title: The central role of creatine and polyamines in fetal growth restriction

city: Udine

first: Raffaella

last: Picco

address: P.le Kolbe 4

department: Department of Medicine

country: Italy

institute: University of Udine

summary: Placental insufficiency is often associated with fetal growth restriction (FGR), a condition associated with both short- and long-term complications for the newborn. In this study, we performed comprehensive transcriptomic and metabolomic analyses to delineate the metabolic profiles that distinguish newborns with FGR from those born with appropriate-for-gestational- age (AGA) status. By comparing our RNA-seq data with placental transcriptome data from the POP dataset, we identified common enrichment categories, notably hypoxia, as well as alterations in creatine and arginine metabolism. In infants with FGR, placental insufficiency tends to promote anaerobic metabolism, resulting in limited ATP production. To counteract this deficiency, arginine is used to synthesise phosphocreatine, an energy-rich compound that is crucial for ATP production. Increased biosynthesis of polyamines  addition, our observations show an upregulation of SAT1 acetyltransferase that contributes to decreased concentrations of spermidine and N1-acetylspermidine as well as increased N1,N8-diacetylspermidine concentrations in the placenta of FGR infants. Increased .In summary, our study improves the understanding of metabolic adaptations associated with placental dysfunction in FGR and provides valuable insights for future therapeutic interventions.

overall_design: Total RNA was extracted from 9 AGA (appropriate weights for gestational age), 9 SGA10 (small for gestational age, below the 10th percentile)  and 5 SGA3 (small for gestational age, below the 3rd percentile) term placenta.

first: Serena

last: Xodo

first: Ambrogio

last: Londero

first: Maria

last: Orsaria

first: Vanessa

last: Tolotto

first: Annalisa

last: Ferino

first: Ylenia

last: Cortolezzis

first: Lorenza

last: Driul

first: Luigi

middle: E

first: Eros

last: Di Giorgio


title: Single-cell RNA-sequencing reveals the effects of right ventricular volume overload on cardiomyocyte proliferation via immune responses

status: Public on Dec 06 2024

city: Shanghai

first: Yuqing

last: Hu

address: 1678 Dongfang Road, Pudong New District, Shanghai

country: China

institute: Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine

type: Expression profiling by high throughput sequencing

summary: Background: Right ventricular volume overload (RVVO) is one of the most important hemodynamic characteristics in children with congenital heart diseases (CHDs) and heart failure, and cardiomyocyte (CM) proliferation is a vital factor for improving cardiac performance. However, whether and how RVVO reboots CM proliferation remains elusive.  Methods and Results: We first created a prepubertal RVVO mouse model by an abdominal- aorta- and inferior- vena- cava- fistula (ACF) surgery on postnatal day 7(P7). Then we performed bulk RNA-seq on RVs of RVVO mice on P14, which showed that the top 30 enriched gene ontology(GO) terms of upregulated genes were associated with cell proliferation and that cell cycle was the fourth top enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway terms. Immunofluorescence staining confirmed the results, showing significantly increased numbers of phosphorylated histone 3/Aurora B-positive CMs in RVs with RVVO when compared to those in control RVs. Single RNA-seq performed on P21 further confirmed the results, showing increased percentage of CMs, with five sub-functional CMs, in which immature CMs increased while mature CMs decreased. In addition, RNA-seq/flow cytometry demonstrated that RVVO induced an immune response. Inhibiting the immune response with cyclosporin A(CsA) caused the gene expression profile of RVVO mice to shift towards that of sham mice, with a significant decrease in cell cycle associated genes’ enrichment. Conclusions: RVVO temporarily reboots prepubertal CM proliferation via immune responses. This study may provide an opportunity to create a novel paradigm to treat pediatric CHDs or heart failure in considering the importance of RVVO and CM proliferation in CHDs or heart failure.

overall_design: We used C57/BL6J mice in this study and performed abdominal- aorta- and inferior- vena- cava- fistula (ACF) surgery on prepubertal mice on postnatal day 7 (P7), which is the edge of the CM proliferation window (P1-P7). Then we collected the right ventricular tissue of mouse pups on postnatal day 21 for single-cell RNA-seq analysis to investigate whether RVVO reactivates CM proliferation.

first: Chunxia

last: Zhou

first: Lincai

last: Ye

first: Haibo

last: Zhang


title: The effects of ketogenic diet on brain gene expressions in type 2 diabetes background

city: Beijing

first: Junling

last: Fu

address: 北京市长椿街45号

institute: 首都医科大学宣武医院

summary:
Aims: Type 2 diabetes mellitus (T2DM) is considered as a risk of neurodegenerative diseases (NDDs). The ketogenic diet (KD) has significant beneficial effects on glycemic control and may act effectively against NDDs. However, the mechanism by which KD is protective against NDDs is still unknown. In the current study, we aimed to explore a possible interaction of KDs on brain functions by determining the effects of KDs on transcriptional changes of brains in the background of T2DM.
Methods: Male db/db mice were fed with KD or normal diet from 9 weeks to 6 months of age, and whole brains were sampled for mRNA-seq analysis. Gene Ontology functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes signaling pathway enrichment analysis were conducted to identify the functions of differentially expressed genes. Proteasomal activities were assessed using biochemical methods.
Results: The KD showed significantly beneficial effects on glycemic control and body weight in db/db mice (P < 0.05). Moreover, KD altered gene expressions in multiple pathways including energy metabolism, biosynthesis, and inflammatory responses in the brain of db/db mice. KD improved in db/db mouse brains the proteasome degradation system, the primary quality control machinery whose defects are involved in most NDDs.
Conclusions: This study suggests that the KD supplement may activate the expression of genes associated with multiple signaling pathway that are closely involved in NDDs. Our results deepen understanding of the molecular mechanisms underlying the improvement of NDDs with KD intervention and may contribute to the development of promising new therapeutic strategies to NDDs.

first: Qianxu

last: Ren

first: Xiaoye

last: Duan

first: Lina

last: Sun

first: Zhijing

last: Mu

first: Wenping

last: Liang

first: Yu

last: Li

first: Zhe

last: Wang

first: Shuangling

last: Xiu


title: Towards improving oil composition and content in oat through metabolic engineering

city: Saint-Anne-de-Bellevue

first: Jaswinder

last: Singh

state: QC

address: 21111 Rue Lakeshore, Plant Science Department, Raymond Building, R2037

country: Canada

institute: McGill University

summary: Energy densification and enrichment of monounsaturated fatty acids increases oat’s nutritional value among small grain cereals. However, optimization of oat oil traits is challenging through conventional breeding. Using the biolistic method for oat’s oil improvement, here we showed that metabolic engineering is a feasible strategy in improving the oil traits of oat. In this study, two constructs containing three genes involved in lipid biosynthesis pathway (AtWRI1, AtDGAT, and SiOLEOSIN) were transformed into oat cultivar ‘Park’ to enhance the oil composition and content in oat grain and leaves. We performed RNA-sequencing in mature seeds and boot leaves of trasngenic lines. Transgene expression contributed to a global transcriptional reprogramming in oat seeds and leaves. Endogenous DGAT, WRI1, and OLEOSIN genes were up regulated while the genes involved in fatty acid biosynthesis expressed in opposite way between oat seeds and leaves. Transcriptomic studies revealed differential gene expression mainly enriched in lipid metabolism.

overall_design: We collected two different tissues from transgenic and wild-type lines with three biological replicates for RNA-seq.

first: Zhou

first: Rajvinder

last: Kaur

first: Thomas

last: Donoso


title: APE1 regulates the transcription of urea cycle genes through stabilizing DNA G-quadruplexes in lung adenocarcinoma [SMART-Seq2]

first: Yanhao

last: Yu

address: Yueyang Street

institute: Center of Excellence in Molecular Cell Science

summary: Lung adenocarcinoma (LUAD) remains the leading cause of cancer deaths worldwide. Apurinic/apyrimidinic endonuclease 1 (APE1), an enzyme integral to DNA repair and redox signaling, is notably upregulated in various cancers, including LUAD. Here we reveal that APE1 amplification, primarily via allele duplication, correlates with poor prognosis in LUAD patients strongly. Using human LUAD cell models and a KRAS-driven genetically engineered mouse model (GEMM), we show that APE1 deletion hampers cell proliferation and tumor growth, highlighting its role in tumorigenesis. Mechanistically, APE1 promoted the transcription of urea cycle genes CPS1 and ARG2 by modulating the presence of G-quadruplex (G4) structures in their promoter regions. Loss of APE1 disrupts the urea cycle and pyrimidine metabolism, inducing metabolic reprogramming and growth arrest, which can be rescued by CPS1 or pyrimidine restoration. These findings uncover APE1’s role in metabolic regulation via G4-mediated transcription, providing a potential therapeutic target LUAD patients with elevated APE1 expression.

overall_design: Gene expression analysis of RNA-seq data for listed cells by Smart-seq2.

first: Chaochao

last: Cen

first: Zhenyu

last: Shao

first: Chao


title: ALS-associated FUS mutation reshapes the RNA and protein composition and dynamic of Stress Granules.

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

institute: Sapienza University of Rome

summary: Stress Granules (SG) formation is a cellular protection mechanism in harmful conditions, constituting a storage for untranslated mRNAs and RNA-binding proteins (RBPs); however, these condensates can turn into pathological aggregates, that in neurons are related to the onset of neurodegenerative diseases, like Amyotrophic Lateral Sclerosis (ALS). Mutations in the RBP FUS, leading to its cytoplasmic mis-localization, are causatively linked to ALS, since they mediate its accumulation in SGs, triggering their transition towards cytotoxic inclusions. Here, we describe the SG transcriptome in a neural context and compare with datasets from other systems, identifying both common rules and diversifying characteristics for SG recruitment of transcripts. We demonstrate that SG dynamics and RNA content are strongly modified by the incorporation of aberrantly localized mutant FUS, switching to a more unstructured, AU-rich SG transcriptome and losing a wide population of GC-rich, structured RNAs. We show that these alterations mainly depend on mutant FUS which favors the SG incorporation of its protein interactors and in turn of their target RNAs. Our data give a comprehensive view of the molecular differences between physiological and pathological SG in ALS conditions, showing how a single mutation is sufficient to impact the RNA and protein population of these condensates.

overall_design: We employed SK-N-BE cells engineered to express wt or mutant FUS under doxycyclin induction, and expressing a GFP-tagged version of the SG marker G3BP1. Cells were harvested after FUS induction and Stress Granules formation via sodium arsenite administration; Stress Granules were purified through centrifugation and immunoprecipitatation for the GFP tag and RNA was extracted to determine the SG transcriptome. DOXY- samples represent controls in which we analyzed the basal transcriptome of SG in these cells, without any interference from overexpressed FUS. For each IP sample, we paired a total RNA input (INP) extracted from the total lysate before the centrifugation steps.

first: Adriano

last: Setti

first: Davide

last: Mariani


title: Human cytomegalovirus infection coopts chromatin organization to modulate TEAD1 transcription factor activity [RNA-Seq]

