title: Rational optimization of a transcription factor activation domain inhibitor

status: Public on Jun 24 2023

city: Berlin

first: Shaon

last: Basu

state: Germany

address: Ihnestrasse 63-73

department: Department of Genome Regulation

institute: Max Planck Institute for Molecular Genetics

summary: Transcription factors are among the most attractive therapeutic targets but are considered largely undruggable. Here we provide evidence that small molecule-mediated partitioning of the androgen receptor, an oncogenic transcription factor, into phase-separated condensates has therapeutic effect in prostate cancer. We show that the phase separation capacity of the androgen receptor is driven by aromatic residues and short unstable helices in its intrinsically disordered activation domain. Based on this knowledge, we developed tool compounds that covalently attach aromatic moieties to cysteines in the receptors’ activation domain. The compounds enhanced partitioning of the receptor into condensates, facilitated degradation of the receptor, inhibited androgen receptor-dependent transcriptional programs, and had antitumorigenic effect in mouse models of prostate cancer and castration resistant prostate cancer. These results establish a generalizable framework to target the phase-separation capacity of intrinsically disordered regions in oncogenic transcription factors and other disease-associated proteins with therapeutic intent.

overall_design: To understand the transcriptomic effects of our lead and engineered AR condensate targeting molecules (EPI-001 and 1ae), we dosed the drugs directly on LNCaP cells in RPMI-1640 5% FBS, for 6 and 24 hours. Vehicle control (DMSO) was matched for each time point. Samples were prepared in three biological replicates for each experimental condition. RNA was then extracted using a Zymo DirectZol Micro kit (Zymo R2062) according to the manufacturer’s protocol. Total RNA-seq libraries were then prepared using 1 µg of resulting RNA from each sample and KAPA RNA HyperPrep Kit with RiboErase (Roche KR1351) according to the manufacturer’s protocol with 10 amplification cycles. Libraries were sequenced on a NovaSeq 6000 with paired-end reads of 100 base pairs, with a read depth of 50 million fragments / library. Three libraries from three corresponding biological replicates  were prepared for each treatment (time, dosage, and compound).

first: Denes

last: Hnisz

first: Xavier

last: Salvatella


title: Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer

status: Public on Jun 14 2023

city: Philadelphia

first: Sarah

last: Alp

state: PA

address: 3601 Spruce Street

country: USA

institute: The Wistar Institute

type: Methylation profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Foxp3 Orchestrates Reorganization of Chromatin Architecture to Establish Regulatory T Cell Identity [ChIP-seq]

city: La Jolla

first: Jesse

middle: R

last: Dixon

state: CA

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute for Biological Studies

summary: Chromatin conformation reorganization is emerging as an important layer of regulation for gene expression and lineage specification. Yet, how lineage-specific transcription factors contribute to the establishment of cell type-specific 3D chromatin architecture in the immune cells remains unclear, especially for the late stages of T cell subset differentiation and maturation. Regulatory T cells (Treg) are mainly generated in the thymus as a subpopulation of T cells specializing in suppressing excessive immune responses. Here, by comprehensively mapping 3D chromatin organization during Treg cell differentiation, we show that Treg-specific chromatin structures were progressively established during its lineage specification, and highly associated with Treg signature gene expression. Additionally, the binding sites of Foxp3, a Treg lineage specifying transcription factor, were highly enriched at Treg-specific chromatin loop anchors. Further comparison of the chromatin interactions between wide-type Tregs versus Treg cells from Foxp3 knock-in/knockout or newly-generated Foxp3 domain-swap mutant mouse revealed that Foxp3 was essential for the establishment of Treg-specific 3D chromatin architecture, although it was not dependent on the formation of the Foxp3 domain-swapped dimer. These results highlighted an underappreciated role of Foxp3 in modulating Treg-specific 3D chromatin structure formation.

overall_design: ChIP-seq in conventional CD4 positive T-cells and T-regs


title: Exclusive heat-not-burn cigarette smoking alters the profile of circulating microRNAs.

status: Public on Jun 13 2023

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background. Traditional combustion cigarette (TCC) smoking is an established risk factor for several types of cancer and cardiovascular diseases. Circulating microRNAs (miRNAs) represent key molecules mediating pathogenetic mechanisms, and potential biomarkers for personalized risk assessment. Several transcriptomics studies have showed that TCC smoking globally changes the profile of circulating miRNAs. The use of heat-not-burn cigarettes (HNBCs) as alternative smoking devices is rising exponentially worldwide, with still unknown long-term effects on health. Comprehensive data on the circulating miRNA profile in chronic HNBC smokers are still lacking.
Purpose. We aimed at defining the profile of circulating miRNAs in serum samples of chronic exclusive HNBC smokers, and identifying potentially pathogenetic circulating miRNA signatures.
Results. Differential expression analysis revealed 101 miRNAs significantly modulated between groups (adjusted p<0.05), with a prevalence of circulating miRNA downregulation in smokers (only 20 miRNAs were upregulated in both groups of smokers). Head-to-head comparison revealed that 65 miRNAs were exclusively modulated in TCC, 26 miRNAs were commonly modulated in both smoker groups, and 10 miRNAs were exclusively modulated in HNBC samples, all versus NS. KEGG pathway analysis performed on target genes of the commonly modulated miRNAs returned cancer-associated and cardiovascular disease pathways. The application of stringent abundance and fold-change criteria to this list nailed down our functional bioinformatic analyses to a network where miR-25-3p and miR-221-3p are main hubs for cardiovascular- and cancer- related molecular pathways, respectively.
Conclusions. Our results define for the first time a global miRNA profile in the serum of exclusive chronic HNBC smokers. Despite the globally lower extent of the differences observed, our data suggest a significant detrimental impact of HNBCs on circulating miRNAs.

overall_design: Serum samples were obtained from subjects previously enrolled in the SUR-VAPES CHRONIC trial, including three groups of 20 healthy young subjects, stratified as chronic HNBC smokers (mean exclusive use of HNBC 1.5±0.5 years), TCC smokers, and non-smokers (NS). Four sub-groups of five subjects each were randomly created for each group (tested for non-statistical differences in available anthropometric and clinical parameters). Three sub-groups were used to create three pooled samples per group for small RNA sequencing, and the fourth sub-group constituted the validation set. Data were analyzed using DEseq2.

first: Vittorio

last: Picchio

first: Claudia

last: Cozzolino

first: Barbara

last: Pardini

first: Erica

last: Floris

first: Sonia

last: Tarallo

first: Xhoulio

last: Dhori

first: Cristina

last: Nocella

first: Lorenzo

last: Loffredo

first: Giuseppe

last: Biondi-Zoccai

first: Roberto

last: Carnevale

first: Giacomo

last: Frati

first: Isotta

last: Chimenti

first: Francesca

last: Pagano


title: The Sequence Basis for Selectivity of Ephrin-B2 for Eph Receptors and Pathogenic Henipavirus G Glycoproteins [EFNB2-D62Q DEEP MUTAGENESIS]

status: Public on Jun 12 2023

city: Urbana

first: Erik

last: Procko

state: IL

address: 600 S Matthews Ave RAL 311

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

summary: Ephrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and also functions as a cell entry receptor for several henipaviruses, which are zoonotic viruses with pandemic potential. Two such viruses, Nipah (NiV) and Hendra (HeV), are highly pathogenic in humans yet do not have any widely approved virus-specific therapeutics or vaccines. Soluble Fc-fusions of EFNB2 (sEFNB2-Fc) are known to bind the attachment glycoprotein G of both viruses and inhibit viral infection of cells. However, the potential of sEFNB2-Fc as a neutralizing agent in vivo is hindered by its binding activity to native Eph receptors. Therefore, using deep mutagenesis, variants of EFNB2 at cell surface are identified with increased binding to the soluble head domain of NiV-G over soluble Fc-fusions of the extracellular domains of Eph receptors. Specificity mutations for NiV-G are found primarily at the binding interface, especially around the G-H binding loop. The mutational landscape offers a preliminary blueprint for engineering sEFNB2-Fc variants with high specificity and affinity for potent neutralization of henipaviruses.

overall_design: The cDNA encoding full-length human EFNB2 isoform 1 (GenBank NP_004084.1) with an N-terminal c-myc tag was diversified by site-saturation mutagenesis at 137 positions (a.a. I31-G168); a glutamine substitution at position D62 was unchanged. This was accomplished by introducing degenerate NNK codons at the respective sites, which fully spanned the known receptor binding domain for Eph receptors and the attachment glycoprotein G of Nipah virus (NiV-G). The EFNB2 library was expressed in human Expi293F cells under conditions where most cells express no more than a single coding variant. The cell culture was then incubated with soluble Fc-fused extracellular domains of EphB3 and EphB4 (subcloned from plasmids from Sino Biological) and simultaneously stained with Alexa 647-conjugated anti-myc to measure surface EFNB2 expression. The cell culture was then incubated with the head domain of NiV-G (a.a. G183-T602; GenBank NP_112027.1). Soluble NiV-G head domain was fused at its C-terminus to sfGFP for fluorescence detection in an oxidizing extracellular environment. After washing, bound NiV-G-sfGFP was found to be proportional to EFNB2 levels. There were unambiguous populations of cells expressing EFNB2 variants with high and low NiV-G-sfGFP binding; these cell populations were collected by FACS and are called NiV-G-High and NiV-G-Low, respectively. Transcripts in the collected cell populations were Illumina sequenced and their frequencies compared to the naive plasmid library. The enrichment or depletion of all 2,740 single amino acid variants in the library was calculated, which acts as a proxy for relative “binding” to NiV-G. This “binding” signal is a product both of EFNB2/NiV-G affinity and surface display of properly folded EFNB2.


title: CD4 T Follicular Helper 1 Cells Promote HIV-1 Env Antibody Persistence

status: Public on Jun 16 2023

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

type: Expression profiling by high throughput sequencing

summary: CD4 T follicular helper cells (Tfh) are essential for establishing serological memory and have distinct helper attributes that impact both the quantity and quality of the antibody response. Therefore, gaining insights into Tfh subsets promoting antibody persistence and functional capacity is crucial for vaccine design. We investigated the potential of inducing a mixed Tfh1/17 response to enhance HIV-1 Envelope (Env) antibodies to a DNA-prime/protein boost platform, utilizing rhesus macaques as our experimental model. Following immunization with Clade C gp140 protein formulated with cationic liposome-based formulation (CAF01), we successfully generated germinal center (GC) Tfh1/17 cells, in contrast to the predominance of GC Tfh1 cells induced with gp140 formulated in monophosphoryl lipid A+QS-21 (MPLA). Analysis of lymph nodes, employing proteomic and transcriptional approaches, demonstrated robust induction of GC responses across vaccine platforms with distinct qualitative and quantitative effects elicited by MPLA versus CAF01. While the induction of GC Tfh1 cells with MPLA and GC Tfh1/17 cells with CAF01 resulted in comparable peak HIV-Env antibody levels, there was a notable difference in antibody persistence. The MPLA group demonstrated significantly greater antibody persistence at week 8 and up to 30 weeks after final immunization compared to CAF01. Inducing GC Tfh1 cells with MPLA furthermore enhanced tier 1 neutralization titers, antibody functions, and Env-specific IgG in the rectal mucosa. Notably, IFNγ+ Env-specific Tfh responses, both in blood and lymph nodes, were higher with MPLA and correlated with Env antibody persistence. These findings suggest that vaccine platforms maximizing GC Tfh1 induction may confer protective immunity against HIV.

