title: Single cell RNA-seq comparing regeneration of young and aged skeletal muscles

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

summary:
Abstract:
Transcription factors (TFs) play key roles in regulating differentiation and function of stem cells, including muscle satellite cells (MuSCs), a resident stem cell population responsible for postnatal regeneration of the skeletal muscle. Sox11 belongs to the Sry-related HMG-box (SOX) family of TFs that play diverse roles in stem cell behavior and tissue specification. Analysis of single-cell RNA-sequencing (scRNA-seq) datasets identify a specific enrichment of Sox11 mRNA in differentiating but not quiescent MuSCs. Consistent with the scRNA-seq data, Sox11 levels increase during differentiation of murine primary myoblasts in vitro. scRNA-seq data comparing muscle regeneration in young and old mice further demonstrate that Sox11 expression is reduced in aged MuSCs. Age-related decline of Sox11 expression is associated with reduced chromatin contacts within the topologically associated domains. Unexpectedly, Myod1Cre-driven deletion of Sox11 in embryonic myoblasts has no effects on muscle development and growth, resulting in apparently healthy muscles that regenerate normally. Pax7CreER or Rosa26CreER driven (MuSC-specific or global) deletion of Sox11 in adult mice similarly has no effects on MuSC differentiation or muscle regeneration. These results identify Sox11 as a novel myogenic differentiation marker with reduced expression in quiescent and aged MuSCs, but the specific function of Sox11 in myogenesis remain to be elucidated.

overall_design: 7 day post injury mononuclear cells from hindlimb skeletal muscle of young (3 months) and old (>20 months) mice were profiled by scRNA-seq and sequenced using IIIumina NovaSeq 6000

first: Stephanie

last: Oprescu

first: Feng

last: Yue


title: Inherited CD19 deficiency impairs signaling in plasma cells

status: Public on Sep 21 2023

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

type: Expression profiling by high throughput sequencing

summary: Background: The human CD19 antigen is expressed throughout B cell ontogeny with the exception of neoplastic plasma cells and a subset of normal plasma cells. CD19 plays a role in propagating signals from the B cell receptor and other receptors such as CXCR4 in mature B cells. Studies of CD19-deficient patients have confirmed its function during the initial stages of B cell activation, however its role in the later stages of B cell differentiation is unclear.  Objective: Using B cells from a newly identified CD19-deficient individual, we investigated the role of CD19 in the generation and function of plasma cells using an in vitro differentiation model.

overall_design: RNA-seq

middle: A

first: Gina

middle: M

last: Doody

first: Kieran

last: Walker


title: Genome wide assessment of gene expression in alpha and beta cells from lean and obese mice

city: Davis

first: Mark

middle: O.

last: Huising

state: CA

address: One Shields Avenue

department: Neurobiology, Physiology and Behavior

country: USA

institute: University of California, Davis

summary: We report the assessment of transcriptome by RNA-Seq of FACS purified Ins1-H2bmCherry purified primary mouse beta cells and Gcg-CreERT2 x YFP positive alpha cells of obese (ob/ob) mice compared to lean littermate controls

overall_design: Examination of transcriptomes in primary alpha and beta cells in lean vs obob beta cells by RNA-Seq. Islets from 5 lean males, 5 lean females, 2 ob/ob males and 3 ob/ob females between 35-38 weeks of age.

first: Jessica

middle: L

last: Huang

first: Alex

last: Mawla

middle: O


title: Clinical significance of apurinic/apyrimidinic endodeoxyribonuclease 1 and microRNAs axis in hepatocellular carcinoma [NanoString]

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

summary: Hepatocellular carcinoma is the most frequent species of liver cancer and the identification of new prognostic factors opens new perspectives for therapy. Circulating and cellular onco-miRNAs are non coding RNAs which can control oncogenesis-related gene expression through post-transcriptional mechanisms and are considered novel prognostic and predictive factors in cancer biology.   The apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) contributes in the quality control and processing of specific onco-miRNAs, and is a negative prognostic factor in many tumors. The present work aims: a) to define APE1 prognostic value in HCC; b) to identify miRNAs regulated by APE1 and their relative target genes, and c) to study their prognostic value.

overall_design: In the study presented here, the miRNome profiling was analyzed in JHH-6 cells following the transient APE1 silencing to identify DEmiRNAs candidates. The experiment was performed in triplicates.

first: Giovanna

last: Mangiapane

first: Devis

last: Pascut

first: Emiliano

last: Dalla

first: Giulia

last: Antoniali

first: Monica

last: Degrassi

first: Claudio

last: Tiribelli

first: Gianluca

last: Tell


title: Effect of PRC2 loss of function on gene and TE expression in Cyanidioschyzon merolae

city: Ikoma

first: Tetsuya

last: Hisanaga

state: Nara

address: Takayama 8916-5

country: Japan

institute: Nara Institute of Science and Technology

summary: To evaluate role of PRC2 on transcriptional regulation in Cyanidioschyzon merolae, we generated loss of function mutants of a Ez homolog in Cyanidioschyzon merolae by homologous recombination based mutagenesis. Then we performed comparative transcriptome analyses using data obtained from Cme(z) and WT.

overall_design: Comparative expression analysis of RNA-seq data for the Cme(z) mutant and wild type.

first: Frederic

last: Berger

first: Teresa

last: Kowar

first: Daniel

last: Schubert


title: Phase Ib trial of inhaled iloprost for the prevention of lung cancer with predictive and response biomarker assessment response biomarker assessment (scRNA-Seq).

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

summary: Iloprost, a prostacyclin analog, has lung cancer preventive activity in preclinical models and improved dysplasia in former smokers in a phase IIb trial. Oral iloprost is currently unavailable.We performed a phase Ib trial of inhaled iloprost in former smokers to assess tolerance and compliance. Participants self-administered nebulized iloprost (5ug) or placebo four (QID) or two (BID) times daily. As QID dose was well tolerated and due to expiration of the placebo, the BID dosing and placebo were eliminated early on in the trial. Bronchoscopy with biopsy at six standard sites was performed at treatment initiation and two months post-iloprost, with exploratory histological analysis. Bulk RNA sequencing, single cell RNA sequencing and an in vitro assay of epithelial progenitor cell iloprost response were performed on a subset of biopsies in an exploratory investigation of response mechanisms and predictive biomarkers. Thirty-four of a planned 48 participants were recruited to the trial. Inhaled iloprost was well tolerated with no adverse events > grade 2. Compliance was 67% in the QID group. The trial was not powered to detect histologic response and none was found. Bulk RNA sequencing of biopsies pre/post iloprost suggest that iloprost is immunomodulatory and downregulates cell proliferation pathways.Single cell RNA sequencing showed an increase in CD8-positive T cells with upregulation of genes in interferon γ signaling. In vitro iloprost response by epithelial progenitor cells correlated with histologic response with kappa coefficient of 0.81 (95% CI 0.47, 1.0). Inhaled iloprost was well tolerated with suboptimal compliance. Molecular analysis suggested that iloprost has immunomodulatory and antiproliferative effects. The progenitor cell iloprost response assay may be a promising avenue to develop predictive biomarkers.

overall_design: Comparative gene expression profiling analysis of scRNA-seq data for inhaled iloprost responders.

first: York

last: Miller

first: Moumita

last: Ghosh

last: Merrick

first: Brandi

last: Kubala

first: Eva

last: Szabo

first: Lisa

last: Bengtson

first: Masha

last: Kocherginsky

first: Irene

last: Helenowski

first: Kelly

last: Benante

first: Tia

last: Schering

first: Hyunmin

first: Duc

last: Ha

first: Raymond

middle: C

last: Bergan

first: Seema

last: Khan

first: Robert

last: Keith


title: Effect of PRC2 loss of function on gene and TE expression in Marchantia polymorpha

first: Tetsuya

last: Hisanaga

summary: To evaluate role of PRC2 on transcriptional regulation in bryophytes, we generated loss of function mutants of a Ez homolog in Marchantia polymorpha by CRISPR/Cas9 based mutagenesis. To avoid lethality of PRC2 knockout, we first mutate MpKNOX2 gene then additionally knocked MpEz1 out. Then we performed comparative transcriptome analyses using data obtained from Mpknox2 ez1 and Mpknox2.

overall_design: Comparative expression analysis of RNA-seq data for the Mpknox2 mutant and two independent Mpknox2 Mpez1 alleles.

first: Frederic

last: Berger


title: Phase Ib trial of inhaled iloprost for the prevention of lung cancer with predictive and response biomarker assessment response biomarker assessment (Bulk RNA-Seq).

first: Jihye

last: Kim

overall_design: Comparative gene expression profiling analysis of RNA-seq data for placebo and inhaled iloprost responders.

first: Daniel


title: Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation [RNA-Seq]

first: Matthew

last: Care

summary: Human B cell differentiation into antibody secreting plasma cells is a critical process in the adaptive immune response whose regulation at the genetic level remains incompletely understood.  To reveal the temporal sequence of transcription factor driven cellular changes we generated chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) data from the in vitro differentiation of human B cells into plasma cells. Data was gathered from three biological replicates using a published 13-day protocol of cytokine addition to drive differentiation. Using a new computational method, cisREAD (cis-Regulatory Elements Across Differentiation), we defined a core set of cis regulatory elements that are confidently linked to the dynamic binding of transcription factors and changes in gene expression. This confirmed known aspects of the differentiation process and revealed novel understanding, including a switch from PU.1/SPIB-driven to AP-1-driven genetic regulation associated with B cell activation.

overall_design: Matched mRNA/ATAC-seq profiles of human naïve B-cells differentiated from day 0 to day 13 plasma cells, from 3 healthy donors.

first: David

middle: R

last: Westhead

first: Reuben

last: Tooze

first: Amber

last: Emmett


title: Transcriptome analysis of six tissues obtained post mortem from sepsis patients

city: São Paulo

first: Fabiano

last: Pinheiro Da Silva

state: São Paulo

address: Av Dr Arnaldo, 455 sala 3189

country: Brazil

institute: Faculdade de Medicina da Universidade de São Paulo

summary: Background: Septic shock is a life-threatening clinical condition characterized by a robust immune inflammatory response to disseminated infection. Little is known about its impact on the transcriptome of distinct human organs. Objective and Methods: To address this, we performed RNA sequencing of samples from the prefrontal cortex, hippocampus, heart, lung, kidney and colon of seven individuals who succumbed to sepsis and seven uninfected controls. Main Results: We identified that the lungs and colon were the most affected organs. While gene activation dominated, strong inhibitory signals were also detected, particularly in the lungs. Principal Conclusions: We found that septic shock is an extremely heterogeneous disease, not only when different individuals are investigated, but also when comparing different tissues of the same patient. However, several pathways, such as respiratory electron transport and other metabolic functions, revealed distinctive alterations, providing evidence that tissue specificity is a hallmark of sepsis. Strikingly, we found evident signals of accelerated ageing in our sepsis population.

overall_design: We performed RNA-seq on frozen autopsy samples of six distinct tissues (prefrontal cortex, hippocampus, heart, lung, kidney and colon) obtained from seven patients who died of septic shock and seven critically ill patients who died of non-infectious diseases.

