title: Dectin-1/CARD9-induction of the TFEB and TFE3 gene network is dispensable for phagocyte anti-Aspergillus activity in the lung.

city: New York

first: Mariano

last: Aufiero

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: Neutrophils play a crucial role in immunity against Aspergillus fumigatus, the most common etiologic agent of mold pneumonia worldwide. Phagocytes rapidly engulf A. fumigatus conidia in the lung to prevent germination and tissue damage. Phagosome maturation, including fusion with the lysosome, is a critical process in killing conidia but if this regulated at the transcriptional level remains unknown. To investigate the transcriptional response in neutrophils to fungal engagement, we compared the transcriptomes of lung neutrophils that were either bystanders or engaged with fungal cells.

overall_design: Sorted pulmonary neutrophils from mice infected with A. fumigatus for 24 hours. Neutrophils were sorted based on whether they were bystanders or fungus-engaged.

first: Neta

last: Shlezinger

first: Anupam

last: Jhingran

first: Tobias

last: Hohl


title: Communication between the HCCLM3 cells and LX2 cells in a 3D  tumor-on-a-chip

status: Public on Jul 31 2023

city: Nanjing

first: Peiliang

last: Shen

address: Xianlin Road 138#

country: China

institute: Nanjing university of Chinese Medcine

type: Expression profiling by high throughput sequencing

summary: The communacation between the Hepatocellular carcinoma (HCC) and hepatic stellate cells(HSC) is not completely understood. Then a tumor-on-a-chip model was used to  evaluate the crosstalk between the HCC cells (HCCLM3) and HSCs (LX2). After 5 days co-culture, we degraded the collagen hydrogel to isolate HCCLM3 cells and LX2 cells for RNA-seq.

overall_design: The mRNA profiles of HCCLM3 cells or LX2 were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Xin

last: Han


title: RNASeq samples of OSKM reprogrammable MEFs treated with various compounds

status: Public on Aug 07 2023

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary: Examination of the impact of vitamin B12 and various one-carbon metabolism and/or epigenetic modifieres during in vitro OSKM reprogramming

overall_design: MEFs carrying a doxycycline-inducible OSKM cassette were reprogrammed in vitro by administering 1mg/mL doxycycline, concomitant with continuous treatmet of various compounds as indicated. RNA was harvested 72h after treatment began.

first: Marta

last: Kovatcheva

first: Manuel

last: Serrano

middle: S

last: Attolini


title: Vitamin B12 is a limiting factor for in vivo reprogramming

summary: Reprogramming in vivo using OCT4, SOX2, KLF4 and MYC (OSKM) triggers cell dedifferentiation, which is considered of relevance for tissue repair and regeneration. However, little is known about the metabolic requirements of this process. We found that antibiotic depletion of the gut microbiota abolished in vivo reprogramming. Analysis of bacterial metagenomes from stool samples of wild type (WT) and OSKM mice treated with doxycycline led us to identify vitamin B12 as a key factor for in vivo reprogramming, which is partly supplied by the microbiome. We report that B12 demand increases during reprogramming due to enhanced expression of enzymes in the methionine cycle, and supplementing B12 levels both in vitro and in vivo enhances the efficiency of OSKM reprogramming.

overall_design: Examination of metagenomes from stool samples of mice expressing doxycycline inducible Oct4, Sox2, Klf4, c-Myc (OSKM) induced for 7 days and wild type (WT) mice treated with doxycycline.

first: Adrià

last: Caballe


title: BlCa: MSL2 is an allelic dosage sensor in mammals

status: Public on Aug 10 2023

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: Biallelic expression is important to ensure adequate mRNA levels as well as protect cells from deleterious heterozygous mutations. However, the factors determining biallelic expression at individual gene loci are unknown. Deletion of the MSL complex component MSL2 in hybrid mouse NPCs uncovers an unprecedented function for MSL2 in allelic regulation. While biallelically expressed in wildtype NPCs, a class of MSL2 targets switches from bi to monoallelic expression upon MSL2 loss. The silenced allele loses nascent transcription, accompanied by dramatic changes in local chromatin landscape such as monoallelic gain of H3K27me3 and DNA methylation. Meanwhile, active histone modifications, RNA POL II, BRD4 and KANSL3 are retained on the active allele. MSL2 targets include several sex-biased genes on autosomes as well as X-chromosomal genes that escape X inactivation. Together, the allele-specific resolution allowed us to unravel an MSL2 mediated safeguarding mechanism to promote biallelic gene expression of sexually dimorphic and dosage-sensitive genes in mammals.

overall_design: Allele specific differential analysis of various sequencing data from ESCs and NPCs of female and male hybrid clones.

first: Yidan

last: Sun

first: Raed

last: Hmadi

first: Meike

last: Wiese


title: Deficiency of hypothalamic taste receptor type 1 member 3 prevents western diet-induced anxiety in mice

status: Public on Aug 05 2023

city: Seoul

first: Jaewon

last: Song

address: Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Accumulating studies support that the western diet (WD), a diet comprised of saturated fat and sugary drinks, contributes to the pathogenesis of anxiety disorders, the most prevalent mental disorders worldwide. However, the underlying mechanisms by which WD causes anxiety, remain unclear. Abundant expression of taste receptor type 1 member 3 (TAS1R3) is identified in the hypothalamus, a key brain area involved in both sensing peripheral nutritional signals and regulating anxiety. Thus, we investigated the role of the hypothalamic TAS1R3 in WD-induced anxiety using wild-type (WT) and Tas1r3 deficient (Tas1r3-/-) mice fed a normal diet (ND) or WD for 12 weeks. We evaluated anxiety levels with the open field test and the elevated plus maze test. Behavior tests showed WD increased anxiety in WT mice, whereas Tas1r3-/- mice were protected from WD-induced anxiety. Analyzing the hypothalamic transcriptome of WD-fed WT and Tas1r3-/- mice, we found 1,437 genes significantly regulated by Tas1r3 deficiency. In addition, bioinformatic analysis revealed that CREB-mediated maintenance of neuronal regeneration, which can prevent the development of anxiety, was enhanced in WD-fed Tas1r3-/- mice compared to WD-fed WT mice. In addition, in vitro studies further confirmed that Tas1r3 knockdown prevented suppression of CREB caused by high levels of glucose, fructose, and palmitic acid in adult hypothalamic neuronal cells. These results imply that TAS1R3 may play a key role in WD-induced alterations in hypothalamic functions, and inhibition of TAS1R3 overactivation in the hypothalamus could offer therapeutic targets to alleviate the effects of the WD on anxiety.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hypothalamus of western diet fed wild-type and western diet fed Tas1r3-/- mice.

