title: Gene expression profiles of the mouse jejunal epithelial cells with breakfast skipping feeding pattern

city: Hangzhou

first: Jian

last: Zhang

address: Yuhangtang Road, Xihu District, Hangzhou, Zhejiang Province

institute: Zhejiang University

summary: Eating habits are closely related to the body's nutrient absorption and metabolic homeostasis. In order to better reveal the changes of intestinal epithelial cells under different dietary patterns, we examined the changes of gene expression profiles in jejunal epithelial cells of mice after 10 days of  breakfast skipping feeding pattern by RNA sequencing.

overall_design: For the feeding pattern adjustment experiment, mice were housed in the same environment and cage. Mice were treated with BSF (Breakfast-skipping feeding, feeding time window: ZT16-ZT24), LSF (Lunch-skipping feeding, feeding time window: ZT12-ZT16 and ZT20-ZT24) and (Dinner-skipping feeding, feeding time window: ZT12-ZT20) for 2 weeks.

first: Ruonan

last: Tian

first: Di

last: Wang


title: Plasticity of the Mammalian Integrated Stress Response [atf4]

status: Public on Jan 22 2025

city: Stockholm

first: Krzysztof

middle: Jan

last: Szkop

state: Solna

address: SciLifeLab, Tomtebodavägen 23

department: Department of Oncology and Pathology

country: Sweden

institute: Karolinska Institutet

type: Expression profiling by high throughput sequencing

summary: Decreased nucleotide exchange activity of the eukaryotic translation initiation factor eIF2B coupled with increased phosphorylation of eIF2alpha (eIF2alpha-p) is a hallmark of the “canonical” integrated stress response (c-ISR). In mammals, however, it is unclear whether decreased eIF2B activity in absence of alterations in eIF2alpha-p which occurs in human disease including leukodystrophies, is synonymous to c-ISR. Herein, we describe a previously unknown mechanism of adaptation to decreased eIF2B activity, distinct from c-ISR, which we term “split” ISR (s-ISR). We demonstrate that s-ISR comprises translation reprogramming of only a subset of c-ISR mRNA targets which is accompanied by distinct transcriptomes. In contrast to c-ISR, s-ISR requires eIF4E-dependent translation of the upstream open reading frame 1 and subsequent stabilization of ATF4 mRNA. This is followed by altered expression of a subset of metabolic genes (e.g., PCK2), resulting in metabolic adaptations to maintain cellular bioenergetics under conditions of low eIF2B activity. Overall, these data demonstrate hitherto-unappreciated plasticity of the mammalian ISR, whereby the loss of eIF2B activity in the absence of increased eIF2-p, activates an eIF4E/ATF4/PCK2 axis to maintain energy homeostasis.

overall_design: Analysis of RNA-sequencing of  ATF4 uORF1 mutant vs WT (3 vs 3)

first: Chien-Wen

last: Chen

first: David

last: Papadopoli

middle: J

first: Bo-Jhih

last: Guan

first: Mohammed

last: Alzahrani

first: Jing

last: Wu

first: Mais

middle: M

last: Asraf

first: Dawid

last: Krokowski

first: Anastasios

last: Vourekas

first: William

middle: C

last: Merrick

first: Anton

last: Komar

first: Antonis

middle: E

last: Koromilas

first: Myriam

last: Gorospe

first: Matthew

last: Payea

first: Fangfang

first: Ashleigh

last: Schaffer

first: Alexander

last: Miron

first: Ilya

last: Bederman

first: Eckhard

last: Jankowsky

first: Christine

last: Vogel

first: Leoš

middle: S

last: Valášek

first: Jonathan

middle: D

last: Dinman

first: Youwei

first: Boaz

last: Tirosh

first: Ola

last: Larsson

first: Ivan

last: Topisirovic

first: Maria

last: Hatzoglou


title: Chromatin accessibility profiles of the mouse jejunum in a bidirectional nutrient supply model

first: Jian

last: Zhang

country: China

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The small intestine is the primary organ for nutrient sensing and absorption, in order to more comprehensively reveal the nutrient sensing and response of  intestinal cells, we used ATAC sequencing to reveal the effects of enteral and serosal nutrients on the intestinal tract in a bidirectional nutrient supply mode.

overall_design: Mice were treated with Control, BSF, DSF and LSF for 2 weeks, and jejunal epithelial cells were collected by flow sorting.

first: Ruonan

last: Tian

first: Di

last: Wang


title: High Throughput Chromosome Conformation Capture identifies differential genome organization in virulent and avirulent strains of Mycobacterium tuberculosis

city: Delhi

first: Rupesh

last: Chaturvedi

state: Delhi

address: School of biotechnology, JNU, Chattarpur

department: School of Biotechnology

country: India

institute: Jawaharlal nehru university

summary: In order to understand the three-dimensional genome organization in M. tuberculosis, in this study we have used exponentially growing mycobacterial culture. We performed Hi-C on both virulent and attenuated strain of M. tuberculosis and analyzed data by using Hi-C explorer tools

sample_organism:
Mycobacterium tuberculosis H37Rv
Mycobacterium tuberculosis H37Ra

overall_design: Comparative chromosome oganization in Mycobacterium tuberculosis strain H37Rv and H37Ra using Hi-C

first: Mohit

last: Mishra

first: Ajay

last: Arya


title: Gene expression profiles of the mouse jejunum at the single-cell level in a bidirectional nutrient supply model

summary: The small intestine is the primary organ for nutrient sensing and absorption, in order to more comprehensively reveal the nutrient sensing and response of different types of intestinal cells, we used single-cell sequencing to reveal the effects of enteral and serosal nutrients on the intestinal tract in a bidirectional nutrient supply mode.

overall_design: To examine the response of different types of cells in the jejunum to the bidirectional nutrition, mice were treated with sham, TPN, or starvation for 24 h, and then 5 cm of jejunal tissue was harvested.To digest the tissues, DNase I (DN25, Sigma-Aldrich) at 1:2000 dilution, Protease Inhibitor Cocktail (HY-K0010, MedChemExpress), Dispase II (40104ES80, Yeasen) and Liberase (5401054001, Roche) at 1:37.5 dilution were added. The tissue was then digested using a gentleMACS Dissociator (Miltenyi Biotec).Library sequencing was performed with the illumina novaseq 6000 pe150.


title: Plasticity of the Mammalian Integrated Stress Response [eIF2B5]

first: Krzysztof

last: Szkop

overall_design: Analysis of RNA-sequencing of  eIF2B-epsilonR191H/R191H vs WT (3 vs 3)

first: Chien-Wen

last: Chen

first: David

last: Papadopoli

first: Bo-Jhih

last: Guan

first: Mohammed

last: Alzahrani

first: Jing

last: Wu

first: Mais

last: Asraf

first: Dawid

last: Krokowski

first: Anastasios

last: Vourekas

first: William

last: Merrick

first: Anton

last: Komar

first: Antonis

last: Koromilas

first: Myriam

last: Gorospe

first: Matthew

last: Payea

first: Fangfang

first: Ashleigh

last: Schaffer

first: Alexander


title: Plasticity of the Mammalian Integrated Stress Response [eIF2B5_eIF4E]

first: Krzysztof

overall_design: Analysis of total and polysome-associated RNA-sequencing of shControl, sheIF2B-epsilon and sheIF2B-epsilon + sheIF4E in MEFs

last: Wang

last: Miron

first: Ilya

last: Bederman

first: Eckhard

last: Jankowsky

first: Christine

last: Vogel

first: Leoš

last: Valášek

first: Jonathan

last: Dinman

first: Youwei

last: Zhang

first: Boaz

last: Tirosh

first: Ola

last: Larsson

first: Ivan

last: Topisirovic

first: Maria

last: Hatzoglou


title: Histone deacetylase-1 is required for epigenomic stability in Neurospora crassa [ChIP-seq]

status: Public on Jan 21 2025

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

country: USA

institute: University of Colorado Colorado Springs

summary: Polycomb group proteins assemble into chromatin modifying complexes that regulate stem cell identity and multicellular development. The trimethylation of lysine 27 on histone H3 (H3K27me3) is catalyzed by the conserved Polycomb Repressive Complex 2 (PRC2). In Neurospora crassa, the typically-subtelomeric pattern of H3K27me3 depends on other chromatin regulators including the H3K36 methyltransferase ASH1, the chromatin remodeling enzyme IMITATION SWITCH, and components of constitutive heterochromatin including the H3K9 methyltransferase DEFECTIVE IN METHYLATION-5 and the H3K9me3-binding protein HETEROCHROMATIN PROTEIN 1 (HP1). How constitutive heterochromatin impacts PRC2 activity is unclear. HP1 forms multiple protein complexes including the HCHC complex, which removes acetyl groups from histones in constitutive heterochromatin, and contains the proteins Histone Deacetylase 1(HDA-1) and Chromodomain Protein-2 (CDP-2). To identify genes required for Polycomb repression in N. crassa, we performed a genetic screen and identified HDA-1 as necessary for PRC2-targeted gene silencing. In the absence of HDA-1, H3K27me2/3 is lost from the subtelomeres and aberrantly accumulates at constitutive heterochromatin domains normally enriched for H3K9me3; CDP-2 is also important for wildtype H3K27me3 localization. The H3K27me2/3 redistribution in Δhda-1 or Δcdp-2 strains is variable and incomplete, and mutant progeny obtained following a sexual cross displayed wild-type H3K27me3 patterns, consistent with HCHC loss leading to progressive changes in H3K27me3 enrichment. Indeed, a newly constructed ∆hda-1 deletion strain displays a wild-type H3K27me3 pattern that relocalizes to constitutive heterochromatic regions after sequential passages. Thus, HCHC-specific deacetylation prevents aberrant recruitment of PRC2 to constitutive heterochromatin.

overall_design: Chromatin Immunoprecipitation-sequencing (ChIP-seq) of the trimethylation of lysine 9 on histone H3 (H3K9me3) and di- and trimethylation of lysine 27 on histone H3 (H3K27me2/3) from the filamentous fungus Neurospora crassa

first: Felicia

last: Ebot-Ojong

first: Aileen

middle: R

last: Ferraro

first: Abigail

last: Deaven

first: Rochelle

last: Yap

first: Farh

last: Kaddar

first: Clayton

last: Hull-Crew

first: Ashley

middle: W

last: Scadden

first: Zachary

middle: A

last: Lewis


title: Histone deacetylase-1 is required for epigenomic stability in Neurospora crassa

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

overall_design: Refer to individual Series


title: Gene expression profiles of the mouse jejunum in a bidirectional nutrient supply model

first: Jian

summary: The small intestine is the primary organ for nutrient sensing and absorption, in order to more comprehensively reveal the nutrient sensing and response of  intestinal cells, we used Bulk RNA sequencing to reveal the effects of enteral and serosal nutrients on the intestinal tract in a bidirectional nutrient supply mode.

overall_design: To examine the response of different types of cells in the jejunum to the bidirectional nutrition, mice were treated with sham, TPN, or starvation for 24 h, and then 5 cm of jejunal tissue was harvested.

