title: RNA-seq data from A. fumigatus strain Af293 with ZfpA wild type, knockout, and overexpression

city: Madison

first: Nancy

last: Keller

state: WI

address: 1550 Linden Drive

department: Medical Microbiology and Immunology

institute: University of Wisconsin-Madison

summary: We generated this RNA-seq dataset to investigate the effects of transcription factor ZfpA (aka. AFUA_8G05010 or AFUB_082490) in the gene expression of A. fumigatus strain Af293. One of the major reasons we were interested in investigating ZfpA was because this TF had been identified as highly regulated by the oxylipins (https://pubmed.ncbi.nlm.nih.gov/33056992/). To that end, we collected RNA from spores and the mycelial tissue under three distinct conditions: (a) wild-type ZfpA, (b) ZfpA knocked out, and (c) ZfpA overexpressed. We had four biological replicates for each set of (tissue, condition) pair. Hence, we had a total of (2 tissues * 3 conditions * 4 replicates) = 24 data samples. The knockout samples could still have reads that map to ZfpA due to the fact that less than 100% of the ZfpA gene was deleted.

overall_design: For the mycelial samples, RNA was extracted from the mycelial tissue 16 hours after inoculation in glucose minimal media at 37 degree celcius and 250 rpm.

first: Dante

last: Calise


title: Next-generation RNA Sequencing and Transcriptome Comparison of Mouse Wild Type and Mesenchymal Bmpr1a conditional knockout  lungs of E15.5

status: Public on Apr 01 2024

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

state: CA

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

country: USA

institute: University of Southern California

type: Expression profiling by high throughput sequencing

summary: Lung mesenchymal knockout of Bmpr1a will lead to lung malformation, including impaired lung branching and cystic lesion. In order to understand the underlying mechanisms, total RNA of wild type and mesenchymal Bmpr1a knockout lungs were isolated and sequenced using the next-generation RNA sequencing technique.

overall_design: BMP receptor 1a (Bmpr1a) flox mice were crossed with Tbx4-rtTA/TetO-Cre transgenic mice and received doxycycline treatment from E6.5 to generate the lung mesenchyme-specific and inducible Bmpr1a conditional knockout (CKO) mice. Lung mRNA profiles of E15.5 fetal wild type and Bmpr1a conditional mice were then generated by deep sequencing, in triplicate.

first: Wei

last: Shi

first: Yongfeng

last: Luo

first: Matthew

middle: E

last: Thornton


title: TET1 reprograms the epithelial ovarian cancer epigenome and reveals casein kinase 2α as a therapeutic target

status: Public on Mar 31 2024

city: Taipei

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

country: Taiwan

institute: Taipei Medical University

summary: Ten-eleven translocation methylcytosine dioxygenase-1, TET1, takes part in active DNA demethylation. This study showed that TET1 expression reprogramed ovarian cancer epigenome and correlated with poor survival in advanced-stage epithelial ovarian carcinoma (EOC).

overall_design: Examination of transcriptional profile of ovarian cancer cell lines, SKOV3 and HeyC2, overexpressed full-length of TET1. Results provide insight into molecular mechanism through which CK2α inhibitor can inhibit a subset of ovarian cancer expression TET1.

first: Lin-Yu

last: Chen

first: Rui-Lan

last: Huang


title: The nuclear receptors ERRα and PPARα co-ordinately control starvation-induced gene expression in hepatocytes.

city: Gent

first: Karolien

last: De Bosscher

address: Technologiepark-Zwijnaarde 75

country: Belgium

institute: VIB-UGent Center for Medical Biotechnology

summary: Peroxisome-proliferator activated receptor α (PPARα) activation reprograms liver gene expression to support fatty acid oxidation during fasting. How PPARα engages in transcriptional programs coping with catabolic fasting responses is insufficiently understood. By applying a protein-protein interaction methodology that also captures transient interactions, we revealed the orphan nuclear receptor estrogen-related receptor α (ERRα) as a novel interaction partner of liganded PPARα and found that this interaction is enhanced following cellular nutrient starvation. Among target genes affected by PPARα-ERRα transcriptional crosstalk in fasted murine livers, multiple components of the electron transport chain were identified. Using pharmacological tools to study hepatic gene subsets under dual PPARα and ERRα control and moving from short-term to prolonged nutrient deprivation, we found that ERRα can switch from being a PPARα target gene suppressor to a marked PPARα target gene activator. Mechanistically, ERRα may control PPARα transcriptional activity via binding onto PPARα’s coactivator interaction site and via facilitating cofactor relays. In sum, a variety of crosstalk mechanisms between PPARα and ERRα seems to co-ordinately drive essential gene regulatory changes in the starving hepatocyte.

overall_design: The transcriptomic signature underlying the ERRα and PPARα crosstalk in murine hepatocytes  using RNA-sequencing of the following conditions: DMSO, PPARα-specific agonist GW7647 (GW), ERRα inverse agonist Compound 29  (C29), GW+C29.

first: Sofie

middle: J

last: Desmet

first: Jonathan

last: Thommis

first: Yunkun

last: Li

first: Rens

middle: M

last: de Vries

first: Steven

last: Timmermans

first: Daria

last: Fijalkowska

first: Dariusz

last: Ratman

first: Evelien

last: Van Hamme

first: Lode

last: De Cauwer

first: Claude

last: Libert

first: Bart

last: Staels

first: Luc

last: Brunsveld

first: Frank

last: Peelman

first: Jan

last: Tavernier


title: CPLANE protein INTU regulates growth and patterning of the mouse lungs through cilia-dependent Hh signaling.

city: University Park

first: Aimin

last: Liu

state: Pennsylvania

address: 201 Life Sciences Building

department: Biology

institute: The Pennsylvania State University

summary: Congenital lung malformations are fatal at birth in their severe forms. Prevention and early intervention of these birth defects require a comprehensive understanding of the molecular mechanisms of lung development. We find that the loss of Inturned (Intu), a cilia and planar polarity effector gene, severely disrupts growth and branching morphogenesis of the mouse embryonic lungs. Consistent with our previous results indicating an important role for Intu in ciliogenesis and hedgehog (Hh) signaling, we find greatly reduced number of primary cilia in both the epithelial and mesenchymal tissues of the lungs. We also find significantly reduced expression of Gli1 and Ptch1, direct targets of Hh signaling, suggesting disruption of cilia-dependent Hh signaling in Intu mutant lungs. An agonist of the Hh pathway activator, smoothened, increased Hh target gene expression and tubulogenesis in explanted lungs in wild type, but not Intu mutants, suggesting impaired Hh signaling response in the absence of Intu. Furthermore, removing both Gli2 and Intu completely abolishes branching morphogenesis of the lung, strongly supporting a mechanism by which Intu regulates lung growth and patterning through cilia-dependent Hh signaling. Moreover, a transcriptomics analysis identifies around 200 differentially expressed genes (DEGs) in Intu mutant lungs, including known Hh target genes Gli1, Ptch1/2 and Hhip. Genes involved in muscle differentiation and function are highly enriched among the DEGs, consistent with an important role of Hh signaling in airway smooth muscle differentiation. In addition, we find a diminishing difference in gene expression between the left and right lungs in Intu mutants, suggesting an important role of Intu in asymmetrical growth and patterning of the mouse lungs.

overall_design: Wild type and Intu mutant lungs were isolated at embryonic day 12.5, and left and right lobes were separated. Total RNAs  were prepared from each sample for sequencing, such that comparisons can be made between wild and mutant, as well as between left and right.

first: Huiqing

last: Zeng

first: Shimaa

last: Ali

first: Aswathy

last: Sebastian

first: Adriana

middle: S

last: Ramos-Medero

first: Istavan

last: Albert

first: Charlotte

last: Dean


title: Molecular dissection of HERV-W dependent microglial- and astroglial cell polarization

status: Public on Mar 30 2024

city: Düsseldorf

first: Joel

last: Gruchot

address: Moorenstraße 5

department: Neurology

country: Germany

institute: Heinrich-Heine-University

summary: The endogenous retrovirus type W (HERV-W) is a human specific entity, which was initially discovered in multiple sclerosis (MS) patient derived cells. We initially found that the HERV-W envelope (ENV) protein negatively affects oligodendrogenesis and controls microglial cell polarization towards a myelinated axon associated and damaging phenotype. Such first functional assessments were conducted ex vivo, given the human specific origin of HERV-W. Recent experimental evidence gathered on a novel transgenic mouse model, mimicking activation and expression of the HERV-W ENV protein, revealed that all glial cell types are impacted and that cellular fates, differentiation, and functions were changed. In order to identify a HERV-W specific signature in glial cells, the current study analyzed the transcriptome of ENV stimulated microglial- and astroglial cells and compared the transcriptomic signature to lipopolysaccharide (LPS) stimulated cells, owing to the fact that both ligands can activate toll-like receptor-4 (TLR-4). Additionally, a comparison between published disease associated glial signatures and the transcriptome of HERV-W ENV stimulated glial cells was conducted. We, therefore, provide here for the first time a detailed molecular description of specific HERV-W ENV evoked effects on those glial cell populations that are involved in smoldering neuroinflammatory processes relevant for progression of neurodegenerative diseases.

overall_design: Transcriptome analysis of primary rat microglial and astroglial cells stimulated with HERV-W ENV or LPS

first: Gruchot

last: Joel

first: Küry

last: Patrick


title: In vivo CRISPR screens reveal SCAF1 and USP15 as novel drivers of pancreatic cancer

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

country: Canada

institute: Lunenfeld- Tanenbaum Research Institute

summary: Functionally characterizing the genetic alterations that drive pancreatic cancer progression is a prerequisite for precision pedicine. Here, we developed a somatic CRISPR/Cas9 mutagenesis screen to assess the transforming potential of 125 recurrently mutated ‘long-tail’ pancreatic cancer genes, which revealed USP15 and SCAF1 as novel and potent pancreatic ductal adenocarcinoma PDAC tumor suppressors, with USP15 functioning in a haplo-insufficient manner. Mechanistically, we found that loss of USP15 leads to reduced inflammatory responses associated with TNFa, TGF-b and IL6 signaling and sensitizes pancreatic cancer cells to PARP inhibition and Gemcitabine. Similarly, genetic ablation of SCAF1 reduced inflammatory responses linked to TNFa, TGF-b and mTOR signaling and increased sensitivity to PARP inhibition. Furthermore, we identified that loss of SCAF1 resulted in the formation of a truncated inactive USP15 isoform at the expense of full length USP15, functionally coupling SCAF1 and USP15. Notably, USP15 and SCAF1 mutations or copy number losses are observed in 31% of PDAC patients. Together, our results demonstrate the utility of in vivo CRISPR screens to integrate human cancer genomics with mouse modeling for selective discovery of novel cancer driver genes such as USP15 and SCAF1 with potential prognostic and therapeutic implications.