first: Woojeong

last: Shon

first: Dongmi

last: Shin


title: Rational design of a SOCS1-edited tumor infiltrating lymphocyte therapy for solid tumors using CRISPR/Cas9 screens [TIL5746_human_invitro]

status: Public on Jul 30 2023

city: Lexington

first: Micah

last: Benson

state: MA

address: 4 Maguire Rd

country: USA

institute: KSQ Therapeutics

summary: Tumor Infiltrating Lymphocyte (TIL) therapy have shown promise  in the treatment of patients with refractory solid tumors, with improvement in response rates and durability of responses nevertheless sought.  To identify targets capable of enhancing the anti-tumor activity  of T cell therapies, large-scale in vitro and in vivo CRISPR/Cas9 screens were performed, with the suppressor of cytokine signaling 1 (SOCS1) gene identified as a top T cell-enhancing target.  In murine CD8 T cell therapy models, SOCS1 served as a critical checkpoint in restraining the accumulation of T central memory cells in lymphoid organs as well as intermediate (Texint) and effector (Texeff) exhausted T cell subsets derived from progenitor exhausted T cell (Texprog) cells in tumors. A comprehensive CRISPR tiling screen of the SOCS1 coding region identified sgRNAs targeting the SH2 domain of SOCS1 as the most potent, with a sgRNA with minimal off-target cut sites used to manufacture KSQ-001, an engineered TIL therapy with SOCS1 inactivated by CRISPR/Cas9.  KSQ-001 possessed increased responsiveness to cytokine signals and enhanced in vivo anti-tumor function in mouse models. These data demonstrate the use of CRISPR/Cas9 screens in the rational design of T cell therapies.

overall_design: A large-scale in vitro CRISPR/Cas9 screen was performed to identify targets that can enhance TIL function. A barcoded sgRNA library encompassing a curated list of 5137 genes involved in T cell function, all predicted cell surface receptors (CSRs), and genes found to be expressed within immune cells and peripheral blood was introduced by lentiviral transduction into pre-REP TIL together with Cas9.  Engineered sgRNA Lib+ TIL were then expanded under REP conditions. One input population of transferred T cells was sequenced and endpoint T cells were collected at day 17 and sequenced.


title: CaBl: MSL2 is an allelic dosage sensor in mammals

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


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

status: Public on Aug 04 2023

city: Philadelphia

first: Sarah

last: Alp

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

summary: To investigate the EBV genome after Decitabine treatment by CTCF ChIP-seq

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

first: Italo

last: Tempera

first: Paul

middle: M

last: Leiberman


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

status: Public on Aug 02 2023

first: Priyankara

middle: J

last: Wickramasinghe

department: Bioinformatics

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 and RNA-seq was performed


title: The Candida albicans reference strain SC5314 contains a rare, dominant allele of the transcription factor Rob1 that modulates biofilm formation and oral commensalism

status: Public on Jul 29 2023

city: Iowa City

first: Damian

middle: Joseph

last: Krysan

state: IA

address: 200 Hawkins Drive

institute: University of Iowa Department of Pediatrics

summary: Candida albicans is a diploid human fungal pathogen that displays significant genomic and phenotypic heterogeneity over a range of virulence traits and in the context of a variety of environmental niches. Here, we show that the effects of Rob1 on biofilm and filamentation virulence traits is dependent on both the specific environmental condition and the clinical strain of C. albicans. The C. albicans reference strain SC5314 is a ROB1 heterozygote with two alleles that differ by a single nucleotide polymorphism at position 946 resulting in a serine or proline containing isoform. An analysis of 224 sequenced C. albicans genomes indicates that SC5314 is the only ROB1 heterozygote documented to date and that the dominant allele contains a proline at position 946. Remarkably, the ROB1 alleles are functionally distinct and the rare ROB1946S allele supports increased filamentation in vitro and increased biofilm formation in vitro and in vivo, suggesting it is a phenotypic gain-of-function allele. SC5314 is amongst the most highly filamentous and invasive strains characterized to date. Introduction of the ROB1946S allele into a poorly filamenting clinical isolate increases filamentation and conversion of an SC5314 laboratory strain to a ROB1946S homozygote increases in vitro filamentation and biofilm formation. In a mouse model of oropharyngeal infection, the predominant ROB1946P allele establishes a commensal state while the ROB1946S phenocopies the parent strain and invades into the mucosae. These observations provide an explanation for the distinct phenotypes of SC5314 and highlight the role of heterozygosity as a driver of C. albicans phenotypic heterogeneity.

overall_design: An RNAseq approach was used to investigate the role of Rob1 in the regulation of gene expression during in vitro hyphal induction conditions. C. albicans strain SN250 (WT) or the same strain with both alleles of Rob1 deleted (ROB1NULL) were grown for 4 hours under three different conditions. Growth at 37C in RPMI media or SPIDER media were used to induce hyphal growth. The third control condition was growth at 30C in YPD media. Each condition was performed in duplicate (A and B). Differential expresssion analysis was performed on the RNAseq gene count data to identify Rob1-dependent gene expression in each of the growth conditions.