last: Pinheiro da Silva

first: André

last: Gonçalves

first: Amaro

middle: N

last: Duarte-Neto

first: Thomaz

last: Dias

first: Hermes

middle: V

last: Barbeiro

first: Cristiane

middle: S

last: Breda

first: Leandro

middle: D

first: Niels

last: Câmara

first: Helder

middle: I

last: Nakaya


title: mRNA splicing is modulated by intronic microRNAs

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

summary: Splicing of transcripts is catalyzed by the spliceosome, a mega-complex consisting of hundreds of proteins and five snRNAs, which employs direct interactions. When U1 snRNA forms high affinity binding, namely more than eight base-pairs, with the 5’SS, the result is usually a suppressing effect on the splicing activity. This likely occurs due to the inefficient unwinding of U1/5’SS base-pairing, or other regulatory obstructions. Here we show in vitro and in patient-derived cell lines that pre-microRNAs can modulate the splicing reaction by interacting with U1 snRNA. This leads to reduced binding affinity to the 5’SS, and hence promotes the inclusion of exons containing 5’SS, despite sequence-based high affinity to U1. Application of the mechanism resulted in correction of the splicing defect in the disease-causing VCAN gene from an individual with Wagner syndrome. This pre-miRNA/U1 interaction can regulate the expression of alternatively spliced exons, thus extending the scope of mechanisms regulating splicing.

overall_design: 3 miR-211 or control plasmid OE; 3 U1 siRNA or conrol oligo OE in the HEK 293T cell-line.

first: Luba

last: Farberov

first: Daphna

last: Weissglas-Volkov

first: Yazeed

last: Zoabi

first: Chen

last: Schiff

first: Barbara

last: Kloeckener-Gruissem

first: John

last: Neidhardt

first: Noam

last: Shomron


title: H4K12 Lactylation-activated c-JUN signaling aggravates bile acid dysfunction in intrahepatic cholestasis during pregnancy

city: Wuhan

first: Tongxin

last: Wang

address: Hongshan Huazhong Agricultural University

country: China

institute: Huazhong Agricultural University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The occurrence of hepatic cholestasis during pregnancy is accompanied by the disorders of glucose and lipid metabolism, especially the acceleration of glycolysis. Here, we reported a novel mechanism that the glycolysis metabolic intermediate lactate-induced histone 4 at K12 (H4K12) hyperlactylation aggravates bile acid (BA) dysfunction in intrahepatic cholestasis during pregnancy by activating c-JUN and in turn facilitating RXRɑ cytoplasmic relocalization. Lactylome analysis in livers of late pregnant sows with high levels of BA revealed induction of H4K12 hyperlactylation. Target correction of aberrant histone lactylation prevented the hepatic BA disorders in both sows and mice models. Mechanistically, H4K12la was enriched in promoter regions of c-JUN and activated its expression Moreover, activated c-JUN facilitated the RXRɑ phosphorylation and cytoplasmic relocalization, which resulted in the activation of whole BA synthesis pathway and inhibition of BA transport pathway. Inhibitor of the glycolysis pathway and lactate inhibitor as nutritional intervention ameliorated BA metabolic disorder in pregnant sows and cholestasis in mice. Our findings demonstrate the catalytic role of lactate on hepatic BA disorders in late pregnancy, we also provided a novel pattern of nutritional intervention to precisely target and regulate bile acid metabolism, and may open the new direction of nutritional epigenetic regulation of metabolic diseases.

overall_design: Liver samples from late gestation sows in high and normal bile acid groups were used to analyze target genes regulated by H4K12la

first: Weilei

last: Yao

first: Lu

last: Huang

first: Longshan

last: Qin


title: Left ventricular hypertrophy and metabolic resetting in the Notch3-deficient adult mouse heart

city: Stockholm

first: Eike-Benjamin

last: Braune

address: Nobels väg 6

department: CMB

country: Sweden

institute: Karolinska Institutet

summary: The heart depends on a functional vasculature for oxygenation and transport of nutrients, and while occlusion of the coronary arteries can lead to myocardial infarction, it remains less explored how a more subtle primary impairment of the vasculature can indirectly affect cardiac function and morphology of the heart. Notch3-deficiency causes vascular smooth muscle cell (VSMC) loss in the vasculature but the consequences for the heart remain largely elusive. Here, we demonstrate that Notch3-/- mice have enlarged hearts with left ventricular hypertrophy and mild fibrosis. Cardiomyocytes were hypertrophic but not hyperproliferative, and the expression of several cardiomyocyte markers, including TnT2, MYH6, MYH7 and Actn2, was altered. Furthermore, expression of genes regulating the metabolic status of the heart was altered: both Pdk4 and Cd36 were downregulated, indicating a metabolic switch from fatty acid oxidation to glucose consumption. Notch3-/- mice furthermore showed lower liver lipid content. Notch3 was expressed in heart VSMC and pericytes but not in cardiomyocytes, suggesting that a perturbation of Notch signalling in VSMC and pericytes indirectly impairs the cardiomyocytes. In keeping with this, Pdgfbret/ret mice, characterized by reduced numbers of VSMC and pericytes, showed left ventricular and cardiomyocyte hypertrophy. In conclusion, we demonstrate that reduced NOTCH3 or PDGFB signalling in vascular mural cells lead to cardiomyocyte dysfunction.

overall_design:
Mice were euthanized, the organs removed and immediately fresh frozen. RNA from heart tissue of c57bl/6j Notch3 +/+ (N3 WT)  and Notch3 -/- (N3 KO) was prepared and sequenced as described.
Clustering was done by 'cBot' and samples were sequenced on HiSeq3000(HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed applying standard parameters of the Illumina pipeline (bcl2fastq) using Nextera index adapters. The quality scale used is Sanger / phred33 / Illumina 1.8+.

first: Francesca

last: Del Gaudio

first: Dongli

last: Liu

first: Maarja

last: Mäe

first: Emil

last: Hansson

first: Qing-Dong

first: Christer

last: Betsholtz

first: Urban

last: Lendahl


title: 5-methyl cytosine profile of the wild type and Mpmet mutant in Marchantia polymorpha

first: Tetsuya

last: Hisanaga

type: Methylation profiling by high throughput sequencing

summary: To understand a role of MpMET in maintenance of cytpsine methylation and transposon silencing, we obtained a genome wide profile of 5-methylated cytosine from the Mpmet mutant of a model liverwort, Marchantia polymorpha.

overall_design: Tagmentation-based whole-genome bisulfite sequencing (T-WGBS) for a whole genome profile of cytosine methylation

first: Arie

last: Fridrich

first: Frederic

last: Berger


title: Analysis of differential gene expression in the degradation of tetracycline by Sphingobacterium sp. WM1

city: Beijing

first: Xiuli

last: Chen

state: Beijing

address: 9/5000  School of Environmental Science

institute: Peking University

summary: We isolated an efficient tetracycline degrading strain Sphingobacterium sp. WM1. To investigate gene expression patterns during tetracycline degradation by strain WM1, we conducted a comparative transcriptomic analysis using cultures of strain WM1 with and without tetracycline addition. The RNA-Seq data revealed that 90.44-96.56% of the reads mapped to the genome of Sphingobacterium sp. WM1 across all samples. Differentially expressed genes (DEGs) analysis (|log2FC| >2; p < 0.01) showed that 693 genes were significantly up-regulated and 592 genes were significantly down-regulated.

overall_design: Control groups (WM1_CK): cultures of strain WM1 without tetracycline addition. Experimental groups (WM1_TC):cultures of strain WM1 with 50 mg/L tetracycline.

first: Shuguang

last: Xie


title: Effect of MpMET loss of function on gene and TE expression in Marchantia polymorpha

summary: To evaluate role of MpMET on transcriptional regulation in bryophytes,   we performed comparative transcriptome  analyses using data obtained from Mpmet-3 described in Ikeda et al., 2018 and the corresponding wild type accession.

overall_design: Comparative  expression analysis of RNA-seq data for the wild type and Mpmet-3 mutant


title: Regulatory role of MAFB transcription factor in cultured human β cells

city: Nashville

first: Xin

last: Tong

state: TN

address: 2213 Garland Ave.

institute: Vanderbilt University

summary: To investigate the function of MAFB in the regulation of human beta cell identity and maturity, we established EndoCbH2 cell lines in which MAFB has been knocked down by shRNA. We then performed gene expression profiling analysis using data obtained from bulkRNA-seq of 3 biological replicates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EndoCbH2 cells and its KD derivatives (shMAFB).

first: Jeeyeon

last: Cha

first: Roland

last: Stein


title: DNA methylation of control lungs

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: Interrogation of the DNA methylome of normal lung tissue adjacent to tumor.

overall_design: Bisulphite converted DNA from 9 normal lung tissue adjacent to tumor

first: M


title: A novel anti-RdDM element that defends cis-regulatory element against ncRNA-dependent, siRNA-driven, and methylation-imposed transcriptional silencing in plants

city: Kearneysville

first: Zongrang

state: WV

address: 2217 Wiltshire Road

department: Appalachian Fruit Research Station

institute: USDA-ARS

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Cell-matrix interactions control biliary organoids polarity,architecture  and differentiation and can be exploited to improve modelling of biliary diseases [scRNA-seq]

city: New Haven

first: Mario

last: Strazzabosco

state: CT

address: 300 Cedar street

department: Internal Medicine

institute: Yale School of Medicine

summary: Diseases of the biliary epithelium (cholangiopathies) are an important cause of morbidity and mortality. Their pathogenesis and treatment remain unclear, in part because of the lack of disease models relevant to humans. 3D biliary organoids hold great promise, however the inaccessibility of their apical pole, and the presence of extracellular matrix (EBM) limit their experimental application. Here we show that when b integrin signaling is inhibited, either by removing the EMC or using blocking antibodies, biliary organoids revert their polarity and expose the apical membrane. Functional, immunohistochemical and TEM studies, along with bulk and single cell transcriptomic demonstrate that organoids in this novel 3D configuration, are less heterogeneous, show increased biliary differentiation, and decreased expression of stem cell markers. This model can be used to study bile transport, interactions with microbial agents, epithelial permeability, cross-talk with other liver and immune cell types and the effect of matrix changes on the biliary epithelium.

overall_design: Liver organoids were generated from liver explants (n=4) and were cultured embedded in the ECM (EMB) or suspended in ECM/media mix (10% BME) or without ECM.

