title: Transcriptional dynamics of sleep deprivation and subsequent recovery sleep in the murine cortex

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

summary: Sleep loss regulates gene expression throughout the brain and impacts learning and memory. However, the molecular consequences of sleep deprivation and the ability of subsequent sleep (recovery sleep) to restore baseline gene expression remain underexplored. Our goal here is to overview transcriptional changes at the gene level in the cortex of adult male wildtype mice in response to sleep loss and recovery sleep. This dataset constitutes an integration of novel data with two publicly available RNA-seq studies and contains 3, 5, and 6 hours of sleep deprivation and 2 and 6 hours of recovery sleep time points.

overall_design:
We analyzed gene expression for 42 RNA-seq samples. Prefrontal cortex tissue was collected after 5 hours of sleep deprivation and 2 hours of subsequent recovery sleep, while cerebral cortex tissue was collected after 3 and 6 hours of sleep deprivation and 6 hours of subsequent recovery sleep. Animals that were left to sleep in their home cage were dissected at the same time of day as the animals in the corresponding treatment group to control for variations due to circadian rhythms. Our dataset is an integration of samples from GSE140345 and GSE113754 with unpublished and not previously analyzed data from our group that was collected at the same time as the samples from GSE113754.
We obtained fastq files for the third-party dataset GSE140345 from SRA using fastq-dump from the SRA toolkit. The reanalyzed samples were GSM4159650, GSM4159652, GSM4159654, GSM4159656, GSM4159658, GSM4159660, GSM4159591, GSM4159593, GSM4159678, GSM4159680, GSM4159682, GSM4159684, GSM4159686, GSM4159688, GSM4159601, GSM4159603, GSM4159605, GSM4159607, GSM4159609, GSM4159611, GSM4159613, and GSM4159615. Raw sequencing reads from the fastq files were quantified with Salmon, and Tximeta was used to summarize counts to the gene level.

first: Alexander

last: Popescu

first: Kaitlyn

last: Ford

first: Elizabeth

last: Medina


title: Adipose stem cells are sexually dimorphic cells with dual roles as preadipocytes and resident fibroblasts [in vitro_SVF]

status: Public on Aug 13 2024

city: Huddinge

first: Martin

middle: Verner

last: Uhrbom

address: Hälsovägen 7C

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institute

type: Expression profiling by high throughput sequencing

summary: Cell identities are defined by intrinsic transcriptional networks and spatio-temporal environmental factors. Here, we explored multiple factors that contribute to the identity of adipose stem cells, including anatomic location, microvascular neighborhood, and sex. Our data suggest that adipose stem cells serve a dual role as adipocyte precursors and fibroblast-like cells that shape the adipose tissue’s extracellular matrix in an organotypic manner. We further find that adipose stem cells display sexual dimorphism regarding genes involved in estrogen signaling, homebox transcription factor expression and the renin-angiotensin-aldosterone system. These differences could be attributed to sex hormone effects, developmental origin, or both. Finally, our data demonstrate that adipose stem cells are distinct from mural cells, and that the state of commitment to adipogenic differentiation is linked to their anatomic position in the microvascular niche. Our work supports the importance of sex and microvascular function in adipose tissue physiology.

overall_design:
To investigate the gene expression profile of in vitro cultivated cells of the stromal vascular fraction (SVF) from pgWAT and iWAT depots in adult male and female mice, we isolated RNA from crude SVF that have been in vitro cultivated for four days and performed bulk RNA sequencing.
There are five mouse RNAseq datasets connected to this study: (1) scRNAseq of stromal vascular fraction (SVF) of pgWAT, (2) bulk RNA-seq from FACS sorted Adipose stem cells (ASC) from pgWAT and iWAT, (3) bulk RNA-seq from isolated floating mature adipocytes from pgWAT and iWAT, (4) bulk RNA-seq from FACS sorted ASC from castrated/ovarectomized/male and female control mice, and (5) bulk RNA-seq from in vitro cultivated SVF cells from pgWAT and iWAT.

first: Lars

last: Muhl

first: Guillem

last: Genové

first: Jianping

last: Liu

first: Henrik

last: Palmgren

first: Ida

last: Alexandersson

first: Fredrik

last: Karlsson

first: Alex

middle: X

last: Zhou

first: Sandra

last: Lunnerdal

first: Sonja

last: Gustafsson

first: Byambajav

last: Buyandelger

first: Kasparas

last: Petkevicius

first: Ingela

last: Ahlstedt

first: Daniel

first: Leif

last: Aasehaug

first: Liqun

last: He

first: Marie

last: Jeansson

first: Christer

last: Betsholtz

first: Xiao

middle: R

last: Peng


title: Adipose stem cells are sexually dimorphic cells with dual roles as preadipocytes and resident fibroblasts [FACS_pgWAT_iWAT_ASC]

first: Martin

last: Uhrbom

overall_design:
To investigate the gene expression profile of adipose stem cells from pgWAT and iWAT depots in male and female mice, we isolated RNA from FACS sorted adipose stem cells (CD45-/CD31-/CD34+/DPP4+/-) from iWAT/pgWAT depots in adult wild-type mice (C57BL6/J) and performed bulk RNA sequencing.
There are five mouse RNAseq datasets connected to this study: (1) scRNAseq of stromal vascular fraction (SVF) of pgWAT, (2) bulk RNA-seq from FACS sorted Adipose stem cells (ASC) from pgWAT and iWAT, (3) bulk RNA-seq from isolated floating mature adipocytes from pgWAT and iWAT, (4) bulk RNA-seq from FACS sorted ASC from castrated/ovarectomized/male and female control mice, and (5) bulk RNA-seq from in vitro cultivated SVF cells from pgWAT and iWAT.

first: Lars

last: Muhl

first: Guillem


title: Adipose stem cells are sexually dimorphic cells with dual roles as preadipocytes and resident fibroblasts [scRNA-seq]

overall_design:
To investigate the gene expression profile of stromal vascular cells from pgWAT in male and female mice, we isolated RNA from FACS sorted single cells and performed Smart-seq2 sequencing.
There are five mouse RNAseq datasets connected to this study: (1) scRNAseq of stromal vascular fraction (SVF) of pgWAT, (2) bulk RNA-seq from FACS sorted Adipose stem cells (ASC) from pgWAT and iWAT, (3) bulk RNA-seq from isolated floating mature adipocytes from pgWAT and iWAT, (4) bulk RNA-seq from FACS sorted ASC from castrated/ovarectomized/male and female control mice, and (5) bulk RNA-seq from in vitro cultivated SVF cells from pgWAT and iWAT.

last: Genové

first: Jianping

last: Liu

first: Henrik

first: Ida


title: Adipose stem cells are sexually dimorphic cells with dual roles as preadipocytes and resident fibroblasts [FACS_castovary_ASC]

overall_design:
To investigate the impact of sex hormones on the gene expression profile of adipose stem cells, we isolated RNA from FACS sorted adipose stem cells (CD45-/CD31-/CD34+/DPP4+/-) from iWAT depot from castrated/ovariectomized/control mice and performed bulk RNA sequencing.
There are five mouse RNAseq datasets connected to this study: (1) scRNAseq of stromal vascular fraction (SVF) of pgWAT, (2) bulk RNA-seq from FACS sorted Adipose stem cells (ASC) from pgWAT and iWAT, (3) bulk RNA-seq from isolated floating mature adipocytes from pgWAT and iWAT, (4) bulk RNA-seq from FACS sorted ASC from castrated/ovarectomized/male and female control mice, and (5) bulk RNA-seq from in vitro cultivated SVF cells from pgWAT and iWAT.

last: Palmgren

last: Alexandersson

first: Fredrik

first: Alex

first: Sandra


title: Genome access is transcription factor specific and defined by nucleosome position [ChIP-Seq]

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mammalian gene expression is controlled by transcription factors (TFs) that engage sequence motifs in a chromatinized genome, where nucleosomes can restrict DNA access. Yet, how nucleosomes affect individual TFs remains unclear. Here, we measure the ability of over one hundred TF motifs to recruit TFs in a defined chromosomal locus in mouse embryonic stem cells. This identifies a set sufficient to enable binding of TFs with diverse tissue specificities, functions, and DNA binding domains. These chromatin-competent factors are further classified when challenged to engage motifs within a highly-phased nucleosome. The pluripotency factors OCT4- SOX2 preferentially engage non-nucleosomal and entry-exit motifs, but not nucleosome internal sites, a preference that also guides binding genome-wide. By contrast, factors such as BANP, REST, or CTCF, engage throughout causing nucleosomal displacement.This reveals that TFs vary widely in their sensitivity to nucleosomes and that genome access is TF-specific and influenced by nucleosome position in the cell.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of the transcriptionf factor OCT4 in WT and SNF2H KO mouse embryonic stem cells.

first: Ralph

last: Grand

first: Marco

last: Pregnolato

first: Lisa

last: Baumgartner

first: Leslie

last: Hoerner

first: Lukas

last: Burger

last: Schubeler


title: Multimodal Hox5 activity generates motor neuron diversity [ATAC-seq]

status: Public on Aug 12 2024

city: Cleveland

first: Polyxeni

last: Philippidou

state: OH

address: 2210 Circle Dr.

department: Neuroscience

country: USA

institute: Case Western Reserve University

summary: Motor neurons (MNs) are the final output of circuits driving fundamental behaviors, such as respiration and locomotion. Hox proteins are essential in generating the MN diversity required for accomplishing these functions, but the transcriptional mechanisms that enable Hox paralogs to assign distinct MN subtype identities despite their promiscuous DNA binding motif are not well understood. Here we show that Hoxa5 can modify chromatin accessibility in all mouse spinal cervical MN subtypes and engages TALE co-factors to directly bind and regulate subtype-specific genes. We identify a paralog-specific interaction of Hoxa5 with the phrenic MN-specific transcription factor Scip and show that heterologous expression of Hoxa5 and Scip is sufficient to suppress limb-innervating MN identity. We also demonstrate that phrenic MN identity is stable after Hoxa5 downregulation and identify Klf proteins as potential regulators of phrenic MN maintenance. Our data identify multiple modes of Hoxa5 action that converge to induce and maintain MN identity.

overall_design: ATAC-seq profiles of control and Hoxa5-deficient cervical motor neurons. The Choline Acetyltransferase (ChAT)::GFP transgenic reporter line was used to sort GFP-positive motor neurons. In total, four samples were used, two biological replicates for control and two for mutants.

first: R

last: KC

first: P


title: Multimodal Hox5 activity generates motor neuron diversity [RNA-seq]

overall_design: Comparative gene expression analysis (RNA-seq data) for cervical and thoracic motor neurons at e12.5. Each cervical or thoracic region contains three biological replicates.

first: A

last: Vagnozzi


title: Multimodal Hox5 activity generates motor neuron diversity [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Hoxa5, Pbx1 and their respective inputs at e12.5. Cervical spinal cords from multiple embryos were combined in each sample.


title: 3D chromatin architecture of drug-tolerant cancer cells at single-cell resolution [scHi-C]

status: Public on Aug 14 2024

city: San Antonio

first: Yufan

last: Zhou

state: TX

address: 7703 Floyd Curl Dr

institute: UT health Science Center at San Antonio

summary: Anticancer drug therapy generally elicits the drug tolerance after long-term treatment. Recent studies suggested that 3D chromatin structures of cancer cells were intimately linked to drug resistance. However, 3D chromatin structures in drug-tolerant cancer cells at single-cell resolution haven’t been elucidated. Here we performed single-cell Hi-C (scHi-C) analysis to examine the 3D chromatin structures in three stages of breast cancer cells.

