title: Sex dependent transcriptomic and reproductive response of the diamondback moth (Plutella xylostella) to cold stress

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

institute: The University of Queensland

summary: Temperature has fundamental influences on fitness and distribution of insects. There have been very few studies on effects of mild cold conditions on insects. We found Plutella xylostella had reduced fitness and females produced few viable eggs when reared at 10°C, a temperature at which they can complete development. Male moths reared at 10°C were not able to fertilize eggs, but the eggs produced by female moths reared at this temperature were viable and could be fertilisied by males moths reared at a warmer temperature (25°C). Subsequently, we examined the transcriptomic changes in mid-fourth instar female and male larvae reared at 10°C and 25°C to investigate sex-dependent developmental and physiological responses of P. xylostella to the mild cold stress. We found 624 differentially expressed genes (DEGs) in females, the majority of which were down-regulated. In males 3239 genes were dysregulated and the majority were up-regulated. Only 280 DEGs were common to both sexes. In females, no DEGs encoded heat shock or cold shock proteins, but some of the DEGs in males did encode these proteins. These differences might suggest that female and male adopt some different strategies in coping with cold stress and/or they were passively affected by coldness to different degrees and in different ways. In addition, DEGs encoding antimicrobial peptides, cytochrome P450 monooxygenases, fatty acid-related enzymes, cuticle proteins, myofilament, and hormone-related proteins were found in both sexes under cold stress. The transcriptome study reveals unexpected sex-dependent thermal responses and provides much new information of how insects that do not diapause cope with a decreased temperature

overall_design: 12 RNAseq libararies. Variables: larval sex (Male and female) and rearing temparture (10 C and 25 C). 3 biological replicates for each traetment.

first: Leyun

last: Wang

first: Michael

last: Furlong

first: Gimme

last: Walter


title: Effect of the marine natural product-derived compound ZJ-101 on MDA-MB-231 cells

status: Public on May 31 2023

city: Rockville

first: Phillip

middle: Raul

last: Sanchez

state: MD

address: 9800 Medical Center Dr, BLDG-C 307W

country: USA

institute: National Center for Advancing Translational Sciences

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Bulk neocortical RNA sequencing of rNLS8 mice (on mixed C57BL/6J × C3H/HeJ background ) +/- active immunization with C-terminal hTDP-43 antigens

city: Munich

first: Dieter

last: Edbauer

state: Select...

address: Feodor-Lynenstr. 17

country: Germany

institute: DZNE

summary: This data set reports RNA sequencing results obtained from whole cerebral cortices of NEFH-tTa/tetO-hTDP43∆NLS transgenic (“rNLS8”) mice that were actively immunized with C-terminal fragments of the human TDP-43 protein. The widely used rNLS8 mouse model overexpresses cytoplasmically mislocalized human TDP-43 in a doxycycline-inducible manner, mimicking ALS/FTD-like CNS pathology and motor dysfunction (Walker et al., 2015). The purpose of this study was to evaluate the safety profile and therapeutic potential of various human TDP-43 epitopes (up to approximately 40 amino acids in length) which were used as antigens for active immunization in a rapidly progressing mouse model of TDP-43 proteinopathy. To this end, we pre-screened 15 peptide antigens, collectively spanning the entire TDP-43 protein sequence, for immunogenicity and safety. Next, we repeatedly immunized “rNLS8” mice with the most promising antigens prior to transgene induction, and performed bulk RNA sequencing of the neocortex, since this region is considerably affected by TDP-43 pathology in both humans and the mouse model. We asked whether active immunization with two different peptide combinations leading to high antibody titers would affect – i.e. prevent – transcriptional alterations upon transgene induction. In summary, we provide a bulk neocortical gene expression profile of actively immunized (and mock-treated) ALS/FTD-resembling “rNLS8” mice.

overall_design: mRNA profiles from whole cerebral cortices of adult rNLS8 mice with a mixed C57BL/6J x C3H/HeJ background. Mice heterozygous for both the NEFH-tTa and the tetO-hTDP43∆NLS allele are referred to as “bigenic”, while “monogenic” mice (carrying only one tetO-hTDP43∆NLS allele) served as asymptomatic controls. The data set includes four different treatment groups:   TDP-10+12: bigenic, treatment with combined peptides 10 and 12 (n=10);   TDP-15: bigenic, treatment with peptide number 15 (n=12);   TDP-PBS: sham treatment with PBS only (n=10);   ctrl-PBS: monogenic, sham treatment with PBS only (n=17).

first: Henrick

last: Riemenschneider

first: Peter

last: Liu


title: Exploring Fur regulon in Escherichia coli

status: Public on Jun 01 2023

city: Shenzhen

first: Conghui

last: You

address: 1068 Xueyuan Blvd.

country: China

institute: Shenzhen University

summary: To get a high resolution understanding of the effect of Fur on global gene expression, we compared by high-resolution RNAseq the transcriptomes of a wild-type E. coli K-12 strain and its Fur deletion derivative grown in minimal medium with or without supplementation of iron. Three independent total RNA extraction and RNAseq assays were performed for each strain in each condition.

overall_design: Examination of the gene expression when E. coli NCM3722 grew in sorbitol carbon sources with iron or not, as well as its fur - mutant (CY405).

first: Chaofan

last: Hou


title: An apicomplexan bromodomain protein, TgBDP1 associates with diverse epigenetic factors to regulate essential transcriptional processes in Toxoplasma gondii

city: Durham

first: Victoria

last: Jeffers

state: NH

address: 46 College Rd

department: MCBS

institute: UNH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The protozoan pathogen Toxoplasma gondii relies on tight regulation of gene expression to invade and establish infection in its host. The divergent gene regulatory mechanisms of Toxoplasma and related apicomplexan pathogens rely heavily on regulators of chromatin structure and histone modifications. The important contribution of histone acetylation for Toxoplasma in both acute and chronic infection has been demonstrated, where histone acetylation increases at active gene loci. However, the direct consequences of specific histone acetylation marks and the chromatin pathway that influences transcriptional regulation in response to the modification is unclear. As a reader of lysine acetylation, the bromodomain serves as a mediator between the acetylated histone and transcriptional regulators. Here we show that the bromodomain protein TgBDP1 which is conserved amongst Apicomplexa and within the Alveolata superphylum, is essential for Toxoplasma asexual proliferation. Using CUT&TAG we demonstrate that TgBDP1 is recruited to transcriptional start sites of a large proportion of parasite genes. Transcriptional profiling during TgBDP1 knockdown revealed that loss of TgBDP1 leads to major dysregulation of gene expression, implying multiple roles for TgBDP1 in both gene activation and repression. This is supported by interactome analysis of TgBDP1 demonstrating that TgBDP1 forms a core complex with two other bromodomain proteins and an ApiAP2 factor. This core complex appears to interact with other epigenetic factors such as nucleosome remodelling complexes. We conclude that TgBDP1 interacts with diverse epigenetic regulators to exert opposing influences on gene expression in the Toxoplasma tachyzoite.

overall_design: CUT&TAG analysis was performed on Toxoplasma tachyzoites expressing an epitope-tagged bromodomain protein TGME49_263580. Included are three experimental replciates using an anti-myc antibody on extracts from the tagged parasite line. Two negative control replicated were performed using anti-myc on the untransfected parental parasite line. One positive control is included that surveyed the distribution of a known histone modification (H3K9ac) using CUT&TAG.

first: Krista

last: Fleck

first: Seth

last: McNutt

first: Feixia

last: Chu


title: Hyperphosphorylation of the Group A Streptococcal Control of Virulence Regulator Increases Promoter Occupancy Specifically at Virulence Factor Encoding Genes

city: Houston

first: William

middle: Charles

last: Shropshire

state: TX

address: 1901 East Road

institute: The University of Texas MD Anderson Cancer Center

summary: The control of virulence two-component gene regulatory system (CovRS) is critical to the pathogenesis of many medically important streptococci.  In emm1 group A streptococci (GAS), CovR directly binds the promoters of numerous GAS virulence factor encoding genes. Elimination of CovS phosphatase activity increases CovR phosphorylation (CovR~P) levels and abrogates GAS virulence. Given the emm type-specific diversity of CovRS function, herein we used ChIP-seq to define global CovR DNA occupancy in the wild-type emm3 strain MGAS10870 (medium CovR~P) and its CovS phosphatase-negative derivative 10870-CovS-T284A (high CovR~P).  In the wild-type emm3 strain, 89% of the previously identified emm1 CovR binding sites present in the emm3 genome were also enriched; additionally, we ascertained unique CovR binding, primarily to genes in mobile genetic elements and other sites of inter-strain chromosomal differences.  Elimination of phosphatase activity specifically increased CovR occupancy at the promoters of a broad array of CovR repressed virulence factor encoding genes, including those encoding the key GAS regulator Mga and M protein.  However, a limited number of promoters had augmented enrichment at low CovR~P levels. Differential motif searches using sequences enriched at high vs. low CovR~P levels revealed two distinct binding patterns. At high CovR~P, a pseudo-palindromic AT-rich consensus sequence consistent with CovR binding as a dimer was determined.  Conversely, sequences specifically enriched at low CovR~P contained isolated “ATTARA” motifs suggesting an interaction with a monomer.  These data extend understanding of global CovR DNA occupancy beyond emm1 GAS and provide a mechanism for previous observations regarding hypovirulence induced by CovS phosphatase abrogation.

overall_design: ChIP-seq analysis using anti-CovR antibody of wild-type (MGAS10870) and high phosphorylation (10870-CovS-T284A) strains

first: Nicola

last: Horstmann

first: Chau

middle: N

last: Tran

first: Anthony

middle: R

last: Flores

first: Samuel

middle: A

last: Shelburne


title: Single-nucleus RNA sequencing of the prefrontal cortex from mice lacking glutaminase 1 in CamKIIa-positive neurons and control mice

city: Shanghai

first: Jialin

middle: C.

last: Zheng

address: Xincun Road 389

institute: Tongji Hospital Affiliated to Tongji University School of Medicine

summary: Autism spectrum disorder (ASD) is a heterogeneous group of disorders with shared diagnostic phenotypes, such as reduced interest in social interaction and communication, and increased stereotyped or restricted interests and behaviors. Little is known about the involvement of alterations of glutaminase 1 (Gls1,  an enzyme that catalyzes the hydrolysis of glutamine into glutamate) in the pathogenesis of ASD. To investigate the role of Gls1 in forebrain neurons , we generated conditional mouse mutants with loss of Gls1 in forebrain CamKIIα-Cre positive neurons  by crossing Gls1flox/flox mice with CamKIIαcre mice.

overall_design: Conditional mouse mutants with loss of Gls1 in forebrain CamKIIα-Cre positive neurons were generated  by crossing Gls1flox/flox mice with CamKIIαcre mice. Mosaic homozygous Gls1 mutant (CamKIIαCre;Gls1flox/flox) mice were not viable. Only mosaic heterozygous Gls1 mice (CamKIIαCre;Gls1+/flox mice, referred to as Gls1_CamKIIαCre mice) and their littermate CamKIIαCre;Gls1+/+ mice (referred to as control mice) were used in this study. Cells from the prefrontal cortex of both groups were isolated for Single-Nucleus RNA sequencing. Three animals were included for each group.

