title: BCAS2 and hnRNPH1 orchestrate alternative splicing for DNA double-strand break repair and synapsis in meiotic prophase I [CLIP-seq]

overall_design: Total cells were isolated from adult WT C57BL/6N mouse testes, and then the cells were cross-linked by ultraviolet light (254 nm) to maintain the covalent binding of RBPs to their cognate RNA. Subsequently, BCAS2 and cross-linked RNAs were immunoprecipitated with an anti-BCAS2 antibody and digested with micrococcal nuclease (EN0181, Thermo Fisher Scientific). An IR800-biotin adapter was ligated to the 3′ ends of the RNA fragments. Then, the BCAS2/RNA complexes were separated by SDS‒PAGE and transferred to a nitrocellulose membrane (HATF00010, Millipore). These RNA and protein complexes from approximately 40 to 60 kDa were extracted from the nitrocellulose membrane, after which proteinase K (9034, Takara) digestion was performed. RNA was isolated with saturated phenol (AM9712, Ambion), ligated with adaptors, and converted to cDNA with a SuperScript III First-Strand Kit (18080-051, Invitrogen). The cDNA was amplified by PCR to prepare the corresponding libraries and then sequenced on illumina NovaSeq 6000.

first: Rong

last: Ye

first: Changchang

last: Cao


title: Refined mechanism of promoter Nucleosome-Depleted Regions resetting after replication

status: Public on Mar 25 2024

city: Geneva

first: Sevil

last: Zencir

address: 30, quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

country: Switzerland

institute: University of Geneva

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Replication disrupts chromatin organization. Thus, rapid resetting of nucleosome positioning is essential to maintain faithful gene expression. The initial step of this reconfiguration occurs at Nucleosome-Depleted Regions (NDRs). While studies have elucidated the role of Transcription Factors (TFs) and Chromatin Remodelers (CRs) in vitro or in maintaining NDRs in vivo, none has addressed their in vivo function shortly after replication. Through purification of nascent chromatin coupled with yeast genetics, we dissected the choreography of events governing the proper positioning of the -1/+1 nucleosomes flanking promoter NDRs. Our findings reveal that CRs are the primary contributors of -1/+1 repositioning post-replication, with RSC acting upstream of INO80. Surprisingly, while Reb1 and Abf1 TFs are not essential for NDR resetting, they are required for NDR maintenance via the promotion of H3 acetylations. Taken together, we propose a two-step model for NDR resetting in S. cerevisiae: first, CRs alone reset promoter NDRs after replication, while a combination of TFs and CRs is required for subsequent maintenance.

overall_design:
Nucleosome occupancy was measured by MNase-seq upon nuclear depletion of Abf1, Reb1, Rpo21, Sth1, Ino80 and Rsc3 in mature and nascent chromatin analyzing ‘Input’ and ‘Edu-labeled’ samples respectively. Edu labeling efficiency was measured by comparing G1-arrested and S-phase EdU labeled samples. Sth1 binding was measured by ChEC-seq upon nuclear depletion of Ino80. The binding of Ino80 was measured by ChEC-seq upon nuclear depletion of Sth1. The effect of the TSA treatment on nucleosome positioning was measured by MNase-seq upon depletion of Sth1, Ino80 and Reb1.
Please note that processed data file generated from both replicates is linked to the corresponding rep1 sample records.

first: Jatinder

middle: K

last: Gill

first: Françoise

last: Stutz

first: Julien

last: Soudet


title: Differential CpG methylation at Nnat in the early establishment of beta cell heterogeneity

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

type: Expression profiling by high throughput sequencing

summary: Aims/hypothesis: Beta cells within the pancreatic islet represent a heterogenous population wherein individual sub-groups of cells make distinct contributions to the overall control of insulin secretion. These include a subpopulation of highly-connected ‘hub’ cells, important for the propagation of intercellular Ca2+ waves. Functional subpopulations have also been demonstrated in human beta cells, with an altered subtype distribution apparent in type 2 diabetes. At present, the molecular mechanisms through which beta cell hierarchy is established are poorly understood. Changes at the level of the epigenome provide one such possibility which we explore here by focussing on the imprinted gene neuronatin (Nnat), which is required for normal insulin synthesis and secretion.  Methods: Single cell RNA-seq datasets were examined using Seurat 4.0 and ClusterProfiler running under R. Transgenic mice expressing eGFP under the control of the Nnat enhancer/promoter regions were generated for fluorescence-activated cell (FAC) sorting of beta cells and downstream analysis of CpG methylation by bisulphite and RNA sequencing, respectively. Animals deleted for the de novo methyltransferase, DNMT3A from the pancreatic progenitor stage were used to explore control of promoter methylation. Proteomics was performed using affinity purification mass spectrometry and Ca2+ dynamics explored by rapid confocal imaging of Cal-520 and Cal-590. Insulin secretion was measured using Homogeneous Time Resolved Fluorescence Imaging.  Results: Nnat mRNA was differentially expressed in a discrete beta cell population in a developmental stage- and DNA methylation (DNMT3A)-dependent manner. Thus, pseudo-time analysis of embryonic data sets demonstrated the early establishment of Nnat-positive and negative subpopulations during embryogenesis. NNAT expression is also restricted to a subset of beta cells across the human islet that is maintained throughout adult life. NNAT+ beta cells also displayed a discrete transcriptome at adult stages, representing a sub-population specialised for insulin production, reminiscent of recently-described “bHI” cells and were diminished in db/db mice. ‘Hub’ cells were less abundant in the NNAT+ population, consistent with epigenetic control of this functional specialization.  Conclusions/interpretation: These findings demonstrate that differential DNA methylation at Nnat represents a novel means through which beta cell heterogeneity is established during development. We therefore hypothesise that changes in methylation at this locus may thus contribute to a loss of beta cell hierarchy and connectivity, potentially contributing to defective insulin secretion in some forms of diabetes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NNAT-positive vs NNAT-negative primary mouse beta cells.

first: Steven

middle: J

last: Millership

first: Guy

middle: A

last: Rutter

first: Dominic

last: Withers

first: Sanjay

last: Khadayate


title: DCK (diquat)-induced lung injury

city: Fuzhou

first: Zhimin

last: Chen

address: Chazhong Road NO.20

country: China

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

summary: Diquat (DQ) poisoning is a severe medical condition with life-threatening implications and multi-organ dysfunction, yet its underlying mechanism remains incompletely understood. This study unveils a critical process in DQ-induced toxicity. DQ disrupts the mitochondrial genome stability in endothelial cells, leading to the accumulation of Z-form DNA. This triggers an interaction between Z-DNA binding protein 1 (ZBP1) and receptor interacting protein kinase 3 (RIPK3), setting off RIPK3-dependent necroptotic and ferroptotic signaling pathways. Depletion of ZBP1 or RIPK3 in endothelial cells effectively inhibits both necroptosis and ferroptosis, reducing organ damage and mortality. Importantly, we discover that RIPK3 plays a dual role. It phosphorylates MLKL to induce necroptosis and phosphorylates FSP1, inhibiting its enzymatic activity and promoting ferroptosis. The phosphorylation of T163 in FSP1 is crucial for suppressing its activity. Combining the deletion of MLKL with vitamin K treatment proves highly effective in mitigating multi-organ damage and lethality caused by DQ.

overall_design:
Lung tissue from pesticide-poisoned mice for exploring mechanisms of pesticide organ damage
Harvested cells at the required densities were combined with gel beads  containing the barcoded information along with a mixture of cells and  enzymes. Oil surfactant droplets in a microfluidic double-cross system were used for encapsulation to generate Gel Beads-In-Emulsions (GEMs). GEMs were passed through a reservoir and collected while the gel beads were lysed to release the barcode sequence. The cDNA fragment was then reverse transcribed before the sample was labeled. The gel beads and the oil droplets are ruptured and PCR amplification was performed using the generated cDNA as a template. The products of all GEMs were mixed and a standard sequencing library is constructed. The cDNA was first enzymatically digested into fragments of about 200300 base pairs (bp), together with the library building process of traditional secondgeneration sequencing such as sequencing junction and primers. Finally, the DNA library was generated by PCR amplification

first: Yanfang

last: Xu


title: Phenotypical states modulate sensitivity and transcriptional reprogramming in patient-derived glioblastoma cells in response to temozolomide and radiation therapy. [RNA-Seq]

city: Detroit

first: oluwademilade

last: Nuga

state: MI

address: 540 E canfield

department: Pharmacology

country: USA

institute: Wayne State University

summary: Differential molecular response involving epigenetic, transcriptomic and proteomic adaptstions of glioblastoma cancer stem-like cells and serum differentiaed cells in response to temozolomide and ionizing radiation

overall_design: Patient derived glioblastoma cancer stem-like cells and 2% FBS differentiated cells exposed to ionizing radiation (4 Gy) and temozolomide with corresponding controls (n=3 technical replicates)

first: Oluwademilade

first: Artem

last: Berezovsky

first: Indrani

last: Dutta

first: Kimberly

last: Bergman

first: Thais

last: Sabedot

first: Katherine

last: Gurdziel

first: Susan

last: Irtenkauf

first: Laura

last: Hasselbach

first: Yuling

last: Meng

first: Claudius

last: Mueller

first: Emanuel

middle: F

last: Petricoin III

last: Brown

first: Sidhesh

last: Aras

first: Laila

last: Poisson

first: Houtan

last: Noushmehr

first: Douglas

last: Ruden

first: Ana

middle: C

last: deCarvalho


title: Phenotypical states modulate sensitivity and transcriptional reprogramming in patient-derived glioblastoma cells in response to temozolomide and radiation therapy. [array]

first: oluwademilade

last: Nuga

summary: Genome wide DNA methylation profiling of patient-derived glioblastoma cells cultured as neurospheres or FBS differentited cells. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in glioblastoma CSCs and serum differentiated cells treated with 4 Gy ionizing radiation or IC30 concentration of temozolomide as well as vehicle control samples. Samples included 3 technical replicates in each treatment group for 2 primary glioblastoma cell lines.

overall_design: Bisulphite converted DNA from the 36 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Steven


title: Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer [RNA-Seq2]

city: Milan

first: Pierluigi

last: Di Chiaro

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

summary: Intratumor morphological heterogeneity of pancreatic ductal adenocarcinoma (PDAC) predicts clinical outcomes but is only partially understood at the molecular level. To elucidate the gene expression programs underpinning intratumor morphological variation in PDAC, we investigated and deconvoluted at single cell level the molecular profiles of histologically distinct clusters of PDAC cells. We identified three major morphological and functional variants that co-exist in varying proportions in all PDACs, display limited genetic diversity, and are associated with a distinct organization of the extracellular matrix: a glandular variant with classical ductal features; a transitional variant displaying abortive ductal structures and mixed endodermal and myofibroblast-like gene expression; and a poorly differentiated variant lacking ductal features and basement membrane, and showing neuronal lineage priming. Ex vivo and in vitro evidence supports the occurrence of dynamic transitions among these variants in part influenced by extracellular matrix composition and stiffness and associated with local, specifically neural, invasion.