first: Ruonan

last: Tian

first: Di

last: Wang


title: Histone deacetylase-1 is required for epigenomic stability in Neurospora crassa [HiC]

overall_design: Chromosome conformation capture coupled with high-throughput sequencing of two independent strains of the filamentous fungus Neurospora crassa deleted of the gene hda-1 (histone deacetylase-1), which is the catalytic subunit of the HCHC histone deacetylase complex


title: Tuft cell IL-17RB restrains IL-25 bioavailability and reveals context-dependent ILC2 hypoproliferation

city: Zurich

first: Christoph

last: Schneider

address: Winterthurerstrasse 190, Y23 J12

department: Physiology

country: Switzerland

institute: University of Zurich

summary: The tuft cell–ILC2 circuit orchestrates rapid type 2 responses upon detecting microbe-derived succinate and luminal helminths. Our findings delineate key mechanistic steps, involving IP3R2 engagement and Ca2+ flux, governing IL-25 production by tuft cells triggered by succinate detection. While IL-17RB plays a pivotal intrinsic role in ILC2 activation, it exerts a regulatory function in tuft cells. Tuft cells exhibit constitutive Il25 expression, placing them in an anticipatory state that facilitates rapid production of IL-25 protein for ILC2 activation. Tuft cell IL-17RB is crucial for restraining IL-25 bioavailability, preventing excessive tonic ILC2 stimulation due to basal Il25 expression. Suboptimal ILC2 stimulation by IL-25 resulting from tuft cell Il17rb-deficiency or prolonged succinate exposure induces a state of hypoproliferation in ILC2s, also observed in chronic helminth infection. Our study offers critical insights into the regulatory dynamics of IL-25 in this circuit, highlighting the delicate tuning required for responses to diverse luminal states.

overall_design: Bulk RNA Sequencing of ILC2s isolated from IL-17RBfl/fl (n=7) and Vil1Cre;IL17RBfl/fl (n=5) mice aged 10 weeks

first: Xiaogang

last: Feng

first: Tilde

last: Andersson

last: Berest


title: Single cell RNA sequencing of MPN patients from humans in South Korea

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

country: South Korea

institute: Catholic University of Korea

summary: we analyzed BM aspirates in reactive BMs, pre-PMFs, overt PMFs, and non-PMF MPNs by single-cell RNA sequencing (scRNA-seq), identifying cell types , including hematopoietic stem and progenitor cell (HSPC) and MK.

overall_design: We performed scRNA-seq on BM mononuclear cells (BM-MNCs) isolated from 17 PMF patients (five pre-PMFs and 12 overt PMFs). Additionally, we analyzed scRNA-seq data of BM-MNCs from two non-neoplastic reactive BMs (one case with idiopathic polycythemia and the other with reactive thrombocytosis)

first: Seung-Hyun

first: Sung-Eun

last: Lee

first: Sujin

last: Yun

first: Da-Eun

last: Min

first: Youngjin

last: Shin

first: Yeun-Jun

last: Chung

first: Sug

middle: H


title: Interplay between CTCF-binding and CTCF-lacking regulatory elements in generating an architectural stripe at the Igh locus

city: Baltimore

first: Fei

last: Ma

state: MD

address: 251 Bayview Blvd

institute: NIA

summary: Three-dimensional genome organization orchestrates recombination and transcription of immunoglobulin heavy chain (Igh) genes. The structure of wild type (WT) alleles includes a prominent architectural stripe that extends from a cluster of CTCF binding elements at the 3’ end of the locus (3’CBE), suggesting interactions of this end with sequences throughout the 2Mb Igh TAD. Here we elucidate interplay between regulatory elements located in the 3’Igh domain (260 kb) that impact the stripe. The CTCF-lacking intronic enhancer, Eì, promotes stripe formation and tethers sub-TADs between flanking CTCF-bound 3’CBE and IGCR1. Substituting Eì with an EF1á promoter in different orientations partially recapitulates epigenetic features of WT Igh alleles, including active histone modifications, sub-TAD formation and interactions with the 3’CBE, but does not restore VDJ recombination. Loss of IGCR1 increases the stripe while inverting the 3’CBE redirects the stripe away from the Igh locus. However, inverted 3’CBE continue to serve as a boundary against aberrant activation of genes outside the Igh domain by Eì. Our observations provide insights into mechanisms by which regulatory elements modulate chromatin structure and stripe formation.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-sequencing) for Nipbl and Wapl using pro-B cell lines with various mutations.

first: Xiang

last: Qiu

first: Noah

last: Ollikainen

first: Hansen

last: Du

first: Fatima

middle: Z

last: Braikia

first: Aisha

last: Bianchi

first: Christopher

last: Dunn

first: Cuong

last: Nguyen

first: Jinshui

last: Fan

first: Supriyo

last: De

first: Ranjan

last: Sen


title: WDR26 depletion alters chromatin accessibility and gene expression profiles in mammalian cells [RNA-seq]

city: London

first: Caroline

last: Schild-Poulter

address: 1151 Richmond Street North

country: Canada

institute: Western University

summary: WD-repeat containing protein 26 (WDR26) is an essential component of the CTLH E3 ligase complex. Mutations in WDR26 lead to Skraban-Deardorff, an intellectual disability syndrome with clinical features resembling other disorders arising from defects in transcriptional regulation and chromatin structure. However, the role of WDR26 and its associated CTLH complex in regulating chromatin or transcription has not been elucidated. Here, we assessed how loss of WDR26 affects chromatin accessibility and gene expression. Transcriptome analysis of WDR26-null HeLa cells revealed over 2000 differentially expressed genes, while ATAC-Seq analysis showed over 32 000 differentially accessible chromatin regions, the majority mapping to intergenic and intronic regions and 13% mapping to promoters. Above all, we found that WDR26 loss affected expression of genes regulated by AP-1 and NF-1 transcription factors and resulted in dramatic changes in their chromatin accessibility. Overall, our analyses implicate WDR26 and the CTLH complex in chromatin regulation.

overall_design: To investigate whether chromatin accessibility is affected in cells depleted of the nuclear CTLH complex, we used RNA-Seq and ATAC-Seq to show that loss of WDR26 in HeLa cells affects CTLH complex chromatin association and results in profound changes in gene expression and chromatin accessibility

first: Gabriel

last: Onea

first: Alireza

last: Ghahramani

first: Haider

last: Hassan

first: Joseph

last: Torchia

first: Nathalie

middle: G

last: Bérubé


title: WDR26 depletion alters chromatin accessibility and gene expression profiles in mammalian cells [ATAC-seq]


title: Stress dynamically modulates Neuronal Autophagy to gate depression onset [snRNA-seq]

status: Public on Jan 20 2025

first: Liang

last: Yang

state: Zhejiang

address: 866 Yuhangtang Road

department: Medicine

summary: Chronic stress remodels brain homeostasis, in which persistent change leads to depressive disorders. As a key modulator of brain homeostasis, it remains elusive whether and how brain autophagy is engaged in stress dynamics. Here, we discover that acute stress activates, whereas chronic stress suppresses, autophagy mainly in the lateral habenula (LHb). Remarkably, systemic administration of distinct antidepressant drugs similarly restores autophagy function in the LHb, suggesting LHb autophagy as a common antidepressant target. Genetic ablation of LHb neuronal autophagy promotes stress susceptibility, whereas enhancing LHb autophagy exerts rapid antidepressant-like effects. LHb autophagy controls neuronal excitability, synaptic transmission and plasticity via on-demand degradation of glutamate receptors. Collectively, this study reveals a causal role of LHb autophagy in maintaining emotional homeostasis against stress. Disrupted LHb autophagy is implicated in the maladaptation to chronic stress, and its reversal by autophagy enhancers provides a novel antidepressant strategy.

overall_design: snRNA-sequencing was performed with fresh LHb sample from chronic restraint stress (CRS) and naïve mice.

first: Chen

last: Guo

first: Zhiwei

last: Zheng

first: Yiyan

last: Dong

first: Xiangnan

last: Zhang

first: Yihui

last: Cui


title: Cut&Run of female mouse primordial germ cells at E11.5 and E12.5 days of gestation for H3K27me3

city: Montpellier

first: Maud

last: Borensztein

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS, Univ of Montpellier

summary: To evaluate the impacts of X-chromosome reactivation on repressive H3K27me3 chromatin marks, allele-specific low input CUT&Run experiments were conducted starting from genomic DNA obtained from FACS-sorted primordial germ cells.

overall_design: PGCs were dissected and FACS sorted from pooled male or pooled female mouse embryos, at E11.5 and E12.5. Low input CUT&RUN was performed for H3K27me3 marks and IgG included as control.

first: Clara

last: Roidor

first: Emmanuelle

last: Beyne

first: Peggy

last: Raynaud


title: Effect of glutamine supplementation on naïve CD4 T cell differentiation from CARD11 R75W mutation patients

city: NYC

first: Lei

last: Huang

address: 701 W 168th St Rm 1404 HHSC

institute: Columbia University

summary: CARD11 LOF mutant patients develop severe atopic phenotpes and increased T-helper 2 (Th2) cytokine production, in addition to other immunopathology. CARD11 LOF impairs lymphocyte receptor–mediated glutamine uptake—thereby reducing signaling in mTORC1. Herein, we investigate whether exogenous glutamine treatment would alleviate Th2 phenotypes of CARD11 LOF mutant T cells.

overall_design: RNA-seq profiling of naïve CD4 T cells from CARD11 R75W patients and healthy donors with different levels of glutamine in the presence of TCR stimulation for 3 days.

first: Joshua

last: Milner


title: Stress dynamically modulates Neuronal Autophagy to gate depression onset

overall_design: RNA-sequencing was performed with fresh LHb, vHippo, mPFC, VTA, LH and NAc samples from chronic restraint stress (CRS) and naïve mice tested using FST 2 days prior to sacrifice. We divided CRS and naïve mice into two groups, respectively. Namely, CRS mice with high FST scores (FST immobility>110 s, n = 3), CRS mice with low FST scores (50 s<FST immobility <110 s, n = 3), naïve mice with high FST scores (50 s< FST immobility <80 s, n = 3), naïve mice with low FST scores (FST immobility <50 s, n = 3).

first: Min

last: Li


title: Hippo Inactivation in the Mammary Epithelium Drives the Evolution of a Tumor-Associated Niche

city: Boston

first: Lina

last: Kroehling

state: MA

address: 91 E Concord St

institute: Boston Unviersity

summary: Basal-like breast cancers exhibit distinct intratumor cell heterogeneity that contributes to disease pathology. In this study we use a genetic mouse model of basal-like breast cancer driven by epithelial-specific inactivation of the Hippo pathway-regulating Lats1 and Lats2 kinases to elucidate epithelial-stromal interactions in the basal-like tumor niche. We demonstrate that basal-like carcinoma initiation is accompanied by the accumulation of distinct cancer-associated fibroblasts, tumor-associated macrophage recruitment, and dramatic extracellular matrix remodeling, phenocopying the stromal diversity observed in human triple-negative breast tumors.Epithelial-stromal signaling dysregulation was observed, including increased TGF-β, PDGF, and CSF intercellular communication. Autonomous activation of the transcriptional effector TAZ was observed in Lats1/2-deleted cells along with non-autonomous activation within the evolving tumor niche. We further demonstrate that small molecule inhibition of the YAP/TAZ-associated TEAD family of transcription factors can block the development of the carcinomas and tumor-associated microenvironment. These observations demonstrate that carcinomas resulting from Hippo pathway dysregulation in the mammary epithelium are sufficient to drive cellular events that promote a basal-like tumor-associated niche and suggest that targeting dysregulated YAP/TAZ-TEAD activity provides an opportunity for therapeutic intervention of basal-like mammary tumors.

