title: Short Peptides based on the conserved regions of MIEN1 protein exhibit anti-cancer activity by targeting the MIEN1 Signaling Pathway

city: West haven

first: Antariksh

last: Tyagi

state: CT

address: 830 West Campus Dr

institute: Yale University

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways in different types of cancers. The goals of this study are to identify differentially expressed genes(DEGs) upon MIEN1 derived anticancer peptide treatment and its analogs by RNA-seq and to compare  quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: MDA-MB-231 cellular mRNA profiles of Peptide-treated and Untreated breast cancer cells

first: Amit

last: Tripathi

first: Jamboor

last: Vishwanatha


title: Electrical stimulation to repair spinal cord injury

status: Public on Jul 01 2023

city: xi'an

first: Erliang

last: Li

address: xin si street

country: China

institute: tangdu hospital

type: Expression profiling by high throughput sequencing

summary:
To investigate  the mechanism of electrical stimulation in the repair of spinal cord injury, we established a rat model of spinal cord injury.
Then, we used RNA-SEQ data obtained from ES treatment and 6 different rat models of spinal cord injury for gene expression profile analysis.

overall_design: Comparative gene expression profile analysis of RNA-seq data of rat models of SCI treated with ES.

first: Bo

last: Liao


title: Gene expression profiles of human adrenocortical NCI-H295R cells treated with cortisol biosynthesis inhibitors

status: Public on Jul 11 2023

city: Seoul

first: Soo Hyun

last: Kim

address: Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu

country: South Korea

institute: Ewha Womans University

summary: We have recently identified a set of benzimidazolylurea derivatives including a representative compound (designated as CJ28), which inhibit both cortisol production and de novo cholesterol biosynthesis. To evaluate its putative mode-of-actions, we examined genome-wide RNA expression profiles of human adrenocortical carcinoma NCI-H295R cell cultures by treatment with CJ28 in comparison with metyrapone (MET), a well-established cortisol biosynthesis inhibitor.

overall_design: NCI-H295R (H295R; ATCC CRL-2128) cells were maintained in DMEM/F12 supplemented with 1% ITS+, 2.5% Nu-Serum and 1% antibiotic-antimycotic solution. Confluent cells were incubated in serum-free media for 12 h and then treated with CJ28 (30 μM), MET (30 μM) or vehicle (VEH; 0.1% DMSO) for 24 h with 4 biological replicates for each group.

first: Sooyoung

last: Chung

first: Soo

middle: H

first: Gi

last: Son

first: Hyun

middle: J

first: Jong-Wha

last: Jung


title: Production of hiPSC-based tumour models

status: Public on Jul 04 2023

city: Magdeburg

first: Ulf

last: Kahlert

address: Leipziger Str 44

country: Germany

institute: Otto-vo-Guericke University

summary: Generation of in vitro models of cancer stem cells for in vivo xenograft models.  hiPSC differentiation into a desired tissue allows studying physiologic processes in human-relevantcell systems. By introducing disease-specific mutations, these cells allow studying genetic origins of diseases in a tissue-specific manner.

overall_design: In vitro models of cancer stem cells for in vivo xenograft model

first: Daniel

last: Picard

first: Ann-Christin

last: Nickel


title: Molecular and Metabolic Analysis of Arsenic-Exposed Humanized AS3MT Mice

status: Public on Jul 03 2023

city: Ithaca

first: Praveen

last: Sethupathy

state: NY

address: Cornell University, College of Veterinary Medicine Room #T7006, Vet Research Tower 618 Tower Rd.

department: Cell and Molecular Biology

country: USA

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Chronic exposure to inorganic arsenic (iAs) has been associated with type 2 diabetes (T2D). However, potential sex divergence and the underlying mechanisms remain understudied. iAs is not metabolized uniformly across species, which is a limitation of typical exposure studies in rodent models. The development of a new “humanized” mouse model overcomes this limitation. In this study, we leverage this model to study sex differences in the context of iAs exposure.
Objectives: The aim of this study iwas to determine if males and females exhibit different liver and adipose molecular profiles and metabolic phenotypes in the context of iAs exposure.
Methods: Our study was performed on wild-type (WT) 129S6/SvEvTac and humanized arsenic +3 methyl transferase (human AS3MT) 129S6/SvEvTac mice treated with 400 ppb of iAs via drinking water ad libitum. After 1 month, mice were sacrificed and the liver and epididymales gonadal adipose depot were harvested for iAs quantification as well as sequencing-based microRNA and gene expression analysis. Serum blood was collected for fasting blood glucose, fasting plasma insulin, and HOMA-IR.
Results: We detected sex divergence in liver and adipose markers of diabetes (e.g., insulin signaling pathways, fasting blood glucose, fasting plasma insulin, and HOMA-IR) only in humanized (not WT) male mice. In humanized female mice, numerous genes that promote insulin sensitivity and glucose tolerance in both the liver and adipose are elevated compared to humanized male mice. We also identified Klf11 as a putative master regulator of the sex divergence in gene expression in humanized mice.
Discussion: Our study underscoreds the importance of future studies leveraging the humanized mouse model to study iAs-associated metabolic disease. The findings also suggest suggested that humanized females are protected  from metabolic dysfunction relative to humanized males in the context of iAs exposure. Future investigations should focus on the detailed mechanisms that underlie the sex divergence, including the potential role of miR-34a and/or Klf11.

overall_design: WT mice and mice expressing humanized AS3MT were exposed to  of iAs via drinking water ad libitum. After 1 month, mice were sacrificed and the liver and gonadal adipose depots were harvested for iAs quantification and sequencing-based microRNA and gene expression analysis. Serum blood was collected for fasting blood glucose, fasting plasma insulin, and homeostatic model assessment for insulin resistance (HOMA-IR).

first: Jenna

middle: E

last: Todero

first: Christelle

last: Douillet

first: Alexandria

last: Shumway

first: Beverly

last: Koller

first: Matt

last: Kanke

first: Daryl

last: Phuong

first: Miroslav S

last: Stýblo


title: Effects of lifelong exercise and age on transcriptome dynamics in MHC I and MHC IIa muscle fibers at baseline and in response to resistance exercise (all samples)

status: Public on Jul 05 2023

city: Manhattan

first: Aliza

last: Rubenstein

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

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

overall_design: Refer to individual Series


title: RNA-sequencing reveals differentially expressed rice genes functionally associated with defense against brown planthopper in NILs pyramiding BPH14 and BPH15

city: Wuhan

first: Liang

last: Hu

address: 1 Nanhu Yaoyuante, Hongshan District

institute: Hubei Academy of Agricultural Sciences

summary: Brown planthopper (BPH) is one of the most destructive pests in rice production. The pyramiding application of BPH-resistance genes BPH14 and BPH15 can effectively improve rice resistance to BPH, however, the molecular mechanisms underlying BPH14/BPH15 pyramiding lines are poorly understood. Here, a mRNA expression profiling analysis was performed on the near isogenic lines (NILs) containing the BPH14, BPH15 or BPH14/BPH15 and their recurrent parent (RP) Wushansimiao. A total of 14492 differentially expressed mRNAs (DEGs) were identified from 12 mRNA profiles of resistant NILs and RP at different feeding stages. In the transcriptome analysis, 531 DEGs appeared to be common among the resistant NILs compared to RP before and after BPH feeding, which were enriched in defense response, phosphorylation and salt stress response. In addition, 258 DEGs shared only in resistant NILs were obtained among the different feeding stages, which were enriched in oxidative stress response, karrikin response and chloroplast organization. 21 DEGs were further selected as candidates for BPH resistance. OsPOX8.1, a potential candidate DEG related to BPH resistance, increased reactive oxygen species levels in rice protoplast. Our results provide valuable information to further explore the defense mechanism of insect-resistant gene pyramiding lines and develop robust strategies for insect control.

overall_design: JL, AY and LH conceived and designed research.

first: Dabing

last: Yang

first: Hongbo

last: Wang

first: Xueshu

last: Du

first: Yanming

last: Zhang

first: Liping

last: Niu

first: Bingliang

last: Wan

first: Mingyuan

last: Xia

first: Huaxiong

last: Qi

first: Tongmin

last: Mou

first: Aiqing

last: You

first: Jinbo

last: Li


title: Totum-070, a nutritional combination of plant extracts, prevents hypercholesterolemia in high fat diet-fed hamsters by inhibiting intestinal cholesterol absorption

status: Public on Jun 30 2023

city: Riom

first: Cédric

last: Langhi

address: 20-22 rue Henri et Gilberte Goudier

country: France

institute: Valbiotis

summary: Atherosclerotic cardiovascular disease is the leading cause of mortality worldwide. Hypercholesterolemia is a risk factor of atherosclerosis. This study evaluated the effects of three doses of Totum-070 (3.5%, 4.25% and 5% of diet for 12 weeks; HFD-Totum-070 groups), a plant-based polyphenol-rich supplement, in hamsters with high-fat diet (HFD)-induced dyslipidemia (HFD group). Several functional tests were performed in vivo to characterize the effect of Totum-070 on lipoprotein metabolism. Molecular mechanisms of action were explored using human Caco2 enterocytes. Totum-070 supplementation reduced total cholesterol (-41%), non-HDL cholesterol (-47%) and triglycerides (-46%) in a dose-dependent manner, compared with HFD, without any effects on food intake or body weight. HFD-induced steatosis also was significantly decreased. Gene expression analysis in liver and intestine highlighted Totum-070 effects on metabolic pathways and a strong anti-inflammatory effect. Upon challenge with olive oil gavage, post-prandial lipemia was strongly reduced. Sterol excretion in the feces was increased in the HFD-Totum-070 groups compared with the HFD group. The dual isotope cholesterol absorption test confirmed the reduction of intestinal cholesterol absorption in Totum-070 supplemented hamsters. These effects were confirmed in Caco2 cells where incubation with Totum-070 inhibited cholesterol uptake and apolipoprotein B secretion. Furthermore, metagenomic analysis of gut microbiota revealed a strong effect of Totum-070 on alpha and beta diversity measures. Compared with the HFD group, the Firmicutes to Bacteroidetes ratio was beneficially reduced in the HFD-hamsters supplemented with Totum-070 groups. Altogether, these findings indicate that Totum-070-mediated inhibition of intestinal cholesterol absorption limits the rise in blood cholesterol in high-fat fed hamsters.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hamster livers from 3 experimental groups: hamsters fed with a Normal Diet (ND), hamsters fed with a High Fat Diet (HFD) and hamsters fed with HFD supplemented with Totum-070 (HFD-T070 5%)

first: Cedric


title: Palovarotene action against heterotopic ossification includes the inhibition of local participating activin-A expressing cell populations

city: Philadelphia

first: Maurizio

last: Pacifici

state: PA

address: 3615 Civic Center Blvd

department: Surgery

institute: The Children's Hospital of Philadelphia

summary: Heterotopic ossification (HO) consists of extraskeletal bone formation. One form of HO is acquired and instigated by traumas or surgery, and another form is genetic and characterizes Fibrodysplasia Ossificans Progressiva (FOP). We and others showed that activin A promotes both acquired and genetic HO and found that the retinoid agonist Palovarotene inhibits both HO forms in mice.  We asked whether Palovarotene's action against HO may include an interference with endogenous activin A expression and/or function. Using a mouse model of acquired HO, we found that activin A and its encoding RNA (Inhba) were prominent in chondrogenic cells within developing HO masses in untreated mice. Single cell RNAseq (scRNAseq) assays verified that  Inhba expression characterized chondroprogenitors and chondrocytes in untreated HO, in addition to its expected expression in inflammatory cells and macrophages. Palovarotene administration caused a sharp inhibition of both HO and amounts of activin A and Inhba transcripts. Bioinformatic analyses of scRNAseq datasets indicated that the drug had reduced interactions and crosstalk amongst cell populations. Our data reveal that Palovarotene markedly reduces the number of local Inhba-expressing HO-forming populations.