overall_design: Total RNA from primary human pancreatic ductal adenocarcinoma cells was processed for multiparallel sequencing. Experiments were carried out in PATC69 cell line cultured on collagen-coated plates of 12kPa and 1kPa stiffness (2 replicates each).


title: Gene expression profiling of mouse breast tumor tissue after injection of 4T1 therapy-induced senesence derived sEVs

city: Singapore

first: Matius

last: Robert

state: Singapore

address: 28 Medical Drive

department: Physiology

country: Singapore

institute: National University of Singapore

summary: TNBC, associated with poor prognosis and high tumour recurrence, are often treated with anti-mitotic drugs. However, cells may bypass treatment-induced cell death via mitotic slippage, resulting in multinucleated polyploid cells and senescence activation. Senescent cancer cells represent a population of residual disease and are highly secretory. The SASP elicited is enriched in soluble cytokines linked to tumor recurrence and distant metastasis. In contrast, sEVs derived from senescent cancer cells represent an underappreciated aspect of SASP and its mechanistic role in mediating paracrine effects remains poorly-understood. Here, we show senescent sEVs as a distinct population of SASP that could elicit anti-tumor activity.

overall_design:
To investigate the effect of sEVs from therapy induced senescent breast cancer cells on mouse tumour growth, we have intratumourally injected Saline, Cont sEV and TIS sEV isolated from DMSO or 100 ng/ml Nocodozole treated 4T1 mouse breast cancer cells into the orthotopic BALB/c breast tumor mouse.
Gene expression profiling analysis were performed using data obtained from RNA-seq of 3 different conditions (tumour tissue) after sEV treatment to orthotopic breast tumour mice.
Comparative gene expression profiling analysis of RNA-seq data from mouse tumour tissue (Saline, Cont sEV, TIS sEV)

first: Karen

last: Crasta

first: Rekha

last: Jakhar


title: The transcription factor Oct6 promotes the dissolution of the naïve pluripotent state by repressing Nanog and activating a formative state gene regulatory network.

city: Belen de Escobar

first: Santiago

last: Miriuka

state: Buenos Aires

address: Ruta 9 Km 52.5

department: LIAN-CONICET

country: Argentina

institute: FLENI

summary: Animal development is controlled by large gene regulatory networks (GRNs) that govern the nearly irreversible changes that occur when a cell differentiates into another cell type. In this work we aimed to determine key transcription factors (TFs) associated with the dissolution of the naïve pluripotent state and the acquisition of a formative identity. We identified Oct6 as one of the earliest TFs induced during the onset of mouse embryonic stem cell (mESCs) differentiation. By generating an Oct6 knockout mESC cell line, we show that it failed to acquire the typical cell morphology associated with the formative state. Transcriptome analysis of these differentiating cells allowed for the identification of nearly 300 differentially expressed genes compared to wild-type cells. Among these were the pluripotency TFs Nanog, Klf2, Nr5a2, Prdm14, and Esrrb, that failed to correctly downregulate. Premature expression of Oct6 in naïve cells induced a rapid morphological transformation that resembled the one observed in differentiating cells. In these conditions, Oct6 induced its own expression as well as that of other TFs such as Sox3, Zic2/3, Foxp1, and formative genes like Dnmt3A and FGF5. Strikingly, Oct6 also repressed the expression of the key pluripotency TF Nanog. Gene expression and single molecule RNA-FISH analysis of Nanog confirmed that this regulation was at the transcriptional level. In summary, our results indicate that Oct6 is a key TF in the dissolution of the pluripotent state. Moreover, they support a model where Oct6 and Nanog form a double negative feedback loop which could act as a toggle switch important for the transition to the formative state.

overall_design: WT and Oct6 KO 46C mouse embryonic stem cells (mESCs) were differentiated to epiblast-like cells (EpiLCs) by culturing them for 48 h in N2B27 defined medium supplemented with 1% KSR, 12 µg/ml bFGF, and 20 µg/ml Activin A, in fibronectin-coated culture dishes. Three paired biological replicates were performed for both WT and KO EpiLCs. Total RNA was submitted to high-throughput sequencing.

first: Ariel

last: Waisman

middle: G


title: Identification and Validation of Frameshift Neoantigens for Mismatch-Repair Deficient Lynch Syndrome

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

summary: Lynch syndrome (LS) patients develop DNA mismatch repair deficient tumors which generate high loads of neoantigens (neoAgs), thus constituting a well-defined population that can benefit from cancer immune-interception strategies, including neoantigen-based vaccines. Using paired whole-exome sequencing and mRNAseq of colorectal cancers (CRC) (n=13) and pre-cancers (n=61) from our LS patient cohort (N=46), we performed in-silico prediction and immunogenicity ranking of highly recurrent frameshift-neoags, followed by their in-vitro validation. We described the somatic mutation landscape in all cancers and pre-cancers, and showed that mutation burden is positively correlated with neoAgs load. Furthermore, our in-vitro validation showed a 65% validation rate of our top 100 predicted neoags. Consistent with neoAgs burden, our transcriptomic results revealed increased infiltration of CD8+ and CD4+ T-cells in microsatellite unstable samples. Overall, our neoAgs catalog and all other findings, improve our understanding of cancer development in LS and guide us towards the advancement of immunoprevention vaccine strategies.

overall_design: All patients included in this study had a confirmed diagnosis of Lynch Syndrome (n = 46) and provided written informed consent at The University of Texas MD Anderson Cancer Center (MDACC). All samples were obtained from study participants through an Institutional Review Board (IRB) approved protocol at MDACC (Protocol PA12-0327). A set of 74 flash-frozen or formalin-fixed paraffin embedded (FFPE) tissue biopsies from polyps or tumors of the lower gastrointestinal tract, with matching normal mucosa and peripheral blood, were collected from 46 LS patients who came to MDACC for a standard of care surveillance colonoscopy. The pathological diagnosis of all tissue samples was confirmed by a gastrointestinal pathologist (M.W.T) at MDACC. Samples were classified as inflammatory polyps (IP), hyperplastic polyps (HP), sessile serrated adenomas (SSA), adenomatous polyps (AP), which included tubular as well as tubullovillous adenomas, and adenocarcinomas, based on pathological diagnosis. Depending on the level of high-grade dysplasia samples were classified into different tissue categories that included pre-cancers, defined as pre-malignant lesions with low or no level of dysplasia, advanced pre-cancers, defined as pre-malignant lesions with high level of dysplasia, and cancers.  DNA and RNA were extracted from all flash-frozen and FFPE tissue samples using the Quick-DNA/RNA Miniprep Kit (Zymo Research, CA) and AllPrep DNA/RNA FFPE Kit (Qiagen, MD), respectively. Genomic DNA was obtained from peripheral blood using Gentra Puregene Blood Kit (Qiagen).

last: Deng


title: Genome-wide Profiles of DNA Damage Represent Highly Accurate Predictors of Chronological Age

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

institute: Huaqiao University

summary: Accurate prediction of a true biological age of an individual represents a very important problem for both the clinics and basic science, as well as for the society as a whole, which led to a wealth of efforts to identify multiple types of various age-related biomarkers. However, the predictive models based on these biomarkers still require major improvements calling for identification of novel age-related biomarkers. Despite multiple studies associating DNA damage with aging, a glaring paucity of DNA damage-based age-related biomarkers exist, in no small part due to the lack of precise methods for genome-wide surveys of different types of DNA damage. Recently, we developed two techniques for genome-wide mapping of the most prevalent types of DNA damage, single-strand breaks and abasic sites, with nucleotide-level resolution. Here, we explored the potential of the data generated using these methods as the source of universal age biomarkers in mammals. Strikingly, we found that patterns of either DNA lesion could very accurately predict age with higher precision than the commonly used transcriptome analysis. These findings show that previously unexplored high-resolution patterns of genome-wide DNA damage contain potential treasure troves of useful information that can significantly enrich both practical applications and basic science

overall_design: An in-depth analysis of the genome-wide profiles of SSBs, AP sites and RNA from several tissues of mice collected from animals of various ages in order to evaluate the potential of DNA damage-based chronological age predictors and to compare their performance to the predictors based on transcriptome.

first: Philipp

last: Kapranov


title: Phenotypical states modulate sensitivity and transcriptional reprogramming in patient-derived glioblastoma cells in response to temozolomide and radiation therapy.

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

overall_design: Refer to individual Series


title: Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer [DNA-seq]

overall_design: Gland forming (GL) and non-gland forming (NGL) tumor areas of 200-500 cells were collected from FFPE tissues in a cohort of 10 primary pancreatic ductal adenocarcinoma (PDAC) patients. Single or multiples areas were processed per patient for a total of 52 samples.


title: Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer [RNA-seq]

overall_design: Gland forming (GL) and non-gland forming (NGL) tumor areas of 200-500 cells were collected from FFPE tissues in a cohort of 30 primary pancreatic ductal adenocarcinoma (PDAC) patients. Single or multiples areas were processed per patient for a total of 102 samples.


title: Knockdown of Plasmodium falciparum Jumonji C2 histone demethylase leads to a global perturbance of gene expression but does not alter var gene transcription

city: São Paulo

first: Gerhard

last: Wunderlich

state: SP

address: Av. Professor Lineu Prestes, 1374, ICB2

country: Brazil

institute: Institute for Biomedical Sciences, University of São Paulo

summary: The gene expression of the human malaria parasite Plasmodium falciparum is dynamically controlled by multiple factors and events including chromatin modifiers. Here, we addressed the effect of a temporary knockdown of the non-essential putative chromatin modifier P. falciparum JumonjiC2 histone demethylase (JmjC2) during asexual blood stages. While ribozyme-mediated transcript-knockdown of PfJmjC2 resulted in the differential transcription of many genes culminating in a delay of cycle progression, ChIPseq analysis pointed to only a few loci with which JmjC2 seemed to associate, including variant gene encoding loci. Knockdown also altered the methylation and acetylation patterns of H3K4 and H3K9, important for global gene regulation, including variant/virulence-associated gene families. However, RT-qPCR based analysis of variant (var) gene transcription of knocked-down or control parasites showed only a partial decrease of dominant var transcripts without changing variant gene transcription patterns. Collectively, JmjC2 appears to be an important, yet dispensable player at least during intraerythrocytic development. The differential transcription of many genes that results from the knockdown of JmjC2 probably reflects a generalized temporary delay in cycle progression.

overall_design: RNA was Trizol-extracted from synchronized triplicate parasite cultures which were treated or not with glucosamine to effect a ribozyme-mediated knockdown of the histone modifier JmjC2. RNA was then converted in cDNA and used for library construction following the Illumina protocol.