overall_design: We utilized a genetic mouse model allowing conditional deletion of Lats1/2 in Krt8+cells to study the impact of epithelial-specific Hippo pathway inactivation on mammary epithelial and stromal cell populations. These mice included Lats1 and Lats2-floxed alleles, a Tamoxifen-inducible Cre recombinase under the control of the Krt8 promoter, and a loxP-stop-loxP(lsl)-EYFP lineage trace to mark Cre+ cells (Lats1/2ff;lsl-EYFP; Krt8CreERT2). After administration of Tamoxifen, mammary glands from these and control (Lats1/2ff;lsl-EYFP) mice were dissociated and live cells were subsequently sorted for single-cell RNA-sequencing. Two mice were used for each condition.

last: Kern

first: Stefano

last: Monti

first: Xaralabos

last: Varelas


title: Bulk RNA-seq of wild-type and Nlrp3-/- bone marrow-derived macrophages with or without LPS and ATP costimulation

city: Shanghai

first: Haihan

last: Gao

address: Xuhui District

department: Department of Orthopaedic Surgery

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: In order to investigate the effect of NLRP3 on the transcription profile of inactive macrophages and active macrophages with LPA and ATP combined stimulation.

overall_design: RNA-seq profiling of wild-type and Nlrp3-/- bone marrow-derived macrophages without stimulation or with 4 hours of LPS preconditioning and subsequently 30 min of ATP stimulation.


title: Transcriptomic analysis of the impact of a short-term leucine deprivation and evaluation of GCN2 involvement in induced gene differential expression in human primary T cells

city: Clermont-Ferrand

first: Aurore

last: Dougé

state: France

address: 28 place Henri Dunant

department: Oncology

institute: University Hospital

summary: We previously demonstrated the proof of concept for the functionality of the NUTRIREG system in T cells. This technology allows for the induction of transgene expression following the consumption of a diet deficient in an essential amino acid, by activating the GCN2-ATF4 signaling pathway. To utilize the NUTRIREG technology for therapeutic purposes in cell therapy with short-term EAA deprivation, we explored the general impact of 6-hour leucine deprivation on primary activated human T cells using RNA-seq technology. We identified 3,431 differentially expressed genes (adjusted p-value < 0.05) between T cells cultured in control media and those cultured in leucine-deprived media for 6 hours. Gene Set Enrichment Analysis revealed that "TNFα signaling via NFκB", "interferon-γ response", and "unfolded protein response" gene sets were positively enriched, while "mTORC1 signaling", "Myc targets", and "oxidative phosphorylation" gene sets were negatively enriched. T cells were cultured with or without a GCN2 inhibitor, which allowed us to assess the involvement of GCN2 kinase in differential gene expression during the 6-hour leucine deprivation. We found that 59% of the differentially expressed genes (DEGs) in our dataset were dependent on GCN2 kinase (n=2028), with 1,140 up-regulated and 888 down-regulated GCN2-dependent genes.

overall_design: Activated human T cells were incubated in 10% FBS-RPMI medium supplemented with IL-2 at 37°C and 5% CO2 for 7 days of expansion. At day 8 post activation, Dulbecco’s Modified Eagle’s Medium (DMEM) (with 10% of dialyzed calf serum) lacking leucine was used (GENAXXON bioscience). A control medium was simultaneously reconstituted by adding all nine EAAs. RPMI-cultured human T cells were collected and washed in PBS with centrifugation at room temperature at 300xg for 5 min. Cells were then resuspended either in reconstituted DMEM control or in DMEM lacking leucine, at a density of 1x106 cells/mL. DMEM was freshly supplemented with IL-2 (50 IU/mL). GCN2 inhibitor (TAP20) was generously provided by Merck KGaA. The compound was resuspended in DMSO and used at a final concentration of 2.5 µM. Cells were cultured in DMEM Control or DMEM lacking leucine +/- GCN2 inhibitor for 6 hours (quadruplicate) and were then collected for mRNA extraction and subsequent RNAseq analysis.

first: Gwendal

last: Cueff

first: Céline

last: Keime

first: Valérie

last: Carraro

first: Pierre

last: Fafournoux

last: Jousse

first: Paul

last: Rouzaire

first: Alain

last: Bruhat


title: Regulatory T-cells in the hypothalamus control immune activation and improve metabolic impairments upon high-calorie environments

city: Munich

first: Carolin

last: Daniel

address: Heidemannstr. 1

department: Diabetes Center

country: Germany

institute: Helmholtz Munich

summary: The hypothalamus in the central nervous system (CNS) plays a key role in the control of systemic metabolism. A calorie-rich diet triggers CNS immune activation, which contributes to impairments of metabolic control, favoring obesity and Type 2 Diabetes (T2D). However, cell types and molecular processes regulating hypothalamic immune activation remain incompletely understood. Here, we report the functionally relevant presence of regulatory T cells (Tregs), key players in the control of immune and tissue homeostasis, in the hypothalamus. Exposure to calorie-rich environments triggers immune activation of hypothalamic CD4+T cells, infiltrating macrophages and microglia while decreasing the presence of hypothalamic Tregs in mice. mRNA expression profiling of hypothalamic CD4+T cells revealed a Th1-like activation state evidenced by high levels of Tbx21, Cxcr3 and Cd226 and a decrease of Ccr7 and S1pr1 expression, a profile typical for recruitment of T cells to and retention at inflammatory sites. Importantly, mechanistic Treg loss- and gain-of-function experiments in vivo, show that Foxp3+Tregs limit hypothalamic immune activation and improve metabolic impairments induced by hyper-caloric feeding. Our findings refine the current model of immuno-metabolic crosstalk in the brain in response to environmental challenges and are of relevance for the future development of immune interventions to support health in obesity and T2D.

overall_design: Foxp3 GFP reporter mice were fed a high-fat high-sugar diet (HFHSD) or a standard diet (SD) for the indicated time points. Additionally, genetically obese ob/ob mice vs. BL6J mice were used. Cells from brains or hypothalami were isolated by homogenization and stained for FACS, followed by sorting of the indicated T cell subsets for purity. Bulk RNA-seq was performed.

first: Daniel

last: Carolin

first: Becker

last: Maike

first: Kälin

last: Stefanie

first: Neubig

last: Anne

first: Lauber

last: Michael

first: Hippich

last: Markus


title: Effect of FN14KO  on mouse lung immune cells after bleomycin injury

first: pei

last: wu

address: 393 Middle Huaxia Road

institute: ShanghaiTech University

summary: TWEAK, also known as TNFSF12, is a multifunctional cytokine that controls many cellular activities in tissue repair and disease by binding to its receptor Fn14.TWEAK-Fn14 signaling has been shown to induce canonical and noncanonical NFkB signaling, triggering pro-inflammatory responses and leukocyte infiltration.In the bleomycin-induced lung fibrosis model, Fn14 KO mice were found to induce a more severe fibrotic phenotype. To explore the effect of Fn14 KO on immune cell populations in this model, we performed single-cell sequencing.

overall_design: Immune cells from six group of mice(WT saline, FN14KO saline, WT bleomycin D7, FN14KO bleomycin D7, WT bleomycin D14, FN14KO bleomycin D14) were isolated by FACS（CD45+ EPCAM- CD31-）and analyzed using scRNAseq.

first: Ying

last: Xi

first: Li

last: Liu

first: Pei

last: Wu

first: Yuqi

last: Wei


title: Effect of tweak stimulation on primary lung fibroblasts

summary: TWEAK, also known as TNFSF12, is a multifunctional cytokine that controls many cellular activities in tissue repair and disease by binding to its receptor Fn14.TWEAK-Fn14 signaling has been shown to induce canonical and noncanonical NFkB signaling, triggering pro-inflammatory responses and leukocyte infiltration.We found that TWEAK-Fn14 signaling was upregulated in IPF while Fn14 was mainly expressed in fibroblasts. Therefore, we added different concentrations of TWEAK to primary mouse lung fibroblasts to activate the TWEAK-Fn14 signaling pathway, and explored the transcriptome changes of TWEAK-Fn14 signaling pathway activation in fibroblasts by RNA-seq technology.

overall_design: We used primary lung fibroblasts without stimulation as a control, and TWEAK recombinant protein was set up three gradients, successively 10ng/ml, 30ng/ml and 100ng/ml. After 48 hours of stimulation, samples were collected for RNA extraction and sequencing.


title: RNAseq of CONTROL engineered and SMAD4 engineered Purified NK cells after 7 day treatment   in the presence/absence of TGFb

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: TGF-β is a suppressive factor curtailing the effectiveness of NK cell adoptive transfer for cancer treatment. Inspired by data of SMAD4 haploinsufficient NK cells, we explored the possibility of knocking out SMAD4 by CRISPR/Cas9 in human NK cells as a novel strategy for circumventing TGF-β suppression. Human SMAD4KO NK cells were resistant to TGF-β inhibition, retaining their anti-tumor function and their proliferation in response to IL-2/IL-15. In addition, SMAD4KO NK cells exposed to TGF-β showed improved tumor-penetration, associated to changes in adhesion molecules and chemokine receptors. Indeed, the cytotoxic activity of SMAD4KO NK cells surpassed that of control NK cells treated with a TGF-β inhibitor, indirectly evidencing the advantage of maintaining SMAD4-independent TGF-β-signaling. Furthermore, SMAD4KO NK cells were also resistant to Activin A inhibition. Overall, disrupting TGF-β/activin A signaling by inactivating SMAD4 represents a promising strategy for simultaneously enhancing the homing and function of NK cell products for cancer immunotherapy.

overall_design: Control and SMAD4 knock out human NK cells were cultured with rIL-2 (200 U/ml) or the combination of rIL-2 and TGFbeta (5 ng/ml). After 5 days, total RNA was extracted and sequenced. The experiment contain data from NK cells obtained from 3 different healthy individuals.

first: A

last: Muntasell

last: Rea


title: Transcriptional memory is conferred by combined heritable maintenance and local removal of selective chromatin modifications

city: Oxford

first: Pawel

last: Mikulski

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

summary: Interferon-γ (IFNγ) transiently activates genes involved in inflammation and innate immunity. A subset of targets maintain a mitotically heritable memory of prior IFNγ exposure resulting in hyperactivation upon reexposure. Here we discovered that the active chromatin marks H3K4me1, H3K14Ac and H4K16Ac are established during IFNγ priming and selectively maintained on a cluster of GBP genes for at least 7 days in dividing cells in the absence of transcription. The histone acetyltransferase KAT7 is required for the accelerated GBP reactivation upon reexposure to IFNγ. In naïve cells, we find the GBP cluster is maintained in low-level repressive chromatin marked by H3K27me3 limiting priming in a PRC2-dependent manner. Unexpectedly, IFNγ results in transient accumulation of this repressive mark but is then selectively depleted from primed GBP genes during the memory phase facilitating hyperactivation of primed cells. Furthermore, we identified a cis-regulatory element that makes transient, long-range contacts across the GBP cluster and acts as a repressor, primarily to curb the hyperactivation of previously IFNγ-primed cells.  Combined our results identify the putative chromatin basis for long-term transcriptional memory of interferon signalling that may contribute to enhanced innate immunity.