first: Virginia

middle: E

last: Glazier

first: Juraj

last: Kramara

first: Tomye

last: Ollinger

first: Norma

middle: V

last: Solis

first: Robert

last: Zarnowski

first: Rohan

last: Wakade

first: Min-Ju

last: Kim

first: Gabriel

last: Weigel

first: Shen-Huan

last: Liang

first: Richard

last: Bennett

first: Melanie

last: Wellington

first: David

middle: R

last: Andes

first: Mark

middle: A

last: Stamnes

first: Scott

middle: G

last: Filler


title: Skin-type-dependent development of murine mechanosensory neurons

status: Public on Jul 27 2023

city: Boston

first: VICTOR

last: BARRERA BURGOS

state: Massachusetts

address: Landmark 401 Park Drive 3 East

department: Biostatistics

institute: Harvard School of Public Health

summary: Mechanosensory neurons innervating the skin underlie our sense of touch. Fast-conducting, rapidly adapting mechanoreceptors innervating glabrous (non-hairy) skin form Meissner corpuscles, while in hairy skin, they associate with hair follicles, forming longitudinal lanceolate endings. How mechanoreceptors develop axonal endings appropriate for their skin targets is unknown. We report that mechanoreceptor morphologies across different skin regions are indistinguishable during early development but diverge post-natally, in parallel with skin maturation. Neurons terminating along the glabrous and hairy skin border exhibit hybrid morphologies, forming both Meissner corpuscles and lanceolate endings. Additionally, molecular profiles of neonatal glabrous and hairy skin-innervating neurons largely overlap. In mouse mutants with ectopic glabrous skin, mechanosensory neurons form end-organs appropriate for the altered skin type. Finally, BMP5 and BMP7 are enriched in glabrous skin, and signaling through type I bone morphogenetic protein (BMP) receptors in neurons is critical for Meissner corpuscle morphology. Thus, mechanoreceptor morphogenesis is flexibly instructed by target tissues.

overall_design: Smart seq of glabrous and hairy skin innevating neurons

first: Charalampia

last: Koutsioumpa

first: Celine

last: Santiago

last: Ginty

first: Victor

last: Barrera


title: Organotypic 3D cell-architecture architecture impacts the expression pattern of miRNAs-network in breast cancer SKBR3 cells

status: Public on Aug 01 2023

city: Chihuahua

first: Mercedes

last: Bermúdez

state: Chihuahua

address: Chihuahua

department: Dentistry

country: Mexico

institute: Universidad autónoma de Chihuahua

summary: The transcriptomic assays showed that cell growth in organoids significantly affected (all p < 0.01) the gene expression patterns of both, miRNAs and mRNAs, finding 20 upregulated and 19 downregulated DE-microRNAs, as well as 49 upregulated and 123 downregulated DE-mRNAs. In silico analysis showed that a subset of 11 upregulated DE-microRNAs target 70 downregulated DE-mRNAs. These genes are involved in 150 gene ontology (GO) biological processes such as regulation of cell morphogenesis, regulation of cell shape, regulation of canonical Wnt signaling pathway, morphogenesis of epithelium, regulation of cytoskeleton organization, as well as in the MAPK and AGE-RAGE signaling KEGG-pathways. Interestingly, hsa-mir-122-5p (Fold Change (FC)=15.4), hsa-mir-369-3p (FC=11.4), and hsa-mir-10b-5p (FC=20.1) regulated up to the 81 % of the 70 downregulated DE-mRNAs

overall_design: we evaluated the effect of 3D cell organization on the expression pattern of miRNAs (by Small-RNAseq) and mRNAs (by microarrays) in the breast cancer SKBR3 cell line and analyzed the biological processes and signaling pathways regulated by the differentially expressed protein-coding genes (DE-mRNAs) and miRNAs (DE-microRNAs) found in the organoids.


title: Circadian clock regulator Bmal1 gates axon regeneration via Tet3-5hmC mediated epigenetics

first: Molly

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: Axon regeneration of dorsal root ganglia (DRG) neurons after peripheral axotomy involves epigenetic reconfigurations that rewire gene regulatory circuits to establish regenerative gene program. However, the mechanisms and transcriptional regulators remain poorly understood. Here, we conducted an unbiased survey of DNA differentially hydroxymethylated regions (DhMRs) in DRG after peripheral lesion, which identified enriched binding motif for Bmal1, a transcription factor and a central regulator of the circadian clock. Through applying conditional deletion of Bmal1, in vitro and in vivo models of axon regrowth, and transcriptomic profiling, we showed that Bmal1 inhibits axon regeneration in part through Tet3-dependent manner. Mechanistically, Bmal1 functions as a gatekeeper of neuroepigenetic injury responses by limiting Tet3 expression and restricting 5hmC modifications. Notably, Bmal1-regulated genes after axotomy not only concern axon guidance and axon regrowth, but also stress responses, energy homeostasis, and neuroinflammation. Furthermore, we uncovered diurnal oscillation of Tet3 and 5hmC in DRG neurons, and this epigenetic rhythm corresponded to time-of-day effect on axon growth potential. Collectively, our studies showed that Bmal1 deletion mimics the conditioning lesion in lifting epigenetic barriers to enhance axon regeneration.

overall_design: For conditional deletion of Bmal1, 19 weeks-old Bmal1 cKO (Bmal1f/f Thy1-CRE-ERT2/EYFP) or control (Bmal1f/f or Bmal1 f/+) mice were injected with Tamoxifen at a dose of 100 mg/kg by intraperitoneal injection once a day for 5 consecutive days. Thoracic and lumbar DRGs were isolated 5 weeks post-tamoxifen treatment ZT2-4 with each mouse representing 1 sample.   Enriched DRG neuronal cultures were prepared and seeded on PLO/Laminin coated plates at ZT8.   RNA was collected at 28 hr post-seeding using QIAGEN RNeasy plus mini kit.  Next-generation sequencing was conducted on the Illumina NovaSeq platform.