overall_design: Female mice were implanted subcutaneously with rhBMP2/Matrigel mixture and received daily doses of vehicle or Palovarotene. As an additional control, companion mice were implanted with Matrigel without rhBMP2 and did not receive Palovatorene. On day 5, ectopic tissue masses were harvested from each mouse group, and their cells were liberated by enzymatic digestion and directly processed for scRNA-seq.

first: Christina

last: Mundy

first: Lutian

last: Yao

first: Kelly

middle: A

last: Shaughnessy

first: Cheri

last: Saunders

first: Eileen

middle: M

last: Shore

first: Eiki

last: Koyama


title: Transdifferentiating alveolar macrophages characterized by Placenta-expressed transcript 1 (Plet1) expression

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: This experiment is performed to analyse the differential expression of genome pattern on both M1 and M2 macrophages during infection in vivo. This experiment could provide us the key genes that regulate the phenotype of macrophages and the difference in expression of pro-survival and anti-apoptotic genes during influenza virus induced acute lung injury.The animlas are infected with (PR8) influenza virus and the bronchoalveolar lavage samples are collected with PBS+EDTA and stained with antibodies. later proceeded with cell sorter to sort out M1 macrophages from D7 pi and M2 macrophages from D21 pi.

overall_design: n = 8 animals were used, macrophages were isolated from bronchoalveolar lavage either at day 7 p.i. (n=4) or at day 21 p.i. (n=4).

first: Balachandar

last: Selvakumar


title: BACH1 is a central regulator of glutathione and iron metabolism, necrotic cell death and host resistance in Mycobacterium tuberculosis infection

city: Bethesda

first: Sivaranjani

last: Namasivayam

address: 33 North Drive

department: NIAID

institute: NIH

summary: Exacerbated oxidative stress response is known to regulate cellular necrosis by triggering lipid peroxidation in an iron-dependent manner and this form of necrotic death has been implicated in Mycobacterium tuberculosis (Mtb) infection and disease. Here we examined the role of Bach1, a transcription factor that represses a major set of antioxidant genes, in regulating host resistance to Mtb. In response to Mtb infection in vitro and in vivo, ablation of Bach1 increased the levels of glutathione as well as enhanced the expression of Gpx4, an enzyme that regulates lipid peroxidation. Consistent with these observations, Bach1-/- macrophages exhibited increased resistance to Mtb-induced necrosis and infected Bach1-deficient mice displayed a striking reduction in bacterial loads as well as pulmonary necrosis and lipid peroxidation reflected in their enhanced survival. In addition, single-cell RNAseq analysis of the lungs of Mtb-infected Bach1-/- mice revealed an enrichment of a gene signature associated with protection against ferroptotic cell death. Finally, deletion of Bach1 in B6.Sst1S mice, an inbred strain that recapitulates the necrotic lung pathology seen in human TB, enhanced host resistance to Mtb while significantly reducing tissue necrosis. These findings identify Bach1 as an important regulator of cellular and tissue necrosis in Mtb infection and as such a potential target for host-direct therapy of tuberculosis.

overall_design: WT and Bach1KO mice were infected with M. tuberculosis via the aerosol route. 23 days post infection lungs were harvested and cells isolated. Sorted live cells were used for scRNAseq processing and analysis


title: RADseq for tumour mutation burden estimation and mutation signature analysis.

city: Melbourne

first: Conor

middle: Friend

last: McGuinness

state: VIC

address: 305 Grattan St

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

summary: The utility of RADseq in an experimental setting is also demonstrated, based on our chasacterisation of an APOBEC mutation signature in an APOBEC3A transfected mouse cell line. 0D5 cells, derived from SSM3 cells, were co-transfected with a mixture containing  pcDNA3.1 vectors expressing either APOBEC3A or APOBEC3B (kindly donated by Vincent Caval), pcDNA3.1 construct expressing deaminase null APOBEC3A linked to a uracil deglycosylase construct and a plasmid encoding mutant GFP and WT mCherry that is a reporter for APOBEC mutagenesis. Cells were grown, and gDNA extracted, prior to preparation of RADseq libraries using a PstI- MspI double-digest. Libraries underwent a Pippin Prep to select fragments in the size range of 220-520 bp (genomic sequence plus 148 bp of adapters). Single-end sequencing (1x101bp) was performed on an Illumina NovaSeq6000 utilizing v1.5 chemistry. Reads were aligned to mm10 using bwa mem and variants called using the GATK4 pipeline.

overall_design: Comparison of variants, tumour mutation burden and mutation signatures in SSM3 cell line derivatives transfected with plasmids encoding APOBEC3A, APOBEC3B, or empty vectors.


title: Effect of IGF2BP3 in the development of glioma

status: Public on Jun 29 2023

city: 上海

first: 玮玮

last: 代

state: 上海

address: 徐汇区东安路131号

institute: 复旦大学

summary: To investigate the  function IGF2BP3 in the regulation of tumor occurrence and development, we established 4 U87MG cell lines in which IGF2BP3 gene has been knocked out and overexpression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U87 cells and its KO/OE derivatives (sg-IGF2BP3 and OE-IGF2BP3)

first: Minfeng

last: Shu

first: Weiwei

last: Dai


title: Effects of HSV infection on glioma cells

status: Public on Jun 27 2023

summary: To investigate the effect of HSV infection on glioma cells, we established a model of HSV infection

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U87 cells and HSV-infected U87 cell

first: Yuling

last: Chen


title: ChIP-seq for Characterization of transcription factor function and patterns fo gene regulation in HepG2 cells

status: Public on Jun 26 2023

city: Huntsville

first: Belle

middle: Aine

last: Moyers

state: AL

address: 601 Genome Way

institute: HudsonAlpha

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcription factors (TFs) are trans-acting proteins that bind cis-regulatory elements (CREs) in DNA to control gene expression. Here, we analyze the genomic localization profiles of 529 sequence-specific TFs and 151 cofactors and chromatin regulators in the cancer cell line HepG2, for a total of 680 broadly-termed DNA-Associated Proteins (DAPs). We use this deep collection to model each TF's impact on gene expression, including identifying a cohort of 26 candidate transcriptional repressors. We examine High Occupancy Target (HOT) sites in the context of three-dimensional genome organization and show biased motif placement in enhancer-promoter connections involving HOT sites. We also find a substantial number of closed chromatin regions with multiple DAPs bound and explore their properties, finding that a MAFF/MAFK TF pair correlates with transcriptional repression. Altogether, these analyses provide novel insights into the regulatory logic of the human cell line HepG2 genome and demonstrate the usefulness of large genomic analyses for elucidation of individual TF functions.

overall_design:
We performed ChIP-seq targeting tagged proteins in HepG2 cell lines to identify peaks corresponding to likely TF binding locations.
For the input FASTQs (All entries with the title "SL######"), no antibody pulldown was performed.  These were crosslinked and sheared, as in ChIP-seq, but sequencing was performed on the whole background.

first: E

middle: C

last: Partridge

first: Mark

last: Mackiewicz

first: Michael

last: Betti

first: Roshan

last: Darji

first: Sarah

middle: K

last: Meadows

first: Kimberly

last: Newberry

first: Laurel

last: Brandesmeier

first: Barbara

last: Wold

first: Eric

last: Mendenhall

first: Richard

last: Myers


title: Extracellular sodium regulates fibroblast growth factor 23 (FGF23) formation

status: Public on Jun 23 2023

city: Zurich

first: Ganesh

last: Pathare

state: Zürich

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

summary: Fibroblast growth factor-23 (FGF23) is a bone-derived hormone that has recently received much attention due to its association with the progression of chronic kidney disease, cardiovascular disease, and associated mortality. Extracellular sodium ion concentration ([Na+]) plays a significant role in bone metabolism. Both hyponatremia (low serum [Na+]) and hypernatremia (high serum [Na+]) have been shown to affect bone remodeling. However, nothing is known about the impact of [Na+] on FGF23 production. Here, we show that elevated [Na+] (by +20 mM) suppressed FGF23 formation, whereas low [Na+] (by -20 mM) led to an increase in FGF23 synthesis in the osteoblast-like cell line UMR-106. Similar bidirectional changes in FGF23 were observed when osmolality was altered by mannitol but not by urea, suggesting a role of tonicity in FGF23 formation. Moreover, these changes in FGF23 were inversely proportional to the expression of NFAT5 (nuclear factor of activated T cells-5), a transcription factor responsible for tonicity-mediated cellular adaptations. On the other hand, arginine vasopressin (AVP), which is often responsible for hyponatremia, did not affect FGF23 production. Next, comprehensive and unbiased RNA-seq analysis of UMR-106 cells exposed to low vs. high [Na+] revealed several novel genes involved in cellular adaptation to altered tonicity. Additional analysis of cells with Crisp-Cas9 mediated NFAT5 deletion indicated that NFAT5 controls numerous genes associated with FGF23 synthesis, thereby confirming its role in [Na+]-mediated FGF23 regulation. In line with these findings, in a pilot study, we found that human hyponatremic patients have higher FGF23 levels. Our results suggest that [Na+] is a critical regulator of FGF23 synthesis.

overall_design: We included 12 datasets in the RNA-Seq data analysis: three biological replicates in each group (control with -NaCl, control with +NaCl, NFAT5KO with -NaCl, and NFAT5KO with +NaCl).


title: scRNA-seq characterization of immune cell types among individuals with or without Long COVID

status: Public on Jun 19 2023

city: San Francisco

first: Kailin

last: Yin

state: California

address: 1650 Owens street

institute: Gladstone Institutes

summary: Long COVID (LC), a type of post-acute sequelae of SARS-CoV-2 infection (PASC), occurs after at least 10% of SARS-CoV-2 infections, yet its etiology remains poorly understood. Here, we used multiple “omics” assays (CyTOF, RNAseq/scRNAseq, Olink) and serology to deeply characterize both global and SARS-CoV-2-specific immunity from blood of individuals with clear LC and non-LC clinical trajectories, 8 months following infection and prior to receipt of any SARS-CoV-2 vaccine. Our analysis focused on deep phenotyping of T cells, which play important roles in immunity against SARS-CoV-2 yet may also contribute to COVID-19 pathogenesis. Our findings demonstrate that individuals with LC exhibit systemic inflammation and immune dysregulation. This is evidenced by global differences in T cell subset distribution in ways that imply ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. Individuals with LC harbored increased frequencies of CD4+ T cells poised to migrate to inflamed tissues, and exhausted SARS-CoV-2-specific CD8+ T cells. They also harbored significantly higher levels of SARS-CoV-2 antibodies, and in contrast to non-LC individuals, exhibited a mis-coordination between their SARS-CoV-2-specific T and B cell responses. RNAseq and Olink analyses similarly revealed immune dysregulatory mechanisms, along with non-immune associated perturbations, in individuals with LC. Collectively, our data suggest that proper crosstalk between the humoral and cellular arms of adaptive immunity has broken down in LC, and that this, perhaps in the context of persistent virus, leads to the immune dysregulation, inflammation, and clinical symptoms associated with this debilitating condition.