overall_design: Cut&Run-seq with immunoprecipitation for H3K4me1, H3K4me3, H3K14ac, H4K16ac, followed by Illumina short-read sequencing (NextSeq 500)

first: Lars

last: Jansen


title: Identifying cross-lineage dependencies of cell-type specific regulators in gastruloids

city: Amsterdam

first: Elzo

last: de Wit

state: Noord-Holland

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

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

overall_design: Refer to individual Series


title: Identifying cross-lineage dependencies of cell-type specific regulators in gastruloids [ATAC-Seq]

summary: Correct gene expression levels in space and time are crucial for normal development. Advances in genomics enable the inference of gene regulatory programs that are active during development. However, this approach cannot capture the complex multicellular interactions that occur in embryogenesis. Compared to model organisms such as fruit flies and zebrafish, the growth of mammalian embryos in utero further complicates the analysis of cell-cell communication during development. However, in vitro models of mammalian development such as gastruloids allow to overcome this limitation. Using time-resolved single-cell chromatin accessibility analysis, we have delineated the regulatory landscape during gastruloid development and thereby identified the critical drivers of developmental transitions. We observed that gastruloids develop from pluripotent cells driven by the transcription factor (TF) dimer OCT4-SOX2 and differentiate along two main branches. A mesoderm branch driven by the TF MSGN1 and a spinal cord branch driven by CDX1, 2, 4 (CDX). Consistent with our lineage reconstruction, ΔCDX gastruloids fail to form spinal cord. Conversely, Msgn1 ablation inhibits the development of paraxial mesoderm, as expected. However, this also abolished spinal cord cells, which is surprising given that MSGN1 is not associated with differentiation along this branch. Therefore, formation of paraxial mesoderm is required for spinal cord development. To validate this, we generated chimeric gastruloids using ΔMSGN1 and wildtype cells, which formed both spinal cord and paraxial mesoderm. Strikingly, ΔMsgn1 cells specifically contributed to spinal cord, suggesting that cell-cell interactions between paraxial mesoderm and spinal cord are necessary for the formation the latter. Our work has important implications for the study of cell-cell communication in development and how the bridge can be made between gene regulatory programs and complex multicellular developmental structures.

overall_design: Analysis of accessible chromatin in wildtype mouse embryonic stem cells.

first: Luca

last: Braccioli

first: Teun

last: van den Brand


title: Cytokine signatures differentiate systemic sclerosis patients at   high versus low risk for pulmonary arterial hypertension [14 plex]

city: Palo Alto

first: Lorinda

last: Chung

address: 1000 Welch Road

institute: Stanford University

summary:
Pulmonary arterial hypertension (PAH) affects approximately 10% of patients with systemic sclerosis (SSc) and is a leading cause of death. We sought to identify serum cytokine signatures that risk stratify SSc patients for this potentially fatal complication.
In the current study we aimed to characterize specific cytokine signatures that differentiate patients with incident SSc-PAH, patients at high risk for SSc-PAH, patients at low risk for SSc-PAH, and healthy controls. We anticipate these data will assist with early identification of patients at high risk for or with incident SSc-PAH. Additionally, we expect this study will identify cytokines that may be involved in the pathogenesis of SSc-PAH and could serve as therapeutic targets.

overall_design: Subjects at high-risk for PAH and with incident PAH based on right heart catheterization (RHC) were enrolled in the multi-center prospective registry, Pulmonary Hypertension Assessment and Recognition of Outcomes in Scleroderma (PHAROS). Low-risk SSc patients were enrolled at Stanford and had normal pulmonary function test and echocardiogram parameters. Serum was available from 71 high-risk patients, 81 incident PAH patients, 10 low-risk patients, and 20 healthy controls (HC). Custom 14 and 65-plex arrays were used for cytokine analysis. Cytokine expression was compared between patient groups by principal component analysis and Tukey’s test result. A multiple hypotheses corrected p-value <0.05 was considered significant.

first: Kathleen

last: Kolstad

first: Avani

last: Khatri

first: Michele

last: Donato

first: Sarah

last: Chang

first: Shufeng

last: Li

first: Virginia

last: Steen

first: Paul

last: Utz

first: Purvesh


title: Modulation of calcium signalling on demand to decipher the molecular mechanisms of primary aldosteronism

status: Public on Jan 19 2025

city: Paris

first: Sheerazed

last: BOULKROUN

address: 56 rue Leblanc

institute: Inserm

summary: Background. Primary aldosteronism is the most common form of secondary hypertension. The most frequent genetic cause of aldosterone producing adenoma (APA) are somatic mutations in the potassium channel KCNJ5. They affect the ion selectivity of the channel, with sodium influx leading to cell membrane depolarization and activation of calcium signalling, the major trigger for aldosterone biosynthesis. Methods. To investigate how KCNJ5 mutations lead to the development of APA, we established an adrenocortical cell model in which sodium entry into the cells can be modulated “on demand” using chemogenetic tools (H295R-S2 α7-5HT3 cells). We investigated their functional and molecular characteristics with regard to aldosterone biosynthesis and cell proliferation.  Results. A clonal cell line with stable expression of the chimeric α7-5HT3 receptor in H295R-S2 cells was obtained. Increased sodium entry through the α7-5HT3 receptor upon stimulation with uPSEM-817 led to cell membrane depolarization, opening of voltage-gated Ca2+ channels and increased intracellular Ca2+ concentrations, resulting in the stimulation of CYP11B2 expression and increased aldosterone biosynthesis. Increased intracellular sodium influx did not increase proliferation, but rather induced apoptosis. RNA sequencing and steroidome analyses revealed unique profiles associated with Na+ entry, with only partial overlap with angiotensin II or potassium induced changes. Conclusion. H295R-S2 α7-5HT3 cells are a new model reproducing the major features of cells harbouring KCNJ5 mutations. Increased expression of CYP11B2 and stimulation of the mineralocorticoid biosynthesis pathway are associated with a decrease of cell proliferation and an increase of apoptosis, indicating that additional events may be required for the development of APA.

overall_design: To investigate the effect of modulating intracellular Na+ concentration in an adrenocrotical cell model (H295R-S2 cells) expressing the chimeric α7-5HT3 receptor, which allow Na+ entry into the cells when treated with a synthetic molecule called PSAM.    The cells were treated 8h or 24h with 10-7M of PSEM and we perfroemd gene expression profiling by RNA-sequencing.

first: Bakhta

last: Fedlaoui

first: Maria-Christina

last: Zennaro

last: Boulkroun


title: TGF-β signaling controls neural crest developmental plasticity via SMAD2/3 [ATAC-seq]

city: Ithaca

first: Megan

last: Rothstein

state: NY

address: 526 Campus Road Rm 433

institute: Cornell University

summary: The neural crest is a highly plastic stem cell population that represents a notable exception to the germ layer theory. Despite being of ectodermal origin, these cells can differentiate into skeletal derivatives like cartilage and bone, tissues that are typically formed by mesoderm. The inductive program that endows the neural crest with these unique properties is still poorly understood. Here, we report that Smad2/3-mediated TGFβ signaling endows cranial neural crest cells with enhanced developmental potential. Our results show that TGFβ signaling modulates neural crest axial identity and directly activates the gene circuits that support skeletal differentiation. Cooperation between TGFβ and low levels of WNT-signaling in the embryonic head activates cranial-specific cis-regulatory elements of anterior genes. Activation of the TGFβ pathway allowed reprogramming of trunk neural crest cells to adopt an anterior identity and led to the development of an improved protocol for the generation of human cranial neural crest cells. Our findings indicate TGFβ signaling is required for the specification of cranial neural crest cells, endowing them with the potential to give rise to the craniofacial skeleton.

overall_design: We performed ATAC-seq analysis on neural crest explant cultures under different TGFB1 and CHIR99021 treatment conditions.

first: Ana Paula

last: Azambuja

first: Tatiane Y

last: Kanno

first: Catriona

last: Breen

first: Marcos

last: Simoes-Costa


title: Identifying cross-lineage dependencies of cell-type specific regulators in gastruloids [scATAC-seq]

first: Elzo

last: de Wit

overall_design: Analysis of accessible chromatin during a timeseries of gastruloid development using wildtype and genetic knockouts of CDX1/2/4 and MSGN1.

first: Luca

last: Braccioli

first: Teun

last: van den Brand


title: TGF-β signaling controls neural crest developmental plasticity via SMAD2/3 [TGF-β KD RNA-seq]

overall_design: We performed RNA-seq analysis on single dorsal neural folds from chicken embryos bilaterally electroporated with control/TGFβ1 morpholinos.


title: Cytokine signatures differentiate systemic sclerosis patients at   high versus low risk for pulmonary arterial hypertension [65-plex]

first: Lorinda

last: Chung

overall_design:
Subjects at high-risk for PAH and with incident PAH based on right heart catheterization (RHC) were enrolled in the multi-center prospective registry, Pulmonary Hypertension Assessment and Recognition of Outcomes in Scleroderma (PHAROS). Low-risk SSc patients were enrolled at Stanford and had normal pulmonary function test and echocardiogram parameters. Serum was available from 71 high-risk patients, 81 incident PAH patients, 10 low-risk patients, and 20 healthy controls (HC). Custom 14 and 65-plex arrays were used for cytokine analysis. Cytokine expression was compared between patient groups by principal component analysis and Tukey’s test result. A multiple hypotheses corrected p-value <0.05 was considered significant.

Submitter note: Two samples (U013 and U132) in the 65-plex are identical, but not because they are duplicates. This is because of the background correction after which all values are zero for these two samples.

first: Kathleen

last: Kolstad

first: Avani

last: Khatri

first: Michele

last: Donato


title: Multiplexed Assays of Human Disease-relevant Mutations Reveal UTR Dimer Composition as a Major Determinant of RNA Stability

city: Taipei City

first: Chien-Ling

last: Lin

address: No. 128, Sec. 2, Academia Road, Nangang District

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: UTRs contain crucial regulatory elements for RNA stability, translation and localization and their integrity is indispensable for gene expression. It has been estimated that ~3.7% of disease-associated genetic variants are located in UTRs. However, functional interpretation of UTR variants is largely incomplete because efficient experimental assessment and computational prediction are both lacking. To systematically assess the effect of UTR variants on RNA stability, we established an unbiased massively parallel reporter assay with 6,555 UTR variants reported in human disease databases. We found that there are common as well as distinct stability regulation elements in each cell line and that, among RNA-binding protein-binding sites, microRNA seed sequences, structural cues and small k-mers, TA-dimers are the most prominent destabilizing sequence.

overall_design: We performed time course assays to examine the relative stability of 6,555 UTR variants collected from the Human Gene Mutation Database (HGMD) and the public archive of interpretations of clinically relevant variants (ClinVar). UTRs fused with GFP coding regions were in vitro transcribed and transfected into human embryonic kidney cells HEK293T or neuroblastoma cells SH-SY5Y. The relative abundance of wild-type (WT) and mutant (mt) alleles was monitored over a time course, and determined by amplicon sequencing. We estimated the decay constant and the half-life (t1/2) of each UTR by its relative abundance over time. We defined stability-altering variants as those with significantly changed decay constant compared to their WT counterpart, determined by weighted linear regression.