first: Chenhui

last: Ji

first: Yalin

last: Tang

first: Yanyan

last: Zhang

first: Xiaoyan

last: Huang

first: Congcong

last: Li

first: Yuhong

last: Yang

first: Qihui

last: Wu

first: Xiaohuan

last: Xia

first: Qingyuan

last: Cai

first: Xin-Rui

last: Qi

middle: C


title: Group B Streptococcus drives major transcriptomic changes in the colonic epithelium

city: tampa

first: Kristen

last: Dominguez

state: FL

address: 9440 leatherwood ave

department: Molecular Medicine

institute: University of South Florida

summary: Group B Streptococcus (GBS) is a leading cause of infant sepsis worldwide. Colonization of the gastrointestinal tract is a critical precursor to late-onset disease in exposed newborns. Neonatal susceptibility to GBS intestinal translocation stems from intestinal immaturity; however, the mechanisms by which GBS exploits the immature host remain unclear. β-hemolysin/cytolysin (βH/C) is a highly conserved toxin produced by GBS capable of disrupting epithelial barriers. However, its role in the pathogenesis of late-onset GBS disease is unknown. Our aim was to determine the contribution of βH/C to intestinal colonization and translocation to extraintestinal tissues. Using our established mouse model of late-onset GBS disease, we exposed animals to GBS COH-1 (WT), a βH/C-deficient mutant (KO), or vehicle control (PBS) via gavage. Blood, spleen, brain, and intestines were harvested 4 days post-exposure for determination of bacterial burden and isolation of intestinal epithelial cells. We used RNA-sequencing to examine the transcriptomes and performed gene ontology enrichment and KEGG pathway analysis. A separate cohort of animals were followed longitudinally to compare colonization kinetics and mortality between WT and KO groups. We demonstrate that disseminated to extraintestinal tissues occurred only in the WT exposed animals. We observed major transcriptomic changes in the colon of colonized animals, but not in the small intestine. We noted differential expression of genes among WT and KO exposed mice indicating that βH/C contributes to alterations in epithelial barrier structure and immune response signaling. Overall, our results demonstrate an important role for βH/C in the pathogenesis of late-onset GBS disease.

overall_design: RNA-Seq

last: Domínguez

first: April

middle: K

last: Lindon

first: Justin

last: Gibbons

first: Sophie

middle: E

last: Darch

first: Tara

middle: M

last: Randis


title: Exposure to lung-migrating helminth protects against murine SARS-CoV-2 infection through macrophage-dependent T cell activation

city: Maryland

first: Oyebola

last: Oyesola

address: Building 4, Room B1 05 4 Memorial Drive Bethesda, MD 20892

department: Type 2 Immunity Section

institute: National Institute of Health

summary: Helminth infection leads to lung remodelling. We used single cell ATAC sequencing (scRNA-seq) to analyze the changes in lung cells following exposure to N. brasiliensis at day 28 and day 45 post helminth infection

overall_design: Single cell suspension of lungs cells was obtained from pooled samples from controls and helminth exposed mice. CD45+ immune cells were enriched in the pooled samples

first: Mingming

last: Zhao

first: P'ng

last: Loke


title: Effect of overexpression of Zfp292 in developing retinas

city: Stanford

first: Yue

last: Sun

state: CA

address: 290 Jane Stanford Way

institute: Stanford University

summary: Control CAG-GFP or CAG-Zfp292 (Zfp292-OE) plasmids were electroporated into P0 mouse pups in vivo. We harvested the retinas 4 days later to allow for robust expression, dissociated the retinas into single cell preps, collected the GFP+ Retinal progenitor cells (RPCs) via FACS sorting from control or Zfp292-OE conditions, and processed the cells for bulk RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Zfp292-OE and control retinal RPC cells.

first: Liang

first: Wang

last: Sui


title: Dysregulated long non-coding RNAs and genes in calcified aortic valve disease

first: Guokun

last: Wang

address: 168 Changhai Road

institute: Changhai Hospital

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

summary: Calcific aortic valve disease (CAVD) is the most common valvular heart disease in the aging population, ranging from initial aortic valve sclerosis to advanced aortic valve stenosis (AVS), but its underlying mechanism remains poorly understood. The present study aimed to explore the differentially expressed long non-coding RNAs and genes in CAVD.

overall_design: Calcified aortic valves ×2 vs. normal aortic valves ×2.

first: Fan


title: Effect of the marine natural product-derived compound ZJ-101 on gene expression in MDA-MB-231 3D Spheroids

first: Phillip

last: Sanchez

summary: Four logs of ZJ-101 were tested on 3D spheroid cultures of MDA-MB-231 cells to identify relevant mechanistic pathways through differentially expressed gene analysis

overall_design: Triplicate 96-well plates of ultra-low attachment cultured MDA-MB-231 spheroids were treated for 24 hours with four doses (0.5, 5.0, 50.0, 500.0 nM) of ZJ-101 and processed for RNA-Seq DEG analysis

first: Wei

last: Zheng


title: The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice

city: Cassina Rizzardi

first: Veronica

middle: Maria

last: Beretta

state: Co

address: Via A. Vivaldi 36

country: Italy

institute: Università degli Studi di Milano

summary: Analysis of the transcriptome of the early developmental stages of the reproductive meristems of Oryza sativa ssp. Japonica cv Nipponbare. We compared the transcriptome obtained from osg1l2 single mutant to a wild type control

overall_design: sampling meristems at early developmental stages enriched in PBMs and ePBM/Ams from osg1l2 and wild type background. Four independent replicates for each genotype were performed

first: Emanuela

last: Franchini

last: Gregis

first: Martin

last: Kater


title: Effect of the marine natural product-derived compound ZJ-101 on MDA-MB-231 gene expression in 2D culture format

summary: Four logs of ZJ-101 were tested on 2D cultures of MDA-MB-231 cells to identify relevant mechanistic pathways through differentially expressed gene analysis

overall_design: Triplicate dishes of 2D cultured MDA-MB-231 cells were treated for 6 hours with four doses (0.5, 5.0, 50.0, 500.0 nM) of ZJ-101 and processed for RNA-Seq DEG analysis


title: Disease activity drives transcriptomic heterogeneity in early untreated rheumatoid synovitis

city: Brussels

first: clement

last: triaille

address: avenue hippocrate

country: Belgium

institute: UCLouvain

summary: The purpose of this study was to investigate the transcriptomic heterogeneity in synovial tissue of early untreated rheumatoid arthritis patients in association with clinical data

overall_design: Comparative gene expression analysis (bulk RNA-seq) of RA synovial tissue biopsie

first: Clément

last: Triaille

first: Axelle

last: Loriot

first: Nisha

last: Limaye


title: ADAR1 Zα domain P195A mutation activates the MDA-5 dependent RNA-sensing signaling pathway in the brain enhanced by haploinsufficiency without overall RNA editing level decrease.

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: The A-to-I RNA editing enzyme ADAR1 critically regulates the cellular RNA sensing signaling pathway, as the RNA-sensing signaling pathway recognizes unedited RNAs as “non-self” to activate the innate immune response. Mutations of ADAR1 cause severe inflammatory tissue injury, as shown in Aicardi-Goutières syndrome (AGS), in which severe inflammation occurs in the brain. The most frequent ADAR1 mutation in AGS is the P193A mutation in the Za domain, which exists in the AGS families coupling with an additional ADAR1 mutation. How this mutation alters the cellular RNAs leading to innate immune activation, has not been fully understood. This study analyzed RNA editing status and innate immune activation in the brains of a mouse model that carries the human ADAR1 P193A-equivalent mouse P195A mutation. We found that this mutation alone can cause excessive ISG expression in the brains, especially in the periventricular areas reflecting the pathologic feature of AGS. Furthermore, we found that ADAR1 P195A mutation did not affect the RNA editing activity in the overall RNA editing level; however, it leads to ISG expression in a dose-dependent manner, causing severer innate immune activation in haploinsufficiency status, whereas wildtype ADAR1 is redundant to suppress innate immune activation. The finding from this study indicated that the intact Z-RNA binding activity of ADAR1 plays a critical role in suppressing self-cellular RNA sensing, and innate immune homeostasis requires a minimum Z-RNA binding capacity of ADAR1.

overall_design: WT_WT, WT_d, 195M_195M, 195M_d, with three repeats each

first: Guo

last: Xinfeng

first: Liu

last: Silvia

first: Sheng

last: Yi

first: Zenati

last: Mazen

first: Billiar

last: Timothy

first: Herbert

last: Alan

last: Qingde


title: Deciphering the cardiovascular potential of human CD34+ stem cells

city: Mulhouse

first: Anne

last: ARIES

address: 87 Av d'Alkirch

country: France

institute: IRHT

summary: Ex vivo monitored human CD34+ stem cells (SCs) injected into myocardium scar tissue have shown real benefits for the recovery of patients with myocardial infarctions. They have been used previously in clinical trials with hopeful results and are expected to be promising for cardiac regenerative medicine following severe acute myocardial infarctions. However, some debates on their potential efficacy in cardiac regenerative therapies remain to be clarified. To elucidate the levels of CD34+ SCs implication and contribution in cardiac regeneration, better identification of the main regulators, pathways, and genes involved in their potential cardiovascular differentiation and paracrine secretion needs to be determined. We first developed a protocol thought to commit human CD34+ SCs purified from cord blood toward an early cardiovascular lineage. Then, by using a microarray-based approach, we followed their gene expression during differentiation. We compared the transcriptome of undifferentiated CD34+ cells to those induced at two stages of differentiation (i.e., day 3 and day 14), with human cardiomyocyte progenitor cells (CMPCs), as well as cardiomyocytes as controls. Interestingly, in the treated cells we observed an increase in the expressions of the main regulators usually present in cardiovascular cells. We identified cell surface markers of the cardiac mesoderm, such as kinase insert domain receptor (KDR) and the cardiogenic surface receptor Frizzled 4 (FZD4), induced in the differentiated cells in comparison to undifferentiated CD34+ cells. The Wnt and TGF- pathways appeared to be involved in this activation. This study underlined the real capacity of effectively stimulated CD34+ SCs to express cardiac markers and, once induced, allowed the identification of markers that are known to be involved in vascular and early cardiogenesis, demonstrating their potential priming towards cardiovascular cells. These findings could complement their paracrine positive effects known in cell therapy for heart disease and may help improve the efficacy and safety of using ex vivo expanded CD34+ SCs.