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

country: USA

institute: Cincinnati Children's Hospital Medical Center

summary: Human cytomegalovirus (HCMV) infects up to 80% of the world’s population and is linked to serious morbidity in immunocompromised individuals and newborns. Here, using multiple genome-scale assays and computational approaches, we show that HCMV infection leads to widespread changes in chromatin accessibility and chromatin looping, with hundreds of thousands of human genomic regions affected 48 hours after infection. Integrative analyses reveal that HCMV infection perturbs the Hippo signaling pathway by drastically diminishing TEA domain transcription factor 1 (TEAD1) activity. Chromatin immunoprecipitation experiments confirm extensive concordant loss of TEAD1 binding and H3K27ac active histone marks upon infection. TEAD transcription factors are direct effectors of the Hippo signaling pathway, and our data support a position for TEAD1 at the top of a hierarchy involving key developmental pathways with differential expression subsequent to HMCV infection. Known gene targets of TEAD1, including Cellular Communication Network Factor 1 (CCN1) and Thrombospondin 1 (THBS1), are significantly downregulated with HCMV infection, reflecting diminished TEAD1-mediated activity. HCMV infection reduces TEAD1 binding through four distinct mechanisms: closing of TEAD1-bound chromatin, reduction of Yes1 associated transcriptional regulator (YAP1) and phosphorylated YAP (pYAP1) levels, reduction of TEAD1 transcript and protein levels, and alteration of TEAD1 exon-6 usage. Collectively, these comprehensive genome-scale analyses reveal novel mechanisms induced by HCMV infection.

overall_design: We performed RNA-seq in human foreskin fibroblasts (HS68) in two conditions. The two conditions are: 1) uninfected; and 2) 48 hours post infection of human cytomegalovirus (HCMV) with the TB40/E clinical isolate. Experiments were performed in two replicates for each condition.

first: Leah

last: Kottyan


title: Human cytomegalovirus infection coopts chromatin organization to modulate TEAD1 transcription factor activity [HiChIP]

overall_design: We performed H3K27ac HiChIP in human foreskin fibroblasts (HS68) in two conditions. The two conditions are: 1) uninfected; and 2) 48 hours post infection of human cytomegalovirus (HCMV) with the TB40/E clinical isolate. Experiments were performed in three replicates for each condition.


title: Fate mapping in mouse demonstrates early secretory differentiation directly from Lgr5+ intestinal stem cells

city: Copenhagen N

first: Kim

middle: B

last: Jensen

address: Belgdamsvej 3B

country: Denmark

institute: University of Copenhagen

summary: The intestinal epithelium has a remarkably high turnover in homeostasis. It remains unresolved how turnover is orchestrated at the cellular level and how the behaviour of stem and progenitor cells ensures tissue maintenance. To address this, we combined quantitative fate mapping in three complementary mouse models with mathematical modelling and single-cell RNA sequencing. Our integrated approach generated a spatially and temporally defined model of crypt maintenance that is based on two cycling populations: crypt-based columnar (CBC) and transit amplifying (TA) cells. Validation experiments substantiated the predictions from the model revealing TA cells as the major contributor to the absorptive lineage, while balanced CBC cell fate choices controlled the numbers of cells in the secretory lineage. By unravelling these mechanisms, we gain insights into the process of tissue turnover and  provide direct evidence to support the notion of CBC cells as the major driver of the intestinal epithelium replenishment.

overall_design: Lgr5-EGFP-IRES- CreERT2;Rosa26-mTmG mice have been labelled with 4-OH-tamoxifen and traced for 48h (n=4) /72h (n=4).  Intestinal epithelial cells have been isolated and stained. Sample from each mouse was stained with a new HTO antibody (Mice traced for 48h #1-4, mice traced 72h #5-8). Single cells were sorted into two eppendorf tubes based on their GFP expression. Cells from 48h/72h clones were sorted as GFPhigh cells, while non-recombined cells were sorted as GFPnegative. Two samples after sorting each had a mix of cells from all the mice. Sample 1 contained GFPneg cells from mice #1,2,5,6 and GFPhigh cells from mice #3,4,7,8. Sample 2 contained GFPneg cells from mice #3,4,7,8 and GFPhigh cells from mice #1,2,5,6.

first: Isidora

last: Banjac

first: Martti

last: Maimets

first: Stine

last: Lind Hansen

first: Kata

last: Krizic

first: Raul

last: Bardini Bressan

first: Cecilia

last: Lövkvist


title: Exosomal miR-183-5p from human hepatocyte-derived liver progenitor-like cells promotes liver regeneration during acute liver failure

first: Yi

last: Chen

address: No.160 Pujian Road

department: Department of Anesthesiology

institute: Renji Hospital, Jiaotong University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Hepatocyte-derived liver progenitor-like cells (HepLPCs) can reversibly differentiate into mature hepatocytes and play important roles in liver regeneration following acute liver failure. However, the mechanisms by which HepLPCs exert these regulatory effects are unclear. Herein, we report that HepLPCs participate in reinitiating liver regeneration and improving survival during acute liver failure, at least in part, via miRNA-183-5p, which is released from HepLPCs in extracellular vesicles. Thus, these findings may identify novel targets and strategies for the treatment of acute liver failure.

overall_design: HepLPC-derived extracellular vesicles (HepLPC-EVs) were isolated from conditioned media and subjected to microRNA (miRNA) sequencing analysis. Primary human hepatocytes were treated with EVs or miRNA mimics and/or inhibitors. C57BL/6J mice were intraperitoneally injected with carbon tetrachloride (CCl4) or acetaminophen (APAP) to induce ALF. These mice were then treated with EVs or a miRNA agomir.


title: Human cytomegalovirus infection coopts chromatin organization to modulate TEAD1 transcription factor activity [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: We performed ATAC-seq in two human cell lines in two conditions. The cell lines are foreskin fibroblasts (HS68) and retinal epithelial (ARPE-19). The two conditions are: 1) uninfected; and 2) 48 hours post infection of human cytomegalovirus (HCMV) with the TB40/E clinical isolate. Experiments were performed in two replicates for each cell type and condition combination.


title: Effect of knockdown Aurora kinase A（AURKA） on gene expression in LX2 cells.

city: guangzhou

first: Guan qi

last: Dai

state: guangdong

address: shiliugang Road 13 courtyard

department: Integrated Hospital of Traditional Chinese Medicine

institute: southern medical university

summary: We performed gene expression profiling analysis using data obtained from RNA-seq of LX2 cells treated with siRNA of AURKA  or siNC.

overall_design: Compare gene expression of LX2 cells transfected with siAURKA or siNC. Each group had three replicates.

first: Guanqi

first: Junhao

last: Lin

first: Xinhui

last: Liu

first: Peng

first: Zhenghui

last: Song

first: Xuefen

last: Zhuang

first: Yun

first: Dong

last: Xiao

first: Aimin

last: Li

first: Yue

last: Luo


title: Identification of influenza virus-encoded vcircRNAs in human A549 cells by RNA-seq

status: Public on Dec 05 2024

first: Zhimin

last: Jiang

address: Yuanmingyuang west road 2

institute: Chinese Agricultural University

summary: The discovery of noncoding RNAs is reshaping paradigms in molecular biology and virology. Circular RNAs (circRNAs), a class of novel noncoding RNAs, their circular conformation endows these transcripts with critical physiological and pathological roles. Here, we employed circRNAs sequencing technologies, following RNase R treatment on influenza virus-infected human pulmonary epithelial cells to identify and characterize influenza virus-derived circRNAs. Back spicing junctions mapping analysis identified lots of circRNAs from 7 viral gene segment apart from M gene and subsequent experiments confirmed the presence of these IAV-encoded circRNAs in infected cells and mice lung. We found that polymerase genes could encode numerous viral circRNA (vcircRNAs) within infected cells, such as NP and PB1. By vcircRNA overexpression and knockdown with small interfering RNA, we found that these vcircRNAs is required for efficient viral replication. Notably, IAV-derived circRNAs biogenesis was formed with canonical GU/AG splicing mechanism in infected A549 cells. Splicing site mutant viruses displayed a significant decrease in the viral replication in vitro and pathogenicity in mice. Overall, our findings will not only uncover the novel RNA transcripts in IAVs infection cycle, but also provide a new perspective to investigate the crosstalk between host and IAVs from vcircRNAs.

overall_design: To identify and characterize influenza virus-encoded circRNAs，we conducted a circRNA sequencing (circRNA-seq) by applying BGISEQ short-read technology combined with RNase R treatment. PR8/H1N1 virus was used to infect A549 cells at a MOI 2 for 12 and 24 hours, then total RNAs were collected and the ribosomal RNA was removed. The RNA-seq was performed after RNase R treatment.

first: Wenliang

last: Pan

first: Yu


title: Therapeutic Effects and Mechanisms of Pomegranate in the Treatment of Hyperlipidemia

city: Hohhot

first: Hao

last: Wang

address: Inner Mongolia Medical University

institute: Inner Mongolia Medical University

summary: Pomegranate exhibits pronounced hypolipidemic properties, and the objective of this study was to delineate the precise mechanism by which pomegranate facilitates the treatment of hyperlipidemia.SD rats were fed with a high fat diet (HFD) to establish an hyperlipidemia model and intervened with pomegranate .Pomegranate significantly lowered body weight gain , liver weight and adipose tissue coefficient, and attenuated the hepatic steatosis.Serum concentrations of triglycerides (TG), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-C) were markedly reduced, concomitant with a significant elevation in high-density lipoprotein cholesterol (HDL-C) levels. Metabolomic analysis revealed that pomegranate treatment significantly modulated 37 metabolites linked to hyperlipidemia, with the primary pathways affected encompassing sphingolipid metabolism, pyrimidine metabolism, and arachidonic acid metabolism. Transcriptomic profiling identified 439 genes differentially expressed following pomegranate treatment, which were associated with various lipid-related and inflammatory pathways, predominantly including the lipid and atherosclerosis signaling pathway, NF-κB signaling pathway, and TNF signaling pathway.

overall_design: RNA-seq analysis of three groups of SD rats (normal control group, model group, and pomegranate-high group) after eight weeks of drug administration

first: Xin

last: Dong

first: Caimeng

last: Xu

first: Shaonan

last: Hu

first: Yuewu

first: Peifeng

last: Xue


title: Human cytomegalovirus infection coopts chromatin organization to modulate TEAD1 transcription factor activity [ChIP-seq]

first: Matthew

last: Weirauch

overall_design: We performed ChIP-seq for H3K27ac, CTCF, and TEAD1 in human foreskin fibroblasts (HS68) in two conditions. The two conditions are: 1) uninfected; and 2) 48 hours post infection of human cytomegalovirus (HCMV) with the TB40/E clinical isolate. Experiments were performed in two replicates for each condition.

first: Leah

last: Kottyan


title: Gene expression profile at single cell level of brain organoid at day56 of ctrl and WS

city: hangzhou

first: zhao

last: xingsen

address: kaixuan road268

institute: zhejiang university

summary: Brain organoid is consist of many different cells， We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of each neural cluster in the intestine.