first: Yun-Lin

last: Wang

first: Jia-Ying

last: Su

first: Yu-Chi

last: Chang

first: Cheng-Han

last: Yang

first: Po-Heng

first: YoonSoon

last: Kang

first: Yu-Tung

last: Hsieh

first: Yen-Tsung

last: Huang


title: Single-cell RNA-seq study of ascending somatosensory assembloids and human primary DRG

city: Stanford

first: Kent

last: Imaizumi

state: CA

address: 318 Campus Drive

summary: Single cell gene expression profileing of hSeO and hdSpO at day 68-72 of differentiation; hASA and individual organoids at day 162-229 of differentiation; and human primary DRG at 15 pcw. Raw data of primary tissues are not provided due to privacy concerns.

overall_design: 4 hSeO samples, 5 hdSpO samples, 4 hASA samples, 4 individual organoid pools, and 7 primary DRG.

first: Ji-il

last: Kim

first: Sergiu

middle: P

last: Pașca


title: Transcriptome sequencing of Riemerella anatipestifer CH-1 and CH-1_zntR under TSB condition

status: Public on Jan 18 2025

city: chengdu

first: Hongmeng

last: Ma

address: No. 211 Huimin Road, Wenjiang District

institute: sichuan agricultural university

summary: Identifying the differentially expressed genes of Riemerella anatipestifer CH-1 and CH-1_zntR under normal condition through RNA sequencing.

overall_design: For RNA extraction, the WT and ΔzntR strains were cultured at 37°C in TSB to an OD600 of ~1.5, and adjusted to OD600 = 0.5 using PBS. Total RNA was extracted from the bacterial pellet using an RNAprep Pure Cell/Bacteria Kit (TIANGEN). We used a NanoDrop 2000 to assess the concentration and quality of RNA samples and then sent samples to Shanghai Majorbio Bio-Pharm Technology Co., Ltd. for RNA sequencing (RNA-seq). Library preparation for RNA transcriptome sequencing was performed using the TruSeqTM Stranded Total RNA Library Prep Kit. The rRNA was first removed from total RNA, and the mRNA was cleaved into ~200 bp fragments using fragmentation buffer. Single-stranded cDNA was synthesized with random primers and the second-strand cDNA was synthesized with dUTP instead of dTTP. The ends of double-stranded cDNA were blunted with the End Repair Mix and an A base was added at the 3’ end. The cDNA was then digested with the UNG enzyme to remove the second-strand. Finally, the remaining first-strand cDNA was quantified using Qubit 4.0 and sequenced on the NovaSeq XPlus platform


title: TGF-β signaling controls neural crest developmental plasticity via SMAD2/3 [hiNCC RNA-seq]

first: Megan

last: Rothstein

overall_design: Examination of transcriptome of human embryonic stem cells and human induced neural crest cells under different differentiation conditions

first: Tatiane

middle: Y

last: Kanno

first: Marcos

last: Simoes-Costa

first: Ana Paula

last: Azambuja


title: MYT1L genome-wide occupancy in human pluripotent stem cell-derived cortical interneurons

city: Saint Louis

first: Kristen

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

summary: We have used our protocol for generating cortical interneurons from human pluripotent stem cells to study MYT1L genome-wide occupancy in human cortical interneurons.

overall_design: 4 replicates of MYT1L CUT&RUN were performed in human embryonic stem cell derived cortical interneurons with 2 replicates of negative controls performed using IgG antibody.

first: Ramachandran

last: Prakasam

first: Gareth

last: Chapman


title: Transcriptomic analysis of ASD and IDD associated pathogenic MYT1L S707Q mutation in human cortical interneurons

summary: We have used our protocol for generating cortical interneurons from human stem cells to study gene expression changes caused by the (S707QfsX56) mutation in the MYT1L gene, using both patient derived (PD) and variant knock in (VKI) models.

overall_design: For each cell line, 4 biological replicates generated from independant differentiations of human pluripotent stem cells were used for transcriptomic analysis by RNA-sequencing.


title: Regulation of RNA polymerase II activity is essential for terminal erythroid maturation

status: Public on Jan 17 2025

city: Rochester

first: Laurie

last: Steiner

address: 601 Elmwood Ave

department: Pediatrics

institute: University of Rochester

summary: RNAseq on HUDEP2 cells overexpressing EV, Hexim1_WT, or Hexim1_YYFF

overall_design: RNAseq

first: Zachary

last: Murphy

first: Jacquelyn

last: Myers

first: Michael

last: Getman

first: Tyler

last: Couch

first: Vincent

last: Schulz

first: Kimberly

last: Lezon-Geyda

first: Cal

last: Palumbo

first: Hongxia

last: Yan

first: Narla

last: Mohandas

first: Patrick

middle: B

last: Gallagher

first: Kristin


title: Angiotensin receptor blockers and CD4 T cell transcriptional and epigenetic states in systemic lupus erythematosus [RNA-seq]

city: Philadlephia

first: Daniel

last: Beiting

state: Pennsylvania

address: 380 S. University Avenue

institute: University of Pennsylvania

summary: In systemic lupus erythematosus (lupus), environmental effects acting within a permissive genetic background lead to autoimmune dysregulation. Dysfunction of CD4+ T cells contributes to pathology by providing help to autoreactive B and T cells, and CD4+ T cell dysfunction coincides with altered DNA methylation and histone modifications of select gene loci. However, chromatin accessibility states of distinct T cell subsets and mechanisms driving heterogeneous chromatin states across patients remain poorly understood. We defined the transcriptome and epigenome of multiple CD4+ T cell populations from lupus patients and healthy individuals. Most lupus patients, regardless of disease activity, had enhanced chromatin accessibility bearing hallmarks of inflammatory cytokine signals. Single cell approaches revealed that chromatin changes extended to naive CD4+ T cells; uniformly affecting naive subpopulations. Transcriptional data and cellular and protein analyses suggested that the TNF family members, TNFɑ, LIGHT, and TWEAK, were linked to observed molecular changes and the altered lupus chromatin state. However, we identified a patient subgroup prescribed angiotensin receptor blockers (ARBs) which lacked TNF-linked lupus chromatin accessibility features. These data raise questions about the role of lupus-associated chromatin changes in naive CD4+ T cell activation and differentiation and implicate ARBs in the regulation of disease-driven epigenetic states

overall_design: RNA Seq Samples from sorted populations of CD4+ T cells. CD4 T cells were enriched from human PBMCs and then sorted for  CD45RA+CD27+ naive TH, CXCR5+PD1+ICOS+CD38+ AcTfh, CXCR5+PD1+ICOSCD38- cTfh, and CXCR5-PD1-CXCR3+ Th1 cells. Cell come from individuals with Lupus and healthy individuals

first: Andrew

last: Hart

first: Terri

last: Laufer


title: TGF-β signaling controls neural crest developmental plasticity via SMAD2/3

first: Megan

last: Rothstein

sample_organism:
Gallus gallus
Homo sapiens

platform_organism:
Gallus gallus
Homo sapiens


title: Angiotensin receptor blockers and CD4 T cell transcriptional and epigenetic states in systemic lupus erythematosus. RNAseq [ATAC-seq]

overall_design: ATAC Seq Samples from sorted populations of CD4+ T cells. CD4 T cells were enriched from human PBMCs and then sorted for  CD45RA+CD27+ naive TH, CXCR5+PD1+ICOS+CD38+ AcTfh, CXCR5+PD1+ICOSCD38- cTfh, and CXCR5-PD1-CXCR3+ Th1 cells. Cell come from individuals with Lupus and healthy individuals


title: A mouse model of cardiac AL amyloidosis unveils mechanisms of tissue accumulation and toxicity of amyloid fibrils

city: Limoges

first: christophe

last: sirac

address: 2 Rue du Pr Descottes

institute: university of Limoges

summary: Immunoglobulin light chain (LC) amyloidosis (AL) is one of the most common types of systemic amyloidosis. The lack of reliable in vivo models hinders the study of the disease in its physiological context. We developped a transgenic mouse model producing high amounts of a human AL free light chain (LC). While mice exceptionnaly develop spontaneous AL amyloidosis and do not exhibit organ toxicity due to the circulating amyloidogenic LC, a single injection of amyloid fibrils, made up of the variable domain (VL) of the human LC, or soluble VL led to amyloid deposits, mainly in heart. The biochemical composition and the fragmentation pattern of the LC in the fibrils are highly similar to that of human AL fibrils, arguing for a conserved mechanism of amyloid fibrils formation. Amyloidosis positive mice also develop an early cardiac dysfunction, with increased NT-proBNP, diastolic dysfunction and remodeling of the extracellular matrix. Overall, this transgenic mice closely reproduces human cardiac AL amyloidosis and shows that a partial degradation of the LC initiate amyloid fibril formations in vivo. Accumulation of AL amyloid fibrils, rather than the soluble LC, drive the initial cardiac dysfunction. This model fills an important gap for research on AL amyloidosis and preclinical evaluation of new therapies.

overall_design: RNA-seq profiling of heart tissues (apex) from DH-LMP2A mice (controls), non-induced transgenic lS mice (AL-) and indiced transgenic lS mice (AL+)

first: Gemma

last: Martinez-Rivas

first: Justine

last: Pollet

first: Christophe

last: Sirac


title: Different PD-L1 Assays Reveal Distinct Immunobiology and Clinical Outcomes in Urothelial Cancer

city: South San Francisco

first: Juliette

last: Roels

address: 1 DNA Way

institute: Genentech

summary: Testing for PD-L1 expression by immunohistochemistry (IHC) is used to predict immune checkpoint blockade (ICB) benefit but has performed inconsistently in urothelial cancer (UC) clinical trials. Different approaches are used for PD-L1 IHC. We analyzed paired PD-L1 IHC data on UC samples using the SP142 and 22C3 assays from the phase 3 IMvigor130 trial and found discordant findings summarized by four phenotypes: PD-L1 positive by both assays (PD-L1 double positive; PD-L1DP), PD-L1 positive by the SP142 assay only (SP142 single positive; SP142SP), PD-L1 positive by the 22C3 assay only (22C3 single positive; 22C3SP), and PD-L1 negative by both assays double negative (PD-L1 double negative; PD-L1DN).  PD-L1DP and SP142SP UCs were associated with more favorable ICB outcomes and increased dendritic-cell (DC) infiltration. SP142 PD-L1 staining co-localized with DC-LAMP, a DC marker, while 22C3 staining was more diffuse. 22C3SP UCs, associated with worse outcomes, were enriched in tumor cell–dominant PD-L1 expression. Multiplex IHC in an independent ICB-treated cohort confirmed that tumor cell–dominant PD-L1 expression was associated with shorter survival. Using different PD-L1 assays, we uncovered that SP142 may preferentially stain PD-L1–expressing DCs, key to orchestrating antitumor immunity, while tumor cell–dominant PD-L1 expression, which underlyies a subset of “PD-L1 positive” specimens, is associated with poor ICB outcomes.

overall_design: ATAC-seq of three luminal and three basal bladder cancer cell lines.