overall_design: Total RNA was extracted from UCB-CD34+- and UCB-CD34+-treated cells and, at different stages of differentiation, cardiac progenitors (CMPCs) and cardiomyocytes (4 pools of quadruplets). Then, the RNA sample quality was evaluated, and RNA integrity was controlled with a Bioanalyzer 2200 (Agilent Technologies, Les Ulis, France). Gene expression profile analysis was performed using a Low Input Quick Amp WT Labeling Kit with one color (Agilent Technologies, Les Ulis, France), and cDNA was reverse-transcribed from RNA samples and fluorescently labeled with cyanine 3. Each sample was hybridized with an Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray and processed according to the manufacturer’s instruction. DNA microarrays were scanned using an Agilent G2505C DNA microarray scanner. The image files were extracted using Agilent Feature Extraction software. The data were filtered and normalized using Agilent Genespring GX software

last: Aries

first: Céline

last: Zanetti

first: Philippe

last: Hénon

first: Bernard

last: Drénou

first: Rachid

last: Lahlil


title: RNA sequencing of skeletal muscle macrophages

city: LOS ANGELES

first: Jesse

last: Zamudio

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

summary: To investigate the functional heterogeneity of muscle macrophages, we sorted 3 macrophage populations from 4wk-old WT and mdx mice based on the expression of Gal3 (gal-3+ Mac), FOLR2 (SkMRM) and CD52 (MDM). We then performed gene expression profiling analysis using data obtained from RNA-seq of the FACs-sorted populations of muscle macrophages.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sorted populations of muscle macrophages reveals unique transcriptomic profiles

first: Armando

last: Villalta


title: The soybean immune receptor GmBIR1 regulates host transcriptome, spliceome, and immunity during cyst nematode infection

city: Knoxville

first: Tarek

last: Hewezi

state: TN

address: 2431 Joe Johnson Drive

department: Plant Sciences

institute: University of Tennessee

summary: To investigate the effect of overexpression of wild-type and kinase deactivated GmBIR1 on soybean transgenic hairy root gene expression

overall_design: Transcriptional profiles of WT-GmBIR1, KD-GmBIR1, and Williams 82 under Heterodera glycines HG Type 0 infected and noninfected with three replicates per treatment

first: Tracy

last: Hawk


title: Identification of Target Genes and Pathways Related to Heat Tolerance in Chinese Holstein Cows

city: Kongens Lyngby

first: Xiao

last: Wang

address: Bagsværdvej 103, ST

country: Denmark

institute: Konge Larsen Aps

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed gene expression profiling analysis using data obtained from miRNA-seq of 12 cows with different heat tolerance.

overall_design: 12 dairy cows were divided into heat-resistant and heat-stressed groups based on rectal temperature and reduction of milk yield using PCA

first: Rongling

last: Li

first: Minghai

last: Hou

first: Liguo

last: Yang


title: Decoding the transcriptome of muscular dystrophy using single-nucleus RNA sequencing

city: Chengdu

first: Xiaokai

state: Sichuan

address: Huiming road #211

institute: Sichuan Agricultural University

summary: Muscular dystrophy is a group of diseases that cause progressive weakness and degeneration of the skeletal muscles that control movement. Lacking polymerase I transcription release factor (PTRF, also known as Cavin1), an essential caveolae component, causes a secondary deficiency of caveolins resulting in muscular dystrophy. Because skeletal muscle is a heterogeneous tissue composed of different metabolic muscle fiber (myofibers) and mononuclear cells, the transcriptome responses of these myofibers and mononuclear cell to muscular dystrophy caused by PTRF deletion has not been explored. Here, we create muscular dystrophy mice caused by the deletion of PTRF gene and apply single-nucleus RNA sequencing (snRNA-seq) to unveil transcriptional changes in the skeletal muscle of mice with muscular dystrophy at single-nucleus resolution.

overall_design: We analyzed quadriceps muscles from 3-month-old WT and PTRF KO mice using single-nucleus sequencing.

first: Keren

last: Long

first: Ruowei

last: Zhang

first: Jiaman


first: Oyebola

last: Oyesola

summary: Helminth infection leads to lung remodelling. We used single cell RNA sequencing (scRNA-seq) to analyze the changes in lung cells following exposure to N. brasiliensis followed by subsequent exposure to SARS-COV2

overall_design: Single cell suspension of lungs cells was obtained from pooled samples from controls and helminth exposed mice and some mice were also infected with SARS-COV2 virus. Cells were analyzed using scRNAseq.

middle: O

last: Oyebola

first: Kerry

last: Hilligan

first: Sivaranjani

last: Namasivayam

first: Nina

last: Howard

first: Alan

last: Sher

first: P'ng

last: Loke


title: Effect of muscular dystrophy caused by PTRF deletion on the transcriptome of skeletal muscles

summary: Muscular dystrophy is a group of diseases that cause progressive weakness and degeneration of the skeletal muscles that control movement. Lacking the caveolae component polymerase I transcription release factor (PTRF) causes a secondary deficiency of caveolins resulting in muscular dystrophy. To investigate the effect of PTRF deletion on skeletal muscle, we created gene-edited mice with PTRF knockout (KO). We then performed RNA-seq of soleus and quadriceps muscles from soleus and quadriceps muscles of 3 months old WT (n=3) and PTRF KO mice (n=3) and analyzed the data for gene expression profiling. 12933 genes were detected across all 12 libraries. The hierarchy clustering of co-expressed genes revealed a clear split between PTRF KO and WT mice for both skeletal muscles. Differential expression analysis identified 1293 and 705 differentially expressed genes (DEGs) in the soleus and quadriceps, respectively. 971 and 534 DEGs were up-regulated, and 322 and 171 DEGs were down-regulated in the soleus and quadriceps of PTRF KO mice, respectively.

overall_design: Gene expression profiling analysis of mRNA-seq data for normal muscles and PTRF knockout muscles (soleus and quadriceps).


title: Comparative gene expression profiling in small intestinal mucosa of Rbm47 intestine-specific knock-out and wt mice

city: Iowa City

first: Jesse

last: Riordan

state: IA

address: 375 Newton Road

institute: University of Iowa

summary: Rationale: RNA binding protein 47 (RBM47) is required for embryonic endoderm development but a role in adult intestine is unknown. Objective: We studied intestine-specific Rbm47 knockout mice (Rbm47-IKO) following intestinal injury and made crosses into Apcmin/+ mice to examine alterations in intestinal proliferation, response to injury and tumorigenesis. We also interrogated human colorectal polyps and colon carcinoma tissue. Findings: Rbm47-IKO mice exhibit increased proliferation, abnormal villus morphology and cellularity, with corresponding changes in Rbm47-IKO organoids. Rbm47-IKO mice adapt to radiation injury and are protected against chemical-induced colitis, with Rbm47-IKO intestine showing upregulation of antioxidant and Wnt signaling pathways as well as stem cell and developmental genes. Furthermore, Rbm47-IKO mice are protected against colitis-associated cancer. By contrast, aged Rbm47-IKO mice develop spontaneous polyposis and Rbm47-IKO, Apcmin/+ mice manifest an increased intestinal polyp burden. RBM47 mRNA was decreased in human colorectal cancer versus paired normal tissue along with alternative splicing of TJP1 mRNA. Public databases revealed stage-specific reduction in RBM47 expression in colorectal cancer, associated independently with decreased overall survival. Conclusions: These findings implicate RBM47 as a cell-intrinsic modifier of intestinal growth, inflammatory and tumorigenic pathways.

overall_design: Small intestine mucosa were scraped from either wild-type C57BL6/J or intestine-specific Rbm47 knock-out mice, and RNA was extracted for sequencing. Pooled samples containing RNA from 3 individual mice (both sexes) were prepared, and 3 such samples were sequenced for each cohort.

first: Saeed

last: Soleymanjahi

first: Valerie

last: Blanc

first: Elizabeth

last: Molitor

first: David

last: Alvarado

first: Yan

last: Xie

first: Vered

last: Gazit

first: Jeffrey

middle: W

last: Brown

first: Kathleen

last: Byrnes

first: Ta-Chiang

last: Liu

first: Jason

last: Mills

first: Matthew

last: Ciorba

first: Deborah

last: Rubin

first: Nicholas

last: Davidson


title: Stress response by phase-separated p62

status: Public on May 30 2023

city: Tokyo

first: Keiko

last: Kan-O

address: Kawadacho 8-1, Shinjuku-ku

department: Department of Respiratory Medicine

country: Japan

institute: Tokyo Women's Medical University

summary: To investigate the role of p62 phosphorylation by ULK1 on NRF2 activation in vivo.

overall_design: We then generated p62S351E/+ mice, phosphomimetic knock-in mice in which Ser351 corresponding to human Ser349 replaced by Glu. The livers from p62+/+ and p62S351E/+ mice at P19 were subjected to mRNA-seq analysis.

first: Masaaki

last: Komatsu

first: Shuhei

last: Takada

first: Hideaki

last: Morishita

first: Tomoaki

last: Koga


title: m6A-sequencing of Mettl14-conditional knock-out retinas and matched control.

first: Yue

last: Sun

summary: Post-transcriptional m6A methylation on mRNA plays a key role in neural development. Here, we specifically depleted Mettl14 (a key component of m6A complex) in retina progenitor cells by crossing Mettl14 fl/fl mice with the Chx10-Egfp/Cre mouse line and investigated Mettl14 depletion-induced m6A alteration in developing retinas using m6A-seq.

overall_design: Immunoprecipitation of m6A-enriched mRNAs (m6A-seq) for control and Mettl14 cKO retinas.

first: Li

last: Liang

first: Sui

last: Wang


title: Transcriptome-wide analysis of low-concentration exposure to Bisphenol A, S and F in prostate cancer cells.

city: MEXICO CITY

first: Mauricio

last: Rodriguez Dorantes

state: Distrito Federal, Mexico

address: Periferico Sur 4809, Arenal Tepepan, Tlalpan,  Ciudad de México, CDMX, México

country: Mexico

institute: INMEGEN

summary:
In this work we use an in vitro model to characterize the transcriptomic effect of low-concentration exposure to bisphenol A, S or F in the two main stages of the disease:
androgen dependency (LNCaP) and resistance (PC-3).  using Affimetrix Clariom D technology

overall_design: LNCaP and PC-3 cells were exposed to bisphenols A, S and F at 5 nM  concentration during 48 hours, then RNA extraction and QC was performed.

first: Sergio

last: Cortés-Ramírez

first: Ana

last: Salazar

first: Monserrat

last: Sordo

first: Patricia

last: Ostrosky-Wegman

first: Miguel

last: Morales-Pacheco

first: Marian

last: Cruz-Burgos

first: Alberto

last: Losada-García

first: Griselda

last: Rodríguez-Martínez

first: Karla

last: Vazquez-Santillán

first: Vilma

last: Maldonado-Lagunas

first: Vanessa

last: González-Covarrubias

first: Imelda

last: González-Ramírez

last: Rodríguez-Dorantes


title: RNAseq of granulocyte-macrophage progenitors (GMP) from bone marrow of mice with hematopoietic knock-out of Rnaseh2b

city: Dresden

first: Alexander

last: Gerbaulet

state: Saxony

address: Fetscherstr. 74

department: Institute for Immunology

institute: Medical Faculty TU Dresden

summary: Bulk transcriptomes of granulocyte-macrophage progenitor cells isolated from bone marrow of Rnaseh2bfl/fl/ Vav-Cre and Cre-negative ctrl mice; The sorted bone marrow cells had the following immunophenotype: lineage- CD201 (EPCR)- CD117+ CD16/32+ CD34+

overall_design: 30,000-100,000 GMP were sorted from Rnaseh2bfl/fl Vav-Cre+ (n=4) or Cre-negative control (n=4) mice and subjected to bulk transcriptome analysis.