overall_design:
SARS-CoV-2 serological analysis and four types of “omics” assays were performed on the same blood specimens from our cohort of LC and non-LC individuals (Fig. 1). Plasma/sera were analyzed for RBD-specific antibody levels, and for the levels of 394 analytes using the Olink platform. PBMCs from the same specimens were subjected to bulk RNAseq, as well as in-depth CD4+ and CD8+ T cell phenotyping using a 39-parameter CyTOF panel designed to simultaneously interrogate the differentiation states, activation states, effector functions, and homing properties of T cells (Table S2). Cells were phenotyped by CyTOF at baseline and following a 6-hour stimulation with SARS-CoV-2 peptides to identify and characterize SARS-CoV-2-specific T cells at the single-cell level through intracellular cytokine staining. The RNAseq/scRNAseq and Olink datasets, as well as the CyTOF datasets corresponding to total and SARS-CoV-2-specific T cells, were visualized and analyzed using a variety of integrative high-dimensional analysis approaches (Fig. 1). In total, we obtained 5 distinct datasets, enabling us to assess humoral response (serology), plasma analytes (Olink), transcriptional signatures at the bulk (RNAseq) and single-cell (scRNAseq) levels, T cell features (CyTOF), and SARS-CoV-2-specific T cell phenotypes and effector functions (CyTOF).
sample_sheet.csv: the details of every sample sequenced including grouping information as well as index information.
sample_cell_count_data.csv: the relevant information considering clustering information, absolute cell counts information as well as cell type information.
Methods_Kailin_et_al_PASC_scRNAseq.txt: the details of every step involved in data processing
sessionInfo.text: the platforms as well as packages used in the whole analysis

last: Peluso

first: Timothy

last: Henrich

first: Nadia

middle: R

last: Roan


title: The ROK-family regulator RokL6 is involved in GlcN toxicity by controlling the transcription of SCO1448 in Streptomyces coelicolor [ChIP-seq]

city: Ledien

first: Gilles

middle: P.

last: van Wezel

address: Sylviusweg 72

department: Institute of Biology Leiden

country: Netherlands

institute: Leiden University

summary: Streptomycetes are saprophytic bacteria that grow on complex polysaccharides, such as cellulose, starch, chitin and chitosan. For the monomeric building blocks glucose, maltose and N-acetylglucosamine the metabolic pathway is well documented, but that of glucosamine (GlcN) is currently unknown. Importantly, GlcN is lethal to Streptomyces coelicolor nagB mutants, which lack glucosamine-6-phosphate deaminase activity. Here we report that spontaneous and directed mutations in the gene for the ROK-family protein RokL6 (SCO1447) relieve GlcN toxicity in nagB mutants of S. coelicolor. RNA sequencing, ChIP-Seq and over-expression studies revealed that RokL6 acts by directly repressing SCO1448, which encodes a sugar exporter; RokL6 thereby only binds to the rokL6-SCO1448 intergenic region in vivo, with consensus binding site C(T)TATCAGG - 7 nt - CCTGATAG(A). The exact transcriptional start sites for rokL6 and SCO1448 were determined using 5’RACE. RokL6 represses the transcription of both rokL6 and SCO1448 by binding to overlapping promoter sequences. Taken together, our data show that RokL6 and SCO1448 are novel GlcN-related genes, whereby RokL6 directly controls the transcription of SCO1448. The latter is a key protein in the defense of S. coelicolor against the toxicity of GlcN in a nagB-mutant background, most likely via the export of GlcN-derived toxic intermediates.

overall_design: To investigare the transcriptional control by RokL6, RNAseq analysis was performed using RNA extracted from Streptomyces coelicolor M145 and its rokL6 null mutant grown on minimal medium agar plates with mannitol or mannitol plus GlcN.

first: Chao

last: Li

first: Mia

last: Urem

middle: P


title: Dynamic enhancer interactome promotes senescence and aging [Hi-ChIP I]

status: Public on Jun 20 2023

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: Gene expression programs are regulated by enhancers which act in a context-specific manner, and can reside at great distances from their target genes. Extensive three-dimensional (3D) genome reorganization occurs in senescence, but how enhancer interactomes are reconfigured during this process is just beginning to be understood. Here we generated high-resolution contact maps of active enhancers and their target genes, assessed chromatin accessibility, and established one-dimensional maps of various histone modifications and transcription factors to comprehensively understand the regulation of enhancer configuration during senescence. Hyper-connected enhancer communities/cliques formed around genes that are highly expressed and within essential gene pathways in each cell state. In addition, motif analysis indicates the involvement of specific transcription factors in hyper-connected regulatory elements in each condition; importantly, MafK, a bZIP family transcription factor, was upregulated in senescence, and reduced expression of MafK ameliorated the senescence phenotypes. Because the accumulation of senescent cells is a key feature of aging, we further investigated enhancer connectomes in the liver of young and aged mice. Hyper-connected enhancer communities were identified during aging, which regulate essential genes that maintain cell differentiation and homeostasis. These findings reveal that hyper-connected enhancer communities correlate with high gene expression in senescence and aging and provide potential hotspots for therapeutic intervention in aging and age-associated diseases.

overall_design: Two biological replicates each of H3K27ac Hi-ChIP in proliferating IMR90 human fibroblasts or the same fibroblasts infected with HRasV12 to induce oncogene-induced senescence (OIS). Data are in five batches of technical repeats (two in rep1, three in rep2) for both conditions.

first: Lu

last: Wang

first: Greg

first: Chen

last: Zhang

first: Aaron

last: Havas

first: Xue

last: Lei

first: Caiyue

last: Xu

first: Wenliang

first: Golnaz

last: Vahedi

first: Peter

last: Adams

first: Shelley

middle: L

last: Berger


title: The ROK-family regulator RokL6 is involved in GlcN toxicity by controlling the transcription of SCO1448 in Streptomyces coelicolor [RNA-seq]


title: The ROK-family regulator RokL6 is involved in GlcN toxicity by controlling the transcription of SCO1448 in Streptomyces coelicolor.


title: Transcriptomic Atlas of Embryonic Human Craniofacial Development

city: Farmington

first: Tara

middle: N.

last: Yankee

state: Connecticut

address: 400 Farmington Ave

institute: UConn Health

summary: A majority of craniofacial development occurs early in pregnancy and to fully understand how craniofacial defects arise, it is essential to observe gene expression during this critical time period. To address this, we performed bulk and single-cell RNA-seq on human craniofacial tissue from embryonic development -4 to 8 weeks post conception. To observe how genes are organized in this system, we have constructed co-expression networks from the bulk RNA-seq. Strong disease candidates are likely genes that are co-expressed with many other genes, serving as regulatory hubs within these networks. We have identified 29 modules of co-expressed genes and ~1800 hub genes and found enrichment of craniofacial relevant biology suggesting that these networks could reveal new disease genes and potential targets of previously identified disease genes. We leveraged large functional genomics databases including GTEx and GnomAD to reveal genes that are specifically expressed in craniofacial tissue. We integrate these data with our co-expression networks in order to prioritize the genes in this study. Our analysis revealed 268 novel or underappreciated disease candidate genes.

overall_design:
RNA-seq performed on dissected human craniofacial tissue from three replicates of 4 time points and a culture model of cranial neural crest cells (CNCCs). Single-nuclei-RNA-seq was performed on two replicates of CS20 craniofacial primary tissue. ChIP-seq performed on CNCCs and chromatin states called to compare to previously published chromatin states from primary craniofacial tissue.

**RAW data for Samples GSM5919238 and GSM5919239 are deposited in dbGAP**

middle: N

first: Andrea

last: Wilderman

first: Emma

last: Wentworth

first: Justin

last: Cotney


title: Ldlr-/-.Leiden mice develop neurodegeneration, age-dependent astrogliosis and obesity-induced changes in microglia immunophenotype which are partly reversed by complement component 5 neutralizing antibody.

status: Public on Jun 18 2023

city: Leiden

first: Martine

last: Morrison

address: Sylviusweg 71

department: MHR

institute: TNO

summary: Abstract  Obesity has been linked to vascular dysfunction, cognitive impairment and neurodegenerative diseases. However, experimental models that recapitulate brain pathology in relation to obesity and vascular dysfunction are still lacking. In this study we performed the histological and histochemical characterization of brains from Ldlr-/-.Leiden mice, an established model for obesity and associated vascular disease. 18 week-old and 50 week-old Ldlr-/-.Leiden male mice were compared with age-matched C57BL/6J mice. We then assessed the effect of high-fat diet (HFD)-induced obesity on  brain pathology in Ldlr-/-.Leiden mice and tested whether a treatment with an anti-complement component 5 antibody, a terminal complement pathway inhibitor recently shown to reduce vascular disease, can attenuate neurodegeneration and neuroinflammation. Histological analyses were complemented with Next Generation Sequencing (NGS) analyses of the hippocampus to unravel molecular pathways underlying brain histopathology. We show that Ldlr-/-.Leiden mice have more severe neurodegeneration and show an age-dependent astrogliosis that is not observed in age-matched C57BL/6J controls. This was substantiated by pathway enrichment analysis using the NGS data which showed that oxidative phosphorylation, EIF2 signaling and mitochondrial dysfunction pathways, all associated with neurodegeneration, were significantly altered in the hippocampus of Ldlr-/-.Leiden mice compared with controls. Obesity-inducing HFD-feeding did not aggravate neurodegeneration and astrogliosis. However, brains from HFD-fed Ldlr-/-.Leiden mice showed reduced IBA-1 immunoreactivity and increased CD68 immunoreactivity compared with chow-fed controls, indicating an altered overall microglial immunophenotype by HFD feeding. The systemic administration of an anti-C5 treatment partially restored the HFD effect on microglial immunophenotype. In addition, NGS data of hippocampi from Ldlr-/-.Leiden mice showed that HFD affected multiple molecular pathways: HFD notably inactivated synaptogenesis and activated neuroinflammation pathways. The anti-C5 treatment restored the HFD-induced effect on molecular pathways to a large extent. This study shows that the Ldlr-/-.Leiden mouse model is suitable to study brain histopathology and associated biological processes in a context of obesity and provides evidence of the potential therapeutic value of anti-complement therapy against obesity-induced neuroinflammation.

overall_design: A reference group of C57BL/6J mice received Standard Chow diet (weaned-50wks). Three groups of Ldlr-/-.Leiden mice received: (i) Standard Chow diet (weaned-50wks), 2 weekly control vehicle injections (30-50wks); (II) Standard Chow diet (weaned-18wks), HFD (High Fat Diet, 18-50wks), 2 weekly control vehicle injections (30-50wks); (III) Standard Chow diet (weaned-18wks), HFD (High Fat Diet, 18-50wks), 2 weekly injections with BB5.1 anti-Complement C5 antibodies (30-50wks). Plasma parameters were evaluated, organs were examined and hippocampal transcriptome analysis was performed.