overall_design: Comparison of transcriptome profiles across CD4 subsets in two vaccine regimens

first: Smita

middle: S

last: Iyer

first: Anil

last: Verma


title: Foxp3 Orchestrates Reorganization of Chromatin Architecture to Establish Regulatory T Cell Identity [CUT&TAG]

first: Jesse

last: Dixon

overall_design: Cut&Tag in T-cell in Foxp3 wild-type and mutant T-regs


title: Foxp3 Orchestrates Reorganization of Chromatin Architecture to Establish Regulatory T Cell Identity


title: Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development [ChIP-seq]

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

country: Spain

institute: IBiS, Universidad de Sevilla-CSIC

summary: Retinoic acid (RA) functions as a ligand for the nuclear RA receptors (RARs), which regulate the expression of target genes by binding to RA response elements. RA signaling is required for multiple processes during chordate embryonic development, such as body axis extension, hindbrain antero-posterior patterning and forelimb bud initiation. Although some RA target genes have been identified, little is known about the genome-wide effects of RA signaling during in vivo embryonic development. Here we stimulate the RA pathway during development by treating zebrafish embryos with all-trans-RA (atRA), the most abundant form of RA, and use a combination of RNA-seq, ATAC-seq, ChIP-seq and HiChIP to gain insight into the molecular mechanisms by which RA signaling control target gene expression. We find that RA signaling is involved in anterior/posterior patterning and development of the central nervous system, participating in the transition from pluripotency to differentiation. atRA treatment also induces alterations in chromatin accessibility during early development and promotes chromatin binding of RARaa and the RA targets Hoxb1b, Meis2b and Sox3, which cooperate in central nervous system development. Finally, we show that RA induces a rewiring of chromatin architecture, with alterations in chromatin 3D interactions that are consistent with target gene expression. This is illustrated by the specific induction of anterior HoxB genes by RARs, among other examples. Altogether, our findings identify genome-wide targets of RA signaling during embryonic development and provide a molecular mechanism by which developmental signaling pathways regulate the expression of target genes by altering chromatin topology.

overall_design: ChIP-seq assays of several trasncription factors in wild-type zebrafish whole embryos, at developmental stages 80% epiboly, 5 somites and 24 hpf, with and without treatment with 0.1µM all-trans retinoic acid (atRA)

first: Marta

last: Moreno-Oñate

first: Lourdes

last: Gallardo-Fuentes

first: Pedro

middle: M

last: Martínez-García

first: Silvia

last: Naranjo

first: Sandra

last: Jiménez-Gancedo

middle: L

last: Gómez-Skarmeta

first: Juan

middle: J

last: Tena


title: Depletion of CRAT in cardiomyocyte results in DCM

status: Public on Jun 02 2023

city: Houston

first: Shengyu

last: Li

state: TX

address: 6670 Bertner Ave, R10-109, floor 10

institute: Houston Methodist Research Insitute

summary: Carnitine acetyltransferase (CRAT) is a mitochondrial enzyme and catalyzes the conversion of acetyl-CoA to acetyl-Carnitine, which enables its export from mitochondria. It was reported that CRAT played a central role in regulating metabolic flexibility and promoting substrate switching from fatty acid to glucose in skeletal myocytes5. Interestingly, CRAT is most abundantly expressed in the heart and its activity is dramatically decreased in the mouse model of HF5,9. However, the specific contribution of this enzyme in the pathogenesis of HF remains largely uncharacterized.

overall_design: Neonatal rat ventricular cardiomyocytes were infected with lentivirus expressing control shRNA (WT) or CRAT shRNA (KO). Cells were harvested after 5 days and RNAs was extracted for RNA-sequencing analysis. We have two WT samples and two KD samples.

first: Hua

last: Mao

first: Aude

last: Angelini

first: Guangyu

last: Wang

first: Xinchun

last: Pi

first: Liang

last: Xie


title: The Sequence Basis for Selectivity of Ephrin-B2 for Eph Receptors and Pathogenic Henipavirus G Glycoproteins [EFNB2 DEEP MUTAGENESIS]

first: Erik

last: Procko

overall_design: The cDNA encoding full-length human EFNB2 isoform 1 (GenBank NP_004084.1) with an N-terminal c-myc tag was diversified by site-saturation mutagenesis at 138 positions (a.a. I31-G168). This was accomplished by introducing degenerate NNK codons at the respective sites, which fully spanned the known receptor binding domain for Eph receptors and the attachment glycoprotein G of Nipah virus (NiV-G). The EFNB2 library was expressed in human Expi293F cells under conditions where most cells express no more than a single coding variant. The cell culture was then incubated with soluble Fc-fused extracellular domain of EphB2 (R&D Systems) and simultaneously stained with Alexa 647-conjugated anti-myc to measure surface EFNB2 expression. The cell culture was then incubated with the head domain of NiV-G (a.a. G183-T602; GenBank NP_112027.1). Soluble NiV-G head domain was fused at its C-terminus to sfGFP for fluorescence detection in an oxidizing extracellular environment. After washing, bound NiV-G-sfGFP was found to be proportional to EFNB2 levels. There were unambiguous populations of cells expressing EFNB2 variants with high and low NiV-G-sfGFP binding; these cell populations were collected by FACS and are called NiV-G-High and NiV-G-Low, respectively. Transcripts in the collected cell populations were Illumina sequenced and their frequencies compared to the naive plasmid library. The enrichment or depletion of all 2,760 single amino acid variants in the library was calculated, which acts as a proxy for relative “binding” to NiV-G. This “binding” signal is a product both of EFNB2/NiV-G affinity and surface display of properly folded EFNB2.


title: Transcriptional changes in the rat brain induced by repetitive transcranial magnetic stimulation (rTMS)_IN_VIVO

status: Public on May 30 2023

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Transcranial Magnetic Stimulation (TMS) is a noninvasive technique that uses pulsed magnetic fields to affect the physiology of the brain and central nervous system.  Repetitive TMS (rTMS) has been used in the study and treatment of neurological conditions including major depression, stroke, epilepsy, schizophrenia, multiple sclerosis, Parkinson’s, and Alzheimer’s disease, as well as other, non-neurological disorders. Among the effects of rTMS, low-frequency protocols (≤ 1Hz) are generally understood to result in cortical inhibition, whereas high-frequency protocols (≥ 3Hz) increase cortical excitability. However, the complex molecular basis of rTMS is largely unexplored. Using three complementary rat models, in vitro, ex vivo, and in vivo, we show complex patterns of hippocampal and neocortical transcriptional response to stimulation in glutamatergic and GABAergic signaling pathways, as well as multiple inflammatory pathways, among others. This broad-based molecular survey helps provide a foundation to tease out the complex molecular mechanisms of the effects of rTMS.

overall_design: Gene expression microarray analysis of 48 mouse brain samples, consisting of matched sets of hippocampus (HIPP, N=24) and parietal cortex (PCTX, N=24) from young sham (Y_Sham, N=4), young iTBS (Y_iTBS, N=4), age-unimpaired sham (AU_Sham, N=4), AU_iTBS (N=5), aged-impaired sham (AI_Sham, N=4) , and AI_iTBS (N=3), obtained 48 hours after either sham or iTBS transcranial magnetic stimulation (rTMS) treatment. TR and TER indicates technical repeats within and between experiments.

first: Marina

last: Weiler

first: Kevin

last: Stieger

first: Kavisha

last: Shroff

first: Jessie

middle: P

last: Klein

first: William

middle: H

last: Wood III

first: Yongqing

last: Zhang

first: Prabha

last: Chandrasekaran

first: Elin

last: Lehrmann

first: Simonetta

last: Camandola

first: Jeffrey

last: Long

first: Mark

last: Mattson

middle: G

last: Becker

first: Peter

last: Rapp


title: Transcriptional changes in the rat brain induced by repetitive transcranial magnetic stimulation (rTMS).


title: Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development [RNA-seq]

first: José

last: Santos-Pereira

overall_design: RNA-seq assays in wild-type zebrafish whole embryos, at developmental stages 80% epiboly, 12 somites and 24 hpf, with and without treatment with 0.1µM all-trans retinoic acid (atRA)

first: Marta

last: Moreno-Oñate

first: Lourdes

last: Gallardo-Fuentes

first: Pedro

last: Martínez-García

first: Silvia

last: Naranjo

first: Sandra

last: Jiménez-Gancedo

last: Gómez-Skarmeta

first: Juan

last: Tena


title: Transcriptional changes in the rat brain induced by repetitive transcranial magnetic stimulation (rTMS)_EX_VIVO

first: Supriyo

last: De

overall_design: Gene expression microarray analysis  of sequential ex vivo hippocampal slices (N=36) from four young (Y), four aged-unimpaired (AU), and four aged-impaired (AI) animals at the one hour time-point after either sham, iTBS or 1Hz transcranial magnetic stimulation (TMS) treatment.

first: Marina

last: Weiler

first: Kevin

last: Stieger

first: Kavisha

last: Shroff

last: Klein

last: Wood III


title: Impact of Bcl11b on the transcriptome of CD8+ T cell subsets[RNA-seq]

status: Public on Jun 08 2023

city: Tampa

first: Dorina

last: Avram

state: Fl

address: 12902 Magnolia Drive, MRC4

department: Department of Immunology

institute: Moffitt Cancer Center

summary: The transcription factor (TF) networks that regulate the differentiation of resident versus circulating memory CD8+ T cells are incompletely understood. Here we show that the TF Bcl11b restricts gut resident memory (Trm) cell differentiation, while promoting splenic T central memory (Tcm) and effector memory (Tem) cell differentiation. The reduction of Bcl11b-deficient splenic Tcm and Tem cells was not due to major alterations in their programs, but rather due to the increased homing of their precursors to the small intestine. However, Bcl11b-deficient resident memory precursor cells upregulated residency program, including the TFs Ahr and Prdm1 (encoding Blimp1), and downregulated Tcf7, which restricts the residency program and promotes tissue egress. Bcl11b directly bound at Ahr and Prdm1, as well as at Tcf7 genes. Abrogating Ahr and Prdm1, or restoration of Tcf7 expression in Bcl11b-deficient cells led to partial correction of the excessive resident memory cell differentiation. Functionally, Bcl11b-deficient memory CD8+ T cells had an impaired recall response, but anti-tumor immunity was increased in adoptive cell therapy. Bcl11b also repressed the residency program in human CD8+ T cells and human Bcl11b low tumor-infiltrating lymphocytes showed increased residency gene expression. Thus, Bcl11b plays a critical role in balancing the circulating and tissue residency programs and reveals a potential novel target for cancer immunotherapies.

overall_design: Examination of changes in transcriptome of memory precursor cells (MP / Mpr), terminal effector cells (TE), and tissue-resident memory T cell precursors (Trmp) in WT and Bcl11b KO cells.