overall_design: We used three sets of human D56 forebrain organoids derived from three sets of CTRL and Williams Syndrome (WS) iPSCs to get changes of WS

first: Xingsen

last: zhao

first: Xue kun

last: li


title: Differential Effects of Prenatal Alcohol Exposure in Mice on Brain Growth and Gene Expression Reveals Early Effects on Cell Cycle and Apoptosis and Delayed Effects on Metabolism in Affected Offspring

city: Rockville

first: Qiaoping

last: Yuan

state: MD

address: 5625 Fishers Lane, Suite 3S32

institute: NIAAA

summary: Fetal Alcohol Spectrum Disorder (FASD) encompasses the deleterious consequences of Prenatal Alcohol Exposure (PAE), including developmental delay, dysmorphologies, cognitive and behavioral issues. The dose and timing of alcohol exposure, maternal and environmental factors, and genetics all impact FASD outcomes, but differential susceptibility to PAE remains poorly understood. In this study, we examined the differential effects of PAE on mouse brain development by measuring brain weight in embryos (embryonic day 14, E14) and neonatal pups (postnatal day 0, P0) exposed alcohol during early development. We used transcriptomics to determine whether offspring differentially affected by PAE also differ in gene expression. PAE offspring were classified as normal, middle, and low-weight brains relative to controls. The normal-weight brains showed no differences in gene expression, suggesting these offspring were both phenotypically and transcriptionally unaffected by PAE. While both middle- and low-weight brains showed changes in gene expression, the middle-weight brains showed the most robust transcriptome differences. In affected E14 offspring, we saw an upregulation of cell cycle and apoptosis by PAE, whereas at P0, we saw a downregulation of metabolic processes. Overall, these findings highlight variability in response to PAE and demonstrate the molecular processes involved in offspring affected by alcohol.

overall_design: Pregnant C57BL6/J mice were treated with 2.9 g/kg of EtOH from embryonic day 7 (E7) to E13. Offspring were harvested at E14 or postnatal day 0 (P0). After taking body and brain weights, the prefrontal cortex was isolated for RNAsequencing using AmpliSeq.

first: Danielle

last: Sambo

first: Ethan

last: Kinstler

first: Yuhong

last: Lin

first: David

last: Goldman


title: Brain microvessel-specific transcriptome profiling after severe cerebral hypoperfusion in mice

first: Zengyu

last: Zhang

state: Shanghai

address: Dong'an Road

department: Neurology

institute: Fudan University

summary: Little is understood about the underlying cellular and molecular mechanisms related to brain microvessel damage and glial activation after severe cerebral hypoperfusion. Efforts to explore the relationship between neuropathological and gene expression changes support a role for identifying novel molecular pathways by transcriptomic mechanisms.

overall_design:
To investigate  brain microvessel-specific transcriptome profiling after severe cerebral hypoperfusion in mice
Brain microvessel-specific gene expression profiling analysis was performed using data obtained from RNA-seq of 3 biological replicates in sham and BCAS mice after hypoperfusion


title: Microglia drive diurnal variation in susceptibility to inflammatory blood-brain barrier breakdown

city: St Louis

first: Erik

last: Musiek

state: MO

address: 4370 Duncan Ave

institute: Washington University in St. Louis

summary: The blood brain barrier (BBB) is critical for maintaining brain homeostasis but is susceptible to inflammatory breakdown. Permeability of the BBB to polar molecules shows circadian variation due to rhythmic transporter expression, while basal permeability to polar molecules in non-rhythmic. Whether daily timing influences BBB permeability in response to inflammation is unknown. Here, we induced systemic inflammation through repeated lipopolysaccharide (LPS) injections either in the morning (ZT1) or evening (ZT13) under standard lighting conditions, then examined BBB permeability to a polar molecule.  We observed clear diurnal variation in inflammatory BBB permeability, with a striking increase in BBB breakdown specifically following evening LPS injection. Evening LPS led to persisting glia activation and inflammation in the brain that was not observed in the periphery. The exaggerated evening neuroinflammation and BBB disruption were suppressed by microglial depletion, were associated with enhanced expression of the Nos2 gene, and could be prevented in vivo by treatment with an iNOS inhibitor. Our data show that diurnal rhythms in microglial inflammatory responses to LPS drive daily variability in BBB breakdown, and reveals time-of-day as a key regulator of inflammatory BBB disruption.

overall_design: To account for the effect of time-of-day on neuroinflammatory responses, we conducted bulk RNAseq on cortex samples from mice treated with i.p. LPS (or PBS control) at ZT1 and ZT13

first: Jennifer

middle: H

last: Lawrence

middle: S


title: APE1 regulates the transcription of urea cycle genes through stabilizing DNA G-quadruplexes in lung adenocarcinoma [RNA-seq]

first: Yanhao

last: Yu

overall_design: Gene expression analysis of RNA-seq data for listed cells and tissues.

first: Chaochao

last: Cen

first: Zhenyu

last: Shao


title: APE1 regulates the transcription of urea cycle genes through stabilizing DNA G-quadruplexes in lung adenocarcinoma

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene expression profile level of mRNA of brain organoid at day56 of ctrl and WS

overall_design: we performed bulk RNA sequencing (RNA-seq) with both CTRL and Williams Syndrome (WS) forebrain organoids to reveals the altered gene expression relating to neuronal development


title: APE1 regulates the transcription of urea cycle genes through stabilizing DNA G-quadruplexes in lung adenocarcinoma [CUT&Tag]

overall_design: CUT&Tag for BG4 and H3K4me3 in WT and APE1 knockout A549 and H1944 cells. CUT&Tag for BG4 in ARG2MUT and CPS1MUT A549 cells.

first: Yiqin

last: Wang


title: E4F1 COORDINATES PYRUVATE METABOLISM AND THE ACTIVITY OF THE ELONGATOR COMPLEX TO ENSURE TRANSLATION FIDELITY DURING BRAIN DEVELOPMENT [Polysome-seq]

city: Montpellier

first: Pierre-François

last: Roux

address: 208 rue des Apothicaires

country: France

institute: Inserm

summary: Pyruvate metabolism defects lead to severe neuropathies such as the Leigh syndrome (LS) but the molecular mechanisms underlying neuronal cell death remain poorly understood. Here, we unravel a connection between pyruvate metabolism and the regulation of the epitranscriptome that is relevant to LS pathogenesis. We identified the transcription factor E4F1 as a key coordinator of AcetylCoenzyme A (AcCoA) production by the pyruvate dehydrogenase complex (PDC) and its utilization as an essential co-factor by the Elongator complex to acetylate tRNAs at the wobble position uridine 34 (U34). E4F1-mediated direct transcriptional regulation of Dlat and Elp3, two genes encoding key subunits of the PDC and of the Elongator complex, respectively, ensured proper translation fidelity and cell survival in the central nervous system (CNS) during mouse embryonic development. Furthermore, analysis of PDH-deficient cells highlighted a crosstalk linking the PDC to ELP3 expression that is perturbed in LS patients.

overall_design: Polysome profiling of mRNA isolated from 14.5 mouse brains.


title: Extracellular vesicles from lung adenocarcinoma cells induce activation of fibroblasts into different cancer-associated fibroblast subtypes

city: Vancouver

first: Cathie

last: Garnis

state: BC

address: 675 West 10th Avenue

department: Integrative Oncology

institute: British Columbia Cancer Research Centre

summary: Lung cancer, particularly lung adenocarcinoma (LUAD), is the leading cause of cancer deaths worldwide, largely due to metastasis. This study investigated the impact of extracellular vesicles (EVs) derived from LUAD cells on lung fibroblasts. EVs were isolated from LUAD cell lines via ultracentrifugation and characterized using Nanoparticle Tracking Analysis and western blot. Lung fibroblasts were treated with PBS, TGFβ or EVs, and their activation was assessed through protein (Western Blot) and RNA analysis (RNA seq and RT-qPCR). Results confirmed TGFβ induced activation and showed that LUAD EVs could also activate fibroblasts, increasing cancer-associated fibroblast (CAF) markers. While EV-induced CAF activation displayed unique features, the EV and TGFβ treatments also shared some differentially expressed genes. Mesenchymal genes POSTN and SPOCK1 were significantly upregulated in TGFβ and EV-treated fibroblasts. The secretion as protein of POSTN from the TGFβ and EV-induced CAFs was confirmed through ELISA. These findings suggest that LUAD EVs play a role in CAF activation through both shared and distinct pathways compared to canonical TGFβ activation, potentially identifying novel gene expression involved in CAF activation.

overall_design: RNA sequencing on human lung fibroblast (H6013) primary cells after exposure to PBS, EVs derived from H1437, EVs derived from H2073 or treated with TGFb.

first: Jessica Angelina

last: Trejo Vazquez

first: Rebecca

last: Towle


title: HDAC1 restricts fungal-induced Th17 polarization to restrain tissue damage

city: Vienna

first: Philipp

last: Penninger

address: Dr. Bohr-Gasse 9

country: Austria

institute: Medical University of Vienna

summary: Epigenetic mechanisms contribute to shaping many aspects of adaptive immunity, including T cell lineage functions in anti-infective surveillance. Histone deacetylases (HDAC) control T cell polarization but a role in fungal-specific T cell responses remains poorly understood. Here we show that CD4+ T cells are an integral part of the adaptive immune defense against invasive fungal infections. Temporally-resolved in vivo transcriptional profiles of splenic Th cells from infected mice harboring a CD4+-specific ablation of HDAC1 reveals its critical role in limiting T cell polarization towards Th17 at the expense of Th1-lineage commitment. Mechanistically, HDAC1 restricts expression of the cytokine receptors gp130 and TGFbRII on the T cell surface thus limiting Stat3 and Smad2/3 signaling in a fungal-specific manner. Controlled release of Th17-associated cytokines IL-17A and GM-CSF is vital to minimize epithelial apoptotic processes in renal tubular epithelial cells (RTECs) in vitro as well as during systemic infections in vivo. Consequently, protecting the host from excessive organ pathology, loss of kidney functionality and limiting fungal burdens, thus reducing sepsis-induced death during fungal infections. Collectively, this work shows that HDAC1 controls T cell lineage polarization, thus playing a critical role in the antifungal immune defense and infection outcome.

overall_design: Mouse line with conditional deletion of HDAC1 in CD4 expressing T cells (HDAC1-cKO) or WT littermate controls were systemically infected with 1*10^4 C. albicans yeast cells per 21,5g body weight and total CD4+ T cells were magnetically sorted using negative selection from spleens 0, 4, 7 and 10 days after infection for RNAseq.

first: Karl

last: Kuchler


title: Cycling Alpha Cells in Regenerative Drug-Treated Human Pancreatic Islets Serve As Key Beta Cell Progenitors

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Diabetes results from an inadequate number of insulin-producing human beta cells. There is currently no effective means to restore beta cell mass in millions of people with diabetes. Although the DYRK1A inhibitors, either alone or in combination with GLP1 receptor agonists (GLP1) or TGF superfamily inhibitors (LY), induce beta cell replication and increase beta cell mass, the precise mechanisms of action remain elusive. We performed single cell RNA sequencing on human pancreatic islets treated with a DYRK1A inhibitor, either alone, or with GLP1 or LY. We identify Cycling Alpha Cells as the most responsive cells to DYRK1A inhibition. Lineage trajectory analyses suggest that Cycling Alpha Cells may serve as precursor cells that transdifferentiate into beta cells. In addition to shedding light onto the mechanisms of action of DYRK1A inhibitors, our findings suggest that the proper target for regenerative drugs in human islets may be Cycling Alpha Cells.