overall_design: Cells were cutlured in DMEMsupplemented with 10% Fetal bovine serum and 1% Pencillin-Streptomycin antibiotic solution and treated with either DMSO as a control or 3uM of Olaparib

first: Sebastien

last: Martinez

first: Ahmad

middle: A

last: Malik


title: AKAP12 UV RNA immunoprecipitation followed by high throughput sequencing

status: Public on Mar 28 2024

city: Belfast

first: Guilherme

last: Costa

address: 97 Lisburn Road

country: United Kingdom

institute: Queen's University of Belfast

summary: Regulation of subcellular mRNA localisation is a fundamental biological mechanism, which adds a spatial dimension to the diverse layers of post-transcriptional control of gene expression. Insights into this phenomenon have been described in a multitude of cell types and across taxonomic kingdoms, highlighting its biological significance.  The cellular compartment in which mRNAs are located may define distinct aspects of the encoded proteins, ranging from production rate and complex formation to localised activity. Ultimately, mRNA localisation supports compartmentalised mechanistic outputs that can respond to local stimuli, orient migration, or even shape cells. We used an unbiased method to profile the RNA-bound proteome in migrating endothelial cells and found that the plasma membrane (PM)-associated A-kinase anchor protein 12 (AKAP12) interacts with various mRNAs, including mRNAs encoding kinases with Actin remodelling activity. To identify transcripts bound by AKAP12, we carried out UV crosslinking experiments followed by RNA immunoprecipitation and high throughput sequencing. Our data offer novel insights in complex mechanisms of spatial control of gene expression.

overall_design: Human umbilical vein endothelial cells (HUVECs) were grown to 90% confluency in complete endothelial growth media, exposed to 254 nm UV light and lysed. Cell lysates were incubated with an antibody targeting AKAP12 and 5% saved for Input sequencing. Next, antibody-AKAP12 complexes were recovered with G protein magnetic beads. After washing, the complexes were eluted from beads, treated with a revere crosslink buffer containing Proteinase K and the RNA recovered via Trizol extraction.

first: Madeleine

last: Rosie Smith


title: Exploring the Dynamic Adaptive Responses of Epimedium pubescens to Phosphorus Deficiency Through Combined Transcriptome and miRNA Analysis [miRNA-Seq]

city: 北京

first: 尚年

last: 刘

state: 北京

address: 马连洼街道马连洼北路151号

country: China

institute: 中国医学科学院药用植物研究所

type: Non-coding RNA profiling by high throughput sequencing

summary: In the early stages (30 days) of phosphorus deficiency stress, Epimedium pubescens leaves cope with short-term phosphorus deficiency by increasing the expression of related genes such as carbon metabolism, flavonoid synthesis and hormone signal transduction pathways, producing sufficient energy, scavenging ROS, and adjusting plant morphology. However, with the extension of stress duration to 90 days, the expression of genes related to phosphorus cycling and phosphorus recovery (PHT1-4, PHO1 homolog3, PAP) was upregulated, and transcriptional changes and post-transcriptional regulation (miRNA regulation and protein modification) were enhanced to resist long-term phosphorus deficiency stress. In addition, bHLH, MYB, NAC, WRKY and other families also play an important role in regulating gene expression and coping with phosphorus deficiency stress, especially MYB60 negatively regulates flavonoid synthesis pathway, which is significantly down-regulated in leaves treated with phosphorus deficiency for 30 days, thereby promoting the accumulation of flavonoid compounds in leaves.

overall_design:
In order to study the response mechanism and flavonoid accumulation of leaves to phosphorus deficiency stress in Epimedium pubescens, we set up two different phosphorus levels (-P: 0mmol/L, +P: 1mmol/L) to sand culture the plants and maintain the consistency of other growth conditions.
We then performed gene expression profiling using data obtained from RNA-seq of leaves from Epimedium pubescens under two phosphorus treatments and at two time points
Comparative analysis of gene expression profiles of RNA-seq data from Epimedium pubescens leaves under 30d-P, 30d+P, 90d-P, 90d+P treatments

first: Shangnian

first: Xiaojing

last: An


title: Transcriptional analysis of T cells derived from individuals with neurodevelopmental disorder carrying de novo heterozygous PSMC3 variants.

city: Nantes

first: Frédéric

last: Ebstein

address: IRS-UN - 8 quai Moncousu - BP 70721

department: L'unité de recherche de l'institut du thorax, Inserm UMR 1087

country: France

institute: French Institute of Health and Medical Research (Inserm)

summary: Gene expression profiling on T cells to investigate the effects of PSMC3 loss-of-function variants on the immune system using the Nanostring nCounter® Human AutoImmune Profiling Panel.

overall_design: Peripheral blood mononuclear cells (PBMC) isolated from blood draws from patients and their parents (father and/or mother) were subjected to polyclonal stimulation with phytohemagglutinin (PHA) and interleukin-2 (IL-2) to expand naive T cells. After 3 weeks of culture, total RNA was isolated from resting T cells for gene expression analysis.

first: Maja

last: Studencka-Turski


title: Exploring the Dynamic Adaptive Responses of Epimedium pubescens to Phosphorus Deficiency Through Combined Transcriptome and miRNA Analysis [RNA-Seq]

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

last: Liu


title: The transcriptional co-repressor Runx1t1 is essential for N-Myc-driven neuroblastoma tumorigenesis [RNA-Seq 2]

city: Randwick

first: Murray

last: Norris

state: NSW

address: Lowy Cancer Research Centre

country: Australia

institute: Children's Cancer Institute

summary: Changes in epigenetic regulation are believed to be a major contributing factor to neuroblastoma development. Using a large-scale in vivo mutagenesis screen in Th-MYCN transgenic mice, we identified a single point mutation in the transcriptional corepressor Runx1t1, that can block N-Myc-driven neuroblastoma tumorigenesis. The loss of function mutation disrupts a highly conserved zinc finger domain (NHR4) within Runx1t1. Crossing an independent Runx1t1 knockout model with Th-MYCN mice, demonstrated that Runx1t1 haploinsufficiency is enough to prevent neuroblastoma development and reverse ganglia hyperplasia. Silencing RUNX1T1 in human neuroblastoma cells resulted in decreased colony formation in vitro, and significant inhibition of tumor growth in vivo. Our results show that RUNX1T1 forms part of a transcriptional LSD1-CoREST3-HDAC repressive complex that regulates the epigenomic landscape and chromatin accessibility, to control neuron-specific pathway genes and maintain an undifferentiated state. Runx1t1 thus represents an entirely novel and highly promising target not previously described in neuroblastoma.

overall_design: Celiac ganglia were dissected from two-week old Th-MYCN homozygote and wild-type mice with 1- or 2-copies of Runx1t1 and cleaned to remove non-ganglion tissue. Total RNA was isolated using the RNeasy Micro kit (50), # 74004 kit and RNA quality was assessed prior to being used (Agilent 2100 Bioanalyzer, Agilent Technologies). Only RNA with an RNA Integrity Number (RIN) of >9.0 was used. Whole transcriptome sequencing was performed at the Ramaciotti Centre for Genomics with SMARTer Stranded Total RNA-seq v2  preparation kit. Prepared libraries were pooled and sequenced on NovaSeq 6000 S1 2x100bp lane generating an average of 60 million reads per sample.

first: Emanuele

last: Valli

first: Jayne

last: Murray

first: Chelsea

last: Mayoh

first: Nisitha

last: Jayatilleke

middle: D


title: Mitotic gene regulation by the N-MYC-WDR5-PDPK1 nexus

status: Public on Mar 29 2024

city: Murfreesboro

first: Rafet

last: Al-Tobasei

state: TN

address: 358 KOM

department: Computer Science Department

institute: Middle Tennessee State University

summary: Background: During mitosis the cell depends on proper attachment and segregation of replicated chromosomes to generate two identical progeny. In cancers defined by overexpression or dysregulation of the MYC oncogene this process becomes impaired, leading to genomic instability and tumor evolution. Recently it was discovered that the chromatin regulator WDR5—a critical MYC cofactor—regulates expression of genes needed in mitosis through a direct interaction with the master kinase PDPK1. However, whether PDPK1 and WDR5 contribute to similar mitotic gene regulation in MYC-overexpressing cancers remains unclear. Therefore, to characterize the influence of WDR5 and PDPK1 on mitotic gene expression in cells with high MYC levels, we performed a comparative transcriptomic analysis in neuroblastoma cell lines defined by MYCN-amplification, which results in high cellular levels of the N-MYC protein.   Results: Using RNA-seq analysis, we identify the genes regulated by N-MYC and PDPK1 in multiple engineered CHP-134 neuroblastoma cell lines and compare them to previously published gene expression data collected in CHP-134 cells following inhibition of WDR5. We find that as expected N-MYC regulates a multitude of genes, including those related to mitosis, but that PDPK1 regulates specific sets of genes involved in development, signaling, and mitosis. Analysis of N-MYC- and PDPK1-regulated genes reveals a small group of commonly controlled genes associated with spindle pole formation and chromosome segregation, which overlap with genes that are also regulated by WDR5. We also find that N-MYC physically interacts with PDPK1 through the WDR5-PDPK1 interaction suggesting regulation of mitotic gene expression may be achieved through a N-MYC-WDR5-PDPK1 nexus. Conclusions: Overall, we identify a small group of genes highly enriched within functional gene categories related to mitotic processes that are commonly regulated by N-MYC, WDR5, and PDPK1 and suggest that a tripartite interaction between the three regulators may be responsible for setting the level of mitotic gene regulation in N-MYC amplified cell lines. This study provides a foundation for future studies to determine the exact mechanism by which N-MYC, WDR5, and PDPK1 converge on cell cycle related processes.

overall_design: We used a MYCN-amplified neuroblastoma cell line that was engineered to express a version of PDPK1 that can be degraded by addition of the dTAG47 molecule. Following 24 hr depletion of PDPK1, RNA was extracted and processed for RNA-seq.

first: April

last: Weissmiller

first: Sarah

last: Streeter

first: Alexandria

last: Williams

first: James

last: Evans

first: Jing

last: Wang

first: Alissa

last: Guarnaccia

first: Andrea

last: Florian

first: Qi

first: William

last: Tansey


title: Mining novel gene targets for improving tolerance to furfural and acetic acid in Yarrowia lipolytica using whole-genome clustered regularly interspaced short palindromic repeats interference library [CRISPR screen]

status: Public on Mar 25 2024

city: Tianjin

first: Qianxi

last: He

address: Yaguan road 135

institute: Tianjin University

summary: Lignocellulosic biomass is an abundant renewable resource with tremendous potential to alleviate climate crisis. Yarrowia lipolytica is an attractive biochemical production host, while the presence of inhibitors furfural and acetic acid in lignocellulosic hydrolysate restricts the efficient utilization of this resource. Given a deficient understanding of the inherent interactions between these inhibitors and cellular metabolism, sufficiently mining relevant genes is necessary. Herein, 14 novel gene targets were discovered using CRISPR interference library in Y. lipolytica, achieving tolerance to 0.35% (v/v) acetic acid (the highest concentration reported in Y. lipolytica), 4.8 mM furfural, or a combination of 2.4 mM furfural and 0.15% (v/v) acetic acid. The tolerance mechanism might involve improvements of signal transduction, PP pathway, and TCA cycle. Transcriptional repression of effective gene targets still enabled tolerance when xylose was a carbon source. This work forms a robust foundation for significantly improving microbial tolerance to inhibitors in lignocellulosic hydrolysate and profoundly revealing underlying mechanism.