first: Florine

last: Seidel

first: Kees

last: Fluiter

first: Robert

last: Kleemann

first: Nicole

last: Worms

first: Anita

last: van Nieuwkoop

first: Martien

last: Caspers

first: Nikolaos

last: Grigoriadis

first: Amanda

last: Kiliaan

first: Frank

last: Baas

first: Iliana

last: Michailidou


title: Single-cell sequencing dissects the transcriptional identity of activated fibroblasts and identifies novel persistent distal tubular injury patterns in kidney

status: Public on Jun 14 2023

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: Mouse E18.5 wildtype kidney single-cell reference.

overall_design: E18.5 wildtype kidneys were analyzed by single-cell RNA-seq.

first: Joo-seop

last: Park


title: Single-cell chromatin accessibility profiling reveals a self-renewing muscle satellite cell state

city: Durham

first: Yarui

last: Diao

state: North Carolina

address: 307 Research Drive, Box 3709

department: Cell Biology

institute: Duke University School of Medicine

summary: Successful skeletal muscle regeneration is primarily mediated by muscle stem cells or satellite cells which express Pax7. In homeostasis, these satellite cells exist in a ‘genuine quiescent’ state, although some satellite cells may also be primed. After an acute injury, satellite cells, enabled by several other niche cells in the muscle tissue, undergo a series of molecular and cellular changes such as activation, proliferation, and differentiation. These processes culminate in the generation of nascent muscle fibers or the restoration of worn-out muscle fibers, leading to the restoration of muscle function. To prevent the depletion of the quiescent satellite cell pool, some satellite cells must resist the ambient differentiation signals and undergo the self-renewal process. While the differentiation process has been well characterized, little is known about the mechanism of satellite cell self-renewal. Furthermore, the molecular identity of self-renewing satellite cells remains unknown. To fill this gap, we utilize single nuclei ATACseq with high temporal resolution to characterize the temporal dynamics of chromatin accessibility in satellite cells and other muscle niche cells during muscle regeneration. This enables us to identify for the first time the self-renewing trajectory undertaken by satellite cells for their long-term repopulation. We also validated these findings using single-cell RNAseq and other protein-level assays. We also utilize gene perturbation to show that SMAD4, a co-SMAD regulating the TGF-beta pathway regulates the cfate choice of self-renewal versus differentiation.

overall_design: 1) Mouse muscle injury (uninjured, 6, 12, 24, 48, 72 hours post injury, 7 days post injury) (2 replicates per sample) and 2) Smad4 f/f:Pax7 CreER/CreER :R26 YFP/YFP mice (i.e., Smad4 iKO) and Smad4 f/+:Pax7 CreER/CreER:R26 YFP/YFP mice (i.e. Smad4 Ctrl)

first: Arinze

last: Okafor

first: Xin

last: Lin

first: Chenghao

last: Situ

first: Xiaolin

last: Wei

first: Yu

last: Xiang

first: Xiuqing

first: Zhenguo

last: Wu


title: Dynamic interplay between IL1 and WNT pathways in regulating dermal adipocyte lineage cells during skin development and wound regeneration

status: Public on Jun 10 2023

city: Xiamen

first: Lingjuan

last: Zhang

address: Xiangan South Street

institute: Xiamen University

summary: Cells were isolated from wounded skin tissue and administered into single cell RNA transcriptome sequencing to deconstruct cell hierarchy of dermal fibroblast population and underlying regulating mechanisms. In brief, 7~9 weeks old male C57BL/6 mice were anesthetized and one full-thickness wound (1.0 cm x 0.5 cm in size) was generated on shaved dorsal skin. Animals were sacrificed at indicated intervals after and wound bed tissues were collected for cell isolation and subsequent 10x Genomics single cell RNAseq. Sequencing was performed on Illumina Novaseq6000 platform (Illumina). The generated raw gene expression matrix was converted into Seurat objects using the R package Seurat v3.0. After low quality cells and outliers were discarded, 10233 cells from non-lesional skin, 7807 cells from wound beds at post-wounding day 2 (PWD2), and 4925 cells from wound tissue at PWD7 were used for downstream analysis. Next, unsupervised clustering and gene expression were visualized with the Seurat 3.0 on R studio, and assignment and identification of cell clusters was based on the expression of validated marker genes. Subsequent in-depth analysis was assisted by GENE DENOVO Inc (Guangzhou, China). Together, our study has identified a specific dermal fibroblast population with high DPP4, Sca1 and WNT2 expression, which is committed into adipocyte upon wounding, and define the differentiation trajectory of this adipocyte precursor during skin regeneration.

overall_design: 7~9 weeks old male C57BL/6 mice were wounded during telogen phase of hair cycling. One full-thickness biopsy (1.0 cm x 0.5 cm in size) was generated on each side of dorsal skin. Biopsies were collected from 3 groups, non-lesional dorsal skin, wound bed tissue at post-wounding day 2 and wound bed tissue at post-wounding day 7. Next, skin cells were isolated and used for subsequent  single cell RNAseq.

first: Ling-juan


title: SIX1+PAX3+ Identify a Progenitor for Myogenic Lineage Commitment from hPSCs

city: Irvine

first: Michael

last: Hicks

state: CA

address: 845 Health Sciences Road, Room 3101

institute: University of California, Irvine

summary: To better characterize the transcriptomic profile of hPSC-derived SMPCS, we performed a comparative analysis on the gene signature of FACS-enriched human embryonic (week 9-10), fetal (week 16-20), and hPSC SMPCs and adult SCs using bulk RNA seq.

overall_design: We performed 20-30 million reads for each enriched sample which enabled a more in-depth view of the molecular composition of enriched cells. We enriched human SMPCs using the surface markers Lin-ERBB3+NGFR+ (Hicks et al., 2018) and adult SCs using Lin-CD82+NCAM+ (Alexander et al., 2016). Additionally, hPSC SMPCs were depleted for the neural crest marker HNK1, while primary-derived cells were lineage depleted for CD45, CD235A, and CD31. FACS enriched populations, were immediately collected and processed for RNA sequencing (N=3-5 per group). Sequence alignment to the human genome (hg38) using HISAT (Kim et al., 2015) and transcriptome assembly in StringTie (Pertea et al., 2015) were analyzed for differential gene expression (DGE) using DESeq2 with a false discovery rate of q=0.05 (Love et al., 2014).

first: Olga

last: Jaime

first: April

last: Pyle


title: ThPOK is a critical and multifaceted regulator of myeloid lineage development

status: Public on Jun 05 2023

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

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

overall_design: Refer to individual Series


summary: In brief, skin resident cells were isolated from dorsal skin of mice and 10x Genomics single cell RNAseq was applied to identify distinct cell populations. Low quality cells and outliers were discarded, and only ～24,409 viable cells were used for downstream analysis. Unsupervised clustering and gene expression were visualized with the Seurat 2.0 on R studio, and assignment of cell clusters was based on expression of validated marker genes. Subsequent in-depth analysis was assisted by GENE DENOVO Inc (Guangzhou, China). Overall, we found that a specific dermal fibroblast population, with high DPP4, Sca1 and WNT2 expression, has robust capacity for adipocyte differentiation and acts key role in maintaining dermis homeostasis.

overall_design: Dorsal skin biopsies were collected from 3 groups, including neonatal , young adult and mature adult C57BL/6 mice.


title: WDR5 facilitates recruitment of N-MYC to conserved gene targets in neuroblastoma cell lines

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

summary: Collectively, the MYC family of oncoprotein transcription factors are overexpressed or deregulated in more than half of all malignancies. The ability of MYC proteins to access chromatin is fundamental to their role in promoting oncogenic gene expression programs in cancer and this function depends on MYC-cofactor interactions. One such cofactor is the chromatin regulator WDR5, which in models of Burkitt’s lymphoma facilitates recruitment of the c-MYC protein to chromatin at select target genes associated with protein synthesis, allowing for tumor progression and maintenance. However, beyond Burkitt’s lymphoma it is unknown whether these observations extend to other cancers or MYC family members, and whether WDR5 can be deemed as a “universal” MYC recruiter. Here, we focus on N-MYC amplified neuroblastoma to determine the extent of colocalization between N-MYC and WDR5 on chromatin while also demonstrating that like c-MYC, WDR5 can facilitate recruitment of N-MYC to known conserved WDR5-bound genes. We conclude based on this analysis that N-MYC and WDR5 colocalize invariantly across cell lines at predicted sites of facilitated recruitment associated with protein synthesis genes. Surprisingly, we also identify N-MYC-WDR5 cobound genes that are associated with DNA repair and cell cycle processes. Dissection of chromatin binding characteristics of N-MYC and WDR5 at all cobound genes reveals that sites of facilitated recruitment are inherently different than most N-MYC-WDR5 cobound sites. Our data reveals that WDR5 acts as a universal MYC recruiter at a small cohort of previously identified genes and highlights novel biological functions that may be coregulated by N-MYC and WDR5 to sustain the neuroblastoma state.

overall_design: We used multiple neuroblastoma cell lines and various genetic approaches to interrogate the N-MYC-WDR5 interaction and its impact on N-MYC binding to chromatin.

last: Weissmiller

first: William

last: Tansey

first: Qi

last: Liu


title: ThPOK is a critical and multifaceted regulator of myeloid lineage development [CITE-Seq]

summary: The transcription factor ThPOK (encoded by Zbtb7b) is well known for its role as a master regulator of CD4 lineage commitment in the thymus. Here, we report a novel role for ThPOK as a critical and multifaceted regulator of myeloid lineage commitment, differentiation and maturation. Using reporter and knockout mouse models combined with CITE-Seq, Smart-Seq2, progenitor transfer and clonogenic assays and we show that ThPOK controls monocyte-DC versus granulocyte lineage production during homeostatic differentiation, and serves as a brake for neutrophil maturation in granulocyte lineage-specified cells through transcriptional regulation of lineage-specific transcription factors and RNA via altered mRNA splicing to reprogram intron retention.

overall_design: Single cell RNA seq of ThPOK wild-type, ThPOK knockout cells.

first: Jayati

last: Basu

first: Andre

last: Olsson

first: Kashish

last: Chetal

first: H

last: Leighton Grimes

first: Dietmar

last: Kappes


title: MPRA for Characterization of transcription factor function and patterns fo gene regulation in HepG2 cells

status: Public on Jun 21 2023

first: Belle

last: Moyers

overall_design: We tested hypotheses regarding ChIP-seq signal and TF binding by testing 170 bp DNA elements cloned upstream of a minimal promoter and expressed barcode sequence in a lentiviral MPRA in HepG2 cells.