overall_design:
Cadaveric human islets were subject to beta cell regenerative drug treatment for 96 hours which was followed by scRNA-seq experiments.
DMSO (control), Harmine (10μM), Harmine + GLP1RA (GLP), and Harmine + LY364947 (LY) treatments.

first: Esra

last: Karakose

first: Xuedi


title: Targeting the IL-5 pathway in severe asthma

city: UPPSALA

first: PERLA

middle: ABIGAIL

last: ALVARADO VAZQUEZ

address: Husargatan 3

country: Sweden

institute: UPPSALA UNIVERSITY

summary:
Therapies targeting interleukin-5 (IL-5) or its receptor (IL-5Rα) are used to treat patients with severe eosinophilic asthma. The therapeutic effect are considered being the suppression of eosinophil activation and elimination. However, the impact of these therapies on mast cells (MCs) and their progenitors has remained largely unexplored.
We investigate whether targeting the IL-5 pathway in severe asthma patients could reduce blood MC progenitors

overall_design: Gene expression was analyzed in isolated MC progenitors before and after of anti- IL-5Rα therapy.

first: Jenny

last: Hallgren

first: Erika

last: Mendez-Enriquez


title: Sex-Specific Astrocyte Regulation of Spinal Motor Circuits by Nkx6.1 [H3K27ac ChIP-seq]

city: Houston

first: Zhung-Fu

last: Lee

state: Texas

address: 2300 Old Spanish Trl, Apt1013

institute: Baylor College of Medicine

summary: To examined the epigenetic alteration in male Nkx6.1 control and cKO spinal cord astrocytes

overall_design: ChIP-seq was applied to analzye H3K27ac epigenetic regulation in adult male mouse Nkx6.1 control and cKO spinal cord astrocytes.

first: Navish

last: Bosquez Huerta

first: Christine

last: Song

first: Akdes

last: Serin-Harmanci

first: Benjamin

last: Deneen


title: Sex-Specific Astrocyte Regulation of Spinal Motor Circuits by Nkx6.1 [RNA-seq]

summary: To profile gene expression expresion in astrocytes between control and Nkx6.1 conditional knockout astrocytes in the mouse spinal cord.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FACS purified astrocytes from mouse spinal cord.


title: Sex-Specific Astrocyte Regulation of Spinal Motor Circuits by Nkx6.1 [Nkx6.1 ChIP-seq]

summary: To profile gene expression expresion in astrocytes between control and Nkx6.1 conditional knockout astrocytes in the mouse spinal cord. Furthermore, we sought to profile DNA binding patterns regulated by Nkx6.1 in spinal cord astrocyte.

overall_design: ChIP-seq was applied to analzye Nkx6.1 binding pattern in adult male and female mouse spinal cord astrocytes.


title: Validation of TLR2/4/9 triple knockout macrophage cell line using RNA sequencing

city: Ann Arbor

first: Michael

middle: J

last: McFadden

state: Michigan

address: 6751 Medical Science II, 1137 Catherine Street

department: Microbiology & Immunology

institute: University of Michigan

summary: In order to validate the identify of TLR2/4/9 triple knockout macrophages isolated from bone marrow from C57/BL6J mice (a gift from Dr. Tod Merkel), RNA sequencing was performed and read density was compared to wild-type macrophages (TLR WT) at the TLR2, TLR4, and TLR9 loci

overall_design: TLR2/4/9 KO macrophages and littermate control TLR WT macrophages were seeded in 6-well plates and RNA was extracted and sequenced to confirm knockout of TLR2/4/9

first: Teresa

last: O'Meara

first: Mary

last: O'Riordan


title: Stress-Induced Premature Senescence in High Five Cell Cultures: A Principal Factor in Cell-Density Effects

city: Shanghai

first: Rui

last: Min

address: meilong road 130,Shanghai,China

institute: East China University of Science and Technology

summary: The Baculovirus Expression Vector System (BEVS) is highly valued in vaccine development, protein engineering, and drug metabolism research due to its biosafety, operational convenience, rapid scalability, and capacity for self-assembling virus-like particles. However, increasing cell density at the time of inoculation severely compromises the production capacity of BEVS, resulting in the “cell density effect”. This study aimed to explore the mechanisms of the cell density effect through time-series analysis of transcriptomes and proteomes, with the goal of overcoming or alleviating the decline in productivity caused by increased cell density. The dynamic analysis of the omics of High Five cells under different CCI (cell density at infection) conditions showed that the impact of the “cell density effect” increased over time, particularly affecting genetic information processing, error repair, protein expression regulation, and material energy metabolism. Omics analysis of the growth stage of High Five cells showed that after 36 h of culture (cell density of about 1×106 cells/mL), the expression of ribosome-related proteins decreased, resulting in a rapid decrease in protein synthesis capacity, which was a key indicator of cell aging. Senescence verification experiments showed that cells began to show obvious early aging characteristics after 36 h, resulting in a decrease in the host cell’s ability to resist stress. Overexpression and siRNA inhibition studies showed that the ndufa12 gene was a potential regulatory target for restricting the “cell density effect”. Our results suggested that stress-induced premature senescence in High Five cell cultures, resulting in reduced energy metabolism and protein synthesis capabilities, was a critical factor contributing to cell density effects, and ultimately affecting virus production. In conclusion, this study provided new insights into managing virus production limitations due to cell density effects and offered innovative strategies to mitigate the adverse effects of cellular aging in biomanufacturing technologies.

overall_design: To explore the intrinsic mechanisms of the cell density effect, we performed a time-series analysis of transcriptomic and proteomics for the CCI1 and CCI3, including four time points during the cell culture stage (12 h, 36 h, 60 h, 84 h) and five time points during the virus infection stage (0 hpi, 6 hpi, 12 hpi, 24 hpi, 72 hpi).

first: Dahe

last: Zhang

first: Mingzhe

last: He

first: Jingyuan

last: Chen


title: Epigenetic and 3D genome reprogramming during the aging of human hippocampus

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: UCSD

summary: Age-related cognitive decline in humans is associated with altered physiology of the hippocampus, a region critical for memory consolidation and spatial navigation. While changes in gene expression have been observed in aging brain cells, our understanding of the regulatory mechanisms underlying these changes and their connection to chromatin structure remains limited. To unravel these complexities, we have applied a comprehensive multi-omics approach, integrating single-nucleus gene expression, chromatin accessibility, DNA methylation, and 3D chromatin architecture data obtained from the hippocampi of 40 neurotypical human donors spanning the adult lifespan. We observed a striking loss of astrocytes, oligodendrocyte precursor cells, and endothelial cells during aging. In particular, we observed a substantial decline in the subset of astrocytes that play a role in maintaining and regulating synaptic transmission. In addition, microglia undergo a dramatic switch from a predominantly homeostatic state to an epigenetically primed inflammatory state that coincides with reprogramming of their DNA methylomes and activation of endogenous retrotransposons. In the aged cells, we detected erosion of the 3D genome architecture, where local chromatin domains are diminished and trans-chromosomal interactions are strengthened. Importantly, age-related changes in chromatin folding have high correspondence with the transcriptome and epigenome in multiple cell types. Our data identifies age-associated changes in cell types/states and gene regulatory features that provide insight into the loss of synapses and cognitive decline that occurs in the human brain during aging.

overall_design: Analysis of single nucleus multiome ATAC-seq + RNA-seq (10x Genomics) of hippocampus from human

first: Nathan

middle: R

last: Zemke

first: Seoyeon


title: Microbe-enhanced high light stress tolerance of Arabidopsis thaliana photosynthesis is coordinated through Iron-dependent redox metabolism

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

summary: High light stress in subtropical and tropical regions strongly limits agricultural production due to photo-oxidative damage, decreased growth and yield. Here, we investigated whether beneficial microbes can protect plants under high light stress. We show that Enterobacter sp. SA187 (SA187) assists Arabidopsis in maintaining growth under high light stress, reducing the accumulation of reactive oxygen species (ROS) and maintaining photosynthesis. Under high light stress, SA187 induces dynamic transcriptional changes related to a fortified iron metabolism and redox system in Arabidopsis. A genetic analysis shows that SA187-induced plant high light stress tolerance is mediated by ethylene signaling via the transcription factor EIN3 to enhance iron metabolism. In summary, we show that Arabidopsis interaction with SA187 results in sustained photosynthesis under high light stress suggesting that beneficial microbes could be effective and cheap means for enhancing high light stress tolerance in crops.

overall_design:
Arabidopsis thaliana plants were grown at 22⁰C under 16 h light and 8 h dark period
Two different light stress regimes (normal light 130 μmol m-2 s-1 and high light 1050 μmol m-2 s-1 ) were implemented on SA187 colonized plants
Total RNA was extracted using Nucleospin RNA plant kit (Macherey-Nagel), we further followed with DNaseI treatment to remove gemomic DNA as per manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Ribo-zero Illumina protocol
RNA-seq was carried out on three independent biological replicates (except two samples)

first: Naganand

last: Rayapuram

first: Anam

last: Fatima

first: Heribert

last: Hirt


title: Differential Activity of MAPK signalling Defines Fibroblast Subtypes in Pancreatic Cancer

city: Verona

first: Davide

last: Pasini

state: VR

address: Piazzale Ludovico Antonio Scuro 10

institute: University of Verona


title: Transcriptional Responses to TREM2 Agonist Antibody Treatment in Cynomologus Monkey Brain - Study 2

city: South San Francisco

first: Brad

middle: A

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary: Monkeys were treated with a single i.v 200 mg/kg dose of hPara.09 or Anti-gD (Isotype control). Brain was harvested on days 4 and 28, and RNA was extracted from the cerebral cortex. The following groups are included: Group 1: Day 4 gD 200mg/kg n=6; Group 2: Day 4 hPara.09 200 mg/kg n=6; Group 3: Day 28 gD 200mg/kg n= 6; Group 4: Day 28 hPara.09 200 mg/kg n=6 (24 animals total). To assess expression heterogeneity between brain samples, 2 different frontal cortex punches were taken from each monkey, resulting in 48 total samples.

first: Gloriia

last: Novikova

first: Chang

last: Cho

first: Anne

last: Biever

first: Alicia

last: Nugent

first: Yuxin

last: Liang


title: Roles of SNORD115 and SNORD116 ncRNA clusters during neuronal differentiation

city: Edinburgh

first: Aleksandra

last: Helwak

address: Max Born Crescent

department: Wellcome Centre for Cell Biology

country: United Kingdom

institute: The University of Edinburgh

summary: In the snoRNA host gene SNHG14, 29 consecutive introns each generate SNORD116, and 48 tandem introns encode SNORD115. Loss of SNORD116 expression, but not of SNORD115, is linked to the neurodevelopmental disease Prader-Willi syndrome. SNORD116 and SNORD115 resemble box C/D small nucleolar RNAs (snoRNAs) but lack known targets. Both were strongly accumulated during neuronal differentiation, but with distinct mechanisms: Increased host-gene expression for SNORD115 and apparent stabilization for SNORD116. For functional characterization we created cell lines specifically lacking the expressed, paternally inherited, SNORD115 or SNORD116 cluster. Analyses during neuronal development indicated changes in RNA stability and protein synthesis. These data suggested that the loss of SNORD116 enhanced some aspects of developmental timing of neuronal cells. Depleted mRNAs included MAGEL2, causal in the PWS-like disorder Schaaf-Yang syndrome. Comparison of SNORD115 and SNORD116 mutants identified small numbers of altered mRNAs and ncRNAs. These were enriched for functions potentially linked to PWS phenotypes.