first: Dalia

last: Halawani

first: Yiqun

last: Wang

first: Aarthi

last: Ramakrishnan

first: Xijing

last: He

first: Li

last: Shen

first: Roland

middle: H

last: Friedel

first: Hongyan

last: Zou


title: Effect of overexpression of A3B and RNA editing calling in mouse tissues

status: Public on Jul 25 2023

city: Heidelberg

first: Alicia

last: Alonso de la Vega

address: Im Neuenheimer Feld 280

institute: Deutsches Krebsforschungszentrum, DKFZ

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

overall_design: Refer to individual Series


title: Effect of overexpression of A3B and RNA editing calling in mouse tissues [WES]

summary: To test if A3B has RNA editing activity we performed SNV calling from WES of 8 mouse livers (Samples 1-8) and 8 pancreas (Samples 7-16)

overall_design: SNV calling of WES data for A3B overexpressing mice

first: Nuri

last: Alpay Temiz


title: LCMR1 Promotes Large-cell Lung Cancer Proliferation and Metastasis through Downregulation of HLA Coding Genes

first: Lu

last: Liu

state: -- None selected --

address: Key Laboratory of Human Functional Genomics of Jiangsu Province

institute: Nanjing Medical University

summary: Lung cancer is notorious for high morbidity and mortality around the world. We previously cloned the gene LCRM1 from human large-cell lung carcinoma cell line, however whether this gene affect the proliferation and metastasis of large-cell lung carcinoma is yet unknown. To fully identify the biofunction of LCMR1 in lung cancer, we performed pan-cancer and cell line based LCMR1 expression profiling. Our analysis indicated that LCMR1 was expressed at higher levels in most solid tumors, especially in NSCLC. The expression profile of LCMR1 in different NSCLC cell lines revealed the highest level in the large-cell lung cancer cell 95D. Furthermore, our functional studies using lentivirus-based knockdown strategies indicates that LCMR1 is critical for large-cell lung cancer proliferation, migration, and invasion in cultured cells, and blocking this gene significantly reduced the growth of 95D cell xenograft mouse model. In mechanism assay, multiple sequence-based assay revealed that LCMR1 diminished the RNA Pol II occupancy at the promoter of HLA coding genes, thus blocks the transcription of these genes. Also, the correlation assay of TCGA database suggested that the expression level of LCMR1 was negatively related with the HLA coding genes, which plays vital role in cancer-specific antigen presenting and anticancer immunity. In conclusion, our studies showed that LCMR1 is required for large-cell lung cancer cell growth and invasion, suggesting its potential as a valid target in clinical treatment.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for 95D cells infected with either LCMR1 shRNA or scramble shNC lentivirus.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA pol II in 95D cell, either blocking LCMR1 or not.

first: Liangan

last: Chen

first: Chunsun

last: Li


title: Unraveling the dataset transcriptomic response of Hydrangea macrophylla stem to mechanical stimulation: de novo assembly and functional annotation

city: Angers

first: Béra

last: LEY-NGARDIGAL

address: 2 Boulevard de Lavoisier

department: Faculté des Sciences

country: France

institute: Université d'Angers

summary: To gain plant compactness, producers use plant growth regulators (PGRs), in particular growth retardants during culture. However, due to their negative environmental impacts, growth retardants are progressively withdrawn from the market. Alternative, eco-friendly methods such as mechanical stimulation (MS), which mimics the effect imposed on plants by the wind, result in reduced stem elongation, increased stem diameter and increased branching, all of which contribute to plant compactness. So far, few plant species were studied under MS and little is known on molecular response mechanisms to MS. This first transcriptomic data after MS in Hydrangea macrophylla cv. ‘Wudu’® will contribute unravelling how plants respond to mechanical stimuli.

overall_design: Mechanical stimulation (MS) of Hydrangea macrophylla stems consisted in 12 consecutive bendings applied at 9 a.m. during 1 h and for a single day. Transcriptomic data were obtained from whole stem collected 15 min before MS (T0) and 1 h, 3 h, 24 h and 72 h after 12 consecutive bendings (S group) or without bendings (NS group). There are therefore 9 different conditions, each with 3 biological replicates i.e. 27 samples. T0 and NS groups constitute the experiment's control groups.

first: B

last: Ley-Ngardigal

first: S

last: Pelletier

first: V

last: Guérin

first: L

last: Huché-Thélier

first: N

last: Brouard

first: H

last: Roman

last: Leduc


title: Androgen receptor condensates as drug targets

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

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: Comparative gene expression profiling analysis of RNA-seq data for AR V7, AR V7 22YtoS and AR V7 22YtoF in PC3 cells.

first: Travis

last: Stracker

first: Jordann

last: Smak


title: Inactivation of the tumor suppressor gene Apc synergizes with H. pylori to induce DNA damage and replication stress in murine gastric stem and progenitor cells

status: Public on Jul 24 2023

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Helicobacter pylori infection is a major risk factor for the development of gastric cancer. The bacteria reside in close proximity to gastric surface mucous as well as stem and progenitor cells. Here, we take advantage of wild type and genetically engineered murine gastric organoids and organoid-derived monolayers to study the cellular targets of H. pylori-induced DNA damage and replication stress, and to explore possible interactions with preexisting gastric cancer driver mutations. We find using alkaline comet assay, single molecule DNA fiber assays and immunofluorescence microscopy of DNA repair factors that H. pylori induces transcription-dependent DNA damage in actively replicating, Lgr5-positive antral stem and progenitor cells and their Troy-positive corpus counterparts, but not in other gastric epithelial lineages. Infection-dependent DNA damage is aggravated by Apc inactivation, but not by Trp53 or Smad4 loss, or Erbb2 overexpression. Our data suggest that H. pylori induces DNA damage in stem and progenitor cells, especially in settings of hyperproliferation due to constitutively active Wnt signaling.

overall_design: C57BL/6J-ApcMin/J (Strain #:002020) and C57BL/6JRj (WT) were obtained from the Jackson laboratory.