title: Characterization of Bacterial Transcriptional Regulatory Networks in Escherichia coli through Genome-Wide In Vitro Run-Off Transcription/RNA-seq (ROSE)

city: Bielefeld

first: David

last: Brandt

address: Universitätsstraße 25

department: CeBiTec

institute: Bielefeld University

summary: The global characterization of transcriptional regulatory networks almost exclusively uses in vivo conditions, thereby providing a snapshot on multiple regulatory interactions at the same time. To complement these approaches, we developed and applied a method for characterizing bacterial promoters genome-wide by in vitro transcription coupled to transcriptome sequencing specific for native 5'-ends of transcripts. This method, called ROSE (run-off transcription/RNA-sequencing), only requires chromosomal DNA, ribonucleotides, RNA polymerase (RNAP) core enzyme, and a specific sigma factor, recognizing the corresponding promoters, which have to be analyzed. ROSE was performed on E. coli K-12 MG1655 genomic DNA using Escherichia coli RNAP holoenzyme (including σ70) and yielded 3226 transcription start sites, 2167 of which were also identified in in vivo studies, and 598 were new. Many new promoters not yet identified by in vivo experiments might be repressed under the tested conditions. Complementary in vivo experiments with E. coli K-12 strain BW25113 and isogenic transcription factor gene knockout mutants of fis, fur, and hns were used to test this hypothesis. Comparative transcriptome analysis demonstrated that ROSE could identify bona fide promoters that were apparently repressed in vivo. In this sense, ROSE is well-suited as a bottom-up approach for characterizing transcriptional networks in bacteria and ideally complementary to top-down in vivo transcriptome studies.

overall_design: We analysed three samples from run-off in vitro transcription reactions on E. coli MG1655 gDNA and five samples from E. coli liquid cultures.

first: Pascal

last: Schmidt

first: Jörn

last: Kalinowski

first: Tobias

last: Busche


title: Transcriptomic analysis of myocardium-specific Creld1 knockout mice at E13.5 and P3

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary:
Purpose: The aim of the study was to decipher the function of Creld1 in the myocardium during embryonic and postnatal heart development.
Methods: We generated conditional knockout (KO) mice lacking Creld1 in cells expressing the Myosine Heavy Chain (MyHC, myocardial cells). Embryonic (E13.5, n=4) and postnatal (P3, n=3) hearts from both wild-type (WT) and KO mice were isolated and postnatal hearts were further split into atria and ventricles. Total RNA was extracted, mRNA purified, converted into cDNA and sequenced using a NextSeq500 system (Illumina).The reads passing default quality filters were aligned to the mouse genome (mm10).
Results: More than 5.1 million aligned reads were retrieved in each sample.The expression profiles of the postnatal KO samples underline drastic anormalies in the hearts and commencing heart failure particularly in the atria. In embryonic KO hearts the transciption of Notch1 signalling components and consequently extracellular matrix (ECM) homeostasis was altered, whereas transcription in Nfatc1 and Vegf signalling pathways was unchanged.
Conclusion: This study shows that myocardial Creld1 is a key morphogenic factor in the developing heart and as it regulates Notch1 signalling and, thereby, the ECM during cardiac wall development.

overall_design: Transcriptomes of myocardium-specific Creld1 knockout mice were compared to wild-type controls at E13.5 and P3.

first: Vera

last: Beckert

first: Sebastian

last: Rassmann

first: Lorenzo

last: Bonaguro

first: Anna

last: Aschenbrenner

first: Elvira

last: Mass

first: Dagmar

last: Wachten


title: Single-cell RNA-sequencing of Mettl14 conditional knock-out retinas and matched controls

first: Yue

last: Sun

summary: Post-transcriptional m6A methylation on mRNA plays a key role in neural development. Here, we specifically depleted Mettl14 (a key component of m6A complex) in retina progenitor cells by crossing Mettl14 fl/fl mice with the Chx10-Egfp/Cre mouse line and investigated cell type and  transcriptome changes in the developing retinas using scRNA-seq.

overall_design: Retinas of Mettl14 fl/fl;Chx10-Egfp/Cre (Mettl14-cKO) mice and age matched controls were collect at P7 and applied to scRNA-seq.

first: Li

last: Liang

first: Sui

last: Wang


title: Directed differentiation of human hindbrain neuroepithelial stem cells recapitulates cerebellar granule neurogenesis [scRNA-seq]

status: Public on May 29 2023

city: Toronto

first: Biren

last: Dave

state: Ontario

address: 686 Bay Street

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: To establish a new model system with which to study cerebellar granule lienage development and disease, human hbNES cells were differentiated to cerebellar granule neurons over a 56 day period.

overall_design: Gene expression profiling of 4 independent hbNES cell lines during a 56 day differentiation protocol.

first: Xin

last: Chen

first: Fraser

last: McCready

first: Connor

last: Charton

first: Rachel

last: Morley

first: Jignesh

last: Tailor

first: James

last: Ellis

first: Xi

last: Huang

first: Peter

last: Dirks


title: Single-cell sequencing of neuroblastoma CHP134 cells treated with doxazosin, isotretinoin (13cRA) and their combination.

city: New Haven, US & Trento, Italy

first: Toma

last: Tebaldi

state: CT

address: 300 George Street

department: CIBIO & Department of Internal Medicine, Yale Cancer Center

institute: Yale University & University of Trento

summary: Neuroblastoma (NB) is an aggressive childhood tumor, with high-risk cases having a 5-year overall survival probability of about 50%. The multimodal therapeutic scheme of NB includes isotretinoin (13cRA), used in the post-consolidation phase as an anti-proliferative and pro-differentiative agent to minimize residual disease and prevent relapse.   Administration of doxazosin, a safe α1-antagonist used in pediatric patients, with 13cRA in NB xenografted mice exerted a marked control of tumor growth, while each of the two drugs alone was ineffective.   To unveil the molecular mechanisms underlying this synergism, single-cell RNA-seq was performed in CHP134 control cells, and cells treated with 13cRA (5 uM), doxazosin (10 uM), and their combination. The data revealed that the transcriptome of single cells was markedly reprogrammed when exposed to 13cRA and to the combination of doxazosin and 13cRA, but not when exposed to doxazosin alone. In detail, we identified 91 genes as specific markers of 307 cells treated with the drug combination: 41 synergistically downregulated and 50 upregulated. Functional analysis of these synergistically expressed genes reported significant enrichment of genes related to apoptosis, control of the cell cycle, and neuronal identity. We, therefore, preclinically identify the α1B adrenergic receptor as a novel pharmacological target in NB. We propose evaluating the addition of α1-antagonists in the post-consolidation therapy of NB to more efficiently control residual disease.    Keywords: isotretinoin, 13cRA, 13-cis retinoic acid, doxazosin, neuroblastoma,single-cell RNA-seq, iCELL8, adrenergic receptors, α-blockers, combinatorial therapy, synergy

overall_design: Single-cell RNA sequencing (scRNA-seq) of 1287 cells after 24h of single (doxazosin OR 13cRA) and combined (doxazosin AND 13cRA) drug incubation

first: Veronica

last: De Sanctis

first: Roberto

last: Bertorelli

first: Viktoryia

last: Sidarovich

first: Sara

last: Longhi

first: Francesca

last: Broso

first: Enrico

last: Sebastiani

first: Alessandro

last: Quattrone


title: Spatiotemporal pathological alternations during syringomyelia formation and resolution

city: Beijing

first: Xianming

last: Wu

state: Chaoyang District

address: Unit 2, No.1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: Syringomyelia is a common clinical lesion associated with arachnoid adhesion, traumatic injury, intramedullary tumor, and congenital or acquired spinal deformities. However, the mechanism of syringomyelia formation and resolution remains controversial. We previously constructed a reversible rat model with extradural compression to closely reproduce the canalicular syringomyelia in the human condition. It is quite necessary to depict the spatiotemporal pathophysiological changes of syringomyelia more precisely by transcriptomic analyses during syrinx development and regression.

overall_design: The spinal cord tissue centered on the syringomyelia segments were collected for bulk-RNA sequencing at different time points after extradural compression in rat model.

first: Chunli

last: Lu

first: Fengzeng

last: Jian

first: Jianwu

last: Dai


title: Spatiotemporal pathological alternations during syringomyelia formation and resolution [scRNA-seq]

overall_design: The spinal cord tissue centered on the syringomyelia segments were collected for single-cell RNA sequencing at different time points after extradural compression in rat model.


title: An integrative omics approach reveals posttranscriptional mechanisms underlying circadian temperature compensation

city: Berlin

first: Bert

last: Maier

address: Charitéplatz 1

institute: Charité Universitätsmedizin Berlin

summary: We apply 3'-End-RNA-seq based sequencing to globally quantify polyadenylation sites and transcript isoform abundance in human U-2 OS cells under wild-type and CPSF6 knock-down conditions at 3 different temperatures (32°C, 37°C and 39°C). We show that CPSF6 knock-down as well as temperature alterations lead to global changes in 3' UTR length and transcript abundance. By means of a differential response analysis with respect to temperature changes in wild type and temperature-decompensated CPSF6 knockdown cells, we reveal candidate genes underlying circadian temperature compensation.

overall_design: Global changes in 3' UTR length and transcript abundance upon CPSF6 knockdown and temperature alterations.

first: Christoph

last: Schmal

first: Reut

last: Ashwal-Fluss

first: Osnat

last: Bartok

first: Sebastian

last: Kadener

first: Achim

last: Kramer


title: Changes in gene expression profiling in the prefrontal cortex from mice lacking glutaminase 1 in CamKIIa-positive neurons

status: Public on May 28 2023

city: Shanghai

first: Jialin

last: Zheng

address: Xincun Road 389

institute: Tongji Hospital Affiliated to Tongji University School of Medicine

summary: Autism spectrum disorder (ASD) is a heterogeneous group of disorders with shared diagnostic phenotypes, such as reduced interest in social interaction and communication, and increased stereotyped or restricted interests and behaviors. Little is known about the involvement of alterations of glutaminase 1 (Gls1,  an enzyme that catalyzes the hydrolysis of glutamine into glutamate) in the pathogenesis of ASD. To investigate the role of Gls1 in forebrain neurons , we generated conditional mouse mutants with loss of Gls1 in forebrain CamKIIα-Cre positive neurons  by crossing Gls1flox/flox mice with CamKIIαcre mice.

overall_design: Conditional mouse mutants with loss of Gls1 in forebrain CamKIIα-Cre positive neurons were generated  by crossing Gls1flox/flox mice with CamKIIαcre mice. Mosaic homozygous Gls1 mutant (CamKIIαCre;Gls1flox/flox) mice were not viable. Only mosaic heterozygous Gls1 mice (CamKIIαCre;Gls1+/flox mice, referred to as Gls1_CamKIIαCre mice) and their littermate CamKIIαCre;Gls1+/+ mice (referred to as control mice) were used in this study. The prefrontal cortex from 3 Gls1_CamkIIaCre mice and 3 control mice were isolated for RNA seq and for comparative gene expression profiling analysis.