first: Romina

last: Fiorotto

first: Valeria

last: Mariotti

first: Zehra

last: Syeda

first: Mytien

last: Nguyen

first: Shakila

last: Taleb

first: Mariangela

last: Amenduni


title: Cell-matrix interactions control biliary organoids polarity,architecture  and differentiation and can be exploited to improve modelling of biliary diseases [bulk RNA-seq]


title: Single-cell analysis of human dermal fibroblasts isolated from a single male donor over 35 years

city: Kita-ku

first: Eji

last: Naru

state: Tokyo

address: 48-18 Sakae-cho

department: Dermatology and Cosmeceutical Research Laboratories

institute: KOSÉ Corporation

summary:
Background: Skin homeostasis is mediated by dermal fibroblasts and is affected by aging. Although age-related heterogeneity in fibroblasts has been reported, the effects of donor and species on this heterogeneity are unclear.
Methods: To analyze age-related transcriptomic changes in human dermal fibroblasts, single-cell RNA sequencing was performed on dermal fibroblasts (ASF-4 cells) collected from the inner forearm of a volunteer over three decades.
Results: Four main cell subpopulations changed with donor age and showed proliferative, homeostasis, fibrotic, and senescence functional annotations. The downregulation of the expression of genes encoding key extracellular matrix production and mechanotransduction components decreased with donor age. Interestingly, dermal fibroblasts have two putative differentiation pathways: one that involves the acquisition of senescent properties and the acquisition of fibrotic properties without the suppression of proliferation. Aging induced fibroblast differentiation in a manner involving the acquisition of senescent properties.
Conclusion:Reconciling the various aspects of fibroblast heterogeneity may provide insight into the mechanisms underlying human skin aging and associated phenomena, including wrinkles, sagging, delayed wound healing, and suppressed scar formation.

overall_design: The mRNA profiles of human dermal fibroblasts obtained from a volunteer at two different ages over a three-decade period (ASF-4-1, 36.2 years; ASF-4-6, 72.8 years).

first: Eriko

last: Itai

first: Kazuhiko

last: Kaji


title: A novel anti-RdDM element that defends cis-regulatory element against ncRNA-dependent, siRNA-driven, and methylation-imposed transcriptional silencing in plants [ARE BSseq]

last: Liu

summary: Cis-regulatory elements (CREs) dictate spatiotemporal expression and tissue specificity of proximal genes. However, when in a transgenic state, many of them become highly vulnerable to RNA-Directed DNA Methylation (RdDM) that is often transcriptionally deleterious and biologically detrimental. This transgene-specific RdDM vulnerability suggests the existence of anti-RdDM elements (AREs) to defend CREs against de novo methylation in vivo.  In this work, we identify such an ARE at the Arabidopsis AGAMOUS (AG) locus, which includes a physically separated enhancer and promoter, both of which are highly vulnerable to transgene silencing.  We demonstrate that this ARE effectively represses RdDM activity at its cognate and heterologous CREs via the inhibition of transcription and processing of potent non-coding RNAs (ncRNAs), which act as substrates for the biogenesis of 24-nt small interfering RNAs (siRNAs) that guide RdDM.  Furthermore, we establish that the ARE exploits hypermethylation in a 108-bp internal region (referred to as M1) as a regulatory signal to recruit methyl reader SU(VAR)3-9 homolog 1 (SUVH1), as well as Harbinger transposon-derived protein 2 (HDP2) associated with HDP1, to carry out ARE-imposed transcriptional and post-transcriptional repression, with the former mediating the repression of ncRNA transcription and the latter repressing both ncRNA transcription and processing.  We also show that M1 methylation is indispensable for the repression of methylation in an adjacent, methylation-vulnerable 737-bp region (dubbed M2) to safeguard the ARE’s functional integrity. Taken together, the present study uncovers a novel anti-RdDM element that defends CREs against ncRNA-dependent, siRNA-driven, and methylation-imposed epigenetic interference to safeguard their regulatory integrity.

overall_design: Comparison of DNA methylation profile among different lines

first: Huawei

first: Yanjun

last: Li

first: Jia

first: Yue

first: Stacy

last: Singer

first: Dennis

last: Bennet

first: Yazhou

last: Yang

first: Jiang

first: Yi

first: Yingzhen

first: Gan-Yuan

last: Zhong

first: Rick

last: Meyer

first: Wenying

last: Xu

first: Zhen

last: Su

first: Hua

last: Lu

first: Ruhui

first: Kunru

last: Wang

first: Binyu

last: Zhao

first: Yong-Qiang

last: An


title: A novel anti-RdDM element that defends cis-regulatory element against ncRNA-dependent, siRNA-driven, and methylation-imposed transcriptional silencing in plants [ARE sRNAseq]

first: Zongrang

overall_design: Analyses of siRNA expression and profile in various Arabidopis lines

first: Huawei

first: Yanjun

first: Jia


title: Clinical significance of apurinic/apyrimidinic endodeoxyribonuclease 1 and microRNAs axis in hepatocellular carcinoma [RNA-Seq]

first: Silvano

last: Piazza

summary: Hepatocellular carcinoma is the most frequent species of liver cancer and the identification of new prognostic factors opens new perspectives for therapy. Circulating and cellular onco-miRNAs are non coding RNAs which can control oncogenesis-related gene expression through post-transcriptional mechanisms and are considered novel prognostic and predictive factors in cancer biology.   The apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) contributes in the quality control and processing of specific onco-miRNAs, and is a negative prognostic factor in many tumors. The present work aims: a) to define APE1 prognostic value in HCC; b) to identify miRNAs regulated by APE1 and their relative target genes, and c) to study their prognostic value.

overall_design: In the study presented here, the miRNome profiling was analyzed in JHH-6 cells following the transient APE1 silencing to identify DEmiRNAs candidates. The experiment was performed in triplicates.

first: Giovanna

last: Mangiapane

first: Devis

last: Pascut

first: Emiliano

last: Dalla

first: Giulia

last: Antoniali

first: Monica

last: Degrassi

first: Claudio

last: Tiribelli

first: Gianluca

last: Tell


title: Genome wide assessment alpha and beta cells from lean and obese mice

first: Mark

last: Huising


title: Clinical significance of apurinic/apyrimidinic endodeoxyribonuclease 1 and microRNAs axis in hepatocellular carcinoma


title: H3K27ac ChIP-seq of SK-Hep-1, Huh7, SNU387, and SNU182 cells

status: Public on Sep 20 2023

city: Jinan

first: Tao

state: Shandong

address: 440 Jiyan Rd

institute: Shandong Cancer Hospital and Institute

summary: To investigate enhancers and super-enhancers in liver cancer cells, we performed H3K27ac ChIP-seq in SK-Hep-1, Huh7, SNU387, and SNU182 cells.

overall_design: We performed H3K27ac ChIP-seq in SK-Hep-1, Huh7, SNU387, and SNU182 cells, and  input groups were sequenced simultaneously

first: Nasha

last: Zhang

first: Teng

first: Ming

last: Yang


title: Transposons repressed by H3K27me3 were co-opted as cis-regulatory elements of H3K27me3 controlled protein-coding genes during evolution of plants

first: Tetsuya

last: Hisanaga

sample_organism:
Marchantia polymorpha
Cyanidioschyzon merolae strain 10D


title: Gene expression profile at single cell level of lung cDC1 and lung cDC2 in steady state

city: Chicago

first: Gye Young

last: Park

state: IL

address: 840 S. Wood St

department: Medicine, Pulmonary

institute: University of Illinois at Chicago

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the heterogeneity of lung cDC1 and lung cDC2.

overall_design: Lung cDC1 and lung cDC2 were isolated by Fluorescence-activated cell sorting (FACS) according to surface markers (XCR1 or CD172a) and analyzed using scRNAseq.

first: Moon

last: Hyung-Geun

first: Kim

last: Seung Jae

first: Park

last: Gye Young


title: CD40L modulates CD4+ T cell polarization and activation through the binding of Receptor for Activated C Kinase 1

city: Amsterdam

first: Claudia

last: van Tiel

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC

summary: Inhibition of the co-stimulatory ligand CD40L has shown beneficial effects in many experimental models of auto-immune disease and inflammation. Here, we show that CD40L deficiency in T-cells in mice causes a reduction of CD4+ T cell activation and specifically a strong reduction in interferon- γ (IFN-γ) producing T helper 1 (Th1) cells. In vitro, we could not reproduce this APC-dependent effects, but found that T-cell CD40L affects cell death and proliferation. We identified receptor of activated C kinase (RACK1), the canonical PKC binding partner and known to drive proliferation and apoptosis, as a mediator of CD40L reverse signaling. Furthermore, we found that CD40L clustering stabilizes IFN-γ mediated Th1 polarization through STAT1, a known binding partner of RACK1. Together this highlights the importance of both CD40L forward and reverse signaling.

overall_design: Comparison of gene expression in murine CD4+ T cells from T cell-specific CD40L-deficient mice and wild-type mice stimulated with αCD40L or isotype control antibodies (n=3 per group)

first: Bram

middle: W

last: van Os

first: Winnie

middle: G

last: Vos

first: Laura

last: Bosmans

first: Myrthe

last: den Toom

first: Linda

last: Beckers

first: Merel

last: Admiraal

first: Marten

last: Hoeksema

first: Menno

middle: P

last: de Winther

first: Esther

last: Lutgens


title: Expression of m6A methylation-modified circRNA in malignant transformation of oral leukoplakia tissue

city: Shanghai

first: Jingwen

address: Zhizaoju Road No.639

institute: Shanghaijiaotong University

summary: Objective This study aimed to investigate the expression and clinical significance of N6-methyladenosine (m6A) modification of circular RNA (circRNA) in oral leukoplakia (OLK) and oral squamous carcinoma cell (OSCC) tissues. Methods Using methylation RNA immunoprecipitation high-throughput sequencing technology (MeRIP-seq) and RNA high-throughput sequencing technology (RNA-seq), the first circRNA transcriptome analysis for detecting m6A methylationome profiles in OLK and OSCC tissues was obtained, followed by bioinformatics analysis. The qRT-PCR technique and protein immunoblotting technique were used to detect the expression of m6A methylesterase in OLK versus OSCC tissues. Results In this study, 275 differential m6A methylation peaks were identified in OLK and OSCC, among which 193 peaks were up-regulated and 82 were down-regulated. Additionally, 198 differential m6A methylation modified circRNAs were observed, with 127 up-regulated and 71 down-regulated (FC ≥ 2, P < 0.05). Most of the identified circRNAs that underwent m6A methylation alterations were derived from overlapping regions. It was found that the differential expression of circRNAs was not correlated with the joint analysis of significantly different m6A-circRNAs between the two groups. Furthermore, downregulation of mETTL14 and FTO protein levels was observed in OSCC tissues, although there were no discernible alterations in RNA levels. Conclusion Our study suggests that m6A methylation modification of circRNA may play a role in the development of oral leukoplakia, and that METTL14 and FTO may be important methylation enzymes that influence the development of oral leukoplakia. These findings may open up new research directions for in-depth investigations to clarify the molecular mechanisms of OLK carcinogenesis.

overall_design: From August 2020 to September 2021, we collected lesion tissues from patients with oral leukoplakia (OLK) and oral mucosal squamous cell carcinoma (OSCC) from the Department of Oral Mucosa of our hospital. For high-throughput sequencing of methylated RNA co-immunoprecipitation, three samples from each of the LK group and the SCC group were selected.