first: E

last: Partridge

first: Mark

last: Mackiewicz

last: Betti

first: Roshan

last: Darji

first: Sarah

last: Meadows

first: Kimberly

last: Newberry

first: Laurel

last: Brandesmeier

first: Barbara

last: Wold

first: Eric

last: Mendenhall

first: Richard

last: Myers


title: Zfp352 over expression ATAC-seq result

status: Public on Jun 01 2023

city: HangZhou

first: Zhengyi

last: Li

state: ZheJiang

address: 866 Yuhangtang Rd, Hangzhou

department: Institute of Genetics

institute: Zhejiang University School of Medicine

summary: Our data delineated bifurcated binding and regulation of ZFP352 towards two distinct retrotransposons, MT2_Mm and SINE_B1/Alu,and whether ZFP352 can regulate mouse genome openness  remains unknown,here we conduct ATAC-seq of Zfp352 over expression sample to detect ZFP352's role in regulating chromatin openness.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ATAC-seq) for ZFP352 protein of Zfp352 over expression sample and Zfp352+Dux over expression sample

first: Hongqing

last: Liang

first: Yang

last: Shen

first: Haiyan

last: Xu


title: ThPOK is a critical and multifaceted regulator of myeloid lineage development [Fluidigm]

first: Nathan

last: Salomonis

first: Jayati

last: Basu

first: Andre

last: Olsson

first: Kashish

last: Chetal

last: Leighton Grimes


title: Zfp352 over expression chip-seq result

summary: Previous study has determined Dux regulates 2CLC trancriptome via binding and activating MERVL,but the mechanism about the change happned during the 2C-exit process are rarely determined.In this study,we try to illustrate how ZFP352 binds genome location to regulate its downstream trancriptome and 2C-exit process.And make some conclusion and hypothesis about ZFP352 co-binding and interact with other trancription factor:Dux,etc to regulate 2C-exit.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for ZFP352 protein of input and Zfp352 over expression samples


title: Time point RNA-seq of Dux over expression samples reveals different transcriptomes of Dux induction in mESC

summary: Prevous study has discoverd 2CLC trancriptome and MERVL can be up-regulated by Dux over expression,but rarely has been found about the whole procedure of Dux-induced 2C-entry and exit process and whether this system can reflect the natural 2-cell embryo development,so we we defined different time point transcription after Dux over expression,and try to establish a link between gene expression profile between gene dynamics in different Dux over expression time point and in early mouse embryo development

overall_design: We then performed gene expression clustering analysis using data obtained from RNA-seq of 0h,12h,24h,36h,48h,72h samples after Dux over expression


title: Fast proliferating and slowly migrating non-small cell lung cancer cells are vulnerable to decitabine and retinoic acid combinatorial treatment

city: Freiburg im Breisgau

first: Sven

last: Diederichs

state: Baden Württemberg

address: Breisacherstrasse 115

department: ZTZ

institute: Universitätsklinikum Freiburg

summary:
Non-small cell lung cancer (NSCLC) patients are often elderly or unfit and thus cannot tolerate standard aggressive therapy regimes. In this study, we test the efficacy of the DNA-hypomethylating agent decitabine (DAC) in combination with all-trans retinoic acid (ATRA), which has been shown to possess little systemic adverse effects. Screening a broad panel of 56 NSCLC cell lines uncovered a decrease in cell viability after the combination treatment in 77% of the cell lines. Transcriptomics, proteomics, proliferation and migration profiling revealed that fast proliferating and slowly migrating cell lines were more sensitive to the drug combination. The comparison of mutational profiles found oncogenic KRAS mutations only in sensitive cells. Additionally, different cell lines showed a heterogeneous gene expression response to the treatment pointing to diverse mechanisms of action. Silencing KRAS, RIG-I or RARB partially reversed the sensitivity of KRAS-mutant NCI-H460 cells.
To study resistance, we generated two cell populations resistant to ATRA and DAC, which migrated faster and proliferated slower than the parental sensitive cells and showed signs of senescence. In summary, this comprehensive dataset uncovers a broad sensitivity of NSCLC cells to the combinatorial treatment with DAC and ATRA and indicates that migration and proliferation capacities correlate with and could thus serve as determinants for drug sensitivity in NSCLC.

overall_design: Differential gene expression analysis of RNA-seq data for two NCI-H460 cell populations resistant to decitabine and all-trans retinoic acid and parental NCI-H460 cells.

first: Giulia

last: Pelos


title: ETV2 primes hematoendothelial gene enhancers prior to hematoendothelial fate commitment

status: Public on Jun 16 2023

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

summary: The lineage-determining transcription factor ETV2 is necessary and sufficient for hematoendothelial fate commitment. We investigated how ETV2-driven gene regulatory networks promote hematoendothelial fate commitment. We resolved the sequential determination steps of hematoendothelial versus cardiac differentiation from mouse embryonic stem cells. Etv2 was strongly induced and bound to the enhancers of hematoendothelial genes in a common cardiomyocyte-hematoendothelial mesoderm progenitor. However, only Etv2 itself and Tal1, not other ETV2-bound genes, were induced. Despite ETV2 genomic binding and Etv2 and Tal1 expression, cardiomyogenic fate potential was maintained. A second wave of ETV2-bound target genes was up-regulated during the transition from the common cardiomyocyte-hematoendothelial progenitor to the committed hematoendothelial population. A third wave of ETV-bound genes were subsequently expressed in the committed hematoendothelial population for sub-lineage differentiation. The shift from ETV2 binding to productive transcription, not ETV2 binding to target gene enhancers, drove hematoendothelial fate commitment. This work identifies mechanistic phases of ETV2-dependent gene expression that distinguish hematoendothelial specification, commitment, and differentiation.

overall_design:
For ATAC-seq, there are 37 samples:
3 each of Day 0, Day 2, Day 4 P+F-, Day 4 P+F+, Day 4 P-F+, Day 6 P+F+, Day 6 P-F+, Day 8 P+F+, and Day 8 P-F+;
4 Day 4 P+F+ under FAB conditions;
2 Day 4 P+F+ under FAB+V conditions; and
4 Day 4 P+F+ under FAB+P conditions.

For RNA-seq, there are 14 samples under the FAB+V conditions:
3 Day 4 P+F-, 2 Day 4 P+F+, 3 Day 4 P-F+, 3 Day 8 P+F+, and 3 Day 8 P-F+.

Under differing conditions, all P+F+, there are 23 samples:
3 Day 4 FAB, 3 Day 4 FAB+P, 3 Day 4 FAB+V, 3 Day 6 FAB, 2 Day 6 FAB+P, 2 Day 6 FAB+V, 3 Day 8 FAB, 2 Day 8 FAB+P, and 2 Day 8 FAB+V.

For ChIP-seq, there are 9 samples labelled as H3K27ac or Input controls with 2 replicates Day 4 P+F+ under FAB+V, 2 replicates Day 4 P+F+ under FAB, 2 replicates at Day 5 under FAB+V, or 1 replicate of each input.

Treatment definitions:
FAB: bFGF+Activin A+BMP4
FAB+P:  bFGF+Activin A+BMP4+PDGFAA
FAB+V:  bFGF+Activin A+BMP4+VEGF

first: Chul

last: Kim

first: Ivan

last: Moskowitz

first: Kohta

last: Ikegami


title: Knocking down Zfp352 delayed mouse embryo development

summary: To explore the function of ZFP352 during mouse early embryonic development, siRNA targeting Zfp352 was injected into the zygotes and the effect of Zfp352 depletion on development was followed.

overall_design: We then performed RNAseq analysis using siRNA targeting Zfp352,and siZfp352 embryo at D2,D3,D4 were sequenced.


title: Zfp352 and Zfp352+Dux over expression chip-seq result

summary: Our data delineated bifurcated binding and regulation of ZFP352 towards two distinct retrotransposons, MT2_Mm and SINE_B1/Alu,further ChIP-seq experiments validated that over-expression of Dux displaced ZFP352 from SINE_B1/Alu and DUX-independent ZFP352 binding sites, but promoted ZFP352 binding onto MT2_Mm and DUX_ZFP352 co-bound sites

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for ZFP352 protein of Zfp352 over expression sample and Zfp352+Dux over expression sample


title: A unique mode of cross regulation in a cell envelope stress signaling system

status: Public on May 30 2023

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University


title: A unique mode of cross regulation in a cell envelope stress signaling system [RNA-seq]

summary: A multi-layered structure known as the cell envelope separates the controlled interior of Gram-negative bacteria from a fluctuating physical and chemical environment. Transcription of genes that determine cell envelope structure and function is commonly controlled by a class of environmental regulators known as two-component signal transduction systems (TCS), which are comprised of 1) sensor histidine kinases and 2) response regulators. To discover TCS genes that contribute to cell envelope function in the intracellular mammalian pathogen, Brucella ovis, we subjected a comprehensive collection of non-essential TCS mutants to compounds that disrupt cell membranes and the peptidoglycan cell wall. Our screen led to the discovery of three TCS proteins with unusual regulatory properties that coordinately function to confer resistance to cell envelope stress and to support B. ovis replication in the intracellular niche. This tripartite regulatory system consists of the conserved cell envelope regulator, CenR, and a previously uncharacterized TCS, EssRS. The CenR and EssR response regulators bind a shared set of sites on the B. ovis chromosomes to control transcription of an overlapping set of genes with cell envelope functions. CenR directly interacts with EssR and functions to stimulate phosphoryl transfer from the EssS kinase to EssR and control steady-state levels of EssR protein in the cell via a post-transcriptional mechanism. Our data provide evidence for a new mode of TCS cross-regulation in which a non-cognate response regulator both regulates activity and influences cellular levels of a cognate TCS system.

overall_design: We compared the differential gene expression between ∆cenR and WT and ∆essRS and WT. Each strain had three replicates

first: Xingru

last: Chen

first: Melene

last: Alakavuklar

first: Aretha

last: Fiebig


title: Selective binding of retrotransposons by ZFP352 facilitates the timely dissolution of totipotency network

first: Zhengyi

last: Li

summary: Acquisition of new stem cell fates relies on the dissolution of the prior regulatory network sustaining the existing cell fates. Currently, extensive insights have been revealed for the totipotency regulatory network around the zygotic genome activation (ZGA) period. However, how the dissolution of the totipotency network is triggered to ensure the timely embryonic development following ZGA is largely unknown.  In this study, we identified the unexpected role of a highly expressed 2C embryo specific transcription factor, ZFP352, in facilitating the dissolution of the totipotency network. We found that ZFP352 has bifurcated binding and regulation towards two different retrotransposon sub-families. ZFP352 coordinates with DUX to bind and regulate the 2C specific MT2_Mm sub-family. On the other hand, without DUX, ZFP352 switched affinity to bind extensively onto SINE_B1/Alu sub-family. This leads to the activation of later developmental programs like ubiquitination pathways, to facilitate the dissolution of the 2C state. Correspondingly, depleting ZFP352 in mouse embryos impaired the 2C to morula transition process. Thus, through differential regulation of MT2_Mm and SINE_B1/Alu, ZFP352 can trigger spontaneous dissolution of the totipotency network. Our study highlights the importance of different retrotransposons sub-families in facilitating the timely and programmed cell fates transition during early embryogenesis.

overall_design:
(1) Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for ZFP352 protein of input and Zfp352 over expression samples
(2) We then performed gene expression clustering analysis using data obtained from RNA-seq of 0h,12h,24h,36h,48h,72h samples after Dux over expression
(3) Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for ZFP352 protein of Zfp352 over expression sample and Zfp352+Dux over expression sample
(4) Chromatin immunoprecipitation DNA-sequencing (ATAC-seq) for ZFP352 protein of Zfp352 over expression sample and Zfp352+Dux over expression sample
(5) RNAseq analysis using siRNA targeting Zfp352 in embryo at D2,D3,D4


title: A unique mode of cross regulation in a cell envelope stress signaling system [ChIP-seq]

overall_design: ChIP-seq using ∆BOV_1929 / pQF-BOV_1929 (D55E)-3xFLAG and ∆BOV_1472 /pQF-BOV_1472 (D64E)-3xFLAG alleles to determine the direct binding targets of each repsonse regulator.


