title: Effect of the res-2 transcription factor gene deletion on protein secretion and stress response in the hyperproducer strain Trichoderma reesei Rut-C30

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

summary: The fungus Trichoderma reesei is one of the most used industrial cellulase producers due to its high capacity of protein secretion. The strain was shown to possess an expanded endoplasmic reticulum, but the genetic factors responsible for this phenotype remain still unidentified. Recently, three new transcription factors were described in Neurospora crassa which were demonstrated to be involved in protein secretion. The orthologous gene of one of them, Res-2, was deleted in the T. reesei hyperproducer strain Rut-C30 and its role on protein secretion analyzed. The mutant strain showed slower growth on all substrates tested, but the presence of the stress agent DTT had contrasting effects. Protein secretion tended to be lower in the deletion strain compared to the parental strain Rut-C30. Analysis of the transcriptomes of the Rut-C30 and the Δres-2 mutant strain in secretion stress conditions reveiled remarkably few differences, but induction of cellulase secretion and/or presence of DTT led to differential expression of genes coding for transporters, redox genes and lipid metabolism. These results suggest that in the T. reesei Rut-C30 strain, Res-2 does not act as a master regulator of the secretion pathway, but contributes to a high protein secretion by adjusting the expression of genes involved in membrane turnover and the redox status of the organism or specific organelles.

overall_design: Rut-C30 and the Δres-2 strain were cultivated in fed flasks and after a 48h batch phase on glucose medium, they were submitted to either a glucose (control condition) or lactose fed-batch. Two other conditions included the exposure to 10 mM DTT for 2 hours at the end of the glucose and the lactose fed-batch. All samples were run in duplicates and mycelia were collected after 48h of fed-batch for RNA extraction.

first: Jawad

last: Alharake

first: Senta

last: Heiss-Blanquet

first: Frédérique

last: Bidard-Michelot

first: Antoine

last: Margeot

first: Catherine

last: Senamaud-Beaufort


title: Effect of depletion of IntS4, IntS6, mts, or Pp2A-29B on gene expression in Drosophila DL1 cells

status: Public on Nov 10 2023

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

type: Expression profiling by high throughput sequencing

summary: To investigate the effect of depletion of Integrator complex subunits IntS4, IntS6, mts, or Pp2A-29B on gene expression

overall_design: Ribo– RNA-seq for 18 samples (3 biological replicate sets of DL1 cells subjected to a Mock treatment or treated with dsRNAs against B-gal (control dsRNA), IntS4, IntS6, mts, or Pp2A-29B)

first: Jeremy

middle: E

last: Wilusz

first: Rina

last: Fujiwara

first: Si-Nan

last: Zhai


title: Blood gene expression profiles following vaccination in 2-month old infants

status: Public on Nov 09 2023

city: Memphis

first: Zhaohui

last: Xu

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

country: USA

institute: St. Jude Children's Research Hospital

summary: Analyzed the gene expression changes in infant of 2 month old after vaccination of HepB, DTaP, Hib, IPV, PCV13, and RV vaccines in 7 days and 30 days

overall_design: Total RNA obtained from whole blood in infants before and after vaccination

first: Raquel

middle: G

last: Cao

first: Asuncion

last: Mejias

first: Octavio

last: Ramilo


title: Effect of overexpression of IntS6 and IntS12 on gene expression in Drosophila DL1 cells

summary: To investigate the effect of IntS6 or IntS12 overexpression on gene expression

overall_design: Ribo– RNA-seq for 9 samples treated with copper for 24h (3 biological replicate sets of control parental DL1 cells, DL1 cells stably maintaining an inducible IntS6 transgene driven by the MtnA promoter (DL1 pMtnA IntS6), and DL1 cells stably maintaining an inducible IntS12 transgene driven by the MtnA promoter (DL1 pMtnA IntS12)) and 9 samples not treated with copper (3 biological replicate sets of control parental DL1 cells, DL1 pMtnA IntS6 cells, and DL1 pMtnA IntS12 cells). The copper treatment was used to induce transgene expression.


title: ZmEREB92 plays a negative role in seed germination by regulating ethylene signaling and starch mobilization in maize

city: Chengdu

first: wenzheng

last: Pei

state: Sichuan Province

address: No. 211, Huimin Road, Fair Street, Wenjiang District, Chengdu, Sichuan Province

department: State Key Laboratory of Crop Gene Exploraion and Utilization in Southwest China

institute: Sichuan Agricultural University

summary: Rapid and uniform seed germination is required for modern cropping system. Thus, it is important to optimize germination performance through breeding strategies in maize, in which identification for key regulators is needed. Here, we characterized an AP2/ERF transcription factor, ZmEREB92, as a negative regulator of seed germination in maize. Enhanced germination in ereb92 mutants is contributed by elevated ethylene signaling and starch degradation. Consistently, an ethylene signaling gene ZmEIL7 and an α-amylase gene ZmAMYa2 are identified as direct targets repressed by ZmEREB92. OsERF74, the rice ortholog of ZmEREB92, shows conserved function in negatively regulating seed germination in rice. Importantly, this orthologous gene pair is likely experienced convergently selection during maize and rice domestication. Besides, mutation of ZmEREB92 and OsERF74 both lead to enhanced germination under cold condition, suggesting their regulation on seed germination might be coupled with temperature sensitivity. Collectively, our findings uncovered the ZmEREB92-mediated regulatory mechanism of seed germination in maize and provide breeding targets for maize and rice to optimize seed germination performance towards changing climates.

overall_design: In order to explore the mechanism of ZmEREB92 regulating seed germination, we generated knockout mutants of ZmEREB92, named ereb92-6. We used the ereb92-6 mutant and wild type maize seeds imbibited for 0h and 6h for Transcriptome sequencing, and set three biological repeats for each line.

first: Jingye

last: Fu

first: Wenzheng

first: Chen

last: Tang

first: Linqian

last: He

first: Ben

last: Ma

last: Zhu

first: Liping

last: Wang

first: Yuanyuan

last: Zhong

first: Gang

last: Chen

first: Qiang


title: Gene expression for eNOS S1176 mutant mice

city: Chicago

first: Monica

last: Lee

address: 835 S Wolcott

institute: University of Illinois at Chicago

summary: Extensive reports in the past decade have shown the importance of eNOS expression in atherogenesis. However, both the eNOS knockout and overexpression mouse models exhibit paradoxical results of increased atherosclerotic lesions. Our genetic approach herein utilizes endogenous point-mutations at the eNOS S1176 site to effectively manipulate eNOS activity rather than total eNOS protein expression levels. Our efforts definitively show that eNOS S1176 phosphorylation is sufficient to mitigate atherosclerotic lesion progression.

overall_design: eNOS S1176A ‘loss-of-function’ and eNOS S1176D ‘gain-of-function’ mice were fed either a standard laboratory diet or a high-fat, high-cholesterol Western Diet for 4weeks. Whole aortas were isolated (2-3 mice per group) for total RNA extraction and quality checks. Satisfactory samples were prepared for hybridization reactions with the NanoString platform (PanCancer Immune Profile Mouse). Each sample reflects a single aorta. mRNA profiling reflects 770 target genes including 20 housekeeping genes, 8 negative and 6 positive spike-in controls.

middle: Y


title: Reduction of TLR7/8-Induced IFN-I Responses by Plasmacytoid Dendritic Cells in a Longitudinal Cohort of Trans Men

city: Hamburg

first: Marcus

last: Altfeld

address: Süderfeldstraße

country: Germany

institute: Leibniz Institute of Virology

summary: Type I interferons (IFN-I) are important mediators of antiviral immunity and autoimmune diseases. Plasmacytoid dendritic cells (pDCs) from females exert an elevated capacity to produce IFN-I in response to activation of toll-like receptor 7 (TLR7) compared to male pDCs, and both hormones and genes encoded by the X chromosome have been implicated in these sex-specific differences. Using longitudinal samples collected from a cohort of trans men receiving testosterone injections as gender-affirming hormone therapy (GAHT), the impact of testosterone on TLR7-mediated IFN-I production by pDCs was assessed. GAHT induced testosterone and estradiol levels within male reference ranges and increased hemoglobin and hematocrit levels, demonstrating biological activity of testosterone. scRNA seq of pDCs showed downregulation of IFN-I-related gene expression signatures, but also revealed inter-donor heterogeneity on the transcriptional level. Longitudinal quantification of IFN-I protein production by pDCs following TLR7-stimulation showed significant and continuous reduction of IFN-I production in trans men, and reduced expression of IFN-I-stimulated genes. These longitudinal studies in trans men demonstrate that testosterone can reduce IFN-I production by pDCs, and provide novel insights into the immune-modulatory role of testosterone in sex differential IFN-I-mediated immune responses.

overall_design: Plasmacytoid DCs (pDCs) from longitudinal blood samples collected from a cohort of trans men receiving testosterone injections as gender-affirming hormone therapy (GAHT) were used in this study. PBMCs were stimulated with CL097 and pDCs were FACS-isolated following single-cell sequencing (10x Genomics) including TotalSeq Hashtag antibodies to combined different treatment conditions per donor.

first: Benjamin

last: Grünhagel

first: Malte

last: Borggrewe

first: Sven

middle: H

last: Hagen

first: Florian

last: Henseling

first: Laura

last: Glau

first: Rebecco-Jo

last: Thiele

first: Maria

last: Pujantell

first: Varshi

last: Sivayoganathan

first: Benedetta

last: Padoan

first: Susanne

middle: M

last: Ziegler

first: Janna

last: Claussen

first: Arne

last: Düsedau

first: Jana

last: Hennesen

first: Madeleine

middle: J

last: Bunders

first: Stefan

last: Bonn

first: Eva

last: Tolosa

first: Christian

middle: F

last: Krebs

first: Christoph

last: Dorn


title: Multiomics of GCN4-dependent replicative lifespan extension models reveals Gcn4 as a regulator of protein turnover in yeast

status: Public on Nov 11 2023

city: Tempe

first: Blaise

middle: L

last: Mariner

state: AZ

address: 427 E Tyler Mall, LSC 356

department: School of Life Sciences and Center for Evolution and Medicine

institute: Arizona State University

summary: We have shown that multiple tRNA synthetase inhibitors can increase lifespan in both the nematode C. elegans and the budding yeast S. cerevisiae by acting through the conserved transcription factor Gcn4 (yeast) / ATF-4 (worms). To further understand the biology downstream of this conserved transcription factor in the yeast model system, we looked at two different yeast models known to have both upregulated Gcn4, and GCN4-dependent increased replicative lifespan. These two models are rpl31aΔ yeast, and yeast treated with the tRNA synthetase inhibitor borrelidin. We used both proteomic and RNAseq analysis of a block experimental design that included both of these models, to identify GCN4-dependent changes in these two longlived strains of yeast. Proteomic analysis of these yeast indicate that the longlived yeast have increased abundance of proteins involved in amino acid biosynthesis. RNASeq of these same yeast uncovered further regulation of protein turnover, identifying the differential expression of genes associated with both autophagy and with the ubiquitin proteasome system. The data presented here further underscore the important role that GCN4 and its orthologs play in the maintenance of protein homeostasis, which is itself an important hallmark of aging. Importantly, these changes could also have wider-ranging implications in the understanding and treatment of diseases of aging characterized by protein aggregation.