first: Yanxiong

last: Shao

first: Yuhan

last: Song

first: Siming

last: Xu

first: Shuyun

last: Ge

first: Haiwen

last: Zhou


title: Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation

city: York

first: Matthew

last: Care

address: Wentworth Way

institute: The University of York


title: Architecture and function of lamellar cells in Meissner corpuscle

first: Viktor

last: Feketa

state: Connecticut

address: 333 Cedar St SHM BE58

department: Cellular & Molecular Physiology

institute: Yale University School of Medicine

summary: Meissner corpuscles detect transient touch and vibration in glabrous skin, but their ultrastructure and mechanism of function are poorly understood. The Meissner corpuscle sensory core contains the terminal neurite(s) of the mechanoreceptor afferent surrounded by Schwann cell-derived lamellar cells. The afferent is thought to be the sole touch-sensing element within the corpuscle, whereas the role of lamellar cells is unclear. Here, we present a high-resolution three-dimensional ultrastructure of an avian Meissner (Grandry) corpuscle in intact skin acquired using the enhanced focused ion beam scanning electron microscopy (FIB-SEM), followed by machine learning based segmentation and reconstruction. We show that the afferent splits within the corpuscle into several disk-shaped endings layered between flattened lamellar cells. Each lamellar cell contains numerous exocytotic dense core vesicles and forms large-area contacts with adjacent afferent disks. Together with single-corpuscle RNA sequencing and electrophysiology, our FIB-SEM data reveal lamellar cells as secretory sensors of touch. We developed a method for direct electrophysiological recordings of afferent activity from an individual corpuscle in the skin and show that activation of a single mechanosensitive lamellar cell is sufficient to trigger action potentials in the afferent. These results reveal comprehensive Meissner (Grandry) corpuscle architecture and demonstrate a dual sensory mechanism comprised of a mechanoreceptor afferent and lamellar cells.

overall_design: Gene expression analysis and differential transcriptomics of single Meissner corpuscles (n = 5 biological replicates) compared to bill skin (n=6 biological replicates) in duck.

first: Yury

last: Nikolaev

first: Elena

last: Gracheva

first: Sviatoslav

last: Bagriantsev


title: Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation [ATAC-Seq]

summary: Human B cell differentiation into antibody secreting plasma cells is a critical process in the adaptive immune response whose regulation at the genetic level remains incompletely understood.  To reveal the temporal sequence of transcription factor driven cellular changes we generated chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) data from the in vitro differentiation of human B cells into plasma cells. Data was gathered from three biological replicates using a published 13-day protocol of cytokine addition to drive differentiation. Using a new computational method, cisREAD (cis-Regulatory Elements Across Differentiation), we defined a core set of cis regulatory elements that are confidently linked to the dynamic binding of transcription factors and changes in gene expression. This confirmed known aspects of the differentiation process and revealed novel understanding, including a switch from PU.1/SPIB-driven to AP-1-driven genetic regulation associated with B cell activation.

overall_design: Matched mRNA/ATAC-seq profiles of human naïve B-cells differentiated from day 0 to day 13 plasma cells, from 3 healthy donors.

first: David

last: Westhead

first: Reuben

last: Tooze

first: Amber

last: Emmett


title: Microbial Bile Acid Metabolism Shapes Effector T Cell Responses During Inflammation in Mouse and Human

city: Duarte

first: Anastasia

last: Kousa

address: 1500 E Duarte Rd

department: Hematology / HCT

institute: City of Hope

summary: To comprehensively investigate the effects of graft-versus-host disease on host metabolism, we carried out RNA-sequencing analysis of bulk liver and epithelial cell fractions of the small and large intestines of bone marrow of mice who received bone marrow (BM) only grafts and mice co-transferred with donor T cells (BMT).

overall_design: We compared the transcriptome of bulk liver and epithelial cell fractions of the small and large intestines between bone marrow only (BM) and bone marrow + T cells (BMT) recipients.

first: Sarah

last: Lindner

first: Oriana

last: Miltiadous

first: Clarissa

last: Campbell

first: Marcel

last: van den Brink


title: Circulating miRNAs detect high versus low visceral adipose tissue inflammation in patients living with obesity

city: Be'er Sheva

first: Nataly

last: Makarenkov

address: David Ben Gurion Blvd 1

institute: Ben Gurion University

summary: Abstract:  Background:  The severity of visceral adipose tissue (VAT) inflammation in individuals with obesity is thought to signify obesity sub-phenotype(s) associated with higher cardiometabolic risk. Yet, this tissue is not accessible for direct sampling in the non-surgical patient. We hypothesized that circulating miRNAs (circ-miRs) could serve as biomarkers to distinguish human obesity subgroups with high or low extent of VAT-inflammation.  Methods: Discovery and validation cohorts of patients living with obesity undergoing bariatric surgery (n=35 and 51, respectively) were included. VAT inflammation was classified into low/high based on an expression score derived from the mRNA levels of TNFA, IL6 and CCL2 (determined by rtPCR). Differentially-expressed circ-miRs were identified, and their discriminative power to detect low/high VAT inflammation was assessed by ROC-AUC analysis. Results: Fifty three out of 263 circ-miRs (20%) were associated with high VAT inflammation according to Mann-Whitney analysis in the discovery cohort. Of those, 12 (12/53=23%) were differentially expressed according to Deseq2, and 6 significantly discriminated between high and low VAT inflammation with ROC-AUC>0.8. Of the resulting 5 circ-miRs that were differentially abundant in all three statistical approaches, 3 were unaffected by hemolysis and validated in an independent cohort. Circ-miRs 181b-5p, 1306-3p, and 3138 combined with HOMA-IR exhibited ROC-AUC of 0.951 (95%CI:0.865-1) and 0.808 (95%CI:0.654-0.963) in the discovery and validation cohorts, respectively, providing strong discriminative power between participants with low versus high VAT inflammation. Predicted target genes of these miRNAs are enriched in pathways of insulin and inflammatory signaling, circadian entrainment, and cellular senescence.   Conclusions: Circ-miRs that identify patients with low versus high VAT inflammation constitute a putative tool to improve personalized care of patients with obesity.

overall_design: miRNA in n=35 plasma samples were from patients with high / intermediate / low VAT inflammation were sequenced

first: Yulia

last: Haim

first: Uri

last: Yoel

first: Yair

last: Pincu

first: Tanya

last: Tarnovscki

first: Idit

middle: F

last: Liberty

first: Ivan

last: Kukeev

first: Lior

last: Baraf

first: Oleg

last: Dukhno

last: Zilber

first: Matthias

last: Blüher

first: Assaf

last: Rudich

first: Isana

last: Veksler-Lublinsky


title: BET inhibition induces synthetic lethality in BRCA2-deficient pancreatic cancer via autophagy-dependent cell death

city: Davis

first: Chang-il

last: Hwang

address: One Shields Ave

department: Microbiology and Molecular Genetics

institute: University of California Davis


title: BET inhibition induces synthetic lethality in BRCA2-deficient pancreatic cancer via autophagy-dependent cell death [CUT&RUN]

summary: To model familial pancreatic cancer patients, we generated isogenic Brca2 deficient pancreatic cancer cell lines with CRISPR/Cas9. To investigate the changes in the enhancer landscape upon BET inhibition, we performed H3K27ac CUT-and-RUN-seq.

overall_design: Upon JQ1 treatment (1 µM) for 72 hrs, the control and Brca2 KO KPC cells were subjected to CUT-and-RUN-seq experiments.

first: EunJung

last: Lee

first: Keely

last: Ji

first: Suyakarn

last: Archasappawat


title: Systemic Epigenome-Wide Association Study of Elk Treponeme- Associated Hoof Disease

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary: Treponeme-associated hoof disease (TAHD) is an emerging disease of elk (Cervus canadensis) in the U.S. Pacific West. Because environmental epigenetics is the primary molecular process that mediates environmental factor impacts on a host organism and disease, the role of epigenetics in TAHD etiology was examined. The current study was designed to examine potential effects of TAHD on systemic epigenetic modifications in infected elk over a range of TAHD lesion severity. Leg tendons that contain predominantly fibroblast connective tissue cells were used to isolate fibroblast cells for epigenetic analysis in unaffected and TAHD-positive male and female Roosevelt and Rocky Mountain elk. DNA methylation in the tendon cells in the different groups was examined. Differential DNA methylation regions (DMRs) between the unaffected and TAHD-positive were identified for both female and male elk. The presence of TAHD was associated with alteration of the connective tissue cell epigenetics and DMR associated genes identified. Therefore, the infected elk were found to have a systemic epigenetic alteration that was associated with the disease despite TAHD pathology being generally limited to feet. Other cell populations with the elk are also anticipated to be affected, and if the elk germline epigenetics is altered then generational transmission of susceptibility to TAHD may impact subsequent generations through epigenetic inheritance. This first study of epigenetic changes associated with disease in elk suggests that TAHD promotes a systemic effect on the elk epigenetics which could exert health impacts on the elk.

overall_design: Study samples were obtained from Rocky Mountain elk collected in Washington, Idaho, and South Dakota and from Roosevelt elk from Washington, Oregon, and California. Treponeme-associated hoof disease was confirmed present or absent for each of the samples used in the study. DNA was isolated from tendon tissue, and methylated DNA was evaluated using methylated DNA immunoprecipitation followed by next generation sequencing (MeDIP-seq). DNA methylation levels along the genome were compared between TAHD-positive and unaffected groups to determine statistically significant Differentially Methylated Regions (DMRs)

first: Margaret

last: Wild

first: Kyle

last: Taylor

first: Eric

middle: E

last: Nilsson

first: Daniel

last: Beck


title: Next Generation Sequencing Quantitative Analysis of altered expression of genes in KRASG12D PDAC tissues

city: Guangzhou

first: Yao

last: Kong

address: Zhongshan Second Road

institute: Guangdong Provincial People's Hospital

summary: KRAS mutation is the most frequently mutated oncogene, occurring in approximately 90% of patients with PDAC, where KRASG12D is the most common allele in PDAC. Recent studies revealed that KRASG12D mutation caused the aberrant gene expression profile by regulating RNA processing to drive tumor progression (9, 17). However, the role of the KRASG12D mutation in triggering the circRNA process during tumor development remains unknown. Our study aims to explore the genes that regulates circRNA biogenesis in the LN metastasis of PDAC.

overall_design: To detect the gees that regulates circRNA biogenesis in LN metastasis of PDAC, the total RNA of KRASG12D PDAC tissues and paired normal adjacent tissues was extracted and the next generation sequencing was conducted to explore the expressing profile difference between PDAC tissues and paired normal adjacent tissues. The result was obtained from three independent experiments.

first: Changhao

last: Chen


title: Tumors produce glucocorticoids by metabolite recycling, not synthesis, and activate Tregs to promote growth