overall_design: To fully understand the 3D chromatin structures of drug-tolerant cancer cells at single-cell resolution, we designed scHi-C approach for analyzing a breast cancer cell model system, MCF7, MCF7M1 and MCF7TR cells. A total of 293 cells (89 MCF7 cells, 91 MCF7M1 cells, 113 MCF7TR cells) were used for scHi-C profiling.

first: Victor

last: Jin


title: Splenocyte mRNA profiles of 4-6 weeks-old p53+/+ Em-Myc and p53DAS/DAS Em-Myc mice

city: Paris

first: Boris

last: BARDOT

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Our study represents the first analysis of splenocyte transcriptomes of Em-Myc transgenic mice lacking alternatively spliced p53 isoforms

overall_design: The experiment was performed in biological replicates on males of each genotype (p53+/+ Em-Myc and p53DAS/DAS Em-Myc) .

first: Anne

last: Fajac

last: Bardot

first: Franck

last: Toledo

first: Marc

last: Gabriel


title: Genome access is transcription factor specific and defined by nucleosome position

last: Schuebeler

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: DAV132 colon-targeted adsorbent prevents antibiotic-related dysbiosis in human volunteers and mitigates anti-PD-1 resistance in murine models

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

institute: UMR INSERM 1231

summary: The deleterious impact of antibiotics (ATB) on the microbiome negatively impacts immune checkpoint inhibitor (ICI) response. We assessed the efficacy of DAV132, a colon-targeted adsorbent in 70 healthy volunteers (HV) randomized to receive ceftazidime-avibactam or piperacillin-tazobactam alone or in combination with oral administration of DAV132. DAV132 significantly decreased fecal but not plasma ATB concentration. When coadministered with either ATB, DAV132 prevented loss of microbiome diversity and induced rapid recovery of the baseline microbiota composition. Moreover, bacterial probe set qPCR-based assay confirmed metagenomics results that DAV132 preserved several commensals such as Alistipes shahii, Blautia obeum and Faecalibacterium praunsnitzii. Fecal microbiota transplantation in murine tumor models from HV treated with ATB alone reduced antitumor responses to anti-PD-1, while transplanted samples from HV treated with ATB+DAV132 circumvented resistance to anti-PD-1. This anti-tumor response in mice was associated with tumor microenvironment increased the ratio of total CD8+ T cells/ regulatory T cells, and three distinct activated CD8+ T cell population whiting the tumor within the tumor, as well as gene expression of interferon gamma (INFγ) in the mesenteric lymph nodes. In addition, a unique gene signature with downregulation of IL-6 and reactive oxygen pathways was found in the mice treated with FMT from ATB+DAV132 sample and treated with anti-PD-1. DAV132 represents a new strategy for overcoming ATB-related dysbiosis and further studies are warranted to evaluate its efficacy in cancer patients on ICI.

overall_design: 2 weeks after FMT with HV stools treated with CZA or CZA+DAV132 for 6 days, C57Bl6 mice were implanted subcutaneously with 0.8 × 10^6 MCA-205 cells. When tumors reached 25 to 35 mm2 in size, mice were treated four times intraperitoneally every three days with αPD-1 mAb (250 μg/mouse; clone RMP1-14, Bio X Cell) or isotype control (clone 2A3, Bio X Cell). The mice were sacrificed 2 days after the last treatment and the tumor were harvested and snap frozen for a tumor bulk RNAseq analysis for gene expression analysis. A duplicate of this experiemnst was performed with the same setting and using the same FMT samples, the tumor were also harvested at the sacrifice and the CD8+ T cells were cell sorted and immediately snap frozen for a specific analysis of the gene expression of this cell population.

first: Meriem

last: Messaoudene

first: Caroline

last: Truntzer

first: Romain

last: Boidot

first: Francois

first: Bertrand

last: Routy


title: Cytoplasmic UHRF1 restrains MHC-I-mediated anti-tumor immune response [bulk RNA-seq]

status: Public on Aug 09 2024

city: Durham

first: Liuyang

last: Wang

state: NC

address: 213 Research Drive

institute: Duke University

summary: Immunotherapy has revolutionized the landscape of cancer treatment. However, both primary and acquired resistance to immunotherapy, emerged during the co-evolution of cancer cells and the tumor microenvironment (TME), commonly restrain long-term tumor control. In exploring the oncogenic activity of Ubiquitin-like with PHD and ring finger domains 1 (UHRF1), we unexpectedly discovered that this epigenetic regulator exhibits altered expression and aberrant cytosolic localization in cancerous tissues. Cytoplasmic translocation of UHRF1 is induced by its phosphorylation on a specific serine in response to signals provided by factors present in the TME, such as TGF-, enabling UHRF1 to bind MHC-I and promote its ubiquitination and degradation via the E3 activity of UHRF1. Down-regulation of MHC-I results in suppression of the antigen presentation pathway to establish a non-T cell-inflamed TME favoring tumor growth. Genetic deletion of UHRF1 synergizes with immune checkpoint blockade (ICB) treatment and induces an anti-tumor memory response by evoking low-affinity T cells upon sustained UHRF1 inactivation. Our study unveils a novel function of UHRF1 in cancer immune evasion and provides a potential target to synergize with immunotherapy and overcome immunotherapeutic resistance.

overall_design: One million sgNT or sgUHRF1 LG1233-OVA cells were subcutaneously injected into female C57BL/6 mice. Tumor tissues were collected on day 27 for RNA-sequencing.

first: Lianmei

last: Tan

first: Tao

last: Yin

first: Poorva

last: Mudgal

first: Qi-Jing

last: Li

first: Xiao-Fan


title: Cytoplasmic UHRF1 restrains MHC-I-mediated anti-tumor immune response

overall_design: This data contains 2 TCR-seq datasets. 1. For LLC-OVA tumor model, LLC-OVA shNT or shUHRF1 cells were subcutaneously injected into male C57BL/6J mice and subsequently treated with either 30 µg IgG or CTLA4 antibodies on days 7, 10 and 14. Total RNA was extracted from tumor tissues day 17 and analyzed by TCRb-seq. 2. For LG1233-OVA tumor model, LG1233-OVA sgNT or sgUHRF1 cells were subcutaneously injected into female C57BL/6J mice. Total RNA was extracted from tumor tissues day 27 and analyzed by TCRb-seq.


title: C286 an orally available retinoic acid receptor Beta agonist drug regulates multiple pathways to achieve SCI repair

status: Public on Aug 08 2024

city: Evry

first: Marco Antonio

last: MENDOZA-PARRA

address: 2 rue Gaston Crémieux

institute: CNRS UMR8030

summary: Retinoic acid receptor beta (RARbeta) is an emerging therapeutic target for spinal cord injuries (SCIs) with a unique multimodal mode of action. We have developed a first in class RARbeta agonist drug, C286, with demonstrated safety in a Phase 1 trial and proven efficacy in a sensory root avulsion rat model. Using genome-wide and pathway enrichment analysis in spinal cords of avulsed rats we show that C286 modulates regenerative pathways amongst which extracellular matrix (ECM) and adhesion molecules were of note. Protein expression analysis showed that C286 upregulates tenascin-C, integrin alpha9 and osteopontin in the injured cord. We further demonstrate the drug's efficacy in a rodent model of spinal cord contusion where it remodulates ECM molecules, hampers inflammation and prevents tissue loss. Treatment with the agonist induced upregulation of RARbeta in dorsal root and spinal neurons. In the single ascending dose (SAD) cohorts in white blood cells from healthy human participants RARbeta2 expression increases with dose and at the highest dose administered the pharmacokinetics are similar to doses used in rat proof of concept (POC) studies. We also show plasma S100B in nerve injured rats as a correlative measure of axonal regeneration. Finally, comparison with other clinically available retinoids which are non RARbeta selective showed these were ineffective in aiding regain of function in avulsed rats. Taken together our data suggests that further clinical testing of C286 in POC trials is justifiable for a broad spectrum of SCIs

overall_design: To study the mechanisms driving nervous injury repair driven by the RAR-beta agonist C286, Sensory root avulsion model in rats has been used. Briefly, animals were treated with vehicle or C286 igand in absence or in presence of  spinal root avulsion injuries. Spinal cord samples were microdissected and used for RNA extraction analysed by next generation sequencing.

first: Jonathan

last: Corcoran

first: Marco

middle: A

last: Mendoza-Parra

first: Maria

last: Goncalves

first: Julian

last: Jack


title: Inducible mucosa-like differentiation of head and neck cancer cells drives the epigenetically determined loss of cell malignancy

city: Bielefeld

first: Ingo

last: Todt

address: Morgenbreede 1

department: Ear, nose and throat medicine

country: Germany

institute: University of Bielefeld

summary: Human papillomavirus-negative head and neck squamous cell carcinoma (HNSCC) is a highly malignant disease with high death rates that have remained substantially unaltered for decades. Therefore, new treatment approaches are urgently needed. Human papillomavirus-negative tumors harbor areas of terminally differentiated tissue that are characterized by cornification. Dissecting this intrinsic ability of HNSCC cells to irreversibly differentiate into non-malignant cells may have striking tumor-targeting potential.

overall_design: Primary head and neck squamous cell carcinoma cell cultures were established in a serum-free medium to investigate the differentiation potential of HNSCC. The cells were differentiated with a serum medium and cultured for 8 days until full differentiation was achieved. Both cultures under the control condition (PNEU) and the differentiation condition (CFM) have been analyzed using RNA-seq.

first: Sarah

last: Gendreizig

first: Felix

last: Oppel


title: Impaired RPE Mitochondrial Energetics Leads Subretinal Fibrosis in Neovascular Age-related Macular Degeneration

city: Oklahoma City

first: Xiang

last: Ma

state: OK

address: 825 NE 13th St

department: Cardiovascular biology

institute: Oklahoma Medical Research Foundation

summary: Subretinal fibrosis permanently impairs the vision of patients with neovascular age-related macular degeneration. Despite emerging evidence revealing the association between disturbed metabolism in retinal pigment epithelium (RPE) and subretinal fibrosis, the underlying mechanism remains unclear. In the present study, single-cell RNA sequencing revealed, prior to subretinal fibrosis, genes in mitochondrial fatty acid oxidation are downregulated in the RPE lacking very low-density lipoprotein receptor (VLDLR), especially the rate-limiting enzyme carnitine palmitoyltransferase 1A (CPT1A). We found that overexpression of CPT1A in the RPE of Vldlr-/- mice suppresses epithelial-to-mesenchymal transition and fibrosis. Mechanistically, TGFβ2 induces fibrosis by activating a Warburg-like effect, i.e. increased glycolysis and decreased mitochondrial respiration through ERK-dependent CPT1A degradation. Moreover, VLDLR blocks the formation of the TGFβ receptor I/II complex by interacting with unglycosylated TGFβ receptor II. In conclusion, VLDLR suppresses fibrosis by attenuating TGFβ2-induced metabolic reprogramming, and CPT1A is a potential target for treating subretinal fibrosis.

overall_design: The RPE-choroid tissues of WT mice and Vldlr-/- mice at the age of 1 month and 2 months were used for scRNA seq.