title: Association of self-identified race and genetic ancestry with the immunogenomic landscape of primary prostate cancer

status: Public on May 31 2023

city: Baltimore

first: Thiago

last: Vidotto

state: MD

address: 1550 Orleans St

institute: Johns Hopkins

type: Methylation profiling by genome tiling array

summary: The genomic and immune landscapes of prostate cancer differ by self-identified race. However, few studies have examined the genome-wide copy number landscape and immune content of matched cohorts with genetic ancestry data and clinical outcomes. Here, we assessed prostate cancer somatic copy number alterations (sCNA) and tumor immune content of a grade-matched, surgically-treated cohort of 145 self-identified Black (BL) and 145 self-identified white (WH) patients with genetic ancestry estimation. A generalized linear model adjusted with age, pre-operative PSA, and Grade Group and filtered for germline copy number variations (gCNV) identified 143 loci where copy number varied significantly by percent African ancestry, clustering on chromosomes 6p, 10q, 11p, 12p, and 17p. Multivariable Cox regression models adjusted for age, pre-operative PSA levels, and Grade Group revealed that chromosome 8q gains (including MYC) were significantly associated with biochemical recurrence and metastasis, independent of genetic ancestry. Finally, regulatory T-cell density in BL and WH patients was significantly correlated with percent genome altered, and these findings were validated in the TCGA cohort. Taken together, our findings identify specific sCNA linked to genetic ancestry and outcome in primary prostate cancer and demonstrate that regulatory T-cell infiltrate varies by global sCNA burden in primary disease.

overall_design: 290 samples derived from primary prostate tumors and 30 benign adjacent samples.

first: Eddie

last: Imada

first: Farzana

last: Faisal

first: Sanjana

last: Murali

first: Adrianna

last: Mendes

first: Harsimar

last: Kaur

first: Siqun

last: Zheng

first: Jianfeng

last: Xu

first: Edward

last: Schaeffer

first: William

middle: B

last: Isaacs

first: Karen

middle: S

last: Sfanos

first: Luigi

last: Marchionni

first: Tamara

last: Lotan


title: The translational oscillation in oocyte and early embryo development

status: Public on May 29 2023

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: Translation is critical for development as transcription in the oocyte and early embryo is silenced. To illustrate the translational changes during meiosis and consecutive two mitoses of the oocyte and early embryo, we performed a genome-wide translatome analysis. Acquired data showed significant and uniform activation of key translational initiation and elongation axes specific to M-phases. Although global protein synthesis decreases in M-phases, translation initiation and elongation activity increases in a uniformly fluctuating manner, leading to qualitative changes in translation regulation via the mTOR1/4F/eEF2 axis. Overall, we have uncovered a highly dynamic and oscillatory pattern of translational reprogramming that contributes to the translational regulation of specific mRNAs with different modes of polysomal occupancy/translation that are important for oocyte and embryo developmental competence. Our results provide new insights into the regulation of gene expression during oocyte meiosis as well as the first two embryonic mitoses and show, how temporal translation can be optimized. This study is the first step towards a comprehensive analysis of the molecular mechanisms that not only control translation during early development, but also regulate translation-related networks employed in the oocyte-to-embryo transition and embryonic genome activation.

overall_design: To decipher protein synthesis and its regulation, we conducted Scarce Sample Polysome Profiling (SSP-profiling) to analyse active translation of mRNA at a genome-wide level. The improved SSP-profiling protocol was followed by RNA sequencing (RNA-seq), which allowed us to analyze mRNA translational profiles of mouse oocytes at the GV, MII stages, zygote, zygote M phase, and 2-cell and 2-cell M-phase stages. A total of 10 fractions from mouse oocytes and embryos were separated by polysomal fractionation, from which first 5 fractions were pooled and labelled as non-polysome (NP) and heavier 5 fraction were pooled and labelled as a polysome (P), followed by RNA-sequencing analysis. This experiment was performed in biological triplicates. In addition, the oocytes or embryos collected from the same batch in each developmental stage were used to profile their transcriptomes by mRNA-seq. This experiment was performed in biological triplicates.

first: Zongliagn

first: Rajan

last: Iyyappan

first: Andrej

last: Susor


title: The establishment of HP1-independent heterochromatin reveals an essential role for HP1 proteins in maintaining epigenetic memory.

status: Public on May 24 2023

city: Waltham

first: Ajay

last: Larkin

state: MA

address: 415 South St

department: MCB

institute: Brandeis University

summary: H3K9 methylation (H3K9me) marks transcriptionally silent genomic regions called heterochromatin. A conserved class of HP1 proteins are critically required to establish and  maintain heterochromatin. HP1 proteins bind to H3K9me, recruit factors that promote heterochromatin formation, and oligomerize to form phase-separated condensates. We do not  understand how HP1 protein binding to heterochromatin establishes and maintains transcriptional silencing. Here, we demonstrate that the S.pombe HP1 homolog, Swi6, can be  completely bypassed to establish silencing at ectopic and endogenous loci when an H3K4 methyltransferase, Set1 and an H3K14 acetyltransferase, Mst2 are deleted. Deleting Set1 and  Mst2 enhances Clr4 enzymatic activity, leading to higher H3K9me levels and increased spreading. In contrast, Swi6 and its capacity to oligomerize were indispensable during epigenetic maintenance. Our results demonstrate the role of HP1 proteins in regulating histone modification crosstalk during establishment and identifies a genetically separable function in  maintaining epigenetic memory.

overall_design: Comparative gene expression profiling analysis of RNA-seq data, performed in triplicate, under several genotypic backgrounds. Strains contained a tethering site to nucleate heterochromatin at an ectopic locus with a TetR-Clr4-I fusion (-Tet). To release the fusion protein, strains were treated with Tetracycline (+Tet).

first: Melissa

last: Seman

first: Alexander

last: Levashkevich

first: Fengting

last: Huang

first: Kaushik

last: Ragunathan


title: Methylation array profiling of peripheral nerve tumors in neurofibromatosis

status: Public on May 22 2023

first: Harish

last: Vasudevan

address: 1450 3rd street

institute: UCSF

summary: Peripheral nerve tumors in neurofibromatosis

overall_design: DNA was extracted from patient derived tumor specimens

first: David

last: Raleigh

first: Frank

last: McCormick


title: A platform for screening microbial effects on primary epithelial cells

status: Public on May 15 2023

city: Gentofte

first: Albin

last: Sandelin

address: Markvangen 26

country: Denmark

institute: University of Copenhagen

summary: CACO2 cells were exposed to four bacteria ( LGG, BB-12, Bifidobacterium infantis DSM33361(hereafter referred to as DSM33361), and Bifidobacterium breve Bif195 (hereafter called Bif195)), and control (untreated)

overall_design: RNA-Seq

first: Kim

last: Jensen


title: Transcriptional response of Saccharomyces cerevisiae to lactic acid enantiomers

status: Public on May 19 2023

city: Irkutsk

first: Polina

last: Drozdova

state: Irkutsk region

address: Lenin str. 3

department: Institute of Biology

country: Russia

institute: Irkutsk State University

summary: The model yeast species Saccharomyces cerevisiae is used in many fundamental and applied research applications, including biosensors and production of many compounds. However, given the enormous work invested in the studies of yeast transcription response to various conditions, there are still substances not explored in this regard. In this work, we explore the transcriptional response of S. cerevisiae to a wide range of concentrations of the D-enantiomer of lactic acid and compare it to the response to L-lactic acid. Of these conditions, we only recorded a transcriptional response to the relatively high concentrations of DLA of 5 and 45 mM, as well as to 45 mM LLA. Our data did not reveal any natural yeast promoters that quantitatively sense D-lactic acid but provide the first description of the transcriptome-wide response to DLA, as well as enrich our understanding of the LLA response.

overall_design: In this work, we explore the transcriptional response of a commonly used S. cerevisiae strain BY4742 to a wide range of concentrations of the D-enantiomer of lactic acid (0.05, 0.5, 5, 45 mM) for the first time and compare it to the response to 45 mM L-lactic acid (LLA). The exposure of the indicated concentrations in shake flask cultures lasted for 3 hours.

first: Anton

last: Gurkov

first: Maxim

last: Timofeyev

first: Ekaterina

last: Borvinskaya


title: Single cell analysis reveals multiple subsets of CD8+ TRM and non-TRM cells with a type 17 signature in the inflamed psoriatic arthritis joint

status: Public on May 17 2023

city: London

first: Leonie

last: Taams

state: london

address: CIBCI, 1.26, New Hunts House

country: United Kingdom

institute: King's College London

summary: CD69+CD103+ tissue-resident memory T-cells (TRM) are increasingly recognised as important drivers of inflammation. To decipher their potential role in inflammatory arthritis, we applied single cell, high-dimensional profiling (CyTOF and scRNAseq) to T-cells isolated from the joint of patients with psoriatic arthritis (PsA) or rheumatoid arthritis (RA). We identified three broad groups of synovial CD8+ TRM cells: cytotoxic and Treg-like TRM cells were present in the inflamed joints of patients with both PsA and RA, while CD161+CXCR6+ type 17-like TRM cells with a pro-inflammatory cytokine profile (IL-17A+TNFa+IFNg+) and a distinct transcriptomic signature and a polyclonal, but distinct TCR repertoire, were specifically enriched in the inflamed joints of patients with PsA.  Type 17-like cells were also enriched in non-TRM CD8+ T-cells in PsA compared to RA. These findings add substantively to the accumulating evidence that the immunopathology of PsA and RA is different, with a particular role for type 17 cells in PsA.

overall_design: Single cell RNAseq analysis of synovial fluid memory CD8+ T cells from patients with psoriatic arthritis

first: Giovanni

last: Povoleri

first: Elizabeth

middle: H

last: Gray

first: Lucy

last: Durham

first: Sylvine

last: Lalnunhlimi

first: Shichina

last: Kannambath

first: Michael

middle: J

last: Pitcher

first: Pawan

last: Dhami

first: Thomas

last: Leeuw

first: Sarah

last: Ryan

first: Kathryn

last: Steel

first: Bruce

middle: W

last: Kirkham


title: The RNA m6A reader YTHDC2 recruits TET1 to demethylate transposable elements DNA and prevent neural fate of human pluripotent stem cells [eclip-seq]

status: Public on May 12 2023

first: Tongyu

last: Sun

state: NC

address: 307 research drive

institute: Duke university

summary:
Covalent modifications of RNA and DNA both regulate numerous biological processes, including development and cancer. The most abundant modification of RNA is that of N6-methyladenosine(m6A), while in the case of DNA, the CpG cytosine methylation characterizes cis-regulatory elements for spatial-temporal gene regulation. Recent studies establish a role for RNA m6A in regulating chromatin through histone modifications. However, whether there is also interplay between RNA and DNA methylation remains unknown. We address this question by studying regulation of the primate-specific transposable element (TE), LTR7/HERV-H, that is specifically activated in human embryonic stem cells (hESCs). Exploiting a novel proteomic approach, we find the RNA m6A-reader, YTHDC2, binds to LTR/HERV-H chromatin through interaction with m6A-modified HERV-H transcripts. Significantly, YTHDC2 recruits DNA demethylase, TET1, to activate LTR7/HERV-H via 5-hydroxymethycytosine(5hmC)-mediated DNA methylation. Furthermore, the YTHDC2/LTR7-axis prevents neural conversion of hESCs. Our results establish previously unknown crosstalk between RNA m6A and DNA methylation and new mechanisms controlling TE activity and hESC fate.
We focused on the regulation of the primate-specific TE family, LTR7/HERV-H that is specifically active in the pluripotent human embryonic stem cells (hESCs) then silenced in differentiated lineages. We develop CARGO-BioID, a CRISPR-based TE-centric proteomics approach, to identify the proteins associated with thousands of copies of endogenous LTR7/HERV-H loci and potentially regulate their activity in hESCs. We found YTHDC2 and TET1 interact with each other and subsequently regulate m6A level on HERVH transcripts and 5hmC level on HERV-H genomic loci, which is critical for LTR7/HERV-H activities.