overall_design: a block-design, considering drug treatment, RPL31A genotype, and GCN4 genotype

first: Mark

middle: A

last: McCormick


title: Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer (PRRX1 OE RNA-Seq)

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Triple-negative breast cancer (TNBC) is a heterogeneous disease with limited treatment options. To characterize TNBC heterogeneity and treatment response, we combined functional and molecular profiling with computational analysis tools. Using these approaches, we defined transcriptional, epigenetic, and metabolic subtypes, and identified subtype-driving super-enhancers. Single cell RNA sequencing analyses revealed relative homogeneity of the three major transcriptional subtypes (luminal, basal and mesenchymal) within tumors. We found that mesenchymal TNBCs are more similar to mesenchymal neuroblastoma and rhabdoid tumors than to other TNBC subtypes, and the PRRX1 transcription factor serves as a key driver of these tumors. By directly regulating the transcription of mesenchymal genes, PRRX1 is sufficient for inducing the mesenchymal subtype but is not required for its maintenance.

overall_design: RNA-seq of 4 TNBC cell lines with TET-inducible expression of wild type or DNA-binding mutant PRRX1, with and without doxycycline treatment, at three time points

first: Bojana

last: Jovanović

first: Daniel

last: Temko

first: Franziska

last: Michor


title: Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer (H3K27ac cell lines ChIP-Seq)

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: H3K27ac ChIP-seq of 30 TNBC cell lines


title: Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer (PRRX1 ChIP-Seq)

overall_design: PRRX1 ChIP-seq of 8 cancer cell lines


title: Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer (PRRX1 KD RNA-Seq)

overall_design: RNA-seq of two TNBC cell lines with and without TET-inducible expression of PRRX1-targeting shRNA's, with and without doxycycline treatment


title: Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer (TNBC cell lines RNA-Seq)

overall_design: RNA-seq of 34 TNBC cell lines


title: Real-time quantitative PCR analysis of human HepaRG cells infected with hepatitis E virus (HEV) [D100 plaque 2]

status: Public on Nov 08 2023

city: Maisons-Alfort

first: Virginie

last: Doceul

address: 7 avenue du Général de Gaulle

country: France

institute: UMR VIROLOGIE INRAE-ANSES-ENVA

summary: We aimed to identify interferon (IFN)-regulated genes that are differentially expressed during chronic HEV infection in human hepatocytes, the main site of HEV replication, using HepaRG cells.

overall_design: HepaRG cells infected with HEV-3f at a MOI of 100 GE/cell and their matched non-infected controls were analyzed at 100 days post-infection. Triplicate samples from 2 independant experiments were analyzed.

first: Léa

last: Meyer

first: Isoline

last: Duquenois


title: Physiologic and Transcriptomic Effects Triggered by Overexpression of Wild Type and Mutant DNA Topoisomerase I in Streptococcus pneumoniae

city: Madrid

first: Pablo

last: Hernandez

state: Madrid

address: Ramiro de Maeztu 9

department: Cellular and Molecular Biology

country: Spain

institute: Centro de Investigaciones Biologicas (CSIC)

summary: We obtained the topARA mutant that encodes a TopoI enzyme that shows reduced topoisomerase activity compared to the wild type gene (topAWT) and confers resistance to the antibiotic seconeolitsine. Alterations in the gene expression profile produced after overexpression of the wild type or the RA mutant of topA gene were studied. In addition, differential gene expression produced by the DNA gyrase inhibitor novobiocin (NOV) was also studied in cultures overexpressing each of the versions of TopA.

overall_design: S. pneumoniae ∆topAPZntopA strain was transformed with plasmid pLS1ROMtopAWT or pLS1ROMtopARA, where topA is under the control of a maltose-inducible promoter. Overnight cultures grown in medium with sucrose (noninducing S medium) were diluted 1000-fold in noninducing S medium or in sucrose+maltose medium (inducing SM medium) and grown to OD=0.4. The last 30 min of culture took place without NOV or with NOV 10xMIC.

first: Miriam

last: García-López

last: Hernández

first: María-José

last: Ferrándiz

first: Adela

last: de la Campa


title: Real-time quantitative PCR analysis of liver tissue from pigs infected experimentally with hepatitis E virus (HEV) [pig liver]

summary: We aimed to identify interferon (IFN)-regulated genes that are differentially expressed during  HEV infection in swine liver tissues.

overall_design: Eight-week-old specific pathogen free Large-White piglets were infected intravenously with 10^6 copies of HEV RNA or mock-infected with PBS. At the peak of excretion (8 days post-infection), liver tissues were snap-frozen in liquid nitrogen. Samples from 2 control pigs, 3 pigs infected with HEV-3c and 3 pigs infected with HEV-3f were analyzed in this study.


title: Real-time quantitative PCR analysis of human HepaRG cells infected with hepatitis E virus (HEV) [pre-array]

summary: We aimed to identify interferon (IFN)-regulated genes that are differentially expressed during chronic HEV infection in human hepatocytes, the main site of HEV replication, using HepaRG cells. We have performed a preliminary screen  using whole-cell RNA extracts prepared from HepaRG mock-infected or infected cells to determine whether HEV was able to trigger an IFN response. Different multiplicities of infection (MOI) (10 and 100 genome equivalent (GE)/cell) and time points (D+7, D+14, D+26, D+40, D+72 and D+100) were analyzed using the PCR array. We have also treated HepaRG cells after overnight treatment with IFN-β to confirm the ability of HepaRG to respond to IFN-I treatment.

overall_design: HepaRG cells infected with HEV-3f at a MOI of 10 or 100 GE/cell and their matched non-infected controls were analysed at different days post-infection. For MOI 10, 1 sample per time point was analysed. For MOI 100, 1 sample containing pooled RNA from triplicate samples was analysed.


title: The hypoxia-inducible factor EPAS1 is required for normal spermatogonial stem cell function in regenerative conditions [Dstat bulkRNAseq]

city: Callaghan

first: Tessa

last: Lord

state: NSW

address: University Dr

country: Australia

institute: University of Newcastle

summary: In this study we explored the role of hypoxia and the hypoxia-inducible transcription factor EPAS1 in regulating spermatogonial stem cell (SSC) function in the mouse. We demonstrated that SSCs reside in hypoxic microenvironments in the testis through utilisation of the oxygen-sensing probe pimonidazole, and by confirming the stable presence of EPAS1, which is degraded at >5% O2. Here we stabilised EPAS1 expression in primary cultures of undifferentiated spermatogonia with the small drug molecule Daprodustat, providing a platform to identify genes whose expression is regulated by EPAS1 in SSCs.

overall_design: Four biological replicates for each treatment (vehicle control or Daprodustat)


title: Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms [RNA-seq]

city: Saint Louis

first: Shiming

last: Chen

state: Missouri

address: 517 South Euclid Avenue

department: Department of Ophthalmology & Visual Sciences

institute: Washington University in St Louis

summary: Homeodomain transcription factors (HD TFs) are instrumental to vertebrate development. Mutations in HD TFs have been linked to human diseases, but their pathogenic mechanisms remain elusive. Here we use Cone-Rod Homeobox (CRX) as a model to decipher the disease-causing mechanisms of two HD mutations, p.E80A and p.K88N, that produce severe dominant retinopathies. Through integrated analysis of molecular and functional evidence in vitro and in knock-in mouse models, we uncover two novel gain-of-function mechanisms: p.E80A increases transactivation of canonical CRX target genes in developing photoreceptors; p.K88N alters CRX DNA-binding specificity resulting in binding at ectopic sites and severe perturbation of CRX target gene expression. Both mechanisms produce novel retinal morphological defects and hinders photoreceptor maturation distinct from loss-of-function models. This study reveals the distinct roles of E80 and K88 residues in CRX HD regulatory functions and emphasizes the importance of transcriptional precision in normal development.

overall_design: Bulk RNA-seq experiments were performed on developing (P10) and adult (P21) mouse retinas to uncover the transcriptome alterations resulted from CRX homeodomain missense mutations, p.E80A, p.K88N, p.R90W, in both heterozygous and homozygous mutant retinas.

first: Yiqiao

last: Zheng

first: Inez

last: Oh


title: Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms [ChIP-seq]

overall_design: CRX ChIP-seq experiments were performed on developing mouse retinas (P14) to understand how homeodomain missense mutations, p.E80A, p.K88N, p.R90W, each affects CRX chromatin binding in homozygous mutant mouse retinas.

first: Xiaodong

last: Zhang


title: The hypoxia-inducible factor EPAS1 is required for normal spermatogonial stem cell function in regenerative conditions

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

overall_design: Refer to individual Series


title: Real-time quantitative PCR analysis of human HepaRG cells infected with hepatitis E virus (HEV) [D100 plaque 1]


title: Young infants display heterogeneous serological responses and extensive but reversible transcriptional changes following initial immunizations

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

institute: THE JACKSON LABORATORY

summary: Infants necessitate vaccinations to prevent life-threatening infections. Our understanding of the infant immune responses to routine vaccines remains limited. We analyzed two cohorts of 2-month-old infants before vaccination, one week, and one-month post-vaccination. We report remarkable heterogeneity but limited antibody responses to the different antigens. Whole-blood transcriptome analysis in an initial cohort showed marked overexpression of interferon-stimulated genes (ISGs) and to a lesser extent of inflammation-genes at day 7, which normalized one month post-vaccination. Single-cell RNA sequencing in peripheral blood mononuclear cells from a second cohort identified at baseline a predominantly naive immune landscape including ISGhi cells. On day 7, increased expression of interferon-, inflammation-, and cytotoxicity-related genes were observed in most immune cells, that reverted one month post-vaccination, when a CD8+ ISGhi and cytotoxic cluster and B cells expanded. Antibody responses were associated with baseline frequencies of plasma cells, B-cells, and monocytes, and induction of ISGs at day 7.

overall_design:
Here, we report on a longitudinal (time-series experiments), systems-level analysis of infants' responses to initial immunizations. We investigated the effects of the 2-month routine vaccination on the PBMCs transcriptome.
***RNA-Seq raw data is to be made available through dbGaP (controlled access; phs002926)***

first: Nima

last: Nouri

first: Asunción

last: Mejías

first: Jacques

last: Banchereau

first: Virginia

last: Pascual

first: Octavio

last: Ramilo


title: 5' UTR-dependent m6A methylation regulates aging and circadian rhythms in Drosophila

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

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


title: Real-time quantitative PCR analysis of liver tissue from pigs infected experimentally with hepatitis E virus (HEV)

first: Virginie

last: Doceul

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa


title: 5' UTR-dependent m6A methylation regulates aging and circadian rhythms in Drosophila [RIP-seq whole]

summary: To evoke further attention to the potential hazard of increasingly accumulative blue light exposure, we construct a series of in vivo Drosophila models employed for multi-omics analyses. This project includes the identification results of untargeted metabolome quantification by LC-MS/MS and the Input and m6A IP data of MeRIP-seq of w1118 male adult whole flies.