first: Wenjing

last: Wu

first: Miwa

last: Hara

first: Carolina

last: Panzarin

first: Jiyang

last: Cai

first: Jian-Xing

first: Yusuke

last: Takahashi


title: Nuclear lamin A/C phosphorylation by loss of Androgen Receptor is a global determinant of cancer-associated fibroblast activation

city: Epalinges

first: Soumitra

last: Ghosh

state: Choose State/Province

address: Chemin des Boveresses 155

department: Biochemistry

institute: University of Lausanne, Switzerland


title: Whole-Transcriptome Sequencing Analysis Identifies of key circRNAs, miRNAs and mRNAs in the development process of yak testis

city: Lanzhou

first: Liyan

last: hu

address: Jiangouyan,Qilihe

department: Key Laboratory of Yak Breeding in Gansu Province

country: China

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: The testis is an important reproductive organ in male mammals, serving as the site for spermatogenesis, androgen synthesis, and secretion. Non-coding RNAs (ncRNAs) plays an important regulatory role in various biological processes. However, the regulatory role of ncRNAs on yak testicular development and spermatogenesis is still largely unclear. In this study, the expression profiles of circRNA, miRNA, and mRNA in testicular tissues were compared between 6 months (Y6M), 18 months (Y18M), and 4 years old (Y4Y), with a significant difference in testicular development using RNA-seq. A total of 22 differentially expressed circRNAs (DE circRNAs), 69 differentially expressed miRNAs (DE miRNAs), and 64 differentially expressed mRNA (DE mRNAs) were detected in testicular samples of Y6M, Y18M, and Y4Y, respectively. Furthermore, GO and KEGG analysis results showed that the source genes of DE circRNAs, predicted target genes of DE miRNAs, and DE mRNAs concentrated on signaling pathways and GO terms that were related to sperm synthesis, vitality, and testicular development, such as cell cycle, Wnt signaling pathway, MAPK signaling pathway, GnRH signaling pathway, and spermatogenesis process. A circRNA-miRNA-mRNA network analysis revealed that some differentially expressed non-coding RNAs (DE ncRNAs) may be involved in testicular spermatogenesis, including miR-574, miR-449a, CDC42, CYP11A1 and et al. At the same time, there are various circRNA-miRNA interaction pairs. This study provides a deep understanding of the regulatory network of ncRNA regulation in yak testicular development, providing data support for further elucidating the molecular mechanisms of yak testicular development.

last: Hu

first: Xingdong

last: Wang

first: Jie

last: Pei

first: Xian

last: Guo


title: Effect of PLX4720 on melanoma-associated fibroblasts co-cultured with melanoma cells

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: The experiment was designed to assess the effect of PLX4720 on the gene expression in human primary melanoma-associated fibroblast co-cultired with 5555 mouse melanoma cells

overall_design:
Total RNA from DMSO or PLX4720-treated melanoma-associated fibroblast (MAF2-mCherry) co-cultured with melanoma cells (5555-mEGFP), FACS sorted. 4 samples previoulsy uploaded under GSE63160
idat files not availabe for this submission.

first: E

last: Hirata

first: G

last: Giangreco

last: Sahai


title: Genome access is transcription factor specific and defined by nucleosome position [NOMe-seq]

first: Dirk

last: Schuebeler

overall_design: Amplicon NOMe-seq in mouse ESCs. Replicates of pools of TF motifs inserted in defined sequence contexts and integrated in the RMCE-locus.

first: Ralph

last: Grand

first: Marco

last: Pregnolato

first: Lisa

last: Baumgartner

first: Leslie

last: Hoerner

first: Lukas

last: Burger

last: Schubeler


title: Effect of flg22 peptide on Arabidopsis seedling roots with endodermis-expressed FLS2 in fls2 mutant background

status: Public on Aug 11 2024

city: Wien

first: Yan

last: Ma

address: Dr.-Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

summary: To compare transcriptional outputs of FLS2 and SGN3 pathways solely within the endodermis, we conducted comparative RNAseq analysis of pCASP1::FLS2 fls2 and wild-type seedling roots treated by flg22 and CIF2 respectively, at three timepoints (30, 120, 480 min) (CIF2 responses data previously published by Fujita et al 2020). The receptor mutant controls sgn3 and fls2, displayed minimal gene responses to respective peptides.

overall_design: Comparing flg22 treatment to H2O treatment at 3 time points (30, 120, 480 min) on pCASP1::FLS2-GFP fls2 (endodermis-expressed FLS2) to assess endodermis-specific FLS2 immune responses in 5-day-old seedling roots. The fls2 receptor mutant is used as a control.

first: Aurélia

last: Emonet

first: Niko

last: Geldner


title: HLTF Prevents G4 Accumulation and Promotes G4-induced Fork Slowing to Maintain Genome Stability

city: Stanford

first: Karlene

middle: Anne

last: Cimprich

state: CA

address: 318 Campus Drive

institute: Stanford University

summary: G-quadruplexes (G4s) form throughout the genome and influence important cellular processes, but their deregulation can challenge DNA replication fork progression and threaten genome stability. Here, we demonstrate an unexpected, dual role for the dsDNA translocase HLTF in G4 metabolism. First, we find that HLTF is enriched at G4s in the human genome and suppresses G4 accumulation throughout the cell cycle using its ATPase activity. This function of HLTF affects telomere maintenance by restricting alternative lengthening of telomeres, a process stimulated by G4s. We also show that HLTF and MSH2, a mismatch repair factor that binds G4s, act in independent pathways to suppress G4s and to promote resistance to G4 stabilization. In a second, distinct role, HLTF restrains DNA synthesis upon G4 stabilization by suppressing PrimPol-dependent repriming. Together, the dual functions of HLTF in the G4 response prevent DNA damage and potentially mutagenic replication to safeguard genome stability.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of HLTF in a U2OS cell line expressing endogenously GFP-tagged HLTF, using a GFP antibody (Abcam, ab290) for IP. This U2OS cell line also constitutively expresses human codon-optimized S. pyogenes Cas9 protein. Cells are either transfected with a non-targeting control single guide RNA (sgRNA) or sgRNA against HLTF. Mouse embryonic stem cells (ESCs) expressing endogenously GFP-tagged MPP8 are used as spike-in control to normalize the ChIP-seq signal.

first: Gongshi

last: Bai

first: Theresa

last: Endres

first: Magdalena

last: P Crossley


title: ATAC-seq of VLDLR+ vs VLDLR- HSCs after acute anemia induction

status: Public on Aug 07 2024

city: Kumamoto

first: Kenichi

last: Miharada

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

summary: Hematopoietic stem cells (HSCs) react to various stress conditions. However, it is unclear whether and how HSCs respond to severe anemia. Here, we demonstrate that upon induction of acute anemia, HSCs rapidly proliferate and enhance their erythroid differentiation potential. In severe anemia, lipoprotein profiles largely change and the concentration of ApoE increases. In HSCs, transcription levels of lipid metabolism-related genes, such as very low-density lipoprotein receptor (Vldlr), are upregulated. Stimulation of HSCs with ApoE enhances their erythroid potential, whereas HSCs in Apoe knockout mice do not respond to anemia induction. VldlrhighHSCs show higher erythroid potential, which is enhanced after acute anemia induction. VldlrhighHSCs are epigenetically distinct because of their low chromatin accessibility, and more chromatin regions are closed upon acute anemia induction. Chromatin regions closed upon acute anemia induction are mainly binding sites of Erg. Inhibition of Erg enhanced the erythroid differentiation potential of HSCs. Our findings indicate that lipoprotein metabolism plays a crucial role in HSC regulation under severe anemic conditions.

overall_design: Chromatin accessibility in VLDLR+HSCs and VLDLR-HSC were compared between steady state condition and PHZ treatment, as well as in vitro culture with ApoE protein.

first: Kiyoka

last: Saito

first: Mark

last: van der Garde

first: Terumasa

last: Umemoto


title: Adipose stem cells are sexually dimorphic cells with dual roles as preadipocytes and resident fibroblasts [bulk_adipocytes]

first: Martin

last: Uhrbom

overall_design:
To investigate the gene expression profile of mature adipocyte in male and female mice in pgWAT and iWAT depots, we isolated RNA from floating mature adipocytes (derived from collagenase treated tissue) and performed bulk RNA sequencing.
There are five mouse RNAseq datasets connected to this study: (1) scRNAseq of stromal vascular fraction (SVF) of pgWAT, (2) bulk RNA-seq from FACS sorted Adipose stem cells (ASC) from pgWAT and iWAT, (3) bulk RNA-seq from isolated floating mature adipocytes from pgWAT and iWAT, (4) bulk RNA-seq from FACS sorted ASC from castrated/ovarectomized/male and female control mice, and (5) bulk RNA-seq from in vitro cultivated SVF cells from pgWAT and iWAT.

first: Lars

last: Muhl

first: Guillem

last: Genové

first: Jianping

last: Liu

first: Henrik

last: Palmgren

first: Ida

last: Alexandersson

first: Fredrik

last: Karlsson

first: Alex

last: Zhou

first: Sandra

last: Lunnerdal

first: Sonja

last: Gustafsson

first: Byambajav

last: Buyandelger

first: Kasparas

last: Petkevicius

first: Ingela

last: Ahlstedt

first: Daniel

first: Leif

last: Aasehaug

first: Liqun

last: He

first: Marie

last: Jeansson

first: Christer

last: Betsholtz

first: Xiao

last: Peng


title: Structural perturbation of chromatin domains with multiple developmental regulators can severely impact gene regulation and development [Cut&Run]

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

summary: Chromatin domain boundaries delimited by CTCF motifs have been shown to restrict the range of enhancers. However, disruption of domain structure often results in mild gene expression changes, and predicting the impact of boundary rearrangements on animal development remains challenging. By targeting clusters of CTCF motifs in a domain with three FGF genes—Fgf3, Fgf4, and Fgf15—we tested whether gene regulation and mouse development may be particularly sensitive to disruption of chromatin domains with multiple developmental regulators. Deletion of a cluster of four CTCF motifs that defines the centromeric boundary of this domain, resulted in ectopic interactions of the FGF genes with brain enhancers located across the deleted boundary, and a strong induction of FGF expression that led to perinatal lethality with encephalocele and orofacial cleft phenotypes. Heterozygous boundary loss was enough to cause these fully penetrant phenotypes, and strikingly, loss of the single CTCF motif within the cluster that is oriented towards the brain enhancers, was sufficient to induce ectopic FGF expression and cause encephalocele. However, such phenotypic sensitivity to perturbation of domain structure did not extend to all CTCF-mediated boundaries of this domain nor to all developmental processes controlled by these three FGF genes. Although precise control of FGF4 levels is essential to regulate blastocyst development, none of our structural perturbations affected implantation. In fact, deletion of a CTCF boundary between Fgf3 and Fgf4, showed that the ability of these neighboring genes to have fully divergent expression patterns in blastocysts is achieved through CTCF-independent mechanisms and relies on remarkable enhancer-promoter specificity in vivo. Our work highlights how small sequence variants at certain domain boundaries can have a surprisingly outsized phenotypic effect and provides important insight into how different developmental contexts affect phenotypic sensitivity to perturbation of chromatin structure.

overall_design: CUT&RUN sequencing was performed in blastocyst derived mouse embryonic stem cells.