overall_design: In this study, a whole-genome CRISPRi library was developed in Y. lipolytica and applied for enforcing the tolerance to furfural and acetic acid. Several novel gene targets were discovered through NGS before and after screening. And to analyze the tolerance mechanism caused by transcriptional repression of the most prominent gene targets, the transcriptome and proteomics were performed.

first: Yingxiu

last: Cao

first: Lixia

last: Fang

first: Yaru

last: Chen

first: Luxin

first: Qiyang

last: Duan

first: Congcong

last: Huang


title: Mining novel gene targets for improving tolerance to furfural and acetic acid in Yarrowia lipolytica using whole-genome clustered regularly interspaced short palindromic repeats interference library [RNA-seq]

overall_design: In this study, a whole-genome CRISPRi library was developed in Y. lipolytica and applied for enforcing the tolerance to furfural and acetic acid. Several novel gene targets were discovered. And to analyze the tolerance mechanism caused by transcriptional repression of the most prominent gene targets, the transcriptome and proteomics were performed.


title: Activation of immune pathways in common bed bugs, Cimex lectularius, in response to bacterial immune challenges - a transcriptomics analysis

status: Public on Mar 18 2024

city: Burnaby

first: Sanam

last: meraj

email: smeraj@sfu.ca, sammeraj26@gmail.com

state: British Columbia

address: 8888 university drive

department: Biological Sciences

institute: simon fraser university

summary: The common bed bug, Cimex lectularius, is an urban pest of global health significance, severely affecting the physical and mental health of humans. In contrast to most other blood-feeding arthropods, bed bugs are not major vectors of pathogens, but the underlying mechanisms for this phenomenon are largely unexplored. Here, we present the first transcriptomics study of bed bugs in response to immune challenges. To study transcriptional variations in bed begs following ingestion of bacteria, we extracted and processed mRNA from immune-related tissues of adult male bed bugs after ingestion of sterile blood or blood laced with the Gram-positive (Gr+) bacterium Bacillus subtilis or the Gram-negative (Gr–) bacterium Escherichia coli. We analyzed mRNA from the bed bugs’ midgut (the primary tissue involved in blood ingestion) and from the rest of their bodies (RoB; body minus head and midgut tissues).

overall_design: To study transcriptional variations in bed begs following ingestion of bacteria, we extracted and processed mRNA from immune-related tissues of adult male bed bugs after ingestion of sterile blood or blood laced with the Gram-positive (Gr+) bacterium Bacillus subtilis or the Gram-negative (Gr–) bacterium Escherichia coli. We analyzed mRNA from the bed bugs’ midgut (the primary tissue involved in blood ingestion) and from the rest of their bodies (RoB; body minus head and midgut tissues) 12 hours after immunization.

last: Meraj

first: Nicolas

last: Salcedo Porras

first: Carl

last: Lowenberger

first: Gerhard

last: Gries


title: End resection and telomere healing of DNA double-strand breaks during nematode programmed DNA elimination

status: Public on Mar 15 2024

city: Knoxville

first: Jianbin

address: 1311 Cumberland Avenue

department: Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

summary: Most DNA double-strand breaks (DSBs) are harmful to genome integrity. However, some forms of DSBs are essential to biological processes, such as meiotic recombination and V(D)J recombination. DSBs are also required for programmed DNA elimination (PDE) in ciliates and nematodes. In nematodes, the DSBs are healed with telomere addition. While telomere addition sites have been well-characterized, little is known regarding the DSBs that fragment nematode chromosomes. Here, we used embryos from the nematode Ascaris to study the timing of PDE breaks and examine the DSBs and their end processing. Using END-seq, we characterize the DSB ends and demonstrate that DNA breaks are introduced before mitosis, followed by extensive end resection. The resection profile is unique for each break site, and the resection generates 3’ overhangs before the addition of telomeres. Interestingly, telomere healing occurs much more frequently on retained DSB ends than on eliminated ends. This biased repair of the DSB in Ascaris is likely due to the sequestration of the eliminated DNA into micronuclei, preventing their ends from telomere healing. Additional DNA breaks occur within the eliminated DNA in both Ascaris and Parascaris, ensuring chromosomal breakage and providing a fail-safe mechanism for nematode PDE.

sample_organism:
Ascaris suum
Parascaris univalens

platform_organism:
Ascaris suum
Parascaris univalens

overall_design: END-seq on Ascaris suum and Parascaris univalens early embryos undergoing programmed DNA elimination. Includes biological replicates for various stages of embryo development.

first: Estrem

last: Brandon

first: Wang

last: Jianbin


title: A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous transposon insertions

city: Cerdanyola del Vallès

first: Carlos

last: de Tomás

state: Barcelona

address: Carrer de la Vall Moronta

country: Spain

institute: CRAG

summary: The vast majority of traditional almond varieties are self-incompatible and the level of variability of the species is very high, resulting in a highly heterozygosity genome. Therefore, information on the different haplotypes is particularly relevant to understand the genetic basis of trait variability in this species. However, although reference genomes for several almond varieties exist, none of them is phased and has genome information at the haplotype level. Here we present a phased assembly of genome of the almond cv. Texas. Our analysis shows that the “Texas” genome has a high degree of heterozygosity, both as SNPs, short indels, and structural variants (SV) level. Many of the SVs are due to heterozygous Transposable Element (TE) insertions, and in many cases they also contain genic sequences. In addition to the direct consequences of this genic variability on the presence/absence of genes, our results show that variants located close to genes tend to be associated with allele-specific gene expression (ASE), which highlights the importance of heterozygous SVs in almond.

sample_organism:
Prunus dulcis
Prunus persica

platform_organism:
Prunus dulcis
Prunus persica

overall_design: Flowers (pink stage) and immature fruits of Prunus dulcis cv Texas and Prunus persica cv Early Gold were collected. For RNA-seq analysis, we used three biological replicates per genotype.

first: Raúl

last: Castanera

last: Vicient

first: Josep

last: Casacuberta


title: The Myc-Associated Zinc Finger Protein (MAZ) controls STAT1-mediated antiviral response by reshaping epigenome

city: Bethesda

first: Gary

last: Felsenfeld

address: 9000 Rockville Pike

institute: NIH

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome

status: Public on Mar 26 2024

city: Moscow

first: Ilya

middle: Andreevich

last: Pletenev

address: Bolshoy Boulevard 30, bld. 1

country: Russia

institute: Skoltech

summary: Chromatin architecture regulates gene expression and shapes cellular identity, particularly in neuronal cells. Specifically, polycomb group (PcG) proteins enable establishment and maintenance of neuronal cell type by reorganizing chromatin into repressive domains that limit the expression of fate-determining genes and sustain distinct gene expression patterns in neurons. Here, we map the 3D genome architecture in neuronal and non-neuronal cells isolated from the Wernicke's area of four human brains and comprehensively analyze neuron-specific aspects of chromatin organization. We find that genome segregation into active and inactive compartments is greatly reduced in neurons compared to other brain cells. Furthermore, neuronal Hi-C maps reveal strong long-range interactions, forming a specific network of PcG-mediated contacts in neurons that is nearly absent in other brain cells. These interacting loci contain developmental transcription factors with repressed expression in neurons and other mature brain cells. But only in neurons, they are rich in bivalent promoters occupied by H3K4me3 histone modification together with H3K27me3, which points to a possible functional role of PcG contacts in neurons. Importantly, other layers of chromatin organization also exhibit distinct structure in neurons, which corroborates with increased cohesin levels in neurons and therefore might be attributed to elevated neuronal loop extrusion activity.

overall_design: Hi-C experiments on NeuN+ and NeuN- cells isolated from human post-mortem brain samples (BA22p)

first: Maria

last: Bazarevich

first: Diana

middle: R

last: Zagirova

first: Anna

last: Kononkova

first: Alexander

middle: V

last: Cherkasov

first: Olga

middle: I

last: Efimova

first: Eugenia

last: Tiukacheva

first: Kirill

last: Morozov

first: Dmitriy

last: Komkov

last: Tvorogova

first: Vera

last: Golimbet

first: Nikolay

last: Kondratyev

first: Sergey

last: Razin

first: Philipp

last: Khaitovich

last: Ulianov

first: Ekaterina

last: Khrameeva


title: Periportal macrophages protect against commensal-driven liver inflammation [spatial transcriptomics]

status: Public on Mar 06 2024

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: The liver is the main gateway from the gut and the unidirectional sinusoidal flow from portal to central veins constitutes heterogenous zonation, such as peri-portal vein (PV) and peri-central vein (CV) zones; however, the functional and molecular differences among liver macrophages in these zones remain poorly understood. Here, intravital multiphoton imaging revealed significantly suppressed in PV zones. Zonation-specific single-cell transcriptome analyses detected an immuno-suppressive macrophage subset highly expressing IL-10 and Marco, a scavenger receptor, enriched in PV zones. Inhibited IL-10 signaling and Marco-deficient conditions impaired the suppressive function of these macrophages. The reduced number of Marco-positive suppressive macrophages in germ-free or antibiotic-treated conditions suggested that gut commensal bacteria were responsible for inducing this specific population. Dextran sulfate sodium-induced colitis led to inflammation in liver PV zones, which was more prominent under Marco-deficient conditions. Marco-positive inflammatory macrophages in the human liver are diminished in primary sclerosing cholangitis (PSC), an intractable disease characterized by chronic inflammation around the portal veins and bile ducts. Collectively, commensal bacteria and their pathogenic substances induce Marco-positive immunosuppressive macrophages, consequently limiting excessive inflammation in PV zones. Failure of this self-limiting system may cause hepatic inflammatory disorders, such as PSC.

overall_design: Spatial transcriptome analysis on the healthy mouse liver using 10X Visium

first: Yu

last: Miyamoto

last: Okuzaki

first: Masaru

last: Ishii


title: Gene expression patterns in cMyBP-CΔC10mut HCM mice and cMyBP-C(t/t) DCM mice

status: Public on Mar 22 2024

city: Tucson

first: Sakthivel

last: Sadayappan

state: AZ

address: 1656 E Mabel Street, Medical Research Building, Rm 315, Cellular and Molecular Medicine

department: Cellular and Molecular Medicine

institute: University of Arizona College of Medicine

summary: A 25-base pair deletion in the cardiac myosin binding protein-C (cMyBP-C) gene (MYBPC3), proposed to skip exon 33, modifies the C10 domain (cMyBP-CΔC10mut) and is associated with hypertrophic cardiomyopathy (HCM) and heart failure, affecting approximately 100 million South Asians. However, the molecular mechanisms underlying the pathogenicity of cMyBP-CΔC10mut in vivo are unknown. To determine whether expression of cMyBP-CΔC10mut is sufficient to cause HCM and contractile dysfunction in vivo, we generated transgenic (TG) mice having cardiac-specific protein expression of cMyBP-CΔC10mut at approximately half the level of endogenous cMyBP-C. At 12 weeks of age, significant hypertrophy was observed in TG mice expressing cMyBP-CΔC10mut. Also RNA Sequencing revealed that genes related to muscle contraction and proteosome biological process are dysregulated. Similarly,to determine whether myocardial inflammation is associated with cardiac dysfunction in dilated cardiomyopathy (DCM) caused by MYBPC3 mutation, we used the well-characterized cMyBP-C(t/t) mouse model of DCM at 3months of age.RNA-seq analysis revealed the upregulation of inflammatory pathways in the DCM hearts.