first: Jiazhuo

last: He

first: Anne

last: Müller

first: Peter

last: Leary


title: Rational design of a SOCS1-edited tumor infiltrating lymphocyte therapy for solid tumors using CRISPR/Cas9 screens

first: Micah

last: Benson


title: High-throughput functional dissection of noncoding SNPs with biased allelic enhancer activity for insulin resistance-relevant phenotypes

status: Public on Jul 28 2023

city: Xi'an China

first: Renjie

last: Zhu

state: Shaanxi

address: No.28 Xianning West Road, Xi'an, Shaanxi 710049, P.R. China

department: School of Life Science and Technology

institute: Xi'an Jiaotong University

summary: The majority of single nucleotide polymorphisms (SNPs) associated with insulin resistance (IR)-relevant phenotypes by genome-wide association studies (GWASs) are located in noncoding regions, complicating their functional interpretation. Here, we utilized an adapted STARR-seq to systematically detect regulatory activity of 5,987 noncoding GWASs SNPs in three IR-relevant cell lines. We identified 876 SNPs with biased allelic enhancer activity across 133 loci, and further uncovered the genetic regulatory mechanisms underlying functional SNPs through integrating multi-omics analyses.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: We selected 5,987 noncoding SNPs associated with IR-relevant phenotypes from GWAS catalog and other published studies.  A 120-bp genomic sequence centered on each SNP was extracted, with identical adapter sequence added on the 5' and 3' region. Oligonucleotides for 150-bp length SNPs on both reference and alternative alleles were synthesized in a CustomArray. Firstly, STARR-seq plasmid library was constructed using hSTARR-seq_ORI vector and amplified oligonucleotides. Secondly, The plasmid library was transfected into three IR-relevant cell lines (A673, HepG2 and preadipocyte) for 24h. Finally, the plasmid library and RNA extracted after transfection were used to construct input and output sequencing libraries respectively. The library preparations were sequenced on an Illumina Novaseq 6000 platform and paired-end reads were generated. Three biological replicates were performed for each cell line.

first: Tie-Lin

last: Yang

first: Yuan-Yuan

last: Duan

first: Xiao-Feng

last: Chen

first: Ren-Jie


title: 9sCa: MSL2 is an allelic dosage sensor in mammals

first: Asifa

last: Akhtar

first: Yidan

last: Sun

first: Raed

last: Hmadi

first: Meike

last: Wiese


title: EIF4A1 is essential in B cells by promoting activation-induced translation

status: Public on Jul 21 2023

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

summary: EIF4A1 and cofactors EIF4B and EIF4H have been well characterised in cancers, including B cell malignancies, for their ability to promote the translation of oncogenes with structured 5’ untranslated regions but very little is known of their roles in non-malignant cells. Using mouse models to delete Eif4a1, Eif4b or Eif4h in B cells we show that EIF4A1, but not EIF4B or EIF4H, is essential for B cell development and the germinal centre response. Following activation, EIF4A1 facilitates an increased rate of protein synthesis, MYC expression and expression of cell cycle regulators. However, EIF4A1-deficient cells remain viable whereas Hippuristanol treatment induces cell death.

overall_design: RNA-seq libraries were prepared from B cells following 24h activation, with four replicates from 8-12-week-old control and Eif4a1 KO mice. Proteomics analysis was also performed from the same samples; data are available using the accession provided in the associated manuscript. Note that replicate 1 for both control and KO were excluded from downstream analysis due to low cell viability following activation.

first: Michael

last: Screen

first: Martin

last: Turner


title: Control of Embryonic Brown Adipocyte Development by GATA6 I

status: Public on Jul 19 2023

first: Patrick

last: Seale

address: 3400 Civic Center Blvd., SCTR 12th Floor

institute: University of Pennsylvania

summary: Brown adipose tissue (BAT) is a thermogenic organ that protects animals against hypothermia and obesity. BAT derives from the multipotent paraxial mesoderm; however, the identity of embryonic brown fat progenitor cells and regulators of adipogenic commitment are unclear.  Here, we performed single cell gene expression analyses of mesenchymal cells during mouse embryogenesis with a focus on BAT development.

overall_design: Live single cells from E10.5-E15.5 mouse embryos were enriched for mesenchymal, dermomyotome (DM) and brown adipose lineage cells as follows: (i) E11.5 and E12.5 DM and mesenchymal cells based on cell surface expression of PDGFRa and/or LRIG1 [30% PDGFRa+, LRIG1(-) cells; 25% PDGFRa(-), LRIG1+ cells, 30% PDGFRa+, LRIG1+ cells, 15% PDGFRa(-), LRIG1(-) cells]. (ii) E13.5-E15.5 fibroblasts through selection of PDGFRa+ cells [75% PDGFRa+; 25% PDGFRa(-)]. (iii) E10.5, E14.5, and E15.5 brown adipose lineage cells based on expression of Early B Cell Factor-2 (Ebf2)-GFP [75% Ebf2-GFP+; 25% Ebf2-GFP(-)].

first: Ethan

middle: C

last: Fein

first: Anthony

last: Angueira

first: Seoyoung

last: Jun


title: C99R mutation in IRF4 drives a novel gain of function binding and gene upregulation in classical Hodgkin lymphoma [Illumina BeadChip]

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

summary: Disease-causing mutations in genes encoding transcription factors (TF) are frequent in hematopoietic malignancies and might affect TF-interactions with respective DNA-binding motifs. Here, we report the characterization of a recurrent somatic mutation c.295T>C in the IRF4 gene in classic Hodgkin lymphoma (cHL) leading to a C99R exchange. IRF4-C99R is located in the center of the IRF4 alpha3-recognition helix contacting the DNA 5´-GAAA-3´ IRF consensus sequence. IRF4-C99R fundamentally alters IRF4 DNA-binding, combining loss-of-binding at canonical IRF motifs and neomorph gain-of-binding at canonical and non-canonical IRF composite elements (CEs), in particular AP-1-IRF-CEs (AICEs). In line, IRF4-C99R profoundly impairs IRF4-dependent plasma cell induction, and specifically up-regulates degenerate-AICE-dependent distinct cHL disease-characteristic genes. These data document an unprecedented mutation-induced shift of TF binding specificity and its impact for lymphoma pathogenesis and TF modulation.