first: Shreeta

last: Chakraborty

first: Joyce

last: Thompson


title: The duct of von Ebner’s glands is a source of Sox10+ taste bud progenitors and susceptible to pathogen infections

city: Athens

first: Hong-Xiang

last: Liu

state: Georgia

address: 425 River Road

department: Animal & Dairy Science

institute: University of Georgia

summary: We have recently demonstrated that Sox10-expressing (Sox10+) cells give rise to mainly type-III neuronal taste bud cells that are responsible for sour and salt taste. The two tissue compartments containing Sox10+ cells in the surrounding of taste buds include the connective tissue core of taste papillae and von Ebner’s glands (vEGs) that are connected to the trench of circumvallate and foliate papillae. Here we present data to support that it is the vEGs, not connective tissue core, that serve as the niche of Sox10+ taste bud progenitors. In this study, we performed single cell RNA-sequencing of the epithelium of Sox10-Cre/tdT mouse circumvallate/vEG complex and used inducible Cre mouse models to map the cell lineages of vEGs and/or connective tissue (including stromal and Schwann cells). Transcriptomic analysis indicated that Sox10 expression was enriched in the cell clusters of vEG ducts that contained abundant proliferating cells, while Sox10-Cre/tdT expression was enriched in type-III taste bud cells and vEG ductal cells. In vivo lineage mapping showed that the traced cells were distributed in circumvallate taste buds concurrently with those in the vEGs, but not in the connective tissue. Moreover, multiple genes encoding pathogen receptors were enriched in the vEG ducts hosting Sox10+ cells. If this is also true in humans, our data indicates that vEG duct is a source of Sox10+ taste bud progenitors and susceptible to pathogen infections.

overall_design: we used single cell transcriptomic analyses on the epithelium of circumvallate/vEG complex and multiple inducible Cre mouse models to map the lineage of cells surrounding circumvallate taste buds including the cells in the connective tissue core and the cells in vEGs. Our data indicates that Sox10+ cells in the duct of vEGs, but not in the connective tissue core of taste papillae, serve as progenitors for taste buds without being transited to basal cells in the stratified tongue epithelium. Moreover, the Sox10+ vEG ducts enrich multiple genes encoding pathogen receptors indicating its potential susceptibility to pathogen infections.

first: Wenxin

last: Yu

first: Maria

middle: E

last: Kastriti

first: Mohamed

last: Ishan

first: Saurav

middle: K

last: Choudhary

first: Md

middle: M

last: Rashid

first: Naomi

last: Kramer

first: Hy

middle: G

last: Do

first: Zhonghou

last: Wang

first: Ting

last: Xu

first: Robert

middle: F

last: Schwabe

first: Kaixiong

last: Ye

first: Igor

last: Adameyko


title: Functional genomic analysis of genes important for Candida albicans fitness in diverse environmental conditions

city: Toronto

first: Emily

middle: Haochen

last: Xiong

state: Ontario

address: 101 College Street

department: Department of Molecular Genetics

country: Canada

institute: University of Toronto

summary: As the limited arsenal of effective antifungals in clinical use is threatened by emerging resistance, the demand for new strategies to combat invasive fungi is urgent. One strategy to expand the therapeutic target space is to identify genes important for pathogen growth in host-relevant environments. Here, we leveraged a pooled functional genomic screening strategy to identify and characterize genes important for fitness of the human fungal pathogen Candida albicans in diverse conditions. Through this approach we identified a novel essential gene with no known Saccharomyces cerevisiae homolog, C1_09670C, and demonstrated that it encodes subunit 3 of replication factor A, Rfa3. Furthermore, we applied robust computational analyses to leverage profile similarity analysis of mutant phenotypes across conditions to identify functionally-coherent gene clusters and predict gene function. Through this approach, we correctly predicted the cell cycle-associated function of C3_06880W, a previously uncharacterized genes required for fitness specifically at elevated temperatures. Protein structure predictions coupled with genetic and biochemical assays confirmed C3_06880W encodes Iml3, a component of the C. albicans kinetochore with key roles in C. albicans virulence in vivo. Overall, this work reveals novel insights into the vulnerabilities of C. albicans.

overall_design: To enable systematic fitness comparisons between diverse growth conditions, we utilized a pooled functional genomics approach for massively parallel analysis of Candida albicans GRACE strains to assess each strain’s fitness profile through quantification of strain-specific barcodes by next-generation sequencing. Specifically, a pooled collection of 2,238 barcoded GRACE strains covering ~35% of the genome was grown in triplicate in the presence and absence of DOX for 24 hours, then sub-cultured into matching fresh medium with or without DOX for an additional 48-hour incubation. ). Screens in all conditions were performed in technical triplicate and biological duplicate apart from the baseline condition (YNB at 30 ˚C), which was tested in five biological replicates. After growth of the cultures, strain-specific molecular barcodes were amplified from extracted gDNA, and pooled barcode PCR products were subjected to next-generation sequencing.

middle: H

first: Xiang

last: Zhang

first: Huijuan

last: Yan

first: Henry

middle: N

last: Ward

first: Zhen-Yuan

last: Lin

first: Cassandra

middle: J

last: Wong

first: Ci

last: Fu

first: Anne-Claude

last: Gingras

first: Suzanne

last: Noble

first: Nicole

last: Robbins

first: Chad

middle: L

last: Myers

first: Leah

last: Cowen


title: Multi-organ Transcriptome Atlas of a Mouse Model of Relative Energy Deficiency in Sport (REDs)

city: La Jolla

first: Laura

last: van Rosmalen

state: California

address: 10010 N Torrey Pines Rd

department: RBIO-P

institute: Salk Institute for Biological Studies

summary: Insufficient energy intake to meet energy expenditure demands of physical activity can result in systemic neuroendocrine and metabolic abnormalities in activity-dependent anorexia and Relative Energy Deficiency in Sport (REDs). REDs affects >40% of athletes, yet the lack of underlying molecular changes has been a hurdle to have a better understanding of REDs and its treatment. To assess the molecular changes in response to energy deficiency, we implemented the ‘exercise-for-food’ paradigm, in which, food reward size is determined by wheel-running activity. By using this paradigm, we replicated several aspects of REDs in female and male mice, with high physical activity, and gradually reduced food intake, which results in weight loss, compromised bone health, organ-specific mass changes and altered rest-activity patterns. By integrating transcriptomics of 19 different organs, we provide a comprehensive dataset that will guide future understanding of REDs and may provide important implications for metabolic health and (athletic) performance.

overall_design: We conducted an extensive analysis of the transcriptome of 19 different metabolic tissues from energy-sufficient (Ctrl) and energy-deficient (Deficient) female and male CBA/CaJ mice (419 samples of bulk RNA-seq passed quality control).

first: Jiaoyue

last: Zhu

first: Geraldine

last: Maier

first: Erica

last: Gacasan

first: Terry

first: Elena

last: Zhemchuzhnikova

first: Vince

last: Rothenberg

first: Swithin

last: Razu

first: Shaunak

last: Deota

first: Ramesh

last: Ramasamy

last: Sah

first: Andrew

last: McCulloch

first: Roelof

last: Hut

first: Satchidananda

last: Panda


title: Expression of genes in HepG2 cells with Knock-out in cholesterol synthesis

city: Ljubljana

first: Cene

last: Skubic

state: - None -

address: Zaloška 4

department: Institute for Biochemistry and molecular genetics

country: Slovenia

institute: University of Ljubljana, Faculty of Medicine

summary:
HepG2 cell line CRISPR-Cas9 generated Knock-out in 4 cholesterol synthesis gene: CYP51, DHCR24, SC5D and HSD17B7
Excess of cholesterol associates with a variety of diseases so its synthesis must be under tight homeostatic control. The early part of cholesterol synthesis with rate-limiting HMGCR and SQLE steps is proceeded by the sterol part where numerous non-polar sterols with poorly defined biological functions are produced. To illuminate their role we developed knockouts (KO) for the consecutive enzymes that metabolize sterols towards cholesterol CYP51A1, DHCR24, SC5D resulted in the accumulation of specific set of sterols in each KO cell. Despite that, we targeted three steps of the cholesterol synthesis housekeeping pathway, the overlap of de-regulated genes was only 9%, suggesting that each set of sterols modulated the hepatic cell transcriptome uniquely. Lanosterol and 24,25-dihydrolanosterol, but not other non-polar sterols, provoked higher cell proliferation, cell cycle changes, and upregulation of metabolic pathways and transcription factors (TFs) associated with cancer progression and immune response like NFKB, SMAD, ESR1 and highly elevated LEF1 a protein from WNT signalling. In contrast, lathosterol and desmosterol caused slower proliferation and apoptosis promotion, through TFs like HNF1A and E2F. We were able to show how sterols from early part of synthesis can promote cell proliferation as sterols from end of synthesis suppress proliferation. These findings challenge the current dogma that sterols produced during cholesterol synthesis have similar biological functions

overall_design: Control HepG2 (named Native) and 4 lines each with Knock-out in one of the cholesterol synthesis genes: CYP51 KO, DHCR24 KO, SC5D KO and HSD17B7 KO were used to obtain tanscriptome data using Clariom S Array, human (902917, Applied Biosystems, Waltham, MA, USA). Each genotype had 3 biological replicates. Cell were seeded on 6-well plate in Dulbecco’s Modified Eagle’s Media (DMEM) high glucose (D6429, Sigma Aldrich, St. Louis, MO, USA), supplemented with 10% FBS (F0804, Sigma Aldrich, St. Louis, MO, USA) and 1% penicillin/streptomycin (P0781, Sigma Aldrich, St. Louis, MO, USA). Cells were cultured in constant 37 °C and 5% CO2. After 24h after seeding cell medium was changed with DMEM high glucose, supplemented with 10% LDP (Lipid Depleted Serum Biosera inc., France),  1% penicillin/streptomycin and 30 µg/ml of cholesterol (Sigma Aldrich). 48h after medium change, cell were washed 2 times with PBS and TRI reagent (T9424, Sigma Aldrich, St. Louis, MO, USA) was used for RNA isolation. Concentration was measured using Nanodrop and RNA quality using Agilent Bioanalyser.  Transcriptome analysis  was performed using Clariom S Array in triplicates from each cell genotype according to manufacturers protocol.

first: Damjana

last: Rozman


title: Structural perturbation of chromatin domains with multiple developmental regulators can severely impact gene regulation and development [Micro-C]

first: Pedro

last: Rocha

overall_design: Promoter capture was performed in the following tissues: Midbrain of E11.5 and E12.5 embryos. Each  sample was pooled from several WT and homozygous mutant embryos.