first: Chenhui

last: Ji

first: Yalin

last: Tang

first: Yanyan

last: Zhang

first: Xiaoyan

last: Huang

first: Congcong

last: Li

first: Yuhong

last: Yang

first: Qihui

first: Xiaohuan

last: Xia

first: Qingyuan

last: Cai

first: Xin-Rui

last: Qi


title: Directed differentiation of human hindbrain neuroepithelial stem cells recapitulates cerebellar granule neurogenesis [ATAC-seq]

first: Biren

last: Dave

first: Xin

last: Chen

first: Fraser

last: McCready

first: Connor

last: Charton

first: Rachel

last: Morley

first: Jignesh

last: Tailor

first: James

last: Ellis

first: Xi

first: Peter

last: Dirks


title: Directed differentiation of human hindbrain neuroepithelial stem cells recapitulates cerebellar granule neurogenesis [RNA-seq]


title: Translatome profiling of neuroblastoma cells CHP134 treated with isotretinoin (13cRA), isorhamnetin (ISR), and their combination

first: Toma

last: Tebaldi

summary: Neuroblastoma (NB) is an aggressive childhood tumor, with high-risk cases having a 5-year overall survival probability of about 50%. The multimodal therapeutic scheme of NB includes isotretinoin (13cRA), used in the post-consolidation phase as an anti-proliferative and pro-differentiative agent to minimize residual disease and prevent relapse. Through a small molecule screening, we identified isorhamnetin (ISR) as a synergistic compound with 13cRA in inhibiting up to 80% of NB cell viability. To unveil the molecular mechanisms underlying this synergism, microarray analysis was performed in CHP134 control cells, and cells treated with 13cRA (5uM), ISR (15uM), and their combination. This analysis revealed that 13cRA ISR synergism is accompanied by a marked increase in the expression of the adrenergic receptor α1B (ADRA1B) gene. Administration of doxazosin, a safe α1-antagonist used in pediatric patients, with 13cRA in NB xenografted mice exerted a marked control of tumor growth, while each of the two drugs alone was ineffective. We, therefore, preclinically identify the α1B adrenergic receptor as a novel pharmacological target in NB. We propose evaluating the addition of α1-antagonists in the post-consolidation therapy of NB to more efficiently control residual disease.  Keywords: isotretinoin, 13cRA, 13-cis retinoic acid, isorhamnetin, ISR, neuroblastoma, polysome profiling, translatome, adrenergic receptors, α-blockers, combinatorial therapy, synergy

overall_design: Microarray analysis was performed to enable a comprehensive view of the changes in the translational status of CHP134 cells in response to the treatment with isotretinoin (13cRA), isorhamnetin (ISR), and their combination, to identify synergistic effects. Polysomal RNA was isolated from vehicle-treated CHP134 cells and CHP134 cells treated with 5 µM 13cRA, 15 uM ISR, and both. Each condition is represented by three biological replicates, i.e. the experiment was repeated starting each time from cells seeding yielding an independent RNA sample. In total, 12 samples corresponding to 4 conditions were subjected to microarray analysis.

first: Pamela

last: Gatto

first: Viktoryia

last: Sidarovich

first: Francesca

last: Broso

first: Valentina

last: Adami

first: Alessandro

last: Quattrone


title: Transcriptome changes in human post-mortem PD striatum

city: New York

first: Caryn

last: Hale

state: New York

address: 1230 York Avenue

institute: Rockefeller University

summary: We analyzed transcriptome differences in postmortem caudate and putamen from controls (n=40) and PD (n=35) as confirmed by autopsy. Further, we analyzed region specific differences in caudate and putamen associated with clinical variables.

overall_design: RNA sequencing analysis in caudate and putamen regions of the striatum from controls and Parkinson’s disease donors.

first: Krithi

last: Irmady

first: Robert

middle: B

last: Darnell

first: Thomas

last: Carroll


title: Lysine Deprivation Suppresses Adipogenesis in 3T3-L1 Cells: A Transcriptome Analysis

city: Hong Kong

first: Man Yuen

last: LEE

address: Hunghom

department: Department of Applied Biology and Chemical Technology

country: Hong Kong

institute: The Hong Kong Polytechnic University

summary: It has been reported that low concentration of lysine suppressed lipid accumulation and transcription of several adipogenic genes in 3T3-L1 preadipocytes, however, the detailed lysine deprivation-specific cellular transcriptomic changes and the altered pathways have not yet been fully decrypted.

overall_design: Using 3T3-L1 cells, we performed RNA sequencing on undifferentiated cells, differentiated cells, and differentiated cells under a lysine-free culture medium

first: Leo

middle: Y

last: LEUNG


title: SRSF10 regulates proliferation of neural progenitor cells and affects neurogenesis in the developing mouse neocortex

first: Xianhua

last: Chen

address: 131 Dongan road,New Research Building, Room B5015

institute: Fudan University

summary: To identify the potential functions of SRSF10 in neural progenitor cells and neocortex development, we constructed SRSF10 flox/flox mice, and conditionally knock out the SRSF10 in the neural progenitor cells by breeding with Nestin-Cre mice.

overall_design: Comparison of gene expression and alternative splicing of RNA-seq data for control mice and SRSF10 conditional knockout mice.

first: Junjie

last: Li


title: Enhanced STAT5a activation opposes Tox and rewires exhausted CD8 T cells towards a hybrid durable effector-like state during chronic stimulation

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

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

overall_design: Refer to individual Series


title: Memory B cell development elicited by mRNA booster vaccinations in the elderly

status: Public on May 27 2023

first: Gabriela

middle: S

last: Silva Santos

state: NY

institute: The Rockefeller University

summary: The study examined antibody and memory B cell responses to SARS-CoV-2 mRNA booster vaccination in the elderly and showed a decrease in memory B cell numbers with an altered antibody repertoire that may contribute to a higher risk for severe disease in the elderly.

overall_design: Peripheral blood mononuclear cells (PBMC) were enriched for B cells, then incubated in Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Zijun

last: Wang

first: Frauke

last: Muecksch

first: Raphael

last: Raspe

first: Frederik

last: Johannsen

first: Martina

last: Turroja

first: Marie

last: Canis

first: Mohamed

last: ElTanbouly

first: Brianna

last: Johnson

first: Viren

last: Baharani

first: Rachel

last: Patejak

first: Kai-Hui

last: Yao

first: Bennett

middle: J

last: Chirco

first: Katrina

middle: G

last: Millard

first: Irina

last: Shimeliovich

first: Anna

last: Gazumyan

first: Thiago

last: Oliveira

first: Paul

middle: D

last: Bieniasz

first: Theodora

last: Hatziioannou

first: Marina

last: Caskey

first: Michel

last: Nussenzweig


title: A three-colour biosensor reveals multimodal stress response at the single cell level and the spatiotemporal dynamics of biofilms.

city: Eggenstein-Leopoldshafen

first: Kersten

last: Rabe

state: Select a state

address: Building 601

department: Institute for Biological Interfaces - 1

institute: Karlsruhe Institute of Technology

summary: We employed the orthogonally detectable red, green, and blue fluorescent proteins in a single vector system, dubbed RGB-S reporter, to enable simultaneous, independent and real-time analysis of the stress response in E. coli to physiological stress, genotoxicity, and cytotoxicity.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: We applied a “mini”- transcriptome  approach to sensor E. coli treated with 2-propanol 2 % by sorting approximately 1 million cells based on the single cell responses into four subpopulations, mono RFP, mono GFP, dual RFP-GFP, and triple RFP-GFP-BFP using FACS.

first: Ahmed

last: Zoheir

first: Morgan

last: Sobol

first: Diana

last: Ordonez

first: Anne-Kristin

last: Kaster

first: Christof

last: Niemeyer


title: NAD+ Metabolism Generates a Metabolic Vulnerability in Endocrine-Resistant Metastatic Breast Tumors

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

summary: Approximately 70% of human breast cancers express estrogen receptor-α (ERα), providing a potential target for endocrine therapy. However, 30%–40% of patients with ER+ breast cancer still experience recurrence and metastasis, with a 5-year relative overall survival rate of 24%. In this study, we identified NAMPT, an important enzyme in nicotinamide adenine dinucleotide (NAD+) metabolism, to be increased in metastatic breast cancer (MBC) cells treated with Fulv. We tested whether blockade of NAD+ production via inhibition of nicotinamide phosphoribosyltransferase (NAMPT) synergizes with standard-of-care therapies for ER+ metastatic breast cancer in vitro and in vivo. A synergistic effect was not observed when KPT-9274 was combined with palbociclib or tamoxifen or when Fulv was combined with other metabolic inhibitors. We show that NAMPT inhibitor KPT-9274 and fulvestrant (Fulv) works synergistically to reduce metastatic tumor burden. RNA-sequencing analysis showed that NAMPT inhibition improved antiestrogenic activity of Fulv, and metabolomics analysis showed that NAMPT inhibition reduced the abundance of metabolites associated with several key tumor metabolic pathways. Targeting metabolic adaptations in endocrine-resistant metastatic breast cancer is a novel strategy, and alternative approaches aimed at improving the therapeutic response of metastatic ER+ tumors are needed. Our findings uncover the role of ERα–NAMPT cross-talk in metastatic breast cancer and the utility of NAMPT inhibition and antiestrogen combination therapy in reducing tumor burden and metastasis, potentially leading to new avenues of metastatic breast cancer treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver tumors derived from MCF7 Y537S cells under various treatments (Fulv, Fulv+NAMPi,Fulv+Palb,Palb,Palb+NAMPTi)

first: Ayca

middle: N

last: Mogol

first: Qianying

last: Zuo

first: Jin

last: Yoo

first: Alanna

middle: Z

last: Kaminsky

first: Ozan

last: Imir

first: Yosef

last: Landesman

first: Christopher

last: Walker

last: Erdogan


title: RNA sequencing of CD103+ cDC1 from melanoma tumors

city: Munich

first: Felix

middle: Archibald

last: Bayerl

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Molecular Immunology

institute: Technical Univerity of Munich

summary:
RNA sequencing was used to characterize in situ tumor infiltrating conventional type 1 dendritic cells (cDC1) in BRAFV600E melanoma tumors transplanted into C57BL/6 wildtype mice.
Our analysis shows PGE2-dependent differences in the gene expression profile of intratumoral cDC1.

overall_design: C57BL6 WT mice were inoculated with 2x10E6 PGE2-producing control BRAFV600E or PGE2-deficient Ptgs1/Ptgs2 BRAFV600E melanoma cells. After 6 days, cDC1 were sorted from tumors and replicates of 10 cells were sequenced using SMART-Seq3.

first: Jan

last: Böttcher

first: Anais

last: Elewaut

first: Anna

last: Obenauf


title: RNA sequencing of human peripheral blood cDC1 treated with PGE2

summary: RNA sequencing was used to characterize PGE2-mediated changes in the gene expression profile of human conventional type 1 dendritic cells (cDC1) purified from PBMCs of healthy donors. Our analysis shows that treatment of cDC1 with PGE2 induces transcriptional changes in resting cDC1. cDC1 activated with a TLR3 ligand after PGE2 pre-treatment show alterations in the expression of activation induced genes.

overall_design: cDC1 (CD370+CD141+CD3- cells) were sort purified from PBMCs of four healthy donors (A,B,C,D). cDC1 were treated or not with PGE2 (1µg/ml) for 24h. In some groups, the TLR3 ligand poly I:C was added to the culture for the last 4h of the experiment to induce cDC1 activation.

first: Sainitin

last: Donakonda


title: RNA sequencing of murine bone marrow cell-derived cDC1 treated with PGE2

summary: RNA sequencing was used to characterize PGE2-mediated changes in the gene expression profile of conventional type 1 dendritic cells (cDC1). Our analysis shows that treatment of cDC1 with PGE2 or conditioned medium from PGE2-producing tumors induces transcriptional changes in resting cDC1. cDC1 activated with a TLR3 ligand after PGE2 pre-treatment show alterations in the expression of activation induced genes.

overall_design:
cDC1 were differentiated from C57BL/6J bone marrow cells in vitro over 14 days using FLT-3 ligand and GM-CSF. CD103+ cDC1 were sort-purified and treated for 4h with PGE2 (100ng/ml) or conditioned medium from PGE2-producing BRAFV600E melanoma cells or PGE2-deficient Ptgs1/Ptgs2-/- BRAFV600E melanoma cells. In some groups, antagonists for the PGE2 receptors EP1, EP2, EP3 or EP4 were added to the culture.