first: Eric

last: Helm

first: Tomas

last: Zelenka


title: Genomic analysis reveals HDAC1 regulates clinically relevant transcriptional programs in Pancreatic cancer

status: Public on May 31 2023

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: We performed ChIP-seq analysis on H3K27ac in MIA PaCa-2 cells with HDAC1 overexpression using the antibody Abcam H3K27ac (Abcam, ab4729), a non-targeting scrableled sgRNA control, and two replicates for each.

overall_design: ChIP sequencing

first: Carter

last: Wright

first: Emily

last: Gordon


title: Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development [ATAC-seq]

first: José

last: Santos-Pereira

overall_design: ATAC-seq assays in wild-type zebrafish whole embryos, at developmental stages 80% epiboly, 12 somites and 24 hpf, with and without treatment with 0.1µM all-trans retinoic acid (atRA)

last: Moreno-Oñate

last: Gallardo-Fuentes

last: Martínez-García


title: Transcriptional changes in the rat brain induced by repetitive transcranial magnetic stimulation (rTMS)_IN_VITRO

overall_design: Gene expression microarray analysis of 36 sequential ex vivo hippocampal slices from four young (Y), four aged-unimpaired (AU) and four aged-impaired (AI, N=X) at the one hour time point after either sham, iTBS or 1Hz transcranial magnetic stimulation (TMS) treatment.

first: Jessie

first: William

first: Yongqing

last: Zhang

first: Prabha

last: Chandrasekaran

first: Elin

last: Lehrmann

first: Simonetta

last: Camandola

first: Jeffrey

last: Long

first: Mark

last: Mattson

last: Becker

first: Peter

last: Rapp


title: Endothelial dysfunction in NR2F2-silenced cells - EA.hy926 cells model

city: Bethesda

first: Gabriela

middle: A

last: Ferreyra

state: MD

address: 9000 Rockville Pike - Building 10 room 4D03

department: CCMD

institute: Clinical Center

summary: Orphan nuclear receptor chicken ovalbumin upstream promoter transcription factor 2 (COUPTF2; NR2F2) is highly expressed in endothelial cells (ECs) and Nr2f2 knockout produces lethal cardiovascular defects. In humans, NR2F2 mutations result in both congenital heart disease and diaphragmatic hernia, conditions associated with the development of pulmonary arterial hypertension (PAH). However, COUPTF2 functions in mature endothelium are uncertain. NR2F2 knockdown in primary human endothelial cells (ECs) led to an interferon-biased inflammatory response, endothelial-to-mesenchymal transition, proliferation, hypermigration, apoptosis-resistance and mitochondrial dysfunction. These phenotypic changes were associated with AKT activation and increased Dickkopf-1 (DKK1) expression, a Wnt/β-catenin pathway inhibitor. DKK1 was also elevated in patients with PAH and secreted in response to loss of bone morphogenetic receptor type 2 (BMPR2), the archetypal PAH-associated genetic defect. Together, these findings demonstrate that endothelial NR2F2 suppresses inflammation and proliferation. Thus, NR2F2 loss disrupts EC homeostasis and may promote pathologic vascular remodeling in the development of PAH.

overall_design: Cells were culture and divided in 4 sets. Independent experiments with 2 condition were performed on each set (control SiRNA vs siRNA against NR2F2). After tRNA collection all samples were process as a batch

first: Edward

last: Dougherty

first: Cumhur

middle: Y

last: Demirkale

first: Robert

last: Danner


title: IL-17 signalling is critical for controlling subcutaneous adipose tissue wasting and parasite burden during chronic Trypanosoma brucei infection

status: Public on May 27 2023

city: Manchester

first: Matthew

middle: Christopher

last: Sinton

state: Greater Manchester

address: Core Technology Facility

department: Division of Immunology, Immunity to Infection and Respiratory Medicine

country: United Kingdom

institute: University of Manchester

overall_design: Refer to individual Series


title: Allometric tissue-scale forces activate mechanoresponsive immune cells to determine pathological foreign body response to biomedical implants

status: Public on Jun 05 2023

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

summary: Allometric tissue-scale forces at the implant-tissue interface drive pathological foreign body response.

overall_design: scRNA-seq was performed on capsule tissue from 20 mice implanted with standard or mechanically stimulated silicone implants.

first: Jagan

last: Padmanabhan

first: Dharshan

last: Sivaraj

first: Geoffrey

middle: C

last: Gurtner


title: Endothelial dysfunction in NR2F2-silenced cells - human lung microvascular endothelial cells model

overall_design: Cells were culture and divided in 5 sets. Independent experiments with 2 condition were performed on each set (control SiRNA vs siRNA against NR2F2). After tRNA collection all samples were process as a batch


title: IL-17 signalling is critical for controlling subcutaneous adipose tissue wasting and parasite burden during chronic Trypanosoma brucei infection [single-cell RNA-seq]

summary: In the skin, Trypanosoma brucei colonises the subcutaneous white adipose tissue (WAT) and harbours a pool of parasites competent for forward transmission. The interaction between parasites, adipose tissue, and the local immune system is likely to drive adipose tissue wasting and weight loss observed in cattle and humans infected with T. brucei.  However, mechanistically, this process is not fully understood. Here, using several complementary approaches including mass cytometry by time of flight, bulk and single cell transcriptomics, we found that T. brucei infection drives a local expansion of several IL-17A-producing cells in the murine WAT, including TH17 and V6+ T cells. We also found that global IL-17 deficiency, or mice lacking IL-17 receptor expression specifically on adipocytes, were protected from infection-induced WAT wasting and weight loss. Unexpectedly, we found that abrogation of IL-17 signalling on adipocytes results in higher burden of extravascular parasites in the WAT. Taken together, our study highlights the central role of IL-17 signalling on adipocytes in controlling WAT responses to infection, suggesting that adipocytes are a critical coordinator of the tissue immune response to T. brucei infection.

overall_design: 3T3-L1 preadipocytes were differentiated to an adipocyte lineage before being treated with 100ng of recombinant IL-17A for 24 hours

first: Praveena

last: Chandrasegaran

first: Paul

last: Capewell

first: Anneli

last: Cooper

first: Alex

last: Girard

first: John

last: Ogunsola

first: Georgia

last: Perona-Wright

first: Dieudonné

last: Ngoyi

first: Nono

last: Kuispond

first: Bruno

last: Bucheton

first: Mamadou

last: Camara

first: Shingo

last: Kajimura

first: Cécile

last: Bénézech

first: Annette

last: MacLeod

first: Juan

middle: F

last: Quintana


title: Trascriptome data in the brain from Propolis treated-Alzheimer's disease model mice

status: Public on Jun 09 2023

city: Tomata

first: Nobuaki

last: Okumura

state: Okayama

address: 194 Ichiba Kagamino

country: Japan

institute: Yamada Bee Company, Inc.

summary: We showed that Brazilian green propolis attenuated Aβ-induced memory and learning impairment. Comprehensive gene expression analysis demonstrated that Brazilian green propolis treatment suppressed inflammation and immune responses via immune cells such as microglia and astrocytes in the brain. These results indicate the potential of Brazilian green propolis as a promising ingredient for preventing AD-type dementia.

overall_design: Five-week-old male Slc:ddY mice were randomly divided into five groups (n=8). The groups were pretreated with vehicle and propolis at a dose of 100, 300 and 900 mg/kg body weight for 8 days, then AD-like phenotypes were induced by intracerebroventricular (ICV) injection of Aβ25‒35. A sham operation group was set as the control. Gene expression analysis was performed using the Clariom S Mouse Array (Thermo Fisher Scientific, Waltham, MA, USA).

first: N

first: T

last: Degawa

last: Ito


title: RNA-seq muscle (AR)

status: Public on May 25 2023

city: ILLKIRCH

first: Delphine

last: Duteil

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary: Identify the genes modulated by Androgen Receptor.

overall_design: We selectively knocked-out AR in myofibers by crossing AR floxed mice to HSA-Cre mice. RNA from gastrocnemius muscle of 9 week-old control (AR floxed mice) and knock-out mice was extracted with trizol according to the manufacturer protocol. RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files). We annotated these reads to the mm10 build of the mouse genome using HOMER. The aligned reads were counted with the homer software (analyze RNA) and DEG’s were identified using EdgeR and DESeq.

first: Anna

middle: I

last: Rerra

first: Daniel

last: Metzger


title: CRISPR-based epigenome editing screens identify transcriptional and epigenetic regulators of human CD8 T cell function [ATAC-seq]

status: Public on May 24 2023

city: Durham

first: Sean

last: McCutcheon

state: NC

address: 101 Science Drive, CIEMAS Rm. 2323

department: Biomedical Engineering

institute: Duke University

summary:
Human CD8+ T cells were transduced with lentivirus encoding for HER2-CAR-2A-GFP or HER2-CAR-2A-BATF3.
T cells were either only stimulated once after thawing (acute stimulation) or repeatedly stimulated with HER2+ SKBR3 cells at a 1:2 effector to target (E:T) ratio every 3 days (chronic stimulation).

overall_design: Comparative chromatin accessibility analysis of ATAC-seq data of acutely (n = 3) and chronically (n = 2) stimulated CD8+ T cells with or without BATF3 overexpression.

first: Charles

last: Gersbach


title: Dynamics of m6A RNA methylome during leukemogenesis reveals a role of PRMT6-MFSD2A signaling axis in maintaining AML stem cells.[RIP-seq]

status: Public on Jun 20 2023

city: Wuhan

first: Haojian

last: Zhang

address: Donghu Rd.

country: China

institute: Wuhan University

summary: We delineate a comprehensive m6A landscape during acute myeloid leukemia (AML) development, and identify PRMT6, regulated by IGF2BP2, acting as a key for leukemia stem cell maintenance by restraining MFSD2A expression and docosahexaenoic acid level.

overall_design: m6A readers (IGF2BP2, YTHDF2, YTHDC1) RIP-seq of primary murine LICs

first: Ying

last: Cheng

first: Zhuying

last: Gao

first: Tiantian

first: Yuhua

last: Wang

first: Guoqiang

last: Han

first: Yashu

last: Li

first: Peipei

first: Jin

last: Hu

first: Tong

first: Chengli

last: Guo

first: Jihua

last: Chai

first: Jing

first: Manman

last: Cui

first: Kexin

first: Weidong

last: Liu

first: Shuxin

last: Yao

first: Pengbo

last: Lu

first: Ziyan

last: Cao

first: Yanbing

last: Zheng

first: Jiwei

last: Chang

first: Rong

last: Yin


title: Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer [RRBS]

status: Public on May 28 2023

city: Philadelphia

first: Sarah

last: Alp

address: 3601 Spruce Street

institute: The Wistar Institute

summary: To investigate the EBV genome after Decitabine treatment by reduced representation bisulfite sequencing, ATAC-seq, and RNA-seq

overall_design: Two EBV positive gastric cancer cell lines were treated with decitabine for 3days

first: Tempera

last: Italo

first: Leiberman

last: Paul M


title: Endothelial dysfunction in NR2F2-silenced cells - human coronary artery endothelial cells model

first: Gabriela

last: Ferreyra

first: Edward

last: Dougherty

first: Cumhur

last: Demirkale

first: Robert

last: Danner


title: Extracellular acidosis promotes colonization of lung metastases by mediating extracellular matrix remodeling and vasculogenic mimicry

status: Public on May 21 2023

city: Taipei

first: Wan-Yi

last: Shie

address: No.1, Changde St., Jhongjheng District, Taipei City 100, Taiwan R.O.C.