overall_design: To inversigate the role of non-coding RNAs from SNORD116 and SNORD115 clusters, we created cell lines with heterozygous deletions in paternal chromosome in LUHMES, neuronal progenitor cells and performed RNAseq analysis during the differentiation to dopaminergic neurons at day 0, 6, 10 and 15.

first: David

last: Tollervey


title: E9.5 TRAF7-*/-* brain transcriptome

city: Oklahoma City

first: Anthony

middle: C

last: Johnson

state: OK

address: 1122 NE 13th St, O'Donoghue Research Building 332

department: Neurosurgey

institute: University of Oklahoma Health Sciences

summary: Here, we describe a spontaneous mouse mutant with a deletion in a predicted gene 2310061I04Rik (Rik) of unknown function located on chromosome 17. A 59 base pair long deletion occurred in the first intron of the Rik gene and disrupted its expression. Riknull mice were born healthy and appeared anatomically normal up to two weeks of age. After that, these mice showed inhibited growth, ataxic gait, and died shortly after postnatal day 24 (P24). Transcriptome analysis at P14 and P23 revealed significantly reduced expression of mitochondrial genes in Riknull brains compared to wild type controls including mt-Nd4, mt-Cytb, mt-Nd2, mt-Co1, mt-Atp6, and others. Similarly, genes specific for myelinating oligodendrocytes also showed reduced expression in P23 Riknull brains compared to controls. Histological examination of anterior thalamic nuclei demonstrated decreased myelination of anteroventral nuclei but not of anterodorsal nuclei in P23 Riknull mice. Myelination of the anterior commissure was also impaired and displayed extensive vacuolation. Consistently with these findings, immunohistochemistry showed reduced expression of Opalin, a glycoprotein expressed in differentiated oligodendrocytes. Taken together, these results suggest that RIK is important for oligodendrocyte maturation and myelination in the developing brain.

overall_design: Brain collected at P14 and placed in RNAlater. Half of the brain (sagittal cut down midline) sent to Novogene for processing.

first: Erdyni

middle: N

last: Tsitsikov

first: Khanh

middle: P

last: Phan

first: Yufeng

last: Liu

first: Alla

middle: V

last: Tsytsykova

first: Rosalia

last: Paterno

middle: M

last: Sherry

first: Ian

middle: F

last: Dunn


title: Distinct molecular profiles underpin mild to moderate equine asthma cytological profiles

city: Guilford

first: Anna Eleonora

last: Karagianni

address: Daphne Jackson Road

institute: Surrey University

summary: This project used a state-of-the-art, multi-omics approach to improve our understanding of the aetiopathogenesis of a highly prevalent, performance-limiting disorder of racehorses; mild to moderate equine asthma (MMEA). This advanced knowledge is a prerequisite to improving prophylactic, management and therapeutic options for this condition. Although a number of risk factors for MMEA have been identified, incomplete understanding of the precise aetiopathogenesis of this syndrome means that options for intervention are currently limited.  This study aimed to apply a multi-omic approach, reveal key inflammatory pathways involved in inflammatory cell recruitment to the lower airways and highlight pathways specific to different MMEA inflammatory cell profiles (MMEA endotypes). Thus, we compared BALF cell gene and protein expression data from horses with normal bronchoalveolar lavage fluid (BALF) cytology (n = 8) with those isolated from horses with neutrophilic (n = 4), mastocytic (n = 8), mixed neutrophilic/mastocytic (n=4) and mixed eosinophilic/mastocytic (n=3) inflammation. Analyses on transcriptomic and proteomic data derived from BALF cells from horses with neutrophilic cytology showed enrichment in classical inflammatory pathways, while horses with mastocytic cytology showed enrichment in pathways involved in hypersensitivity reactions related to non-classical inflammation that could mimic a Th2 immune response. The mixed eosinophilic/mastocytic group also presented with a non-classical inflammatory profile while, the mixed neutrophilic/mastocytic group revealed profiles consistent with both neutrophilic inflammation and hypersensitivity. Our adopted multi-omics approach (both gene and protein expression) has enabled a more holistic assessment of the immunological status of the lower airways associated with the different cytological profiles of equine asthma.

overall_design: Bronchoalveolar lavage fluid cell gene and protein expression data from horses with normal bronchoalveolar lavage fluid cytology (n = 8) with those isolated from horses with neutrophilic (n = 4), mastocytic (n = 8), mixed neutrophilic/mastocytic (n=4) and mixed eosinophilic/mastocytic (n=3) inflammation was analysed using RNAseq and proteomic analysis, respectively.

first: Anna

first: Eric

last: Richard

first: Erιka

last: Hue

last: Courouce-Malblanc

first: Scott

last: Pirie


title: RNA sequencing reveals that Taar5 gene knockout in mice up-regulate the striatal expression of genes involved in neuronal connectivity and synaptogenesis

city: Saint-Petersburg

first: Nataliia

middle: Victorovna

last: Katolikova

address: Universitetskaya emb. 7-9-11

department: Institute of Translational Biomedicine

country: Russia

institute: Saint-Petersburg State University

summary: Our study revealed the slight but significant shifts in the striatal expression profile related to TAAR5 depletion. We have found, that TAAR5-KO mice are characterised by activation of transcription and post-transcriptional mRNA modification processes in striatum and suppression of the expression of genes involved in cell differentiation, especially in gliogenesis, and Ras signal transduction.

overall_design: We perform RNA sequencing analysis of striatum of TAAR5-KO and WT mice (n = 6 for each group)

first: Anastasia

last: Vaganova

first: Zoya

last: Fesenko

first: Evgeniya

last: Efimova

first: Sergei

last: Chekrygin

first: Daria

middle: D

last: Shafranskaya

first: Andrey

last: Prjibelski

first: Raul

last: Gainetdinov


title: Inorganic Pyrophosphate influence Stem Cells from Human Exfoliated Deciduous Teeth

city: Bangkok

first: Ravipha

last: Suwittayarak

address: Wang mai

department: Dentistry

country: Thailand

institute: Chulalongkorn University

summary: To explore the cellular response of stem cell derived from human exfoliated deciduous teeth (SHED) in response to inorganic pyrophosphate (PPi). SHED was extracted from human primary exfoliated teeth. The cellular responses including cell proliferation, apoptosis, migration, transcriptomic expression was investigated afterward PPi treatment at the distinct concentration. Additionally, Alizarin red, oil red O, and alcian blue staining were performed to evaluate the multipotency. Inorganic pyrophosphate (PPi) had no although effect on cell cycle, yet enhanced migratory cell, compared to control. Additionally, PPi abolished the gene expression of osteogenic genes and also calcium deposition. Interestingly, the inhibition of mineralization by PPi was not reversed though Pi3K and MAPK family, including ERK, P38, and JNK signalling pathway. On the contrary, PPi induced the ALPL and COL1A1 gene expression and reduced RANKL mRNA and protein in the condition medium, resulting in a decrease of osteoclast formation. The transcriptomic profiles illustrated PPi modulated interferon ⍺/𝛾, TGF-β1, NOTCH signalling pathway, and metabolism of lipid. In summary, our study revealed that PPi enhanced migratory ability, however inhibited osteo/odontogenic, adipogenic and chondrogenic differentiation. This study implicated that PPi can modulate cellular responses of SHED.

overall_design: SHED cell, isolated from exfoliated deciduous teeth, was treated with inorganic pyrophosphate (PPi) to investigate cell response and regenrative potential of SHED

first: Nunthawan

last: Nowwarote

first: Chatvadee

last: Kornsuthisopon

first: Waleerat

last: Sukarawan

first: Brian

middle: L

last: Foster

first: Hiroshi

last: Egusa

first: Thanaphum

last: Osathanon


first: ln

last: wang

address: Room 309, C building No. 154, Jianchuan Road 953 Nong, Minhang District

institute: shanghai

summary: Increasing evidence has revealed a close relationship between circular RNAs (circRNAs) and the regulatory process of cell aging. Exploring the role and mechanism of circRNAs in cellular senescence may help to identify new anti-aging therapeutic targets. In the present study, we investigated the role and regulatory mechanism of hsa_circ_012707 in renal aging.High-throughput sequencing was performed to detect the differential expression of circRNAs in kidney tissues of the old and young groups. qRT-PCR confirmed that the expression of hsa_circ_0127071 in kidney tissue of the old group was significantly higher than that of the young group. SA-β-Gal, Masson Assay is used to evaluate the role of hsa_circ_0127071 in the aging process of kidney tissue.Using RIP, RNA pull down, and WB to study the interaction between hsa_circ_0127071 and aging related pathway proteins.In this study, we found that the expression of hsa_circ_0127071 in kidney tissue of the old group was significantly higher than that of the young group. The activity of JAK2/STAT5 signaling pathway was decreased after silencing EIF4A3, which could delay the aging process. On the basis of silencing EIF4A3 expression, the JAK2/STAT5 signaling pathway was activated by EPO processing, and the senescence of HGMCs increased. After treatment with LOS, the activity of JAK2/STAT5 pathway was decreased and the aging process of HGMCs was delayed. Our findings showed that hsa_circ_0127071 promoted renal aging, and confirmed the regulatory role of EIF4A3/hsa_circ_0127071/JAK2/STAT5 in the regulation of renal aging, providing a new therapeutic target for drug design and early diagnosis.

overall_design: In conclusion, this study intends to use human kidney tissues and human mesangial cells for validation experiments through transcriptional gene assay, KEGG pathway and other prediction, aiming to explore that EIF4A3-induced hsa_circ_0127071 promotes human glomerular mesangial cells senescence via JAK2/STAT5 signaling pathway. in order to provide a new therapeutic target for the prevention and treatment of renal aging.

first: Ying

last: Chen

first: Lining

last: Wang


title: 14 days old 2310061I04Rik-null brain transcriptome

first: Anthony

last: Johnson

first: Erdyni

last: Tsitsikov

first: Khanh

last: Phan

first: Yufeng

last: Liu

first: Alla

last: Tsytsykova

first: Rosalia

last: Paterno

first: David

last: Sherry

first: Ian

last: Dunn


title: Failed reprogramming of transformed cells due to induction of apoptosis and senescence impairs tumor progression in lung cancer

city: Cambridge

first: Jianfeng

last: Ge

state: Cambridgeshire

address: 37, ST THOMAS'S SQUARE

institute: University of Cambridge

summary: Cell reprogramming to pluripotency applied to the study of cancer has identified transformation and pluripotency as two independent and incompatible cell fates. A detailed knowledge of the relationship between transformation and reprogramming could lead to the identification of new vulnerabilities and therapeutic targets in cancer. Here, we explore this interplay and find that OSKM expression limits tumor cell growth by inducing apoptosis and senescence. We identify Oct4 and Klf4 as the main individual reprogramming factors responsible for this effect. Mechanistically, the induction of cell cycle inhibitor p21 downstream of the reprogramming factors acts as mediator of cell death and senescence. Using a variety of in vivo systems, including allografts, orthotopic transplantation and KRAS-driven lung cancer mouse models, we demonstrate that OSKM expression impairs tumor growth and reduces tumor burden

overall_design: mRNA profilling in OSKM expressing cells

first: Pablo

last: Pedrosa

first: Zhenguang

last: Zhang

first: Manuel

last: Collado

first: Daniel

last: Muñoz-Espín


title: Transcriptional Responses to TREM2 Agonist Antibody Treatment in Cynomologus Monkey Brain [single nuclei RNA sequencing]

first: Kevin

last: Huang

state: California

institute: Genentech

summary: In order to search for pharmacodynamic biomarkers of a TREM2 agonist antibody (Para09) in primates we performed single nuclei RNA-Seq on cortical tissue from cynomolgus monkeys after single IV injected doses. Changes in proliferation genes such as MKI67 were observed, as well as genes associated with glial activation, such as CHI3L1. This experiment demonstrates that our antibody induces transcriptional changes in the brain after peripheral administration.