overall_design: Illumina BeadChip HT-12 V4.0 expression data from BJAB cells with Tet-inducible control, IRF4WT and IRF4C99R cells treated with 0, 6, 24 and 48 hours doxycycline

first: Nikolai

last: Schleußner

first: Vedran

last: Franke

first: Oriol

last: Crespo

first: Benjamin

last: Edginton-White

first: Salam

last: Assi

first: Lionel

last: Huber

first: Nadine

last: Obier

first: Peter

last: Cockerill

first: Ralph

last: Küppers

first: Sylvia

last: Hartmann

middle: L

last: Hansmann

first: Rudolf

last: Grosschedl

first: Constanze

last: Bonifer

first: Thomas

last: Bukur

first: Stephan

last: Mathas


title: Control of Embryonic Brown Adipocyte Development by GATA6

first: Patrick

last: Seale


title: C99R mutation in IRF4 drives a novel gain of function binding and gene upregulation in classical Hodgkin lymphoma

last: Cauchy


title: C99R mutation in IRF4 drives a novel gain of function binding and gene upregulation in classical Hodgkin lymphoma [ChIP-Seq]

overall_design: IRF4 and JunB ChIP-Seq from IRF4WT NHL and IRF4WT, IRF4C99R HL-derived cell lines

last: Schleußner

first: Martin


title: Rational design of a SOCS1-edited tumor infiltrating lymphocyte therapy for solid tumors using CRISPR/Cas9 screens [IVP59_mc38gp100]

first: Micah

last: Benson

summary: Tumor Infiltrating Lymphocyte (TIL) therapy have shown promise  in the treatment of patients with refractory solid tumors, with improvement in response rates and durability of responses nevertheless sought.  To identify targets capable of enhancing the anti-tumor activity  of T cell therapies, large-scale in vitro and in vivo CRISPR/Cas9 screens were performed, with the suppressor of cytokine signaling 1 (SOCS1) gene identified as a top T cell-enhancing target.  In murine CD8 T cell therapy models, SOCS1 served as a critical checkpoint in restraining the accumulation of T central memory cells in lymphoid organs as well as intermediate (Texint) and effector (Texeff) exhausted T cell subsets derived from progenitor exhausted T cell (Texprog) cells in tumors. A comprehensive CRISPR tiling screen of the SOCS1 coding region identified sgRNAs targeting the SH2 domain of SOCS1 as the most potent, with a sgRNA with minimal off-target cut sites used to manufacture KSQ-001, an engineered TIL therapy with SOCS1 inactivated by CRISPR/Cas9.  KSQ-001 possessed increased responsiveness to cytokine signals and enhanced in vivo anti-tumor function in mouse models. These data demonstrate the use of CRISPR/Cas9 screens in the rational design of T cell therapies.

overall_design: For each library, three replicates of  input population of transferred T cells were sequenced. For each library, two groups of endpoint T cells at day 14 were collected, and 7 replicates of mice were included within each group.


title: High-sensitive spatially resolved T cell receptor sequencing with SPTCR-seq

city: Freiburg im Breisgau

first: Jasim

last: Kada Benotmane

state: - Select -

address: Breisacherstraße 64

department: Clinic for Neurosurgery

institute: Albert-Ludwigs-University Freiburg

summary: Understanding the spatial distribution of T cells is pivotal to decrypting immune dysfunction in cancer. Current spatially resolved transcriptomics fall short in directly annotating T cell receptors (TCRs), limiting the comprehension of anti-cancer immunity. We introduce a novel technology, Spatially Resolved T Cell Receptor Sequencing (SPTCR-seq), integrating target enrichment and long-read sequencing for highly sensitive TCR sequencing. This approach yields an on-target rate of ~85%, and via a bespoke computational pipeline, it provides meticulous spatial mapping, error correction, and UMI refinement. SPTCR-seq outperforms PCR-based methods, offering superior reconstruction of the complete TCR architecture, inclusive of V, D, J regions and the vital complementarity-determining region 3 (CDR3). Applying SPTCR-seq, we reveal local T cell diversity, clonal expansion, and transcriptional evolution across spatially distinct niches in glioblastoma, identifying critical involvement of NK and B cells in spatial T cell adaptation. SPTCR-seq, by bridging spatially resolved omics and TCR sequencing, stands as a robust tool for exploring T cell dysfunction in cancers and beyond.

overall_design: The Spatial Transcriptomics-based T Cell Receptor sequencing (SPTCR) approach begins by generating full-length cDNA from fresh frozen glioblastoma tissue samples. This cDNA is enriched for T cell receptor (TCR) sequences using custom probes, then undergoes long-read nanopore sequencing for a thorough interpretation of TCR diversity. Following sequencing, computational processing is employed for TCR annotation, error correction, and clonality analysis. SPTCR combines this information with spatial transcriptomics data, mapping TCR sequences to their original spatial context within the tumor. Finally, integration with imaging mass spectrometry metabolomics data allows for a unique exploration of TCR clonal expansion, exhaustion, and metabolism within the tumor microenvironment. The spatial transcriptomics data related to this study has been deposited on DataDryad and is accessible to the public (DOI: 10.5061/dryad.h70rxwdmj). The spatial metabolomics data can be found on the OSF platform using this link: https://osf.io/8qbdz/?view_only=5287d7f6263e4ba680ca8c396aeefeee. Further processed files and detailed steps of our analysis have also been made available on OSF: https://osf.io/65y3t/?view_only=6571f0c374ce4bf294b9cbd10ade62cf.