overall_design: Briefly, we colonized Drosophila melanogaster w1118 under the photoperiodic cycles of 12 h low-intensity blue light exposure: 12 h darkness (BD) and consistent darkness (DD) until 10- (namely BD10 and DD10) and 25-day-old (namely BD25 and DD25) after eclosion, respectively. We then performed polyadenylated (poly-A) MeRIP-seq and untargeted metabolome analysis for the male adult whole flies, and performed poly-A RNA-seq for the male adult heads and the 3-day-old male adult whole flies grew from the earlier eggs as the F1 generation (namely BD8F1, BD23F1, DD8F1, and DD23F1, respectively) for assessing the influences of parental photoperiods and natural aging.

first: Jia

last: Huang

first: Fan

last: Zhou


title: Single-Cell Transcriptomics Reveals Peripheral Immune Responses in Non-Segmental Vitiligo

status: Public on Nov 07 2023

city: Xi'an

first: Pengju

last: Yang

state: Shaanxi

address: No. 277, Yanta West Road, Xi'an

institute: The First Affiliated Hospital of Xi’an Jiaotong University

summary: Vitiligo is a common autoimmune depigmented dermatology due to the destruction of melanocytes. Much evidence suggests that vitiligo is associated with systemic immune activation. Previous studies have focused on immune cell infiltration in and around lesion areas, while few studies have investigated the cell types and function of circulating immune cells in peripheral blood. We collected peripheral blood from five patients with progressive non-segmental vitiligo (PV) and three healthy controls (HC).Single-cell RNA sequencing(scRNA-seq) is used to investigate the mechanisms of peripheral immune responses in vitiligo patients.

overall_design: We collected peripheral blood from five patients with progressive non-segmental vitiligo (PV) and three healthy controls (HC). The peripheral blood mononuclear cell (PBMC) fraction was isolated by Ficoll-Paque density gradient centrifugation, and scRNA-seq was performed on isolated cell populations to obtain single-cell transcriptomes and characterize key genes and intracellular signaling pathways.

first: Mei

last: Luan

first: Kuanhou

last: Mou

first: Pan

last: Li


title: Aberrant DNA Methylation in Dimethylarsinic Acid-induced Rat Bladder Carcinogenesis

status: Public on Nov 06 2023

city: Osaka

first: Tomoki

last: Yamamoto

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

country: Japan

institute: Osaka Metropolitan University Graduate School of Medicine

type: Methylation profiling by high throughput sequencing

summary: DNA methylation profile in rat bladder carcinogenesis treated with dimethylarsinic acid.

overall_design: The DNA methylation status of bladder cancer induced in 10-week-old rats treated with DMA for 2 years was compared to the bladder mucosa of rats normally reared for the same period.

first: Min

last: Gi

first: Satoshi

last: Yamashita

first: Hideki

last: Wanibuchi


title: Mechanisms of cellular crosstalk in the gastric tumour microenvironment are mediated by YAP1 and STAT3

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

institute: Monash University

summary: The association of proinflammatory pathways and activation of the Hippo pathways are largely uncharacterised. In the present study we aimed to assess the functional relationship between Stat3 and  Yap1  ablation in  a gastric cancer model, the gp130FF mutant mouse in which Yap1 was conditionally deleted with the Tff1 driven-Cre-recombinase.

overall_design: To explore the biological role of YAP1 in gastric cancer we evaluated the transcriptomic profiles of gastric tumor samples obtained from gp130FF and gp130FF;Yap1floxed mice.

first: Pathum

last: Thilakasiri

first: Sarah

last: To

first: David

last: Chisanga

first: Moritz

last: Eissmann

first: Ryan

last: O’Keefe

first: Annalisa

last: Carli

first: Belinda

last: Duscio

first: Rhynelle

last: Dmello

last: Williams

first: John

last: Mariadason

first: Ashleigh

last: Poh

first: Bhupinder

last: Pal

first: Benjamin

last: Kile

first: Vissers

last: Joep

first: Kieran

last: Harvey

first: Michael

last: Buchert

first: Matthias

last: Ernst

first: Ashwini

last: Chand


title: 5' UTR-dependent m6A methylation regulates aging and circadian rhythms in Drosophila [RNA-seq whole]

first: Xiaoyun

last: Wang

summary: To evoke further attention to the potential hazard of increasingly accumulative blue light exposure, we construct a series of in vivo Drosophila models employed for multi-omics analyses. This project includes the RNA-seq data of w1118 F1 generation male adult whole flies.

first: Jia

last: Huang

first: Fan

last: Zhou


title: Analysis of the consequences of the constitutive  loss of Prdm12 in developing trigeminal ganglia

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Prdm12 is required to repress visceral markers  in developing trigeminal ganglia

overall_design: RNA-seq analysis  of the transcriptome of dissected trigeminal ganglia  of E13.5 Prdm12 KO  and control  embryos.

first: Simon

last: Vermeiren


title: The hypoxia-inducible factor EPAS1 is required for normal spermatogonial stem cell function in regenerative conditions [EPAS1 scRNAseq]

first: Tessa

last: Lord

summary: To understand the role of the hypoxia-inducible transcription factor EPAS1 in regulating spermatogonial stem cell (SSC) function, a conditional knockout mouse was generated (EPAS1-cKO) where Epas1 was ablated only in the germ cells (Ddx4-Cre, Epasfl/-). For single cell RNA sequencing analysis, control and EPAS1-cKO males were pre-treated with the chemotherapeutic reagent busulfan to instigate regenerative conditions, and a germ cell-enriched cell population was collected 14 days later. Transcriptome profiling revealed that EPAS1 deficiency alters gene expression and key cellular processes in undifferentiated spermatogonia, including metabolism and proteostasis. Overall, these transcriptomic changes resulted in an impaired capacity for SSCs to restore spermatogenesis after busulfan treatment.

overall_design: Comparing germ cell populations from the testes of control mice to mice with germline ablation of Epas1. Mice were treated with busulfan (20mg/kg) 14 days prior to analysis to instigate regenerative conditions.


title: Biological and genetic characterization of a newly established human external auditory carcinoma cell line, SCEACono2

city: La Jolla

first: Kuniaki

last: Sato

state: CA

address: 3855 Health Sciences Dr Room 2345

department: Moores Cancer Center

institute: University of California San Diego

summary: Squamous cell carcinoma of the external auditory canal (EACSCC) is an extraordinarily rare and aggressive malignant disease. Establishment of EACSCC cell line with robust molecular characteristics is essential for the basic and translational research of EACSCC. In this study, we showed the newly established EACSCC cell line SCEACono2, derived from a patient with well-to-moderately differentiated EACSCC. To elucidate the transctomic features of SCEACono2, we performed RNA-seq and revealed its unique characteristics and compared with publicly available head and neck squamous cell caricnoma (HNSCC)-derived cell lines HSC4 and SCC9.

overall_design: Library preparation from RNA extracted from cultured cells and RNA sequencing were performed using a DNBSEQ-G400 sequencer at the Beijing Genomics Institute (Shenzhen, China). The sequenced reads were aligned to the human reference genome GRCh38 using STAR v2.7.9a with Gencode v38 annotations. Gene count tables were generated with RSEM v1.3.1.

first: Noritaka

last: Komune

first: Mayumi

last: Ono

first: Takashi

last: Nakagawa


title: Histone code dynamics during nitrogen response in tomato

city: West Lafayette

first: Ryan

last: Patrick

state: Indiana

address: 625 Agriculture Mall Dr

institute: Purdue University

summary: In plants, environmental stimuli trigger rapid transcriptional reprogramming of relevant gene suites. Regulation occurs down to the local chromatin landscape of the genes, and while epigenetic modifications proceed in a manner dependent on specific organ and tissue contexts, detailed investigations at this level remain limited. To better understand the organ specificity of dynamic chromatin modifications in response to external signals, we treated nitrogen-limited tomato seedlings with a supply of nitrate and measured the genome-wide changes of four histone marks, the permissive histone marks H3K27ac, H3K4me3, and H3K36me3 and repressive mark H3K27me3, in shoots and roots separately. We observed dynamic histone acetylation and methylation events which are largely organ-specific in scope at functionally relevant gene loci. Integration of transcriptomic and epigenomic datasets generated from the same tissue samples revealed largely syngenetic relations between changes in transcript levels and histone modifications, with the exception of H3K27me3 where an increased level at genes up-regulated in response to nitrate supply is observed in only the shoots. This non-canonical pattern of H3K27me3 deposition could possibly function to prevent over-expression of certain activated genes. To study the determinant roles of histone code in predicting gene regulation at the genome-wide level we applied a machine learning approach. While gene regulation could be best predicted using all four histone marks together, we observed different rules regarding the importance of individual histone marks between shoots, where H3K36me3 is the most successful mark in predicting gene activation and repression events, and the roots, where H3K4me3 is the strongest individual predictor. In summary, our integrated study substantiates a view that during plant environmental responses, the histone code dynamics that govern relationships between chromatin modification and gene regulation are highly dependent on tissue specific contexts.

overall_design:
Three replicates of ChIP-Seq from root and shoot in nitrogen supplied (6 hours) or nitrogen replete control, with input and immunopreciptation for H3K4me3, H3K27ac, H3K27me3, and H3K36me3, for a total of 60 samples.

Three replicates of RNA-Seq in the root and shoot tissue in the two nitrogen conditions (total of 12 samples) were used for expression analysis.

For H3K9me2 analyses, three replicates from input or from immunoprecipitation for each of the conditions were used for a total of 12 samples.

first: Russell

last: Julian

first: Ying

last: Li


title: A complex with poly(A) binding protein cytoplasmic 1 and EWS facilitates oncogenic ETS transcription factor function in prostate cells

city: Bloomington

first: Peter

last: Hollenhorst

state: IN

address: 1001 E 3rd Street

department: Medical Sciences

institute: Indiana University

summary: The ETS transcription factor ERG is aberrantly expressed in approximately 50% of prostate tumors due to chromosomal rearrangements such as TMPRSS2/ERG. The ability of ERG to drive oncogenesis in prostate epithelial cells requires interaction with distinct co-activators, such as the RNA-binding protein EWS. Here, we find that ERG has both direct and indirect interactions with EWS, and the indirect interaction is mediated by the poly-A RNA-binding protein PABPC1. PABPC1 directly bound both ERG and EWS. ERG expression in prostate cells promoted PABPC1 localization to the nucleus and recruited PABPC1 to ERG/EWS binding sites in the genome. Knockdown of PABPC1 in prostate cells abrogated ERG-mediated phenotypes and decreased the ability of ERG to activate transcription. These findings define a complex including ERG and the RNA-binding proteins EWS and PABPC1 that represents a novel therapeutic target for ERG-positive prostate cancer and identify a novel nuclear role for PABPC1.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for PABPC1 in RWPE-Empty Vector and RWPE-ERG cells.

first: Benjamin

last: Greulich

first: Saranya

last: Rajendran

first: Nicholas

last: Downing

first: Taylor

middle: R

last: Nicholas

middle: C


title: Transcriptomic profile of neutrophils subsets in healthy donors and cancer patients

city: Woluwe Waint Lambert

first: Pierre

last: van der Bruggen

address: Avenue Hippocrate 75

country: Belgium

institute: de Duve institute


title: 5' UTR-dependent m6A methylation regulates aging and circadian rhythms in Drosophila [RNA-seq head]

first: Xiaoyun

last: Wang

summary: To evoke further attention to the potential hazard of increasingly accumulative blue light exposure, we construct a series of in vivo Drosophila models employed for multi-omics analyses. This project includes the RNA-seq data of w1118 male adult heads.