first: T

last: Macedo-Silva

first: R

middle: B

last: Duque Araujo

first: A

middle: P

last: Besenbruch

first: L

last: Ortega Sepulveda

first: J

last: Fernandes

first: D

last: Barbosa

last: Martins-Jr

last: Setubal

first: P

middle: M

last: Ribolla

last: Alonso

first: G


title: Soluble ST2 induces cardiac contractile dysfunction by repressing mitochondrial electron transport chain genes in cardiomyocytes during fulminant myocarditis

status: Public on Mar 24 2024

city: Wuhan

first: Yan

last: Zhuang

state: Hubei

address: 1095# Jiefang Ave

department: Tongji Hospital

institute: Huazhong University of Science and Technology

summary: Fulminant myocarditis (FM) is an acute fatal disease characterised by myocardial inflammation. Our previous study identified soluble growth stimulation- expressed gene 2 (sST2) as a sensitive and specific biomarker for early diagnosis of FM. However, its function in FM remains unclear.In the present study, we observed a marked elevation of sST2 in the plasma and hearts of mice with FM induced by coxsackievirus B3 (CVB3) and explored the main cellular sources of sST2 in FM. Moreover, using recombinant sST2 protein administration and unbiased transcriptomics analyses, we investigated the role and underlying mechanisms of sST2 in FM. Importantly, we found that sST2 has a novel non-classical function in cardiomyocytes, other than acting as an IL-33 decoy receptor. These findings reveal a novel role and action mechanism of sST2 in FM and suggest that sST2 may be a potential therapeutic target for FM.

overall_design:
To explore how sST2 aggravates cardiac deterioration in mice and how sST2 induces contractile dysfunction in cardiomyocytes, RNA sequencing was performed on the hearts of mice with FM and cultured primary neonatal mouse cardiomyocytes (NMCMs) infected with CVB3
Transcriptome sequencing was performed on the hearts of CVB3-induced FM  and normal control mice. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the upregulated differentially expressed genes (DEGs), the chemokine signalling pathway was significantly enriched
To identify whether the potential target genes were directly regulated by YY1 in NMCMs and affected by sST2 treatment, we integrated the DEGs from NMCM RNA-seq with or without sST2 treatment with YY1-binding genes identified by YY1 CUT&Tag-seq

first: Zhuo

last: Zhang

first: Huihui

last: Li

first: Kudusi

last: Abuduwufuer

first: Donghui

first: Zheng

last: Wen

first: Chen

last: Chen

first: Dao

middle: W

last: Wang


title: The effect of the modulation of L2-hydroxyglutarate content in pachytene-diplotene cells of male mice

city: Jerusalem

first: Eli

last: Pikarsky

address: Ein Karem

department: The Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University-Hadassah Medical School

summary: We found that testis of male mice contain high concentrations of L2-hydroxyglutarate (L2HG) specifically in germ cells at pachytene/ diplotene (PD) stage of spermatogenesis. In order to elucidate the function of 2HG we decreased its level by incubating  PD cells with 24 mM oxamate and to rescue the putative phenotype by incubation with 24 mM oxamate together with 0.3 mM cell permeable L2HG.

overall_design: PD cells were isolated by sorting of enzyme-digested testicular cells from transgenic mice expressing tdTomato under germ cells specific promotor.  PD cells were incubated for 48 hrs with 24 mM oxamate  or with 24 mM oxamate together with 0.3 mM octyl L-2HG.

first: Nina

last: Mayorek


title: Gene expression profiling of MDA-MB-231 cells incubated with therapy induced senescence derived small extracellular vesicles

first: Matius

last: Robert

overall_design:
To investigate the effect of sEVs from therapy induced senescent breast cancer cells on recipient breast cancer cells, we have incubated MDA-MB-231 cells for 72h with No sEV, Cont sEV, TIS sEV isolated from donor MDA-MB-231 cells (DMSO or Nocodozole treated).
We then performed gene expression profiling analysis using data obtained from RNA-seq of recipient MDA-MB-231 cells after 72 h sEV treatment.
Comparative gene expression profiling analysis of RNA-seq data from MDA-MB-231 cells (No sEV, Cont sEV, TIS sEV)

first: Karen

last: Crasta

first: Rekha

last: Jakhar


title: CRISPRTE: A web-based tool to generate single guide RNA targets transposable elements

city: Haining

first: Yixin

last: Guo

address: 718 East Haizhou Rd.

institute: Zhejiang University

summary: CRISPR/Cas systems have gained prominence as powerful tools for genome engineering. Recent investigations into the crucial role of transposable elements (TEs) have stimulated research interest in manipulating TEs to elucidate their functions. Nevertheless, designing single guide RNAs (sgRNAs) that are both specific and efficient for TE manipulation presents a formidable challenge, considering the repetitive nature and high copy numbers of TEs. Although various sgRNA design tools have been developed for gene editing, an optimized sgRNA designer explicitly for TE manipulation has yet to be established. To bridge this gap, we presented CRISPR-TE, a web-based application featuring an accessible graphical user interface, available at https://www.crisprte.cn. CRISPR-TE could identify all potential sgRNAs for TEs and offers a comprehensive solution for efficient TE targeting at both the single duplicate and subfamily levels. We also demonstrated that young TEs can be targeted with higher coverage at the subfamily level. Finally, we validated the overexpression of SVAD, a human-specific TE, using dCas9-VP64 activator incorporated with three sgRNAs designed by our tool. Collectively, our findings suggest that CRISPR-TE may serve as a versatile framework for designing sgRNAs aimed at TE targeting.

overall_design: Comparative gene and transposable element expression profiling analysis of RNA-seq data for 293T_Suntag cells and 293T_Suntag_SVAD cells

first: Yixinguo

first: Wanlu

last: Liu


title: A single cell atlas of the murine pancreatic ductal tree identifies novel cell populations with potential implications in pancreas regeneration and exocrine pathogenesis.

city: Tallahassee

first: Li

address: Thrasher Medical Researcher Building, Suite 2300-D

department: College of Medicine

institute: Florida State University

summary: Pancreatic ducts form an intricate network of tubules that secrete bicarbonate and drive acinar secretions into the duodenum. This network is formed by centroacinar cells, terminal, intercalated, intracalated ducts, and the main pancreatic duct. Ductal heterogeneity at the single-cell level has been poorly characterized. Here, we used scRNA-seq to comprehensively characterize mouse ductal heterogeneity at single-cell resolution of the entire ductal epithelium from centroacinar cells to the main duct. Moreover, we used organoid cultures, injury models and pancreatic tumor samples to interrogate the role of novel ductal populations in pancreas regeneration and exocrine pathogenesis. In our study, we have identified the coexistence of 15 ductal populations within the healthy pancreas and characterized their organoid formation capacity and endocrine differentiation potential. Cluster isolation and subsequent culturing let us identify ductal cell populations with high organoid formation capacity and endocrine and exocrine differentiation potential in vitro, including Wnt-responsive-population, ciliated-population and FLRT3+ cells. Moreover, we have characterized the location of these novel ductal populations in healthy pancreas, chronic pancreatitis and tumor samples, hightlihgting a putative role of WNT-responsive, IFN-responsive and EMT-populations in pancreatic exocrine pathogenesis as their expression inceases in chronic pancreatitis and PanIN lesions. In light of our discovery of previously unidentified ductal populations, we unmask the potential roles of specific ductal populations in pancreas regeneration and exocrine pathogenesis.

overall_design: Tg(Sox9-EGFP) EB209 Gsat obtained from J.Ferrer laboratory (CRG) were utilized in this study. Sox9:eGFP positive cells were sorted from small, medoim and large ducts via FACS. Ten thousand sorted cells from each ductal fraction were pooled from 3 male mice in two independent experiments and used for scRNA-seq.

first: Yue

first: Meritxell

last: Rovira


title: Gene expression of A549 cells after cocultured with Trichomonas tenax

city: Tainan City

first: Wei-Chen

last: Lin

address: No.1, University Road

country: Taiwan

institute: National Cheng Kung University

summary: To investigate the gene expression of lung epithelial cells effected by Trichomonas tenax, we chose A549 lung epithelial cells and cocultured with Trichomonas tenax at MOI1.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Trichomonas tenax-treated A549 cells


title: Increased long-distance interactions related to heterotic expression in Arabidopsis hybrids (clf)

city: Beijing

first: Xu

middle: Zhao

last: Gao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

institute: Peking University

summary: In plants, the genomic structure of hybrids changed compared with their parents. However, the effects of genomic structure changes on heterotic expression in hybrids remain elusive. By comparing interspecific hybrids between Col×C24 and their backcross C24×Col in Arabidopsis with Hi-C analysis, we found that the three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents. The compartment strength related to the increased A-B compartment interactions decreased in hybrids. In the boundaries of topologically associated domains (TADs) like regions in hybrids, the values of Interchromosomal Fraction of Interactions (ICF) and Distal-to-Local [log2] (DLR) were higher than or close to the highest value of their parents. While in the hybrids of CURLY LEAF (clf) mutants, which affects the long-distance interactions, the heterosis phenotype disappeared and the ICF and DLR in hybrids were lower than their parents. In addition, compared with the clf mutant, the differential expressed genes located in TAD boundaries and loop regions in the wild type changed more obviously. In the long-distance interaction and the loop region between WT and clf, there were obvious differences in the functional enrichment for DEGs. The genes with cell cycle and mitotic related process were specifically enriched in clf. By analyzing ChIP-seq data, we found that the enrichment of H3K27me3 were higher in the hybrids in WT, which may lead to more long-distance interactions. Our findings may therefore propose a new epigenetic explanation of the heterotic expression in Arabidopsis hybrids and provide new insights into crop breeding and yield increasing.

overall_design: Three replicates for RNA-seq of Col, C24, ColM, and C24M in clf

first: Zhaoxu

first: Yanning

last: Su

first: Hang

last: He


title: Transcriptome dynamics of mutualistic poxvirus infection of tropical fruit fly hosts

city: Hilo

first: Kelsey

last: Coffman

state: HI

address: 64 Nowelo St

department: Tropical Pest Genetics and Molecular Biology Research Unit

institute: USDA-ARS

summary: Parasitoid wasps are one of the most species-rich groups of animals on Earth, due to their ability to successfully develop as parasites of nearly all types of insects. Unlike most known parasitoid wasps that specialize within one or a few host species, Diachasmimorpha longicaudata is a generalist that can survive within multiple genera of tephritid fruit fly hosts, including many globally important pest species. D. longicaudata has therefore been widely released to suppress pest populations as part of biological control efforts in tropical and subtropical agricultural systems. In this study, we investigated the role of a mutualistic poxvirus in shaping the host range of D. longicaudata across three genera of agricultural pest species: two of which are permissive hosts for D. longicaudata parasitism and one that is a nonpermissive host. We found that permissive hosts Ceratitis capitata and Bactrocera dorsalis were highly susceptible to virus infection, displaying rapid virus replication and abundant fly mortality. However, the nonpermissive host Zeugodacus cucurbitae largely overcame virus infection, exhibiting substantially lower mortality and no virus replication. Further investigation of transcriptional dynamics during virus infection demonstrated hindered viral gene expression and limited changes in fly gene expression within the nonpermissive host compared to the permissive species, indicating that the host range of the viral symbiont may dictate the host range of D. longicaudata wasps. These findings also reveal that viral symbiont activity may be a major contributor to the success of D. longicaudata as a generalist parasitoid species and a globally successful biological control agent.

sample_organism:
Ceratitis capitata
Bactrocera dorsalis
Zeugodacus cucurbitae

overall_design: We deep-sequenced total polyadenylated mRNA from 81 whole body fly samples: 3 biological replicate samples were collected at 0, 12, and 24 h post injection for both 1x and 0.1x viral doses, along with a saline-injected mock “dose” in three different fly species.