For analyses of changes upon cDC1 activation, cDC1 were treated for 24h with PGE2 and stimulated for the last 4h with the TLR3 ligand poly I:C.

first: Rupert

last: Öllinger


title: Transcriptional profiling of immunity to the MF-59 – adjuvanted influenza vaccine in children

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary:
In this study, we performed a systems-level analysis of immune responses to the trivalent inactivated influenza vaccine adjuvanted with MF-59 in children (15-24 months old) and in young healthy adults. We analyzed transcriptional responses elicited by vaccination in peripheral blood, as well as cellular and antibody responses following primary and booster vaccinations.
The pediatric population is a major target of vaccination, yet there is a paucity of studies on the transcriptional response of immunity to vaccination in this special population. In this study, we performed a systems-level analysis of immune responses to the trivalent inactivated influenza vaccine adjuvanted with MF-59 in children (15-24 months old) and in young healthy adults. We analyzed transcriptional responses elicited by vaccination in peripheral blood, as well as cellular and antibody responses following primary and booster vaccinations. Our analysis revealed that primary vaccination induced a persistent transcriptional signature of innate immunity; booster vaccination induced a transcriptional signature of an enhanced memory-like innate response, which was consistent with enhanced activation of myeloid cells assessed by FACS. Furthermore, we identified a transcriptional signature of type 1 IFN response post booster vaccination and at baseline that was correlated with the local reactogenicity to vaccination, and defined an early signature of the hemagglutinin antibody titers. These results highlight an adaptive behavior of the innate immune system in evoking a memory-like response to secondary vaccination and define molecular correlates of reactogenicity and immunogenicity in infants.

overall_design: 90 children, aged 15 to 24 months, were randomized into three cohorts. Each participant received two doses of seasonal TIV vaccine with MF59 adjuvant, 28 days apart. Peripheral blood was collected. Due to the limitations on the number of blood draws that could be obtained from a child, we utilized a staggered sample collection design. Pre-vaccination baseline samples were obtained from individuals in cohort A. Pre-boost baseline samples were obtained from those in cohorts B and C. Children in Cohort A were sampled also at Day 1 post primary vaccination. Children in cohorts B and C were sampled at Day 1 and Day 3 post boost vaccination, respectively. Blood was also collected from all subjects 28 days after the boost vaccination to access the serological responses. Thirty young healthy adult volunteers (cohort D) received a single ATIV injection, and blood was collected from all adult subjects prior to vaccination, and at days 1, 3 and 28 post vaccination.

first: Bali

last: Pulendran


title: Long non-coding RNA and circular RNA and coding RNA profiling of plasma exosomes of osteosarcoma by RNA seq

city: Nanning

first: Yun

last: Liu

address: NO 6, Shuangyong Road, Nanning City, Guangxi Province, China

institute: The First Affiliated Hospital of Guangxi Medical University

summary: Research show that the plasma exosomes derived from osteosarcoma play a key role in the process of tumor metastasis. Here, we established RNA-seq dataset for lncRNAs, circRNAs and mRNAs in plasma exosomes from 10 OS patients and 5 healthy donors. This database provides a significant resource for relevant researchers to excavate dysregulated lncRNAs, circRNAs and mRNAs of plasma exosomes in OS versus normal conditions.

overall_design: Extract plasma exosomes from osteosarcoma patients and normal volunteers, and sequence these exosomes to find differentially expressed RNA.

first: Jili

last: Lu

first: Haijun

last: Tang


title: Comparison of the therapeutic effects between stem cells and exosomes in primary ovarian insufficiency: As promising as cells but different persistency and dosage.

city: Chicago

first: Hang-soo

last: Park

address: 5821 S Drexel Ave

institute: University of Chicago

summary: Primary ovarian insufficiency (POI) refers to the loss of ovarian function under the age of 40 and results in amenorrhea and infertility. Our previous studies have shown that transplantation of mesenchymal stem cells (MSCs) and MSC-derived exosomes in chemotherapy-induced POI mouse ovaries can reverse the POI and eventually achieve pregnancy. Based on our recent studies, MSC-derived exosomes have almost equal therapeutic potentials as transplanted MSCs. However, it is still unclear whether exosomes can completely replace MSCs in POI treatment. In this study, we induced POI in C57/BL6 mice by chemotherapy (CXT) using a standard protocol. We compared the RNA expression pattern in ovarian tissue after MSC or exosome treatment. our data suggest that a minimal 10-fold increase, and ideally 100-fold increase, in the exosome concentration is required to generate more analogous results to MSC treatment.

overall_design: To find difference between exosome treatment and MSC treatment (10,000 cells), we injected same amount of exosome particle produced from 10,000 cells(1-fold), higher amounts of exosome particles (10-fold and 100-fold) into the POI model and analyzed ovarian follicles. Next, we compared the RNA expression pattern in ovarian tissue. Expriment 1 (Exp1) is MSC treated set, experiment 2 (Exp2) is UC-exosome treated set, experiment 3(Exp3) is BM-exosome treated set.

first: Ayman

last: Al-Hendy


title: Loss of TDP-43 causes ectopic endothelial sprouting and migration defects through increased fibronectin, vcam 1 and integrin α4/β1

status: Public on May 26 2023

city: Tübingen

first: Vikas

last: Bansal

state: BW

address: Otfried Müller Strasse 23

institute: German Center for Neurodegenerative Diseases (DZNE)-Tübingen

summary: Aggregation of the Tar DNA-binding protein of 43 kDa (TDP-43) is a pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) and likely contributes to disease by loss of nuclear function. Analysis of TDP-43 function in knockout zebrafish identified an endothelial directional migration and hypersprouting phenotype during development prior lethality. In human umbilical vein cells (HUVEC) the loss of TDP-43 leads to hyperbranching. We identified elevated expression of FIBRONECTIN 1 (FN1), the VASCULAR CELL ADHESION MOLECULE 1 (VCAM1), as well as their receptor INTEGRIN α4β1 (ITGA4B1) in HUVEC cells. Importantly, reducing the levels of ITGA4, FN1, and VCAM1 homologues in the TDP-43 loss-of-function zebrafish rescues the angiogenic defects indicating the conservation of human and zebrafish TDP-43 function during angiogenesis. Our study identifies a novel pathway regulated by TDP-43 important for angiogenesis during development.

overall_design: Comparative transcriptome profiling by RNA sequencing of Control vs TDP-43 knock down in HUVEC cells

first: Katrin

last: Hipke

first: Stefan

last: Bonn

first: Bettina

last: Schmid


title: Interferon inhibits a model RNA virus via a limited set of inducible effector genes [GW_CRISPR_Screen]

city: Dallas

first: John

last: Schoggins

state: TX

address: 6000 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

summary: Host cells produce interferon (IFN) in response to viral infections. Secreted interferon results in the transcription and production of hundreds of interferon-stimulated genes (ISGs). A genome-wide CRISPR screen using IFN beta-treated U-2 OS cells was performed to determine which ISGs were required in order for host cells to suppress Venezuelan equine encephalitis virus (VEEV) infection.

overall_design: Human U-2 OS cells were transduced with a human genome-wide CRISPR knockout (Brunello) library, selected for transduced cells, treated with IFNβ, infected with Venezuelan equine encephalitis virus encoding a GFP reporter, and GFP-positive cells that became infected despite IFNβ suppression were collected by FACS. The screen was performed as 2 independent biological replicates at approximately 417x and 460x library coverage.

first: Matthew

last: McDougal

first: Anthony

last: De Maria

first: Maikke

last: Ohlson

first: Ashwani

last: Kumar

first: Chao

last: Xing


title: RNA sequencing of brown adipose tissue in Letmd1 Knockout mice

city: Daejeon

first: Anna

state: Yuseong-gu

address: 125, Gwahak-ro

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

summary: We performed RNA sequencing on brown adipose tissue in wild-type and Letmd1 knockout mice to investigate the gene expression patterns in Letmd1 deficient mice.

overall_design: Bulk RNA sequencing of the total interscapular browns adipose tissue depot from 5-week-old WT and Letmd1KO mice.

first: Kwang-eun

last: Kim

first: Isaac

first: Sang

middle: H

last: Lee

first: Kun-Young

first: Minkyo

last: Jung

first: Xiaoxu

last: Li

first: Maroun

last: Sleiman

first: Su-Jeong

first: Dae-Soo

first: Jaehoon

first: Dae-Sik

last: Lim

first: Eui-Jeon

last: Woo

first: Eun

first: Baek

last: Han

first: Kyoung-Jin

last: Oh

middle: C

first: Johan

last: Auwerx

first: Ji

last: Mun

first: Hyun-Woo

last: Rhee

first: Won

middle: K

first: Kwang-Hee

last: Bae

first: Jae

last: Suh


title: Interferon inhibits a model RNA virus via a limited set of inducible effector genes [RNA-seq]

first: John

last: Schoggins

summary: To investigate the transcripts induced by the cytokine interferon (IFN) β in U-2 OS cells, we treated U-2 OS cells with IFNβ 20U/mL for 6 and 24 hours and performed RNA-Seq to determine differentially expressed genes.

overall_design: U-2 OS cells were mock treated or treated with IFNβ (20U/mL) for 6 or 24 hours

first: Matthew

last: McDougal

first: Anthony

middle: M

last: De Maria

first: Maikke

last: Ohlson

first: Ashwani

first: Chao


title: Supraphysiological Androgens Promote the Tumor Suppressive Activity of the Androgen Receptor Through cMYC Repression and Recruitment of the DREAM Complex [CUT&RUN]

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

summary: The androgen receptor (AR) pathway regulates key cell survival programs in prostate epithelium. Targeting the AR has a remarkable therapeutic index and represents a near-universal driver and therapeutic vulnerability in metastatic prostate cancer. Though most approaches directed toward the AR focus on inhibiting AR signaling, laboratory and now clinical data have shown that high dose, supraphysiological androgen treatment (SPA), results in growth repression and improved out-comes in subsets of prostate cancer patients. However, the mechanism(s) contributing to SPA re-sponse and resistance remain unclear. To characterize SPA signaling, we integrated metrics of gene expression changes induced by SPA together with cistrome data and protein-interactomes. These analyses determined that the Dimerization partner, RB-like, E2F and Multi-vulval class B (DREAM) complex mediates growth repression and downregulation of E2F targets in response to SPA. Notably, prostate cancers with complete genomic loss of RB1 responded to SPA treatment whereas loss of DREAM complex components such as RBL1/2 promoted resistance. Overexpres-sion of MYC resulted in complete resistance to SPA and attenuated the SPA/AR-mediated repres-sion of E2F target genes. These findings support a model of SPA-mediated growth repression that relies on the negative regulation of MYC by AR leading to repression of E2F1 signaling via the DREAM-SIN3A-HDAC complex. As RB1 and DREAM complex stability are regulated by MYC, a key determinant of tumor sensitivity to SPA, treatment may hinge on effectively repress-ing MYC activity. The integrity of MYC signaling and DREAM complex assembly may conse-quently serve as determinants of SPA responses and as pathways mediating SPA resistance.