first: Jia

last: Huang

first: Fan

last: Zhou


title: Pyrvinium pamoate targets to multiple vulnerabilities of Merkel cell carcinoma

city: Tucson

first: Jiawen

last: Yang

state: Arizona

address: 1515 N Campbell Ave

department: University of Arizona Cancer Center

institute: The University of Arizona

summary: Among several WNT signaling perturbagens, we identified pyrvinium pamoate, an FDA-approved anthelminthic drug that exhibits anti-tumor abilities in multiple cancers. Through the integration of transcriptomic, network, and molecular analyses, we discovered that pyrvinium is broadly effective against Merkel cell carcinoma cell lines, and it targets multiple proposed MCC tumorigenesis pathways. Our study revealed that pyrvinium exerts anti-tumor activity in MCC not only through perturbing the canonical and non-canonical WNT signaling pathway but also non-specifically inhibiting cell growth - via the activation of the p53-mediated apoptosis pathway, modulation of mitochondrial function, and induction of endoplasmic reticulum (ER) stress.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WaGa/MKL1 cell lines treated with DMSO and 1 μM pyrvinium pamoate for 6h and 24h

first: Megha

last: Padi


title: Transcriptomic profile of neutrophils subsets in healthy donors and cancer patients II

summary: We distinguished immature non-suppressive CD45low LDN and mature suppressive CD45high LDN from each other based on their expression of CD45 and CD16 and isolated at least 10,000 cells for each cell type in matched samples from the blood of NSCLC patients, and performed RNA sequencing to determine transcriptomic profile associated with suppression of T cell proliferation

overall_design: Comparative gene expression profile of neutrophil subsets from healthy donors and cancer patients

first: Christophe

last: Vanhaver

first: Annika

last: Bruger

first: Alexandre

last: Bayard

first: Thibault

last: Hirsch


title: Transcriptomic profile of neutrophils subsets in healthy donors and cancer patients I


title: Gene expression profile at single cell level of J558 allograft mouse model treated with the CDC7-specific inhibitor TAK-931 [scRNA-seq]

status: Public on Nov 05 2023

city: Kashiwa

first: Akihiro

last: Ohashi

state: Chiba

address: 6-5-1 Kashiwanoha

department: Exploratory Oncology Research and Clinical Center

institute: National Cancer Center Japan

summary: To comprehensively evaluate in vivo inflammatory effects of TAK-931 in tumor microenvironment, scRNA-seq was conducted in the J558 allograft mouse model. The tSNE plots and the expression dot plots showed cellular components in the allografts classified by the indicated TME markers: cancer cell (J558 allograft), monocyte, CD8+ T cell, CD4+ T cell, NK cell, endothelial cell, fibroblast, and undefined, demonstrating that TAK-931 treatment prominently promoted tumor infiltration of both adaptive (CD8+ T cell and CD4+ T cell) and innate (NK cells and monocytes) immune cells in the allografts.

overall_design: The J558-allografted BALB/c female mice were orally administered vehicle or TAK-931 at 60 mg/kg, QD for 6 days. One sample from each group was used for scRNA-seq.

first: Yukie

last: Kashima

first: Chiaki

last: Mashima

first: Tomoko

last: Morita

first: Miyuki

last: Yoshiya


title: Changes in gene expression time 0 vs. 1hr post-cataract sugery wounding in the lens

status: Public on Nov 04 2023

city: Philadelphia

first: Janice

middle: Lynn

last: Walker

state: PA

address: 1020 Locust Street; 571 JAH

department: Pathology and Genomic Medicine

institute: Thomas Jefferson University

summary: Early changes in the transcriptome associated with lens wounding in an ex vivo post-cataract surgery chicken model. Here we report the changes in the transcriptome that occur 1hr vs. time 0 post-cataract surgery wounding. Our data provide a molecular framework for understanding the early gene changes associated with the injury response of the lens.

overall_design:
To determine changes in the transcriptome that occur time 0 compared to 1 hour (1h) post lens wounding.
We here report the changes in the transcriptome that occur 1hr vs. time 0 post-cataract surgery wounding.
Comparative gene expression profiling analysis of RNAseq data for ex vivo chick post-cataract surgery explants performed at time 0 and 1h post-injury

first: Morgan

middle: D

last: Basta


title: Gene expression profile at single cell level of HeLa cells treated with the CDC7-specific inhibitor TAK-931 [scRNA-seq]

summary: We performed scRNA-seq analyses to determine the transcriptional landscape of the TAK-931-induced aneuploid cells at the single-cell levels. HeLa cells were treated with DMSO or TAK-931 (300 nM) for 72 h. In the t-SNE plots, the DMSO- and TAK-931-treated cells were classified in two distinct clusters. Indicating that the major population of the TAK-931-treated aneuploid HeLa cells was transformed to a cell contexture that was transcriptionally distinct from that of DMSO-treated control cells. The hallmark of an inflammatory response was remarkably enriched in the TAK-931 treatment cluster. In addition, the positive cells of inflammatory cytokine/chemokine-related genes, such as CXCL8, IL1B, TNHSF14 and TNFRSF1B, were significantly accumulated in the TAK-931-treatment cluster.

overall_design: Transcriptome analyses were conducted to capture the signaling networks comprehensively in the TAK-931-induced aneuploidcells. HeLa cells were treated with DMSO or TAK-931 (300 nMa) for 72 h.


title: Transcriptome analysis of J558 allograft mouse model treated with the CDC7-specific inhibitor TAK-931 [RNA-seq]

summary: To comprehensively evaluate in vivo inflammatory effects of TAK-931 in tumor microenvironment, RNA-seq was conducted in the J558 allograft mouse model. The GSEA revealed significant enrichment of inflammatory hallmarks in TAK-931-treated allografts. Metascape analyses also visualized that the network modules of the inflammatory signaling pathways were predominantly enriched.

overall_design: The J558-allografted BALB/c female mice were orally administered vehicle or TAK-931 at 60 mg/kg, QD for 6 days. Vehicle and TAK-931 treated J558 allografts were analyzed using two independent samples.


title: Dynamics of host response to Merkel cell polyomavirus oncogenes

state: AZ

address: 1071 East Lowell St.

department: Molecular and Cellular Biology

institute: University of Arizona

summary: Merkel cell polyomavirus (MCPyV) small tumor antigen (ST), truncated large tumor antigen (TLT), early region (ER), and GFP control inducible vectors were introduced into IMR90 human lung embryonic fibrobrasts. After induction, cells were extracted and sequenced in triplicate every 4 hours for the first 24 hours, then every 8 hours until 48 hours. The purpose of this experiment was to identify the dynamic host response to MCPyV oncogenes, using both differential expression analysis and transcriptional network reconstruction, and to provide a systems-level understanding of the initial steps toward Merkel cell carcinoma.

overall_design: Expression of MCPyV ER, TLT, ST or GFP was induced in IMR90 fibroblasts, and triplicate RNA samples were extracted and sequenced over 10 timepoints within 48 hours

first: Christian

last: Berrios

first: Paris

last: Vail


title: Affymetrix Chip data of the transcriptome of human clinical study for acupuncture mechanisms on rheumatoid arthritis

city: Rome

first: Christine

last: Nardini

address: Via dei Taurini 9

country: Italy

institute: PICB

summary:
We report the application of Affymetrix technology for high-throughput mRNA profiling of rheumatoid arthritis (RA) patients, with acupuncture+Methotrexate and Methotrexate treatments.

Clinical Trial ID: https://clinicaltrials.gov/study/NCT01619176

overall_design: 9 patients were enrolled according to ACR and delivered with 2 therapies, i.e. Acupuncture+Methotrexate (AP, 6 patients) and Methotrexate (MTX, 3 patients). Peripheral blood sampling was carried out before therapy, after 2 weeks in AP group and after 3 months for both therapies. Finally, 18 total RNA samples (two samples for each patient) were extracted from blood samples (peripheral blood mononuclear cells, PBMC ) and analyzed using Affymetrix microarray technology (Affymetrix U133 Plus 2.0 array).

first: Valentina

last: Devescovi

first: Yuanhua

last: Liu


title: In situ regeneration of inner hair cells in the damaged cochlea by temporally regulated coexpression of Atoh1 and Tbx2

city: Beijing

first: Zhiyong

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

summary: Cochlear inner hair cells (IHCs) are primary sound receptors, and thus in efforts to develop treatments for hearing impairment. IHC regeneration in vivo has been widely attempted, although not yet in the IHC-damaged cochlea. Moreover, the extent to which new IHCs resemble wild-type IHCs remains unclear, as does whether new IHCs can yield hearing improvement. Here, we developed an in vivo mouse model wherein wild-type IHCs were pre-damaged and nonsensory supporting cells were transformed into IHCs by ectopically expressing Atoh1 transiently and Tbx2 permanently. Notably, the new IHCs expressed the functional marker vGlut3 and presented similar transcriptomic and electrophysiological properties as wild-type IHCs. Furthermore, the formation efficiency and maturity of new IHCs were higher than those previously reported, although marked hearing improvement was not achieved, at least partly due to defective mechanoelectrical transduction (MET) in new IHCs. Thus, we successfully regenerated new IHCs resembling wild-type IHCs in multiple aspects in the damaged cochlea. Our findings suggest that the defective MET is a critical barrier preventing the restoration of hearing capacity and should thus facilitate future IHC regeneration studies.

overall_design: We have generated a new genetic mouse model wherein the endogenous inner hair cells (IHCs) are damaged, and at the same time transient Atoh1 and permanent Tbx2 expression are specifically induced in the neonatal cochlear inner border cells/inner phalangeal cells (IBCs/IPhs). Briefly, the IBCs/IPhs are transformed into new IHCs expressing functional IHC marker vGlut3. Comprehensive assays including fate mapping analysis, immunostaining, transcriptomic analysis, ultrastructure morphological and electrophysiological analysis, support that those new IHCs are functional at the single cell level and that they are divergent from the IBCs/IPhs and most closely to the endogenous IHCs.

first: Xiang

last: Li

first: Zhenghong

last: Bi

first: Minhui

last: Ren

first: Yunpeng

last: Gu

first: Tong

last: Zhu

first: Yu

last: Zhang

first: Jie

first: Chao

first: Guangqin

last: Wang

first: Lei

last: Song


title: Transcriptome analysis of HeLa cells treated with the CDC7-specific inhibitor TAK-931 [RNA-seq]

first: Akihiro

last: Ohashi

summary: The results showed that 48-h treatment upregulated 138 genes and 72-h treatment upregulated 504 genes. In the Metascape analyses, the TNF signaling pathway was a dominant network module in the 48-h treatment group, while the inflammatory-related modules were more intensively accumulated, and the signaling networks expanded to the surrounding various modules in the 72-h treatment. Our signaling module results indicate that the TAK-931-induced cellular senescence progressed in a time-dependent manner, and mTOR pathways plays important roles in viability for TAK-931-induced senescent cells.