overall_design: The study included two mice models and its respective control. 1. cMyBP-CΔC10mut mice (SS2)and non transgenic mice(SS1). 2. cMyBP-C(t/t)  (SS5) and control mice (SS4)

first: Diederik

last: Kuster

first: Thomas

middle: L

last: Lynch

first: David

middle: Y

last: Barefield

first: Mayandi

last: Sivaguru

first: Gina

last: Kuffel

first: Michael

last: Zilliox

first: Kyoung

last: Lee

first: Roger

last: Craig

first: Rajasekaran

middle: N

last: Soorappan

first: Mohamed

last: Ismahil

first: Anil

middle: G

last: Jegga

first: Christian

last: Troidl

first: Sumanth

last: Prabhu


title: A whole-genome CRISPR screen identifies the spindle accessory checkpoint as a locus of nab-paclitaxel resistance in pancreatic cancer cells.

status: Public on Mar 21 2024

first: PRIYA

last: MONDAL

state: MD

address: 37 Convent Dr.

institute: NCI

summary: Pancreatic adenocarcinoma is one of the most aggressive and lethal forms of cancer. Chemotherapy is the primary treatment for pancreatic cancer, but resistance to the drugs used remains a major challenge. A genome-wide CRISPR interference and knockout screen in the PANC-1 cell line with the drug nab-paclitaxel has identified a group of spindle assembly checkpoint (SAC) genes that enhance survival in nab-paclitaxel.  Knockdown of these SAC genes (BUB1B, BUB3, and TTK) attenuates paclitaxel-induced cell death. Cells treated with the small molecule inhibitors BAY 1217389 or MPI 0479605, targeting the threonine tyrosine kinase (TTK), also enhance survival in paclitaxel. Overexpression of these SAC genes does not affect sensitivity to paclitaxel. These discoveries have helped to elucidate the mechanisms behind paclitaxel cytotoxicity. The outcomes of this investigation may pave the way for a deeper comprehension of the diverse responses of pancreatic cancer to therapies including paclitaxel. Additionally, they could facilitate the formulation of novel treatment approaches for pancreatic cancer.

overall_design: Whole Genome CRISPR SCREEN

first: Priya

last: Mondal

first: George

last: Alyateem

first: Allison

last: Mitchell

last: Gottesman


title: RNA-binding preference of the Roquin-1 CCCH-type zinc finger

city: Marburg

first: Julia

middle: E.

last: Weigand

address: Marbacher Weg 6

department: Pharmacy

institute: University of Marburg

summary: Zinc finger (ZnF) domains are widespread RNA-binding domains, recognizing single stranded and double stranded RNAs. Together with other RNA-binding domains, ZnFs enhance the affinity and specificity of RNA-binding proteins (RBPs). The ZnF-containing RBP Roquin controls mRNA decay by recognizing stem-loop elements in the 3'-UTR of its target mRNAs. Stem-loop elements are bound in a shape-specific manner by the unique ROQ domain with nanomolar affinity. The ZnF was suggested to play an essential role in RNA decay by Roquin. However, its RNA motif preference was not investigated so far. Here, we use RBNS to elucidate the RNA binding preference of the isolated Roquin-1 ZnF domain. We find that the ZnF preferentially recognizes single-stranded AU-rich elements (ARE).

overall_design: RNA Bind-n-Seq (RBNS) to systematically explore the binding specificity of Roquins ZnF domain. A 20-nt random RNA pool (1 µM) flanked by short constant adapter sequences was incubated with different concentrations of the Strep-tagged ZnF domain (1, 5, 20 µM).

first: Lasse

last: Oberstrass

first: Andreas

last: Schlundt

first: Jan-Niklas

last: Tants


title: Targeting IL-1b–mediated inflammatory signaling overcomes transfusion dependence in early-stage myelodysplastic syndromes

status: Public on Mar 20 2024

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Myelodysplastic syndromes (MDS) are a group of incurable hematopoietic stem cell (HSC) neoplasms characterized by peripheral blood cytopenias and a high risk of progression to acute myeloid leukemia. MDS represent the final stage in a continuum of HSCs’ genetic and functional alterations and are preceded by a premalignant phase, clonal cytopenia of undetermined significance (CCUS). Dissecting the mechanisms of CCUS maintenance may uncover therapeutic targets to delay or prevent malignant transformation. Here, we demonstrate that DNMT3A and TET2 mutations, the most frequent mutations in CCUS, induce aberrant HSCs’ differentiation towards the myeloid lineage at the expense of erythropoiesis by upregulating IL-1b–mediated inflammatory signaling and that canakinumab rescues red blood cell transfusion dependence in early-stage MDS patients with driver mutations in DNMT3A and TET2. This study illuminates the biological landscape of CCUS and offers an unprecedented opportunity for MDS intervention during its initial phase, when expected survival is prolonged.

overall_design: Single cell RNA sequencing on HSPCs and bone marrow cells from MDS patients comparing Canakinumab treatment and no treatment

first: Vera

last: Adema

first: Simona

last: Colla


title: Turnover of PPP1R15A mRNA encoding GADD34 controls responsiveness and adaptation to cellular stress

status: Public on Mar 19 2024

city: Heidelberg

first: Alessia

last: Ruggieri

address: Im Neuenheimer Feld 344

department: Dpt. of Infectious Diseases, Molecular Virology

institute: Heidelberg University

summary: The integrated stress response (ISR) is a key cellular signaling pathway activated by environmental alterations that represses protein synthesis to restore homeostasis. To prevent sustained damage, the ISR is counteracted by the upregulation of Growth Arrest and DNA Damage inducible 34 (GADD34), a stress-induced regulatory subunit of protein phosphatase 1 that mediates translation reactivation and stress recovery. Here, we uncover a novel ISR regulatory mechanism that post-transcriptionally controls the stability of PPP1R15A mRNA encoding GADD34. We established that the 3' untranslated region of PPP1R15A mRNA contains an active AU-rich element recognized by proteins of the ZFP36 family, promoting its rapid decay under normal conditions and stabilization for efficient expression of GADD34 in response to stress. We identify the tight temporal control of PPP1R15A mRNA turnover as a key step in establishing the ISR molecular memory, which sets the threshold for cellular responsiveness and mediates adaptation to repeated stress conditions.

overall_design: Two replicates of Huh7 control cell clone #1  as well as two replicates of Brf1/TTP DKO cell clone #18  have been treated with DMSO for 3h prior to a 10-min treatment with 5 µg/ml actinomycin D in DMSO. Cells were harvested, total RNA  extracted and sequenced.

last: Magg

first: Alessandro

last: Manetto

first: Katja

last: Kopp

first: Chia

middle: C

last: Wu

first: Mohsen

last: Naghizadeh

first: Doris

last: Lindner

first: Lucy

last: Eke

last: Welsch

first: Stefan

last: Kallenberger

first: Johanna

last: Schott

first: Volker

last: Haucke

first: Nicolas

last: Locker

first: Georg

last: Stoecklin


title: LINC00894 promotes neuronal survival by regulating the expression of ATF3.

status: Public on Mar 03 2024

city: jiangsunantong

first: hu

middle: han

last: jing

address: Chongchuan District Xincheng Bridge street

institute: nantonguniversity

summary: There is evidence suggesting that LINC00894 may have a biological role in the brain, but the exact function of this gene remains largely unknown. In this study, we discovered that LINC00894 regulates neuronal cell apoptosis. Using RNA-seq, we identified a gene cluster regulated by LINC00894 in M17 neuroblast cell line, and qRT-PCR analysis demonstrated that LINC00894 may affect cell viability by modulating the expression of ATF3 in neuronal cells.

overall_design: To investigate the function of LINC00894 in M17 neuroblast cell line, we constructed the LINC00894 knockdown vector by CRISPR-Cas9.We then performed gene expression profiling analysis using data obtained from RNA-seq.


title: Loss of tumor suppressors promotes a non-cell-autonomous inflammatory tumor microenvironment and enhances LAG3+T cell mediated immune suppression

status: Public on Mar 01 2024

first: Jae Young

last: So

address: 37 Convent Drive, Rm 3134

department: LCBG

institute: NCI/NIH


title: The hsa_circ_0002371/hsa-miR-502-5p/ATG16L1 axis modulates the survival of intracellular Mycobacterium tuberculosis and autophagy in macrophages

status: Public on Mar 13 2024

city: shanghai

first: jinyi

last: zhang

address: Songhu Road No.2005

institute: fudan university

summary: Circular RNAs (circRNAs) play a critical role in pathological mechanisms of Mycobacterium tuberculosis (Mtb) and can be used as a new biomarker for active tuberculosis (ATB) diagnosis. Therefore, we identified significantly dysregulated circRNAs in ATB patients and healthy controls (HC) and explored its molecular mechanism. We found that hsa_circ_0002371 was significantly up-regulated in PBMCs of ATB patients and H37Rv- or BCG-infected THP-1 human macrophages. Functional experiments demonstrated that hsa_circ_0002371 inhibited autophagy of BCG-infected THP-1 human macrophages and promoted intracellular BCG survival rate. Mechanistically, hsa_circ_0002371 promoted the expression of hsa-miR-502-5p, and hsa_circ_0002371 overexpression-induced protective effects in BCG-infected THP-1 human macrophages was largely overturned by the inhibition of hsa-miR-502-5p. Notably, hsa-miR-502-5p inhibited autophagy via suppressing autophagy related 16 like 1 (ATG16L1) in BCG-infected macrophages and thus promoting intracellular BCG growth. In summation, hsa_circ_0002371 increased the suppression of hsa-miR-502-5p on ATG16L1 and inhibited autophagy to promote Mtb growth in macrophages. In Conclusion, our data suggested that hsa_circ_0002371 was significantly up-regulated in the PBMCs of ATB patients compared with HC. The hsa_circ_0002371/hsa-miR-502-5p/ATG16L1 axis promoted the survival of intracellular Mtb and inhibited autophagy in macrophages. Our findings suggested hsa_circ_0002371 could act as a potential diagnostic biomarker and therapeutic target.

overall_design: To compare the differentially expressed circRNAs in healthy and active pulmonary tuberculosis patients.

first: Jinyi

last: Zhang

first: Yumo

last: He

first: Qiaoling

last: Ruan

first: Aixiao

last: Bi

first: Jingyu

last: Zhou

first: Shufeng

last: Weng

first: Huixia

last: Ma

first: Taiyue

last: Lin

first: Honghai

last: Wang

first: Ying

last: Xu


title: Enterococcus feacalis effect on Enteorhemorraghic E. coli

city: Madison

first: Thibaut

last: Rosay

state: Wisconsin

department: MMI

institute: UW Madison

summary: Previous experiments have shown that E. feacalis increases EHEC virulence, this RNAseq aims to understand the molecular mechanism underlaying this phenotype

overall_design: 6h coculture of E. feacalis with EHEC in DMEM low glucose in anaerobic condition

first: Fernando

middle: H

last: Martins

first: Vanessa

last: Sperandio


title: FGF signaling modulates mechanical force/WNT signaling in progenitors during tooth root development

status: Public on Feb 28 2024

first: Fei

last: Pei

address: 2250 Alcazar St

institute: USC

summary: The goal of this study is to compare transcriptome profiling (RNA-seq) of apical part of molar at postnatal 7.5 days after TMX induction between control and Fgfr1 mutant mice

overall_design: Methods: mRNA profiles of control and Fgfr1 mutant mice were generated by deep sequencing, in triplicate, using NextSeq500 High Output. The quality of RNA samples was determined using an Agilent 2100 Bioanalyzer.