first: Angela

middle: N

last: Kauwe

first: Gaelen

middle: R

last: Burke

first: Scott

last: Geib


title: Gene expression of NCI-H292 cells after cocultured with Trichomonas tenax

summary: To investigate the gene expression of lung epithelial cells effected by Trichomonas tenax, we chose NCI-H292 lung epithelial cells and cocultured with Trichomonas tenax.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Trichomonas tenax-treated NCI-H292 cells


title: Sterol biosynthesis is regulated by a sophisticated regulatory network involving multiple transcription factors in fungi

first: pengju

last: YU

address: No.1 Beichen West Road

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: Ergosterol, a pivotal constituent of the fungal cell membrane, plays a crucial role in diverse cellular activities. Fungi inherently regulate ergosterol homeostasis, a process traditionally associated with the control of a major transcription factor, like SREBP, activated in response to ergosterol depletion, regardless of which ergosterol biosynthesis step is affected. Contrary to the established paradigm, our investigation demonstrates that the inhibition of ergosterol biosynthesis at specific steps triggers distinct transcriptional responses in erg genes across fungi, including Neurospora crassa, Aspergillus fumigatus, and Fusarium verticillioides. In N. crassa, the targeted responses are orchestrated by several transcription factors that have undergone functional rewiring. Specifically, ERG24 inhibition by amorolfine activates transcription factors SAH-2 and AtrR, resulting in the upregulation of erg24, erg2, erg25 and erg3. Additionally, ERG11 inhibition by azoles activates transcription factor NcSR, leading to the upregulation of erg11 and erg6. Our findings unveil a novel sophisticated regulation model of sterol biosynthesis in fungi which potentially enhances fungal survival in complex environments, thus providing new insights into sterol homeostasis maintenance and a deeper understanding of drug resistance mechanisms in fungi.

overall_design: To thoroughly investigate the targeted regulatory mechanism of ergosterol biosynthesis, we sequenced the transcriptome of N.crassa treated with various sterol synthesis inhibitors. Additionally, we analyzed the gene expression profiles of three key transcription factors—SAH-2 (NCU04731), AtrR (NCU01478), and NcSR (NCU08594)—in knockout strains using data from RNA-seq.

first: Pengju

last: Yu


title: DNA methylation analysis by DREAM of UV irradiated melanocytes

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

type: Methylation profiling by high throughput sequencing

summary: Ultraviolet radiation (UVR) is the greatest risk factor for melanoma development. While the role of UVR in DNA mutagenesis is generally accepted, the role of UVR-induced mutations in melanomagenesis remains controversial.  To understand better how UVR is contributing to melanoma development, we investigated the non-mutational effect of UVR on the epigenome, specifically DNA methylation.  Aberrant DNA methylation changes are a hallmark in melanoma and there are few reports on the effects of UVR on DNA methylation. We exposed melanocytes to UVR and cultured them for one-month to detect heritable and stable changes in DNA methylation. We found both hyper and hypo methylated sites after UVR exposure. While many of these changes occurred outside of promoters and areas of active gene expression, there were changes in promoter DNA methylation changes that correlated with changes in gene expression.  These changes also correlated with those found in melanoma and UVR sensitive sites were prognostic of patient overall survival. Our work shows  UVR-induced DNA methylation changes in melanocytes and may be a novel non-mutational mechanism in which UVR contributes to melanoma development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Melanocyte cells were UV irradiated with a broad spectrum wave band ( UVA & UVB) for a total dos of 175 J/m2. Cells were cultured for one month before performing digital restriction enzyme analysis of methylation (DREAM). Genomic DNA was digested by SmaI which recognizes unmethylated CpG sites in the sequence CCCGGG and cuts leaving a 5'-GGG signature. Next, digestion by XmaI was performed which can cut methylated CpG sites in the sequence CCCGGG and leaves a 5'-CCGGG signature. High throughput sequencing was used to map these sites to the genome. Methylation ratios were calculated as the total number of XmaI signature reads over the total number of reads for each specific site. Methylation ratios were adjusted for differences in restriction enzyme efficiency based on values from spiked in methylation standards.

first: Sarah

last: Preston-Alp

first: Jean-Pierre

last: Issa

first: M

last: Zaidi


title: Synergistic Activity of Adefovir Dipivoxil and Venetoclax to Target the Bioenergetic Metabolism of Acute Myeloid Leukemia

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: The overall outcome of patients with acute myeloid leukemia (AML) remains poor and more effective strategies are urgently needed. Adefovir dipivoxil (ADV) is an oral prodrug of the nucleotide analogue adefovir that inhibits viral DNA polymerase and is a Food and Drug Administration (FDA)-approved drug for the treatment of hepatitis B virus. Preliminary evidence of the anti-leukemic activity of ADV was recently reported in a patient with acute promyelocytic leukemia. Herein we report on the anti-leukemic activity of ADV, alone and in combination with venetoclax (VEN), an oral FDA-approved BCL-2 inhibitor, for the treatment of AML. We observed a significant increase in apoptosis and reduction of cell growth both in AML cell lines and CD34+ blasts, but not in healthy donor CD34+ cells, after exposure to ADV. The combination of ADV and VEN had synergistic anti-leukemic activity and significantly reduced leukemia stem cell (LSC) burden and prolonged survival of AML murine (i.e., MllPTD/WT/Flt3ITD/ITD) and patient derived xenograft (PDX) models, likely by interfering with the bioenergetic metabolism of leukemic blasts and decreasing their apoptotic threshold. Our results provide a rationale for translating this “all oral” regimen to the clinic for treatment of AML patients, especially those requiring low intensity therapy.

overall_design:
To gain insights into the molecular mechanisms underlying the anti-leukemic activity of ADV alone and in combination with VEN, we performed RNA-Seq on AML CD34+ blasts from R/R AML patients (n=6) treated with vehicle, ADV (5 μΜ), VEN (100 nΜ), or ADV+VEN for 24 hours.

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due to patient privacy concern
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first: Bin

last: Zhang

first: Min-Hsuan

last: Chen


title: Increased long-distance interactions related to heterotic expression in Arabidopsis hybrids

first: Xu

overall_design: Three replicates for RNA-seq of Col, C24, ColM, and C24M in WT


title: Effect of stroke on the transcriptome of epithelial cells in the small intestines

city: Melbourne

first: Deanna

middle: S

last: Deveson Lucas

state: Victoria

address: 15 Innovation walk, Monash University, Clayton

country: Australia

institute: Monash University

summary: To investigate the effect of stroke on the transcriptome of intestinal epithelial cells, mice underwent permanent middle cerebral artery occlusion (pMCAO) or sham surgery for 24 hours

overall_design: EpCAM+ epithelial cells from the whole small intestines were isolated via FACS

first: Kathryn

last: Kumar

first: Connie

last: Wong

middle: D

last: Lucas


title: Effect of stroke on the transcriptome of muscularis macrophages in the small intestines

summary: To investigate the effect of stroke on the trasnscriptome of intestinal muscularis macrophages, mice underwent permanent middle cerebral artery occlusion (pMCAO) or sham surgery for 24 hours

overall_design: The whole small intestines were peeled to isolate the muscle layer and CX3CR1-GFP+ muscularis macrophages were collected via FACS

first: Prame

last: Kathryn

first: Wong

last: Connie

first: Deveson

middle: L

last: Deanna


title: Epigenetic states in P. infestans

city: Nanjing

first: Haidong

last: Shu

state: Jiangsu

address: Weigang NO.1

department: Department of Plant Pathology

institute: Nanjing Agricultural University

overall_design: Refer to individual Series


title: Effect of stroke on the transcriptome of lamina propria macrophages in the small intestines

summary: To investigate the effect of stroke on the trasnscriptome of intestinal lamina propria macrophages, mice underwent permanent middle cerebral artery occlusion (pMCAO) or sham surgery for 24 hours

overall_design: The whole small intestines were peeled to isolate the mucosal layer and CX3CR1-GFP+ lamina propia macrophages were collected via FACS

middle: K


title: A genetic mouse model of malignant peripheral nerve sheath tumor with postnatal Nf1 and p53 loss recapitulates the histology and transcriptome of human tumors

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

summary: We established a new genetically engineered mouse (GEM) model of malignant peripheral nerve sheath tumors (MPNST) based on postnatal deletion of a Nf1;Trp53 cis-conditional allele by the tamoxifen-inducible Plp-CreER (NP-Plp). We also generated two Lats1;2 conditional knockout models by using Nestin-Cre (Lats-Nes) and Plp-CreER (Lats-Plp), both of which also develop tumors similar to MPNST (GEM-PNST). To evaluate these models, transcriptome analyses were performed to compare these models and with human MPNST, plexiform neurofibromas (PNF), and neurofibromas (NF).

overall_design: Transcriptome comparison of various mouse models of maligant peripheral nerve sheath tumor (NP-Plp, NPcis, Lats-Nes, and Lats-Plp) and human MPNST, PNF, and NF tumors.

first: Xinwei

last: Cao

first: Akira

last: Inoue


title: ATAC-seq of Phytophthora infestans T30-4 mycelium

summary: Phytophthora infestans, the causal agent of potato late blight, is a devastating plant disease that leads to Irish potato famine and threatens world-wide food security. Despite the genome of P. infestans has provided fundamental resource for studying the aggressiveness of this pandemic pathogen, the epigenomes remain poorly understood. Here, utilizing liquid chromatography-tandem mass spectrometry (LC-MS/MS), we demonstrate post-translational modifications (PTM) at P. infestans core histone H3. The PTMs not only include these prevalent modifications in eukaryotes, and also some novel marks, such as H3K53me2 and H3K122me3. We focused on the trimethylations of H3K4, H3K9 and H3K27 and H3K36, and profiled P. infestans epigenomes employing Native Chromatin Immunoprecipitation followed by sequencing (N-ChIP-seq). In parallel, we mapped P. infestans chromomatin accessibility by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). We found that adaptive genomic compartments display significantly higher levels of H3K9me3 and H3K27me3, and are generally in condense chromatin. Interestingly, we observed that genes encoding virulence factors, such as effectors, are enriched in open chromatin regions that barely have the four histone modifications. With a combination of genomic, epigenomic, transcriptomic strategies, our study illustrates the epigenetic states in P. infestans, which will help to study genomic functions and regulations in this pathogen.

overall_design: Two replicates of  P. infestans T30-4 mycelium stage sample were performed.