overall_design: Monkeys were treated with anti-hTREM2 agonist Para09 or an isotype control via intrathecal injection and brain samples were collected 2 days later. Single-nuclei was extracted from frontal cortex

first: Alicia

last: Nugent

first: Anne

last: Biever

first: Brad

last: Friedman

first: Michelle

last: Dourado


title: Transcriptional Responses to TREM2 Agonist Antibody Treatment in Cynomologus Monkey Brain

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

overall_design: Refer to individual Series


title: 23 days old 2310061I04Rik-null brain transcriptome

first: Anthony

last: Johnson

overall_design: Brain collected at P23 and placed in RNAlater. Half of the brain (sagittal cut down midline) sent to Novogene for processing.

first: Erdyni

last: Tsitsikov


title: Dysregulation of microbiota gut-retina axis in neovascular age-related macular degeneration: beneficial ocular effects of a lutein, zeaxanthin and saffron based prebiotic supplementation

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

summary: This work investigates the effects of a prebiotic mix containing lutein, zeaxanthin, and saffron, recognized for their anti-inflammatory properties, on ophthalmological and microbial parameters in neovascular AMD (nAMD) patients.

overall_design: Total DNA was extracted from the stool of healthy old subjects and ADM (Age-related macular degeneration) patients. Moreover, the total DNA was extracted from stool samples of the same ADM patients after the completion of the prebiotic treatment. The total DNA was amplified to collect amplicons of variable V3–V4 regions (primers 341F and 805R) of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

first: Amedeo

last: Amedei

first: Leandro

last: Di Gloria

first: Simone

last: Baldi


title: Modulation of tsRNA and mRNA expression by mesenchymal stem cells in COPD model mice

city: Changsha

first: Lihua

last: Xie

address: No.138, Tongzipo Road

institute: The Third Xiangya Hospital of Central South University

summary: Chronic obstructive pulmonary disease (COPD) is characterized by lung parenchymal destruction and small airway remodeling, involving processes like inflammation, cell apoptosis, epithelial-mesenchymal transition (EMT), and collagen deposition. There are currently no targeted drugs for airway remodeling. Bone marrow mesenchymal stem cells (BMSCs) show promise in COPD treatment, yet their impact on airway remodeling and underlying mechanisms remain elusive. Transfer RNA-derived small RNAs (tsRNAs) are non-coding RNAs implicated in disease regulation, but their role in COPD and their modulation by BMSCs remain unexplored. Our study assessed BMSC effects on airway remodeling in a COPD mouse model and constructed tsRNA and mRNA expression profiles. Based on the differentially expressed tsRNA-mRNA target pairs identified by tsRNA and mRNA sequencing, we constructed a tsRNA regulatory network linked to COPD airway remoding. The modulation of tsRNA by MSCs may represent one of the pathways through which they ameliorate COPD airway remodeling. Our research will enrich the understanding of BMSC therapy for COPD and provide greater insight into the molecular mechanisms underlying the progression and treatment of airway remodeling.

overall_design: To investigate the effects of MSCs on the expression of tsRNA and mRNA in COPD, the expression patterns of tsRNA and mRNA were examined in lung tissues from control group, COPD model group, and model mice treated with MSCs.

first: Ting

last: Jin

first: Guoan

last: Li

first: Xianyang

last: Liu

first: Shenghua

last: Sun


title: TMED10 inhibition suppresses cell-surface PD-1 expression and overcomes T cell dysfunction

city: Amsterdam

first: Daniel

last: Peeper

state: Outside the US or Canada

address: Plesmalaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

summary: PD-1 immune checkpoint blockade (ICB) is revolutionizing cancer therapy, but little is known about the mechanisms governing its expression. In a whole-genome, dual- marker FACS-based CRISPR-Cas9 screen in primary murine CD8 T cells, we found that inactivation of the EMP24/GP25L/p24 protein family, most prominently TMED10, reduced PD-1 cell-surface stability, thereby augmenting T cell activity. Treatment with TMED inhibitor AGN192403 led to lysosomal degradation of the TMED-PD-1 complex and reduced PD-1 expression in intratumoral CD8 T cells in mice, thus reversing T cell dysfunction. Clinically corroborating these findings, single-cell RNA analyses  revealed a positive correlation between TMED expression in tumor-infiltrating CD8 T cells (TIL), and both a T cell dysfunction signature and lack of ICB response. Similarly, patients receiving a TIL product with high TMED expression had a shorter overall survival. Our results uncover a novel mechanism of PD-1 regulation, and provide a possible opportunity for PD-1 small molecule inhibition

overall_design: C57BL/6 Rag2-/- mice were inoculated with B16F10-OVA cells. On day 4, ACT was performed, administering CD8+ OT-I sgCtrl or sgTmed10. On day11, spleen and tumor were isolated and digested. Tumor samples were analyzed using flow cytometry and RNA sequencing. Moreover, CD8+ bead isolation was performed to enrich for intratumoral CD8+ T cell population ahead of RNA sequencing. Overall, RNAseq data was derived from T cells before inoculation, from treated tumors and ultimately, from CD8+ enriched intratumoral fractions.

first: David

last: Vredevoogd


title: TET-Mediated DNA Demethylation is Required for Inducible Vasculogenic Reprogramming of the Skin

city: Pittsburgh

first: CHANDAN K

last: SEN

state: PA

address: 221 Republic Street

institute: University of Pittsburgh

summary: Tissue nanotransfection (TNT) based topical electrophoretic delivery of Etv2, Foxc2, and Fli1 (EFF) plasmids achieve induced vasculogenesis (iV) in the skin by inducing vasculogenic fibroblasts (VF). scRNA-seq analysis revealed TET-dependent gain of VF in dermal fibroblasts in response to EFF. Emergence of VF required TET-dependent demethylation of fibroblast-borne endothelial genes in vivo. Fibroblast-specific inducible overexpression of EFF in TARGATT mice caused induction of TET1/2/3, followed by transition of fibroblast to VF in vivo. TET induction was associated with elevated 5-hmC abundance in VF. TET-dependent demethylation of fibroblast-borne endothelial genes caused the formation of VF and rescued perfusion in diabetic ischemic limbs. TNTEFF rescued perfusion and closure of diabetic wounds. TET enzymes, suppressed in diabetics, play a pivotal role in causing endogenous EFF-induced VF state change of skin fibroblasts. TNT delivery of EFF transcription factors upregulate TET expression. This work is the first to recognize the significance of TET in the inducible formation of blood vessels to rescue diabetic ischemic tissue.

overall_design: Primary Dermal Fibroblast; Normal, Human, Adult (ATCC ® PCS-201-012) were used.

first: Chandan

middle: K

last: Sen

first: Kanhaiya

last: Singh

first: Ahmed

last: Safwat Abouhashem

first: Mervin

last: Yoder

first: Sujit

last: Mohanty

first: Rajneesh

last: Srivastava

first: Sashwati

last: Roy


title: Metabolic Disruption in Zebrafish Larvae Due to Exposure to the Pesticides Tefluthrin or Acetochlor

city: Bloomington

first: Jason

last: Tennessen

state: IN

address: 1001 E. Third St

department: Department of Biology

institute: Indiana University

summary: This study investigates the pesticides' (Tefluthrin or Acetochlor) effects on gene expression

overall_design: Hatched zebrafish larvae were treated with two different concentrations of acetochlor (0.78 µM or 7.8 µM) or tefluthrin (60 nM or 2.3 µM) from 48 hpf until 72 hpf.

first: Fahmi

last: Mesmar

first: Maram

last: Muhsen

last: Tourigny

first: Maria

last: Bondesson


title: Dissecting the novel molecular interactions of solute carrier family 4 member 4 (SLC4A4) for prostate cancer (PCa) progression

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: To investigate the SLC4A4 as a potential therapeutic target for prostate cancer patients

overall_design: We performed shLSLC4A4 in Prostate Cancer cells and performed gene expression profiling analysis using data obtained from RNA-seq of PCa cells

first: Asif

last: Rashid

first: Hiu

last: Fung

first: Alexander

last: Tang


title: A 50-gene high-risk profile predictive of COVID-19 and Idiopathic Pulmonary Fibrosis mortality originates from a molecular imbalance in monocyte and T-cell subsets that reverses in survivors with post-COVID-19 Interstitial Lung Disease

city: Tampa

first: Theodoros

last: Karampitsakos

address: 560 Channelside D

institute: University of South Florida

summary: Background: We previously identified a 50-gene signature that distinguished two groups of patients with increased risk of COVID-19 and IPF mortality. In this study we aimed to validate our previous findings and to study the source and trajectory of circulating immune cells expressing these 50 genes in patients with COVID19, post-COVID-19 Interstitial Lung Disease (ILD) and Idiopathic Pulmonary Fibrosis (IPF). Methods: Whole blood and Peripheral Blood Mononuclear cells (PBMC) were obtained from 216 hospitalized patients with COVID-19, five patients with post-COVID-19-ILD, six patients with IPF and four controls from the University of South Florida (USF)/Tampa General Hospital (TGH). We measured the expression of the 50-gene signature using the nCounter analysis system (Nanostring), and the levels of Interleukin 6 (IL6), interferon γ-induced protein (IP10), Secreted Phosphoprotein 1 (SPP1) and transforming growth factor beta (TGF-β) in these patients by Luminex and Elisa tests. A 7-gene PCR assay was generated to validate the identification of COVID-19 endotypes. For single-cell RNA sequencing (scRNA-seq) we used Chromium Single Cell Controller (10X Genomics). For analysis of gene expression, we used the Scoring Algorithm of Molecular Subphenotypes (SAMS), Cell Ranger and Seurat packages. For statistical analysis, we used Kaplan-Meier survival curves, CoxPH models, Two-way ANOVA, T-test, Fisher’s exact and the Wilcoxon rank test.  Results: We identified the presence of three genomic risk profiles based on the 50-gene signature, and a subset of seven genes, associated with low, intermediate, or high-risk of mortality in COVID-19. These risk groups had significant differences in IL6, IP10, SPP1 and TGFβ-1 levels. By applying scRNA-seq, we discovered a novel subtype of Monocytic-Myeloid-Derived Suppressive cells (M-MDSCs) expressing CD14+HLA DRlowCD163+ and high levels of the 7-gene signature. We denominated these cells as 7Gene-M-MDSC. These cells were not observed in survivors with post-COVID-19-ILD. The 43-gene signature was mostly expressed in naive CD4 T and memory CD4 T cells, Tregs, memory CD8 T GZMB+, memory CD8 T GZMK+ and naive CD8 T cells. While increased expression of genes in the 43 gene signature was seen in T cell subsets from survivors with post-COVID-19 ILD, the expression of these genes remained low in IPF. Conclusion: A 50-gene, high-risk genomic profile in peripheral blood of COVID-19 can accurately predict COVID-19 mortality. This profile is characterized by a simultaneous increase in expression of seven genes originating from 7Gene-M-MDSCs and decreased expression of 43 genes originating primarily in T cell subsets.  While increased expression of these 43 genes can be seen in survivors with post-COVID-19 ILD, their expression remains low in IPF.