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary: Glucocorticoids are steroid hormones with potent immunosuppressive properties. Their primary source is the adrenals, where they are generated via de novo synthesis from cholesterol. In addition, many tissues have a recycling pathway in which glucocorticoids are regenerated from inactive metabolites by the enzyme 11β-HSD1 (encoded by Hsd11b1). Here we find that multiple tumor types express Hsd11b1 and produce active glucocorticoids. Genetic ablation of Hsd11b1 in such cells had no effect on in vitro growth but reduced in vivo tumor progression, which corresponded with increased frequencies of tumor-infiltrating CD8+ T cells (TIL) expressing activation markers and producing effector cytokines. Tumor-derived glucocorticoids were found to promote signatures of Treg activation and suppress signatures of Tconv activation in tumor-infiltrating Treg. Indeed, CD8+ T cell activation was restored and tumor growth reduced in mice with Treg-specific glucocorticoid receptor deficiency. Importantly, pharmacologic inhibition of 11β-HSD1 reduced tumor growth to the same degree as gene knockout, and rendered immunotherapy-resistant tumors susceptible to PD-1 blockade. Given that HSD11B1 expression is upregulated in many human tumors and that inhibition of 11β-HSD1 is well-tolerated in clinical studies, these data suggest that targeting 11β-HSD1 may be a beneficial adjunct in cancer therapy.

overall_design: B16.F10 mouse melanoma cells were implanted into Nr3c1-flox/flox and Nr3c1-flox/flox Foxp3-YFP/Cre recipient mice. Tumors were dissociated, Treg cells purified by FACS, total RNA extracted, and bulk RNA-seq performed by next generation sequencing.

first: Matthew

last: Taves

first: Shizuka

last: Otsuka

last: Cam

first: Jonathan

last: Ashwell


title: Development of potent antibody drug conjugates against ICAM1+ cancer cells in preclinical models of cholangiocarcinoma

city: ZHEJIANG

first: Bing

last: Zhu

state: 浙江

address: No.150 Dongfang street, Qiantang district, Hangzhou

institute: Institute of Basic Medicine and Cancer Chinese Academy of Sciences

summary:
We observed an interesting contradictory phenomenon that ICAM1-Dxd showed a very weak cytotoxicity on CCA cell lines in vitro, whereas it mediates more potent tumor attenuation than ICAM1-MMAE in vivo, suggesting the potency of ICAM1-Dxd may arise from its multifaceted biological activities instead of merely cytotoxicity.
To elucidate its underlying biomechanism, we performed a transcriptomic RNA sequencing (RNA-seq) to profile the signaling pathways and key genes affected by ICAM1-Dxd treatment in PDX tumor tissues.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PDX tumor tissues with different treatments (ICAM1-Dxd, ICAM1-MMAE, ICAM1 mAb,PBS)

first: Peng

last: Guo

first: Jie-Er

last: Ying


title: Integrated Analysis of Transcriptome and Secretome of Sensory Neurons Reveals Sex Difference in Pathways Relevant to Insulin Sensitivity and Insulin Secretion

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

summary: Sensory neurons in the dorsal root ganglia (DRG) convey somatosensory and metabolic cues to the central nervous system and release substances locally from stimulated terminal endings in peripheral organs. Sex-biased variations driven by the sex chromosome complement (XX and XY) have been implicated in the sensory-islet crosstalk. However, the identity of the molecules underlying male-female differences is not known. Here, we aim to characterize the molecular repertoire and the secretome profile of the spinal sensory neurons in sexually immature male and female mice to identify molecules with sex-biased insulin sensing- and/or insulin secretion-modulating activity. We used transcriptomics and proteomics to uncover differentially expressed genes and secreted molecules in DRG sensory neurons derived from 3-week-old male and female C57BL/6J mice. Comparative transcriptome and proteome analyses revealed differential gene expression and protein secretion in DRG neurons in males and females. Interestingly, gene ontology annotation highlighted sex differences in epigenetic regulation, cell cycle, DNA replication and insulin signaling pathways. Secretome analysis uncovered several sex-based variations in conventionally and unconventionally sensory-secreted proteins with potential roles in β-cell function-modulating activity. Collectively, we provide a valuable resource of molecular and secretory targets that can be leveraged for understanding sex differences in DRG sensory neurons. Some of these candidates have translational value as they can inform the development of novel sex-based therapeutic opportunities for individuals with compromised β-cell activity.

first: Sohyun

last: Moon

first: Jerry

middle: Y

first: Abdelfattah

last: El Ouaamari


title: BET inhibition induces synthetic lethality in BRCA2-deficient pancreatic cancer via autophagy-dependent cell death [RNA-Seq]

first: Chang-il

last: Hwang

state: CA

summary: To model familial pancreatic cancer patients, we generated isogenic Brca2 deficient pancreatic cancer cell lines with CRISPR/Cas9. To investigate the changes in the transcriptome profiles upon BET inhibition, we performed RNA-seq.

overall_design: Upon JQ1 treatment (1 µM) for 72 hrs, the control and Brca2 KO KPC cells were subjected to RNA-seq experiments.

first: EunJung

last: Lee

first: Keely

last: Ji

first: Suyakarn

last: Archasappawat


title: Comparing the adrenal gland microbiota composition between healthy subjects and patient with adrenal corticoma

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

summary: The aim of this study is to evaluate the presence of intratumoral microbiome in 26 human ACC tissues versus 9 healthy adrenals.

overall_design: Total DNA was extracted from the biopsies of the subjects, 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: Michela

last: Luconi

first: Giulia

last: Cantini

first: Amedeo

last: Amedei

first: Leandro

last: Di Gloria

first: Elena

last: Niccolai


title: Gene expression profile at single cell level of  islet cells from normoglycemic or hyperglycemic mice

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

institute: HUJI

summary: The purpose of the experiment was  to investigate the heterogeneity  of islet cell response, especially beta-cells to hyperglycemia induced by severe insulin resistance in mice.

overall_design: Mice were implanted with osmotic pumps containing PBS or S961 insulin receptor antagonist (12nM).  S961-treated  mice developed hyperglycemia within 24h. Pancreatic islets were isolated 5 days after transplantation, dissociated into single cell suspension and stained for propidium iodide. Propidium iodide-negative live cells were FACS-sorted and single cells captured in droplet emulsions to generate libraries using a Chromium Single-cell instrument (10X Genomics).

first: Yuval

last: Dor

first: Tehila

last: Dahan

first: Agnes

last: Klochendler


title: Cell-matrix interactions control biliary organoids polarity,architecture and differentiation and can be exploited to improve modelling of biliary diseases.

city: New Haven

first: Mario

last: Strazzabosco

address: 300 Cedar street

institute: Yale School of Medicine

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

overall_design: Refer to individual Series


title: Single-nucleus RNA-sequencing reveals NRF1/NFE2L1 as a key determining metabolic state and fate decision of brown adipocytes in mice [bulk RNA-seq]

city: Shenyang

first: Wei

last: Shen

state: Liaoning

address: No. 77 Puhe Road, Shenyang North New Area

department: School of Public Health

institute: China Medical University

summary: Brown adipose tissue (BAT) is a major site of nonshivering thermogenesis (NST) in mammals and might play an important role in human obesity and energy homeostasis. Recent single-cell/nucleus RNA-sequencing studies have revealed heterogeneity in thermogenesis among brown adipocytes, such as the findings of low thermogenesis and regulated thermogenesis in brown adipocytes. Activating and enhancing function adipocytes (BAC) has acquired attention as a possible therapeutic intervention for metabolic diseases. Nuclear factor-erythroid 2-related factor 1 (NFE2L1, also known as Nrf1), a CNC-bZIP protein, is a master regulator of multiple cellular functions and responds to various stress in many cells and tissues. NFE2L1 acts as a guardian role in BAC function providing increased proteometabolic quality control for adapting to cold or obesity. Our previous studies demonstrated that NFE2L1-dependent lipolytic activity is crucial for white adipose tissue (WAT) plasticity and lipid homeostasis. To further clarify the role of NFE2L1 in adipocytes, we focused on the phenotype and gene expression profiling of BAT in adipocyte-specific Nfe2l1-knockout [Nfe2l1(f)-KO] mice. We found that deletion of Nfe2l1 decreased core body temperature and cold intolerance under cold exposure. Compared with floxed mice, the BAT of Nfe2l1(f)-KO mice expressed substantially lower levels of many genes related to lipolysis, thermogenesis, oxidative capacity of mitochondria, cellular respiration while higher genes related to inflammation, pyroptosis. By snRNA-seq, we found that Nfe2l1-knockout resulted in increased antigen processing and presentation (APP), necroptosis and NOD-like receptor signal pathway (NOD) signaling pathways in most subpopulations of BAC, with devastating effects on a normal subpopulation of BAC with low thermogenesis and high necroptosis genes expression. Absent of Nfe2l1 impairs the function of BAC, causing a morphological “whitening” phenotype with adipocyte hypertrophy and severe inflammation. Moreover, the adipose inflammation and pyroptosis in Nfe2l1(f)-KO mice could be mitigated by cold exposure or β3-agonist treatment. These findings provided a deeper insight into the function of NFE2L1 in the metabolic programming of brown adipocytes.

overall_design: Bulk RNA-sequencing profiles of BAT from Flox and Nfe2l1(f)-KO mice at 4 and 14~16 weeks.

first: Suping

last: Ren

first: Zhuo

last: Zuo

first: Yongyong

last: Hou


title: Single-nucleus RNA-sequencing reveals NRF1/NFE2L1 as a key determining metabolic state and fate decision of brown adipocytes in mice [scRNA-seq]

overall_design: Single-nucleus RNA-sequencing profiles of BAT from Flox and Nfe2l1(f)-KO mice at 4 weeks.


title: Single-cell RNA sequencing reveals cellular and molecular heterogeneity in fibrocartilaginous enthesis formation

city: chang sha

first: zhang

last: tao

address: xiangya street

institute: xiangya hospital

summary: The attachment site of the rotator cuff (RC) is a classic fibrocartilaginous enthesis, which is the junction between bone and tendon with typical characteristics of a fibrocartilage transition zone. Enthesis development has historically been studied with lineage tracing of individual genes selected a priori, which does not allow for the determination of single-cell landscapes yielding mature cell types and tissues. Here, in together with open source GSE182997 datasets (3 sample) provided by Fang et al, we applied Single-cell RNA sequencing (scRNA-seq) to delineate the comprehensive postnatal RC enthesis growth and the temporal atlas from as early as postnatal day 1 up to postnatal week 8. And we furtherly performed single cell spatial transcriptomic sequencing on postnatal day 1 mice enthesis, in order to deconvoluted bone-tendon junction (BTJ) chondrocytes onto spatial spots. In summary, we deciphered the cellular heterogeneity and the molecular dynamics during fibrocartilage differentiation. Combined with current spatial transcriptomic data, our results provide a transcriptional resource that will support future investigations of enthesis development at the mechanistic level and may shed light on the strategies for enhanced RC healing outcomes.