first: Matthew

last: Galsky

first: Deepali

last: Rishipathak

first: Romain

last: Banchereau

first: Sanjeev

last: Mariathasan


title: Angiotensin receptor blockers and CD4 T cell transcriptional and epigenetic states in systemic lupus erythematosus [Multiomics]

overall_design: single cell multi-ome Samples (ATACseq and nuclear RNA) from sorted naive CD4+ T cells. CD4 T cells were enriched from human PBMCs and then sorted for  CD45RA+CD27+ naive TH cells. Cell come from individuals with Lupus and healthy individuals


title: A biophysical basis for the spreading behavior and limited diffusion of Xist [ChIP-Seq]

city: Boston

first: Jeannie

middle: T

last: Lee

address: Massachusetts General Hospital, 185 Cambridge street

department: molbio

institute: Massachusetts  General Hospital, Harvard Medical School

summary: Here we reveal a biophysical basis for the spreading behavior of Xist RNA on the inactive X-chromosome (Xi). Xist and HNRNPK together drive a liquid-liquid phase separation (LLPS) that encapsulates the Xi. HNRNPK and Xist exert mutual pulling forces that lead to RNA internalization into the condensate. While HNRNPK is sufficient for condensate formation, Xist induces a further phase transition into a "soft" droplet by altering elasticity, adhesiveness, and wetting properties of the condensate in vitro. Once phase transition occurs, other Xist-interacting factors are internalized and concentrated within the condensate. We attribute LLPS to HNRNPK's RGG and Xist's Repeat B (RepB) motifs. Mutating these motifs causes Xist diffusion, disrupts Polycomb recruitment, and precludes the required mixing of Xi chromatin for establishing the Xi superstructure. Thus, phase transitions driven by RepB and HNRNPK create a membrane-less subnuclear compartment for the localization and limited diffusion of Xist ribonucleoprotein complexes on the Xi.

overall_design: Calibrated ChIP-seq on WT female HNRNPK mutant MEFs

first: Danni

last: Wang

first: Mingrui

last: Ding

first: Hui

last: Chen

first: Barry

last: Kesner

first: Niklas-Benedikt

last: Grimm

first: Uri

last: Weissbein

first: Anna

last: Lappala

first: Jiying

last: Jiang

first: Carlos

last: Rivera

first: Jizhong

last: Lou

first: Pilong

last: Li


title: A biophysical basis for the spreading behavior and limited diffusion of Xist [RNA-Seq]

overall_design: RNA-seq on WT  and HNRNPK 6A mutant of day 0 and differenated day 7 mESCs


title: A biophysical basis for the spreading behavior and limited diffusion of Xist [CHART-seq]

overall_design: CHART-seq on WT  and HNRNPK 6A mutant of differenated day 7 mESCs


title: Pre- and postsynaptic MEF2C promote experience-dependent, input-specific development of Layer 4 to Layer 2/3 excitatory synapses

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

summary: Experience and activity-dependent transcription is a candidate mechanism to mediate development and refinement of specific cortical circuits. Here we provide evidence that the activity-dependent transcription factor Myocyte-Enhancer Factor 2C (MEF2C) is required in both presynaptic layer 4 (L4) and postsynaptic L2/3 somatosensory (S1) cortical neurons for development of their synaptic connection. In contrast, synaptic inputs from local L2/3, contralateral S1, or ipsilateral frontal/motor cortex are unaffected by postsynaptic Mef2c deletion in L2/3 neurons. Postsynaptic MEF2C is required for L4 to L2/3 synapse function during, but not after, an early postnatal, experience-dependent period. Furthermore, homozygous and heterozygous Mef2c deletion in presynaptic L4 neurons weakens L4 to L2/3 excitatory synaptic inputs by decreasing presynaptic release probability. Our results suggested that experience or activity-dependent transcriptional activation of MEF2C promotes development of L4→L2/3 synapses. In support of this idea, expression of transcriptionally active MEF2C (MEF2C-VP16) rescued weak L4 to L2/3 synaptic strength in sensory deprived mice. Consistent with a presynaptic function for MEF2C, we find that MEF2C regulates the activity-dependent expression of many presynaptic assembly genes, including transsynaptic cell adhesion proteins and regulators of neurotransmitter release. This work provides mechanistic insight into the experience-dependent development of specific cortical circuits.

overall_design: Organotypic slice cultures were prepared from P6 pups that were either: CaMKii-α Cre +/-; Mef2c fl/fl or Mef2c fl/fl. These cultures were grown for 8 days in-vitro (DIV) and then treated with either: 1% DMSO and 1% water or 100 μM  Picrotoxin and 100 μM 4-aminopyridine. Then RNA was made and turned into 150 basepair paired end cDNA libraries and sequenced on a NextSeq2000 to give ~80-100 million reads per sample

first: Sean

last: Watson

first: Jennifer

last: Putman

first: Zhe

last: Zhang

first: Kimberly

last: Huber


title: Transcriptome profiling of the posterior salivary glands of the cuttlefish Sepia officinalis from the Portuguese West coast

city: Caparica

first: Pedro

middle: M.

last: Costa

address: Campus de Caparica

department: Department of Life Sciences

country: Portugal

institute: NOVA School of Science and Technology, NOVA University of Lisbon

summary: Transcriptomic profiling (RNA-Seq) of the posterior salivary glands of Sepia officinalis L. 1758 (Mollusca: Coleoidea), wild type, collected from the Portuguese West coast (2020).

overall_design: Three samples (independent replicates) were analyzed. Total RNA from all samples was used to build the main library.

first: Cátia

last: Gonçalves

first: Inês

last: Moutinho Cabral

first: Ana

last: Grosso


title: Thymopentin ameliorates experimental colitis by inhibiting neutrophil extracellular traps: an alternative way to restore immune balance in IBD?

city: Shanghai

last: Cui

address: No.1058, Huan Zhen Bei Road, Baoshan District, Shanghai

institute: Department of General Surgery, Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: RNA sequencing was performed to investigate the mechanisms underlying TP5.

overall_design: The downstream signaling of TP5 was analyzed using RNA sequencing (RNA-seq) of the colon tissues of TNBS-induced and DSS-induced colitis mice.

first: Ye

first: Dongxing

last: Cao

first: Keyu

last: Qian


title: Extensive location bias of the GPCR-dependent translatome via site-selective activation of mTOR

city: Durham

first: Nikoleta

last: Tsvetanova

state: NC

address: 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

summary: G protein-coupled receptors (GPCRs) modulate various physiological functions by re-wiring cellular gene expression in response to extracellular signals. Control of gene expression by GPCRs has been studied almost exclusively at the transcriptional level, neglecting an extensive amount of regulation that takes place translationally. Hence, little is known about the nature and mechanisms of gene-specific post-transcriptional regulation downstream of receptor activation. Here, we apply an unbiased multiomics approach to delineate an extensive translational regulatory program initiated by the prototypical beta2-adrenergic receptor (β2-AR) and provide mechanistic insights into how these processes are orchestrated. Using ribosome profiling (Ribo-seq), we identify nearly 120 novel gene targets of adrenergic receptor activity for which expression is exclusively regulated at the level of translation. We next show that all translational changes are induced selectively by endosomal β2-ARs and report that this proceeds through activation of the mammalian target of rapamycin (mTOR) pathway. Specifically, within the set of translational GPCR targets we discover significant enrichment of genes with 5' terminal oligopyrimidine (TOP) motifs, a gene class classically known to be translationally regulated by mTOR. We then demonstrate that endosomal β2-ARs are required for mTOR activation and subsequent mTOR-dependent TOP mRNA translation. This site-selective crosstalk between the pathways is observed in multiple cell models with native β2-ARs, across a range of endogenous and synthetic adrenergic agonists, and for other GPCRs with intracellular activity. Together, this comprehensive analysis of drug-induced translational regulation establishes a critical role for location-biased GPCR signaling in fine-tuning the cellular protein landscape.

overall_design: To investigate transcription and translation responses downstream of β2-AR, we conducted parallel RNA-seq and Ribo-seq in HEK293 cells. Cells were incubated with DMSO or Dyngo (dynamin inhibitor) for 20 minutes, then stimluated with 1uM Isoproterenol. RNAseq samples were isolated through standard library preparation. Ribo-seq samples were prepared by isolating ribosome-protected-fragments and small RNA library preparation

first: Matthew

last: Klauer

first: Katherine

last: Hall

first: Caitlin

last: Jagla


title: Ortholog replacement reveals stable TFIIIC complexes are required for proper mitotic chromosome segregation

city: Taipei

first: Akshi

last: Gupta

state: Taiwan

address: IMB, 128, Academia Rd., Nangang, N411 lab

summary: Transcription factors are speculated to play crucial roles in adaptive evolution. Here we investigated how essential transcription factors (eTFs) change using ortholog replacement assays. Several orthologous eTFs from other yeast species could not fully complement the mutants in Saccharomyces cerevisiae, suggesting that these eTFs have changed their functions or interactions to become incompatible. We further characterized TFIIIC, a protein complex assisting RNA polymerase III transcription, that exhibits complete or partial incompatibility in several subunits. In the orthologous Tfc7-replacement line, the binding of TFIIIC to tRNA genes is reduced, but the abundance of tRNAs is not severely affected. However, Tfc7-replacement cells often mis-segregate chromosomes during mitosis and their fitness is further reduced in the spindle checkpoint mutant. Chromatin immunoprecipitation experiments showed that unstable TFIIIC binding results in defective cohesion loading, leading to chromosome mis-segregation. Swapping the highly divergent C-terminal domain of Tfc7 orthologs rescues its interaction with Tfc1 and cell fitness, suggesting that incompatibility is caused by altered interactions between complex subunits. Our results reveal separatable essential functions of a well-studied protein complex.

overall_design: ChIP-seq of Saccharomyces cerevisiae S288C TFIIIC complex subunit TFC3 in wild type like Sc-TFC7 and orthologous replacement line Kl-TFC7

first: Jun-Yi

last: Leu


title: SMC translocation is unaffected by an excess of nucleoid associated proteins in vivo

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

summary: Genome organization is important for DNA replication, gene expression, and chromosome segregation. In bacteria, two large family of proteins, nucleoid-associated proteins (NAPs) and the SMC complexes, play important roles organizing the genome. NAPs are abundant DNA-binding proteins that can bend, wrap, bridge and compact DNA, while SMC complexes load on the chromosome, translocate on the DNA, and extrude DNA loops. How SMC loop extrusion is influenced by various NAPs remains unknown. In this study, we expressed a collection of representative prokaryotic chromosome-associated proteins in Bacillus subtilis, which introduce distinct DNA structures and pose different challenges for SMC loop extrusion. By fluorescence microscopy and chromatin immunoprecipitation experiments, we observed that these proteins bound to the genome in characteristic manners. Through genome-wide chromosome conformation capture assays, we found that the SMC complex can traverse these DNA-binding proteins without slowing down. Our findings reveal that the DNA loop extrusion activity of the SMC complex is unaffected by the chromosome-associated proteins and highlight the robustness of SMC motors on the busy chromatin.

overall_design: Hi-C experiments were performed on wild type and mutant cells of Bacillus subtilis PY79 growing in rich medium.