country: Taiwan

institute: National Taiwan University

summary:
Acidosis is a hallmark of the tumor microenvironment caused by the metabolic switch from glucose oxidative phosphorylation to glycolysis. It has been largely associated with tumor growth and progression, nevertheless, how acidosis promotes metastatic dissemination remains largely unknown.
In this study, we established a long-term acidosis model using patient-derived lung cancer cells. By comparing xenograft inoculates at the cluster sizes of lung cancer circulating tumor cells, the acidosis cells display significantly higher incidence of secondary tumor establishment than their neutral pH counterparts.
Transcriptomics analyses reveal a profound remodeling of the extracellular matrix in the acidosis cells, featuring the upregulation of ITGA4 and HAS3 genes, In clinical specimen, overexpression of both ITGA4 and HAS3 proteins are associated with primary tumors with metastatic ability, and their distribution is markedly accentuated around vascular mimicry structures in secondary tumors.
We show that acidosis cells display higher ability of vascular mimicry in vitro, and are enriched in ABC transporter-dependent side population cells.
Our data support that acidosis drives tumor metastatic colonization via enhanced extracellular matrix remodeling and vascular mimicry. Assessment on the prognostic value of tumor acidosis for metastasis and possible treatment directions are discussed.

overall_design: This submission contains RNA-Seq data of transcriptome analysis of CLS1 cells under the tratments of long-term pH6.6 culture, long-term pH7.4 control, 24hrs pH6.6 culture, and 0hr control.


title: CRISPR-based epigenome editing screens identify transcriptional and epigenetic regulators of human CD8 T cell function [CRISPRi/a TF scRNA-seq characterization]

first: Sean

last: McCutcheon

summary: Human CD8+CCR7+ T cells from three donors were transduced with CRISPRi and CRISPRa TF gRNA libraries and expanded for 10 days. After 10 days, we used single-cell RNA sequencing (scRNA-seq) to analyze the transcriptomic effects of silencing or activating each gene candidate.

overall_design: The transcriptome profiles of cells with the same targeting gRNA were compared to cells with only non-targeting gRNAs.

first: Charles

last: Gersbach


title: mRNA expression of young, mid-old, and old fibroblasts

status: Public on May 19 2023

city: Suwon

first: Soon Sang

last: Park

address: Worldcup-Ro 206

country: South Korea

institute: Ajou University School of Medicine

summary: Examination of the difference in mRNA expression profile between young, mid-old, and old fibroblasts

overall_design: Young fibroblasts (P8), mid-old fibroblasts (P27), and old fibroblasts (P57)

first: Soon

first: Young-Kyeong

last: Lee

first: Young

last: Kim

first: Tae


title: AR in skeletal muscle

first: Delphine

last: Duteil

summary: Determine AR cistrome in skeletal muscle and correlate it with the presence of H3K4me2.

overall_design: Muscle nuclei were extracted as described (Joshi et al., 2016). After sonication, chromatin was immunoprecipitated with anti-AR and anti-H3K4me2 antibodies. sequenced with an Illumina Hiseq 4000 as paired-end 100 bp reads, and mapped to the mm10 reference genome using Bowtie 2 (Langmead and Salzberg, 2012). Uniquely mapped reads were retained for further analysis. MACS2 algorithm (https://github.com/taoliu/MACS/) (Zhang et al., 2008) was used for peak calling with non-immunoprecipitated chromatin as control.


title: Mapping disease-associated regulatory circuits by cell type from single-cell multiomics data (COVID-19 scATAC-seq)

city: New York

first: Elena

last: Zaslavsky

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

summary: Resolving chromatin remodeling-linked gene expression changes is important for understanding disease states. We describe MAGICAL (Multiome Accessible Gene Integration Calling And Looping), a hierarchical Bayesian approach that leverages paired scRNA-seq and scATAC-seq data from different conditions to map disease-associated transcription factors, regulatory sites and genes as regulatory circuits. By introducing hidden Bayesian variables to allow modeling noise and signal variation across cells and conditions in both transcriptome and chromatin data, in systemic evaluations MAGICAL achieved high accuracy on circuit prediction at cell-type resolution. We applied MAGICAL to study Staphylococcus aureus sepsis from peripheral blood mononuclear single cell data that we generated from infected subjects and healthy uninfected controls. MAGICAL identified sepsis-associated regulatory circuits predominantly in CD14 monocytes, known to be sepsis activated. We addressed the challenging problem of distinguishing methicillin-resistant- (MRSA) and methicillin-sensitive Staphylococcus aureus (MSSA) infections, where differential expression analysis failed to show predictive value. MAGICAL, however, identified epigenetic circuit biomarkers that distinguished MRSA from MSSA.

overall_design: scATAC sequencing of PBMCs from 6 samples with mild SARS-CoV-2 infection and 3 healthy controls

first: Xi

last: Chen


title: CRISPR-based epigenome editing screens identify transcriptional and epigenetic regulators of human CD8 T cell function [RNA-seq]

summary:
Human CD8+ T cells from three donors were transduced with lentivirus encoding for BATF3-2A-GFP or GFP and expanded for 10 days.
Total RNA was isolated from each sample and submitted for RNA-seq. We then performed gene expression profiling analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human CD8 T cells (n = 3 donors) with or without BATF3 overexpression.


title: CRISPR-based epigenome editing screens identify transcriptional and epigenetic regulators of human CD8 T cell function

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


title: Transcriptome data (mRNA and non-coding RNAs) of Bim-deficient Treg cells and aged Treg cells, respectively

city: Hangzhou

first: Di

last: Wu

state: Zhejiang

address: No. 268, Kaixuan Road

institute: Zhejiang University

summary: CD4+YFP+ Treg cells were sorted from the peripheral lymph nodes and spleens of Foxp3-Cre mice (8-10-weeks-old), Foxp3-Cre;Bim-fl/fl mice (8-10-weeks-old), or Foxp3-Cre mice (older than 18-months-old), respectively. Detailly, peripheral lymph nodes and spleens were harvested from mice, and grinded into single cells, then the CD4+-T cells were isolated by Mouse CD4 T Lymphocyte Enrichment Set-DM (BD Biosciences, 558131), followed with FACS sorting (SONY Cell Sorter, SH800S) to purify CD4+YFP+ Treg cells with purities >99%.  RNA samples were prepared with the miRNeasy Mini Kit (Qiagen, 21704), then reverse transcribed, amplified, labeled (Affymetrix GeneChip pico kit, 703308), and hybridized to Clariom D Arrays, mouse (Affymetrix, 902931).

overall_design: Bim regulates Treg cells function and aging. We try to explore the mechanisms by analyzing the transcriptome data of (1) young Foxp3-Cre Treg cells; (2) young Bim-deficient Treg cells; (3) aged Treg cells


title: Transcriptome analysis of a model cyanobacterium Synechococcus elongatus PCC7942 under salt stress and protein synthesis-inhibiting stress conditions

status: Public on May 17 2023

city: Nagoya

first: Hakuto

last: Kageyama

state: Aichi

address: 1-501, Shiogamaguchi, Tempaku-ku

institute: Meijo University

summary: Here, we treated the model cyanobacterium Synechococcus elongatus PCC7942 with streptomycin, which selectively binds to bacterial ribosomes, at a concentration of 50 µg/mL and performed transcriptome analysis using RNA sequencing. In addition to antibiotic stress, we treated salt stress (0.4 M NaCl) and performed RNA sequencing analysis.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Synechococcus elongatus PCC7942 cells were subjected to antibiotic stress or salt stress. Then, total RNA was extracted and analyzed by RNA-seq analysis.

first: Rungaroon

last: Waditee-Sirisattha


title: Mapping disease-associated regulatory circuits by cell type from single-cell multiomics data

overall_design: Refer to individual Series


title: Interferon e restricts Zika infection at the female reproductive tract

status: Public on May 11 2023

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: Interferon ε (IFNε), a unique type I IFN, is thought to protect the host against sexually transmitted infections. Unlike conventional type I IFNs (e.g., IFNα/β), whose expression is undetectable at baseline, IFNε expression is detectable in the epithelium of mucosal tissues, particularly the female reproductive tract (FRT). We found that IFNε expression was not limited to epithelial cells at the FRT. Importantly, in contrast to previous reports, IFNε expression in plasmacytoid dendritic cells and primary cervical epithelial cells was induced by viral infection and by activation of TLR3 or 4 in PBMCs. Induction of IFNε mRNAs was also found in cervicovaginal tissues (CVT) of Zika virus (ZIKV)-infected mice. Mice with IFNε deficiency (Ifnε-/-) did not have impaired induction of interferon-stimulated genes except IFNl, but had altered epithelial and collagen structure in the CVT. Ifnε-/- mice exhibited increased susceptibility to ZIKV infection via an intravaginal route but not via a subcutaneous route, indicating that the protective effect of IFNe was specific to the FRT. Infected Ifnε-/- mice had higher and more sustained viral loads than infected wild-type (WT) mice. Detection of ZIKV infection by single molecule in situ hybridization confirmed that virus spread faster in Ifnε-/- mice than in WT mice. Recombinant murine IFNε protected Ifnar1-/- mice against ZIKV infection when administered through an intravaginal route but not when administered through a subcutaneous route, indicating that the specific role of IFNe at the FRT is independent of IFNAR1 signaling. Our findings indicate that IFNε mediates a novel FRT-specific protective effect on mucosal immunity that limits Zika virus spread.

overall_design: female C57BL/6J (WT) and IFN epsilon deficiency mice generated by using CRISPR-Cas9  at 6-12 weeks were treated with Depo-Provera for 12 days. Cervicovaginal tissues were harvested and total RNAs were prepared for RNAseq analyses.

first: Theresa

last: Chang


title: mRNA expression of mid-old fibroblasts co-cultured with young and mid-old fibroblasts

summary: Examination of the difference in mRNA expression profile between mid-old fibroblasts co-cultured with mid-old fibroblasts and mid-old fibroblasts co-cultured with young fibroblasts

overall_design: Mid-old fibroblasts (P28) are co-cultured with mid-old fibroblasts (P28) or young fibroblasts (P8)


title: Identify the key signaling pathway involved in the Tet2 deficiency-induced clonal hematopoiesis

status: Public on May 15 2023

city: Shanghai

first: Shaoqin

last: Rong

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary: To investigate the signaling pathway required for the Tet2 mutant associated clonal hematopoiesis, we identified the activated signaling pathway in Tet2-deficient hematopoietic stem/progenitor cells  compared to WT cells and using transgentic mouse model to validate our findings. In short, the cGAS-STING pathway is activated in Tet2-deficient HSPCs and promotes the development of CH associated with Tet2 deficiency.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and Tet2-deficient hematopoietic stem/progenitor cells

first: Jiaying

last: Xie

first: Yuheng

last: Shi


title: Identifying the regulon of the Sinorhizobium meliloti JspA protease

status: Public on May 10 2023

city: Stanford

first: Melanie

last: Barnett

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

summary: Sinorhizobium meliloti establishes symbiotic relationship with compatible leguminous plants by inducing root nodule formation, colonizing such nodules, and fixing molecular nitrogen for the host in exchange for carbon compounds.  This mutualistic process requires complex communication and tight regulation to allow yet constrain infection to specific tissues.  Production of succinoglycan, or exopolysaccharide-I (EPS-I), enables S. meliloti to invade the root cortex via infection threads.  A previous genetic screen identified jspA (SMc03872), encoding an extracytoplasmic protease, as a regulator of EPS-I production.  To elucidate its molecular role, we performed transcriptome analyses of strains overexpressing wild-type or mutant alleles of jspA.  We observed changes in gene expression suggesting that JspA contributes to symbiosis efficiency by modulating the critical ExoR-ExoS-ChvI signaling pathway.