overall_design: The humeral head- supraspinatus tendon samples were dissected from the left shoulders of C57/BL6 mice at postnatal day-1, day-7, day-14, and day-28. In general, samples were harvested from pooled sibling limbs of two litters (five to six limbs per pool). Following dissection, the humeral heads and tendons were trimmed to retain the enthesis part, and all the samples were minced immediately and digested in type I collagenase (1mg/ml, Gibico) and type II collagenase (1mg/ml, Gibico) diluted in low-glucose DMEM (Gibco) solution at 37 °C for 30-40 min. Freshly isolated cells were resuspended into FACS buffer containing 2% FBS (Gbico) in PBS. Cell suspensions were stained with antibodies including Ter119-Alexa700 and Cd45- Alexa700 (Biolengend) to remove blood cells. DAPI (BD) stain was used to exclude dead cells. Flow cytometry was performed on BD FACS Aria II, single cells were gated using doublet-discrimination parameters and collected in FACS buffer. 8000-10,000 cells were loaded for each age group by Chromium instrument and its chemistry kit V3 (10X Genomics) according to the manufacturer’s guidance. Each cell was encapsulated with a barcoded Gel Bead in a single partition, then amplified to generate single-cell cDNA libraries and sequenced on an Illumina NovaSeq 6000 platform at a sequencing depth of ~500 million reads. The Cellranger pipeline (version 6.1.1) was used to align the raw reads to the mouse reference genome GRCm38 and to generate feature-barcode matrices. All the low-quality reads were filtered with default parameters.

first: wan

last: liyang

first: lu

last: hongbin


title: Insulin Receptor Loss Impairs Mammary Tumorigenesis in Mice

city: Toronto

first: Vuk

last: Stambolic

state: Ontario

address: 101 College Street

country: Canada

institute: University of Toronto/University Health Network

summary:
To investigate the role of Insr in processes affecting tumor initiation, we generated Comma1D luminal cells with a CRISPR Insr knockout.
We then performed RNA-seq followed by differential gene expression analysis and pathway enrichment analysis.

overall_design: Differential gene expression analysis of RNA-seq data for wild-type Comma1D cells and Comma1D cells with CRISPR Insr knockout.

first: Lauren

last: Podmore

first: Caterina

last: Iorio

first: Kevin

last: Nixon


title: Effect of assisted reproduction on maternal immune cells

city: Philadelphia

first: Scott

middle: Michael

last: Gordon

state: PA

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

summary: To investigate differences in gene expression between bulk NK cells from naturally cycling endometrium versus bulk NK cells from superovulated endometrium, we performed bulk RNAseq of sort-purified endometrial NK cells.

overall_design: Paired-end bulk RNA sequencing to compare gene expression in sorted CD45+CD3-CD56+ cells from human endometrium during the natural window of implantation versus in the context of superovulation

first: Monica

last: Mainigi


title: Bulk RNA sequencing of cytotoxic T lymphocytes of OT1 mice

first: daniel

last: beiting

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: We found that MC38 tumor-conditioned medium(TCM) treatment significantly impacted multiple pathways including cholesterol metabolism pathway of CTLs. Further analysis of cholesterol metabolism pathway, we observed that Cholesterol-25-hydroxylase(Ch25h) expression was significantly downregulated after treated with TCM compared to treated with fibroblasted-conditioned medium(FCM). In the meanwhile, we found that activating transcription fator 3(Atf3) was signifcantly upregulated after TCM treatment. Finally, we investigated the Atf3-Ch25h axis regulating CTLs function in tumor context.

overall_design: Splenocytes were isolated from WT OT1 mice and stimulated with OVA peptide for 48 hours followed by FCM or TCM treatment for 8 hours. After that, RNA was extracted using mini RNA isolation kit and concentration was measured using nanodrop2000.

first: Zhen

last: Lu

first: Daniel

last: Beiting

first: Serge

last: Fuchs


title: N6-methyladenosine (m6A) RIP-seq in SK-Hep-1 cells

city: Jinan

first: Tao

last: Su

address: 440 Jiyan Rd

institute: Shandong Cancer Hospital and Institute

summary: To explore the m6a modification in SK-Hep-1 cells, we performed RNA immunoprecipitation with an antibody against m6a (SYSY), and sequencing was performed using Illumina NovaSeq 6000

overall_design: RIP assay was performed using m6a (SYSY) antibody in SK-Hep-1 cells and the enriched RNA was sequenced with input sample

first: Nasha

last: Zhang

first: Teng

last: Wang

first: Ming

last: Yang


title: Effect of knockdown LINC01089 on gene expression in SK-Hep-1 cells

summary: To explore the effect of LINC01089 on gene expression and alternative splicing, we established stable LINC01089 knockdown cell lines in SK cells and perfromed RNA-seq.

overall_design: We established stable LINC01089 knockdown cell lines in SK cells through lentiviral infection.Then the knockdown groups (sh1089-1 and sh1089-2) and control cells (shNC) were subjected to RNA-seq to explore the effect of LINC01089 on gene expression


title: A unique epigenomic landscape defines CD8+ tissue-resident memory T cells [multiome]

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Multiome datasets of CD8+ T cells in LCMV and HSV infections

first: Frank

middle: A

last: Buquicchio

first: Raissa

last: Fonseca

first: Ansuman

middle: T

last: Satpathy

first: Laura

last: Mackay


title: Genome-wide Map of R-loop Reveals its interplays with Transcription and Genome Integrity during Germ Cell Meiosis

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

summary: R-loop is a three-strand nucleic acid structure composed of mRNA and DNA. In mammalian meiotic cells, R-loop mainly distributed at promoter-related regions, and combined with systematically transcriptome analysis showed R-loop was closely related to transcription in meiotic process. Moreover, knockout of Rnaseh1 in meiotic cells caused mice completely sterile with R-loop accumulation and abnormal DSB repairing in spermatocytes. Further analysis showed R-loop accumulation in leptotene/zygotene influenced transcriptional regulation in pachytene stage. Thus, mutual regulation of R-loop and transcription plays essential role in spermatogenesis.

overall_design: A total of 12 samples were analyzed in this study, including WT and Rnaseh1 knock-out spermatogenic cells from two stages, leptotene/zygotene and pachytene. Each biological samples has three replicates.

first: Yu

last: Jiang

first: Fei

last: Huang

first: Lu

last: Chen

first: Yunwen

last: Wu

first: Mengyan

last: Jia

first: Hengyu


title: Metabolic dependencies of metastasis-initiating cells in breast cancer [RNA-seq]

city: Lausanne

first: Candice Megan

last: Young

state: Vaud

address: Rue du Bugnon 25A

department: SV

country: Switzerland

institute: EPFL

summary: We investigated gene expression changes in response to acetate treatment, which results in increased MIC-frequency, H3K27ac, and metastatic potential.

overall_design: Comparative gene expression analysis between cells that have been treated for 48 hours with vehicle or acetate treatment

first: Candice

middle: M

first: Laurent

last: Beziaud

first: Pierre

last: Dessen

first: Angela

last: Madurga-Alonso

first: Joerg

last: Huelsken


title: Cannabidiol (CBD) exposure during gestation leads impaired cardiac function exclusively in male rat offspring

city: London

first: Daniel

middle: B

last: Hardy

address: 1151 Richmond St

department: Physiology & Pharmacology

institute: Western University

summary: The primary objective of this study was to investigate the imapcts of maternal exposure to CBD on offsrping cardiac function and to gain mechanistic insights underlying the functional impacts. Pregnant rats were randomly assigned to a treatment group; (1) vehicle control, (2) 3 mg/kg/day or (3) 30 mg/kg/day i.p. CBD from gestational day 6-22. Primary findings indicate that excusively male offsrping exhibit impaired cardiac function. The primary findings in the heart transcriptome data indicates several GO terms suggesting altered pathways involving mitochondrial metabolism and developmental pathways.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq (Genome Québec Innovation Centre, QU, Canada) data for hearts of three-week-old male wistar rat offsrping exposed to 3 or 30 mg/kg/day CBD in gestation (7 vehicle control animals, 6 CBD3 animals and 5 CBD30 animals).

first: Kendrick

last: Lee

first: Sebastian

last: Vanin

first: Mina

last: Nashed

first: Mohammed

middle: H

last: Sarikahya

first: Steven

middle: R

last: Laviolette

first: David

last: Natale


title: Single nuclei RNAseq of human fetal cardiac cells from the epicardium of 10PCW and 11PCW

city: Los Angeles

first: Stanislao

last: Travisano

address: 4650 Sunset Blvd

department: Cardiothoracic Surgery

institute: Children's Hospital Los Angeles

summary: Here we characterize human fetal cardiac lymphatic vessel development and reveal a new role for cells that reside in the epicardium as a source of progenitors involved in cardiac lymphatic differentiation. The single nuclei (sn) Multiome data of the human heart reveal the plasticity and the heterogeneity of the cardiac lymphatic endothelium. We have captured nuclei from a novel population of lymphatic progenitors in the epicardium and performed an integrative snRNAseq and snATACseq analysis to define the gene expression and gene regulatory landscape of these cardiac lymphatic cells in human fetal hearts.

overall_design:
Micro-dissection of the epicardial layer of the human fetal hearts surface was performed at post-conception week 10 and 11 before lysis of the nuclei and processing for 10x Genomics "Chromium Single Cell Multiome ATAC + Gene Expression". Expression profiling by high throughput sequencing and Genome binding/occupancy profiling by high throughput sequencing from 2 different time points 10 PCW (n=2) and 11 PCW (n=3).
ATAC-seq data not provided due to patient privacy concerns

first: Ching-Ling

last: Lien


title: Epigenomic analysis reveals a unique DNA methylation program of metastasis-competent circulating tumor cells in colorectal cancer

city: Santiago de Compostela

first: Angel

last: Diaz-Lagares

state: A Coruña

address: C/ Choupana s/n

department: ONCOMET

institute: Health Research Institute of Santiago (IDIS)

type: Methylation profiling by genome tiling array

summary: Metastasis is the main cause of cancer-related deaths in patients with solid tumors, including colorectal cancer (CRC). Circulating tumor cells (CTCs) and epigenetic alterations are involved in the development of metastasis. It is important to characterize the DNA methylation pattern of metastasis-competent CTCs to better understand the metastatic process and obtain new clinical applications for cancer patients. Therefore, the aim of this study was to investigate the DNA methylation landscape of metastasis-competent CTCs in CRC. The DNA methylome of the human colorectal cancer-derived cell line CTC-MCC-41 was compared with primary (HT29, Caco2, HCT116, RKO) and metastatic (SW620 and COLO205) CRC cells using a genome-wide methylation analysis.

overall_design: The DNA methylome of the human colorectal cancer-derived cell line CTC-MCC-41 was compared with primary (HT29, Caco2, HCT116, RKO) and metastatic (SW620 and COLO205) CRC cells using a genome-wide methylation analysis. The association between the methylation and the transcriptional profile of CTC-MCC-41 was also evaluated. Differentially methylated CpGs were validated with pyrosequencing and qMSP.


title: Learning the sequence code for mRNA and protein abundance in human immune cells

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

institute: Sanquin

summary: mRNA and protein abundance are defined by transcriptional and post-transcriptional regulatory mechanisms. Here, we develop a machine learning pipeline, termed SONAR, to decipher the endogenous sequence code that determines mRNA and protein abundance in human cells. SONAR models predict up to 62% of mRNA and 63% of protein abundance independent of promoter or enhancer information, and reveal a strong—yet dynamic—cell-type specific sequence code. We also find that the effect of sequence features is dependent on their location within the mRNA transcript. Using SONAR, we design synthetic 3’UTRs, with which protein expression levels can be manipulated and tailored to a specific cell-type. Beyond its fundamental findings, our work provides novel means to improve immunotherapies and biotechnology applications.