first: X


title: TGF-β signaling controls neural crest developmental plasticity via SMAD2/3 [CUT&RUN]

first: Megan

last: Rothstein

summary: The neural crest is a highly plastic stem cell population that represents a notable exception to the germ layer theory. Despite being of ectodermal origin, these cells can differentiate into skeletal derivatives like cartilage and bone, tissues that are typically formed by mesoderm. The inductive program that endows the neural crest with these unique properties is still poorly understood. Here, we report that Smad2/3-mediated TGFβ signaling endows cranial neural crest cells with enhanced developmental potential. Our results show that TGFβ signaling modulates neural crest axial identity and directly activates the gene circuits that support skeletal differentiation. Cooperation between TGFβ and low levels of WNT-signaling in the embryonic head activates cranial-specific cis-regulatory elements of anterior genes. Activation of the TGFβ pathway allowed reprogramming of trunk neural crest cells to adopt an anterior identity and led to the development of an improved protocol for the generation of human cranial neural crest cells. Our findings indicate TGFβ signaling is required for the specification of cranial neural crest cells, endowing them with the potential to give rise to the craniofacial skeleton.

overall_design: Examination of binding by SMAD2/3, as well as H3K27ac occupancy in chick neural crest cells

first: Tatiane

last: Kanno

first: Marcos

last: Simoes-Costa

first: Ana Paula

last: Azambuja


title: A biophysical basis for the diffusion-restricted behavior of Xist RNA

first: Jeannie

last: Lee

overall_design: In situ Hi-C on WT female HNRNPK mutant MEFs

first: Danni

first: Mingrui

last: Ding

first: Hui

last: Chen

first: Barry

last: Kesner

first: Niklas

last: Grimm

first: Uri

last: Weissbein

first: Anna

last: Lappala

first: Jiying

last: Jiang

first: Carlos

last: Rivera

first: Jizhong

last: Lou

first: Pilong

last: Li


title: Modulation of predicted key driver genes of an atherosclerosis-associated gene regulatory network in human endothelial cells

status: Public on Jan 16 2025

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

summary: Carotid stenosis is a major cause of ischemic strokes both in males and females, but the clinical manifestation and carotid plaque histology differ. Single-cell RNA-Seq of endarterectomy samples from women and men revealed marked differences at the cell subtype level depending on sex. To provide clinical and pathophysiological context, cell subtypes displaying sex differences were integrated with 135 tissue-specific gene-regulatory networks (GRNs) of the STARNET study, leading to the identification of several atherosclerotic arterial wall sex-differential and cell-type-specific GRNs. PLVAP and FAM110D, two predicted key drivers of the male-dominant, endothelial cell-associated network GRN195 were overexpressed in human arterial endothelial cells (HAECs) to modulate the GRN and study its effect on cellular functions, including cell adhesion and proliferation.

overall_design: RNA-Seq profiling of primary and immortalized human aortic endothelial cells (HAECs) overexpressing PLVAP, FAM110D or negative control vector.

first: Prosanta

last: Singha

first: Katyayani

last: Sukhavasi

first: Minna

middle: U

last: Kaikkonen

first: Johan

middle: L

last: Björkegren


title: The Exserohilum turcicum effector EtEC81 reprograms alternative splicing in maize and activates immunity [RIP-Seq]

city: Beijing

first: Haiyue

last: Yu

address: Yuanmingyuanxilu No.2

institute: Chinese Academy of Agricultural Sciences

summary: Some pathogen-derived effectors reprogram mRNA splicing in their host plant to regulate plant immune responses. The fungus Exserohilum turcicum is the causal agent of northern corn leaf blight, a damaging maize (Zea mays) disease. However, the low efficiency of genetic transformation of E. turcicum has hampered research on its effectors and whether E. turcicum effectors interfere with RNA splicing remained unknown. Here, using an alternative splicing (AS) reporter system, we identified the secreted protein EtEC81 (Exserohilum turcicum effector 81), which modulates the AS of maize pre-mRNAs and negatively regulates the pathogenicity of E. turcicum. EtEC81 physically interacts with EtEC81-interactiNG protein 1 (ZmEIP1), which associates with maize spliceosome components, regulating AS and positively regulating the defense response against E. turcicum. EtEC81 binding further enhanced the effect of ZmEIP1 on AS. Transcriptome analysis revealed 119 common events with altered AS in maize plants transiently overexpressing ZmEIP1 or EtEC81, suggesting that these factors cause the mis-regulation of cellular activities and thus induce immune responses. We used RT-qPCR to verify representative AS events in the plants transiently overexpressing ZmEIP1 and EtEC81. Together, our results suggest that the EtEC81 effector targets ZmEIP1 to reprogram pre-mRNA splicing in maize.

overall_design: The RIP assay was performed as previously described with minor modification65-67. Briefly, total RNA was extracted from maize plants for incubation with MBP-EtEC81 and MBP, respectively. MBP-EtEC81 and MBP were purified with amylose resins (NEB, E8201) washed six times with MBP lysis and washing buffer (150 mM NaCl, 50 mM Tris-HCl pH 7.5, 1 mM EDTA, 1 mM PMSF, 20 units/mL RNase inhibitor [Promega, N251A]). A total of 10 μg RNA and 10 μg purified protein were mixed and treated with 0.5% fromaldehyde for 30 min for cross-linking, following with 125 mM glycine for 5 min to stop the reaction. Add up to 1 mL MBP lysis and washing buffer, and saved 100 μL mixture as input. Then the remaining RNA-protein solution was incubated with 50 μL amylose resins overnight at 4℃ with rotation. The RNA/MBP and RNA/MBP-EtEC81 resin complexes were thoroughly washed six times with MBP lysis and washing buffer. The immunoprecipitated RNAs and input-RNA were extracted with TRIzol reagent (Invitrogen, 15596018). Library construction and sequencing were performed by Novogene Inc (Beijing, China). The library was sequenced on an illumina Novaseq platform (HiSeq-PE150). Raw reads were firstly subjected to quality control using FastQC (v.0.20.1). The filtered reads were mapped to the Zea mays reference genome (https://download.maizegdb.org/Zm-B73-REFERENCE-GRAMENE-4.0/Zm-B73-REFERENCE-GRAMENE-4.0.fa.gz) using BWA mem (v0.7.12). The MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. The RIP target were identified based on the default parameters (P-value<0.05, and Fold change>2).


title: Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics

city: Gent

first: Marieke

last: Dubois

address: Technologiepark 71

country: Belgium

institute: PSB, Vlaams Instituut voor Biotechnologie (VIB)

summary: Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is a crucial first step towards engineering improved drought resilience. The molecular responses to drought are however very complex as they depend on multiple factors including the severity of drought, the profiled organ, its developmental stage and even the cell types therein. As such, deciphering the transcriptional responses to drought is specifically challenging.In the study associated with this data submission, we investigated tissue-specific responses to mild drought in young Arabidopsis thaliana (Arabidopsis) leaves using single-cell RNA sequencing (scRNA-seq, deposited under another id, GSE273033). To preserve transcriptional integrity during cell isolation, we fixed the RNA prior to cell isolation using the transcription inhibitor actinomycin D, demonstrating the benefits of fixation for studying mild stress responses at single-cell level. The transcriptome data deposited here corresponds to the bulk RNA-sequencing experiments described in this study. The samples presented here are undigested leaves, leaves digested by cell wall degradation without fixation, and leaves digested by cell wall degradation with RNA fixation. All sample types were collected from plants growing under well-watered and mild drought conditions.

overall_design: Arabidopsis Col-0 was grown either under well-watered conditions or exposed to mild drought. Per condition and per biological replicate, third true leaves were collected as "Undigested leaf" samples. They were harvested in 3 biological replicates. Third true leaves were also collected for tissue digestion, either without ("digested") or with RNA fixation("fixed, digested"). The obtained cells were subsequently processed for single-cell RNA sequencing (data deposited separately, GSE273033) or collected for bulk RNA sequencing (this deposition). These samples were harvested in two biological replicates.

first: Rubén

last: Tenorio Berrio

first: Eline

last: Verhelst

first: Thomas

last: Eekhout

first: Carolin

last: Grones

first: Lieven

last: De Veylder

first: Bert

last: De Rybel


title: High Expression of SERPINE1 and CTSL in Keratinocytes in Pressure Injury Caused by Ischemia-reperfusion Injury

city: Yantai

first: Dong

last: Wang

state: --- Select One ---

address: Binzhou Medica University, No. 346 Guanhai Road, Binhai Road Street, Laishan District, Yantai, Shandong Province

institute: Binzhou Mecical University

summary: Pressure Injury (PI) is a complex disease process which is influenced by multiple factors, among which ischemia-reperfusion (I/R) injury is closely related to the progression of PI. But, its biomarkers are still unclearly. Understanding its physiological mechanisms and related molecular biomarkers is the key to developing effective prevention and therapeutic strategies. This study through obtained the candidate genes of the differentially expressed genes (DEGs) from the PI rat model by transcriptome sequencing, PI single-cell sequencing database, and genes related to ischemic-reperfusion (I/R) injury from GeneCards database to analyze and screen prognostic related target genes. There were finally 7 candidate genes obtained from the intersection of the three datasets. Gene Ontology (GO) and Kyoto Encyclopedia of Genomes (KEGG) pathway analysis revealed that the DEGs were enriched in complement and coagulation cascades, and the keratinocyte differentiation is a significant factor. Then, two hub genes Serine protease inhibitor clade E member 1 (SERPINE1) and Cathepsin L (CTSL) were identified through three machine learning algorithms. The two hub genes were assessed using the nomogram and Receiver Operating Characteristic (ROC) approaches, and the findings indicated that these two genes had a high prognosis value. The two genes both play crucial roles in vasculogenesis, coagulation and degradation of the extracellular matrix, which is essential for wound healing. The results of immunohistochemistry demonstrated that SERPINE1 and CTSL are significantly upregulated in skin tissue from PI caused by I/R injury, and their mRNA expression levels significantly correlate with PI outcomes. According to our research we referred that the SERPINE1 and CTSL might be the potential biomarkers of PI.

overall_design: In order to investigate the genetic changes of pressure injury induced by ischemia-reperfusion injury, we constructed a rat model of pressure ulcer.

first: Lexuan

last: Bi

first: Yaxin

last: Liu

first: Lei

last: Zhang

first: Xiaoli


title: Polyploidy of MDA-MB-231 cells drives increased extravasation with enhanced cell-matrix adhesion

city: CAMBRIDGE

first: Satomi

last: Hirose

address: 500 Technology Square

department: Mechanical Engineering

institute: Massachusetts Institute of Technology

summary: Metastasis, the leading cause of cancer-related deaths, involves a complex cascade of events, including extravasation. Despite extensive research into metastasis, the mechanisms underlying extravasation remain unclear. Molecular targeted therapies have advanced cancer treatment, yet their efficacy is limited, prompting exploration into novel therapeutic targets. Here, we showed the association of polyploidy in MDA-MB-231 breast cancer cells and their extravasation, using microfluidic systems to reproduce the in vivo microvascular environment. We observed enhanced extravasation in polyploid cells alongside upregulated expression of genes involved in cell-substrate adhesion and cell mechanical dynamics. These findings offer insights into the relationship between polyploidy and extravasation, highlighting potential targets for cancer therapy.

overall_design: We found a subgroup of MDA-MB-231 cells that shows increased extravasation in a microvascular network generated in a microfluidic device in vitro. We then performed RNA-seq to investigate the characteristics of that subgroup.