overall_design: eclip-seq

first: Yarui

last: Diao


title: The RNA m6A reader YTHDC2 recruits TET1 to demethylate transposable elements DNA and prevent neural fate of human pluripotent stem cells [RIP-seq_2]

overall_design: RIP-seq


title: The RNA m6A reader YTHDC2 recruits TET1 to demethylate transposable elements DNA and prevent neural fate of human pluripotent stem cells [RNA-seq_2]

overall_design: RNA-seq


title: Proper parental histone allocation is required for mouse embryonic stem cell differentiation and histone post-transcription modification inheritance

city: Shenzhen

first: haiyun

last: gan

address: xueyuan lu 1068

institute: Shenzhen Institute of Advanced Technology

summary: To understand whether parental histone PTM landscape plays roles in cell differentiation, we perturbed parental histone PTM allocation by mutating histone chaperone MCM2 on its histone binding domain (MCM2-2A mutation), disrupted only the histone transferring of MCM2 protein in mouse embryonic stem cells (ESCs). Combining single-cell transcriptomics and epigenomics with lineage barcoding, we found that MCM2-2A mutant ESCs cannot be fully differentiated to neuronal precursor cells (NPCs), causing by the redistribution of H3K27me3, and subsequently NPC related gene expression. Here, we show that the parental histone allocation plays an important role in the establishment of chromatin landscapes, altering ESC differentiational potential, shaping expression programs and cell heterogeneity.

overall_design: We used mouse embryonic stem cell and differentiation neuronal precursor cells (Wild type and MCM2-2A mutant cells). H3K27me3, H3K4me3 and H3K9me3 CUT&Tag, H3.3 CUT&Tag in ESCs, H3K27me3 eSPAN in ESCs, H3.3 espan in ESCs, scRNA-seq of ESCs and D7 NPCs, scCUT&Tag of H3K27me3 in ESCs, MINCE-seq in ESCs, Repli-ATAC-seq in ESCs, ATAC-seq in ESCs and CUT&RUN in ESCs, D3 NPCs and D7 NPCs were implemented. Parts of experiments above were also implemented in POLE3-/-, HIRA-/- and HIRA-/- MCM2-2A ESCs.

first: Qing

last: Wen

first: Congcong

last: Tian

first: Jiaqi

last: Zhou

first: Haiyun

last: Gan


title: The RNA m6A reader YTHDC2 recruits TET1 to demethylate transposable elements DNA and prevent neural fate of human pluripotent stem cells [ChIP-seq_2]

overall_design: ChIP-seq


title: The RNA m6A reader YTHDC2 recruits TET1 to demethylate transposable elements DNA and prevent neural fate of human pluripotent stem cells [RNA-Seq]

overall_design: RNA-Seq on H1 hESCs.


title: The RNA m6A reader YTHDC2 recruits TET1 to demethylate transposable elements DNA and prevent neural fate of human pluripotent stem cells [RIP-Seq]

overall_design: RIP-Seq on H1 hESCs.


title: The RNA m6A reader YTHDC2 recruits TET1 to demethylate transposable elements DNA and prevent neural fate of human pluripotent stem cells [CUT&RUN]

overall_design: CUT&RUN on H1 hESCs.


title: The RNA m6A reader YTHDC2 recruits TET1 to demethylate transposable elements DNA and prevent neural fate of human pluripotent stem cells [ChIP-seq]

overall_design: ChIP-seq on H1 hESCs.


title: The RNA m6A reader YTHDC2 recruits TET1 to demethylate transposable elements DNA and prevent neural fate of human pluripotent stem cells [ATAC-Seq]

overall_design: ATAC-seq on H1 hESCs.


title: Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells

type: Methylation profiling by high throughput sequencing

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

relation:
SuperSeries of: GSE210834
SuperSeries of: GSE210835
SuperSeries of: GSE210859
SuperSeries of: GSE210862
SuperSeries of: GSE210864
SuperSeries of: GSE210865
SuperSeries of: GSE224669
SuperSeries of: GSE224670
SuperSeries of: GSE224671
SuperSeries of: GSE224672

overall_design: Refer to individual Series


title: Psoriatic arthritis skin lesions and uninvolved bulk RNA-seq

status: Public on May 10 2023

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

institute: University of Glasgow

summary: Investigation of the transcriptomic differences that occur in psoriatic skin lesions, compared to non arthritic skin or non-lesion arthritic skin.

overall_design: Bulk RNA-seq of human skin biopsy for healthy controls, psoriatic arthritis lesions and psoriatic arthritis uninvolved.

first: Hanna

last: Johnson

first: Gerard

last: Graham


title: Sorting receptor SORCS2 facilitates a protective stress response in pancreatic islets

city: Aarhus c

first: Per

last: Qvist

state: Danmark

address: Høegh-Guldbergs Gade 10

department: Biomedicine

institute: Aarhus University

summary: Objective: SORCS2 is an intracellular sorting receptor genetically associated with body mass index (BMI) in humans, yet its mode of action remains unknown. Elucidating the receptor function that defines its role in metabolic health is the objective of this work.                                                              Methods: Combining in vivo metabolic studies in SORCS2-deficient mouse models with ex vivo structural and functional analyses as well as single-cell transcriptomics of murine pancreatic tissues, we studied the pathophysiological consequences of receptor dysfunction for metabolism.  Results: Our studies identified an important role for SORCS2 in islet stress response essential to sustain glucose-stimulated insulin release. In detail, we show that SORCS2 is predominantly expressed in islet alpha cells. Loss of expression impairs the ability of these cells to produce osteopontin, a secreted factor that facilitates insulin release from beta cells under stress. In line with diminished osteopontin levels, beta cells in SORCS2-deficient islets show changes in gene expression related to aggravated stress, protein misfolding, as well as mitochondrial dysfunction; and they exhibit defects in insulin granule maturation and a blunted response to glucose stimulation in vivo and ex vivo. Impaired glucose tolerance in receptor mutant mice coincides with alterations in body weight and composition.  Conclusion: Our data identified a novel concept in protective islet stress response involving the alpha cell receptor SORCS2, and they provide experimental support for association of SORCS2 with metabolic control in humans.

overall_design: Pancreatic islets from 3 animals per genotype (Sorcs2+/+ and Sorcs2-/- ; ~ 400-600 islets per sample )

first: Oleksandra

last: Kalnytska

last: Conrad

first: Séverine

last: Kunz

first: Vanessa

last: Schmidt

middle: E

last: Willnow


title: Tolerogenic Dendritic Cells Engineered with IL-10 and Antigen Control Pathogenic T Cell Responses and Promote Type 1 T Regulatory Cells

status: Public on May 02 2023

city: Milano

first: Silvia

last: Gregori

state: Italy

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

summary: Dendritic cells (DC) play a critical role in the maintenance of tissue homeostasis and in promoting tolerance, thus acting as regulatory cells. Tolerogenic DC (tolDC) represent the cells of choice to fulfill the goal of restoring antigen (Ag)-specific tolerance since they can dampen Ag-specific T cell responses, induce pathogenic T cell exhaustion, and Ag-specific regulatory T cells. Here we efficiently generate tolDC by genetic engineering of monocytes with bidirectional lentiviral vectors co-encoding for immunodominant Ag-derived peptides (Ovalbumin or Matrix Protein 1, Insulin and Gliadin) in combination with IL-10 (DCIL-10/Ag). DCIL-10/Ag secrete high amounts of IL_x0002_10 in the absence of pro-inflammatory cytokines and efficiently modulate Ag-specific CD4+ and CD8+ T cell activation and proliferation in vitro in healthy subjects and Celiac Disease patients. DCIL-10/Ag promote Ag-specific CD49b+LAG-3 + T cells, which display the type 1 T regulatory (Tr1) cell gene signature in vitro. In vivo administration of DCIL-10/Ag promote Ag-specific Tr1 cells and prevent type 1 diabetes development in two murine models of disease. In conclusion, we generate an innovative approach based on the use of autologous engineered DC, which effectively modulate pathogenic CD4+ and CD8+ T cell responses in vitro and in vivo by promoting Ag_x0002_specific Tr1 cells suitable for cell-based therapy for restoring tolerance in T cell mediated diseases

overall_design: RNA-Seq of 6 samples from 3 independent donors; from each donor 1 Control and 1 test sample were generated

first: Laura

last: Passerini

first: Grazia

last: Andolfi

last: Passeri

first: Giorgia

last: Giacomini


title: Maternal antibiotic exposure enhances neonatal ILC2 responses and aggravates allergic airway inflammation in adults

status: Public on May 08 2023

city: Tianjin

first: Jie

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: Tianjin Medical University

summary: The maternal microbiota plays an important role in shaping and priming infant immunity, although the cellular and molecular mechanisms underlying these effects remain obscure. Here we report that prenatal antibiotic exposure caused significant elevation of group 2 innate lymphoid cells (ILC2s) in neonatal lungs, in both cell numbers and functionality. Downregulation of type 1 interferon signaling in ILC2s caused by diminished production of microbiota-derived metabolite butyrate represents the underlying mechanism. Mice lacking butyrate receptor GPR41 (GPR41-/-) or type 1 interferon receptor (Ifnar1-/-) recapitulated the phenotype of neonatal ILC2s upon maternal antibiotic exposure. Furthermore, prenatal antibiotic exposure induced persistent epigenetic changes in ILC2s and had a long-lasting deteriorative effect on allergic airway inflammation in adulthood. Prenatal supplementation with butyrate ameliorated airway inflammation in adult offspring born to antibiotic-exposed dams. These observations demonstrate an essential role for the maternal microbiota in the control of type 2 innate immunity at the neonatal stage, which provides a therapeutic window for treating asthma in early life.

overall_design: A total of 1,000 lung ILC2s(prenatal antibiotic exposure group and control group) were sorted and lysed in 5 μL lysis buffer  for RNA-sequencing

first: Haixu

last: Xu

first: Zhaohai

last: Cui

first: Lijuan

last: Zhang


title: Gene expression profiles of a non-gestational choriocarcinoma and its corresponding patient-derived xenograft tumor

status: Public on May 03 2023

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

summary: Non-gestational choriocarcinoma (NGC) is a rare subtype of malignant germ cell tumor. We established a patient-derived xenograft (PDX) model using tumor tissue from an 18-year-old patient with NGC. Then, we performed mRNA-seq analysis using the fresh-frozen tissues of the original tumor and the PDX model.

overall_design: The fresh NGC tumor was subcutaneously transplanted into NSG mice. When the tumor diameter reached approximately 2 cm, the tumors were harvested and passed. The generation harboring the patient-derived material was termed P1, with subsequent generations numbered consecutively (P2, P3, P4, etc.). The tumor tissue of P3  was used for analysis.