overall_design: A parallel reporter assay was performed to test the effect of synthetic 3'UTR sequences on GFP protein expression. HeLa cells, HEK cells, CD8+ T cell and CD4+ T cells were transduced with a GFP-3'UTR retroviral library containing ±500 distinct synthetic 3'UTR sequences. Transduced cells were subsequently sorted for GFPhi or GFPlo cells. gDNA was isolated from these populations, 3'UTR sequences were amplified and sequenced to asses abundances

first: Benoît

last: Nicolet


title: Real-time quantitative PCR analysis of microRNAs in a mice model of Neurogenic Heterotopic Ossifications (NHOs)

city: Clamart

first: Jules

last: GUEGUEN

address: 1 Rue Lieutenant Raoul Batany

country: France

institute: French Armed Forces Biomedical Research Institute (IRBA)

summary: Neurogenic heterotopic ossifications are intramuscular bone formations developing following central nervous system injury. The pathophysiology is poorly understood and current treatments for this debilitating condition remain unsatisfying. Here we explored the role of miRNAs in a clinically relevant mouse model that combines muscle and spinal cord injury (SCI), and in patients’ cells. We found an osteo-suppressive miRNAs response in injured muscle that was hindered when the spinal cord injury was associated. In isolated fibro-adipogenic progenitors from damaged muscle (cells at the origin of ossification), spinal cord injury induced a downregulation of osteo-suppressive miRNAs while osteogenic markers were overexpressed. The overexpression of selected miRNAs in patient’s fibro-adipogenic progenitors inhibited mineralization and osteo-chondrogenic markers in vitro. Altogether, we highlighted an osteo-suppressive mechanism involving multiple miRNAs in response to muscle injury that prevents osteogenic commitment and which is ablated by the neurologic lesion in heterotopic ossification pathogenesis. This provides new research hypotheses for preventive treatments.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: These data were generated from RT-qPCR miRNA arrays on pooled samples (n=3 independant biological replicates) from control (SHAM+PBS), damaged (SHAM+CDTX), spinalized (SCI+PBS) or NHOs developping (SCI+CDTX) muscles from mice gastrocnemius biopsy at 2 or 4 days after induction. MicroRNAs screening was performed using miRNome Mouse&Rat panel I+II (V5, 339322, Qiagen). These results were subsequently validated in RT-qPCR for each individual donor (n=6 independant biological replicates) in the linked manuscript.

last: Gueguen

first: Dorothée

last: Girard

first: Bastien

last: Rival

first: Juliette

last: Fernandez

first: Marie-Emanuelle

last: Goriot

first: Sébastien

last: Banzet


title: Age-associated changes in murine endothelial gene expression and chromatin accessibility correlate with impaired blood-brain barrier integrity and elevated risk of intracerebral hemorrhage [RRBS]

city: Saarbruecken

first: Gilles

last: Gasparoni

state: Saarland

address: Campus

department: Genetics Department

country: Germany

institute: Saarland University

summary: Intracerebral hemorrhage (ICH), a devastating form of stroke, is a leading global cause of human death and disability. The major risk factors for ICH include increasing age, hypertension and cerebral amyloid angiopathy. Despite high mortality and morbidity associated with ICH, the mechanisms leading to blood-brain barrier (BBB) dysfunction with age and development of hemorrhagic stroke is poorly understood. In the vasculature of the central nervous system, endothelial cells (ECs) constitute the core component of the BBB and provide a physical barrier due to tight junctions, adherens junctions, and basement membrane layers. In this study, we show in brains of mice that incidents of intracerebral bleeding increase with advancing age. After isolation of an enriched population of cerebral ECs, we studied gene expression in ECs isolated from murine brains of increasing ages of 2, 6, 12, 18, and 24 months. The study reveals age-dependent dysregulation of 1388 genes in the ECs, including many involved in the maintenance of BBB and vascular integrity. Since epigenetic mechanisms regulate gene expression, we also investigated age-dependent changes at the levels of CpG methylation and accessible chromatin in cerebral ECs. Our study reveals correlations between age-dependent changes in chromatin structure and gene expression. We find significant age-dependent downregulation of the apelin receptor (Aplnr) gene along with an age-dependent reduction in chromatin accessibility of the promoter of this gene. Aplnr is known to play a crucial role in positive regulation of vasodilation and is implicated in vascular health. Interestingly, we also observe an age-dependent reduction in the protein expression levels of the apelin receptor in the brain, potentially implicating the apelin receptor to be critical for the increased risk of intracerebral hemorrhage with ageing.

overall_design: Reduced Representation Bisulfite Sequencing.

first: Kshitij

last: Mohan

first: Abdulrahman

last: Salhab

first: Michael

last: Orlich

first: Robert

last: Geffers

first: Steve

last: Hoffmann

first: Ralf

last: Adams

first: Jörn

last: Walter

first: Alfred

last: Nordheim


title: Age-associated changes in murine endothelial gene expression and chromatin accessibility correlate with impaired blood-brain barrier integrity and elevated risk of intracerebral hemorrhage

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

overall_design: Refer to individual Series


title: Identification of 5-methylcytosine associated genes in osteoarthritis

city: zhengzhou

first: yang

last: yu

state: henan province

address: jianshe road

department: Department of orthopedics

institute: the First Affiliated Hospital of Zhengzhou University

summary: Our study aimed to identify common m5C features in OA. We identified we found 35828 m5C peaks and mapped up to 11720 annotated genes in OA samples, and we found 16259 m5C peaks and mapped up to 7504 annotated genes in normal samples, indicating an overall hypermethylated level in the OA cartilage.

overall_design: We collected three OA knee cartilage tissues and three normal knee cartilage tissues to obtain the transcriptome-wide m5C modification profile of genes in OA by methylated RNA immunoprecipitation next-generation sequencing (MeRIP-seq).

first: Yang

last: Yu

first: Shitao

last: Lu

first: Jianzhong

last: Xu


title: A Novel Transcription Factor Combination for Direct Reprogramming to a Spontaneously Contracting Human Cardiomyocyte-like State

city: Chicago

first: Hananeh

last: Fonoudi

address: 320 E Superior st.,

department: Pharmacology

institute: Northwestern University

summary: To investigate the transcriptome changes during reprogramming of of human cardiac fibroblasts to cardiomyocytes

overall_design: Comparative gene expression profiling analysis of RNA-seq data for three primary cardiac fibroblasts (1274-20, 1289-20,1309-21) before and after reprogramming

first: Marisol

last: Romero-Tejeda

first: Paul

last: Burridge


title: In-Flight Human Skeletal Muscle Tissue Chip Autonomous Payload: Validation of Fiber Type and Metabolic Changes Due to Space Flight

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

summary: Our muscle tissue chip platform provides a novel approach to studying the cell autonomous effects of microgravity on muscle cell biology

overall_design: CD56 myoblasts-derived from young active and old sedentary muscle biopsies, differentiated into functional myobundles, that exhibited classic skeletal muscle bio-functions, were subjected to microgravity. We report on the differences in gene expression  profiling between the flight young- vs old-derived myobundles and ground young- vs old-derived myobundles. A minimum of three biological replicates was used for RNA seq.

first: Maddalena

last: Parafati

first: Shelby

last: Giza

first: Tushar

middle: S

last: Shenoy

first: Siobhan

last: Malany


title: ZmRPN1 confers quantitative variation in pollen number and boosts hybrid seed production in maize

city: Beijing

first: Luguang

last: Jiang

state: Beijing

address: No.2 Yuanmingyuan West Road, Haidian, Beijing

institute: China Agricultural University

summary: The number of pollen grains is a critical determinant of reproductive success in seed plants and varies among species and individuals. However, in contrast with many mutant-screening studies relevant to anther and pollen development, the natural genetic basis for variations in pollen number remains largely unexplored. To address this issue, we carried out a genome-wide association study in modern maize, ultimately revealing that a large variance of the absence or presence of sequences in the promoter region of Zea mays RPN1 (ZmRPN1) alters its expression level and thereby contributes to pollen number variation. Molecular analyses showed that ZmRPN1 interacts with ZmMSP1, an ortholog of the male germline cell number regulator in Arabidopsis and rice, and facilitates ZmMSP1 localization to the plasma membrane. Importantly, ZmRPN1 dysfunction resulted in a substantial increase in pollen number, consequently boosting seed production by increasing female-male planting ratio. Together, our findings uncover a key gene controlling pollen number, and therefore modulation of ZmRPN1 expression could be efficiently used to develop elite pollinators for modern hybrid maize breeding.

overall_design: RNA-seq liabraries were prepared using S3-S5 stage anthers from zmrpn1-1 and wild-type plants


title: Vitrification preserves follicular transcriptomic dynamics during ex vivo ovulation

city: Pitscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

institute: Rutgers University

summary: Vitrification is a method for long-term biological sample cryopreservation without causing intra- and extra-cellular ice formation. We recently established a novel closed vitrification system to cryopreserve mouse ovarian follicles. Using the 3D alginate hydrogel encapsulated in vitro follicle growth (eIVFG) method, we have demonstrated that compared to freshly-harvested follicles, vitrified follicles have normal follicle and oocyte reproductive outcomes. Our recent study further demonstrated the faithful preservation of molecular signatures of follicle-stimulating hormone (FSH)-stimulated follicle maturation in vitrified follicles. However, it is unknown whether ovulation, another crucial gonadotropin-dependent follicular event, and involved ovulatory gene regulatory pathways are well conserved in vitrified follicles. Fresh and vitrified follicles grown for 8 days by eIVFG were collected at 0, 1, 4 and 8-hour post human chorionic gonadotropin (hCG) treatment for the single-follicle RNA sequencing. Principal component analysis (PCA) and Pearson’s correlation analysis revealed that vitrified follicles have similar transcriptomic profiles to fresh follicles. Furthermore, the expression of several genes essential for ovulation were comparable between vitrified and fresh follicles. In summary, these results demonstrate that our closed vitrification system preserves follicular transcriptomic dynamics during ex vivo ovulation. Together with our previous findings that vitrification preserves FSH-stimulated follicle maturation, the integration of vitrification of immature follicles and eIVFG has a great potential to serve as an additional fertilization preservation approach for young cancer patients and endangerers species. Moreover, follicle vitrification enables a high-content ovarian follicle biobank, which can greatly improve the throughput of eIVFG for studying ovulation biology, anovulatory disease, toxicology, and novel contraceptive drug development targeting ovulation.