first: Tatsuya

last: Osaki

first: Roger

last: Kamm


overall_design:
MDA-MB-231 cells were transfected to express cytoplasmic tdTomato and further tagged with H2B-EGFP. MDA-MB-231-H2B-EGFP-CMV-RFP cells were sorted using FACS into EGFP-positive and EGFP-negative subpopulations.
MDA-MB-231-H2B-EGFP-CMV-RFP cells were also sorted depending on nuclei size into small nucleus and large nucleus subpopulations.
Real-time RT-PCR gene expression profiling. Total RNA from each sample was collected from 2D culture.

first: Kamm

last: Roger


title: Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [10x-v3-RNA-seq]

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

summary: During early mammalian development, the endoderm layer undergoes complex patterning to form the foundations of the respiratory and digestive systems. This intricate process, guided by a series of cell fate decisions, remains only partially understood. Our research introduces a pioneering genetic tracing code across 14 distinct endodermal regions by developing a group of mouse strains. By integrating high-throughput and high-precision single-cell RNA sequencing with sophisticated imaging techniques across various mouse models, we comprehensively resolve the spatiotemporal and genetic lineage differentiation processes of the endoderm at a single-cell resolution. Our findings reveal a previously unrecognized multipotentiality within early endodermal regions for differentiation into diverse organ primordia. Furthermore, this research illuminates the complex and underestimated phenomenon of multiple origins in the development of endodermal organs, prompting a reevaluation of differentiation models for these organs. This work not only advances our understanding of developmental biology, but also has significant implications for regenerative medicine and the development of organoid models, providing new insights into the intricate mechanisms that guide organogenesis.

overall_design: scRNA-seq of tracing linegae for the development of endoderm

first: Keran

last: Li

first: Peilong

first: Qiqi

last: Zheng

first: Xin

first: Xuan

last: Fang

first: Linchen

first: Chengran


title: Increased global DNA methylation by Dnmt3a disrupts skeletal muscle homeostasis, promotes age-related muscle atrophy, and reduces muscle metabolic elasticity

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

type: Methylation profiling by high throughput sequencing

summary: Loss of muscle mass and function—a hallmark of skeletal muscle aging—is known as sarcopenia. Moreover, mammalian aging is reportedly driven by loss of epigenetic information. However, the effect of epigenetic alterations on skeletal muscle homeostasis is unknown. In this study, we show that chronic elevation of global DNA methylation results in a myopathy-like phenotype and age-related changes in skeletal muscle. Overexpression of muscle de novo methyltransferase 3a (Dnmt3a) increased central nucleus-positive myofibers, predominantly in fast-twitch myofibers, and shifted muscle fiber type to stress-resistant slow-twitch myofibers, accompanied by increased inflammatory and senescent signatures, decreased mitochondrial OXPHOS complex I protein level, and reduced basal autophagy in skeletal muscle. Chronic Dnmt3a overexpression decreased muscle mass and strength, and impaired tolerance to endurance exercise with age. This age-related decline in endurance exercise capacity was accompanied by an augmented inflammatory signature in a manner that is enhanced with age and promoted muscle atrophy. Network analysis identified Akt1 as a potential hub gene. Dnmt3a expression not only reduced sensitivity to starvation-induced muscle atrophy by suppressing the FoxO-regulated autophagy and ubiquitin–proteasome systems, but also reduced the restorability from starvation-induced muscle atrophy. These data suggest that increased global DNA methylation disrupts skeletal muscle homeostasis, promotes age-related muscle atrophy, and reduces muscle metabolic elasticity.

overall_design: Genomic DNAs were extracted from skeletal muscle (gastrocnemius) of Dnmt3a-Tg and age-matched WT mice. Libraries for whole-genome bisulfite sequencing was prepared as described in Miura F et al (2019), NAR, 47, e85.

first: Mamoru

last: Oyabu

first: Yuto

last: Ohira

first: Mariko

last: Fujita

first: Kiyoshi

last: Yoshioka

first: Runa

last: Kawaguchi

first: Yukino

last: Hatazawa

first: Huascar

last: Pedro Ortuste Quiroga

first: Hiromitsu

last: Araki

first: Masaki

last: Okano

first: Izuho

last: Hatada

first: Yoshihiro

last: Ogawa

first: Takashi

last: Ito

first: Kengo

last: Ishihara

first: Yusuke

last: Ono

first: Yasutomi

last: Kamei


title: Innate Immune Training of Osteoclastogenesis promotes Inflammatory Bone Loss

city: Dresden

first: Marko

last: Barovic

state: Saxony

address: Fetscherstr. 74

department: Institute for Clinical Chemistry and Laboratory Medicine

institute: TU Dresden

summary: scRNAseq of myeloid cells from arthritic hind paws upon induction of trained immunity or control treatment

overall_design: CD45+CD11b+ synovial myeloid cells from hind paws of b-glucan or PBS pre-treated mice (7 days prior to K/BxN STA induction) were sorted at day 17 after arthritis induction using a FACS Aria III sorter (BD, Heidelberg, Germany). The cell concentration was adjusted to 1000–1600 cells per μl (1.537 cells/μl in PBS sample and 1150 cells/μl in b-glucan sample). Approximately 10.000 cells were loaded and then processed with Chromium Next GEM Single Cell 3' v3.1 dual-index kit (10X Genomics) at the Dresden Concept Genome Center, Dresden, Germany. According to the manufacturer’s instructions, the cDNA was synthesized and subjected to library preparation and sequencing on the Novaseq 6000 platform (Illumina).

first: Nora

last: Haacke

first: Hui

last: Wang

first: Shu

last: Yan

first: Lydia

last: Kalafati

first: George

last: Hajishengallis

first: Triantafyllos

last: Chavakis


title: Increased global DNA methylation disrupts skeletal muscle homeostasis, promotes age-related decline in muscle function, and reduces muscle plasticity

first: Fumihito

last: Miura

summary: Loss of muscle mass and function—a hallmark of skeletal muscle aging—is known as sarcopenia. Moreover, mammalian aging is reportedly driven by loss of epigenetic information. However, the effect of epigenetic alterations on skeletal muscle homeostasis is unknown. In this study, we show that chronic elevation of global DNA methylation results in a myopathy-like phenotype and age-related changes in skeletal muscle. Overexpression of muscle de novo methyltransferase 3a (Dnmt3a) increased central nucleus-positive myofibers, predominantly in fast-twitch myofibers, and shifted muscle fiber type to stress-resistant slow-twitch myofibers, accompanied by upregulation of chemokine and immune system-related genes and reduced basal autophagy in skeletal muscle. Dnmt3a overexpression reduced muscle androgen receptor signaling, decreased muscle mass and strength, and impaired tolerance to endurance exercise with age. Network analysis identified Akt1 as a potential hub gene. Dnmt3a expression reduced sensitivity to starvation-induced muscle atrophy by suppressing the FoxO-regulated autophagy and ubiquitin–proteasome systems. These data suggest that increased global DNA methylation disrupts skeletal muscle homeostasis, promotes age-related decline in muscle function, and reduces muscle plasticity.

overall_design: Genomic DNAs were extracted from skeletal muscle (tibialis anterior) of Dnmt3a-Tg and age-matched WT mice, or Dnmt3a-KO and age-matched WT mice. Libraries for whole-genome bisulfite sequencing was prepared as described in Miura F et al (2019), NAR, 47, e85.

first: Mamoru

last: Oyabu

first: Yuto

last: Ohira

first: Mariko

last: Fujita

first: Kiyoshi

last: Yoshioka

first: Runa

last: Kawaguchi

first: Yukino

last: Hatazawa


title: Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq-add]

first: Cheng-ran

last: Xu

overall_design: scRNA-seq of tracing lineage for the development of endoderm

first: Keran

last: Li

first: Peilong

last: Yu

first: Qiqi

last: Zheng

first: Xin

first: Xuan

last: Fang

first: Linchen

first: Chengran


title: Microarray analysis of transgenic mice specifically overexpressing Dnmt3a in skeletal muscle (Dnmt3a Tg mice)

city: Kyoto

first: Yasutomi

last: Kamei

address: 1-5 Shimogamo-Hangicho, Sakyo-ku

institute: Kyoto Prefectural University

summary: DNA methylation occurs as 5-methylcytosines mainly at cytosine-guanine dinucleotides, so-called CpG sites, and such methylation is a well-studied epigenetic mechanism for transcriptional regulation. Genomic DNA methylation patterns are established by the actions of the de novo methyltransferases Dnmt3a and Dnmt3b, and are maintained by the methyltransferase Dnmt1. Expression of Dnmt3a mRNA is relatively high in skeletal muscle, suggesting a major role in transcriptional regulation. Thus, we created transgenic mice specifically overexpressing Dnmt3a in skeletal muscle (Dnmt3a Tg mice). In this study, we performed a microarray analysis of skeletal muscle in wild-type control and Dnmt3a Tg mice. The microarray data shows upregulation of a set of slow-twitch myofiber-specific genes and downregulation of fast-twitch myofiber-specific genes in Dnmt3a-Tg muscle compared with WT muscle.

overall_design: For microarray analysis, RNA was isolated from the gastrocnemius skeletal muscle of control mice (7 weeks of age) and Dnmt3a Tg mice (7weeks of age). Samples from wild-type and Dnmt3a Tg mice (N = 3 for each group) were pooled before use.


title: The meninges host a unique compartment of regulatory T cells that bulwarks adult hippocampal neurogenesis [scRNA-Seq]

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Our knowledge about the meningeal immune system has recently burgeoned, particularly how innate and adaptive effector cells are mobilized in response to brain challenges. However, information on how meningeal immunocytes guard brain homeostasis in healthy individuals remains sparse. This study highlights the heterogeneous and polyfunctional regulatory T (Treg) cell compartment in mouse meninges. A Treg subtype specialized in controlling Th1-cell responses and another subtype devoted to controlling responses in B-cell follicles were substantial components of this compartment, foretelling the finding that punctual Treg-cell ablation rapidly unleashed interferon-gamma production by meningeal lymphocytes, unlocked their access to the brain parenchyma, and altered meningeal B-cell profiles. Distally, the hippocampus took on a reactive state, with activation of multiple glial-cell types; within the dentate gyrus, neural stem cells showed exacerbated death and desisted from further differentiation, associated with inhibition of spatial-reference memory. Thus, meningeal Treg cells are a multifaceted bulwark to brain homeostasis at steady-state.

overall_design: We investigated the transcriptional heterogeneity of meningeal CD4+ T cells  via single-cell RNA and Tcr sequencing (scRNA-seq/ scTcr-seq), and investigate the changes in the hippocampal niche after punctual Treg cell depletion via diphtheria toxin (DT) injections into Foxp3-DTR+ and littermate Foxp3-DTR- controls (scRNA-seq) .For standard genome-wide scRNA-seq analyses, non neuronal non microglia (Live CD45- Thy1-) were sorted by flow cytometry and encapsulated using the Chromium Single Cell 3′ v2 platform. For coupled scRNA-seq and scTcr-seq, CD4+ T cells from meninges of Foxp3Gfp mice and b6 wildtype mice  were sorted and encapsulated using the Chromium Single Cell 5′ v3 and V(D)J platform (10x Genomics).

first: Miguel

last: Marin-Rodero

first: Diane

last: Mathis


title: The meninges host a unique compartment of regulatory T cells that bulwarks adult hippocampal neurogenesis

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

overall_design: Refer to individual Series