first: Shreeta

last: Chakraborty


title: Antigen-specific T helper cells predict intensity and longevity of immune responses to SARS-CoV-2 booster vaccination

status: Public on Aug 06 2024

city: Augsburg

first: Lukas

last: Page

state: Bavaria

address: Stenglinstrasse 2

department: Institute for Laboratory Medicine and Microbiology

institute: University Hospital of Augsburg

summary:
SARS-CoV-2 spike (S) specific T-cell and antibody (AB) responses after primary BNT162b2 vaccination (Pfizer Inc., New York, NY, USA and BioNTech SE, Mainz, Germany) partially depend on the phenotypic composition of pre-existing T-helper (Th) cell populations (Saggau et al., 2022, Immunity). However, adaptive cellular responses and their impact on sustained immune protection after booster vaccination are incompletely understood. We therefore monitored cellular and humoral immune responses before and up to 6 months after the 3rd BNT162b2 vaccination to identify early determinants of sustained responses. As part of an ongoing registry study (Corona Registry Study number 20–426, approved by the ethics committee of the Ludwig Maximilians University Munich), volunteers were recruited among employees of the University Hospital of Augsburg. All subjects had received primary vaccination with two doses of BNT162b2 and were enrolled before their third dose of BNT162b2 (first booster). Exclusion criteria were active infections, receipt of immunomodulatory therapy, pregnancy, positive nucleocapsid-specific (N) IgG titers, and underlying conditions associated with significant impairment of anti-COVID-19 immunity (e.g., diabetes mellitus, cancer, prior stem cell transplantation, or autoimmune diseases). Lithium heparin-anticoagulated whole blood and serum samples were collected immediately before the third vaccination (T0), as well as 1 (T1), 3 (T3), and 6 months (T6) after booster vaccination. No additional booster doses were given during the study period. Serum samples were tested for nucleocapsid (N), S (COBAS e801 immunoassay analyzer with Elecsys Anti-SARS-CoV-2 and Anti-SARS-CoV-2 S (Hitachi Ltd., Tokyo, Japan and Roche Diagnostics GmbH, Basel, Switzerland), and neutralizing AB responses (Haselmann et al., 2020, Clin Chem Med Lab). Subjects developing N IgG or those with incomplete follow-up were excluded. Whole blood was stimulated with co-stimulatory factors anti-CD28 and anti-49d (1 µg/mL Miltenyi Biotec, Bergisch Gladbach, Germany) only, representing the unstimulated/background sample, or additionally S peptides (0.6 nMol/peptide/mL Prot_S, Miltenyi Biotec, Bergisch Gladbach, Germany), as described previously (Lauruschkat et al., 2021, J Fungi (Basel), Weis et al., 2020, Med Mycol). Samples were subsequently analyzed by flow cytometry (data not relevant for this file/analysis) and 13-plex multiplex cytokine assay (LegendPlex Essential Immune Response Panel, BioLegend, San Diego, USA). Significant associations between readouts were identified by multiple testing-adjusted rank correlation analysis.
We found moderate correlation between S IgG (r=0.47), S-induced IL-2 (r=0.58) and IFN-γ (r=0.43) at T1 and T6. S IgG, S-induced IL-2, and S-induced IFN-γ at T6 were significantly associated with increased IL 2 & IL 4, IP 10 & MCP1, and IFN-γ & IP 10 levels at T1, respectively (data presented at the 7th Joint Microbiology & Infection Conference of the German Society for Hygiene and Microbiology (DGHM) and the Association for General and Applied Microbiology (VAAM), Wuerzburg, Germany). Subsequently, the preserved T1 RNA samples of the top and bottom half responders at T6 (based on S IgG, S-induced IL-2, and IFN-γ measurements) were isolated via RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) and analyzed by nCounter Immune Exhaustion Panel (Nanostring, Seattle, USA) as described below. At the time of GEO submission of this data (August 2024), the associated manuscript is under review by Frontiers in Immunology.

overall_design: Top and bottom half of responders 1 month and 6 months after vaccination have been determined as described above. 12 pairs of unstimulated (reference sample) and Prot_S stimulated samples were analysed by nCounter Sprint Immune Exhaustion Panel (total of 24 samples). Transcriptomic data of background-corrected S-induced transcriptional changes at T1 were subsequently analyzed to determine the impact on short- and long-term vaccine responses, i.e. top / bottom half IgG, IL-2, and IFN-γ responder status (as described above) at T1 and T6.

first: Kevin

last: Dennehy

first: Katharina

last: Mueller

first: Philipp

last: Girl

first: Eva

last: Loell

first: Hellen

last: Buijze

first: Johanna-Maria

last: Classen

first: Helmut

last: Messmann

first: Christoph

last: Roemmele

first: Reinhard

last: Hoffmann

first: Sebastian

last: Wurster

first: Andre

last: Fuchs

first: Friederike

last: Liesche-Starnecker


title: Multi-omics analysis reveals the impact of influenza A virus host adaptation on immune signatures in pig tracheal tissue

city: Kongens Lyngby

first: Helena

last: Aagaard Laybourn

address: Søltofts Plads

country: Denmark

institute: Technical University of Denmark

summary: Influenza A virus (IAV) infection is a global respiratory disease, which annually leads to 3-5 million cases of severe illness, resulting in 290,000-650,000 deaths. Additionally, during the past century, four global IAV pandemics have claimed millions of human lives. The epithelial lining of the trachea plays a vital role during IAV infection, both as point of viral entry and replication as well as in the antiviral immune response. Tracheal tissue is generally inaccessible from human patients, which makes animal models crucial for the study of the tracheal host immune response. In this study, pigs were inoculated with swine- or human-adapted H1N1 IAV to gain insight into how host adaptation of IAV shapes the innate immune response during infection. In-depth multi-omics analysis (global proteomics and RNA sequencing) of the host response in upper and lower tracheal tissue was conducted, and results were validated by microfluidic qPCR. Additionally, a subset of samples was selected for histopathological examination. A classical innate antiviral immune response was induced in both upper and lower trachea after infection with either swine- or human-adapted IAV with upregulation of genes and higher abundance of proteins associated with viral infection and recognition, accompanied by a significant induction of interferon stimulated genes with corresponding higher proteins concentrations. Infection with the swine-adapted virus induced a much stronger immune response compared to infection with a human-adapted IAV strain in the lower trachea, which could be a consequence of a higher viral load and a higher degree of inflammation. Central components of the JAK-STAT pathway, apoptosis, pyrimidine metabolism, and the cytoskeleton were significantly altered depending on infection with swine- or human-adapted virus and might be relevant mechanisms in relation to antiviral immunity against putative zoonotic IAV. Based on our findings, we hypothesize that during host adaptation, IAV evolve to modulate important host cell elements to favor viral infectivity and replication.

overall_design: To investigate the host response in swine tracheal tissues to either swine- or human-adapted IAV three days after inoculation by RNA-seq.   Group 1 (control) consisted of six pigs, while group 2 and 3 included eight pigs each. Group 1 was mock inoculated intranasally in one nostril by a MAD nasal device (Teleflex) containing 3 mL culture medium only, while group 2 and 3 were inoculated with 3 ml of 10^7 TCID50/ml of a swine-adapted H1N1 strain, A/Swine/Denmark/3974/2017 (swH1N1), or a human-adapted H1N1 strain, A/Denmark/238/2020 (huH1N1), respectively. The pigs were euthanized 3 days post inoculation, and tracheal tissue was collected for RNA-seq.


city: Bunkyo-ku

first: Yasuhito

last: Sakuraba

state: Tokyo

address: Yayoi 1-1-1

department: Agro-Biotechnology Research Center

institute: The University of Tokyo

summary: To examine the effect of hasty KO mutation on miRNA expression, we performed miRNA-seq analysis using Arabidopsis Col-0 WT and hasty KO mutant that were grown under control and low nitrogen conditions.

overall_design: Shoot tissues from 10 day-old Col-0 WT and hasty KO mutants that were initially grown under standard nutrient conditions for 5 days and then grown under low nitrogen conditions for 5 days were used for miRNA-seq analysis.

first: Shuichi

last: Yanagiswa


title: Noncoding Mendelian epigenomics - single cell ATACseq mouse cMN data

city: Boston

first: Elizabeth

middle: C

last: Engle

address: 3 Blackfan Circle

institute: Boston Childrens Hospital

summary: Although Mendelian disorders are overwhelmingly attributed to protein-coding pathogenic variants, a majority of unsolved cases do not harbor obvious causal pathogenic variants in the coding sequence, suggesting a potential non-coding etiology. However, classification of pathogenicity in non-coding sequence remains prohibitive due to a vastly increased search space and the lack of a standardized rubric for interpretation. Here, we present an integrated single cell multiomic framework to nominate pathogenic non-coding variants for the congenital cranial dysinnervation disorders (CCDDs). The CCDDs are Mendelian neurodevelopmental disorders that result from aberrant development of cranial motor neurons in the embryonic brainstem. We created a non-coding reference atlas of single cell chromatin accessibility profiles for 86,089 embryonic mouse cranial motor neurons (cMNs). We found that high-quality single cell ATAC-seq (scATAC) profiles alone were a strong predictor of enhancement (64% in vivo validation rate). To further aid in interpretation, we integrated single cell histone modification and gene expression information to distinguish individual enhancers and their cognate genes. Relatively subtle differences in cellular composition of input data often led to substantial differences in predicted enhancer strength, cognate gene, and tissue of activity. Next, we mapped candidate non-coding variants from 899 whole genome sequences from 270 CCDD pedigrees to the murine cMN-specific regulatory elements and trained a machine learning classifier to accurately predict the functional effects of patient variants within these elements. We then performed high coverage scATACseq and site-specific footprinting analysis on an allelic series of CRISPR-humanised mice to validate our machine learning predictions and render important clues to the mode of pathogenicity. Finally, we performed peak- and gene-centric allelic aggregation to nominate non-coding variants, including those regulating MN1 and EBF3, respectively. Altogether this work extends non-coding variant analysis to Mendelian disease and presents a generalizable framework for nominating novel non-coding variants in other rare disorders.

overall_design: Single cell ATACseq of mouse developing cranial motor neurons, spinal motor neurons, and surrounding neuronal tissue at e10.5 and e11.5

first: Arthur

last: Lee


title: Noncoding Mendelian epigenomics - single cell RNAseq mouse cMN data

overall_design: Single cell RNA seq of mouse developing cranial motor neurons and surrounding neuronal tissue at e10.5 and e11.5


title: Nuclear lamin A/C phosphorylation by loss of Androgen Receptor is a global determinant of cancer-associated fibroblast activation [ChIP-Seq]

first: Soumitra

last: Ghosh

summary: Alterations of nuclear structure and function, and associated impact on gene transcription, are a hallmark of cancer cells. Little is known of these alterations in Cancer-Associated Fibroblasts (CAFs), a key component of the tumor stroma. Here we show that loss of androgen receptor (AR), which triggers early steps of CAF activation in human dermal fibroblasts (HDFs), leads to nuclear membrane alterations with increased micronuclei formation and frequent ruptures, with similar alterations occurring in fully established CAFs. AR associates with nuclear lamin A/C and loss of AR results in a substantially increased lamin A/C nucleoplasmic redistribution. Mechanistically, AR functions as a bridge between lamin A/C with the protein phosphatase PPP1. In parallel with a decreased lamin-PPP1 association, AR loss results in a marked increase of lamin A/C phosphorylation at Ser 301, which is also a feature of CAFs. Phospho-Ser301 Lamin A/C binds to the transcription promoter regulatory region of multiple CAF marker genes upregulated by AR loss, and expression of a  lamin A/CSer301 phosphomimetic mutant is sufficient for conversion of normal fibroblasts into tumor-promoting CAFs. The findings point to an AR - lamin A/C - PPP1 axis and lamin A/C phosphorylation at ser 301 as critical determinants of CAF activation.

overall_design: Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) was conducted for Lamin A/C, Phospho-Ser301 Lamin A/C, and the histone modification H3K27Ac in human dermal fibroblast (HDF) cells, both with and without androgen receptor (AR) silencing.