overall_design: Transcriptome analyses were also conducted to capture the signaling networks comprehensively in the TAK-931-induced senescent aneuploid cells. HeLa cells were treated with DMSO or TAK-931 (300 nM) for 24 h, 48 h, or 72 h and then subjected to RNA sequencing (RNA-seq) by NovaSeq 6000.

first: Yukie

last: Kashima

first: Yumi

last: Hakozaki

first: Tomoko

last: Morita


title: A dual role of RBM42 in modulating splicing and translation of CDKN1A/p21 during DNA damage response

status: Public on Nov 03 2023

city: Haifa

first: Tamar

last: Lahav

address: Zor

department: Biology

country: Israel

institute: Technion

summary: p53-mediated cell cycle arrest during DNA damage is dependent on the induction of p21 protein, encoded by the CDKN1A gene. p21 inhibits cyclin-dependent kinases required for cell cycle progression to guarantee accurate repair of DNA lesions. Hence, fine-tuning of p21 levels is crucial to preserve genomic stability. Currently, the multilayered regulation of p21 levels during DNA damage is not fully understood. Herein, we identified the human RNA binding motif protein 42 (RBM42) as a novel regulator of p21 levels during DNA damage. Genome-wide transcriptome and interactome analysis revealed that RBM42 alters the expression of p53-regulated genes during DNA damage. Specifically, we demonstrated that RBM42 facilitates CDKN1A splicing by counteracting the splicing inhibitory effect of RBM4 protein. Unexpectedly, we also show that RBM42, underpins translation of various splicing targets, including CDKN1A. Concordantly, transcriptome-wide mapping of RBM42-RNA interactions using eCLIP further substantiates the dual function of RBM42 in regulating splicing and translation of its target genes, including CDKN1A. Collectively, our data show that RBM42 couples splicing and translation machineries to fine-tune gene expression during DNA damage response.

overall_design: Enhanced crosslinking and immunoprecipitation (eCLIP) for RBM42 upon DNA damage and mock treatment on HCT116 cells. For each treatment we performed 2 replicates and comapred the eCLIP to size match input control

first: Bella

last: Ben-Oz

first: Feras

last: Machour

first: Marian

last: Nicola

first: Amir

last: Argoetti

first: Galia

last: Polyak

first: Rawad

last: Hanna

first: Oded

last: Kleifeld

first: Yael

last: Mandel-Gutfreund


title: Dapagliflozin alleviates renal inflammation and protects against diabetic kidney diseases dependent and independent of glucose levels

status: Public on Nov 02 2023

city: Shanghai

first: Anxiang

last: Cai

state: None Selected

address: No.1630 dongfang road, pudong new district

institute: Department of Nephrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China

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

overall_design: Refer to individual Series


title: CBLL1 is hypomethylated and correlates with cortical thickness in transgender men before gender affirming hormone treatment

city: A Coruña

first: Rosa

last: Fernandez

state: None / N/A

address: Campus Elviña

department: Psychology

institute: University of A Coruña

summary: We measured whole-genome DNA methylation by the Illumina Infinium Human Methylation 850 array and reported its correlation with cortical thickness (CTh) in 22 transgender men (TM) experiencing GD versus 25 cisgender men (CM) and 28 cisgender women (CW). With respect to the methylation analysis, TM vs. CW showed significant differences in 35 CpGs, while 2,155 CpGs were found when TM vs. CM were compared. With respect to correlation analysis, TM showed differences in methylation of CBLL1 and DLG1 genes that correlated with global and left hemisphere CTh. Both genes were hypomethylated in TM compared to the cisgender groups. Early onset TM showed a positive correlation between CBLL1 and several cortical regions in the frontal (left caudal middle frontal), temporal (right inferior temporal, left fusiform) and parietal cortices (left supramarginal and right paracentral). This is the first study relating CBLL1 methylation with CTh in transgender persons and supports a neurodevelopmental hypothesis of gender identity

overall_design: Bisulphite converted DNA from the 75 samples were hybridised to the Illumina Infinium Human Methylation 850 array

last: Fernández

first: Leire

last: Zubiaurre-Elorza

first: Andrea

last: Santisteban

first: Natalia

last: Ojeda

first: Sarah

last: Collet

first: Meltem

last: Kiyar

first: Guy

last: T’Sjoen

first: Sven

last: Mueller

first: Antonio

last: Guillamon

first: Eduardo

last: Pásaro


title: Role of affinity in plasma cell development in the germinal center light zone

city: NEW YORK

first: Thiago

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: Protective immune responses to many pathogens depend on the development of high affinity antibody-producing plasma cells in germinal centers. Transgenic models suggest that there is a stringent affinity-based barrier to plasma cell development. Whether a similar high affinity barrier regulates plasma cell development under physiologic circumstances, and the nature of the plasma cell fate decision has not been defined precisely. Here we use a fate mapping approach to examine the relationship between germinal center (GC) B cells selected to undergo additional rounds of affinity maturation, germinal center pre-plasma cells and plasma cells. The data show that initial plasma cell selection overlaps with germinal center B cell selection, but that the plasma cell compartment accumulates a less diverse and higher affinity collection of antibodies over time. Thus, whereas the GC continues to diversify over time, affinity-based pre-plasma cell selection sieves the germinal center to enable accumulation of a more restricted group of high affinity antibody secreting plasma cells.

overall_design: c-Myc-GFP or C57Bl6/J male mice were immunized with NP-Ova in Alhydrogel and GC B cells (LZ and DZ) and Plasma cells were FACS-sorted on day 14

first: Mohamed

last: ElTanbouly

first: Victor

last: Ramos

first: Andrew

last: MacLean

first: Spencer

last: Chen

first: Maximilian

last: Loewe

first: Sandra

last: Steinbach

first: Tarek

last: Ben Tanfous

first: Brianna

last: Johnson

first: Melissa

last: Cipolla

first: Anna

last: Gazumyan

first: Michel

last: Nussenzweig


title: Dapagliflozin alleviates renal inflammation and protects against diabetic kidney diseases dependent and independent of glucose levels [RNA-seq]

first: Anxiang

last: Cai

summary: Diabetic kidney disease (DKD) has become the leading cause of end-stage renal disease worldwide. Therefore, efforts to understand DKD pathophysiology and prevent its development at the early phase are highly warranted. Here, we analyzed kidneys from healthy mice, diabetic mice, and diabetic mice treated with the sodium-glucose cotransporter 2 inhibitor dapagliflozin. Our combined method of ATAC and RNA sequencing revealed Csf2rb, Btla, and Isg15 as the key candidate genes associated with hyperglycemia, azotemia, and albuminuria. Their protein levels were altered together with multiple other inflammatory cytokines in the diabetic kidney, which was alleviated by dapagliflozin treatment. Cell culture of immortalized renal tubular cells and macrophages unraveled that dapagliflozin could directly effect on these cells in vitro as an anti-inflammatory agent independent of glucose concentrations. We further proved that dapagliflozin attenuated ischemia/reperfusion-induced chronic kidney injury and renal inflammation in mice. Overall, our data emphasize the importance of inflammatory factors to the pathogenesis of DKD, and provide valuable mechanistic insights into the renoprotective role of dapagliflozin.

overall_design: Briefly, 8-week-old male C57BL/6 mice and BKS.Cg-Dock7m +/+ Leprdb/J(db/db) mice were housed under controlled ambient conditions with standard chow, a 12-h light/dark cycle (lights on at 7 a.m.), and were maintained at 25℃. For experiments, mice were divided into three groups: control group (Ctrl, C57BL/6 mice, n=5), diabetic group (Case, db/db mice, n=6), and treatment group (Dapa, db/db mice treated with dapagliflozin [1.0 mg/kg/day, AstraZeneca, Cambridge, UK], n=6) for 6 weeks. Dapagliflozin was administrated in the drinking water by oral gavage once daily in the treatment group, and mice in the Ctrl and Case groups were administrated with the same volume of saline. When the experiment was completed, all mice in the three groups were sacrificed by cervical dislocation after CO2-induced narcosis. Immediately afterward, the kidneys were collected and analyzed.

first: Jianxiao

last: Shen

first: Xiaoqian

last: Yang

first: Xinghua

last: Shao

first: Leyi

last: Gu

first: Shan

last: Mou

first: Xiajing

last: Che


title: DNA polymerase ε harmonizes topological states and R-loops formation to maintain genome integrity in Arabidopsis

city: BeiJing

first: Qin

last: Li

state: BeiJing

address: Tsinghua University,Hai Dian, Beijing

institute: Tsinghua University

summary: Genome topology is tied to R-loop formation and genome stability. However, the regulatory mechanism remains to be elucidated. By establishing a system to sense the connections between R-loops and genome topology states, we show that inhibiting DNA topoisomerase 1 (TOP1i) triggers the global increase of R-loops (called topoR-loops) and DNA damages, which are exacerbated in the DNA damage repair-compromised mutant atm. Further suppressor screen identifies a mutation in POL2A, the catalytic subunit of DNA polymerase ?, liberating the TOP1i-induced topoR-loop accumulation and genome instability in atm. Additionally, we find a highly conserved junction domain between the exonuclease and polymerase domains in POL2A that is required for modulating topoR-loops near DNA replication origins and facilitating faithful DNA replication. Our results suggest that DNA replication is in concert with genome topological states to fine-tune R-loops and thereby maintain genome integrity, revealing a presumably conserved regulatory mechanism of TOP1i resistance in chemotherapy for ATM-deficient cancers.

overall_design: ssDRIP performed using S9.6 antibody of root with TOP1i or DMSO (control) treatment in Col-0 (WT), atm, asr20 and pol2a mutants

first: Jincong

last: Zhou

first: Shuai

first: Weifeng

last: Zhang

first: Yingxue

last: Du

first: Kuan

first: Yingxiang

last: Wang

first: Qianwen

last: Sun


title: Single cell RNA-sequencing studies to examine the heterogeneity of infarct macrophages

city: Bronx

first: Silvia

last: Hernandez

address: 1300 Morris Park Avenue

department: Medicine-Cardiology

institute: Albert Einstein College of Medicine

summary: Cardiac macrophages exhibit remarkable heterogeneity that is accentuated after myocardial infarction. In order to characterize the transcriptional profile of cardiac macrophage subpopulations after infarction we performed scRNA-seq in FACS-sorted macrophages from normal and infarcted CSF1R-EGFP (macrophage reporter) mouse hearts. CSF1R-EGFP 12-16 week-old mice were subjected to permanent coronary occlusion, and 7 days after surgery macrophage suspensions were harvested from infarcted and control mice. Non-neutrophils (Ly6G-) were gated to identify EGFP+ macrophages, which were sorted with the FACSAria Sorter (BD Biosciences). Subsequently, scRNA-seq was performed.

overall_design: Cardiac Macrophages from CSF1R-EGFP mice were isolated by Fluorescence-activated cell sorting (FACS) based on the presence of EGFP signal after exclusion of Ly6G+ cells. Previous to cell isolation surgery was preformed for the infarct groups (n=3). Seven days after surgery, hearts were harvested for baseline (n=1, 3 control hearts pooled) and infarcted (n=3) mice. Before digestion, the non-infarcted region (remote zone) was excised from the heart and excluded from the digestion. Samples were analyzed using scRNA-seq.