first: Jiyang

last: Zhang

first: Daniela

middle: D

last: Russo

first: Yingzheng

last: Wang

first: Qiang

first: Mary

last: Zelinski

first: Alex

last: Shalek

first: Brittany

last: Goods


title: Single-nucleus RNA-sequencing reveals NRF1/NFE2L1 as a key determining metabolic state and fate decision of brown adipocytes in mice

city: Shenyang

first: Wei

last: Shen

address: No. 77 Puhe Road, Shenyang North New Area

institute: China Medical University


title: RNAseq of Pdgfb' brain cells obtained by from young male mice

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: RiboTag mice B6N.129-Rpl22tm1.1Psam/J (# 011029, Jackson Laboratories), which carry a conditional Rpl22 allele (Sanz et al., 2009; doi: 10.1073/pnas.0907143106),were crossed with Pdgfb-iCreER mice that are tamoxifen-inducible form of Cre recombinase in vascular endothelial cells (Claxton et al., 2008; doi: 10.1002/dvg.20367),to generate Ribotag-Pdgf-β1 Cre mice

overall_design: we compared the effect of ischemia (ipsilateral cortex, CI) versus control (contralateral cortex, CC) at day 1.

first: Maria

last: Arbaizar-Rovirosa

first: Mattia

last: Gallizioli

first: Anna

last: Planas

first: Juan

middle: J

first: Julia

last: Sidorova


title: RNAseq of sorted CD31+ endothelial cells obtained by FACS from brain of young (3-4 months) male mice 1 day post-ischemia

summary: CD31+brain  endothelial cells obtained from the brain of C57BL/6 mice 1 day after ischemia (tMCAo) or control mice

overall_design: we compared the effect of ischemia (G1) versus control (G3) at day 1.


title: Bulk RNA-seq of CRISPRi ADGRG6-kd iAT2 following cigarette smoke exposure

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

summary: We performed bulk transcriptomic profiling of induced human pluripotent stem cells (iPSCs)-derived type 2 alveolar epithelial cells (iAT2). iPSCs stably expressed CRISPRi (dCas9-KRAB) under the control of doxycyline. iAT2s were transduced with a lentivirus expressing gRNA targeting the transcriptional start site of ADGRG6. Cells were treated with or without doxycyline to intiate CRISPRi-knockdown. Cells were plated at an air-liquid interface, then subsequently exposed to air or 5% cigarette smoke using a VitroCell smoke robot.  Cells were harvested for bulk RNA sequencing 8 hours post cigarette smoke exposure

overall_design: Bulk transcriptomic analysis of iPSC-derived type 2 alveolar epithelial cells (iAT2) comparing wild-type cells with CRISPRi-mediated knockdown of ADGRG6 following exposure to air or 5% cigarette smoke exposure

first: Rhiannon

last: Werder

first: Andrew

last: Wilson


title: CHK1-driven SENP2 S344 phosphorylation under laminar flow prevents endothelial activation-regulated fibrosis and atherogenesis while preserving endothelial lineage

city: Houston

first: Shengyu

last: Li

state: TX

address: 6670 Bertner Ave, R10-109, floor 10

institute: Houston Methodist Research Insitute

summary: BACKGROUND: The deSUMOylase SENP2 exerts athero-protective effects by inhibiting endothelial cell (EC) activation through attenuating ERK5 and p53 SUMOylation. Publicly available datasets show that SENP2 S344  is phosphorylated by Checkpoint Kinase 1 (CHK1), but the functional role remains unknown.     METHODS: Mouse SENP2 S343A (human S344A) phosphodeficient knock in (KI) mutant was generated by CRISPR/Cas9, and vascular-specific function was assessed via bone marrow transplantation (BMT). ECs from KI and wild type (WT) mice were exposed to smooth (laminar flow; l-flow) or grooved (disturbed flow; d-flow) cone-and-plate devices and characterized by RNA sequencing (RNA-seq).      RESULTS: L-flow increased CHK1 S280 and SENP2 S344 phosphorylation, which inhibited ERK5 and p53 SUMOylation and atherogenesis in vivo. BMT-generated vascular specific SENP2 S344A KI showed more atherogenesis but thinner fibrous cap formation specifically in the aortic arch area (d-flow) compared to that of WT mice. Ionizing radiation (IR) decreased CHK1 expression and SENP2 S344 phosphorylation, which might account for differences between systemic and BMT-generated vascular specific SENP2 S344A KI models. RNA-seq data analysis showed that SENP2 S344 phosphorylation in ECs in response to l-flow inhibited EC activation and fibrotic changes without interfering EC lineage phenotype. Lastly, l-flow-induced expression of genes was regulated by SENP2 S344 phosphorylation through ERK5 activation and inhibited EC apoptosis.     CONCLUSIONS: We uncovered a novel mechanism by which l-flow inhibits EC activation, including proliferation, migration, inflammation, and fibrotic changes, via upregulating CHK1-mediated SENP2 S344 phosphorylation to attenuate atherogenesis. We also uncovered a unique expression pattern of fibrotic changes without affecting EC lineage, which is distinct from endothelial-to-mesenchymal transition and therefore should be considered a unique type of EC activation for its potential role in vulnerable plaque formation.

first: Minh

last: Nguyen

first: Masaki

last: Imanishi

first: Khanh

last: Chau

first: Kyung

last: Ko

first: Sivareddy

last: Kotla

first: Venkata

last: Samanthapudi

first: Ling-Ling

last: Lee

first: Priyanka

last: Banerjee

first: Loka

last: reddy Velatooru

first: Rei

last: Abe

first: Elena

last: McBeath

first: Keigi

last: Fujiwara

first: Mae

last: Borchrdt

first: Estefani

last: Berrios Turcios

first: John

last: Cooke

first: Guangyu

first: Jun-ichi

first: Nhat-Tu

last: Le


title: Alteration of global transcription by the phytochemical Kaempferol in Acinetobacter baumannii AB5075

city: Uxbridge

first: Rubén

last: de Dios

state: Middlesex

address: Kingston Lane

department: Life Sciences

institute: Brunel University London

summary:
We perform RNA-seq comparing a treatment with 0.375 mM Kaempferol  to a mock treatment (DMSO) in A. baumannii AB5075 in order to describe the alterations in global transcription produced by this phytochemical.
A. baumannii AB5075 cultures were grown in LB medium in the presence of 0.375 mM Kaempferol or a DMSO control (3 biological replicates per condition) until reaching mid-exponential phase. At this point, cells were harvested, treated with RNAlater for preservation of total RNA and stored at -80 C. After that, total RNA was extracted from each sample.
As a result,  99 genes appeared upregulated in the presence of Kaempferol whereas 18 were downregulated. In highlights, the gene functional groups showing the strongest transcriptional alterations were those related to iron acquisition, siderophore biosynthesis and iron transport genes.

overall_design: Three independent replicates of A. baumannii AB5075 were grown to mid-exponential phase in cation-adjusted Muller-hinton (pH 7.2) medium supplemented with 0.375 mM Kaempferol and compared to three independent replicates grown in the same conditions but receiving a mock treatment (equivalent volume of DMSO).

first: Kavita

last: Gadar

first: Nikol

last: Kadeřábková

first: Despoina

last: Mavridou

first: Ronan

last: McCarthy


title: CFL1-induced super enhancer RNA m6A modification promotes local chromatin accessibility and oncogenes transcription in pancreatic cancer [m6A-seq]

city: Guangzhou

first: Rui

last: Li

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary:
Herein, we describe the landscape of m6A on super enhancer RNAs (seRNAs) in pancreatic ductal adenocarcinoma (PDAC) and demonstrate a regulatory axis involving m6A-seRNAs, H3K4me3 modification, chromatin accessibility and oncogenic transcription.
our study has revealed the CFL1-YTHDC2-MLL1 epigenetic regulatory axis plays critical roles of dynamic m6A deposition in seRNAs and local chromatin state, which may be a novel oncogenic mechanism in PDAC and shed light on the crosstalk between epitranscriptome and epigenome.

overall_design: m6A-seq data of PANC-1

first: Hongzhe

last: Zhao

first: Xudong

last: Huang


title: Age-associated changes in murine endothelial gene expression correlate with impaired blood-brain barrier integrity and elevated risk of intracerebral hemorrhage.

city: Oxford

first: Kshitij

last: Mohan

address: CVMed, Level 5, John Radcliffe Hospital

department: Radcliffe Department of Medicine

institute: University of Oxford

summary: We studied changes in gene expression in Endothelial Cells isolated from murine brains of increasing ages of 2, 6, 12, 18, and 24 months. We then performed linear regression analysis to compare the changes in gene expression in the endothelial cells with age.

overall_design: We performed RNA-seq on 6 biological replicates (3 males and 3 females) of 2,6,12,18 and 24 months. We then compared the changes in gene expression with age using linear regression after correcting for differences in sex.

first: Robert

last: Geffers

first: Gilles

last: Gasparoni


title: Proteogenomics reveals two distinct biological pilocytic astrocytoma subgroups

city: Homburg (Saar)

first: Marc

last: Remke

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

summary:
Pilocytic astrocytoma (PA) is the most common pediatric brain tumor and driven by aberrant MAPK signaling, typically mediated by BRAF alterations. While five-year overall survival rates exceed 95%, tumor recurrence constitutes a major clinical challenge in incompletely resected tumors despite chemotherapeutic or radiation based therapies. Therefore, we used proteogenomics to discern the biological heterogeneity of PA to improve classification of this tumor entity and identify novel therapeutic targets.
Our proteogenomics approach integrates RNA sequencing and LC/MS-based proteomic profiling data from a cohort of 58 confirmed, primary PA samples. An integrative genomics approach was conducted to discern the biological heterogeneity of PA and to identify aberrant pathway activation in these biological subgroups.
In summary, pilocytic astrocytomas segregate into two groups where younger patients are significantly associated with Group 1. Importantly, we validate the two distinct biological subgroups in two non-overlapping cohorts. The biological heterogeneity seen here may improve biological classification and reveal novel therapeutic targets specifically useful for non-resectable tumors with high risk of recurrent or progressive disease.

overall_design: Bisulphite converted DNA from the samples were hybridised to the Illumina Infinium MethylationEPIC Kit array.

first: Daniel

last: Picard


title: Single-cell RNA-seq of CRISPRi ADGRG6-kd in iAT2

first: Pushpinder

last: Bawa

summary: We performed single cell transcriptomic profiling of induced human pluripotent stem cells (iPSCs)-derived type 2 alveolar epithelial cells (iAT2). iPSCs stably expressed CRISPRi (dCas9-KRAB) under the control of doxycyline. iAT2s were transduced with a lentivirus expressing gRNA targeting the transcriptional start site of ADGRG6. Cells were treated with or without doxycyline to intiate CRISPRi-knockdown. Prior to capture, cells were labelled with hashing antibodies (HTO). Cells were captured for 10x Genomics Single cell capture (V3 protocol), and GEX and HTO libraries were sequenced. HTODemux function was used to demultiplex the samples. Knockdown of ADGRG6 caused cells to cluster separately from wild-type cells.

overall_design: Single-cell transcriptomic analysis of iPSC-derived type 2 alveolar epithelial cells (iAT2) comparing wild-type cells with CRISPRi-mediated knockdown of ADGRG6

first: Rhiannon

last: Werder

first: Andrew

last: Wilson