first: Jovan

last: Isma

first: G

last: Dotto

first: Paola

last: Ostano


title: A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders

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

overall_design: Refer to individual Series


title: Noncoding Mendelian epigenomics - bulk ATAC mouse cMN data

overall_design: Bulk ATACseq of mouse developing cranial motor neurons, spinal motor neurons, and surrounding neuronal tissue at e10.5 and e11.5


title: Transcriptome profiling based on the presence of Usf2 and nutrient starvation

city: Seoul

first: Young Suk

last: Yu

address: 1-Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Intricate regulation of lysosome and autophagy processes is essential for maintaining cellular homeostasis and basal metabolism. While the consequences of disrupting or attenuating lysosome and autophagy systems have been extensively studied, little is known about the impact of hyper-activation of lysosomal and autophagy genes on homeostasis. Our research uncovers previously unknown transcriptional repression mechanism by upstream stimulatory factor 2 (USF2), which inhibits lysosomal and autophagy genes in nutrient-rich conditions. USF2 binds to the CLEAR motif within lysosomal genes along with HDAC1, which diminishes H3K27 acetylation levels, restrains chromatin accessibility, and lowers lysosomal gene expression. Under starvation, USF2 competes with TFEB, a master transcriptional activator of lysosomal and autophagy genes, to bind target gene promoters in phosphorylation-dependent manner. Phosphorylation of the S155 site by GSK3b plays a pivotal role in controlling USF2's DNA binding activity for the repression of lysosomal genes while GSK3b-mediated phosphorylation of TFEB enhances its cytoplasmic retention. Applying these discoveries has potential for treating diseases associated with protein aggregation, including alpha-1 antitrypsin deficiency. These findings demonstrate that the USF2 repression mechanism could be a potent therapeutic strategy for various lysosome and autophagy-related diseases.

overall_design: To investigate the roles of Usf2 in the regulation of autophagy and lysosome, we performed mRNA expression profiles of Usf2 WT and Usf2 KO MEF cells with normal media, glucose starvation media, or amino acid starvation media

first: Young

middle: S

first: Jaebeom

last: Kim

first: Sung

last: Baek


title: Genome binding/occupancy profiling of USF2 under glucose starvation and changes in H3K27ac based on the presence of USF2

overall_design: To determine where USF2 is recruited, we performed ChIP-sequencing (ChIP-seq) in WT MEFs after glucose starvation. To investigate the roles of Usf2 in the regulation of H3K27ac, we performed ChIP-seq using Usf2 WT and Usf2 KO MEF cells


title: Nuclear lamin A/C phosphorylation by loss of Androgen Receptor is a global determinant of cancer-associated fibroblast activation [Affymetrix]

summary:
Alterations of nuclear structure and function, and associated impact on gene transcription, are a hallmark of cancer cells. Little is known of these alterations in Cancer-Associated Fibroblasts (CAFs), a key component of the tumor stroma. Here we show that loss of androgen receptor (AR), which triggers early steps of CAF activation in human dermal fibroblasts (HDFs), leads to nuclear membrane alterations with increased micronuclei formation and frequent ruptures, with similar alterations occurring in fully established CAFs. AR associates with nuclear lamin A/C and loss of AR results in a substantially increased lamin A/C nucleoplasmic redistribution. Mechanistically, AR functions as a bridge between lamin A/C with the protein phosphatase PPP1. In parallel with a decreased lamin-PPP1 association, AR loss results in a marked increase of lamin A/C phosphorylation at Ser 301, which is also a feature of CAFs. Phospho-Ser301 Lamin A/C binds to the transcription promoter regulatory region of multiple CAF marker genes upregulated by AR loss, and expression of a lamin A/CSer301 phosphomimetic mutant is sufficient for conversion of normal fibroblasts into tumor-promoting CAFs. The findings point to an AR - lamin A/C - PPP1 axis and lamin A/C phosphorylation at ser 301 as critical determinants of CAF activation.
Determining transcriptomic profile of Phospho Ser 301 mimetic mutant (S301D) and WT lamin A/C expressing HDFs.

overall_design: Determine the transcriptomic profile of Phospho Ser 301 mimetic mutant (S301D) and WT lamin A/C expressing human dermal fibroblasts (HDFs).


title: Structural perturbation of chromatin domains with multiple developmental regulators can severely impact gene regulation and development [RCMC]

first: Pedro

last: Rocha

overall_design: RCMC was performed in the following tissues: blastocyst-derived mouse embryonic stem cells and midbrain of E11.5 and E12.5 embryos. For ES cells, 2 individual homozygous embryos were processed and analyzed seperately.  WT controls are littermates from isolated embryos. Midbrain samples were pooled from several WT and homozygous mutant embryo.

first: Shreeta

last: Chakraborty


title: Nuclear lamin A/C phosphorylation by loss of Androgen Receptor is a global determinant of cancer-associated fibroblast activation [ATAC-Seq]

summary:
Alterations of nuclear structure and function, and associated impact on gene transcription, are a hallmark of cancer cells. Little is known of these alterations in Cancer-Associated Fibroblasts (CAFs), a key component of the tumor stroma. Here we show that loss of androgen receptor (AR), which triggers early steps of CAF activation in human dermal fibroblasts (HDFs), leads to nuclear membrane alterations with increased micronuclei formation and frequent ruptures, with similar alterations occurring in fully established CAFs. AR associates with nuclear lamin A/C and loss of AR results in a substantially increased lamin A/C nucleoplasmic redistribution. Mechanistically, AR functions as a bridge between lamin A/C with the protein phosphatase PPP1. In parallel with a decreased lamin-PPP1 association, AR loss results in a marked increase of lamin A/C phosphorylation at Ser 301, which is also a feature of CAFs. Phospho-Ser301 Lamin A/C binds to the transcription promoter regulatory region of multiple CAF marker genes upregulated by AR loss, and expression of a  lamin A/CSer301 phosphomimetic mutant is sufficient for conversion of normal fibroblasts into tumor-promoting CAFs. The findings point to an AR - lamin A/C - PPP1 axis and lamin A/C phosphorylation at ser 301 as critical determinants of CAF activation.
Determining chromatin accessibility changes associated with androgen receprtor (AR) silencing in human dermal fibroblasts using Assay for Transposase-Accessible Chromatin with sequencing (ATAC-Seq).

overall_design: Soumitra, Ghosh


title: Structural perturbation of chromatin domains with multiple developmental regulators can severely impact gene regulation and development [CHiC]

overall_design: Capture HiC (CHiC) was performed in the following tissues: blastocyst-derived mouse embryonic stem cells, differentiated XEN cells and midbrain of E11.5 embryos. For ES and XEN cells, 2 individual homozygous embryos were processed and analyzed seperately.  WT controls are littermates from isolated embryos. Midbrain samples were pooled from several WT and homozygous mutant embryo.


title: Translation inhibition with CHX in mouse embryonic stem cells in bulk

status: Public on Aug 05 2024

city: Nijmegen

first: Oscar

last: Garcia-Blay

state: Gelderland

address: Heyendaalseweg 135

department: Biophysical Chemistry

country: Netherlands

institute: Institute for Molecules and Materials (Radboud University)

summary: Gene-expression noise can influence cell-fate choices across pathology and physiology. However, a crucial question persists: do regulatory proteins or pathways exist that control noise independently of mean expression levels? Our integrative approach, combining single-cell RNA sequencing with proteomics and regulator enrichment analysis, reveals 32 putative noise regulators. The approach utilizes global translation inhibition  (i.e., potential protein regulators), and single-cell RNA sequencing (scRNA-seq) to quantify the changes in noise of all transcripts (i.e., potential mRNA targets). This dataset corresponds to a control bulk RNAseq experiment experiment upon translation inhibition with cycloheximide to validate the changes in mean observed with single-cell.

overall_design: Mouse embryonic stem cells (mESCs) were seeded and growth in serum/LIF conditions. 24 hours post-seeding, cells were treated with cycloheximide for 3 or 6 hours, or EtOH as control. After treatment RNA was extracted in preparation for RNA sequencing. RNA samples were shipped in dry ice and single-cell RNA sequencing was performed.

first: Óscar

last: García-Blay

first: Maike

last: Hansen


title: Total RNA-seq and long-read RNAseq (Nanopore) upon Son KD in mouse embryonic stem cells

summary: Gene-expression noise can influence cell-fate choices across pathology and physiology. However, a crucial question persists: do regulatory proteins or pathways exist that control noise independently of mean expression levels? Resulting from a previous screen, the protein SON was identified as a potential noise regulator. We perform Son KD and utilize (1) total RNA sequencing (RNA-seq) to analyze differences in splicing efficiency of introns upon Son KD; and (2) Nanopore sequencing to analyze changes in isoform usage. These datasets correspond to the aforementioned total RNA-seq and long-read polyA+ cDNA Nanopore sequencing upon Son KD.

overall_design: Mouse embryonic stem cells (mESCs) were seeded and growth in serum/LIF conditions. 24 hours post-seeding, knock down of Son was induced with siRNA transfection (Lipofectamine 2000). After treatment RNA was extracted and frozen in preparation for  RNA sequencing. For total RNA-seq, RNA samples were shipped in dry ice to sequencing company  and rRNA depletion and RNA sequencing was performed. Long-read nanopore sequencing was performed in house.


title: Systems Biology to Identify Biomarkers of Neonatal Vaccine Immunogenicity [methylation]

first: Ofer

last: Levy

state: MA

address: 300 Longwood Avenue

department: Infectious Disease

institute: Boston Children's Hospital

type: Methylation profiling by genome tiling array

summary: Infection is the most common cause of death in early life, especially for newborns and can be reduced by immunization but insufficient knowledge of how vaccines protect the very young limits their optimal use. To gain insight into how vaccines induce protection of the most vulnerable, our project employs two novel approaches studying newborn responses to hepatitis B vaccine (HBV): (a) systems biology that uses technologies which comprehensively measure global changes in molecules such as transcriptomics (RNA) and proteomics (proteins), as well as cell composition of the blood and (b) use of human newborn blood components, collected prior to immunization, to model vaccine responses in vitro (outside the body). Characterizing vaccine-induced molecular patterns (signatures) that correspond to vaccine-mediated protection will accelerate development and optimization of vaccines against early life infections of major global health importance.

overall_design: longitudinal neonatal cohort study

first: Tobias

last: Kollmann

first: Robert

last: Hancock

first: Joann

last: Arce

first: Beate

last: Kampmann

first: David

last: Martino


title: Son KD in mouse embryonic stem cells

summary: Gene-expression noise can influence cell-fate choices across pathology and physiology. However, a crucial question persists: do regulatory proteins or pathways exist that control noise independently of mean expression levels? Resulting from a previous screen, the protein SON was identified as a potential noise regulator. We perform Son KD and utilize single-cell RNA sequencing (scRNA-seq) to quantify the changes in mean/noise of all transcripts. This dataset corresponds to the aforementioned scRNA-seq experiment upon Son KD.

overall_design: Mouse embryonic stem cells (mESCs) were seeded and growth in serum/LIF conditions. 24 hours post-seeding, knock down of Son was induced with siRNA transfection (Lipofectamine 2000). After treatment cells were dechached and frozen in preparation for single-cell RNA sequencing. A portion of the cells were utilized to validate the knock down at the protein level. Cells were brought in dry ice to sequencing facility  and single-cell RNA sequencing was performed from a freshly thawed sample after fast sorting of viable cells, through single-cel barcoding (10x Genomics'Chromium) and sequencing  (NextSeq 2000, Single Cell 3'v3 chemistry).