platform_organism:
Sinorhizobium meliloti
Medicago truncatula

overall_design: To identify genes whose expression depends on a functional JspA protease, we used custom Affymetrix GeneChips to compare the transcriptomes of three strains: wild-type S. meliloti Rm1021 ectopically expressing jspA (JOE4140) from a taurine-inducible promoter (PtauA: Mostafavi et al., 2014; BMC Microbiol 14: 295) on a plasmid (pJC535), a similar strain expressing a mutant jspA allele (with E148A mutation in the protease active site) (JOE4400, carrying pJC555), and a reference strain carrying the empty vector, pCM130 (JOE3200). Three biological replicates were performed for each of the three strains.

first: Raymond

last: Lopez-Magaña

first: Jason

last: Brice

first: Zhenzhong

last: Huang

first: Sharon

last: Long

first: Joseph


title: Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections

status: Public on May 02 2023

city: La Jolla

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Single-cell genetic and epigenetic analyses parse the brain’s billions of neurons into thousands of “cell-type” clusters, each residing in different brain structures. Many of these cell types mediate their unique functions by virtue of targeted long-distance axonal projections to allow interactions between specific cell types. Here we have used Epi-Retro-Seq to link single cell epigenomes and associated cell types to their long-distance projections for 33,034 neurons dissected from 32 different source regions projecting to 24 different targets (225 source→target combinations) across the whole mouse brain. We highlight uses of this large data set for interrogating both overarching principles relating projection cell types to their transcriptomic and epigenomic properties and for addressing and developing specific hypotheses about cell types and connections as they relate to genetics. We provide an overall synthesis of the data set with 926 statistical comparisons of the discriminability of neurons projecting to each target for every dissected source region. We integrate this dataset into the larger, annotated BICCN cell type atlas composed of millions of neurons to link projection cell types to consensus clusters. Integration with spatial transcriptomic data further assigns projection-enriched clusters to much smaller source regions than afforded by the original dissections. We exemplify these capabilities by presenting in-depth analyses of neurons with identified projections from the hypothalamus, thalamus, hindbrain, amygdala, and midbrain to provide new insights into the properties of those cell types, including differentially expressed genes, their associated cis-regulatory elements and transcription factor binding motifs, and neurotransmitter usage.

overall_design:
In Epi-Retro-Seq, the retrograde viral tracer rAAV2-retro-Cre is injected in the target region in an INTACT mouse, turning on Cre-dependent nuclear-GFP expression in neurons that project to the injected target, throughout the mouse brain. The brain is then sectioned into eighteen 600-micron coronal slices, and the brain regions of interest are mannually dissected from each slice. Nuclei are sampled from 4 mice (2 male and 2 female) for each projection target. Nuclei from each of the dissected source regions are prepared, from which GFP+/NeuN+ nuclei (the GFP-labeled projection neurons) are isolated as single nuclei using fluorescence activated nuclei sorting (FANS) and assayed using snmC-Seq2/3 to profile their genome-wide DNA methylation signatures. Low-quality nuclei were removed.

This project includes the following series:
GSE150170 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150170
GSE230818 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230818
GSE231230 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE231230
GSE231326 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE231326
GSE231414 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE231414
GSE231442 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE231442

first: Jingtian

last: Zhou

first: Zhuzhu

last: Zhang

first: May

first: Hanqing

last: Liu

first: Yan

last: Pang

first: Anna

last: Bartlett

first: Angeline

last: Rivkin

first: Will

middle: N

last: Lagos

first: Elora

last: Williams

first: Cheng-Ta

last: Lee

first: Paula

last: Assakura Miyazaki

first: Andrew

last: Aldridge

first: Qiurui

last: Zeng

first: J

last: Salinda

first: Naomi

last: Claffey

first: Michelle

last: Liem

first: Conor

last: Fitzpatrick

first: Lara

last: Boggeman

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Cynthia

last: Valadon

last: Nery

first: Rosa

last: Castanon

first: Neelakshi

last: Patne

first: Minh

last: Vu

first: Mohammad

last: Rashid

first: Matthew

middle: W

last: Jacobs

first: Tony

last: Ito-Cole

first: Julia

last: Osteen

first: António

last: Pinto-Duartec

first: Bertha

last: Dominguez

first: Jared

middle: B

last: Smith

first: Carolyn

last: O'Connor

first: Kuo-Fen

first: Eran

last: Mukamel

first: Xin

last: Jin

first: M

last: Behrens


title: Circadian ribosome profiling reveals a role for the Period2 upstream opening reading frame in sleep

status: Public on May 05 2023

city: Suita

first: Arthur

last: Millius

state: Osaka

address: iFReC 6F

department: iFReC

institute: Osaka University

summary: Many mammalian proteins have circadian cycles of production and degradation, but de novo transcription is only responsible for a small fraction of this rhythmicity. We used ribosome profiling to quantify RNA translation in liver from circadian-entrained mice transferred to constant darkness conditions over a 24-h period and compared translation levels to absolute protein production for 16 circadian proteins. We observed a delay between translation and peak protein levels for several circadian genes covering a wide range of translation efficiencies. We found extensive binding of ribosomes to upstream open reading frames (uORFs) in circadian mRNAs, including the core clock gene Period2 (Per2). Increased uORFs in 5' UTRs was associated with decreased ribosome binding in downstream ORFs and reduced expression of synthetic reporter constructs in vitro and in single cells. Mutation of the Per2 uORF increased luciferase and fluorescence reporter expression in 3T3 cells without altering phase or period. Genomic Per2 uORF mutation using CRISPR/Cas9 increased PER2 expression in PER2:Luc MEFs and reduced sleep in Per2 uORF mutant mice. These results suggest that post-transcriptional processes shape translation of mRNA transcripts, which can impact physiological rhythms and sleep.

overall_design: Circadian ribosome profiling of two C57BL/6N mouse livers from each timepoint CT00, CT04, CT08, CT12, CT16, CT20, and CT24

first: Dimitri

last: Perrin

first: Hiroki

middle: R

last: Ueda


title: HiC and H3K27ac HiChIP of clonal Jurkat T cells infected HIV-1 model NL4-3-D6-drEGFP

status: Public on May 01 2023

city: New Haven

first: Ya-Chi

last: Ho

state: Connecticut

address: 295 Congress Avenue,BCMM 354E

institute: Yale University

summary: HIV-1 integration introduces ectopic transcription factor binding sites into host chromatin. We postulate that the integrated provirus serves as an ectopic enhancer that recruits additional transcriptional factors to the integration locus, increases chromatin accessibility, changes 3D chromatin interactions, and enhances both retroviral and host gene expression. We used 4 well-characterized HIV-1-infected cell line clones having unique integration sites and low to high levels of HIV-1 expression. Using single-cell DOGMA-seq, which captured the heterogeneity of HIV-1 expression and host chromatin accessibility, we found that HIV-1 transcription correlated with HIV-1 accessibility and host chromatin accessibility. HIV-1 integration increased local host chromatin accessibility within ~5–30 kb distance. CRISPRa and CRISPRi-mediated HIV-1 promoter activation and inhibition confirmed integration site-dependent HIV-1-driven changes of host chromatin accessibility. HIV-1 did not drive chromatin confirmation changes at the genomic level (by Hi-C) or the enhancer connectome (by H3K27Ac HiChIP). Using 4C-seq to interrogate HIV-1-chromatin interactions, we found that HIV-1 interacted with host chromatin ~100–300 kb from the integration site. By identifying chromatin regions having both increased transcription factor activity (by ATAC-seq) and HIV-1-chromtain interaction (by 4C-seq), we identified enrichment of ETS, RUNT, STAT, and ZNF transcription factor binding that may mediate HIV-1-host chromatin interactions. Our study found that HIV-1 promoter activity increased host chromatin accessibility, increased HIV-1-host chromatin interactions in an integration site dependent manner, within the existing chromatin boundaries without impacting broader host chromatin structure.

overall_design: Unstimulated Jurkat CD4+ T cells with or without an HIV-1 provirus were profiled.

first: Jack

last: Collora


title: ChIP-seq data analysis of TgAP2XII-1 on the whole genome of Toxoplasma gondii tachyzoites [XII-1 ChIPseq]

first: Bang

last: Shen

address: No. 1 SHizishan St

institute: Huazhong Agricultural University

summary: Transcriptomic analyses revealed the gene expression changes after AP2XII-1 depletion. To see which of these differentially expressed genes are directly targeted by AP2XII-1, we used chromatin immunoprecipitation, followed by deep sequencing (ChIP-Seq) to assess the binding positions of AP2XII-1 in the parasite’s genome.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for TgAP2XII-1 in Toxoplasma tachyzoites.

first: Fuqiang

last: Fan


title: RNA-seq data analysis of TgAP2XII-1 on Toxoplasma gondii merozoites development [ME49 XII-1 RNAseq]

summary: To investigate transcriptional role of TgAP2XII-1 on type II Toxoplasma gondii (ME49 Tir1), an auxin inducible degron system was introduced to control the protein expression of TgAP2XII-1 and the target protein could be totally degradated in 3h after adding IAA.

overall_design: Transgenic parasite ME49 iKD AP2XII-1-mAID-3HA was treated with IAA for 0h or 60h, then total RNA were extracted for deep sequencing.


title: RNA-seq data analysis of TgAP2XII-1 on Toxoplasma gondii merozoites development

summary: To investigate transcriptional role of TgAP2XII-1 on type I Toxoplasma gondii (RHΔhxgprt Tir1), an auxin inducible degron system was introduced to control the protein expression of TgAP2XII-1 and the target protein could be totally degradated in 3h after adding IAA.

overall_design: Transgenic parasite iKD AP2XII-1-mAID-3HA was treated with IAA for 0h, 12h or 24h, then total RNA were extracted for deep sequencing.