first: Han


title: High fat diet ameliorates mitochondrial cardiomyopathy in CHCHD10 mutant mice

status: Public on Mar 23 2024

city: New York

first: Nneka

last: Southwell

state: New York

address: 407 E 64th St Fl 5

department: Brain and Mind Research Institute

institute: Weill Cornell Graduate School

summary: Mutations in CHCHD10, a mitochondrial protein with undefined functions, are associated with autosomal dominant mitochondrial diseases.  Chchd10 knock-in mice harboring a heterozygous S55L mutation (equivalent to human pathogenic S59L) develop a fatal mitochondrial cardiomyopathy caused by CHCHD10 aggregation and proteotoxic mitochondrial integrated stress response (mtISR). In mutant hearts, mtISR is accompanied by a metabolic rewiring characterized by increased reliance on glycolysis rather than fatty acid oxidation. To counteract this metabolic rewiring, heterozygous S55L mice were subjected to chronic high fat diet (HFD) to decrease insulin sensitivity and glucose uptake and enhance fatty acid utilization in the heart. HFD ameliorated the ventricular dysfunction of mutant hearts and significantly extended the survival of mutant female mice affected by severe pregnancy-induced cardiomyopathy. Gene expression profiles confirmed that HFD increased fatty acid utilization and ameliorated cardiomyopathy markers. Importantly, HFD also decreased accumulation of aggregated CHCHD10 in the S55L heart, suggesting activation of quality control mechanisms. Overall, our findings indicate that metabolic therapy can be effective in mitochondrial cardiomyopathies associated with proteotoxic stress.

overall_design:
To investigate how modulating metabolic substrate utilization benefits an animal model of proteotoxic mitochondrial cardiomyopathy, we exposed wild-type (WT) and S55L Het mutant mice to either HFD or a control diet (CD).
We performed heart gene expression analyses from RNA-seq data on four groups: WT CD, Het CD, WT HFD, and Het HFD.

first: Onorina

last: Manzo

first: Sandra

last: Bacman

first: Dazhi

last: Zhao

first: Nicole

last: Sayles

first: Jalia

last: Dash

first: Keigo

last: Fujita

first: Marilena

last: D'Aurelio

first: Annarita

last: Di Lorenzo

first: Giovanni

last: Manfredi

first: Hibiki

last: Kawamata


title: RNA-seq of Phytophthora infestans T30-4 two infection stages

overall_design: Two replicates of P. infestans 2 dpi and 3 dpi stage samples were performed.

last: Chen


title: Characterization of the role of SETDB1 in Muscle stem cells during skeletal muscle regeneration [scRNA-seq]

city: Lyon

first: Pauline

last: GARCIA

address: 8 avenue Rockefeller

country: France

institute: INMG

summary: Muscle regeneration is process where different type of cells are interacting together to ensure a proper muscle regeneration. As Muscle stem cells are the central protagonist of muscle regeneration, we performed single cell RNA-seq to observe the change between the different cell types when SETDB1 is absent in Muscle stem cells.

overall_design: Cells were isolated from the conditional mice model Setdb1-cKO and were isolated by Fluorescence-activated cell sorting (FACS) using Hoeschst and Propidium iodide staining and analyzed using scRNAseq.

first: Fabien

last: Le Grand

last: Garcia


title: Analysis of lncRNA expression in endometriosis infertility, tubal disease infertility and normal subjects

first: Que

last: Xiaohong

state: None Selected

address: No. 24, Bai Lu Road, Siming District

institute: Fujian Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: We found differential expression of lncRNA in the endometrium of patients with endometriosis compared to controls.

overall_design: Our study used the Arraystar Human LncRNA Microarray V4.0, a microarray designed for global profiling of human lncRNA and protein-coding transcripts. Three infertile patients with endometriosis, three patients with tubal causes of infertility and three normal patients were analyzed as controls.

first: Xiaohong

last: Que

first: Lulu

last: Ren

first: Lin

last: Yang

first: Lemeng

last: Wang

first: Junzui

last: Li

first: Rongfeng

last: Wu

first: Qionghua


title: ChIP-seq of Phytophthora infestans T30-4 mycelium

first: Haidong

last: Shu

overall_design: Two replicates of four histone methylations (H3K4me3, H3K9me3, H3K27me3, H3K36me3) were performed, and non-enrich input samples were also seuqneced.

first: Han


title: Effect of glycolysis on hepatic stellate cell transcriptome

city: Rochester

first: Alexander

middle: Quinn

last: Wixom

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary:
To investigate the role of glycolysis in the regulation of HSC transcriptome, we treated our cells with or without glucose, to block or induce glycolysis, respectively.
We then performed gene expression profiling analysis using data obtained from RNA-seq of all the conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HSCs treated with or without glucose.

first: Enis

last: Kostallari

first: Shalil

last: Khanal


title: Investigation of circular RNA expression profiles in ultrasound-guided radiofrequency ablation-treated transplanted tumor models of human liver cancer

first: Shuang

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

summary: Following RFA treatment, 76 DE-circRNAs were detected (|fold changes |>1.5, P-value <0.05), among which 21 were up-regulated and 55 were down-regulated.

overall_design: We established a subcutaneous tumor transplantation model in 8 immunodeficient mice (Balb/c nude mice), of which 4 mice received incomplete ultrasound-guided RFA treatment and 4 mice received no treatment and were designated as the control group. Using Agilent Scanner G2505C to analyze the circRNA expression profile and its change in the HepG2-transplanted nude mice treated with incomplete RFA .

first: Dongyue

last: Wen

first: J

first: P

last: Lin

last: Pang

first: G

first: Y

last: He

first: H


title: Characterization of the role of SETDB1 in Muscle stem cells during skeletal muscle regeneration [ChIP-seq]

first: Pauline

last: GARCIA

summary: We are characterizing the role of an H3K9 histone methyltransferase. As these proteins have the capacity to modulate chromatin, we investigate the chromatin modulation using H3K9Me3 Chip-seq.

overall_design: Muscle Stem Cells were isolated from the conditional mice model Setdb1-cKO and were isolated by Magnetic-activated cell sorting (MACS) and cultured in vitro. We treated the cells with either Ethanol or 4-hydroxytamoxifen in order to induce Setdb1 deletion and after 72 hours of treatment performed the H3K9Me3 Chip-Seq.

first: Fabien

last: Le Grand

first: Petit

last: Valentin

first: Ait-Si-Ali

last: Slimane


title: Effect of Hyperoxia Exposure on the Neonatal Lungs of WT C57BL6 and PTAFR KO C57BL6 mice

city: Birmingham

first: Tamas

last: Jilling

state: AL

address: UAB Station

department: Department of Pediatrics

institute: The University of Alabama at Birmingham

summary: To assess the role of signaling via platelet-activating factor (PAF) in a murine model of BPD, we used WT and PTAFR KO mice on a C57BL6 background

overall_design: Neonatal mice were exposed to hyperoxia (FiO2=85%) and normoxia (FiO2=21%) from postanatl day 3 (p3) to p14

first: Namasivayam

last: Ambalavanan

first: Jegen

last: Kandasamy

first: Aaron

middle: J

last: Yee


title: Characterization of the role of SETDB1 in Muscle stem cells during skeletal muscle regeneration [ATAC-seq]

summary:
We are characterizing the rol of an H3K9 histone methyltransferase. As these proteins have the capacity to modulate chromatin, we investigate the chromatin modulation using ATAC-seq
Muscle Stem Cells were isolated from the conditional mice model Setdb1-cKO and were isolated by Magnetic-activated cell sorting (MACS) and cultured in vitro

overall_design: Comparative gene expression profiling analysis of ATAC-seq data for muscle stem cells and muscle stem cells deleted for SETDB1

last: Garcia


title: Transcriptomic characterization of in vitro human iPSC-derived motor neuron systems for the exploration of cell autonomous mechanisms and modifiers of TDP-43 perturbation associated neurotoxicity

city: Cambridge

first: Kristina

last: Holton

state: MA

address: 7 Divinity Ave

department: HSCRB

institute: Harvard University

summary: Transactive Response DNA-binding protein 43 (TDP-43) is a multifunctional nuclear protein ubiquitously expressed in all tissues. Although it is primarily nuclear, Amyotrophic Lateral Sclerosis (ALS) patients frequently present with cytoplasmic aggregates of TDP-43 in motor neurons on post-mortem examination. Although only about 5% of all ALS patients have a TARDBP mutation (Ghasemi and Brown 2018; Ingre et al. 2015), which is known to cause these insoluble cytoplasmic aggregates, 97% of ALS patients will develop cytoplasmic, insoluble TDP-43 aggregates regardless of whether they have a mutation in TARDBP or not (Ling et al. 2013). Overexpression of wild-type TDP-43 has previously been shown to be a valid model of inducing neurotoxicity as well as a limited amount of cytoplasmic re-localization and aggregation characteristic of ALS (Elden et al. 2010; Wils et al. 2010). In the search for modifiers of toxicity as conferred by TDP-43 overexpression in these models, knockout of Ataxin-2 (ATXN2) was proposed as a protective intervention in the context of TDP-43 perturbation in non-human model systems (Elden et al. 2010, Becker et al. 2017). This promising finding had not previously been validated in a human motor neuron system, nor had a thorough investigation been conducted to determine the mechanism of neuroprotection that ATXN2 knockout employs to drive the therapeutic effect. This sequencing study examines both ATXN2 intact and ATXN2 knockout motor neurons in the context of TDP-43 perturbation to explore global transcriptomic changes that arise from these changes in cellular state that are associated with progression of ALS (ATXN2 intact) and what pathways could be implicated in protection from ALS-associated neurodegeneration (ATXN2 Knockout).

overall_design:
To investiage global transcriptomic changes resulting from TDP-43 perturbation via overexpression, we performed bulk RNA sequencing on isogenic motor neuron lines with and without induced TDP-43 perturbation at the same time point. Samples compared are an Empty Vector Control and a YFP expression only control as negative controls, wild-type TDP-43 overexpression, and cytoplasmically locked TDP-43 expression (TDP-43ΔNLS). The cytoplasmic TDP-43 condition was included because it is represenative of the end physiological state of ALS patients. There are four biological replicates of each sample present in this study.
This study also examines the role of Ataxin-2 (ATXN2), a proposed modifier of TDP-43 associated neurodegeneration, by including isogenic motor neuron lines (from the same background as the above mentioned TDP-43 perturbed lines) harboring Ataxin-2 knockout (conferred via CRISPR). This allows for comparison and discovery of factors that are exclusively modulated when Ataxin-2 is knocked out and whether those have an effect on the set of factors perturbed when TDP-43 is overexpressed or cytoplasmically constrained. Ataxin-2 knockout samples are available in this data set also in the Empty Vector, YFP only, TDP-43 overexpression, and TDP-43ΔNLS conditions. These samples are also presented as the results of four biological replicates each.

first: Stanley

last: Gill

first: Kevin

last: Eggan

first: Lee

last: Rubin


title: The effect of Aryl hydrocarbon receptor (AHR) inhibitor CH-223191 on differentiation of human colon organoids

status: Public on Mar 22 2024

city: London

first: Brigitta

last: Stockinger

address: 1 Midland Road

institute: The Francis Crick Institute

summary: To investigate the effect of AHR deficiency on organoid differentiation or in stem cell state we performed RNA-seq of human colon organoids treated with CH-223191 or DMSO  in stem cell conditions or during differentiation

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of 3 different control patient organoid lines at day 4 of differentiation or in stem cell state.