title: Genomic context sensitizes regulatory elements to genetic disruption [RNA]

city: New York

first: Matthew

middle: T

last: Maurano

state: New York

address: 435 East 30th Street

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

summary: DNase-seq mapping in engineered  mesendodermal cells differentiated from mouse embryonic stem cells (mESCs) using CHIR.

overall_design: Single DNase-seq sample in WT mesendodermal cells used as a reference

first: Raquel

last: Ordoñez

first: Weimin

first: Gwen

last: Ellis

first: Yinan

last: Zhu

first: André

last: Ribeiro-dos-Santos

first: Ran

last: Brosh

first: Emily

last: Huang

first: Megan

last: Hogan

first: Jef

last: Boeke


title: Genomic context sensitizes regulatory elements to genetic disruption [DNAse-seq]

summary: Enhancer function is frequently investigated piecemeal using truncated reporter assays or single deletion analysis, thus it remains unclear to what extent their function is influenced by surrounding genomic context. Using our Big-IN technology for targeted integration of large DNAs, we analyzed the regulatory architecture of the Igf2/H19 locus, a paradigmatic model of enhancer selectivity. We assembled payloads containing a 157-kb functional Igf2/H19 locus and engineered mutations to genetically direct CTCF occupancy at the imprinting control region (ICR) that switches the target gene of the H19 enhancer cluster. Contrasting the activity of payloads delivered to the endogenous locus or to a safe harbor locus (Hprt) revealed that the functional elements comprising the Igf2/H19 locus are highly sensitive to their native context. Exchanging components of the Igf2/H19 locus with the well-studied Sox2 locus showed that the H19 enhancer cluster in particular functioned poorly out of context, and required its native surroundings to activate Sox2 expression. Conversely, the Sox2 locus control region (LCR) could activate both Igf2 and H19 outside its native context, but its activity was only partially modulated by CTCF occupancy at the ICR. Analysis of regulatory DNA actuation across different cell types revealed that, while the H19 enhancers are tightly coordinated within their native locus, the Sox2 LCR acts more independently. We show that these enhancer clusters typify broader classes of loci genome-wide. Our results show that unexpected dependencies may influence even the most studied functional elements, and our synthetic regulatory genomics approach permits large-scale manipulation of complete loci to investigate how locus architecture relates to function.

overall_design:
DNase-seq mapping in engineered  mesendodermal cells differentiated from mouse embryonic stem cells (mESCs) using CHIR.
Single DNase-seq sample in WT mesendodermal cells used as a reference

last: Zhang

middle: M


title: Soma-to-Germline miRNA inheritance via Yolk Promotes Stress Resilience in Progeny [mRNA]

status: Public on Mar 12 2024

city: Paris

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 4eme Etage

department: Development and stem cell biology

institute: Institut Pasteur

summary: At the onset of reproduction, oviparous animals synthesize large amounts of yolk in somatic tissues to provide lipids and other nutrients to their progeny. However, whether the yolk transports other types of molecules, such as RNAs with gene regulatory functions, remains largely unexplored. Here, we have biochemically purified the yolk in the nematode Caenorhabditis elegans and show it contains microRNAs (miRNAs). We provide evidence that the yolk transports such miRNAs from the mother’s intestine to the embryos via the lipoprotein yolk receptor RME-2. These yolk-enriched miRNAs inherited by the embryos regulate the transcriptomes of developing larvae. Moreover, environmental stresses and maternal age modulate the transfer of yolk-enriched miRNAs, providing stress resilience benefits to progeny. This discovery establishes a novel paradigm in intergenerational gene regulation, where the gut-germline axis orchestrates the transmission of environmental cues through yolk-enriched miRNAs. Our work reveals a new mechanism underlying the soma-to-germline transfer of epigenetic information in animals.

overall_design: RNA sequencing profiles of 2-cell embryos or freshly hatched L1 larvae from drosha pasha intestinal degron strain.

first: Névé

last: Aupérin

first: Meetali

last: Singh

first: Loan

last: Bourdon

first: Pierre-Henri

last: Commere

first: Almira

last: Chervova

first: Hélène

last: Lopez-Maestre

first: Aikaterini

last: Gkaraveli


title: Soma-to-Germline miRNA inheritance via Yolk Promotes Stress Resilience in Progeny [small RNA]

overall_design: small RNA sequencing profiles of sorted yolk by VIT-2::GFP and 2-cell embryos under different conditions of growth and genotypes.


title: Single Cell RNA Sequence Reveals a Distinct Immune Landscape in Acute Aortic Dissection.

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

institute: Kobe University Graduate School of Medicine

summary: We investigated the relationship between a developemnt of aortic dissection and inflammatory cells. Il-1b high expression macrophage contributed to developing an aortic dissection.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: single cell transcreptome of dissected aortic wall  in human and mouse

first: Taishi

last: Inoue


title: Differential DNA methylation occurs in RUNX1 heterozygous mutations harboring hematopoietic progenitor cells

status: Public on Feb 26 2024

city: Yokohama

first: Yuki

last: Tanaka

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

type: Genome variation profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below

overall_design: Refer to individual Series


title: Genomic context sensitizes regulatory elements to genetic disruption [DNA]

first: Matthew

last: Maurano

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design:
Sequencing and coverage data produced as part of the Big-IN genome engineering sequence verification pipeline.
(1) payload sequencing data. (2) Targeted sequencing (Capture-seq) data from mouse embryonic stem cell (mESC) lines engineered to harbor landing pads (LPs) and various payloads at Igf2/H19, Sox2, and Hprt loci

first: Raquel

last: Ordoñez

first: Weimin

first: Gwen

last: Ellis

first: Yinan

last: Zhu

last: Ribeiro-dos-Santos

middle: S


title: PI3Kg inhibition circumvents inflammation and mortality in SARS-CoV-2 and other infections

city: La Jolla

first: Judith

middle: Anne

last: Varner

address: Center for Novel Therapeutics 9310 Athena Circle 9310 Athena Circle

department: Pathology

institute: University of California, San Diego

summary: Virulent infectious agents such as SARS-CoV-2 and Methicillin Resistant Staphylococcus Aureus (MRSA) induce tissue damage that recruits neutrophils and monocyte/macrophages, leading to T cell exhaustion, fibrosis, vascular leak, epithelial cell depletion, and fatal organ damage. Neutrophils, monocytes and macrophages recruited to pathogen-infected lungs, including SARS-CoV-2 infected lungs, express phosphatidylinositol 3-kinase gamma (PI3K a signaling protein that coordinately controls granulocyte and monocyte trafficking to diseased tissues and immune suppressive, pro-fibrotic transcription in myeloid cells. PI3K deletion and inhibition with the clinical PI3K inhibitor eganelisib promoted survival in models of infectious diseases, including SARS-CoV-2 and MRSA, by suppressing inflammation, vascular leak, organ damage and cytokine storm. These results demonstrate essential roles for PI3K in inflammatory lung disease and support the potential use of PI3K inhibitors to suppress inflammation in severe infectious diseases.

overall_design: Human ACE2 transgenic mice were inoculated with SARS-CoV-2 and treated with the PI3Kgamma inhbitor IPI-549 or vehicle. Lungs of treated mice (4 IPI-549 and 3 Vehicle) were isolated  three days later and stored in TRIZOL until RNA was isolated, and ribodepleted libaries were synthesized and sequenced.

first: Ryan

last: Shepard

first: Isa

last: Pratumchai

first: Anghesom

last: Ghebremedhin

first: Hui

last: Chen

middle: A

first: John

last: Teijaro


title: Genomic context sensitizes regulatory elements to genetic disruption [CUT&RUN]

overall_design:
CTCF CUT&RUN of mouse embryonic stem cells (mESCs) and mesendodermal cells differentiated using CHIR.
CTCF CUT&RUN on 6 samples with different configurations of CTCF recognition sequences at the Igf2/H19 ICR

last: Zhang

first: André

first: Ran

last: Brosh

first: Emily

last: Huang

first: Megan

last: Hogan

first: Jef

middle: D

last: Boeke


title: Ankrd11, a chromatin regulator and a KBG syndrome risk gene, is a critical regulator of cardiac neural crest cell biology and heart development [MERSCOPE]

status: Public on Feb 25 2024

city: Montreal

first: Jo Anne

last: Stratton

address: 3801 Rue University

institute: McGill University

summary: ANKRD11 (Ankyrin Repeat Domain 11) is a chromatin regulator and a risk gene for KBG syndrome, a rare developmental disorder characterized by multiple organ abnormalities, including cardiac defects. However, the role of ANKRD11 in heart development is unknown. The neural crest plays a leading role in embryonic heart development, and its dysfunction is implicated in congenital heart defects. We demonstrate conditional knockout of Ankrd11 in the murine embryonic neural crest results in persistent truncus arteriosus, ventricular dilation, and impaired ventricular contractility. We further show these defects occur due to aberrant cardiac neural crest cell organization leading to outflow tract septation failure. Finally, knockout of Ankrd11 in the neural crest leads to impaired expression of various transcription factors, chromatin remodelers and signaling pathways, including mTOR, BMP and TGF-β in the cardiac neural crest cells. In this work, we identify Ankrd11 as a novel regulator of neural crest-mediated heart development and function.

overall_design: 3 Ankrd11-nchet and 3 Ankrd11-ncko E11.5 anatomically matched embryo slices encompassing the medial OFT region were imaged using a custom panel of 140 RNA probes for genes that are known to be important for OFT development and/or that were previously shown to be expressed in the OFT during the septation process in a scRNAseq dataset.

first: Yana

last: Kibalnyk

first: Elia

last: Afanasiev

first: Ronan MN

last: Noble

first: Adrianne ES

last: Watson

first: Irina

last: Poverennaya

first: Nicole L

last: Dittmann

first: Maria

last: Alexiou

first: Kara

last: Goodkey

first: Amanda

last: Greenwell

first: John R

last: Ussher

first: Igor

last: Adameyko

first: James

last: Massey

first: Daniel

last: Graf

first: Stephane L

last: Bourque

first: Anastassia

last: Voronova


title: The Myc-Associated Zinc Finger Protein (MAZ) controls STAT1-mediated antiviral response by reshaping epigenome [ChIP-Seq]

first: Gary

last: Felsenfeld

address: 9000 Rockville Pike

institute: NIH

summary:
The objectives of this study are to understand the regulatory roles of MAZ in biological processes using the NGS-deriveed ChIP-seq, DNA-MEDIP-seq and RNA-seq data in HAP1 control cells and MAZ knockout cells.  Our comparative analysis of these data generated from the HAP1 control and MAZ KO cells shows that MAZ is required for recruiting STAT1 to its target sites by reshaping epigenetic landscape in the human genome, thereby mediating antiviral response cells.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for STAT1 and H3K4me3, H3K27Ac in HAP1 cells.