overall_design: This data series contains LNCaP cells and isogenic TP53/RB1 knockout cells that also have RBL1, RBL2, or both knocked out. These are also isogenic clones. IgG serve as input controls for MACS2. 4xKO samples lack RB1/RBL1/RBL2 and can serve as antibody-specific background controls for .tdf or Bigwig files. Each condition is in represented by biological triplicates (1-3)

first: Michael

last: Nyquist

first: Ilsa

last: Coleman

first: Jared

last: Lucas

first: Dapei

first: Hannah

last: Meade

first: Elahe

last: Mostaghel

first: Stephen

middle: R

last: Plymate

first: Eva

last: Corey

last: Haffner

first: Peter

last: Nelson


title: Interferon inhibits a model RNA virus via a limited set of inducible effector genes [ISG_CRISPR_Screen]

summary: Host cells produce interferon (IFN) in response to viral infections. Secreted interferon results in the transcription and production of hundreds of interferon-stimulated genes (ISGs). An ISG-targeted CRISPR screen using IFN beta-treated U-2 OS cells was performed to determine which ISGs were required in order for host cells to suppress Venezuelan equine encephalitis virus (VEEV) infection.

overall_design: Human U-2 OS cells were transduced with a human interferon-stimulated gene CRISPR knockout library, selected for transduced cells, treated with IFNβ, infected with Venezuelan equine encephalitis virus encoding a GFP reporter, and GFP-positive cells that became infected despite IFNβ suppression were collected by FACS. The screen was performed as 3 independent biological replicates at approximately 1270x, 430x, and 1160x library coverage.

last: Kumar

last: Xing

middle: W


title: Supraphysiological Androgens Promote the Tumor Suppressive Activity of the Androgen Receptor Through cMYC Repression and Recruitment of the DREAM Complex [ChIP-seq]

overall_design: This data series contains LNCaP and isogenic TP53/RB1 LNCaP knockout cells lines treated with high-dose R1881. ChIP-seq was performed for E2F1, LIN37, or LIN9. E2F1 ChIP-seq was perfromed in triplicate. LIN37 and LIN9 are single samples. These factors control expression of E2F target genes that are repressed as a result of androgen receptor activity. Input samples were used with MACS2. IgG files are availble as negative controls.

last: Li


title: Gene expression of S100a8/a9 predicts Staphylococcus aureus-induced septic arthritis in mice

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

summary: To identify specific predictive biomarkers for septic arthritis, transcriptome sequencing analysis was performed on Staphylococcal aureus infected mouse RNA samples. We then evaluated differentially expressed genes from RNA-seq of Day 0, Day 2 and Day 10 samples of arthritic and non-arthritic mice.

overall_design: Compartive S100a8 and S100a9 gene expression analysis of RNA-seq data for Arthritis, non arthritis and control samples for different time points.

first: Meghshree

last: Deshmukh

first: Zhicheng

last: Hu

first: Majd

last: Mohammad

first: Anders

last: Jarneborn

first: Rille

last: Pullerits

first: Tao

last: Jin

first: Pradeep

last: Kopparapu


title: Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen B. burgdorferi [SPD RNA-seq]

city: Bethesda

first: Philip

last: Adams

state: MD

address: 9000 Rockville Pike

department: NICHD

institute: National Institutes of Health

summary: Transcription termination is an essential and dynamic process that can tune gene expression in response to diverse molecular signals. Yet, the genomic positions, molecular mechanisms, and regulatory consequences of termination have only been studied thoroughly in model bacteria. We employed complementary RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi – the etiological agent of Lyme disease. By systematically mapping B. burgdorferi RNA ends at single nucleotide resolution, we delineated complex gene arrangements and operons and mapped untranslated regions (UTRs) and small RNAs (sRNAs). We experimentally tested modes of B. burgdorferi transcription termination and compared our findings to observations in E. coli, P. aeruginosa, and B. subtilis. We discovered 63% of B. burgdorferi RNA 3′ ends map upstream or internal to open reading frames (ORFs), suggesting novel mechanisms of regulation. Northern analysis confirmed the presence of stable 5′ derived RNAs from mRNAs encoding gene products involved in the unique infectious cycle of B. burgdorferi. We suggest these RNAs resulted from premature termination and regulatory events, including forms of cis-acting regulation. For example, we documented that the polyamine spermidine globally influences the generation of truncated mRNAs. In one case, we showed that high spermidine concentrations increased levels of RNA fragments derived from an mRNA encoding a spermidine import system, with a concomitant decrease in levels of the full-length mRNA. Collectively, our findings revealed new insight into transcription termination and uncovered an abundance of potential RNA regulators.

overall_design: Identification of spermidine specific differentially expressed genes in RNAseq experiment

middle: P

first: Emily

last: Petroni

first: Caroline

last: Esnault

first: Daniel

last: Tetreault

first: Ryan

last: Dale

first: Gisela

last: Storz


title: Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen B. burgdorferi [3′RNA-seq]

overall_design: Identification of 3′ ends by 3′RNA-seq (Term-seq) experiment


title: Y-complex nucleoporins independently contribute to nuclear pore assembly and gene regulation in neuronal progenitors

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

summary: From their essential function in building up the nuclear pore complexes, nucleoporins have expanded roles beyond nuclear transport. Hence, their contribution to chromatin organization and gene expression has set them as critical players in development and pathologies. We previously reported that Nup133 and Seh1, two components of the Y-complex subunit of the nuclear pore scaffold, are dispensable in mouse embryonic stem cells but required for their survival during neuroectodermal differentiation. Here, a transcriptomic analysis revealed that Nup133 regulates a subset of genes at early stages of neuroectodermal differentiation, including Lhx1 and Nup210L, encoding a newly validated nucleoporin. These genes were also misregulated in Nup133∆Mid neuronal progenitors, in which NPC basket assembly is impaired, as previously observed in pluripotent cells. However, a four-fold reduction of Nup133, despite affecting basket assembly, is not sufficient to alter Nup210L and Lhx1 regulation. Finally, these two genes are misregulated in Seh1-deficient progenitors that only show a mild decrease in NPC density. Together these data reveal a shared function of Y-complex nucleoporins in gene regulation during neuroectodermal differentiation.

overall_design: We compared the transcriptome of WT and Nup133-/- mESCs at the pluripotent state and after 2 or 3 days of differentiation towards neuroectodermal lineage. We therefore used cell lines from two distinct genetic background, namely the HM1 control cell line (Selfridge et al., 1992, PMID: 1440055) and its CRISPR/Cas9-edited Nup133-/- derivatives (#14 and #19), and the blastocyst-derived control (#1A4) and Nup133-/- (merm, #319) mESC lines (cell lines described in Souquet et al., 2018 - PMID: 30428363).

first: Clarisse

last: Orniacki

first: Annalisa

last: Verrico

first: Stéphane

last: Pelletier

first: Benoit

last: Souquet

first: Fanny

last: Coulpier

first: Laurent

last: Jourdren

first: Serena

last: Benetti

first: Valérie

last: Doye


title: Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen B. burgdorferi.

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

overall_design: Refer to individual Series


title: hapln1a+ cells guide coronary growth during heart morphogenesis and regeneration [Dev, hapln1a+ cells]

city: ATLANTA

first: Jinhu

last: Wang

state: Georgia

address: 101 WOODRUFF CIRCLE WMB 2304

institute: Emory University

summary: As cardiac regeneration requires new coronary vessels, exploring the underlying mechanisms behind revascularization will facilitate the development of regenerative therapies for heart failure. Although multiple tissues and chemokines likely orchestrate coronary formation, the interaction between coronary growth and guidance cues remains unclear. Here, by applying single-cell RNA-sequencing (scRNA-seq) analysis, we examined gene expression in zebrafish epicardial cells during coronary vascularization and identified hapln1a-expressing epicardial cells enriched with vascular-regulating genes. Fluorescence reporter assays indicated hapln1a+ cells not only envelop coronary vessels, but also form cellular shear structures in ahead of coronary tips. Live imaging analyses demonstrated coronary growth along the pre-formed shears, with depletion of hapln1a+ cells blocking this growth. Further, we found hapln1a+ cells also pre-lead coronary tips in the regenerating area and hapln1a+ cell loss inhibits coronary revascularization. To characterize the molecular nature of hapln1a+ cells during coronary growth, we profiled hapln1a+ cells in juvenile and regenerating hearts and detected expression of the cell adhesion and migration regulator serpine1 in hapln1a+ cells adjacent to coronary tips. Pharmacological inhibition of serpine1 function blocked coronary vascularization and revascularization. Altogether, our studies reveal that hapln1a+ cells are required for coronary production during heart morphogenesis and regeneration, by establishing a microenvironment to facilitate guided coronary growth.

overall_design: hapln1a+ cells of zebrafish heart were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of eGFP signal and analyzed using scRNAseq.

first: Jisheng

last: Sun


title: Heart morphogenesis and regeneration


title: hapln1a+ cells guide coronary growth during heart morphogenesis and regeneration [Reg, hapln1a+ cell]


title: Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen B. burgdorferi [BCM RNA-seq]

first: Philip

last: Adams

overall_design: Identification of Rho-dependent termination by RNAseq experiment


title: Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen B. burgdorferi [bulk RNA-seq]

overall_design: Quantification of total RNA in B. burgdorferi

first: Emily

last: Petroni


title: Interferon inhibits a model RNA virus via a limited set of inducible effector genes

first: John

last: Schoggins


title: Bulk RNAseq of control, XBP1-deficient or XBP1/IRE1-deficient cDC1s from subcutaneous B16- melanoma bearing mice

city: Santiago

first: Fabiola

last: Osorio

address: Av Independencia 1027, wing I, lower floor

department: Immunology

country: Chile

institute: Universidad de Chile

summary: The unfolded protein response (UPR) sensor IRE1 and its target, the transcription factor XBP1s critically regulate the function of dendritic cell (DC) subtypes. However, the contribution of the IRE1/XBP1s axis in DCs to the antitumor immunity is not entirely understood. Here, using reporter mice we found that DCs, in particular type 1 conventional DCs (cDC1s), are major targets of IRE1 RNase activity in melanoma tumors. Deletion of XBP1s in CD11c+ cells resulted in augmented tumor growth, impaired effector T cell responses and decreased accumulation of TCF-1+CD8+ T cells with a precursor exhausted profile. Transcriptomic studies revealed that XBP1 deletion in tumor cDC1s induced regulated IRE1 dependent decay (RIDD) of mRNAs, which accounted for the dysregulated T cell immunity in melanoma. Thus, a strict regulatory circuit involving IRE1 RNase and XBP1s in DCs ensures optimal antitumor T cell immunity in melanoma models.

overall_design: Bulk-RNAseq of intratumoral cDC1s isolated from B16 bearing control (wild-type) mice or conditional deficient mice for XBP1 or XBP1/IRE1 in CD11c+ cells. Each data point comes from 2-4 pooled mice with the same genotype and replicates correspond to independent pools.