first: Bijun

last: Chen

first: Ruoshui

first: Anis

last: Hanna

first: Yang

last: Liu

first: Richard

last: Ma

first: Deyou

last: Zheng

first: Nikolaos

last: Frangogiannis


title: Enhanced Production of Mesencephalic Dopaminergic Neurons from Lineage-Restricted Human Undifferentiated Stem Cells [RNA-seq 2]

status: Public on Nov 01 2023

city: Aarhus

first: Mark

last: Denham

address: Høegh-Guldbergs Gade 10

department: Biomedicine

country: Denmark

institute: Aarhus University

summary: The differentiation of human pluripotent stem cells (hPSCs) into mesencephalic dopaminergic (mesDA) neurons requires a precise combination of extrinsic factors that recapitulates the in vivo environment and timing. Current methods are capable of generating authentic mesDA neurons after long-term culture in vitro; however, when mesDA progenitors are transplanted in vivo, the resulting mesDA neurons are only minor components of the graft. This low yield hampers the broad use of these cells in the clinic. In this study, we genetically modified pluripotent stem cells to generate a novel type of stem cells called lineage-restricted undifferentiated stem cells (LR-USCs), which robustly generate mesDA neurons. LR-USCs are prevented from differentiating into a broad range of nondopaminergic cell types by knocking out genes that are critical for the specification of cells of alternate lineages. Specifically, we target transcription factors involved in the production of spinal cord and posterior hindbrain cell types. When LR-USCs are differentiated under caudalizing condition, which normally give rise to hindbrain cell types, a large proportion adopt a midbrain identity and develop into authentic mesDA neurons. We show that the mesDA neurons are electrophysiologically active, and due to their higher purity, are capable of restoring motor behavior eight weeks after transplantation into 6-hydroxydopamine (6-OHDA)-lesioned rats. This novel strategy improves the reliability and scalability of mesDA neuron generation for clinical use.Competing Interest StatementThe authors have declared no competing interest.

overall_design: Gene expression analysis of RNA-seq data for H9, GBX2 knockout and 4X cells at day 32 after differentiation using a caudal neural differentation protocol.


title: Dapagliflozin alleviates renal inflammation and protects against diabetic kidney diseases dependent and independent of glucose levels [ATAC-seq]

first: Anxiang

last: Cai

first: Jianxiao

last: Shen

first: Xiaoqian

last: Yang

first: Xinghua

last: Shao

first: Leyi

last: Gu

first: Shan

first: Xiajing


title: The role of MSK1 in pancreatic adenocarcinoma (PDAC) progression

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham


title: Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer (Cell lines scRNA-Seq)

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Triple-negative breast cancer (TNBC) is a heterogeneous disease with limited treatment options. To characterize TNBC heterogeneity and treatment response, we combined functional and molecular profiling with computational analysis tools. Using these approaches, we defined transcriptional, epigenetic, and metabolic subtypes, and identified subtype-driving super-enhancers. Single cell RNA sequencing analyses revealed relative homogeneity of the three major transcriptional subtypes (luminal, basal and mesenchymal) within tumors. We found that mesenchymal TNBCs are more similar to mesenchymal neuroblastoma and rhabdoid tumors than to other TNBC subtypes, and the PRRX1 transcription factor serves as a key driver of these tumors. By directly regulating the transcription of mesenchymal genes, PRRX1 is sufficient for inducing the mesenchymal subtype but is not required for its maintenance.

overall_design: scRNA-seq of 19 TNBC cell lines, sequenced across two batches

first: Bojana

last: Jovanović

first: Daniel

last: Temko

first: Franziska

last: Michor


title: Integrated network pharmacology and cellular assay reveal the biological mechanisms of Limonium sinense (Girard) Kuntze against breast cancer

city: Southampton

first: Hualong

last: Zhao

state: Not US or Canada

address: University Road

department: Biological Sciences

country: United Kingdom

institute: University of Southampton

summary: Limonium Sinense (Girard) Kuntze (L. sinense) has been widely used for the treatment of anaemia, bleeding, cancer, and other disorders in Chinese folk medicine. The aim of this study is to predict the therapeutic effects of L. sinense and investigate the potential mechanisms using integrated network pharmacology methods and in vitro cellular experiments. A total of 15 active ingredients of L. sinense and their corresponding 389 targets were obtained. KEGG enrichment analysis revealed that the biological effects of L. sinense were primarily associated with Pathways in cancer. DisGeNET enrichment analysis highlighted the potential role of L. sinense in the treatment of breast cancer. Cellular experiments demonstrated that the L. sinense ethanol extract (LSE) exhibited a significant growth inhibitory effect on multiple breast cancer cell lines in both 2D and 3D cultures. This study predicts the biological activities of L. sinense and demonstrates the inhibitory effect of LSE on breast cancer cells, highlighting the potential application of L. sinense in cancer treatment.

overall_design: MDA-MB-468 cells were treated with Limonium Sinense Ethanol extract (LSE) for 48 hours at 500 μg/mL, and untreated cells were used as control.

first: Jialian

last: Wang

first: Yihua


title: Functional maturation of human iPSC-derived pyramidal neurons in vivo is dependent on proximity with the host tissue

city: Paris

first: Uwe

last: Maskos

address: 25-28 Rue du Dr Roux

department: DEPARTMENT OF NEUROSCIENCE

institute: Institut Pasteur

summary: Human induced pluripotent stem cells (hiPSCs) have been used extensively in vitro to model early events in neurodevelopment. Because of a number of shortcomings, previous work has established a potential to use these cells in vivo after transplantation into the mouse brain. Here, we describe a systematic approach for the analysis of transplanted hiPSC-derived neurons and glial cells over time in the mouse brain. Using functional two-photon imaging of GCaMP6fexpressing human neural cells, we define and quantify the embryonic-like features of their spontaneous activity. This is substantiated by detailed electron microscopy (EM) of the graft. We relate this to the synaptic development the neurons undergo up to seven months in vivo. This system can now be used further for the genetic or experimental manipulation of developing hiPSC-derived cells addressing neurodevelopmental diseases like schizophrenia or Autism Spectrum Disorder.

overall_design: validation of the homogenity of human neural precursor cells before transplantation

first: Célia

last: Rais

first: Daniela

last: Santos

first: Giulia

last: Sansone

first: Stéphane

last: Blanchard

first: Jean-Pierre

last: Bourgeois

first: Bernd

last: Jagla

first: Baptiste

last: Saudemont

first: Laurène

last: Schlick

first: Stéphanie

last: Pons


title: Gene-expression study of primary human anti-CD19 CAR T cells in vitro with or with out stimulation with target cells

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Assessing transcriptomic differences between activation and non-activation of CAR T cells expressing different Chimeric Antigen Receptors

overall_design: mRNA extraction after 24h of antigen starvation or 24h of CAR activation

first: Melanie

last: Boerries

first: Misol

last: Velasco

first: Susana

last: Minguet


title: Sustained store-operated calcium entry utilizing activated chromatin state leads to instability in iTregs

first: Huiyun

last: Lyu

address: Tsinghua University, Zhengyutong Building D301

department: Institute for Immunology

summary: Thymus-originated tTregs and in vitro induced iTregs are subsets of regulatory T cells. While they share the capacity of immune suppression, their stabilities are different, with iTregs losing their phenotype upon stimulation or under inflammatory milieu. Epigenetic differences, particularly methylation state of Foxp3 CNS2 region, provide an explanation for this shift. Whether additional regulations, including cellular signaling, could directly lead phenotypical instability requires further analysis. Here we show that upon TCR triggering, store-operated calcium entry (SOCE) and NFAT nuclear translocation are blunted in tTregs, yet fully operational in iTregs, similar to Tconvs. On the other hand, tTregs show minimal changes in their chromatin accessibility upon activation, in contrast to iTregs that demonstrate an activated chromatin state with highly accessible T cell activation and inflammation related genes. Assisted by several cofactors, NFAT driven by strong SOCE signaling in iTregs preferentially binds to primed opened T helper (TH) genes, resulting in their activation normally observed only in Tconv activation, ultimately leads to instability. Conversely, suppression of SOCE in iTregs can partially rescue their phenotype. Thus our study adds two new layer, cellular signaling and chromatin accessibility, of understanding in Treg stability, and may provide a path for better clinical applications of Treg cell therapy.

overall_design: To systemicly study the similarity among iTregs, Tconvs and tTregs, we performed RNA-seq and ATAC-seq of iTregs, together with resting/activated tTregs and Tconvs.To validate the role of calcium and NFAT in iTreg instability, we used inhibitors cyclosporine A (CsA) and CM-4620 to suppress calcium signal and NFAT, respectively. Then, we performed RNA-seq and ATAC-seq on these cells.

first: Guohua

last: Yuan

first: Yan

last: Shi


title: Electrical Stimulation Mitigates Muscle Degradation Shift in Gene Expressions during 12-hour Mechanical Ventilation

city: Nishinomiya

first: Yutaka

last: Hirata

state: Hyogo

address: 1-1 Mukogawa-cho

department: Integrative Physiology

institute: Hyogo Medical University

summary: Ventilator-induced diaphragm dysfunction (VIDD), a dysfunction of the diaphragm muscle caused by prolonged mechanical ventilation (MV), is an important factor that hinders successful weaning from ventilation. We evaluated the effects of electrical stimulation of the diaphragm muscle (pulsed current with off-time intervals) on genetic changes during 12 hours of MV (E-V12). Rats were divided into four groups: control, 12-hour MV, sham operation, and E-V12 groups. Transcriptome analysis using an RNA microarray revealed that 12-hour MV caused upregulation of genes promoting muscle atrophy and downregulation of genes facilitating muscle synthesis, suggesting that 12-hour MV is a reasonable method for establishing a VIDD rat model. Of the genes upregulated by 12-hour MV, 18 genes were not affected by the sham operation but were downregulated by E-V12. These included genes related to catabolic processes, inflammatory cytokines, and skeletal muscle homeostasis. Of the genes downregulated by 12-hour MV, 6 genes were not affected by the sham operation but were upregulated by E-V12. These included genes related to oxygen transport and mitochondrial respiration. These results suggested that 12-hour MV shifted gene expression in the diaphragm muscle toward muscle degradation and that electrical stimulation counteracted this shift by suppressing catabolic processes and increasing mitochondrial respiration.

overall_design: The study involved 16 rats divided into four groups (CON, V12, S-V12, E-V12): Control (CON): Rats not subjected to ventilation, diaphragm harvested after anesthesia. Ventilatory management (V12): Rats with tracheostomy, mechanically ventilated for 12 hours. Sham operation (S-V12): Rats with tracheostomy and abdominal incision, no electrical stimulation applied during 12 hours of mechanical ventilation. Ventilatory management and electrical stimulation (E-V12): Rats with tracheostomy and abdominal incision, continuous electrical stimulation applied during 12 hours of mechanical ventilation with diaphragmatic contraction monitoring. Transcriptome analysis of the diaphragm was performed using the Clariom S Assays Array.