overall_design: For scRNA-seq, we used cryopreserved PBMC from healthy controls and patients with COVID-19 (from Cohort 1), post-COVID-19 ILD and IPF as described above in the human specimen and design section. A single-cell suspension from PBMC from each patient was quantified and analyzed for viability using the Cell counter 3 (Countess 3, Invitrogen) and then loaded onto the 10X Genomics Chromium Single Cell Controller for isolation of single cells (10X Genomics).

first: Jose

last: Herazo-Maya

first: Bochra

last: Tourki

first: Minxue

last: Jia


title: Effects of Nogo-A deletion on the trigeminal ganglion

status: Public on Dec 04 2024

city: Zürich

first: Laurence

last: Pirenne

address: Weststrasse 133

country: Switzerland

institute: University of Zürich

summary: Nogo-A is a major regulator of neural development and regeneration in the central nervous system, but its role in tooth innervation remains largely unknown. Neurons of the trigeminal ganglion innervate the teeth. We showed that Nogo-A is expressed in the trigeminal ganglion and tooth-related nerve fibres. Nogo-A deletion in mice leads to a less complex neuronal network when compared to wild-type animals. Bulk RNA sequencing on the trigeminal ganglia of Nogo-A KO and wild-type mice revealed gene expression changes associated with alterations in neurotrophin signalling and neuronal synaptic formation during the development and maturation of the trigeminal neurons.

overall_design: The trigeminal ganglia were isolated from wild-type and Nogo-A KO mice at embryonic day 14 (E14) and postnatal day 25 (P25). Total RNA was extracted and sequenced. n = 4 wild-type and n = 4 Nogo-A KO animals were analysed for each stage; each sample contains one trigeminal ganglion.

first: Anamaria

last: Balic

first: Thimios

last: Mitsiadis


title: Monitoring ORF10's Impact on Host Transcriptome Using Doxycycline-Inducible A549 and 293T Cell Lines.

city: Philadelphia

first: Jeffrey

middle: Allen

last: Haltom

address: 3501 Civic Center Blvd

department: Center for Mitochondrial and Epigenomic Medicine

institute: Children's Hospital of Philadelphia

summary: To monitor ORF10s effects on the host transcriptome, doxycycline-inducible cell lines were create in A549 and 293T(HEK) cells expressing ORF10. Because doxycycline itself can alter gene expression, we used doxycycline-inducible cell lines driving GFP as control. Empty vectors were used as well.

overall_design: ORF10 was cloned into pLVX-EF1alpha-IRES-Purovector, swapped into a TRE construct, and used to generate lentivirus. A549 and 293T cells were grown for four days and then transduced and selected with puromycin to generate doxycycline inducible cell lines. Clones were generated and allowed to grow out and samples were then tested for baseline ORF10 expression and then ORF10 induction with doxycycline. Cell lines that had no to minimal ORF10 expression at baseline and then had robust induction were used for downstream assays. GFP and empty vector was swapped with ORF10 as a conrol. ORF10 without doxycycline is included as well.


title: Pre-vaccination transcriptomic profiles of immune responders to the MUC1 peptide vaccine for colon cancer prevention

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: Self-antigens abnormally expressed on tumors, such as MUC1, have been targeted by therapeutic cancer vaccines. We recently assessed in two clinical trials in a preventative setting whether immunity induced with a MUC1 peptide vaccine could reduce high colon cancer risk in individuals with a history of premalignant colon adenomas. In both trials, there were immune responders and non-responders to the vaccine. Here we used PBMC pre-vaccination and 2 weeks after the first vaccine of responders and non-responders selected from both trials to identify early biomarkers of immune response involved in longterm memory generation and prevention of adenoma recurrence. We performed flow cytometry, phosflow, and differential gene expression analyses on PBMCs collected from MUC1 vaccine responders and non-responders pre-vaccination and two weeks after the first of three vaccine doses. MUC1 vaccine responders had higher frequencies of CD4 cells pre-vaccination, increased expression of CD40L on CD8 and CD4 T-cells, and a greater increase in ICOS expression on CD8 T-cells. Differential gene expression analysis revealed that iCOSL, PI3K AKT MTOR, and B-cell signaling pathways are activated early in response to the MUC1 vaccine. We identified six specific transcripts involved in elevated antigen presentation, B-cell activation, and NF-kB1 activation that were directly linked to finding antibody response at week 12. Finally, a model using these transcripts was able to predict non-responders with accuracy. These findings suggest that individuals who can be predicted to respond to the MUC1 vaccine, and potentially other vaccines, have greater readiness in all immune compartments to present and respond to antigens. Predictive biomarkers of MUC1 vaccine response may lead to more effective vaccines tailored to individuals with high risk for cancer but with varying immune fitness.

overall_design: In this study, we analyzed PBMC samples collected from both trials at baseline (pre-vaccination) and 2 weeks post-first of 3 vaccines (week 0, week 2 and week 10) from vaccine responders and non-responders to identify comprehensive gene and pathway biomarkers related to vaccine response.

first: Cheryl

first: Vineet

last: Raghu

first: Brian

last: Richardson

first: Leah

last: Zagore

first: Banumathi

last: Tamilselvan

first: Jackelyn

last: Golden

first: Michael

last: Cartwright

first: Robert

middle: E

last: Schoen

first: Olivera

last: Finn

first: Panayiotis

last: Benos


title: Visceral adipocyte-derived extracellular vesicle miR-27a-5p elicits glucose intolerance by inhibiting pancreatic b-cell insulin secretion

city: Nanjing

first: Chen

last: Liu

address: 101 Longmian Avenue

institute: Nanjing Medical University

summary: Pancreatic β-cell dysfunction caused by obesity can be associated with alterations in the levels of microRNAs (miRNAs). However, the role of miRNAs in such processes remains elusive. Here, we show that pancreatic islet miR-27a-5p, which is markedly increased in obese mice and impairs insulin secretion, is mainly delivered by visceral adipocyte-derived extracellular vesicles (EVs). Depleting miR-27a-5p significantly improves insulin secretion and glucose intolerance in db/db mice. Supporting the function of EVs’ miR-27a-5p as a key pathogenic factor, intravenous injection of miR-27a-5p-containing EVs shows their distribution in mouse pancreatic islets. Tracing the injected AAV-miR-27a-5p (AAV-miR-27a) or AAV-FABP4-miR-27a-5p (AAV-FABP4-miR-27a) in visceral fat results in upregulating miR-27a-5p in EVs and serum, and elicits mouse pancreatic β-cell dysfunction. Mechanistically, miR-27a-5p directly targets L-type Ca2+ channel subtype CaV1.2 (Cacna1c) and reduces insulin secretion in β-cells. Overexpressing mouse CaV1.2 largely abolishes the insulin secretion injury induced by miR-27a-5p. These findings reveal a causative role of EVs’ miR-27a-5p in visceral adipocyte-mediated pancreatic β-cell dysfunction in obesity-associated type 2 diabetes mellitus.

overall_design: Total RNA from islets of NCD and HFD mice was isolated using the RNeasy mini kit (Qiagen), following the protocol for total RNA isolation. RNA integrity and concentration were assessed using an RNA Nano 6000 Assay Kit for the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA), according to the manufacturer’s instructions.


title: TGF-β protects dormant metastasis from immune mechanosurveillance

city: New York

first: Zhenghan

last: Wang

state: NY

address: 417 East 68th St

department: CBG

institute: Memorial Sloan Kettering Cancer Centerr

summary: Cancer cells disseminated to distant sites enter a period of dormancy before generating overt metastases. The ability of these cells to elude immune surveillance determines their persistence as latent disease. We report that TGF-β promotes dormancy in lung adenocarcinoma (LUAD) mouse models by placing disseminated SOX2+ and NKX2-1+ progenitors in a quiescent state that biomechanically averts killing by cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells. In these primitive progenitors, TGF-β induces an atypical epithelial-to-mesenchymal transition (EMT) lacking actin stress fibers. TGF-β drives expression of the actin-depolymerizing factor gelsolin that changes a migratory, stress fiber-rich mesenchymal phenotype into a cortical actin-rich, spheroidal state. This transition lowers the stiffness of metastatic progenitors and their killing by mechanosensitive CTLs and NK cells. Thus, LUAD primitive progenitors activate a biomechanical process to evade immune-mediated elimination during prolonged dormancy periods. Inhibiting this process clears tissues of dormant metastatic cells.

overall_design: Expression profiling by high throughput sequencing of H2087-LCC, a dormant metastatic derivative from stage I LUAD cell line H2087,  treated with SB505124 for 3 days, TGF-b for 3 days and TGF-b for  7 days.

first: Joan

last: Massagué


title: Aedes aegypti NeSt1 interacts with human CD47 to enhance Zika virus infectivity

city: New Haven

first: Alejandro

last: Marin Lopez

state: CT

address: 300 Cedar St

department: Internal Medicine

institute: 300 Cedar St

summary: Aedes aegypti is a vector of many infectious agents, including flaviviruses like Zika virus. We demonstrate that Nest1, a 34kDa mosquito salivary protein, facilitates Zika virus dissemination in human skin explants. Our aim was to analyze the effect of Nest1 at a transcriptomic level (RNAseq) in human skin explants, in the presence and absence of virus (ZIKV), at different timepoints (day 1, 2,3 ,and 4)

overall_design: Human skin explants were inoculated with 3 micrograms of Nest1 protein or buffer as control, in the presence and absence of ZIKV. Groups: Buffer, NeSt1, ZIKV.Buffer and ZIKV.NeSt1. Timepoints: Day 1, Day 2, Day 3 and Day4. 4 replicates per tretament.