first: Felipe

last: Flores-Santibanez

first: Clint

last: De-Nolf

first: Sofie

last: Rennen

first: Sophie

last: Janssens


title: Clariom S Microarry Gene Expression Data from murine pancreatic ductal adenocarcinoma cells (Pan02) transduced to either overexpress or knockdown murine NLRX1 (and their respective controls)

status: Public on May 25 2023

city: Blacksburg

first: Irving

middle: Coy

last: Allen

state: VA

address: 295 Duck Pond Dr

institute: Virginia Tech

summary:
NLRX1 is an immune signaling protein that has shown to be both tumor suppressing or tumor promoting, depending on the type of cancer. We demonstrate that NLRX1 has tumor suppressive abilities in vitro in Pan02 cells. We used this microarray to evaluate genes and pathways NLRX1 regulates in these cells to cause the observed in vitro phenotypes.
Abstract from associated publication: Pancreatic cancer is a deadly malignancy with limited treatment options. NLRX1 is a unique, understudied member of the Nod-like Receptor (NLR) family of pattern recognition receptors that regulates a variety of biological processes that are highly relevant to pancreatic cancer. The role of NLRX1 in cancer remains highly enigmatic, with some studies defining its roles as a tumor promoter, while others characterize its contributions to tumor suppression. These seemingly contradicting roles appear to be due, at least in part, to cell type and temporal mechanisms. Here, we define roles for NLRX1 in regulating critical hallmarks of pancreatic cancer using both gain-of-function and loss-of-function studies in murine Pan02 cells. Our data reveals that NLRX1 increases susceptibility to cell death, while also suppressing proliferation, migration, and reactive oxygen species production. We also show that NLRX1 protects against upregulated mitochondrial activity and limits energy production in the Pan02 cells. Transcriptomics analysis revealed that the protective phenotypes associated with NLRX1 are correlated with attenuation of NF-kB, MAPK, AKT, and inflammasome signaling. Together, these data demonstrate that NLRX1 diminishes cancer-associated biological functions in pancreatic cancer cells and establishes a role for this unique NLR in tumor suppression.

overall_design: 8 RNA samples from murine Pan02 cells (pancreatic adenocarcinoma). Data compare transduced Pan02 cells with overexpressed NLRX1 (Pan02OE) versus their controls (Pan02OE-CTL), and compare Pan02 cells with knocked down NLRX1 (Pan02KD) versus their controls (Pan02KD-CTL), in either normal cell culture conditions or after a challenge with low dose H2O2. 4 cell lines x 2 conditions = 8 samples. MRSL from manufacturer is also included for a total of 9 samples.

first: Margaret

last: Nagai-Singer


title: Expression data from human lung FFPE samples

city: Matsumoto

first: Sachie

last: Hiratsuka

address: 3-1-1 Asahi

department: Medicine

institute: Shinshu University

summary:
Fibrinogen deposition promotes metastasis in lung because fibrinogen binds circulating tumor cells and the fibrinogen-tumor cell complex is allowed to invade in the lung tissue.
We used microarrays to compare gene expression profiles of the tissues near and apart from fibrinogen deposition in non-cancer patients and cancer patients.

overall_design: Formalin fixed paraffin embedded (FFPE) lung tissues from non-cancer and cancer patients. Slide sections were prepared and blood vessels with or without fibrinogen deposition were isolated by using laser microdissection. Total 20,000 vessels were obtained for each group [Fibrinogen(-)-non-cancer, Fibrinogen(+)-non-cancer, Fibrinogen(-)-cancer, Fibrinogen(+)-cancer]. Total RNAs were extracted from the pooled tissue fragments and these samples were analyzed by microarray.

first: Takeshi

last: Tomita


title: Old and newly synthesized histones are asymmetrically distributed in Drosophila intestinal stem cell divisions

city: Baltimore

first: Daniel

last: Ringwalt

address: 3400N Charles St

department: Biology

institute: Johns Hopkins University

summary: We report that preexisting (old) and newly synthesized (new) histones H3 and H4 are asymmetrically partitioned during the division of Drosophila intestinal stem cells (ISCs). Furthermore, the inheritance patterns of old and new H3 and H4 in postmitotic cell pairs correlate with distinct expression patterns of Delta, an important cell fate gene. To understand the biological significance of this phenomenon, we expressed a mutant H3T3A to compromise asymmetric histone inheritance. Under this condition, we observe an increase in Delta‐symmetric cell pairs and overpopulated ISC‐like, Delta‐positive cells. Single‐cell RNA‐seq assays further indicate that H3T3A expression compromises ISC differentiation. Together, our results indicate that asymmetric histone inheritance potentially contributes to establishing distinct cell identities in a somatic stem cell lineage, consistent with previous findings in Drosophila male germline stem cells.

overall_design: H3 wild-type- or H3T3A-expressing intestines were dissected, and the tissue samples were analyzed using scRNA-seq.

last: Zion

first: Kristina

last: Rinaldi

first: Elizabeth

last: Kahney

first: Yingying

last: Li

first: Xin

last: Chen


title: Effect of Domatinostat treatment on MKL1 cells

city: Long Beach

first: Ling

last: Gao

email: ling.gao@va.gov, lingg3@hs.uci.edu

state: California

address: 5901 E.7th Street

institute: Department of Veterans Affairs

summary:
To investigate the effect of HDAC inhibition, we treated MKL1 cells with 10µM of domatinostat or vehicle control (DMSO) for 24h, and carried out bulk RNA-seq
We then performed gene expression profiling analysis using data obtained from RNA-seq of vehicle control (DMSO treated) and domatinostat treated samples (in duplicates)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for untreated and treated MKL1 cells.

first: Aarthi

last: Kannan

first: Bhaba

last: Das


title: NF-kB subunits direct kinetically distinct transcriptional cascades in antigen receptor-activated B cells [RNA-seq II]

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: The NF-kB family of transcription factors orchestrates signal-induced gene expression in a diversity of cell types.  Cellular responses to NF-kB activation are regulated at the level of cell- and signal-specificity, as well as differential use of family members (subunit specificity).  Here we used time-dependent multi-omics to investigate selective functions of Rel and RelA, two closely related NF-kB proteins, in primary B lymphocytes activated via the B cell receptor.  Despite large numbers of shared binding sites genome wide, Rel and RelA directed kinetically distinct cascades of gene expression in activated B cells.  Single cell RNA-Seq revealed marked heterogeneity of Rel- and RelA-specific responses and sequential binding of these factors was not a major mechanism of protracted transcription.  Moreover, nuclear co-expression of Rel and RelA led to functional antagonism between the two factors.  By rigorously identifying target genes of each NF-kB subunit, these studies provide insights into exclusive functions of Rel and RelA in immunity and cancer.

overall_design: Mouse splenocytes were staining with antibodies for B220, AA4.1, CD23 and CD21/35. FO and MZ B cells were FACS sorted, and activated with anti-IgM and collected at various time points (unstimulated, 1, 4, 18h). Total RNA was prepared and bulk RNA-seq was performed.

first: Mingming

last: Zhao

first: Chauhan

last: Prashnat

first: Cheryl

last: Sherman-Baust

first: Amit

last: Singh

first: Mary

last: Kaileh

first: Satabdi

last: Nandi

first: Krystyna

last: Mazan-Mamczarz

first: Hongkai

last: Ji

first: Jamie

last: Joy

first: Yongqing

last: Zhang

first: Jinshui

last: Fan

first: Kevin

last: Becker

first: Png

last: Loke

first: Weiqiang

last: Zhou

first: Ranjan

last: Sen


title: hapln1a+ cells guide coronary growth during heart morphogenesis and regeneration [Dev, tcf21+ cells]

first: Jinhu

last: Wang

overall_design: Epicardial cells of zebrafish heart were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of eGFP signal and analyzed using scRNAseq.

first: Jisheng

last: Sun


title: Effect of faecal water exposure from control or antibiotic-treated mice on gene expression of Caco-2 cells

city: Woluwe-Saint-Lambert

first: Laure

last: Elens

address: Avenue Emmanuel Mounier 72

department: LDRI

institute: UCLouvain

summary: To investigate the effect of polar microbial metabolites on intestinal gene expression, we exposed Caco-2 cell to faecal water from control mice or the same mice under antibiotherapy (for 7-10 days).

overall_design: Comparative gene expression profiling analysis of RNA-seq data of Caco-2 cells exposed for 48 hours to the vehicle (PBS), the faecal water from control mice, the faecal water from antibiotic-treated mice, or the antibiotic cocktail.

middle: B

last: Bindels

first: Alexandra

middle: L

last: Degraeve

first: Axelle

last: Loriot

first: Laurent

last: Gatto


title: Effect of upregulation of LINE-1 retrotransposon on translation in the mouse testis

first: Alex

last: Bortvin

address: 3520 San Martin drive

department: Embryology

institute: Carnegie Institution for Science

summary: We used piRNA-deficient Maelstrom (Mael) knockout mice to investigate the effect of LINE-1 retrotransposon upregulation on translation efficiency (TE) in the germline. We collected Mael+/- and Mael-/- testes at postnatal day 16 (P16), when LINE-1 upregulation in Mael-/- spermatocytes is manifest, and performed ribosome profiling. RNA-seq analysis of the same samples was performed in parallel to evaluate the contribution of transcriptional changes to variations in footprint levels.

overall_design: Comparative ribosome profiling analysis of P16 Mael-/- testes and their Mael+/- controls. Three biological replicates per genotype are reported.

first: Chiara

last: De Luca


title: Characterization of the RNA present in L1 ORF1p macromolecular complexes from Mael-/- mouse testes

summary: piRNA-deficient Maelstrom (Mael) null mice are characterized by a strong upregulation of LINE-1 (L1) retrotransposon in meiotic spermatocytes. This defect turns out in the accumulation of L1 RNA and ORF1p in their cytoplasm and the formation of prominent ribonucleoprotein aggregates. We used 3-months-old Mael-/- male mice to characterize the RNA present in those ORF1p aggregates. To favor the isolation of complexed versus free ORF1p protein, we first fractionated Mael-/- testis extracts (that we refer to as TOTAL) by sucrose gradient ultracentrifugation, in the presence of EDTA. We then pooled the sucrose fractions where ORF1p macromolecular complexes sediment (fractions 5-8) and used this pool as the INPUT for an anti-ORF1p co-immunoprecipitation (IP) followed by RNA-seq.

overall_design: Enrichment of RNAs in anti-ORF1p co-immunoprecipitation samples (IP) was calculated over the background controls (Beads Only - BO), over the pools of sucrose fractions 5-8 (INPUT), and over the testis extracts originally loaded on sucrose gradients (TOTAL). Three biological replicates are reported.

first: Anuj

last: Gupta


title: Inflammation induces bitter taste oversensitization via epigenetic changes in Tas2r gene clusters

city: Philadelphia

first: Hong

address: 3500 Market Street

institute: Monell Chemical Senses Center

summary: T2R bitter receptors, encoded by Tas2r genes, are not only critical for bitter taste signal transduction but also important for defense against bacteria and parasites. However, little is known about whether and how Tas2r gene expression are regulated. Here, using single-cell assays for transposase-accessible chromatin with sequencing (scATAC-seq), we found that the chromatin accessibility of Tas2rs was highly cell type specific and lipopolysaccharide (LPS)-induced inflammation increased the accessibility of many Tas2rs. scATAC-seq also revealed substantial chromatin remodeling in immune response genes in taste tissue stem cells, suggesting potential long-term effects. Together, our results suggest an epigenetic mechanism connecting inflammation, Tas2r gene regulation, and altered bitter taste, which may explain heightened bitter taste that can occur with infections and cancer treatments.

overall_design: Nucleus preparations from peeled tongue epithelium from the circumvallate papillae of control (PBS) or LPS-treated adult C57BL/6J mice (N=6 mice per group) were used for scATAC-seq analyses.

first: Cailu

last: Lin

first: Masafumi

last: Jyotaki

first: John

last: Quinlan

first: Shan

last: Feng

first: Minliang

first: Peihua

last: Jiang

first: Ichiro

last: Matsumoto

first: Liquan

last: Huang

first: Yuzo

last: Ninomiya

first: Robert

middle: F

last: Margolskee

first: Danielle

last: Reed