first: Hideki

last: Nakai

first: Hidemasa

last: Furue

first: Yoshitaka

last: Oku


title: MicroRNA-mediated attenuation of branched-chain amino acid catabolism promotes ferroptosis in chronic kidney disease [RNA-seq]

city: Augusta

first: Sang Ho

last: Kwon

state: Georgia

address: 1120 15th Street

department: Cellular Biology and Anatomy

institute: Augusta Univeristy

summary: Chronic kidney disease (CKD) complicates cisplatin-based chemotherapy of cancer patients. Here we investigate microRNA (miRNA)-regulated transcriptomic activity to unveil biological processes associated with cisplatin-induced kidney injury. Implementing chimeric-eCLIP-seq approach to a mouse model for cisplatin-induced CKD, we identify direct pairs of miRNA and their target messenger RNA in the injured kidney. We find a dedicated transcriptomic program directed by a group of miRNAs that alter metabolic pathways centered on mitochondria in the injured kidneys. Specifically, cisplatin-induced miRNA, miR-429-3p suppresses the mitochondria pathway that catalyzes branched-chain amino acid (BCAA), eventually leading to lipid peroxidation-dependent cell death, called ferroptosis. Thus, the identification of miRNA-429-3p-mediated stimulation of ferroptosis suggests a therapeutic potential for BCAA pathway modulation in ameliorating CKD and cisplatin-associated nephrotoxicity.

overall_design:
To investigate the miRNA effect on CKD, cisplatin induced CKD mouse and control mouse were prepared.
eCLIPseq (to obtain miRNA-mRNA interaction through Ago2 complex), small RNAseq (to obtain miRNA), and RNAseq (to obtain mRNA) were performed.

first: Hisakatsu

last: Sone

first: Tae

last: Lee

first: Byung

first: Dan

last: Heo

first: Sekyung

last: Oh

first: Sang-Ho


title: MicroRNA-mediated attenuation of branched-chain amino acid catabolism promotes ferroptosis in chronic kidney disease.

type: Non-coding RNA profiling by high throughput sequencing


title: MicroRNA-mediated attenuation of branched-chain amino acid catabolism promotes ferroptosis in chronic kidney disease [miRNA-seq]


title: MicroRNA-mediated attenuation of branched-chain amino acid catabolism promotes ferroptosis in chronic kidney disease [CLIP-seq]


title: Pathogenic TH17 cells utilize BHLHE40 to instruct myeloid cells during autoimmune neuroinflammation

city: St. Louis

first: Brian

middle: Todd

last: Edelson

state: MO

address: 660 S. Euclid Ave., Box 8118

institute: Washington University School of Medicine

summary: TH17 cells are implicated in the pathogenesis of multiple sclerosis and experimental autoimmune encephalomyelitis (EAE). We previously reported that the transcription factor BHLHE40 marks cytokine-producing pathogenic TH cells during EAE, and that its expression in T cells is required for clinical disease. Here, using dual reporter mice, we show BHLHE40 expression within TH1/17 and ex-TH17 cells following EAE induction. Il17a-Cre-mediated deletion of BHLHE40 in TH cells led to less severe EAE with reduced TH cell cytokine production. Characterization of the leukocytes in the central nervous system during EAE by scRNA-sequencing identified differences in the infiltrating myeloid cells when BHLHE40 was present or absent in TH17 cells. Our studies highlight the importance of BHLHE40 in promoting TH17 cell encephalitogenicity and instructing myeloid cell responses during active EAE.

overall_design: Live CD45+ cells from the central nervous system were FACS sorted from either naïve mice or immunized Bhlhe40fl/fl, Cd4-Cre+ Bhlhe40fl/fl, or Il17a-Cre+ Bhlhe40fl/fl mice 14 days post-EAE immunization for scRNA-seq.

first: Melissa

last: Cook

first: Irina

last: Shchukina

first: Chih

last: Lin

first: Tara

last: Bradstreet

first: Elizabeth

last: Schwarzkopf

first: Nicholas

middle: N

last: Jarjour

first: Ashlee

last: Webber

first: Konstantin

last: Zaitsev

first: Maxim

last: Artyomov

middle: T


title: Mechanopathology of biofilm-like Mycobacterium tuberculosis cords

city: Lausanne

first: Maxime

last: Jan

state: Suisse

address: University of Lausanne

department: CIG

country: Switzerland

institute: University of Lausanne

summary: Mycobacterium tuberculosis (Mtb) cultured in the absence of detergent forms biofilm-like cords, a clinical identifier of virulence. Using lung-on-chip and mouse infection models, we show that cord growth in alveolar cells contributes to the suppression of innate immune signalling via nuclear compression. Thereafter, extracellular cords cause contact-dependent phagocyte death but grow intercellularly between epithelial cells. These “mechanopathological” mechanisms explain the greater proportion of alveolar lesions with increased immune infiltration and dissemination defects in cording-deficient Mtb infections.  Compression of WT Mtb lipid monolayers induces a phase transition that enables mechanical energy storage. Agent-based simulations demonstrate that the increased energy storage capacity is sufficient for the formation of stable cords that maintain structural integrity despite mechanical perturbation. Moreover, bacteria in cords remain translationally active despite prolonged antibiotic exposure and regrow rapidly upon cessation of treatment. This study provides a conceptual framework for the biophysics of cord architectures and their functional roles in tuberculosis infection and therapy, independent of mechanisms ascribed to single bacteria.

overall_design: To investigate the differences between the pulmonary immune responses of C3HeB/FeJ mice at 8 weeks post infection of wild-type or cording-deficient Mycobacterium tuberculosis strains using the aerosol route. Uninfected mice serve as the control. Bulk RNA seq was performed on RNA extracted from lung samples from sex-mixed mice using Trizol

first: Vivek

middle: V

last: Thacker

first: Richa

last: Mishra

first: Nicolas

last: Guex


title: Single cell RNA sequencing of murine ankle joints over time reveals distinct transcriptional and cellular changes in response to Borrelia burgdorferi infection

city: Charlestown

first: Neal

middle: Patrick

last: Smith

address: 149 13th Street

institute: Massachusetts General Hospital

summary: Borreliella burgdorferi is the causative agent of Lyme disease, which is the most common vector-borne disease in the United States.  While cases of Lyme disease are geographically limited to the Northeast, mid-Atlantic, and Midwest states, there are still estimates of almost 500,000 cases annually in the United States alone. In this study, we sought to assess transcriptional changes that occur in response to B. burgdorferi infection in the ankle joints of C57BL/6 mice. To this end, we performed single cell RNA sequencing (scRNA-seq) to transcriptionally profile cells, identify population heterogeneity, and analyze how cellular environments change over time. Sequencing of immune and non-immune cells in the mouse ankle joint was performed over five distinct time points, starting with uninfected animals and progressing to eight weeks post-infection in two-week increments.

overall_design: Mice were inoculated subcutaneously in the center of the abdomen with 105 spirochetes in 100 µl or with 100 µl BSK-II medium for uninfected controls. B. burgdorferi infection was confirmed by culturing of live spirochetes from the ears in BSK-II medium at time of sacrifice and visualization of spirochetes using dark-field microscopy. At two, four, six and eight weeks post-infection, mice were sacrificed and ankle joints harvested. Ankle joints were processed as previously described. Briefly, joint tissue was digested for 1 hour at 37 ºC in RPMI containing 0.2 mg/ml liberase TL (Roche) and 1 unit/ml DNase (Thermo), inverting every 15 minutes. Cells were then filtered through a 40 µm filter and washed in PBS containing 2% FBS and 1 mM CaCl2. Live cells were obtained through magnetic sorting using the EasySep Dead Cell Removal (Annexin V) Kit (StemCell Technologies) per manufacturer’s instructions. Following dead cell removal, cells were washed in MACS buffer (PBS containing 0.5% BSA and 2 mM EDTA) and CD45+ and CD45- cells separated using CD45 MicroBeads and a MiniMACS Separator per manufacturer’s instructions (Miltenyi Biotec).

middle: P

first: Jennifer

last: Helble

first: Alexandra-Chloe

last: Villani

first: Linden

last: Hu


title: Enhanced Production of Mesencephalic Dopaminergic Neurons from Lineage-Restricted Human Undifferentiated Stem Cells

first: Mark

last: Denham

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

overall_design: Refer to individual Series


title: Breast Cancer Therapies Reduce Risk of Alzheimer’s Disease and Promote Estrogenic Pathways and Action in Brain

city: TUCSON

first: Roberta

last: Brinton

address: 1230 N Cherry Ave, PO Box 210242

department: The Center for Innovation in Brain Science

institute: University of Arizona

summary: Worldwide an ever-increasing number of women are prescribed estrogen modulating therapies (EMTs) for the treatment of breast cancer.  In parallel, aging of the global population of women will contribute to risk of both breast cancer and Alzheimer’s disease. To address the impact of anti-estrogen therapies on risk of Alzheimer’s and neural function, we conducted medical informatic and molecular pharmacology analyses to determine the impact of EMTs on risk of Alzheimer’s followed by determination of EMT estrogenic mechanisms of action in neurons. In a propensity matched data set of 260,232 women with breast cancer, medical informatic analyses indicated that EMTs were associated with reduced risk of AD which was driven by patients receiving tamoxifen or aromatase inhibitors whereas raloxifene was ineffective independently validating earlier reports. Mechanistically, a comparative analysis of EMTs vs estradiol was conducted to determine whether EMTs exerted estrogenic action in neural cells in-vitro and in brain in-vivo. Outcomes of mechanistic analyses indicated that select EMTs induced estrogenic action and pathways in neural cells including promoting neuronal morphological plasticity, electrophysiological indicators of synaptic connectivity, mitochondrial number and function and induction of transcriptomic pathways consistent with estrogenic outcomes. Collectively, these data provide both clinical and mechanistic data indicating that select EMTs exert estrogenic agonist action in neural tissue that are associated with reduced risk of Alzheimer’s disease while simultaneously acting as effective estrogen receptor antagonists in breast.

overall_design: To determine and validate the impact of SERM treatment on the CNS, 6-month-old female Sprague Dawley rats were ovariectomized and treated with EMT. Briefly, rats underwent surgery (ovariectomy or sham) at 6 months by Charles River Laboratories. After a 2-week wash-out period, rats were randomly distributed into 8 equal groups based on treatment type. Each rat was then treated according to their assignment group (i.e., SHAM, OVX+Vehicle, OVX+EMT) at clinically relevant concentrations based on allometric dose scaling (Human Equivalent Dose Conversion [mg/kg]). The resulting dosing regimen was once daily IP injections of estradiol E2 (0.16mg/kg), tamoxifen (3.23mg/kg), raloxifene (9.68mg/kg), anastrozole (4.03mg/kg), or exemestane (0.16mg/kg). Tissues of interest were collected at 7 days post onset of treatment and processed for transcriptomics.

first: Gregory

last: Branigan

first: Georgina

last: Torrandell-Haro

first: Shuhua

last: Chen

first: Yuan

last: Shang

first: Samantha

last: Perez-Miller

first: Zisu

last: Mao

first: Marco

last: Padilla-Rodriguez

first: Helena

last: Cortes Flores

first: Francesca

last: Vitali

last: Diaz Brinton


title: Omics data integration suggests a potential idiopathic Parkinson’s disease signature

city: Esch sur Alzette

first: Alise

last: Zagare

state: Belval

address: 7 Avenue des Hauts-Fourneaux

country: Luxembourg

institute: University of Luxembourg

summary: Identification of early transcriptomic and metabolic alterations consistent across different idiopathic Parkinson’s disease (IPD) patients might reveal the potential basis of increased dopaminergic neuron vulnerability and primary disease mechanisms. In this study, we combine systems biology and data integration approaches to identify differences in transcriptomic and metabolic signatures between IPD patient and healthy individual-derived midbrain neural precursor cells. Characterization of gene expression and metabolic modeling reveal pyruvate, several amino acid and lipid metabolism as the most dysregulated metabolic pathways in IPD neural precursors. Furthermore, we show that IPD neural precursors endure mitochondrial metabolism impairment and a reduced total NAD pool. Accordingly, we show that treatment with NAD precursors increases ATP yield hence demonstrating a potential to rescue early IPD-associated metabolic changes.