title: Tubercidin treatment in mouse embryonic stem cells

summary: Gene-expression noise can influence cell-fate choices across pathology and physiology. However, a crucial question persists: do regulatory proteins or pathways exist that control noise independently of mean expression levels? Resulting from a previous screen, a possible role of nuclear speckles in noise regulation was highlighted. We utilize tubercidin treatment and single-cell RNA sequencing (scRNA-seq) to quantify the changes in mean/noise of all transcripts upon nuclear speckle disruption. This dataset corresponds to the aforementioned scRNA-seq experiment upon tubercidin treatment.

overall_design: Mouse embryonic stem cells (mESCs) were seeded and growtn in serum/LIF conditions. 24 hours post-seeding, cells were treated with tubercidin for 3 or 6 hours, or DMSO as control. After treatment cells were dechached and prepared for single-cell RNA sequencing. Single-cell RNA sequencing was performed from fresh cells, through single-cell barcoding (10x Genomics'Chromium) and sequencing  (NextSeq 2000, Single Cell 3'v3 chemistry).


title: Noncoding Mendelian epigenomics - single cell CUT&Tag mouse cMN data

first: Elizabeth

last: Engle

overall_design: Single cell CUT&Tag of mouse developing cranial motor neurons at e10.5 and e11.5 using antibody against H3K27Ac histone modification (ab177178)

first: Arthur

last: Lee


title: Noncoding Mendelian epigenomics - single cell multiome mouse cMN data

overall_design: Single cell multiome of mouse developing cranial motor neurons and spinal motor neurons at e11.5


title: RUNX1 interacts with lncRNA SMANTIS to regulate monocytic cell functions [RNA_iPSC_diff_Mono]

city: Frankfurt

first: Simonida

last: Zehr

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe University, Frankfurt am Main, Germany,

summary: Monocytes are important for acute myeloid leukemia (AML), but the influence of long non-coding RNAs (lncRNAs) in this context is unknown. Previously we demonstrated that lncRNA SMANTIS maintains endothelial angiogenic functions and endothelial-monocyte adhesion. Here, the role of SMANTIS in monocytes was examined. SMANTIS was higher expressed in monocytes than in endothelial cells, lost in macrophages, and varied in patients with different AML subtypes. Interaction studies revealed that SMANTIS binds RUNX1, a transcription factor frequently mutated in AML, primarily through its Alu-element. RNA-seq after CRISPR/Cas9-mediated deletion of SMANTIS or RUNX1 revealed an association with cell adhesion and both limited the monocyte adhesion to endothelial cells. Mechanistically, SMANTIS KO reduced RUNX1 genomic binding, and interfered the interaction of RUNX1 with EP300. Collectively, SMANTIS interacts with RUNX1 and limits cell adhesion, which may thus offer a novel therapeutic strategy for AML.

overall_design: To investigate whether SMANTIS is specifically expressed in monocytes, and not macrophages, RNA-seq was performed after differentiation of inducible pluripotent stem cells (iPSCs, 20 aggregates / cm2) into monocytes or further into macrophages.  iPSC (d0), monocytes (d15), and further differentiated monocytes (d21) were used for RNA-sequencing.

first: Lisa

last: Weiss

first: Timothy

last: Warwick

first: Stefan

last: Günther

first: Sebastian

last: Wolf

first: Tessa

last: Schmachtel

first: Judit

last: Izquierdo Ponce

first: Katalin

last: Pálfi

first: Tom

last: Teichmann

first: Alicia

last: Schneider

first: Julia

last: Stötzel

last: Knapp

first: Andreas

last: Weigert

first: Rajkumar

last: Savai

first: Michael

last: Rieger

first: Thomas

last: Oellerich

first: Ilka

last: Wittig

first: James

last: Oo

first: Ralf

last: Brandes

first: Matthias

last: Leisegang


title: chromatin accessibility profiling by ATAC-seq based on the presence of Usf2

first: Young Suk

last: Yu

overall_design: To investigate the roles of Usf2 in the regulation of chromatin accessibility, we performed ATAC-seq using Usf2 WT and Usf2 KO MEF cells

first: Young

first: Jaebeom

last: Kim

first: Sung

last: Baek


title: RUNX1 interacts with lncRNA SMANTIS to regulate monocytic cell functions [CUT&RUN]

first: Simonida

last: Zehr

overall_design: DNA-sequencing of CUT&RUN (Cleavage Under Targets & Release Using Nuclease) assay

first: Lisa

last: Weiss

first: Timothy

last: Warwick

first: Stefan

last: Günther

first: Sebastian

last: Wolf

first: Tessa

last: Schmachtel

first: Judit

last: Izquierdo Ponce


title: Noncoding Mendelian epigenomics - bulk RNA mouse cMN data

first: Elizabeth

last: Engle

overall_design: Bulk RNAseq of mouse developing cranial motor neurons at e10.5 and e11.5

first: Arthur

last: Lee


title: THE EPIGENOME PLAYS A MAJOR ROLE IN TOMATO 3D CHROMATIN ORGANIZATION [RNA-seq]

city: Gif-sur-Yvette

first: Xiaoning

last: HE

address: 630 Rue Noetzlin

summary: Understanding the 3D genome organization in the nucleus is becoming increasingly crucial given its involvement in many processes from transcription to the integrity of the nucleus itself, which play a role in every stage of an organism's life. Beyond the linear genome defined by its nucleotide sequence, this organization is also governed by its epigenome, but how the latter controls the 3D architecture of the nucleus is poorly understood. To decipher the epigenome influence on the formation of all levels of the nuclear organization, we studied tomato mutants defective for DDM1, a chromatin remodeler determining for the constitutive heterochromatin establishment. We observed that the ddm1 mutant exhibited weakened compartmentalization with lower insulation, more inter-compartment contacts and an increase in long-range contacts. This disorganization is accompanied by a reconfiguration of the epigenome, ultimately resulting in a reprogramming of its transcriptome. By integrating all our data, we have shown that this redistribution of the epigenome is linked to the global disorganization of the nucleus notably via new interactions mediated by H3K27me3, and is also related to new interactions between genes and/or TEs which display the same epigenetic characteristics. Altogether, our results strongly suggest that epigenetic features drive the formation of distinct compartments by playing a segregating role between active and inactive chromatin, becoming an essential characteristic for the identity of genes and TEs in terms of genome organization.

overall_design: To assess the effect of the epigenome reconfiguration on transcriptome reprogramming, we performed RNA-seq analyses in WT and mutant. Then,  we performed DESeq2 analysis and found differentially expressed genes in ddm1.

last: He

first: Chloé

middle: D

last: Lopes

first: Leonardo

middle: I

last: Bistrain

first: Nicolas

last: Bouché

first: David

last: Latrasse

first: Cécile

last: Raynaud

first: Moussa

last: Benhamed


title: RUNX1 interacts with lncRNA SMANTIS to regulate monocytic cell functions [RNA_THP1_SMANTIS_RUNX1_KO]

last: Zehr

overall_design: RNA sequencing (n = 3) of THP-1, an accepted human leukemia monocytic cell line. LentiCRISPRv2-mediated knockouts were generated using a dual-guide RNA (gRNA) system approach to knockout SMANTIS, and a single gRNA approach to knock out RUNX1.For the non-target control (NTC) also a single gRNA approach was used.

first: Katalin

last: Pálfi

first: Tom

last: Teichmann

first: Alicia

last: Schneider

first: Julia

last: Stötzel

last: Knapp

first: Andreas

last: Weigert

first: Rajkumar

last: Savai

first: Michael

middle: A

last: Rieger

first: Thomas

last: Oellerich

first: Ilka

last: Wittig

first: James

last: Oo

first: Ralf

last: Brandes

first: Matthias

last: Leisegang


title: RUNX1 interacts with lncRNA SMANTIS to regulate monocytic cell functions [ATAC-seq]

first: Simonida

overall_design: ATAC sequencing (n = 3) of THP-1, an accepted human leukemia monocytic cell line. LentiCRISPRv2-mediated knockouts were generated using a dual-guide RNA (gRNA) system approach to knockout SMANTIS, and a single gRNA approach to knock out RUNX1.For the non-target control (NTC) also a single gRNA approach was used.

first: Lisa

last: Weiss

first: Timothy

last: Warwick

first: Stefan

last: Günther

first: Sebastian

last: Wolf

first: Tessa

last: Schmachtel

first: Judit

last: Izquierdo Ponce


title: Nuclear lamin A/C phosphorylation by loss of Androgen Receptor is a global determinant of cancer-associated fibroblast activation [ChIP-Seq2]

city: Epalinges

first: Soumitra

last: Ghosh

address: Chemin des Boveresses 155

institute: University of Lausanne, Switzerland

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of total Lamin A/C in HDF cells with and without AR silencing.

first: Mazzeo

last: Luigi

first: G

last: Dotto


title: Single-cell RNA-seq analysis of rat molars reveals cell-identity and driver genes associated with dental mesenchymal cell differentiation

city: Guangzhou

first: Yingchun

last: Zheng

state: Guangdong

address: Guangdong province

institute: Southern Medical University

summary: To explore the cell-identity and driver genes related to dental mesenchymal cell differentiation during the late bell hard tissue formation stage, the first and second mandibular molars (M1 and M2) of rat at postnatal days 5 were dissected for enzymatic digestion and subjected to single-cell RNA sequencing (scRNA-seq).

overall_design: We performed single-cell transcriptome of the first and second mandibular molars tooth germ of 5 days postnatal rat.

first: Ting

last: Lu

first: Leitao

last: Zhang

first: Zhongzhi

last: Gan

first: Aoxi

last: Li

first: Chuandong

last: He

first: Fei

first: Sha

first: Jian

first: Fu

last: Xiong


title: BET inhibition rescues ciliogenesis and ameliorates pancreatitis-driven phenotypic changes in mice with Par3 loss

city: Chicago

first: Mario

last: Shields

state: Illinois

address: 303 E Superior St

department: Medicine

institute: Northwestern University

summary: The apical-basal polarity of pancreatic acinar cells is essential for maintaining tissue architecture. However, the mechanisms by which polarity proteins regulate acinar pancreas tissue homeostasis are poorly understood. Here, we evaluate the role of Par3 in acinar pancreas injury and homeostasis. While Par3 loss in the mouse pancreas disrupts tight junctions, Par3 loss is dispensable for pancreatogenesis. However, with aging, Par3 loss results in low-grade inflammation, acinar degeneration, and pancreatic lipomatosis. Par3 loss also exacerbates pancreatitis-induced acinar cell loss, resulting in pronounced pancreatic lipomatosis and failure to regenerate. Moreover, Par3 loss in mice harboring mutant Kras causes extensive pancreatic intraepithelial neoplastic (PanIN) lesions and large pancreatic cysts. We also show that Par3 loss restricts injury-induced primary ciliogenesis. Significantly, targeting BET proteins enhances primary ciliogenesis during pancreatitis-induced injury and, in mice with Par3 loss, limits pancreatitis-induced acinar loss and facilitates acinar cell regeneration. Combined, this study demonstrates how Par3 restrains pancreatitis- and Kras-induced changes in the pancreas and identifies a potential role for BET inhibitors to attenuate pancreas injury and facilitate pancreas tissue regeneration.

overall_design: Wildtype or Par3 conditional knockout mice were pre-treated with DMSO control or JQ1 for 7 days then pancreatitis is induced with cerulein for 5 days. RNA was isolated from pancreas tissue for RNA-seq.