first: Jan

last: Kückelhaus

first: Paulina

last: Will

first: Junyi

last: Zhang

first: Vidhya

last: Ravi

first: Kevin

last: Joseph

first: Roman

last: Sankowski

first: Jürgen

last: Beck

first: Catalina

last: Lee-Chang

first: Oliver

last: Schnell

first: Dieter

last: Heiland


title: Rational design of a SOCS1-edited tumor infiltrating  lymphocyte therapy for solid tumors using CRISPR/Cas9 screens [scRNA-seq]

summary: Tumor Infiltrating Lymphocyte (TIL) therapy have shown promise  in the treatment of patients with refractory solid tumors, with improvement in response rates and durability of responses nevertheless sought.  To identify targets capable of enhancing the anti-tumor activity of T cell therapies, large-scale in vitro and in vivo CRISPR/Cas9 screens were performed, with the suppressor of cytokine signaling 1 (SOCS1) gene identified as a top T cell-enhancing target.  In murine CD8 T cell therapy models, SOCS1 served as a critical checkpoint in restraining the accumulation of T central memory cells in lymphoid organs as well as intermediate (Texint) and effector (Texeff) exhausted T cell subsets derived from progenitor exhausted T cell (Texprog) cells in tumors. A comprehensive CRISPR tiling screen of the SOCS1 coding region identified sgRNAs targeting the SH2 domain of SOCS1 as the most potent, with a sgRNA with minimal off-target cut sites used to manufacture KSQ-001, an engineered TIL therapy with SOCS1 inactivated by CRISPR/Cas9.  KSQ-001 possessed increased responsiveness to cytokine signals and enhanced in vivo anti-tumor function in mouse models. These data demonstrate the use of CRISPR/Cas9 screens in the rational design of T cell therapies.

overall_design: CD45+ tumor infiltrating lymphoctyes were harvested 7 days post-transfer from small B16ova tumor-bearing mice and analyzed using scRNA-Seq . Droplet-base 5’ single-cell RNA sequencing (scRNA-Seq) was performed by the 10x Genomics platform to capture gene expression and V(D)J transcripts and clonotypes for T cells. For the sgSocs1 (KSQ001) and sgOlfr (Olfactory) treatment groups, four mice per group were pooled into two samples. For the sgPD-1 (PD-1) treatment group, two mice were pooled into one sample.


title: Centrosome clustering in osteoclasts regulated by CCR5-mediated signaling, involved in bone homeostasis

status: Public on Jul 18 2023

city: Sapporo

first: Ji-Won

last: Lee

state: Does Not Apply

address: N13W7, Kita-Ku

department: Graduate school of Dental Medicine

country: Japan

institute: Hokkaido University

summary: To investigate the effect of intracellular signals mediated by chemokine receptor 5 (CCR5) on osteoclast differentiation, bone marrow cells were harved from Ccr5-deficient mice (KO) and their littermates (WT) mice.

overall_design: Bone marrow cells were harvested from tibia of 8 weeks-old male Ccr5-deficient mice and WT. Cells were induced into bone marrow macrophages with M-CSF for 2 days, and further differentiated into osteoclast precursors (pOCs) with RANKL for 2 days. pOCs were then subjected to RNA-sequencing.


title: Rational design of a SOCS1-edited tumor infiltrating lymphocyte therapy for solid tumors using CRISPR/Cas9 screens [IVP27_B16Ova]

address: 4 Maguire Rd

institute: KSQ Therapeutics

overall_design: Two plasmid samples are sequenced for two sgRNA libraries; For each library, two replicates of  input population of transferred T cells were sequenced. For each library, endpoint T cells were collected at two timepoints: day 14 and day 21, and 7 replicates of mice were included within each group.


title: Human SUP-B15 cells: CNV compared to reference genome.

city: Fortaleza

first: Caio

middle: Bezerra

last: Machado

state: Ceará

address: St. Coronel Nunes de Melo, 1000

department: Drug Research and Development Center (NPDM)

country: Brazil

institute: Federal University of Ceará (UFC)

type:
Genome variation profiling by array
Genome variation profiling by SNP array

summary: Copy Number Variaton (CNV) detection of human BCR-ABL positive acute lymphoblastic leukemia (ALL) cell line, SUP-B15.

overall_design: SUP-B15 genome was compared to reference human DNA from SureTag Complete DNA labeling kit (Agilent).

middle: B

first: Wallax

last: Ferreira

first: Edivaldo

last: Oliveira

first: Caroline

last: Moreira-Nunes


title: Scalable single-cell profiling of chromatin modifications with sciCUT&Tag

status: Public on Jul 13 2023

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Cleavage Under Targets & Tagmentation (CUT&Tag) is an antibody-directed in situ chromatin profiling strategy that is rapidly replacing precipitation-based methods. The efficiency of the method enabled chromatin profiling in single cells but is limited by the numbers of cells that can be profiled.  Here, we describe a combinatorial barcoding strategy for CUT&Tag that harnesses a nanowell dispenser for simple, high-resolution high-throughput single-cell chromatin profiling. We describe a pipeline for single-cell indexed CUT&Tag (sciCUT&Tag) that uses SNPs to facilitate doublet-cell removal and minimize batch effects. We illustrate the optimized protocol by analysis of mouse and human cell lines, as well as human peripheral blood mononuclear cells. We have also used sciCUT&Tag for simultaneous profiling of multiple chromatin epitopes in single cells. The reduced cost, improved resolution and scalability of sciCUT&Tag make it an attractive platform to profile chromatin features in single cells.

overall_design: We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.

first: Jacob

last: Greene

first: Derek

last: Janssens

first: Steven

last: Wu

first: Christine

last: Codomo

first: Sam

last: Minot

first: Scott

middle: N

last: Furlan

first: Kami

last: Ahmad


title: Single-cell RNA-seq dictionary of in vivo immune responses to cytokines

status: Public on Jul 17 2023

first: Ang

last: Cui

address: 415 Main St.