title: Jurkat T cells


title: Mapping disease-associated regulatory circuits by cell type from single-cell multiomics data (S. aureus scRNA-seq)

first: Elena

last: Zaslavsky

overall_design: scRNA sequencing of PBMCs from 10 samples with MRSAs, 11 samples with MSSAs and 23 healthy controls

first: Xi

last: Chen


title: Circular RNAs drive oncogenic chromosomal translocations through R-loop-mediated genome instability [DRIP-seq]

city: Adelaide

first: Simon

last: Conn

state: South Australia

address: Sturt Road, Bedford Park

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

summary: Studying the role of circular RNAs in cancer initiation by profiling the interaction of circRNAs with DNA in human cells. The first step of oncogenesis is the acquisition of a repertoire of genetic mutations to initiate and sustain the malignancy. An important example of this initiation phase in leukaemia is the formation of a potent oncogene by chromosomal translocations between the histone methyltransferase Mixed Lineage Leukaemia (MLL) gene and one of over 100 translocation partner genes. Here we show that circular RNAs (circRNAs) - which are a family of covalently-closed, alternatively-spliced RNA molecules - bind DNA, forming circRNA:DNA hybrids (circR-loops) at their cognate loci, and promote transcriptional pausing and DNA breaks. The MLL recombinome concentrates these circR-loops and by overexpressing circRNAs from MLL in human cells we could generate de novo chromosomal translocations, mimicking the MLL recombinome. We anticipate our findings will illuminate this critical phase in cancer initiation and provide a framework to investigate the action of endogenous RNA molecules underlying various genetic aberrations through a process of Endogenous RNA-Directed DNA Damage (ER3D).

overall_design: Biological duplicates of each sample type were sequenced to identify R-loops (DRIPseq)

first: John

last: Toubia

first: Shashikanth

last: Marri


title: Mapping disease-associated regulatory circuits by cell type from single-cell multiomics data (S. aureus scATAC-seq)

overall_design: scATAC sequencing of PBMCs from 10 samples with MRSAs, 11 samples with MSSAs and 23 healthy controls


title: Integrative genetic and genomic networks identify microRNA associated with COPD and ILD

status: Public on Apr 30 2023

city: Boston

first: Joshua

middle: David

last: Campbell

state: MA

address: 72 East Concord St.

institute: Boston University

summary: Chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD) are clinically and molecularly heterogeneous diseases. We utilized clustering and integrative network analyses to elucidate roles for microRNAs (miRNAs) and miRNA isoforms (isomiRs) in COPD and ILD pathogenesis.  Short RNA sequencing was performed on 351 lung tissue samples of COPD (n=145), ILD (n=144) and controls (n=64). Five distinct subclusters of samples were identified including 1 COPD-predominant cluster and 2 ILD-predominant clusters which associated with different clinical measurements of disease severity.  Utilizing 262 samples with gene expression and SNP microarrays, we built disease-specific genetic and expression networks to predict key miRNA regulators of gene expression. Members of miR-449/34 family, known to promote airway differentiation by repressing the Notch pathway, were among the top connected miRNAs in both COPD and ILD networks. Genes associated with miR-449/34 members in the disease networks were enriched among genes that increase in expression with airway differentiation at an air-liquid interface. A highly expressed isomiR containing a novel seed sequence was identified at the miR-34c-5p locus. 47% of the anticorrelated predicted targets for this isomiR were distinct from the canonical seed sequence for miR-34c-5p. Overexpression of the canonical miR-34c-5p and the miR-34c-5p isomiR with an alternative seed sequence down-regulated NOTCH1 and NOTCH4. However, only overexpression of the isomiR down-regulated genes involved in Ras signaling such as CRKL and GRB2. Overall, these findings elucidate molecular heterogeneity inherent across COPD and ILD patients and further suggest roles for miR-34c in regulating disease-associated gene-expression.

overall_design: Libraries for 45 samples were prepared with the Illumina Small RNA Sample Prep Kit v1.5 and sequenced on the Genome Analyzer IIx. 6 of these libraries were also sequenced on the HiSeq 2000. The libraries for an additional 320 samples were prepared with the Illumina TruSeq Small RNA Sample Prep Kit and sequenced on the Illumina HiSeq 2000 with multiplexing 10 samples per lane. One additional sample was found to be a biological duplicate. Samples were clustered using the distribution of read lengths after trimming and alignment. 13 samples were excluded for being outliers based on the clustering of read length distributions. After exclusion of 7 replicate samples and 13 poor-quality samples, 351 samples were included in the final analysis set.

first: Ana

last: Pavel

first: Jennifer

last: Beane

first: Avrum

last: Spira

first: Marc

middle: E

last: Lenburg

middle: D


title: Trisomy 21 and RNA-seq of family

status: Public on Apr 29 2023

city: Boulder

first: Mary

middle: Ann

last: Allen

state: Co

address: UCB 596  JSCBB

department: BioFrontiers

institute: University of Colorado

summary: RNA-seq of lymphoblastoid cells from a family of individuals (one of which has Trisomy 21) was used to determine the molecular origin of dosage compensation in Trisomy 21.

overall_design: lymphoblastoid cells from a family of individuals were used for RNA-seq

first: Robin

last: Dowell

first: Sam

last: Hunter


title: Ablation of MYB-dependent leukaemia phenotype in MLL-driven AML correlates with increased expression of MAFB

city: Birmingham

first: Carl

last: Ward

address: Edgbaston

institute: University of Birmingham

summary: The transcription factor MYB plays a pivotal role in haematopoietic homeostasis and its aberrant expression is involved in the genesis and maintenance of acute myeloid leukaemia (AML).  Our previous work on CEBPA mutants has demonstrated that not all AML types display the same dependency on MYB expression, rather this depends on the nature of the driving mutations.  However, whether this difference in MYB expression dependency is a general trend in AML still remains to be further elucidated. In this study, we investigate the importance of MYB in human leukaemia by performing siRNA-mediated knock-down in cell lines modelling AML driven by different genetic lesions.  We show that the reduction in proliferation and the concomitant induction of myeloid commitment observed in MLL-driven leukaemia upon suppression of MYB expression is not seen in AML cells with a complex karyotype.  By performing transcriptome analysis, we demonstrate that reduction of MYB in the cell line that responds to its manipulation leads to a strong activation of MAFB expression.  Correlating with these observations, stratification of publicly available patient data reveals a reciprocal relationship between the expression of MYB and MAFB, highlighting a novel connection between those two factors in such AML.

overall_design: Gene expression analysis of MOLM14 and FUJIOKA cells with and without MYB knock-down

first: C

first: P

last: Cauchy

first: D

middle: S

last: Walton

first: M

middle: L

last: Clarke

last: Blakemore

last: Garcia

last: Esteban

first: J

last: Frampton

first: G

last: Volpe


title: Long-read RNA-Seq analysis of the full-length F8 transcript in iPSCs

status: Public on Apr 24 2023

city: Tochigi

first: Tsukasa

last: Ohmori

address: 3311-1 Yakushiji, Shimotsuke,

institute: Jichi Medical University

summary: We repaired the variant in iPSCs derived from a patient with moderate hemophilia A.  To confirm the restoration of the full-length F8 transcript in the gene-corrected iPSCs, we performed long-read RNA-Seq analysis in iPSCs with the EF1α promoter.

overall_design: Full-length F8 transcript in healthy donor-derived iPSCs or variant-corrected or uncorrected patient-derived iPSCs

first: Takafumi

last: Hiramoto


title: Transcriptional impacts of Myc deficiency in murine bone marrow NK cells

status: Public on Apr 19 2023

city: Bellinzona

first: Greta

last: Guarda

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine

summary: Despite the function of Myc oncogene has been extensively studied, little is known concerning its role in Natural killer (NK) cells. By performing RNA-sequencing analyses comparing Myc-deficient to Myc-sufficient NK cells, we aim at determining the biological function of Myc in these innate lymphocytes.

overall_design:
To this aim we generated Ncr1cre Mycfl/fl mice, in which Myc expression is deleted in NK cells at the immature stage. We sorted the immature CD27SP NK (sorted as NK1.1+CD27+CD11b−CD3/19−) cells from the bone marrow of the Ncr1cre Mycwt/wt (WT) or Ncr1cre Mycfl/fl (KO) mice and subjected them to RNA-sequencing analysis.

Ncr1cre Mycfl/fl and Ncr1cre Mycwt/wt mice were generated by crossing Ncr1cre and Mycfl/fl mice which were previously described (Narni-Mancinelli et al., 2011, 10.1073/pnas.1112064108; Trumpp et al., 2001, 10.1038/414768a). All mice were backcrossed multiple times on a C57BL/6 background.


title: Effect of trans-vaccenic acid(TVA) treatment on gene expression of mouse CD8+ T cells

status: Public on May 08 2023

city: Chicago

first: Matthew

middle: Oliver

last: Ross

state: United States

address: 929 E 57th St (loading dock behind 5741 S. Drexel Ave) GCIS E507

department: Chemistry

institute: University of Chicago

summary:
To investigate the TVA's effect on mouse CD8+ T cells in vitro, we treated activated mouse CD8+ T cells with 20 µM TVA for various timepoints (or untreated cell control) followed by kethoxal labeling of single stranded DNA (ssDNA)
We then performed differential analysis of ssDNA levels following the KAS-pipe pipeline

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparative ssDNA profiling analysis of KAS-seq data for human and mouse CD8+ T cells treated with 20 µM TVA vs. untreated cells.

first: Fan

last: Hao

first: Chuan

last: He

first: Jing

last: Chen


title: Gene expression profile at single cell level of sclerotome-derived fibroblasts from 52 hours post fertilization (hpf) transgenic zebrafish trunks.

status: Public on Apr 18 2023

city: Calgary

first: Peng

last: Huang

state: Alberta

address: 3330 Hospital Drive N.W.

department: Department of Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

summary: The sclerotome region of the somite (labelled by nkx3.1:Gal4-VP16; UAS:NTR-mCherry) gives rise to numerous fibroblasts populations in the zebrafish trunk. We performed single cell RNA sequencing (scRNA-seq) on sclerotome-derived fibroblasts from 52 hpf embryos to determine population heterogeneity and plasticity.

overall_design: scRNA-seq was performed on mCherry-positive cells from trunk regions of 52 hpf Tg BAC(nkx3.1:Gal4-VP16)ca101; Tg(UAS:NTR-mCherry)ca264 zebrafish isolated by Fluorescence-activated cell sorting (FACS). The single cell library was prepared using 10X Genomics 3’ gene expression profiling droplet-based scRNA-seq technology (v3.1 chemistry) according to manufacturer’s protocols. Sequencing was performed on the using the Illumina NovaSeq S2 flow cell.

first: Arsheen

middle: M

last: Rajan

first: Nicole

last: Rosin

first: Elodie

last: Labit

first: Jeff

last: Biernaskie

first: Shan

last: Liao


title: Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss

city: Chengdu

first: jin

last: long

address: Hui ming

institute: Sichuan Agricultural University

summary: Obesity can be considered a worldwide epidemic that has become a major threat to the quality of human life at modern society. Understanding the molecular mechanisms that underlie obesity related phenotypes can help to improve treatment options and drug development.

overall_design: Here, we employed miniature pigs as a model and generated a total of 249 high-resolution chromatin contact maps for four distinct ATs (one subcutaneous and three visceral adipose tissues) during dietary-induced weight gain and loss (WGWL) at adult. We found dramatic alteration of both functional and metabolic related transcriptome and multiple scale of chromatin architecture in distinct ATs response to WGWL.