first: Anke

last: Liebert

first: Michael

last: Shapiro


title: Olig2 targetome in SHH subgroup of medulloblastoma

city: Toronto

first: Chi-chung

last: Hui

state: Ontario

address: 686 Bay Street. Room 16-9712

department: Developmental & Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

summary: Several basic helix-loop-helix (bHLH) transcription factors are upregulated in Sonic Hedgehog subgroup of medulloblastoma (SHH MB). Olig2, a neural bHLH transcription factor known to regulate differentiation of neural cell populations, is broadly expressed in mouse models of SHH MB. ChIP-Seq of Olig2 revealed its binding to a large number of sites near genes known to promote SHH MB tumorigenesis, suggesting a potential role for Olig2 in regulating transcriptional programme of MB.

overall_design: Examination of Olig2-bound DNA in P13 Sufu;Spop double knockout and SmoM2 overexpression medulloblastoma in mice

first: Wen-Chi

last: Yin


title: Single-cell Multi-omics Analysis of Human Testicular Germ Cell Tumor Reveals its Molecular Features and Microenvironment II

city: Bei jing

first: Xiaojian

last: Lu

state: Bei jing

address: No.3, Datusi Road, Chaoyang District, Beijing

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology，Chinese Academy of Sciences

summary: Seminoma is the most common malignant solid tumor in 14 to 44 year-old men. However, its molecular features and tumor microenvironment (TME) is largely unexplored. Here, we performed a series of studies via genomics profiling (single cell multi-omics and spatial transcriptomics) and functional examination using seminoma samples and a seminoma cell line. We identified key gene expression programs shared between seminoma and primordial germ cells, and further characterized the functions of TFAP2C in promoting tumor invasion and migration. We also identified 15 immune cell subtypes in TME, and found that subtypes with exhaustion features were located closer to the tumor region through combined spatial transcriptome analysis. Furthermore, we identified key pathways and genes that may facilitate seminoma breaking through the seminiferous tubules. These findings advanced our knowledge of seminoma tumorigenesis and produced a multi-omics atlas of in situ human seminoma microenvironment, which could help discover potential therapy targets for seminoma.

overall_design: Expression profiling by high throughput sequencing

first: Xichen

last: Nie

first: Hao

last: Bo

first: Jingtao

last: Guo


title: Differential expression of Pseudomonas fluorescens SBW25 during growth using glucose or MHPP as carbon sources

city: Richland

first: Joshua

last: Elmore

state: WA

address: 902 Battelle Blvd

institute: PNNL

summary: Identify genes involved in catabolism of the compound Methyl 3-(4-hydroxyphenyl)propionate

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Pseudomonas fluorescens SBW25 grown on different carbon sources

first: Andrew

last: Wilson


title: Characterization of the role of SETDB1 in Muscle stem cells during skeletal muscle regeneration [RNA-seq]

first: Pauline

last: GARCIA

summary:
Muscle regeneration is process where different type of cells are interacting together to ensure a proper muscle regeneration. As Muscle stem cells are the central protagonist of muscle regeneration, we performed single cell RNA-seq to observe the change between the different cell types when SETDB1 is absent in Muscle stem cells.
Muscle Stem Cells were isolated from the conditional mice model Setdb1-cKO and were isolated by Fluorescence-activated cell sorting (FACS).

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for muscle stem cells and muscle stem cells deleted for SETDB1

Please note that the processed data columns are associated with each sample as below:
sample title processed data column
Control_OIL_biol rep 1 OSETDB1OIL273_S12
Control_OIL_biol rep 2 SETDB1OIL274_S8
Control_OIL_biol rep 3 SETDB1OIL276_S11
Setdb1_KO_TAM_biol rep1 SETDB1TAMO263_S7
Setdb1_KO_TAM_biol rep2 SETDB1TAMO265_S9
Setdb1_KO_TAM_biol rep3 SETDB1TAMO275_S10

first: Fabien

last: Le Grand

first: Giordani

last: Lorenzo


title: Peripheral immunomodulatory effects of Apolipoprotein E4 on Alzheimer's disease - Immune Enrichment

city: Chicago

first: David

last: Gate

state: IL

address: 303 E Chicago Ave, Chicago, IL 60611

department: Neurology

institute: Northwestern University

summary: Apolipoprotein E (APOE) is a lipid and cholesterol transport molecule known to influence Alzheimer's disease (AD) risk in an isoform-specific manner. In particular, the APOE E4 allele is the largest genetic risk factor for late-onset sporadic AD. Our recent findings uncovered activated, clonally expanded T cells in AD cerebrospinal fluid (CSF). This T cell phenotype occurred concomitantly with altered expression of APOE in CSF monocytes. Yet, whether APOE variants differentially affect peripheral immunity systems remains unknown. In this study, we performed targeted immune profiling using single-cell epigenetic and transcriptomic analysis of peripheral blood mononuclear cells (PBMC). We analyzed 55 age-matched healthy control (HC) and AD patients with equal distribution of APOE E3/E3, E3/E4, and E4/E4 genotypes. We reveal dysregulation in monocytes and clonally expanded T cells that are distinct to AD patients carrying the APOE E4/E4 genotype. Additionally, we find APOE isoform-dependent chromatin accessibility differences that correspond to RNA expression changes. Cumulatively, these results uncover APOE isoform-dependent changes to peripheral immunity in AD.

overall_design: Peripheral blood mononuclear cells from healthy control and Alzheimer's disease patients, matched for age, sex, and APOE genotype. Samples were thawed, FACS sorted for live cells, and profiled using Immune Enrichment

first: Abhirami

last: Ramakrishnan

first: Natalie

last: Piehl


title: Inflammation-dependent differentiation of two distinct regulatory T cell populations in the visceral adipose tissue shapes systemic metabolism [RNA-seq II]

city: Clayton

first: Wei

last: Shi

address: 15 Innovation Walk

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

summary: Visceral adipose tissue (VAT) is an endocrine organ critical for energy storage and metabolic homeostasis. Its function, at least in part, is controlled by immune cells, including Foxp3+ regulatory T (Treg) cells, which restrain VAT inflammation and glucose intolerance. Here we uncover that the VAT harbours two distinct Treg cell populations, prototypical ST2+ Treg cells, that are enriched in males and depend on the cytokine IL-33 and the transcription factor PPAR and a previously uncharacterized population of VAT Treg cells that express the chemokine receptor CXCR3+, are enriched in females and depend on the transcription factor T-bet. We further show that the transcription factor GATA3 promoted differentiation of ST2+ VAT Treg cells and together with PPAR and IL-33 repressed the differentiation of CXCR3+ Treg cells. CXCR3+ VAT Treg cells developed from naïve Treg cells in a cytokine IFN- dependent manner. Finally, we demonstrate that ST2+ Treg cells promoted glucose tolerance, while CXCR3+ Treg cells limited VAT inflammation in a sex specific manner. This study for the first time establishes how inflammation determines the developmental trajectories of two functionally and molecularly distinct Treg cell types in the VAT.

overall_design: Bulk RNA sequencing of  VAT Treg cells obtained from male and female wildtype, Gata3KO and Tbet KO mice. In the KO mice, Gata3 and Tbet transcription factors are ablated in a Treg specific manner using Foxp3Cre

first: Ajithkumar

last: Vasanthakumar

first: Yang

last: Liao

last: Chisanga

first: Axel

last: Kallies


title: Recognition of copy-back defective interfering rabies virus genomes by RIG-I triggers efficient immune response against vaccine strains

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: Using next-generation sequencing (NGS) combined with bioinformatics tools, we characterized two major 5’copy-back defective interfering (5’cb DI) genomes generated during SAD replication. Furthermore, we identified a specific interaction of 5’cb DI genomes and RIG-I that correlated with a high stimulation of the type I IFN signaling

sample_organism:
Homo sapiens
Lyssavirus rabies
Rabies virus SAD B19

overall_design: Three biological replicates of RABV THA and SAD strains infected (MOI 0.5) HEK 293 ST_RLR cells were performed.

first: Wahiba

last: Aouadi

first: Valérie

last: Najburg

first: Hugo

last: Varet

first: Lauriane

last: Kergoat

first: Frédéric

last: Tangy

first: Florence

last: Larrous

first: Anastassia

middle: V

last: Komarova

first: Hervé

last: Bourhy


title: Characterization of the role of SETDB1 in Muscle stem cells during skeletal muscle regeneration

first: Pauline

last: GARCIA

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

overall_design: Refer to individual Series


title: Synovial Macrophage Activation Profiles in Experimental Knee Osteoarthritis

first: Tom

last: Appleton

address: 1151 Richmond Street

institute: Western University

summary: To investigate differences in gene expression of synovial macrophages in experimental rat knee post traumatic osteoarthritis.

overall_design:
12-week-old Sprague Dawley rats underwent a surgical arthrotomy and induction of post traumatic osteoarthritis via transection of the medial meniscotibial ligament and anterior cruciate ligament or sham surgery consisting of an arthrotomy but no transections. 4- or 12-weeks after surgery, synovial tissue was dissected and enzymatically digested into a single cell suspension. Synovial macrophages were sorted with CD11b/c magnetic beads and isolated using magnet assisted cell sorting technology.
biological replicates: n=40 rats underwent synovial arthrotomy and induction of PTOA or sham surgery (n=20 per group) for the 4-week endpoint. N=30 rats underwent synovial arthrotomy and induction of PTOA or sham surgery (n-15 per group) for the 12-week endpoint. To facilitate adequate RNA quantity post cell isolation, synovial tissue (n=4 rats; 4-week, and n=3 rats; 12-week) were pooled into individual enzymatic digestions. 5 pooled samples per condition (PTOA or sham) at 4-weeks post surgery and 4 pooled samples (PTOA or sham) at 12-weeks post surgery were sequenced and used as comparator groups for downstream sequencing analysis.

first: Garth

last: Blackler

first: Yue

last: Lai-Zhao

first: Joseph

last: Klapak

first: Holly

middle: T

last: Philpott

first: Kyle

last: Pitchers

first: Andrew

last: Maher

first: Benoit

last: Fiset

first: Logan

middle: A

last: Walsh

first: Elizabeth

last: Gillies

first: C


title: Inflammation-dependent differentiation of two distinct regulatory T cell populations in the visceral adipose tissue shapes systemic metabolism [RNA-seq III]

first: Wei

last: Shi

institute: Monash University

overall_design: Bulk RNA sequencing of female and male VAT Dendritic cells and macrophages and total VAT tissue from male and female mice fed HFD or normal diet.

first: Ajithkumar

last: Vasanthakumar

first: David

last: Chisanga

first: Yang

last: Liao

first: Axel

last: Kallies


title: O-GlcNAcylation governs astrocytes reactivation and involves in Alzheimer’s disease

city: hangzhou

first: wenzheng

last: qu

address: Kaixuan Road

institute: Zhejiang University

summary: To reveal the mechanisms that Ogt controls inflammatory response of astrocytes, we first performed RNA-seq with Ctrl and Ogt cKO astrocytes isolated from the brains of adult mice. Given the inflammation in the brain of Alzheimer’s disease, we next performed RNA-seq with astrocytes isolated from the brains of adult Ctrl and 5X APP Alzheimer’s mice model (AD), and Aβ treated astrocytes, respectively. Taken together, these findings suggest that differentially expressed genes shared between cKO astrocytes, AD astrocytes and Aβ-treated astrocytes are related with inflammation.