overall_design: ChIP-Seq of HAP1/K562 control cells and MAZ knockdown/kockout cells were generated by deep sequencing in duplicate using Illumina GAIIx. The ChIP-seq sequence reads were aligned with Bowtie2 followed by calling peaks with MACS2 software. Distribution  of STAT1, H3K4me3, H3K27Ac and DNA methylation was analyzed using Deeptools and other software.

first: Tiaojiang

last: Xiao

first: Xin

last: Li


title: Characterization of an Osmr Conditional Knockout Mouse Model

status: Public on Feb 18 2024

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Oncostatin M (OSM) is a member of the interleukin-6 (IL-6) family of cytokines and has been found to have anti-inflammatory and pro-inflammatory properties in various cellular and disease contexts. OSM signals through two receptor complexes, one of which includes OSMRb. Here, we investigated OSM-OSMRb signaling in adult mouse hematopoietic stem cells (HSCs) using the conditional Osmrfl/fl mouse model B6;129-Osmrtm1.1Nat/J. We crossed Osmrfl/fl mice to interferon-inducible Mx1-Cre, which is robustly induced in adult HSCs. From these mice, we isolated HSCs by flow cytometry, stimulated with or without recombinant OSM for 1 hour, and assessed gene expression changes in control versus Osmr knockout HSCs by RNA-seq. This data may be utilized to investigate OSMRb-dependent and -independent OSM signaling as well as the transcriptional effects of an IL-6 family cytokine on mouse HSCs to further define its anti-inflammatory versus pro-inflammatory properties.

overall_design:
We sought to assess levels of Osmr transcript and Osmr signaling in prospectively isolated hematopoietic stem cells (HSCs) from the bone marrow of mice using fluorescence-activated cell sorting (Lineage- Sca-1+ c-Kit+ Flt3- CD150+ CD48-). HSCs from Osmrfl/fl Mx1-Cre female mice (2-4 months of age) and control Mx1-Cre female mice (2-4 months of age) were placed into serum-free StemSpan SFEM II media with 100ng/ml SCF, 50ng/ml TPO, and with or without 500ng/mL of recombinant murine OSM 60min, then flash frozen for RNA sequencing (RNA-seq). Significantly differentially expressed genes were defined based on stringent cutoffs (p < 0.01 and log2(FC) > 2 or < -2). N= 3-6 mice per group, experiment done two independent times.

UPDATE: [07-10-2024] The titles and characteristics of the Samples were updated. The associated data did not change.

first: Logan

last: Schwartz

first: Timothy

last: Stearns

middle: J

last: Telpoukhovskaia


title: Impaired T3 transport and action underlies the pathophisiology of the Allan-Herdon-Dudley syndrome

status: Public on Mar 11 2024

city: Chicago

first: Federico

last: Salas-Lucia

state: IL

address: 5841 S Maryland Ave

department: Medicine

institute: The University of Chicago

summary: Patients with mutations in the thyroid hormone (TH) cell transporter MCT8 gene develop severe neuropsychomotor retardation known as the Allan-Herndon-Dudley syndrome (AHDS). It is assumed that this is caused by a reduction in TH signaling in the developing brain during both intrauterine and postnatal developmental stages, and treatment remains understandably challenging. Given species differences in brain TH transporters and the limitations of studies in mice, we generated cerebral organoids (COs) using human iPSCs from MCT8-deficient patients. We found that MCT8-deficient COs exhibit (i) alterations in early neurodevelopment, resulting in smaller neural rosettes with thinner cortical units, (ii) impaired T3 transport in developing neural cells, as assessed through deiodinase-3-mediated T3 catabolism, (iii) reduced expression of genes involved in cerebral cortex development, and (iv) reduced T3-inducibility of TH-regulated genes. In contrast, the TH-analogs 3,5-diiodothyropropionic acid and 3,3’,5-triiodothyroacetic acid triggered normal responses (induction/repression of T3-responsive genes) in MCT8-deficient COs, constituting a proof-of-concept that lack of T3 transport underlies the pathophysiology of AHDS, and demonstrating the clinical potential for TH analogues to be used in treating AHDS patients. MCT8-deficient COs represent a species-specific relevant preclinical model that can be utilized to screen drugs with potential benefits as personalized therapeutics for AHDS patients.

overall_design: three biological replicates were analyzed for WT line (4 pooled COs per replicate) and two biological replicates for each MCT8-deficient line (4 pooled COs per replicate)

first: Sergio

last: Escamilla

first: Antonio

last: Bianco

first: Alexandra

last: Dumitrescu

first: Samuel

last: Refetoff


title: Analysis of DDX39A and DDX56 interacting proteins

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: DDX39A and DDX56 recombinant proteins were assayed using commercial protein microarrays in order to detect potential interaction partners.

overall_design: V5-tagged DDX39A, DDX56 and GFP (negative control) were purified from HEK293T cells and incubated separately on microarrays (ProtoArray v5.1, Invitrogen) containing more than 9000 unique proteins arrayed in duplicates under native conditions to maximize functionality and to allow native interactions.

middle: P

last: Acebron

first: Christof

last: Niehrs


title: Histone H3.1 is a chromatin embedded redox sensor triggered by tumor cells developing adaptive phenotypic plasticity and multi-drug resistance

status: Public on Feb 20 2024

first: Matthew

middle: J.

last: Schipma

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

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


title: Histone H3.1 is a chromatin embedded redox sensor triggered by tumor cells developing adaptive phenotypic plasticity and multi-drug resistance [ChIP-Seq]

summary: Chromatin structure is regulated through histone post-translational modifications as well as histone variants. Although highly homologous, histone variants display unique amino acid sequences associated with specialized functions in gene transcription regulation. Abnormal incorporation of histone variants into chromatin contributes to cancer initiation, progression, metastasis, as well as, therapy resistance. The current study reports a novel epigenetic function of histone H3.1 as a redox sensor embedded in heterochromatin. We found that this new function depends on oxidation by nuclear ROS and lead to changes in the transcriptional profile of MCF10A cells.

overall_design: ChIP-seq for H3.1/H3.2 and H3.3 histone variants 4h or 24h after treatment with D-Alanine (ROS generated in the nucleus)

first: Flavio

middle: R

last: Palma

first: Marcelo

last: Bonini


title: Dissecting depression symptoms: multi-omics clustering uncovers immune-related subgroups and cell-type specific dysregulation

status: Public on Mar 05 2024

city: Munich

first: Janine

last: Knauer-Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

summary: In a subset of patients with mental disorders, such as depression, low-grade inflammation and altered immune marker concentrations are observed. However, these immune alterations are often assessed by only one data type and small markers panels. Here, we used a transdiagnostic approach and combined data from two cohorts to define subgroups of depression symptoms across the diagnostic spectrum through a large-scale multi-omics clustering approach in 237 individuals. The method incorporated age, body mass index (BMI), 43 plasma immune markers and RNA-seq data from peripheral mononuclear blood cells (PBMCs). Our initial clustering revealed four clusters, including two immune-related depression symptom clusters characterized by elevated BMI, higher depression severity and elevated levels of immune markers such as interleukin-1 receptor antagonist (IL-1RA), C-reactive protein (CRP) and C-C motif chemokine 2 (CCL2 or MCP-1). In contrast, the RNA-seq data mostly differentiated a cluster with low depression severity, enriched in brain related gene sets. This cluster was also distinguished by electrocardiography data, while structural imaging data revealed differences in ventricle volumes across the clusters. Incorporating predicted cell type proportions into the clustering resulted in three clusters, with one showing elevated immune marker concentrations. The cell type proportion and genes related to cell types were most pronounced in an intermediate depression symptoms cluster, suggesting that RNA-seq and immune markers measure different aspects of immune dysregulation. Lastly, we found a dysregulation of the SERPINF1/VEGF-A pathway that was specific to dendritic cells by integrating immune marker and RNA-seq data. This shows the advantages of combining different data modalities and highlights possible markers for further stratification research of depression symptoms.

overall_design: The total RNA-seq of PBMCs from 229 participants with stress-related mental disorders and 33 healthy controls was determined as well as from 11 participants with stress-related mental disorders for a replication analysis.

first: Jonas

last: Hagenberg

first: Elisabeth

middle: B

last: Binder


title: Loss of tumor suppressors promotes a non-cell-autonomous inflammatory tumor microenvironment and enhances LAG3+T cell mediated immune suppression [RNA_seq_Cas9_PT]

city: Bethesda

first: Jae Young

last: So

summary: Low response rate, treatment relapse, and resistance remain key challenges in the application of immune checkpoint blockade (ICB). Here we report that loss of specific tumor suppressors (TSs) induces an inflammatory response and promotes an immune suppressive tumor microenvironment.  Importantly, low expression of these TSs is associated with a higher expression of immune checkpoint inhibitory mediators. Using CRIPSR/Cas9 in vivo loss-of-function screening, we identified NF1, TSC1, and TGF-b RII as TSs that regulate immune composition. Loss of each of these three TSs leads to alterations in chromatin accessibility and enhances IL6-JAK3-STAT3/6 inflammatory pathways. This results in an immune suppressive landscape characterized by increased LAG3+ CD8 and CD4 T cells. ICB targeting LAG3 in combination with PD-L1 decreased metastatic progression in preclinical triple negative breast cancer (TNBC) mouse models of NF1-, TSC1- or TGF-b RII- deficient tumors. Together, our studies identify LAG3 as a new ICB target for patients whose cancer displays inactivation of these TSs. In addition, our studies reveal an unexpected role for TSs in the regulation of metastatic spread via non-cell-autonomous modulation of the immune compartment.

overall_design: To investigate gene expression changes of downstream molecules by knockout of Nf1, Tsc1, Tgfbr2 in 4T1 tumors.


title: Loss of tumor suppressors promotes a non-cell-autonomous inflammatory tumor microenvironment and enhances LAG3+T cell mediated immune suppression [RNA_seq_vitro]

overall_design: To investigate gene expression changes of downstream molecules by nkockout of Nf1, Tsc1, Tgfbr2 in 4T1 cell in vitro.


title: Loss of tumor suppressors promotes a non-cell-autonomous inflammatory tumor microenvironment and enhances LAG3+T cell mediated immune suppression [ATAC_seq]

overall_design: To investigate epigenetic alterations of downstream molecules by knockout of Nf1, Tsc1, Tgfbr2 in 4T1 cell in vitro.