first: Hidayatullah

last: Munshi


title: Post-prandial cardiac hypertrophy is sustained by mechanics, epigenetic, and metabolic reprogramming in pythons [ATAC-Seq]

status: Public on Aug 04 2024

city: Boulder

first: Mary

middle: Ann

last: Allen

state: Co

address: UCB 596  JSCBB

department: BioFrontiers

institute: University of Colorado

summary: Constricting pythons, known for their ability to consume infrequent, massive meals, exhibit rapid and reversible cardiac hypertrophy following feeding. Our primary goal was to investigate how python hearts achieve this adaptive response after feeding. Isolated myofibrils increased force after feeding without changes in sarcomere ultrastructure and without increasing energy cost. Ca2+ transients were prolonged after feeding with no changes in myofibril Ca2+ sensitivity. Feeding reduced titin-based tension, resulting in decreased cardiac tissue stiffness. Feeding also reduced the activity of sirtuins, a metabolically-linked class of histone deacetylases, and increased chromatin accessibility. A transcription factor enrichment analysis on transposase-accessible chromatin with sequencing (ATAC-Seq) revealed the prominent role of transcription factors YY1 and NRF1 in post-feeding cardiac adaptation. Gene expression was also changed in favor of translation and metabolism. Finally, metabolomics analysis and ATP production assay demonstrated that cardiac adaptation after feeding not only increased energy demand but also energy production. These findings have broader implications for our understanding of cardiac adaptation across species and hold promise for the development of innovative approaches to address cardiovascular diseases.

overall_design:
To determine the chromatin accessibility profile of post-prandial python hearts, the cardiomyocytes of fasted and 24 post fed Python regius were extracted for ATAC-sequencing analysis.
The cardiomyocytes from three fasted and three fed pythons were included in the study.
Transcription factor expression analysis (TFEA) was performed between fasted and 24 hour post fed python cardiomyocytes.

first: Claudia

last: Crocini

first: Kathleen

last: Woulfe

first: Christopher

last: Ozeroff

first: Stefano

last: Perni

first: Joseph

last: Cardiello

first: Cierra

last: Walker

first: Kristi

last: Anseth

first: Leslie

last: Leinwand


title: THE EPIGENOME PLAYS A MAJOR ROLE IN TOMATO 3D CHROMATIN ORGANIZATION [Hi-C]

first: Xiaoning

last: HE

overall_design: Hi-C of WT and ddm1 mutants

first: Chloé

last: Lopes

first: Leonardo

last: Bistrain

first: Nicolas

last: Bouché

first: David

last: Latrasse

first: Cécile

last: Raynaud

first: Moussa

last: Benhamed


title: Claustrum/dorsal Endopiriform cortex complex cell identity is determined 1 by Nurr1 and regulates hallucinogenic-like states.

city: Solna

first: Yuvarani

last: Masarapu

address: SciLifeLab, Tomtebodavägen 23

institute: SciLifeLab

summary: The Claustrum/dorsal Endopiriform cortex complex (CLA) is an enigmatic brain region with 19 extensive glutamatergic projections to multiple cortical areas. The transcription factor Nurr1 is 20 highly expressed in the CLA, but its role in this region is not understood. By using conditional 21 gene-targeted mice, we show that Nurr1 is a crucial regulator of CLA neuron identity. Although 22 CLA neurons remain intact in the absence of Nurr1, the distinctive gene expression pattern in 23 the CLA is abolished. CLA has been hypothesized to control hallucinations, but little is known 24 of how the CLA responds to hallucinogens. After the deletion of Nurr1 in the CLA, both 25 hallucinogen receptor expression and signaling are lost. Furthermore, functional ultrasound 26 imaging and Neuropixel electrophysiological recordings revealed that the effects of 27 hallucinogenic receptor agonists on functional connectivity between the prefrontal and 28 sensorimotor cortices are altered in Nurr1-ablated mice. Our findings suggest that Nurr1-29 targeted strategies provide new avenues for functional studies of the CLA.

overall_design: Spatially resolved transcriptional profiling of striatum from wild-type mice and Nr4a2 knockdown mice. Transcriptome capture in each tissue section with spatial resolution using the 10x genomics kit Visium Spatial Gene Expression assay for Fresh Frozen tissues

first: Ioannis

last: Mantas

first: Ivana

last: Flais

last: Masaparu

first: Tudor

last: Ionescu

first: Solène

last: Frapard

first: Felix

last: Jung

first: Pierre

last: Le Merre

first: Marcus

last: Saarinen

first: Katarina

last: Tiklova

first: Behzad

last: Yaghmaeian Salmani

first: Linda

last: Gillberg

first: Xiaoqun

last: Zhang

first: Karima

last: Chergui

first: Marie

last: Carlén

first: Stefania

last: Giacomello

first: Bastian

last: Hengerer

first: Thomas

last: Perlmann

first: Per

last: Svenningsson


title: POSTN secreted from glioblastoma stem cells can recruit microglia and upregulate CD70 expression in microglia through the αVβ3/PI3K/AKT/NFκB pathway

city: Soochow

first: Hao

last: Wang

state: Jiangsu

address: 899 Pinghai Road

department: Department of Neurosurgery & Brain and Nerve Research Laboratory

institute: The First Affiliated Hospital of Soochow University

summary: Our findings revealed that POSTN secreted from GSCs can recruit microglia and upregulate CD70 expression in microglia through the αVβ3/PI3K/AKT/NFκB pathway, which in turn promotes Treg development and functionality and supports the formation of an immunosuppressive tumor microenvironment.

overall_design: Comparative gene expression profiling analysis of RNA-seg data of HMC3 cells treated with PBS or human recombinant POSTN.

first: Youxin

last: Zhou


title: Functional genomics identifies a small secreted protein that plays a role during the biotrophic to necrotrophic shift in the root rot pathogen Phytophthora medicaginis

city: Sydney

first: Jonathan

middle: Michael

last: Plett

state: New South Wales

address: 50 Bourke street

department: Soil Biology and Genomics

country: Australia

institute: Western Sydney University

summary:
Introduction: Hemibiotrophic Phytophthora are a group of agriculturally and ecologically important pathogenic oomycetes causing severe decline in plant growth and fitness. The lifestyle of these pathogens consists of an initial biotrophic phase followed by a switch to a necrotrophic phase in the latter stages of infection. Between these two phases is the biotrophic to necrotrophic switch (BNS) phase, the timing and controls of which are not well understood particularly in Phytophthora spp. where host resistance has a purely quantitative genetic basis.
Methods: To investigate this we sequenced and annotated the genome of Phytophthora medicaginis, causal agent of root rot and substantial yield losses to Fabaceae hosts. We analysed the transcriptome of P. medicaginis across three phases of colonisation of a susceptible chickpea host (Cicer arietinum) and performed co-regulatory analysis to identify putative small secreted protein (SSP) effectors that influence timing of the BNS in a quantitative pathosystem.
Results: The genome of P. medicaginis is ~78 Mb, comparable to P. fragariae and P. rubi which also cause root rot. Despite this, it encodes the second smallest number of RxLR (arginine-any amino acid-leucine-arginine) containing proteins of currently sequenced Phytophthora species. Only quantitative resistance is known in chickpea to P. medicaginis, however, we found that many RxLR, Crinkler (CRN), and Nep1-like protein (NLP) proteins and carbohydrate active enzymes (CAZymes) were regulated during infection. Characterisation of one of these, Phytmed_10271, which encodes an RxLR effector demonstrates that it plays a role in the timing of the BNS phase and root cell death.
Discussion: These findings provide an important framework and resource for understanding the role of pathogenicity factors in purely quantitative Phytophthora pathosystems and their implications to the timing of the BNS phase.

sample_organism:
Cicer arietinum
Phytophthora medicaginis

overall_design: In total six samples were generated for the double stranded interfering RNA knockdown experiment to test the function of Phytmed_10271 in Phytophthora medicaginis during their biotrophic to necrotrophic switch in chickpea roots. Three of the samples were from dsiRNA treated roots targeting Phytmed_10271 and the other three samples were from roots treated with scrambled dsiRNA unable to target any endogenous P. medicaginis genes.  Additionally, 16 samples were generated for RNA-sequencing of which the 16 samples included 1 replicate each of 16 timepoints 8, 16, 20, 28, 32, 36, 40, 44, 48, 60, 84, 96, 108, 120, 132 and 144 hours post P. medicaginis inoculation in chickpea var. 'Sonali' roots.

first: Donovin

middle: W

last: Coles

first: Sean

last: Bithell

first: Thommas

last: Jeffries

first: Willam

last: Cuddy


title: RUNX1 interacts with lncRNA SMANTIS to regulate monocytic cell functions [RNA_THP1_diff_OCL]

first: Simonida

last: Zehr

overall_design: RNA sequencing (n = 2) of THP-1, an accepted human leukemia monocytic cell line. LentiCRISPRv2-mediated knockouts were generated using a dual-guide RNA (gRNA) system approach to knockout SMANTIS, and a single gRNA approach to knock out RUNX1.For the non-target control (NTC) also a single gRNA approach was used.

first: Lisa

last: Weiss

first: Timothy

last: Warwick

first: Stefan

last: Günther

first: Sebastian

last: Wolf

first: Tessa

last: Schmachtel

first: Judit

last: Izquierdo Ponce

first: Katalin

last: Pálfi

first: Tom

last: Teichmann

first: Alicia

last: Schneider

first: Julia

last: Stötzel

last: Knapp

first: Andreas

last: Weigert

first: Rajkumar

last: Savai

first: Michael

last: Rieger

last: Oellerich

first: Ilka

last: Wittig

first: James

last: Oo

first: Ralf

middle: P

last: Brandes

first: Matthias

last: Leisegang


title: Crosslinking of Ly6a metabolically reprograms CD8 T cells for cancer immunotherapy.

city: Tel Aviv

first: Carmit

last: Levy

state: israel

address: kalchekin 35

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

summary: T cell inhibitory mechanisms prevent autoimmune reactions, while cancer immunotherapy aims to remove these inhibitory signals, Chronic UV exposure attenuates autoimmunity through promotion of unknown immune-suppressive mechanisms. Here we showed that mice with subcutaneous melanoma were not responsive to anti-PD1 immunotherapy following chronic UV irradiation, given prior to tumor injection, due to the suppression of T cell killing ability in skin-draining lymph nodes. Using mass cytometry and single-cell RNA-sequencing analyses, we discovered that skin-specific, UV-induced suppression of T-cells killing activity is mediated by upregulation of Ly6ahigh T-cells subpopulation. Independently of the UVB effect, Ly6ahigh T cells were induced by chronic type-1 interferon in the tumor microenvironment. Treatment with an anti-Ly6a antibody enhanced the anti-tumoral cytotoxic activity of T cells and reprogrammed their mitochondrial metabolism via the Erk/cMyc axis. Remarkably, treatment with anti-Ly6a antibody significantly inhibited tumor growth in mice resistant to anti-PD1 therapy. Applying our findings in humans could lead to a new immunotherapy treatment for patients with resistance to existing treatments.

overall_design:
single-cell RNA sequencing was conducted on skin drain lymph nodes (sDLN) cells from mice following UVB or mock irradiation. C57BL/6J mice were dorsally shaved and chronically exposed to low-dose UVB irradiation or were mock-irradiated as controls.
The dose of UVB was increased gradually to mimic the protocol used for human UVB phototherapy. Starting at an initial dose of 50 mJ/cm2, a sub-erythematic dose in this mouse strain, the UVB dose was increased by 30% at each treatment reaching a final dose of 200 mJ/cm2.

first: Yuval

last: Sade

first: Keren

last: Reshef