overall_design: Two replicates of mRNA in astrocytes isolated from the brains of  adult Ctrl and Ogt cKO mice, 5-month-old Ctrl and 5X APP Alzheimer’s mice model (AD), Ctrl and Aβ treated adult astrocytes, respectively

first: Xiaoxue

last: Dong

first: Wenzheng

last: Qu

first: Jinyu

last: Zhang

first: Xuekun

last: Li


title: RNA sequencing of maternal plasma

city: shenyang

first: Shanshan

last: Jia

state: China

address: Shengjing Hospital, China Medical University Street #36, SanHao,  HePing Distric

institute: Shengjing Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA sequency was performed on maternal plasma from pregnant women carrying nsCLP foetuses or healthy foetuses. The aim of this study is to explore potential promising biomarkers for diagnosing nsCLP.

overall_design: 5 pregnant women carrying nsCLP foetuses (nsCLP group) and 5 pregnant women carrying normal foetuses (control group) were included in this study.

first: Zhengwei

last: Yuan


title: Hepatic loss-of-function phenotype in the peripheral benzodiazepine receptor (PBR) also known as the mitochondrial translocator protein (TSPO), knockout mice (TSPO-/- mice).

city: Ithaca

first: Vimal

last: Selvaraj

state: NY

address: 204 Morrison Hall

department: Animal Sciences

institute: Cornell University

summary: This study was intended to dissect the role of PBR/TSPO in hepatic metabolism. As it was determined that the purported role for PBR/TSPO in steroidogenesis was a misconception, the precise function and regulation of this therapeutic target remains a mystery. Via examining gene expression changes associated with PBR/TSPO deficiency in the liver, these results evaluate specific phenotypic perturbations linked to PBR/TSPO function.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from liver samples of Tspo fl/fl and Tspo -/- mice.

first: Lan

last: Tu

first: Prasanthi

last: Koganti


title: The Role of MAP3K1 in the Development of the Female Reproductive Tracts

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: University of Cincinnati, 160 Panzeca Way

institute: University of Cincinnati

summary: Mitogen-Activated Protein 3 Kinase 1 (MAP3K1) is a dynamic signaling molecule with myriad cell-type specific functions not yet fully understood. Here we describe a role of MAP3K1 in the development of female reproductive tract (FRT). MAP3K1 kinase domain deficient females (Map3k1ΔKD) exhibit imperforate vagina, labor failure and sterility. The defects correspond to shunted Müllerian duct (MD), precursor of the FRT, in embryos, and contorted caudal vagina and abrogated vagina-urogenital sinus fusion in newborns. Although MAP3K1 acts through JNK and ERK to activate WNT in epithelial cells, it is dispensable for epithelial but crucial for mesenchymal WNT activity at the caudal embryonic MD in vivo. Moreover, conditional media derived from MAP3K1-compentent, but not -deficient, epithelial cells activate TCF-luciferase reporter in fibroblasts, suggesting MAP3K1 induces secreted activators from epithelial cells to activate WNT in fibroblasts. Correspondingly, the expression of Wnt7b is high in wild type, but low in Map3k1 knockout caudal MD epithelium and MAP3K1-deficient keratinocytes. Our data reveal a temporal-spatial paracrine MAP3K1-WNT crosstalk in the regulation of caudal MD elongation and FRT development.

overall_design: Three independent samples of human epithelial HaCaT cells genetically-modified to have increased (SAM) MAP3K1 expression were compared to three independent samples of human epithelial HaCaT cells genetically-modified to have  decreased (shRNA) MAP3K1 expression.

first: Ying

last: Xia

first: Eiki

last: Kimura

first: Jingjing

last: Wang


title: The predictive biomarkers of TNFα-blocking agent responsiveness are specific for adalimumab and etanercept

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

institute: INSERM U905

summary: The objective of this study was to identify specific gene expression profiles able to predict the response of rheumatoid arthritis patients treated with methotrexate (MTX)/adalimumab (ADA) or MTX/etanercept (ETA). Twenty RA patients were received subcutaneously Adalimumab (40 mg each other week) and eleven RA patients were received Etanercept (50 mg per week). The drug efficacy was evaluated with the DAS28 score after 3 months of treatment according to the EULAR response criteria. A blood sample was carried out in patients just before the first injection of treatment in order to isolate peripheral blood mononuclear cells (PBMC) and extract total RNA.

overall_design: Two color experiments : patient(Cy5)/Control pool (Cy3).

first: Thierry

last: Lequerre


title: The CAP1 represses MRTF-SRF–dependent gene expression in the mouse cerebral cortex by an actin-dependent mechanism

city: Marburg

first: Sharof

last: Khudayberdiev

state: Hessen

address: Karl-von-Frisch Str 2

country: Germany

institute: Inst. Phys. Chem. Marburg University

summary: Serum response factor (SRF) is a ubiquitously expressed transcription factor that is essential for brain development and function. SRF activity is controlled by two competing classes of coactivators, myocardin-related transcription factors (MRTF) and ternary complex factors, which introduce specificity into gene expression programs. Here, we explored the MRTF-mediated regulatory mechanism in mouse cortical neurons. Using gene-reporter assays and pharmacological and genetic approaches in isolated mouse cortical neurons, we found that cyclase-associated protein 1 (CAP1) repressed neuronal MRTF-SRF activity. CAP1 promoted cytosolic retention of MRTF by controlling cytosolic G-actin levels that required its helical folded domain and its CARP domain. This function of CAP1 was not redundant with that of its homolog CAP2 and was independent of cofilin1 and actin-depolymerizing factor. Deep RNA sequencing and mass spectrometry in cerebral cortex lysates from CAP1 knockout (CAP1-KO) mice supported the in vivo relevance for the CAP1-actin-MRTF-SRF signaling axis. Our study identified CAP1 as a repressor of neuronal gene expression and led to the identification of likely MRTF-SRF target genes in the developing cerebral cortex, whose dysregulation may contribute to impaired formation of neuronal networks in CAP1-KO mice. Together with our previous studies that implicated CAP1 in actin dynamics in axonal growth cones or excitatory synapses, we established CAP1 as a crucial actin regulator in neurons.

overall_design:
To investigate the role of actin binding protein CAP1 in regulation of gene expression in neurons
In order to identify the list of differentially expressed genes in cerebral cortex lysates from E18.5 brain-specific CAP1-KO (Cap1flx/flx,Nestin-CRE) and CAP1-CTR (Cap1 flx/flx) mice the total RNA was extracted.

first: Kerstin

last: Weiss

first: Anika

last: Heinze

first: Dalila

last: Colombaretti

first: Nathan

last: Trausch

first: Uwe

last: Linne

first: Marco

middle: B

last: Rust


title: Hippo-YAP/TAZ signaling coordinates adipose plasticity and energy balance by uncoupling leptin expression from fat mass

status: Public on Mar 21 2024

city: Daejeon

first: Sungwoo

last: Choi

address: 291 Daehak-ro

country: South Korea

institute: KAIST

summary: Adipose tissues serve as an energy reservoir and endocrine organ, yet the mechanisms that coordinate these functions remain elusive. Here, we show that transcriptional coregulators YAP and TAZ mediate the crosstalk between fat mass and leptin levels to maintain metabolic homeostasis. Activating YAP/TAZ in adipocytes by Lats1 and Lats2 deletion results in a profound reduction in fat mass by converting mature adipocytes into delipidated progenitor-like cells. Surprisingly, Lats1/2 knockout mice did not exhibit lipodystrophy-related metabolic dysfunction, attributed to a paradoxical increase in circulating leptin levels. Mechanistically, YAP/TAZ-TEAD signaling upregulates leptin expression by directly binding an upstream enhancer site of the leptin gene. We further show that YAP/TAZ activity is linked to, and functionally required for, leptin regulation during fasting and refeeding. These results suggest that adipocyte Hippo-YAP/TAZ plays an essential role in coordinating adipose storage capacity and systemic energy balance through dual control of adipocyte plasticity and leptin gene transcription.

overall_design: SVF were isolated from the iWAT of 4-week-old Lats1fl/fl; Lats2fl/fl; Rosa-LSL-tdTomato (control, Con) and Adipoq-Cre; Lats1fl/fl; Lats2fl/fl; Rosa-LSL-tdTomato (AKO) mice. SVF cells were  flow-sorted to exclude CD45 positive leukocytes. Singlets were selected based on gating. CD45-& tdT+ cells from AKO SVF and CD45-& tdT- cells from Con SVF were sorted for single-cell RNA-sequencing.

first: Ju-Gyeong

last: Kang

first: Myungsun

last: Park

first: Haeyon

last: Jeon

first: Young

middle: H

last: Kim

first: Jong-Eun

first: Jae

last: Suh

first: Dae-Sik

last: Lim


title: AMAR-seq: automated multimodal sequencing of DNA methylation, chromatin accessibility, and RNA expression with single-cell resolution

city: Xiamen

first: Xi

last: Zeng

address: No. 422, Siming South Road

institute: Xiamen University

summary: Parallel single-cell multimodal sequencing is the most intuitive and precise tool for cellular status research. In this study, we propose AMAR-seq to automate methylation, chromatin accessibility and RNA sequencing on a chip with single-cell precision. We validated the accuracy and robustness of AMAR-seq in comparison with standard single-omics methods. The high gene detection rate and genome coverage of AMAR-seq enabled us to establish a genome-wide gene expression regulatory atlas, implement single-cell copy number variation analysis, and construct a single-gene, single-base resolution gene expression, DNA methylation, and chromatin accessibility landscape. Applying AMAR-seq to investigate the process of mouse embryonic stem cell differentiation, we revealed the dynamic coupling of the epigenome and transcriptome which may contribute to the unravelling of the molecular mechanisms of early embryonic development. Collectively, these results illustrate that the employment of AMAR-seq can deeply and accurately establish single-cell multi-omics regulatory networks in a single-cell context in a cost-efficient and automated manner, which paves the way for incisive dissection of complex life procedures.

overall_design:
In total, 19 K562 cell line samples and 24 mESC samples were analyzed. We examined genome-wide DNA methylation, gene expression and chromatin accessibility profiles of 12 K562 single cells, two bulk K562 samples and 24 mESC single cells. We analysed DNA methylome of 3 K562 single cells by scBS-seq and transcriptome of 4 K562 single cells with smart-seq2 workflow, respectively. Mouse embryonic stem cells were grown on 6-cm culture dishes with MEF feeder cells and cultured in a complete medium supplemented with leukemia inhibitory factor (LIF) to prevent differentiation. To induce undirectional differentiation, mESCs were dissociated and replated onto 0.1% gelatin-coated dishes, and cultured without LIF in a feeder-free manner. We collected mESCs at day 0 and differentiated cells at day 3, day 6 day 9.
For library construction methods:
NOMe-seq (http://www.genome.org/cgi/doi/10.1101/gr.143008.112)
scNOMe-seq (https://elifesciences.org/articles/23203)

first: Xiaoping

last: Yang

first: Zhixing

last: Zhong

first: Zhi

last: Zhu

first: Jin

last: Li

first: Jia

last: Song

first: Chaoyong


title: Expression profile of shMCT-1 in 4T1 metastatic murine triple-negative breast cancer (TNBC) cell lines in response to anti-IL6R immunotherapy

city: Zhunan

first: Hsin-Ling

last: Hsu

state: Miaoli

address: 35 Keyan Road

department: Institute of Molecular and Genomic Medicine

institute: National Health Research Institutes

summary: Malignant T-cell amplified sequence (MCT-1 or MCTS1) is an oncoprotein that regulates translation re-initiation, ribosomal recycling, and tumorigenicity. Given that MCT-1 amplifies interleukin-6 (IL-6) trans-signaling by elevating interaction between interleukin-6 receptor (IL-6R) and glycoprotein 130 (gp130), we aimed to dissect whether targeting IL-6R alters transcriptional profile of TNBC cells with different MCT-1 background. Through RNA-seq, we have characterized that anti-IL6R immunotherapy suppressed genes involved in cell proliferation and metastatic cascades but enriched genes associated in cell adhesion in 4T1 murine TNBC cells with shMCT-1.