first: Zhiguang

last: Xiao

first: Sara

last: Zahraeifard

first: Jae

middle: Y

first: Li

last: Yang


title: The interferon-rich skin environment regulates Langerhans cell ADAM17 to promote photosensitivity in lupus

status: Public on Feb 23 2024

city: New york

first: Yurii

last: Chinenov

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

summary: The autoimmune disease lupus erythematosus (lupus) is characterized in part by photosensitivity, where patients can develop inflammatory skin lesions with even ambient ultraviolet radiation (UVR) exposure. Evidence points to a role for type I interferon (IFN-I) in photosensitivity, but mechanistic understanding remains limited. We have shown that photosensitivity in lupus models is at least in part attributable to Langerhans cell (LC) dysfunction. Healthy LCs limit photosensitivity via a disintegrin and metalloprotease 17 (ADAM17), a sheddase that normally limits UVR-induced skin inflammation by releasing soluble epidermal growth factor receptor (EGFR) ligands to support keratinocyte survival. On the other hand, LCs from lesional and even non-lesional lupus model skin show reduced ADAM17 activity and mRNA expression. Non-lesional human lupus skin also showed evidence of LC dysfunction, and, here, we asked how the lupus skin environment contributes to this dysfunction. We show that non-lesional skin in human CLE and multiple photosensitive lupus models share gene expression patterns consistent with a high IFN environment and LC dysfunction. IFN-I inhibits murine and human LC ADAM17 activity, and anti-IFNAR1 in lupus models restores LC ADAM17 function and reduces photosensitivity in EGFR and LC ADAM17-dependent manners. Reactive oxygen species (ROS) are a mediator of ADAM17 activity, and we show that lupus models have reduced UVR-induced LC ROS generation that is restored by anti-IFNAR1. Our findings suggest shared pathogenic mechanisms of photosensitivity in human and murine lupus skin and a model whereby the IFN-I-rich microenvironment in non-lesional lupus skin inhibits UVR-induced ADAM17 activity, predisposing to photosensitivity. Our data also suggest that the beneficial effects of the recently FDA-approved anifrolumab (anti-IFNAR1) on human lupus skin could act in part by restoring LC function.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for

first: Thomas

last: Li

first: Noa

last: Schwartz

first: Andrea

last: Daamen

first: David

last: Oliver

first: Marija

last: Dacic

first: Ali

last: Jabbari

first: Inez

last: Rogatsky

first: Theresa

last: Lu


title: Genomic context sensitizes regulatory elements to genetic disruption

first: Matthew

last: Maurano


title: U2AF1 mutations confer resistance to chemotherapy in AML

city: Shanghai

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Patients with primary refractory acute myeloid leukemia (AML) have a dismal long-term prognosis. Elucidating the resistance mechanisms to induction chemotherapy could help identify strategies to improve AML patient outcomes. Herein, we retrospectively analyzed the multi-omics data of more than 1,500 AML cases and found that patients with spliceosome mutations had a higher risk of developing refractory disease. RNA splicing analysis revealed that the mis-spliced genes in refractory patients converged on translation-associated pathways, promoted mainly by U2AF1 mutations. Integrative analyses of binding and splicing in AML cell lines substantiated that the splicing perturbations of mRNA translation genes originated from both the loss and gain of mutant U2AF1 binding. In particular, the U2AF1-S34F and U2AF1-Q157R mutants orchestrated the inclusion of exon 11 (encoding a premature termination codon) in the eukaryotic translation initiation factor 4A2 (EIF4A2). This aberrant inclusion led to reduced eIF4A2 protein expression via nonsense-mediated mRNA decay. Consequently, U2AF1 mutations caused a net decrease in global mRNA translation that induced the integrated stress response (ISR) in AML cells, which was confirmed by single-cell RNA-seq. The induction of ISR enhanced the ability of AML cells to respond and adapt to stress, contributing to chemoresistance. A pharmacologic inhibitor of ISR, ISRIB, sensitized U2AF1 mutant cells to chemotherapy. These findings highlight a resistance mechanism by which U2AF1 mutations drive chemoresistance and provide a therapeutic approach for AML through targeting the ISR pathway.

overall_design:
scRNA-seq on 12,853 cells from two AML patients carrying U2AF1-S34F mutations. Law restrictions prohibit us from publicly sharing raw sequencing data, which however can be made available upon reasonable request and permission of the local ethics committee.

***************************************************************
Law restrictions prohibit us from publicly sharing raw sequencing data, which however can be made available upon reasonable request and permission of the local ethics committee.
***************************************************************

first: Junmin


title: NCoR1 limits angiogenic capacity by altering Notch signaling

status: Public on Feb 12 2024

city: Frankfurt

first: Simonida

last: Zehr

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe University, Frankfurt am Main, Germany,

summary:
Corepressors negatively regulate gene expression by chromatin compaction. Targeted regulation of gene expression could provide a means to control endothelial cell phenotype. We hypothesize that by targeting corepressor proteins, endothelial angiogenic function can be improved. To study this, the expression and function of nuclear corepressors in human umbilical vein endothelial cells (HUVEC) and in murine organ culture was studied. RNA-seq revealed that nuclear receptor corepressor 1 (NCoR1), Silencing Mediator of Retinoid and Thyroid hormone receptors (SMRT) and repressor element-1 silencing transcription factor (REST) are the highest expressed corepressors in HUVECs. Knockout and knockdown strategies demonstrated that the depletion of NCoR1 increased the angiogenic capacity of endothelial cells, whereas depletion of SMRT or REST did not. Interestingly, the effect was VEGF signaling independent. NCoR1 depletion significantly upregulated angiogenesis-associated genes, especially tip cell genes, including ESM1, DLL4 and NOTCH4, as observed by RNA- and ATAC-seq. Confrontation assays comparing cells with and without NCoR1-deficiency revealed that loss of NCoR1 promotes a tip-cell position during spheroid sprouting. Moreover, a proximity ligation assay identified NCoR1 as a direct binding partner of the Notch-signaling-related transcription factor RBPJk. Luciferase assays showed that siRNA-mediated knockdown of NCoR1 promotes RBPJk activity. Furthermore, NCoR1 downregulation prompts upregulation of several elements in the Notch signaling cascade. Downregulation of NOTCH4, but not NOTCH1, prevented the positive effect of NCoR1 knockdown on spheroid outgrowth. Collectively, these data indicate that decreasing NCOR1 expression is an attractive approach to promote angiogenic function.

This SuperSeries is composed of the SubSeries listed below.

overall_design: RNA sequencing (n=3) and ATAC sequencing (n=3) of of human umbilical vein endothelial cells (HUVEC) treated with either negative control siRNA or siRNA HSS114352, which knocks down NCoR1 expression. Please refer to individual Series


title: Transcirptomic data from Isolated Tfh cells from AITL patients and healthy donors

status: Public on Feb 09 2024

city: Toulouse

first: Marie

last: Tosolini

address: 2 avenue Hubert Curien

department: CRCT

institute: INSERM

overall_design: Detection of RNA expression data  used by agio immunoblastic T cell lymphoma (AITL) Tfh cells as compared to healthy counterpart cells

first: Els

last: Verhoeyen

first: Philippe

last: Gaulard

first: François

last: Lemoinne


title: Micro-C XL  of Saccharomyces cerevisiae

status: Public on Feb 08 2024

city: Srinagar

first: Ajaz ul Hamid

last: Wani

state: Jammu and Kashmir

address: Hazratbal

department: Biotechnology

country: India

institute: University of Kashmir

summary: We report change in the chromatin contacts at nucleosomal resolution upon deletion of ATP-dependent chromatin remodellers(Isw1,Isw2 and Chd1) in Saccharomyces cerevisiae.

overall_design: Both wildtype and triple knockout strains chromatin were crosslinked with two different crosslinkers, digested with MNase. After end repairing biotin labelling and ligation was done. After DNA purification size selection was done and NGS library was prepared and sequenced

first: Ajazul

first: Fouziya

last: Rashid


title: Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi

city: Planegg

first: Wolfgang

last: Enard

address: Großhadernerstr. 2

institute: Ludwig-Maximilians-Universität München

summary: Comparisons of molecular phenotypes across primates provide unique information to understand human biology and evolution and single-cell RNA-seq CRISPR interference screens are a powerful approach to analyze them. Here, we generate and validate three human, three gorilla and two cynomolgus iPS cell lines that carry a dox-inducible KRAB-dCas9 construct in the AAVS1 locus. We show that despite variable expression levels of KRAB-dCas9 among lines, comparable downregulation of target genes and comparable phenotypic effects are observed in a single-cell RNA-seq CRISPR interference screen. Hence, we provide valuable resources for performing and further extending CRISPRi screens in human and non-human primates.

sample_organism:
Macaca fascicularis
Gorilla gorilla
Homo sapiens

overall_design: Three human, three gorilla, and two cynolmolgus inducible KRAB-dCas9 iPS cell lines with an integrated SOX2-targeting gRNA were culture in +dox or -dox conditions for 4 days to compare between SOX2-knockdown (+dox) and normal condition (-dox).

first: Fiona

last: Edenhofer

first: Anita

last: Térmeg

first: Mari

last: Ohnuki

first: Jessica

last: Jocher

first: Eva

last: Briem

first: Zane

last: Kliesmete

first: Ines

last: Hellmann


title: Inhibition of ACSS2-mediated crotonylation alleviates kidney fibrosis via IL- 1β-dependent macrophage activation and tubular cell senescence [ChIP-Seq]

city: chengdu

first: Ting

last: Xiang

address: chengdu

institute: West China Hospital of Medicine: Sichuan Universit

summary: Chronic kidney disease (CKD) is characterized by sustained inflammation and progressive fibrosis, however therapies to slow CKD progression are limited. Histone lysine crotonylation (Kcr) as a novel post-translational modification is widespread as acetylation (Kac), but its roles in CKD are largely unknown. In the study, we firstly reported that the nuclear histone Kcr in tubular epithelial cells was significantly elevated in fibrotic kidney of patients and mice, which was positively correlated with the progression of disease. Interestingly, abnormal increase of histone 3 lysine 9 crotonylation (H3K9cr) in kidneys of unilateral ureteric obstruction (UUO) and folic acid nephropathy (FAN) was completely different to the stable expression of H3K9ac, indicating that H3K9cr may exert extraordinary functions in kidney fibrosis. By screening these crotonylated/acetylated factors, crotonyl-CoA-producing enzyme ACSS2 (acyl-CoA synthetase short chain family member 2) remarkably promoted H3K9cr without influencing H3K9ac to trigger proinflammatory cytokine IL-1β transcription. Furthermore, genetic and pharmacologic inhibition of ACSS2 both attenuated kidney injury and fibrosis, as well as suppressed H3K9cr-mediated IL-1β expression, which thus to alleviate IL-1β-dependent macrophage activation and tubular cell senescence. Collectively, our finding uncovers that H3K9cr plays a critical, previously unrecognized role in kidney fibrosis, where ACSS2 represents an attractive target for strategies that aim to slow fibrotic kidney disease progression

overall_design: To understand the functions of ACSS2 in kidney fibrosis, we established ACSS2 konckout mouse

first: Lingzhi

last: Li

first: Liang

last: Ma


title: Tumor-infiltrating monocytic myeloid-derived suppressor cells contribute to the development of an immunosuppressive tumor microenvironment in gastric cancer

status: Public on Jan 22 2024

city: Fukuoka

first: Chikanori

last: Tsutsumi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Surgery and Oncology, Graduate School of Medical Sciences

institute: Kyushu University

summary: The present study suggests that TI-M-MDSCs, especially IER3+ ones, may play a predominant role in the development of the immunosuppressive and ICI-resistant GC TIME.