overall_design: RNA sequencing analysis of three healthy individual and three age-gender matched idiopathic Parkinson's disease patient-derived neuroepithelial stem cells

first: German

last: Preciat

first: Sarah

last: Nickels

first: Anna

middle: S

last: Monzel

first: Gemma

last: Gomez-Giro

first: Graham

last: Robertson

first: Christian

last: Jaeger

first: Jafar

last: Sharif

first: Haruhiko

last: Kaseki

first: Xi

last: Luo

first: Nico

last: Diederich

first: Enrico

last: Glaab

first: Ronan

last: Fleming

first: Jens

last: Schwamborn


title: Enhanced Production of Mesencephalic Dopaminergic Neurons from Lineage-Restricted Human Undifferentiated Stem Cells [scRNA-seq]

first: Mark

last: Denham

overall_design: Single cell  RNA-seq data for H9 and 4X cells at day 16, 28 and 62  days of differentiation.

first: Morten

last: Venø


title: Enhanced Production of Mesencephalic Dopaminergic Neurons from Lineage-Restricted Human Undifferentiated Stem Cells [RNA-seq 1]

overall_design: Gene expression analysis of RNA-seq data for H9, GBX2 knockout and 4X cells in the undifferentiated state and differentiated to day 4 caudal neural progenitors (CNPs).


title: ABCA12-mediated ceramide efflux governs breast cancer stem cell function

first: Jihong

last: Cui

state: NY

address: 1301 Morris Park Avenue, Room 108/114

institute: Albert einstein college of medicine

summary:
Cancer stem cells (CSCs) drive tumor growth, metastasis, relapse, and chemoresistance. However, it’s unclear how lipid metabolism, especially sphingolipids metabolism, regulates CSCs and chemoresistance.
In this study, we developed spontaneous tumor models expressing a Sox9-GFP transgenic reporter and demonstrated that cancer cells expressing high levels of SOX9 functioned as CSCs in both primary tumors and metastases. Transcriptomics analyses uncovered that SOX9high CSCs upregulate ABCA12 lipid transporter.
Functionally, downregulation of ABCA12 impaired cancer stemness and chemoresistance of SOX9high cells. Through lipidomic analysis, we demonstrated that ABCA12 regulates SOX9 expression and cancer stemness by controlling ceramide abundance.
Blocking ceramide hydrolysis using acid ceramidase inhibitor D-NMAPPD sensitized tumors to chemotherapy and prevented enrichment of SOX9high CSCs. These data suggest a potential strategy for targeting CSCs and overcoming chemoresistance. We further demonstrated that ceramide inhibits the YAP/TAZ signaling that is required for SOX9 expression in breast CSCs.

overall_design: Four Sox9-GFP; C3(1)/Tag tumors were used in this study. Each tumor was dissected into a single cell suspension. From this suspension, Lineage-/Sox9-GFP neg, low and high tumor cells were FACS sorted. RNA was isolated from these populations and RNA-seq was preformed for comparison the gene expression.

first: Wenjun

last: Guo


title: Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer

first: Kornelia

last: Polyak


title: Effect of indel in promoter of CDC20 on gene expression in A375 human melanoma cell line.

first: Charles

last: Kaufman

address: 4518 McKinley Ave. McDonnell Science BuidinRM 558

institute: Washington University in St. Louis

summary:
CDC20 promoter variants are present in ~26% of cutaneous melanomas.
We generated an indel in the promoter of CDC20 and performed RNA-sequencing to determine the effect on CDC20 expression and other secondary transcriptional changes.

overall_design: RNA-sequencing of WT A375, A3 (small indel ~ 4-5 bp ), and A10 (larger, >20 bp CDC20 promoter deletion)

first: Paula

last: Godoy


title: Molecular and spatial design of human cerebellar development

city: Beijing

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

institute: Chinese Academy of Sciences

summary: Human cerebellar development is precisely orchestrated by molecular regulatory networks. Here, we combined single-cell transcriptomics, spatial transcriptomics and chromatin accessibility states to systematically depict an integrative temporal-spatial landscape of human fetal cerebellar development. The multiomic data reveal molecular networks, providing an informative regulatory map to show how and when cell fates are determined. Spatial transcriptomics illustrated the distinct molecular signatures of the progenitors, Purkinje cells and granule cells located in different regions of the developing cerebellar cortex. We identified RORB as a new marker of developing human Purkinje cells, which was not expressed in mice. In addition, the RL progenitors highly expressed the human-specific gene ARHGAP11B , and ARHGAP11B expression led to cerebellar cortex expansion and folding in mice. We finally mapped the genes and single-nucleotide polymorphisms (SNPs) of diseases related to cerebellar dysfunction onto cell types, indicating the cellular basis and possible pathogenesis mechanisms of neuropsychiatric disorders.

overall_design:
Gestational week 12 to 27
10x Genomics Visium sequencing for more 50,000 nucleis from human fetal cerebellum.

first: S

last: Zhong

first: Q

last: Wu

first: X

last: Wang


title: Molecular mechanisms for changing brain connectivity in mice and humans

status: Public on Oct 31 2023

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University


title: Molecular mechanisms for changing brain connectivity in mice and humans (blood samples)

summary: The goal of this study was to examine commonalities in the molecular basis of learning in mice and humans. In our previous work on mouse learning we suppressed activity in the anterior cingulate cortex (ACC) and hippocampus (HC) and found the stages for which each area was critical in performing a 2-choice visuospatial discrimination task. Our current study began by examining gene expression changes in mouse ACC and HC as a result of learning a new skill. Genes upregulated in both brain areas were used as candidates to examine commonalities between genes upregulated in mouse and human blood.  We used microarrays to identify candidate genes and real-time PCR to compare the mouse results with two forms of human learning. One form involved training in a working memory task (network training), the other a generalized training shown to change many networks (meditation).  We identified two genes that were upregulated in both mice and humans following training. We believe these genes act to regulate pathways that influence NF-κB, a factor previously found to be related to enhanced synaptic function and learning.

overall_design: The experiment consists of 12 Mouse Gene 2.0 ST arrays, profiling pooled RNA samples obtained from blood obtained from untrained and trained animals both pre- and post-training-period.

first: Pascale

last: Voelker

first: Michael

middle: I

last: Posner


title: Discovery and Anti-inflammatory Activity of a Cyanobacterial Fatty Acid Targeting the Keap1/Nrf2 Pathway

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

summary: We discovered a cyanobacterial fatty acid that contains an α,β-unsaturated carbonyl system a key motif required for the activation of the Keap1/Nrf2−ARE pathway that is involved in the activation of antioxidant and phase II detoxification enzymes. The compound was screened in ARE luciferase reporter gene assay which induced Nrf2 activity at 32 and 10µM. Given the established crosstalk between oxidative stress and inflammation, we aimed at investigating the antiinflammatory potential of our compound using RAW264.7 mouse macrophage. We carried RNAseq to capture the effects of the comound on transript levels and identify additional pathways invloved in inflammation that could be modulated.

overall_design: RAW264.7 mouse macrophage cells were treated with three concentrations (32, 10, 3.2 µM) of the fatty acid in addition to solvent control (DMSO) for 1h followed by stimulation with Lipopolysaccharide (LPS). The RNA was collected after 12h. RNA from cells treated with DMSO without LPS stimulation were also obtained.

first: Fatma

last: Al-Awadhi

first: Emily

last: Simon

first: Ranjala

last: Ratnayake

first: Hendrik

last: Luesch


title: Novel Role for Alpha-2-Macroglobulin (A2M) as a Disease Modifying Protein in Senile Osteoporosis

city: Jupiter

first: Christopher

middle: Lee

last: Haga

state: Florida

address: 130 Scripps Way, BldgA261A

department: Molecular Medicine

institute: UF Scripps Biomedical Research

summary: Identification of the downregulation of A2M in bone marrow isolated from elderly (24-month-old) vs mature (3-month-old) mice.

overall_design: RNA-sequencing of whole bone marrow from 3-month-old C57Bl/6 mice versus 24-month-old C57Bl/6 mice.

first: Donald

middle: G

last: Phinney

first: Siddaraju

last: Boregowda


title: Gene expression data from C57BL/6J mice exposed to 3 days of hypoxia

city: London

first: Olena

last: Rudyk

address: St Thomas Hospital, The Rayne, Lambeth Wing, Westminster Bridge Rd

department: School of Cardiovascular and Metabolic Medicine & Sciences

institute: King's College London

summary:
Pulmonary hypertension (PH) is a chronic vascular disease characterised, amongst other abnormalities, by hyperproliferative smooth muscle cells and a perturbed cellular redox and metabolic balance. Oxidants induce cell cycle arrest to halt proliferation; however, little is known about the redox-regulated effector proteins that mediate these processes. Here, we report a novel kinase-inhibitory disulfide bond in cyclin D-CDK4 and investigate its role in cell proliferation and PH.
We used an Affymetrix microarray to look at the gene expression profile of mouse lungs exposed to normobaric hypoxia (10% oxygen) or normoxia and identified genes that were differentially expressed in response to hypoxia.

overall_design: C57BL/6J mice were subjected to either normoxia (21% oxygen) or normobaric hypoxia (10% oxygen) for 3 days and then anaesthetized with an intraperitoneal injection of pentobarbitone (300 mg/kg) supplemented with heparin (150 U). mRNA extraction from the lung was performed using the RNeasy Plus Universal kit (Qiagen). ~5 μg of SPIA-amplified complementary DNA was fragmented and biotin-labelled using the Encore Biotin module (NuGEN), and hybridisation cocktails were prepared as recommended by NuGEN. Samples were hybridized to Mouse Gene 2.0 ST arrays using standard protocols as recommended by the manufacturer (Affymetrix).

first: Hannah

last: Knight

first: Giancarlo

last: Abis

first: Manpreet

last: Kaur

last: Green

first: Susanne

last: Krasemann

first: Kristin

last: Hartmann

first: Steven

last: Lynham

first: James

last: Clark

first: Lan

last: Zhao

first: Clemens

last: Ruppert

first: Astrid

last: Weiss

first: T

last: Schermuly

first: Phillip

last: Eaton


title: Molecular mechanisms for changing brain connectivity in mice and humans (brain samples)

first: Boston University

last: Microarray and Sequencing Resource

overall_design: The experiment consists of 12 Mouse Gene 2.0 ST arrays, profiling pooled RNA samples obtained from two different brain regions (the anterior cingulate cortex (ACC) and hippocampus (HC)) of untrained and trained animals.

first: Pascale

last: Voelker

first: Michael

last: Posner