overall_design: Samples include two independent biological replicates of the scramble cells and MCT-1 silencing (shMCT-1) cells treated with anti-IL6R


title: ALK upregulates POSTN and WNT signaling to drive neuroblastoma

city: Los Angeles

first: Miller

last: Huang

state: CA

address: 4650 Sunset Blvd, #57

department: Pediatrics

institute: Children's Hospital Los Angeles

summary: The goal of this study is to identify the mechanism for how ALK promotes tumorigenesis in neuroblastoma.  We developed a human stem cell model of neuroblastoma and generated isogenic tumors using MYCN and MYCN/ALK.  RNAseq analysis of both tumors revealed an enrichment in focal adhesion signaling and allowed us to find POSTN as a key mediator of ALK-mediated tumor growth.

overall_design: The samples are human stem cell derived trunk neural crest cells that were implanted into mice and developed into tumors. We have samples of WTC11 MYCN, WTC11 MYCN/ALK and 1323 MYCN tumors. The data provided is RNA-seq analysis of each of the samples in triplicate

first: Alvin

last: Farrel

first: John

middle: M

last: Maris

first: William

last: Weiss


title: DNA methylation alterations across time and space in paediatric brain tumours

city: Gothenburg

first: Helena

last: Carén

address: Medicinaregatan 1F

country: Sweden

institute: University of Gothenburg

type: Methylation profiling by genome tiling array

summary: DNA methylation is increasingly used for tumour classification and has expanded upon the > 100 currently known brain tumour entities. A correct diagnosis is the basis for suitable treatment for patients with brain tumours, which is the leading cause of cancer-related death in children. DNA methylation profiling is required for diagnosis of certain tumours, and used clinically for paediatric brain tumours in several countries. We therefore evaluated if the methylation-based classification is robust in different locations of the same tumour, and determined how the methylation pattern changed over time to relapse.

overall_design: We sampled 3-7 spatially separated biopsies per patient, and collected samples from paired primary and relapse brain tumours from children. Altogether, 121 samples from 46 paediatric patients with brain tumours were profiled with EPIC methylation arrays.

first: Anna

last: Wenger

first: Sandra

last: Ferreyra Vega


title: Pax37 gene function in Oikopleura dioica supports a neuroepithelial-like origin for its house-making Fol territory

city: Bergen

first: Simon

last: Henriet

address: Thormøhlensgate 55

country: Norway

institute: University of Bergen

summary: Larvacean tunicates feature a spectacular innovation not seen in other animals - the trunk oikoplastic epithelium (OE). This epithelium produces a house, a large and complex extracellular structure used for filtering and concentrating food particles. Previously we identified several homeobox transcription factors expressed during early OE patterning. Among these are two Pax3/7 duplicates that we named Pax37A and Pax37B. The vertebrate homologs, PAX3 and PAX7 are involved in developmental processes related to neural crest and muscles. In the ascidian tunicate Ciona intestinalis, Pax3/7 is playing a role in the development of cells deriving from the neural plate border, including trunk epidermal sensory neurons and tail nerve cord neurons, as well as in the neural tube closure. Here we have investigated the roles of Oikopleura dioica Pax37A and Pax37B in the development of the OE, using CRISPR-Cas9 mutant lines and analyzing scRNA-seq data from wild-type animals that we compared with scRNA-seq data from C. intestinalis. We revealed that Pax37B but not Pax37A is essential for the differentiation of cell fields that produce the food concentrating filter of the house: the anterior Fol, giant Fol and Nasse cells. Trajectory analysis supports that these cells have a neuroepithelial-like transcriptional signature. We propose that the highly specialized secretory epithelial cells of the Fol region either maintained or evolved neuroepithelial features such as “glue” secreting collocytes of ascidians. Their development seems to be controlled by a fragmented GRN that also operates in ascidian epidermal neurons.

overall_design: To reveal downstream genes that are regulated by Pax37b, we compared the transcriptomes of Pax37b-/- individuals to wild-type transcriptomes

first: David

last: Lagman

first: Anthony

last: Leon

first: Cieminska

last: Nadia

first: Wei

last: Deng

first: Marios

last: Chatzigeorgiou

first: Daniel

last: Chourrout


title: Genome-wide chromatin accessibility (ATAC-Seq) of primary murine nephron progenitor cells.

first: Alison

middle: Jarmas

last: Perl

state: Ohio

address: 3333 Burnet Ave.

institute: CCHMC

summary: This series contains ATAC-Seq data generated from mouse nephron progenitor cells (NPCs) isolated from different strains/mutants and developmental timepoints as indicated.

overall_design: Evaluation of genome-wide chromatin accessibility in freshly-isolated murine nephron progenitor cells from different developmental timepoints and strains/mutants with varying nephron endowments.

first: Praneet

last: Chaturvedi

first: Raphael

last: Kopan


title: Activation of GFRAL+ Neurons Induces Hypothermia and Glucoregulatory Responses Associated with Nausea and Torpor

first: Johan

last: Ruud

address: Medicinaregatan 11

summary: GFRAL-expressing neurons actuate aversion and nausea, are targets for obesity treatment and may mediate metformin effects by long-term GDF15-GFRAL agonism. If GFRAL+ neurons acutely regulate glucose and energy homeostasis is however underexplored. Here, we report that cell-specific activation of GFRAL+ neurons using a variety of techniques causes a torpor-like state, including hypothermia, the release of stress hormones, a shift from glucose to lipid oxidation, and impaired insulin sensitivity, glucose tolerance and skeletal muscle glucose uptake but augmented glucose uptake in visceral fat. Metabolomic analysis of blood and transcriptomics of muscle and fat indicate alterations in ketogenesis, insulin signaling, adipose tissue differentiation and mitogenesis, or energy fluxes. Our findings reveal that acute GFRAL+ neuron activation induces endocrine and gluco- and thermoregulatory responses associated with nausea and torpor. While chronic activation of GFRAL signaling promotes weight loss in obesity, these results show that acute activation of GFRAL+ neurons causes hypothermia and hyperglycemia.

overall_design: To investigate the impact of chemogenetic GFRAL+ neuron activation on gene expression in tissues that showed lowered (quadriceps) or increased (perigonadal white adipose tissue; pgWAT) glucose uptake, we performed RNAseq on RNA isolated from these tissues. Samples were collected from hM3DGq male mice that were either Gfral Cre-positive or negative. For quadriceps, material was obtained from CNO-injected clamped mice, for pgWAT the material was obtained at 1h or 6h after CNO-injection (activation of Gfral neurons). Replicates: For quadriceps, 10 vs 10; for pgWAT CNO 1h, 9 vs 9; for pgWAT CNO 6h, 6 vs 6.

first: Linda

last: Engström Ruud

first: Ferran

last: Font-Gironès

first: Joanna

last: Zajdel


title: Genome-wide chromatin conformation capture (Hi-C) of primary murine nephron progenitor cells

summary: This series contains Hi-C data generated from postnatal day 0 mouse nephron progenitor cells (NPCs) isolated from three different genotypes representing control, low and high nephron number mouse lines.

overall_design: Evaluation of genome-wide chromatin conformation in freshly-isolated murine nephron progenitor cells

first: Yaping

last: Liu


title: RNA-seq analysis between WT mice and knock out mice

city: Tianjin

first: Linlin

address: Weijin Road 97

institute: Nankai university

summary: We seprated the primodial germ cells using MACS from E12.5 stages in WT and Rif1-knock out mice, and using modified Smart-seq2 methods to get 1,000 cells library.

overall_design: we did 2 repeats for each sample and have WT data as control for 2 repeats.


title: Dual Targeting of FLT3 and LSD1 Disrupts the MYC Super Enhancer Complex in Acute Myeloid Leukemia.

city: Portland

first: William

middle: Montgomery

last: Yashar

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Knight Cancer Institute

institute: OHSU

summary: Clinical responses to kinase inhibitor therapy in acute myeloid leukemia (AML) are limited by the inevitable development of resistance. A major contributor to resistance is early epigenetic adaptation, leading to persistence of a small number of leukemia cells. Here we show that inhibition of the epigenetic regulator lysine-specific deme-thylase 1 (LSD1) augments the response to inhibitors of the FLT3 kinase in AML. We demonstrate that combined FLT3 and LSD1 inhibition results in synergistic cell death of FLT3-mutant AML cells via proliferative arrest and apoptosis. The drug combination synergistically activates a pro-differentiative epigenetic and transcriptional program while simultaneously suppressing the activity of MYC target genes. High resolution multi-modal epigenetic analyses revealed that combined FLT3 and LSD1 resulted in the suppression of MYC-bound promoters and the activation of PU.1-bound enhanc-ers. Forced expression of MYC partially abrogated the drug effect, and regulon en-richment analysis in primary AML samples nominated STAT5 as a putative regulator of MYC gene expression. STAT5 is highly bound to the MYC blood super-enhancer and inhibition of FLT3 results in a loss of STAT5 binding and a loss of super enhancer acti-vation. Furthermore, knockdown of STAT5 augments LSD1-inhibitor induced cell death. LSD1 inhibition also directly represses MYC target genes which show specific accumulation of the repressive LSD1 substrate H3K9me1. We validated these findings in 67 primary AML samples including 19 FLT3-ITD positive AML samples, with the vast majority demonstrating improved responses with the drug combination. High MYC regulon activity was a predictor of response to the drug combination and RNA-seq on drug treated AML samples revealed suppression of MYC target genes. Finally, single cell ATAC seq on primary AML blasts treated ex-vivo with combined FLT3 and LSD1 inhibition results in a shift from MYC super enhancer-high to a MYC super enhancer-low cell state. Collectively, these studies provide preclinical rationale for the investiga-tion of dual FLT3 and LSD1 inhibition in clinical trial.

overall_design: A human FLT3-ITD-mutant cell line and primary AML samples were analyzed by multi-omic profiling, including bulk RNA-seq, ChIP-seq, CUT&Tag, CUT&RUN, ATAC-seq, and single cell ATAC-seq

first: Brittany

last: Smith

first: Jake

last: Van Campen

first: Garth

last: Kong

first: Jommel

last: Macaraeg

last: Coleman

first: Brian

last: Druker

first: Julia

middle: E

last: Maxson

first: Theodore

middle: P

last: Braun