overall_design: We performed scRNA-seq analysis from 12 tumors and 10 non-tumor samples, who performed gastrectomy.

first: Kenoki

last: Ohuchida


title: Histone H3.1 is a chromatin embedded redox sensor triggered by tumor cells developing adaptive phenotypic plasticity and multi-drug resistance  [RNA-Seq]

first: Matthew

last: Schipma

overall_design: mRNA was collected from control cells and 4h or 24h after treatment with D-Alanine (ROS generated in the nucleus)

first: Flavio

last: Palma

first: Marcelo

middle: G

last: Bonini


title: Effect of mechanical constriction forces on breast cell lines transcripts

status: Public on Feb 16 2024

city: London

first: Julia

last: Perea Paizal

address: Imperial College London, Department of Bioengineering

institute: Imperial College London

summary: During metastatic dissemination, circulating tumour cells (CTCs) enter capillary beds, where they experience mechanical constriction forces. A high-throughput microfluidic platform mimicking human capillaries to investigate the impact of mechanical constriction forces on malignant and normal breast cell lines was developed. Cells were collected after transiting the constrictions, followed by RNA extraction and sequencing. The non-malignant cell line experienced transcriptional changes, particularly downregulation of epithelial markers, while the metastatic cell lines showed minimal alterations.

overall_design: In this study, the effects of capillary constriction forces on the transcriptomics of the breast cell lines MDA-MB-231, LM2 and MCF-10 were investigated. Cells transited microfluidic constrictions of 5x5x150µm3 (width by height by length) dimensions under physiological hydrostatic pressures (7-33cmH2O) and were collected upon transit, followed by RNA-seq. Controls of untransited cells for each cell line were included. For each condition (control and cells that had transited the constriction), duplicates were included.


title: Energy Balance Drives Diurnal and Nocturnal Brain Transcriptome Rhythms

status: Public on Feb 14 2024

first: Laura

last: van Rosmalen

state: California

address: 10010 N Torrey Pines Rd

department: RBIO-P

institute: Salk Institute for Biological Studies

summary: Plasticity in the daily timing of activity has been observed in a wide variety of species, yet the underlying mechanisms driving nocturnality and diurnality remain to be discovered. By regulating how much wheel-running activity will be rewarded with a food pellet, we can manipulate energy balance, and switch mice to be nocturnal or diurnal. Here we present the rhythmic transcriptome of 21 tissues, including 17 brain regions (hypothalamic, thalamic, cortical), sampled every 4 hours over a 24-hour period from nocturnal and diurnal male CBA/CaJ mice. Rhythmic gene expression across tissues comprised a different set of genes with minimal overlap between nocturnal and diurnal mice. We show that genes other than clock genes in the suprachiasmatic nucleus (SCN) of nocturnal and diurnal mice change, and the habenula was the most affected tissue. Our results indicate that adaptive flexibility in daily timing of behavior is supported by gene expression dynamics in many tissues and brain regions, especially in the habenula, which suggests a crucial role for the observed nocturnal-diurnal switch.

overall_design: Diurnal mRNA expression profiles from 21 tissues including 17 brain sites from nocturnal and diurnal mice. 493 libraries were sequenced. Each library was sequenced 1-3 times.

first: Shaunak

last: Deota

first: Geraldine

last: Maier

first: Hiep

last: Le

first: Terry

last: Lin

first: Ramesh

middle: K

last: Ramasamy

first: Roelof

last: Hut

first: Satchidananda

last: Panda


title: NCoR1 limits angiogenic capacity by altering Notch signaling [ATAC-seq]

first: Simonida

last: Zehr

summary: Corepressors negatively regulate gene expression by chromatin compaction. Targeted regulation of gene expression could provide a means to control endothelial cell phenotype. We hypothesize that by targeting corepressor proteins, endothelial angiogenic function can be improved. To study this, the expression and function of nuclear corepressors in human umbilical vein endothelial cells (HUVEC) and in murine organ culture was studied. RNA-seq revealed that nuclear receptor corepressor 1 (NCoR1), Silencing Mediator of Retinoid and Thyroid hormone receptors (SMRT) and repressor element-1 silencing transcription factor (REST) are the highest expressed corepressors in HUVECs. Knockout and knockdown strategies demonstrated that the depletion of NCoR1 increased the angiogenic capacity of endothelial cells, whereas depletion of SMRT or REST did not. Interestingly, the effect was VEGF signaling independent. NCoR1 depletion significantly upregulated angiogenesis-associated genes, especially tip cell genes, including ESM1, DLL4 and NOTCH4, as observed by RNA- and ATAC-seq. Confrontation assays comparing cells with and without NCoR1-deficiency revealed that loss of NCoR1 promotes a tip-cell position during spheroid sprouting. Moreover, a proximity ligation assay identified NCoR1 as a direct binding partner of the Notch-signaling-related transcription factor RBPJk. Luciferase assays showed that siRNA-mediated knockdown of NCoR1 promotes RBPJk activity. Furthermore, NCoR1 downregulation prompts upregulation of several elements in the Notch signaling cascade. Downregulation of NOTCH4, but not NOTCH1, prevented the positive effect of NCoR1 knockdown on spheroid outgrowth. Collectively, these data indicate that decreasing NCOR1 expression is an attractive approach to promote angiogenic function.

overall_design: ATAC sequencing (n = 3) of human umbilical vein endothelial cells (HUVEC) treated with either negative control siRNA or siRNA HSS114352, which knocks down NCoR1  expression.

first: Tom

last: Teichmann

first: Pedro

last: Malacarne

first: Stefan

last: Günther

first: Beatrice

last: Pflüger-Müller

first: Timothy

last: Warwick

first: Ralf

last: Brandes


title: Sequential transcriptional waves and NFκB-driven chromatin remodeling direct drug-induced dedifferentiation in cancer

status: Public on Feb 13 2024

city: SEATTLE

first: Wei

last: Wei

state: Washington

address: 401 Terry Ave N

institute: Institute For Systems Biology

overall_design: Refer to individual Series


title: An immunophenotype coupled transcriptomic atlas of human hematopoietic progenitors

status: Public on Jan 26 2024

city: Cincinnati

first: Xuan

last: Zhang

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's hospital

summary: Understanding the cellular heterogeneity and lineage potential of human bone marrow hematopoietic progenitors is required to understand normal differentiation and the mechanisms of hematological disease. Central to this objective are protocols that enable the delineation, isolation and functional characterization or known and novel cell populations, which are traditionally empowered by flow cytometry. Recognizing the need for tackling cellular heterogeneity, we have designed a use case for compiling next-generation processing methods via existing and highly curated single-cell interrogation technologies. Multi-omics approaches, such as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), enable concurrent transcriptomic and immunophenotyping at a single-cell level but necessitate precision antibody titration mixes that can be directly integrated with parallel flow cytometry strategies. To bridge this gap, we performed a molecular titration of 266 antibodies using primary human bone marrow cells spanning race and sex to approximate diversity. Through machine learning and user curation, we created an optimized titrated bone marrow CITE-seq panel of 132 antibodies. Multimodal integration of these data using a game-theory driven approach, improved our ability to resolve new stable stem, progenitor, and transitional cell populations, readily defined by unique RNA and ADT markers. Leveraging complexity-matching high-dimensional flow cytometry (pyInfinityFlow), we consolidated the findings from CITE-seq and subsequently developed novel isolation strategies for maturing granulocytes, late-stage erythroid progenitors and improved purification of megakaryocyte/erythrocyte progenitors (MEP). Finally, we integrated CITE-seq with flow cytometry data from matching donors, successfully identified 37 cell surface markers consistently expressed across donors and technologies. The compiled bone marrow cell atlas serves as an advanced digital analytical resource for progenitor analyses in health and disease.

overall_design: CITE-seq molecular titration on four donors varing race and sex. Human bone marrow relevant ADTs and their best working concentration are determined. 132 ADTs titrated mix is used on four more donors and used to construct the atlas

first: Baobao

last: Song

first: Maximillian

last: Carlino

first: Guangyuan

last: Li

first: Kyle

last: Ferchen

first: Mi

last: Chen

first: Evrett

last: Thompson

first: Bailee

middle: N

last: Kain

first: Dan

last: Schnell

first: Kairavee

last: Thakkar

first: Stuart

last: Hay

first: David

last: Bernardicius

first: Siyuan

last: Ma

first: Sierra

last: Bennett

first: Josh

last: Croteau

first: Ornella

last: Salvatori

first: Melvin

last: Lye

first: Austin

middle: E

last: Gillen

first: Craig

last: Jordan

first: Harinder

last: Singh

first: Diane

last: Krause

first: Nathan

last: Salomonis

first: H

middle: L

last: Grimes


title: Hi-C in Saccharomyces cerevisiae strains,

first: Ajaz ul Hamid

last: Wani

summary: We report change in the chromatin contacts upon deletion of ATP-dependent chromatin remodellers (ISW1, ISW2 and CHD1) in Saccharomyces cerevisiae.

overall_design: Both wildtype and triple knockout strains chromatin were crosslinked, digested with DpnII, biotin labelled and ligated. After DNA purification biotin was removed from free ends and then sonicted.Size selection was done by ampure beads and NGS library was prepared and sequenced

first: Ajazul

last: Hamid Wani

first: Fouziya

last: Rashid


title: Thyroid Hormones Promotes Terminal Differentiation of Medulloblastoma Tumor Cells

city: Philadelphia

first: Duancheng

last: Guo

state: PA

address: 333 Cottman AVE

institute: Fox Chase Cancer Center

summary: Hypothyroidism is commonly detected in patients with medulloblastoma (MB), a pediatric brain tumor, which is generally considered as a treatment-related complication. Although reduced levels of thyroid hormone (TH) significantly correlate with poor survival of patients with MB, the possible link between TH signaling and MB pathogenicity is unknown. Here, we found that TH regulating terminal differentiation of tumor cells. Reduction in the levels of TH frees the unliganded TH receptor, TRα, to bind to EZH2 and repress expression of NeuroD1, a transcription factor that drives terminal differentiation of neuronal progenitors as well as MB cells. Moreover, TH promotes extensive differentiation and reduced proliferation of tumor cells from multiple molecular subtypes of MB including the hedgehog (HH) group as well as group 3 (G3) MB. Consequently, TH treatment significantly inhibits the in vivo growth of SHH- and G3-MB by promoting tumor cell differentiation, with no obvious increase in tumor cell death, indicating that TH signaling represents a novel therapeutic entry-point for broad treatment of MB.

overall_design:
We assess the genetic profiles of tumor cells. Tumor cells from mice with conditional deletion of Ptch1, an established model for SHH-MB, were treated with T3 or PBS, by RNA sequencing. KEGG pathway analyzy neuronal differentiation related pathways. The neuronal differentiation associated genes and SHH pathway target genes was analyzed as well.
RNA sequencing on tumor cells from mice with conditional deletion of Ptch1, an established model for SHH-MB, as well as human PDOX Shh and Group3 subtypes were assessed for comparisons between T3 treatments and PBS controls.

first: Zeng-jie

last: Yang

first: Yijun

first: Shengyou

last: Liao