriched in quiescent and cytokine-producing HSC (cyHSC), protected from hepatocyte death and HCC development. In contrast, type I collagen, enriched in activated myofibroblastic HSC (myHSC), promoted proliferation and tumour development via increased stiffness and TAZ activation in pretumoural hepatocytes and via activation of discoidin domain receptor 1 in established tumours. An increasing HSC dysbalance between cyHSC and myHSC during liver disease progression was associated with elevated HCC risk in patients. In summary, the dynamic shift of HSC subpopulations and their mediators during CLD is associated with a switch from HCC protection to HCC promotion.

overall_design:
- Single Cell RNAseq of isolated HSC from fibrotic livers induced by CCl4 (RS039, n=1), TAZ+FPC-NASH diet (RS042, n=1) and HF-CDAA diet (RS043, n=1)
- Bulk RNA sequencing of isolated HSC from FPC-treated mice (n=5), or by CCl4 (n=4)
- Bulk RNA-sequencing from normal (n=8), adjacent (n=10) and HCC (n=10) mouse livers with or without HSC inhibition induced by YAP deletion in HSC during hepatocarcinogenesis induced by DEN+CCl4

first: Aveline

last: Filliol

first: Ajay

last: Nair


title: Atlas of target genes of thyroid hormone (TH) in mice

first: Yanis

last: ZEKRI

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for TRa in GABAergic neurons from adult striatum

last: Zekri

first: Romain

last: Guyot

first: Frédéric

last: Flamant


title: High throughput sequencing for circRNAs and mRNAs in XPO4 knockout NIH/3T3 cell [RNA-seq]

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

institute: University of Science and Technology of China

type: Non-coding RNA profiling by high throughput sequencing

summary: Numerous RNAs are exported from the nucleus, abnormalities of which lead to cellular complications and diseases. We report the identification of Exportin 4 (XPO4) as a conserved circular RNA (circRNA) exportin. Cellular insufficiency of XPO4 causes nuclear circRNA accumulation, circRNA:DNA (ciR-loop) formation, linear RNA:DNA (liR-loop) buildup, and DNA damage. These results provide insights into the mechanism and biomedical links of circRNA nuclear export.

overall_design: Examination of circRNA expression level and gene expression level in NIH/3T3 cells.


title: Functional characterization of enhancer activity during a long terminal repeat's evolution

city: St. Louis

first: Alan

middle: Y

last: Du

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University at St. Louis School of Medicine

summary: Many transposable elements (TEs) contain transcription factor binding sites and are implicated as potential regulatory elements. However, TEs are rarely functionally tested for regulatory activity, which in turn limits our understanding of how TE regulatory activity has evolved. We systematically tested the human LTR18A subfamily for regulatory activity using massively parallel reporter assay (MPRA) and found AP-1 and C/EBP-related binding motifs as drivers of enhancer activity. Functional analysis of evolutionarily reconstructed ancestral sequences revealed that LTR18A elements have generally lost regulatory activity over time through sequence changes, with the largest effects occurring due to mutations in the AP-1 and C/EBP motifs. We observed that the two motifs are conserved at higher rates than expected based on neutral evolution. Finally, we identified LTR18A elements as potential enhancers in the human genome, primarily in epithelial cells. Together, our results provide a model for the origin, evolution, and co-option of TE-derived regulatory elements.

sample_organism:
Homo sapiens
Escherichia coli DH5[alpha]

overall_design: MPRA of the LTR18A transposable element subfamily and reconstructed ancestral sequences in K562 and HepG2

first: Ting

last: Wang


title: Effect of NAMPT inhibition on gene expression in LPS/IFNg-stimulated primary mouse astrocytes

city: Tel Aviv

first: Lior

last: Mayo

state: Israel

address: Britannia Bldg. Room 204, Tel Aviv univeristy

country: Israel

institute: Tel Aviv Unoversity

summary: To investigate the role of NAMPT activity on astrocyte pro-inflmmatory activation

overall_design: Comparative gene expression profiling analysis of RNA-seq data for astrocytes activated for 6 h with LPS/IFNγ or left untreated (Con) in the presence of FK866 or Vehicle control

first: Tom

last: Meyer

first: Dor

last: Shimon


title: Widespread alternative polyadenylation regulation reprograms the prostate cancer cell transcriptome upon androgen receptor inhibition.

city: Rome

first: Marco

last: Pieraccioli

address: Largo Francesco Vito 1

country: Italy

institute: Catholic University of the Sacred Heart rome

summary: Prostate cancer (PC) onset and progression relies on the androgen receptor (AR) signaling. Anti-androgenic hormonal therapy (HT) is initially efficacious, but most patients evolve to a castration resistant stage (CRPC) for which no cure is currently available. Most proposed mechanisms of acquired resistance to HT focus on the transcriptional activity in CRPC cells. In this study, however, we have uncovered a new role of AR in alternative cleavage and polyadenylation (APA) regulation.

overall_design: We have profiled the global effect of Enzalutamide on alternative polyadenylation by 3’READS-seq analysis using RNA isolated from LNCaP cells following 24 hours treatment with Enzalutamide or vehicle control DMSO (3 biological replicates).

first: Cinzia

last: Caggiano

first: Gabriele

last: Babini

first: Chuwei

last: Zhong

first: Bin

last: Tian

first: Pamela

last: Bielli

first: Claudio

last: Sette


title: TLR2-induced CD8+ T cell deactivation shapes dendritic cell differentiation in the bone marrow during sepsis

status: Public on Aug 11 2022

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

institute: University Hospital Essen

summary:
Sepsis is associated with profound immune dysregulation that increases the risk for life-threatening secondary infections: Dendritic cells (DCs) undergo functional reprogramming due to yet unknown changes during differentiation in the bone marrow (BM).
We investigated whether T cells alter the gene expression in the bone marrow during sepsis using microarrays.

overall_design: CD8 T cells from wildtype or TLR2 ko mice were transferred into wildtype mice immediately before induction of sepsis by cecal ligation and puncture. After 24 h, bone marrow cells were isolated for RNA extraction and microarrays.

first: Anne

middle: C

last: Antoni

first: Ekaterina

last: Pylaeva

first: Jadwiga

last: Jablonska

first: Ludger

last: Klein-Hitpaß

first: Marcel

last: Dudda

first: Stefanie

middle: B

last: Flohé


title: Stem cell-derived mouse embryos develop within an extra-embryonic yolk sac to form anterior brain regions and a beating heart

city: Cambridge

first: Florian

last: Hollfelder

address: 80 Tennis court road

institute: University of Cambridge

summary: We report the analysis by inDrop single cell sequencing of mouse embryos at embryonic day E6.5, E7.5 and E8.5 as well as the analysis of stem cell derived synthetic embryos generated with the previously reported protocol (Amadei et al., 2021) and cultured to day 5, day 6 and day 8 of development. We find that all the cell types present in the natural embryos examined at these timepoints were also present in their synthetic counterparts. Furthermore, in these synthetic structures we observed formation of neuroectoderm and surface ectoderm, a beating heart, gut and primordial germ cells and development occurred inside extraembryonic membranes (yolk sac and amnion) similarly to what occurs in natural development. We conclude that these synthetic embryos are a unique tool to recapitulate mouse post-implantation development.

overall_design: Analysis of similarities and differences in the transcriptomes among mouse embryos and stem cell derived synthetic embryos, generated with the recently reported protocol (Amadei et al., 2021) and the new protocol established in this study

first: Gianluca

last: Amadei

first: Charlotte

last: Handford

first: Joachim

last: De Jonghe