first: Rolando

last: Garcia Milian

first: Saravanan

last: Thangamani

first: Allen

last: Esterly

first: Erol

last: Fikrig


title: Molecular effects of arsenic and smokeless tobacco aqueous extract in cultured cells  [RNA-seq]

city: LYON

first: Samrat

last: Das

address: 25 avenue Tony Garnier

institute: International Agency for Research on Cancer (IARC)

summary: Chronic arsenic exposure can lead to various health issues including cancer. There has been a growing concern about co-exposure to various prevalent lifestyle habits and their role in the enhancement of arsenic toxicity. Smokeless tobacco (SLT) products are extensively consumed in many South Asian countries, where their use frequently co-occurs with exposure to arsenic from contaminated groundwater. To decipher the oral epithelial cell responses to arsenic and SLT alone and in co-exposure, we performed multi-omics analyses of DNA methylome, transcriptomic reprogramming and genotoxic effects in controlled experimental settings. Chronic exposure studies revealed hypomethylation of genes involved in inflammation response and apoptosis, further corroborated by the upregulation of genes involved in these processes due to arsenic and the combined treatment in acute exposure setting. Next, to validate the omics results at the phenotypic level, we observed a dose dependent decrease in cell viability, induction of DNA damage, cell cycle changes, and an increase in apoptotic cells, with the most pronounced effects observed under arsenic and SLT co-exposure conditions. The observed DNA damage was likely the result of apoptosis induction, as chronic exposure experiments based on whole-exome sequencing did not reveal increased mutagenicity following the arsenic and/or SLT exposure. Our integrative omics study provides insights into both chronic and acute responses to arsenic and SLT co-exposure, with both types of responses converging on some of the same mechanisms. We identified large-scale epigenomic and transcriptomic reprograming associated with arsenic and SLT co-exposure, alongside genotoxic effects presumably manifesting as consequences of apoptosis induction. The findings point to a role of arsenic and SLT in altering key molecular responses, especially in the context of the co-exposure, and call for further studies in humans in the areas of exposure, to validate the observed mechanisms.

overall_design: hTERT Normal oral keratinocytes cells were grown in T25 flasks (seeding density ~ 3 - 5 × 105 cells). Upon reaching a confluency of around 70%, the cells were treated with media containing the test substances and were grouped into various time points based on exposure period (2 hrs, 4 hrs and 8 hrs). Two experimental control groups were included, the baseline untreated control (0 hr), and time-matched untreated control (harvested at 8 hrs). Each timepoint condition consisted of four experimental replicates. After exposure, the media containing the test substances were removed from the flasks and the cellular RNA was extracted using standard methods (TRIzol™ Reagent, Cat. No. 15596026, Invitrogen). Estimation of yield was done by Qubit analysis (Qubit 3.0 Fluorometer, Life Technologies, Invitrogen™, Thermo Scientific Fisher) . RNA integrity was analysed on High Sensitivity RNA ScreenTape (Cat. No. 5067- 5579, Agilent), using the 4200 TapeStation automated electrophoresis instrument (Agilent). All samples exhibited RNA Integrity Number (RIN) above 8.4. 500 ng RNA per sample was used to prepare libraries (QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina (FWD)), Cat. No. 015, Lexogen).


title: M1 microglia-derived exosomes promote A1 astrocyte activation and aggravate ischemic injury via miR-331-5p/MAVS/NF-kB pathway

first: Zhongyuan

last: Li

address: Changle Road No.68

institute: Nanjing First Hospital

summary: Ischemic stroke (IS) is one of the most serious neurological diseases, characterized by high mortality and disability rates. Glia cells, particularly microglia and astrocytes, occupy a pivotal position in the progression of IS. In response to stroke, microglia undergo polarization, transforming into either pro-inflammatory M1 phenotype or anti-inflammatory M2 phenotype. Analogously, astrocytes would polarize to pro-inflammatory A1 phenotype or anti-inflammatory A2 phenotype. It has been documented that A1 astrocytes can be activated by M1 microglia, although precise underlying mechanism remains elusive. In our study, we emulated ischemic injury using a middle cerebral artery occlusion/reperfusion (MCAO/R) model in mice and  an oxygen-glucose deprivation/reoxygenation (OGD/R) model in primary astrocytes. Our findings revealed that M1 microglia could activate A1 astrocytes by secreting exosomes. According to RNA sequencing, circSTRN3 was enriched in M1 microglia-derived exosomes. Based on the review of literature and bioinformatics analysis, it was suggested that circSTRN3 could sponge miR-331-5p, while miR-331-5p could bind to MAVS and participate in the activation of NF-kB pathway and A1 astrocytes. Western blotting and qRT-PCR experiments verified this process. Furtherly, overexpression of circSTRN3 could aggravate neurological deficits, increase infarct volume, and promote cell death in MCAO/R model, whereas miR-331-5p inhibited this process. Furthermore, we conducted tests on circSTRN3 and miR-331-5p in exosomes isolated from the peripheral blood of IS patients, thereby confirming the correlation among circSTRN3, miR-331-5p, and the stroke severity score. Taken together, our study indicated that M1 microglia-derived exosomes could promote A1 astrocyte activation and exacerbate ischemic brain injury through the circSTRN3-miR331-5P/MAVS/NF-KB pathway.

overall_design: circRNA profiles of exosomes from microglia after previous normoxia condition(M0) or OGD/R model(M1)


title: Transcriptional Responses to TREM2 Agonist Antibody Treatment in Cynomologus Monkey Brain [bulk RNA-seq]

city: South San Francisco

first: Brad

last: Friedman

address: 1 DNA Way

institute: Genentech, Inc.

summary: In order to search for pharmacodynamic biomarkers of a TREM2 agonist antibody (Para09) in primates we performed bulk RNA-Seq on cortical tissue from cynomolgus monkeys after single IV injected doses. Changes in proliferation genes such as MKI67 were observed, as well as genes associated with glial activation, such as CHI3L1. This experiment demonstrates that our antibody induces transcriptional changes in the brain after peripheral administration.

overall_design:
Monkeys were treated with anti-hTREM2 agonist Para09 or an isotype control via intrathecal injection and brain samples were collected 2 days later. Bulk RNA was extracted from frontal cortex.

Please note that the treatment 1, 2, 3 represents:
treatment 1: "Anti-gD 200 mg/kg"
treatment 4: "Para09 50 mg/kg"
treatment 5: "Para09 200 mg/kg"

first: Gloriia

last: Novikova

first: Anne

last: Biever

first: Alicia

last: Nugent

first: Mitchell

last: Rezzonico

first: Bill

last: Meilandt


title: The mechanism of XYP-001 in treating pulmonary fibrosis

city: Hangzhou

first: Yicheng

last: Xie

address: 3333 Binsheng Rd

institute: Children’s Hospital Zhejiang University School of Medicine

summary: We performed single-cell sequencing on the mice lung tissues of bleomycin induced pulmonary fibrosis model group and XYP-001 (Itraconazole) treatment group.

overall_design: ICR female mice (22 – 25 g) were obtained from Shanghai Jihui Experimental Animal Breeding Co., Ltd (certificate: SCXK 2022-0009), divided into three groups: Control group (n = 12, did nothing), Model group (n = 12, 25 µL of 1 mg/mL bleomycin sulfate solution diluted with PBS (9041-93-4, Aladdin, China) was administered into the mice lungs by spray on day 0), XYP-001 treatment group (n = 12, model with 2.5 mg/mL XYP-001 (20100302, Joincare Haibin Pharmaceutical Co., Ltd., China) nebulized inhalation administration for 1 hour every day from day 0 to day 20). On day 21 lung tissues of mice were collected (left upper lobe of lung) and stored on ice in tissue preservation solution (DMEM:fetal bovine serum=9:1). Mix 6 animals each group (model group and XYP-001 treatment group) into one sample and send it for scRNAseq (10× Genomics) within 1 hour.


title: The Dlk1-Dio3 noncoding RNA cluster coordinately regulates mitochondrial respiration and chromatin structure to establish proper cell state for muscle differentiation

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: The coordinate regulation of metabolic activity and epigenetics to establish cell state-specific gene expression patterns during lineage progression is among the most important aspects of cell differentiation. Cell states are defined by their epigenetic landscape and have cell state-specific metabolic demands. Defining the regulatory factors involved in the interplay between metabolism and cell state would represent a significant step forward in understanding the genetic circuitry that drives differentiation of progenitor cells into highly specialized cell types for proper tissue formation. Expression levels of the imprinted Dlk1-Dio3 noncoding RNA (ncRNA) mega-cluster have been shown to correlate with distinct metabolic profiles in a variety of progenitor cells, suggesting it functions as a key regulator of metabolism and cell state. Here, we directly demonstrate that the Dlk1-Dio3 ncRNA locus is a central player coordinating mitochondrial metabolic activity and genome-wide epigenetic changes in myoblasts and differentiated myotubes. Stable muscle cell lines were generated harboring two distinct deletions in the proximal promoter region resulting in either greatly upregulated or severely attenuated transcription of the entire mega-cluster of Dlk1-Dio3 ncRNAs. Both mutant lines displayed impaired myotube formation along with perturbed mitochondrial respiration and widespread changes in chromatin accessibility and histone methylation. Global gene expression patterns and pathway analyses indicated a reprogramming of cell state which created a differentiated-like molecular profile in proliferating myoblasts. Our results strongly suggest that the Dlk1-Dio3 ncRNA locus is a nodal regulator coordinating metabolic activity and the epigenome to maintain proper cell state in the myogenic lineage.

overall_design: To investigate the importance of dosage of the Dlk1-Dio3 ncRNA cluster in muscle cell state and differentiation we created two novel mutant C2C12 myoblast lines with CRISPR/Cas9-induced deletions in the proximal promoter region of Meg3.

first: Amanda

last: Pinheiro

first: Francisco

last: Naya


title: Adaptation to diverse transcription factor knockouts reveals robustness of transcription regulatory network

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr

institute: UCSD

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

overall_design: To investigate impact of TF KO's on the transcriptome, TF's were KO'd and evolved. Midpoint and endpoint isolates were taken.


title: Molecular effects of arsenic and smokeless tobacco aqueous extract in cultured cells

type: Methylation profiling by genome tiling array

overall_design: htert-immortalized normal oral keratinocytes (NOK) cells underwent the respective, controlled treatment protocols. Briefly, each week the cells were exposed for 24 hr, and following treatment, the exposure medium was replaced with normal media and cells were left for recovery. Exposures were repeated in for a period of 5 weeks. Following the repeated exposure protocol, genomic DNA was extracted from the cells using standard protocol.  For each sample, 500ng DNA were bisulfite converted to enable quantitative assessment of methylation level over 850K CpG sites. Following this treatment, methylation profiles were obtained with Infinium® Methylation EPIC bead arrays (Illumina), using recommended protocols for amplification, labelling, hybridisation, and scanning. For each treatment condition triplicate wells were analysed. Samples: Samples: Parental (4 biological replicates), NT (Non treated time matched control, 3 biological replicates), SA (Sodium arsenite treated: 10µM, 3 biological replicates), SLT (smokeless tobacco aqueous extract treated: 3000 µg/mL, 3 biological replicates), SA+SLT [co-exposed: (SA: 7µm)+(SLT: 1000 µg/mL), 3 biological replicates].


title: XIST and MUC1-C form an autoregulatory pathway in driving cancer progression

first: Atrayee

last: Bhattacharya

address: 450 Bookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: MUC1-C /XIST autoregulatory axis is of importance in cancer progression where MUC1-C regulates XIST lncRNA levels in cancer

overall_design: RNA Seq in DU145 prostate cancer cell line with tet-XIST shRNA (from GenePharma (Shanghai, China)) silencing. Transduced cells were selected for growth in 1-2 g/ml puromycin or 100 g/ml geneticin. For inducible gene silencing, cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline (DOX; Millipore Sigma).

first: Keyi

last: Wang