first: Long

last: Jin

first: Danyang

last: Wang

first: Jiaman

last: Zhang

first: Zhihua

first: Mingzhou

last: Li


title: Single cell trajectory mapping of human pluripotent stem cells differentiating towards lung and hepatocyte progenitors

status: Public on Apr 17 2023

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

summary: The molecular details for the specification of lung progenitors from human pluripotent stem cells (hPSCs) are unclear. Here, we use single cell RNA-sequencing with high temporal resolution along an optimized differentiation protocol to determine the transcriptional hierarchy of lung specification from human hPSCs. To chart a comprehensive map of the transcriptional states underlying the differentiation of lung progenitors and hepatoblasts in parallel, we performed a 16-day time-series scRNA-seq using the Drop-Seq workflow (Macosko et al., 2015). Single cell suspensions were processed daily, resulting in the analysis of a total of 10,667 cells that were used for downstream analysis.

overall_design: Single-cell transcriptomics on human induced stem cell during early differentiation

first: Chaido

last: Ori

first: Ilias

last: Angelidis

first: Fabian

middle: J

last: Theis

first: Herbert

last: Schiller

first: Micha

last: Drukker


title: A model for studying homeostatic plasticity in human stem cell derived neuronal networks

status: Public on Apr 14 2023

city: Nijmegen

first: Sofia

last: Puvogel

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: RadboudUMC

summary: To investigate the functional and molecular effects of neuronal activity suppresion at the network level, we co-cultured human-derived iPSCs neurons with rat astrocytes and treated them with TTX.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Transcriptomic profilling of co-cultures of human-derived iPSCs neurons and rat astrocytes treated either with TTX or vehicle.  Three biological replicates of vehicle-treated (Veh) and 48 h-TTX treated (TTX) co-cultures (6 samples in total). RNA-seq reads were mapped against the hybrid human and rat reference genome (GRCh38+ Rnor6.0), which allowed  to discriminate between human neurons and rat astrocytes-derived transcripts.

first: Xiuming

last: Yuan

first: Jon-Ruben

last: van Rhijn

first: Anna

last: Esteve-Codina

first: Mandy

last: Meijer

first: Simon

last: Rouschop

first: Eline J.H

last: Van Hugte

first: Astrid

last: Oudakker

first: Chantal

last: Schoenmaker

first: Dirk

last: Schubert

first: Barbara

last: Franke

first: Nael

last: Nadif Kasri


title: Reactivity-Based RNA Profiling (RBRP) determined transcriptome interactions of small molecule drugs

status: Public on Apr 13 2023

first: Linglan

last: Fang

state: California

address: 369 N-S AXIS STAUFFER I, RM-107-CHEMISTRY-KOOL LAB

summary: We developed Reactivity-Based RNA Profiling (RBRP) approach to determine the off-target transcriptome interactions of small molecule drugs. Deep sequencing was used to locate and quantify drug-promoted acylation of RNA 2´-hydroxyl groups as a proxy of RNA-drug interaction in HEK293.

overall_design: The sequencing experiments were performed in two biological replicates. Comparative analysis of deep sequencing data using a customized pipeline identifies drug binding events.

first: Eric

last: Kool


title: Active maintenance of CD8+ T cell naïvety through regulation of global genome architecture

status: Public on Apr 10 2023

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

institute: Monash Bioinformatics Platform

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

overall_design: Refer to individual Series


title: Trisomy 21 and GRO-seq of family

first: Mary

last: Allen

summary: GRO-seq of lymphoblastoid cells from a family of individuals (one of which has Trisomy 21) was used to determine the molecular origin of dosage compensation in Trisomy 21.

overall_design: lymphoblastoid cells from a family of individuals were used for GRO-seq

middle: A

first: Robin

last: Dowell

first: Sam

last: Hunter


title: Circular RNAs drive oncogenic chromosomal translocations through R-loop-mediated genome instability

last: Conn


title: PolyA RNA-seq from Human esophageal biopsy samples from eosinophilic esophagitis patients

status: Public on Apr 08 2023

city: Aurora

first: Calies

last: Menard-Katcher

state: CO

institute: University of Colorado School of Medicine

summary: Analysis of steady-state mRNA levels in 27 samples from healthy controls and patients with fibrostenotic EoE and non-fibrostenotic EoE. Participants range 5 – 18 years old. EoE participants had >15 eosinophils per hpf (eos/hpf) and were classified as fibrostenotic (FS) or non-fibrostenotic (non-fs). FS EoE: having either a) a stricture and/or b) grade 2 or 3 concentric esophageal rings and an esophageal distensibility < 15 mm. Non-fs EoE: no clinical evidence for stricture, circumferential rings or history of food impaction. Included control subjects had no identified abnormalities on endoscopy or histology. Results provide insight into the pathways involved in fibrostenotic remodeling in EoE.

overall_design: Comparison of non-fibrostenotic EoE (n=11) and fibrostenotic EoE (n=9) samples to controls (n=7).

first: Matthew

last: Galbraith


title: Effects of alcohol and PARP inhibition on RNA ribosomal engagement in cortical excitatory neurons

first: Rajiv

middle: Pandit

last: Sharma

state: IL

address: 1601 W Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago

summary: The objective of the study is to describe the effects of EtOH on excitatory pre-frontal cortical neuronal ribosomal-engagement (RE) transcripts from total-RNA and provides insights into Poly (ADP-ribose) polymerase (PARP)-mediated regulation of EtOH effects (using the PARP inhibitor ABT-888).

overall_design: Mice whose ribosomes were tagged with EGFP expressed only in CaMKIIα expressing cells were used for the study. PFC samples were homogenized in the appropriate buffer and TRAP-RNA (collected by anti-EGFP antibody incubation) and total-RNA samples were extracted. Following quantification and quality control, the samples were subjected to rRNA depletion, library preparation and 50bp paired-end sequencing (NovaSeq 6000) using the Illumina platform. Data were analyzed using standardized bioinformatic packages and normalized based on treatment status, i.e., Control, EtOH or EtOH+ABT-888, as well as by sample type, i.e., Input or TRAP.

first: Harish

last: Krishnan

first: Gian

last: Paolo Vallerini

first: Hooriyah

last: Rizavi

first: Hannah

last: Gavin

first: Marina

last: Guizetti

first: George

last: Chlipala

first: David

middle: P


title: Active maintenance of CD8+ T cell naïvety through regulation of global genome architecture [ATAC-seq]

summary: The differentiation of naïve CD8+ cytotoxic T lymphocytes (CTLs) into effector and memory states results in large scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organisation reflect or underpin these transcriptional programs. We utilised Hi-C to map changes in the spatial organisation of long-range genome contacts within naïve, effector and memory virus-specific CD8+ T cells. We observed that the architecture of the naive CD8+ T cell genome was distinct from effector and memory genome configurations with extensive changes within discrete functional chromatin domains.  However, deletion of the BACH2 or SATB1 transcription factors was sufficient to remodel the naïve chromatin architecture and engage transcriptional programs characteristic of differentiated cells. This suggests that the chromatin architecture within naïve CD8+ T cells is preconfigured to undergo autonomous remodelling upon activation, with key transcription factors restraining differentiation by actively enforcing the unique naïve chromatin state.

overall_design: In situ HI-C was performed on CD4+ CD8+ thymocytes, naïve OT-1 CD8+ T cells, and Influenza A-virus-specific, effector and memory OT-1 CD8+ T cells from C57Bl6/J mice, and from naive BACH2-/- and CD4+CD8+ and naive SATB1m1Anu/M1Anu1 mice. ATAC-Seq was also perfomerd on naïve, effector and memory OT-1 CD8+ T cells.

first: Brendan

last: Russ

first: Kirril

last: Tsyganov

first: Sara

last: Quon

first: Bingfei

last: Yu

first: Jasmine

last: Li

first: Jason

middle: K

last: Lee

first: Moshe

last: Olshansky

first: Zhaohren

last: He

first: Paul

middle: F

last: Harrison

first: Adele

last: Barugahare

first: Michael

last: See

first: Simone

last: Nussing

first: Alison

last: Morey

first: Vibha

last: Udupa

first: Taylah

last: Bennett

first: Axel

last: Kallies

first: Cornelis

last: Murre

first: Phillipe

last: Collas

last: Powell

first: Ananda

last: Goldrath

first: Stephen

last: Turner


title: Dissecting crosstalk between embryonic and extra-embryonic tissues with stem cell co-culture [I]

city: Kunming

first: Mq

last: Peng

state: Yunnan

address: No. 727, Jingming South Road, Chenggong District

institute: Kunming University of Science and Technology

summary: Faithful embryogenesis requires the precise coordination between embryonic and extraembryonic tissues. Although embryonic and extraembryonic stem cells have been derived from several mammalian species including humans, they are cultured in different conditions, which makes it difficult to study their intercommunication. Here, by simultaneously activating FGF, TGF-β and WNT pathways, we derived stable pluripotent stem cells (PSCs), trophoblast stem cells (TSCs) and extraembryonic endoderm stem cells (XENs) from mouse blastocysts under the same condition (FTW). Co-culture of PSCs and XENs in the same environment uncovered, among other interactions, a previously unrecognized control of proliferation of epiblast cells by extraembryonic endoderm cells. FTW condition also supported de novo derivation of XENs from cynomolgus monkey and human blastocysts, and enabled setting up co-culture of human iPSCs and XENs. Crosspieces comparison revealed conserved and divergent processes and genes regulating XENs and ligand-receptor interactions between pluripotent and extraembryonic endoderm cells. Our study establishes a unique stem cell co-culture strategy to examine embryonic and extraembryonic lineage crosstalk during early mammalian development, and opens the door for developing more faithful in vitro models and differentiation protocols.

sample_organism:
Macaca fascicularis
Homo sapiens
Mus musculus

overall_design: Totally 47 samples were sequenced, including 5 human samples, 10 mouse samples , 10 monkey single cell samples and 7 bulk samples. All human and mouse samples with two replicates and monkey sample with one replicate.

first: Jun

last: Wu

first: Tao

last: Tan

first: Yulei

last: Wei

first: E

last: Zhang

first: Leqian

last: Yu


title: Analysis of Circulating Extracellular Vesicle microRNAs in Breast Cancer Patients with Obesity: a Potential Role for Let-7a

status: Public on Apr 04 2023

city: Caserta

first: Gilda

last: Cobellis

address: Viale Abramo Lincoln

institute: University of Campania "Luigi Vanvitelli"

summary: To study the impact of the obesity condition on circulating Extracellular Vesicle-miRNA expression signature in breast cancer patients, and identify potential obesity-related miRNAs that may be associated with progression.

overall_design: Comparative EV-miRNA expression profiling analysis of RNA-seq data for circulating EVs in breast cancer patients categorized based on their Body Mass Index  in Normal weight (NW; 18 > BMI < 24.9 Kg/m2) and overweight/obese (OW/Ob BMI > 25 Kg/m2).

first: Stefania

last: Catalano

first: Ines

last: Barone

first: Cinzia

last: Giordano

first: Luca

last: Gelsomino


title: Human corneal endothelial cell cultures obtained from discarded tissues using a xenogeneic free culture medium

status: Public on Apr 03 2023

city: Debrecen

first: Noemí

last: Caballero-Sánchez

address: Egyetem tér 1

department: Biochemestry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary:
To investigate the use of Plasma Rich in Growth Factors (PRGF) as the unique source of growth factors in primary cultures of human corneal endothelial cells obtained from discarded tissues.
We  performed gene expression profiling analysis using data obtained from RNA-seq of 8 different cell cultures. 4 of them obtained with a standard culture medium and the other 4 using a xeno free PRGF based culture medium

overall_design: Comparative gene expression analysis of RNA-seq data for Corneal endothelial cells cultured with different media.