first: Yukari

last: Oda

first: Akira

last: Yokoi

first: Kaoru

last: Niimi


title: Genomic i-Motifs Display Diverse Binding Preferences Towards Small Molecules, Transcription Factors, and Antibodies

status: Public on Apr 30 2023

city: Frederick

first: Srinath

last: Seshadri

address: 1050 Boyle St.

institute: NCI/CCR

summary: In this study, we have designed custom DNA microarray slides containing 10,976 distinct iM-forming sequences found in human promoters, centromeres, and telomeres, with varied lengths of cytosine repeats from two to ten bases and loops ranging from one to ten bases. We screen this array against a relevant small molecule, an antibody, and four endogenous transcription factors to elucidate differences in iM binding and recognition in the genome.

sample_organism:
Homo sapiens
unidentified

overall_design:
Four identical custom Agilent 8X60K DNA i-motif arrays were screened against increasing concentrations of mitoxantrone, Cy5-labelled iMab monoclonal antibody, or GST-tagged hnRNP K. Additionally, we screened leftover blocks on the microarrays against GST-tagged hnRNP LL, hnRNP A1, and ASF/SF2 protein.
Please note that, as Each array has 8 sectors/blocks (i.e. 8 samples hybridized on a single array), the raw outputs (directly from innoscan) have been modified as per sector/block corresponding to each sample.

first: Kamyar

last: Yazdani

first: Desiree

last: Tillo

first: Charles

last: Vinson

first: John

last: Schneekloth Jr


title: Metabolic rescue of α-synuclein-induced neurodegeneration through propionate supplementation and intestine-neuron signaling in C. elegans

status: Public on Apr 28 2023

city: HK

first: Chaogu

last: Zheng

address: The University of Hong Kong, Pokfulam Road

department: School of Biological Science

country: Hong Kong

institute: University of Hong Kong

summary: Vitamin B12 depletion or propionate supplementation can reverse the transcriptomic aberration in the C. elegans model of PD with neuronal overexpression of alpha-synuclein A53T

overall_design: C. elegans strains with pan-neuronal or dopaminergic neuron-specific overexpression of human alpha-synuclein A53T proteins were fed with either wild-type or B12-depleted cobS(-); cobA(-) K12 E. coli. The PD animals were also supplemented with either propionic acid or vitamin B12 to assess their effects on the transcriptome. Wild-type C. elegans carrying a transgene that expressed GFP in the dopaminergic neurons was used as a control strain. Animals were collected at L4 stage and subjected to whole-organism RNA sequencing. Ribosomal RNAs were depleted from the total RNA during the library construction.


title: Micro-Capture-C  to determine the long-range interaction of HBG1/2 promoter with the locus control region (LCR), a powerful upstream enhancer in  -175 A>G mutantant HUDEP-2 cells.

city: Memphis

first: Jonanthan

last: Yen

address: 262 Danny Thomas Pl

department: Hematology

institute: St. Jude Children's Research Hospital

summary: Naturally occurring mutations in the γ-globin promoters can result in hereditary persistence of fetal hemoglobin (HPFH), a benign condition that ameliorates the severity of β-hemoglobinopathies through increased post-natal fetal hemoglobin (HbF) expression. Base editing to recreate the HPFH mutations is a promising approach to induce HbF. Compared with Cas9-generated indels, base-editing approaches were more potent, with the −175 A>G conversion resulting in the strongest induction of HbF by creating a new TAL1 binding motif that stimulates long-range interaction with the locus control region (LCR), a powerful upstream enhancer.  Micro-Capture-C analysis showed that introducing the −175 A>G variant stimulated long-range interaction between the γ-globin promoters and the LCR in erythroid progenitor cell line. Together, these findings show that the −175 A>G variant creates a bipartite GATA–TAL1 motif, resulting in the assembly of a GATA1/TAL1/LMO2/LDB1 complex, which activates γ-globin gene transcription by enhancing its physical association with the LCR.

overall_design: Micro-Capture-C  experiments were performed in wild type hemizygous HUDEP-2 cells (HUDEP2∆εγδβ cells), HUDEP2∆εγδβ cells harboring  -175 A>G mutation at -globin promoter the γ-globin promotesr (HBG2/HBG1).  Wild type HUDEP-1 is used as a control.

first: T

last: Mayuranathan

first: Jonathan


title: Potent and uniform fetal hemoglobin induction via base editing


title: Smart-seq2 single-cell RNA sequencing of mouse liver non-parenchymal cells

status: Public on Apr 29 2023

city: Huddinge

first: Ping

last: Chen

address: Alfred Nobels allé 8

department: Department of Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

summary: Smart-seq2 scRNA-seq of liver non-parenchymal cells from 3 high-fat diet and 3 control mice.

overall_design: scRNA-Seq


title: Time-dependent recruitment of GAF, ISGF3 and IRF1 complexes to GAS, ISRE and composite genes shapes IFNa and IFNg activated transcriptional responses and explains functional overlap [RNA-seq]

status: Public on May 04 2023

city: Poznan

first: Hans

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

department: Laboratory of Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz University

summary:
Although the core type I and type II IFN signaling pathways are distinct, their expression profiles show considerable overlap and are difficult to discern. Using a genome-wide RNAseq-ChIPseq integrative approach, our results identify a novel class of IFN-I and IFN-II responsive genes that use ISRE and GAS composite sites to recruit STAT1 and STAT2-containing ISGF3 and GAF-like complexes and IRF1 for optimal expression. Moreover, they support the existence of an analogous transcriptional regulatory mechanism of IFNα and IFNγ inducible genes, in which STAT1 and STAT2-containing ISGF3 and GAF-like complexes and IRF1 are recruited to individual or combined ISRE and GAS composite sites in an IFN- and time-dependent manner.
In addition, we present proof for the involvement of an ISRE and GAS composite-dependent regulatory system in IFN-activated positive feedback regulation of the STAT1, STAT2, IRF9 and IRF1 genes and long-term response to IFNs, which depends on phosphorylation and expression of ISGF3, IRF1 and GAF-like components. These findings provide further insight in the existence of a novel intracellular amplifier circuit that offer an explanation for the existing molecular and functional overlap between IFN-I and IFN-II activated ISG expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the human hepatocellular carcinoma cell lines – Huh7.5 WT, Huh7.5 IRF9KO, Huh7.5 STAT1KO, Huh7.5 STAT2KO, Huh7.5 IRF1KO and Huh7.5 IRF9/IRF1 dKO treated with IFN alpha and IFN gamma

middle: A


title: The RNA m6A reader YTHDC2 recruits TET1 to demethylate transposable elements DNA and prevent neural fate of human pluripotent stem cells [MeDIP-Seq]

city: Durham

first: Tongyu

last: Sun

overall_design: MeDIP-Seq on H1 hESCs.

first: Yarui

last: Diao


title: Transcriptomic analysis of LMP1 TES domain single or double mutant in EBV-negative Akata Burkitt Lymphoma Cells

status: Public on Apr 25 2023

city: Boston

first: Bidisha

last: Mitra

address: 181 Longwood Avenue, 8th floor

department: Medicine

institute: Brigham and Women's Hospital

summary: RNA-seq was used to characterize the LMP1 TES domain-mediated regulation of B-cell genome wide target genes. We created an inducible stable  EBV-negative Akata Burkitt Lymphoma cell line expressing LMP1 wildtype, TES1 functional only, TES2 functional only and TES1/2 non-functional.

overall_design: Comparative gene expression profiling analysis of RNA-seq data  EBV-negative Akata Burkitt Lymphoma Cells upon expression of LMP1 wildtype, TES1 only, TES2 only and loss of function of both TES domains.  Uninduced cell lines (with the respective transgenes) were used as control.

first: Rui

last: Guo

first: Eric

last: Burton

first: Laura

last: Murray-Nerger

first: Benjamin

last: Gewurz


title: Decreased SRSF7 expression induces cellular senescence via generating MDM2 variants

status: Public on Apr 27 2023

city: Suwon

first: Su Bin

last: Lim

state: Gyeonggi-do

address: Worldcup-Ro 164, Yeongtong-Gu

institute: Ajou University School of Medicine

summary: To evaluate the role of alternative splicing in cellular senescence, we analyzed transcriptomics by RNAseq in SRSF3 and SRSF7 suppressed human diploid fibroblasts.

overall_design: A transcriptomic analysis by suppression of SRSF3 and SRSF7 with siRNA transfection in human diploid fibroblasts.

first: Jiwon

last: Hong

first: Su


title: Transcriptomic analysis of EBV LMP1 TES domain(s) single or double mutant and CD40L treatment in EBV-negative BL41 Burkitt-Lymphoma Cells

summary: RNA-seq was used to characterize the LMP1 TES domain-mediated regulation of B-cell genome wide target genes. We created an inducible stable  EBV-negative BL41 Burkitt Lymphoma cell line expressing LMP1 wildtype, TES1 functional only, TES2 functional only and TES1/2 non-functional. wildtype EBV-negative BL41 (no LMP1 transgene) cells were also subjected to CD40L (recombinant CD40 ligand) to study the B-cell target gene regulation in comparison to LMP1 wildtype-mediated.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in EBV-negative BL41 Burkitt Lymphoma Cells upon expression of LMP1 wildtype, TES1 only, TES2 only and loss of function of both TES domains. Uninduced cell line (with the LMP1 wildtype transgene) were used as control. Cell untreated with CD40L were used a control for experimental samples (treated with CD40L)


title: Transcriptome-wide deamination analysis

summary: Adenosine base editing to recreate the HPFH mutations is a promising approach to induce HbF. To measure Cas-independent off-target editing of mRNA, we electroporated CD34+ cells from three different donors with RNP consisting of ABE7.10 or ABE8e complexed with the -globin −175 A>G targeting sgRNA. Six days later, this was followed by high-depth RNA-seq. The rates of A-to-I conversion were similar in edited and unedited control cells, which is consistent with previous reports that off-target RNA editing was not detected after high-level adenine base editing of HUDEP2 cells or HSPCs.

overall_design: Total RNA-seq were performed in untreated, mock electroporated and ABE7.10 and ABE8e RNP complexed with the g-globin -175-targeting sgRNA in CD34+ HSPCs.


title: Gene expression profiles of differentially expressed genes in Enterococcus faecalis 14 ΔpnpA mutant strain

status: Public on Apr 20 2023

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

institute: University of Lille

summary: To explain the particular behavior of the mutant ΔpnpA strain, we performed a  comparative transciptomic analysis of RNA isolated from a derivative strain ΔpnpA mutant versus the wild-type (WT) , after 3h and 6 h of growth in GM17 medium under semi-aerobic conditions.

overall_design:
Expression data of the 3 wild-type samples were filtered and the average was calculated for each gene, for 3h and also for 6h condition. A fold change (FC) value was calculated between ΔpnpA individual samples and the mean of WT for each point of kinetics. Differentially expressed genes (DEGs) were selected for a FC threshold > 2.0 or < 0.5.
Please note that the gpr files contains raw data obtained from the 4-plex/block slides and the .xlsx file (linked to each sample) contains the corresponding sample raw data (obtained from the selected block).

first: Rabia

last: Ladjouzi

first: Djamel

last: Drider