first: Sergio

last: Alonso-Alonso

first: Natalia

last: Vázquez

first: Manuel

last: Chacón

first: Susana

last: Del Olmo

first: Carlota

last: Suárez

first: Belén

last: Alfonso-Bartolozzi

first: Laszlo

last: Nagy

first: Jesús

last: Merayo-Lloves

first: Álvaro

last: Meana


title: Transcription dosage compensation does not occur in Down syndrome

status: Public on Apr 28 2023

first: Mary

last: Allen


title: The RNA-seq of HCC specimens and the RIP-seq of HNRNPD in PLC cells and WT (DMSO or Compound C) and circLARP1B-Def (DMSO) PLC/PRF/5 cells

status: Public on Apr 02 2023

city: Hefei

first: Yucong

last: Wang

state: Anhui

address: 443 Huangshan Road

institute: USTC

summary:
To investigate functional transcripts in metastatic HCC, we performed high-throughput RNA sequencing (RNA-seq) of tumors from 3 metastatic HCC and 3 non-metastatic HCC. And we performed RIP-seq human PLC/PRF/5 cells to investigate the HNRNPD binding transcripts.
To investigate function of  circLARP1B on AMPK pathway, we performed high-throughput RNA sequencing (RNA-seq) of WT (DMSO or Compound C) and  circLARP1B-Def (DMSO) PLC/PRF/5 cells.

overall_design:
We performed ribosomal RNA (rRNA) depleted RNA sequencing (RNA-seq) of HCC tissues and PLC cells.
We performed ribosomal RNA (rRNA) depleted RNA sequencing (RNA-seq) of PLC/PRF/5 cells.

first: Jingxin

last: Li

first: Xiaolin


title: Active maintenance of CD8+ T cell naïvety through regulation of global genome architecture [Hi-C]

first: Monash

last: Platform

first: Brendan

last: Russ

first: Kirril

last: Tsyganov

first: Sara

last: Quon

first: Bingfei

last: Yu

first: Jasmine

first: Jason

last: Lee

first: Moshe

last: Olshansky

first: Zhaohren

last: He

first: Paul

last: Harrison

first: Adele

last: Barugahare

first: Michael

last: See

first: Simone

last: Nussing

first: Alison

last: Morey

first: Vibha

last: Udupa

first: Taylah

last: Bennett

first: Axel

last: Kallies

first: Cornelis

last: Murre

first: Phillipe

last: Collas

first: David

last: Powell

first: Ananda

middle: W

last: Goldrath

first: Stephen

last: Turner


title: The role of AF10 (Mllt10) in maintaining cell identity

status: Public on Apr 01 2023

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin


title: Spatiotemporally Deciphering the Unknown Role of Persistent HPV Infection in Precancer to Cervical Cancer Progression: Integrating Single-Cell RNA-Sequencing Landscape and Spatial Transcriptomics Atlas [scRNA-seq]

city: Shanghai

first: Chenyan

last: Guo

address: 419 Fangxie Road, Shanghai, China

institute: Fudan University Obstetrics and Gynecology Hospital

summary: The mechanism underlying the cervical carcinogenesis mediated by persistent HPV infection remains elusive. Here we pioneeringly deciphered both temporal transition and spatial distribution of the cellular subsets during the disease progression from normal cervix, precancer lesions to cervical cancer by integrating scRNA-seq with ST. We not only identified three ‘HPV-related epithelial clusters’ unique to normal, HSIL and cervical cancer respectively, but also discovered node genes which potentially determined the disease progression. Moreover, we observed a gradual transition of multiple immune cells from positive immune response to dysregulation and exhaustion, to an immune-suppressive microenvironment during the malignant program. Besides, the cellular interaction analysis further verified a ‘homeostasis-balance-malignancy’ change within cervix microenvironment during disease escalation. Together, these findings not only deciphered mysterious persistent HPV infection spatiotemporally from the process of precancer to cervical cancer but also provided unprecedented possibilities for accurate diagnosis, precise treatment and prognosis evaluation for precancer and cervical cancer.

overall_design: Nine cervical tissue samples of different disease stages from normal, HPV-infected, precancer to cancer were collected from colposcopy examination and analyzed using scRNAseq and spatial transcriptomics .


title: Mechanism of stem cells from human exfoliated deciduous teeth derived exosomes in the treatment of steroid-induced osteonecrosis of the femoral head

status: Public on Mar 31 2023

city: Guangzhou

first: chen

middle: wei

last: fen

address: 4F, Building 1, Standard Property Unit 3, International Biotech Island

institute: Forevergen

summary: The exosomes secreted by SHED can be endocytosed by BMSC, and can partially reverse the inhibition of glucocorticoids on the viability and osteogenic differentiation of BMSC. Transcriptome data analysis combined with qPCR showed that three pathways, Rap1, PI3K-Akt and CAMs (Cell adhesion molecules), may be related to this experimental phenomenon.

overall_design: Primary dental pulp cells were isolated and cultured from human deciduous tooth pulp, and SHED was isolated and purified by limiting dilution method and exosomes were isolated from SHED cell supernatants by ultracentrifugation. Cell surface markers CD31, CD34, CD45, CD73, CD90 and CD105 were detected by flow cytometry. ALP and Alizarin Red staining were used to identify osteogenic differentiation ability, and exosomes were identified using TEM (transmission electron microscopy), NanoFCM and Weatern Blot. PKH67 fluorescent labeling tracked the uptake of exosomes by BMSC. Transcriptome combined with qPCR to explore its mechanism.

first: Fei

last: Liu

first: Xinmin

last: Wang

first: Jie

last: Xu

first: Jian

last: Lv


title: Genome annotation of the blackstripe livebearer Poeciliopsis prolifica, a placental Poeciliid for understanding fish placenta evolution

status: Public on Mar 26 2023

city: Auburn University

first: Xu

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

summary: The objective of our study is to obtain a high-quality reference genome of Poeciliopsis prolifica with gene annotation and identify the exonic SNP in inbred lines by RNA sequencing to provide the essential genetic toolkit for evolutionary and comparative genomic studies for P. prolifica and facilitate the reseach of placental evolution.

overall_design: Whole-body of male P. prolifica was used for high molecular weight  genomic DNA extraction and genome sequencing and the juvenile whole-body fish from line A (n=3) and line B (n=3) were used for RNA sequencing.


title: RNA-seq analysis with MFN2-deficient human iPS cells

city: Toyoake

first: Takahiko

last: Sato

state: Aichi

address: 1-98, Dengakugakubo, Kutsukakecho

institute: Fujita Health University

summary: We performed Next-generation sequencing analyses with control or MFN2-deficient human iPS cells.

overall_design: Examination of  the effects of MFN2 deficiency in human iPS cells.


title: Isolation, characterization, proteome, miRNAome, and the embryotrophic effects of chicken egg yolk nanovesicles (vitellovesicles)

status: Public on Mar 22 2023

city: Daejeon

first: Islam

last: Saadeldin

address: Dehak ru

institute: Chungnam National University

summary: We provide a detailed analysis of miRNA in the egg yolk vesicles.

overall_design: Egg yolk of freshly oviposited commercially purchased eggs (n=3) were aseptically aspirated and diluted 10 times with phosphate-buffered saline (PBS). Egg yolk vesicles were isolated through ultracetrifugation and used for RNA extraction and sequencing.

first: Jongki

last: Cho

first: Sanghoon

last: Lee

first: Seonggyu

last: Bang


title: Transcriptome profiling of bladders of CYP-treated C57BL6/J mice (male and female)

status: Public on Mar 17 2023

city: Ljubljana

first: Dominika

last: Peskar

address: Vrazov trg 2

department: Institute for Cell Biology

country: Slovenia

institute: Faculty of Medicine

summary: In the present study, we aimed to identify a complete transcriptome profile of the bladders of CYP-treated mice, a commonly used animal model of IC/BPS disease. Our study represents a reference database for the understanding of the mouse model, which is crucial for the more successful translation of the data obtained on this model to human patients.

overall_design: Comparative gene expression analysis of RNA-seq data for C57BL6/J mice (Ctrl males/Females vs CYP Males/Females, CYP mice vs Ctrl mice, Ctrl males vs Ctrl females; 3 animals per group)

first: Tadeja

last: Kuret

first: Katja

last: Lakota

first: Andreja

last: Erman


title: Genome wide enhancer loops (HiChIP) and 3-D high order chromatin features associated with EWS-FLI1 in Ewing Sarcoma. [microC]

status: Public on Mar 16 2023

city: Charlestown

first: Rui

last: Dong

address: 149 13th Street

institute: Massachusetts General Hospital

summary: Tumor cell identity is the product of complex interactions between oncogenic drivers and mechanisms regulating normal differentiation pathways. Cell fate transitions observed in embryonic development involve structural changes in genomic organization that provide proper lineage specification, however, whether similar events also occur within tumor cells and contribute to cancer evolution remains largely unexplored. Here we modeled this process in the pediatric bone cancer Ewing sarcoma and investigated high resolution looping and large-scale 3D nuclear conformation changes associated with EWS-FLI1, the oncogenic fusion protein that drives this tumor. We find that chromatin interactions in Ewing sarcoma cells are dominated by highly connected looping hubs centered on EWS-FLI1 binding sites, wmicroCh directly control the activity of linked enhancers and promoters to establish oncogenic expression programs. Depletion of EWS-FLI1 leads to the loss of looping networks associated with the fusion protein and, strikingly, also results in widespread nuclear reorganization through the establishment of new patterns of looping and large-scale inter-compartment connectivity that resemble the chromatin configuration of mesenchymal stem cells, a candidate cell of origin of this tumor. Our data thus demonstrate that major architectural features of nuclear organization in cancer cells can be linked to a single oncogenic event and readily reversed to re-establish latent differentiation programs.

overall_design: Using in-situ microC and H3K27ac Hi-ChIP, we profiled the organization and establishment of EWS-FLI1 mediated enhancer connectome in Ewing sarcoma model cells, A673 and SKNMC. The re-organization of enhancer network is further compared to the MSCs, a potential cell or origin or Ewing Sarcoma. Pooled microC and Hi-ChIP libraries of each condition, shGFP/shFLI, from Ewing cells and wildtype MSCs were used in the study.

first: Rajendran

last: Sanalkumar

first: Miguel

middle: N

last: Rivera

first: Nicolò

last: Riggi


title: scRNA-seq analysis of murine TECs after irradiation

status: Public on Mar 30 2023

city: Yokohama

first: Taishin

last: Akiyama

state: Kanagawa

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

institute: RIKEN

summary: Influence of irradiation on heterogeneity of thymic epithelial cells remains elusive. We performeds single cell RNA-seq of TECs from mice 15 days after irradiation.

overall_design: Thymic epithelial cells (EPCAM+, CD45-, reticulocyte negative) were isolated from murine thymus 15 days after sublethal dose irradiation and its control

first: Kenta

last: Horie

first: Maki

last: Miyauchi

first: Nobuko