institute: Broad Institute

summary: Cytokines mediate cell-cell communication in the immune system and represent important therapeutic targets. While there have been in-depth studies of individual cytokines, we lack a global view of the responses of each major immune cell type to each cytokine. To address this gap we created the Immune Dictionary — a compendium of single-cell transcriptomic profiles of over 17 immune cell types in response to each of 86 cytokines in murine lymph nodes in vivo. A cytokine-centric view of the dictionary revealed that most cytokines induce highly cell-type-specific responses. For example, the inflammatory cytokine IL-1β induced distinct gene programs in almost every cell type. A cell-type-centric view identified both known and previously uncharacterized cytokine-induced polarization states in every immune cell type, such as a polyfunctional state of NK cells induced by IL-18. Based on the dictionary, we developed companion software, Immune Response Enrichment Analysis (IREA), for assessing immune cell polarization and cytokine activities in any transcriptomic data, and applied it to infer cytokine networks in tumors following immune checkpoint blockade therapy. Our dictionary generates new hypotheses for cytokine functions, illuminates pleiotropic effects of cytokines, expands our knowledge of activation states in each immune cell type, and provides a framework to deduce the roles of specific cytokines and cell-cell communication networks in any immune response.

overall_design: We systematically profiled single-cell transcriptomic responses in vivo to 86 cytokines. The 86 cytokines were selected to represent most of the members in each major cytokine family, including: IL-1 (IL-1α/1β/Ra/18/33/36α/36Ra), common γ chain (IL-2/4/7/9/15/21), common β chain (GM-CSF/IL-3/IL-5), IL-6 (IL-6/11/27*/31, LIF, OSM, CT-1, NP), IL-12 (IL-12/23/27*/Y), IL-10 (IL-10/19/20/22/24), IL-17 (IL-17A-F), interferon (IFN-α1/β/ε/κ/γ/λ2), TNF (TNFSF1-15, 13B, 18), complement (C3a, C5a), and a small number of representative cytokines from other protein families with less well-characterized immune functions (e.g.,Persephins, Adiponectin). Carrier-free cytokines were freshly reconstituted and administered into distinct wild-type C57BL6/J mice (3 mice per cytokine as biological replicates). PBS (vehicle) treated samples were included in each batch as controls. Draining lymph nodes were collected 4 hours after treatment and freshly processed using an optimized protocol for viable cell recovery. Data quality, including batch-to-batch consistency, was experimentally strictly controlled for and computationally verified. Single-cell profiling of lymph node cells was performed Chromium Single Cell 3’ Library & Gel Bead v3 Kit (10x Genomics) to generate single-cell transcriptomes for 386,703 cells that passed quality control.

first: Teddy

last: Huang

first: Shuqiang

last: Li

first: Aileen

last: Ma

first: Jorge

last: Perez

first: Chris

last: Sander

first: Derin

last: Keskin

first: Catherine

first: Ernest

last: Fraenkel

first: Nir

last: Hacohen


title: Time-course of transcriptomic change in the lungs of F344 rats repeatedly exposed to a multiwalled carbon nanotube in a 2-year test

city: Tokyo

first: Motoki

last: Hojo

address: 3-24-1 Hyakunincho, Shinjuku-kuku

department: Department of Pharmaceutical and Environmental Sciences

institute: Tokyo Metropolitan Institute of Public Health

summary: Despite intensive toxicological studies of carbon nanotubes (CNTs) over the last two decades, only a few studies have demonstrated their pulmonary carcinogenicities in chronic animal experiments, and the underlying molecular mechanisms are still unclear. To obtain molecular insights into CNT-induced lung carcinogenicity, we performed a transcriptomic analysis using a set of lung tissues collected from rats in a 2-year study, in which lung tumors were induced by repeated intratracheal instillations of a multiwalled carbon nanotube, MWNT-7. The RNA-seq-based transcriptome identified a large number of significantly differentially expressed genes at Year 0.5, Year 1, and Year 2. Ingenuity Pathway Analysis revealed that macrophage-elicited signaling pathways such as phagocytosis, acute phase response, and Toll-like receptor signaling were activated throughout the experimental period. At Year 2, cancer-related pathways including ERBB signaling and some axonal guidance signaling pathways such as EphB4 signaling were perturbed. qRT-PCR and immunohistochemistry indicated that several key molecules such as Osteopontin/Spp1, Hmox1, Mmp12, and ERBB2 were markedly altered and/or localized in the preneoplastic lesions, suggesting their participation in the induction of lung cancer. Our findings support a scenario of inflammation-induced carcinogenesis and contribute to a better understanding of the molecular mechanism of MWCNT carcinogenicity.

overall_design: To investigate the chronic effect of the multiwalled carbon nanotube to lungs, we repeatedly administered MWNT-7 to male F344 rats for 2 years. Throuh the experiment, we harvested rat lungs from vehicle control group and MWCNT-treated group at 6 months (Year 0.5), 1 year (Year 1), and 2 years (Year 2) after the begenning of the experiment (3 rats per time point per group). We then performed comparative gene expression profiling analyses for MWCNT-treated vs vehicle control at each time point.


title: Th1/17 polarization and potential treatment by an anti-interferon-γ DNA aptamer in Hunner-type interstitial cystitis

first: Yoshiyuki

last: AKIYAMA

state: Please select...

department: Urology

institute: The University of Tokyo

summary: Hunner-type interstitial cystitis (HIC) is a rare, enigmatic inflammatory disease of the urinary bladder with no curative treatments. In this study, we aimed to characterize the unique cellular and immunological factors specifically involved in HIC by comparing with cystitis induced by Mycobacterium bovis bacillus Calmette–Guérin, which presents similar clinicopathological features to HIC. Here, we show that T helper 1/17 polarized immune responses accompanied by prominent overexpression of interferon (IFN)-γ, enhanced cGAS-STING cytosolic DNA sensing pathway, and increased plasma cell infiltration are the characteristic inflammatory features in HIC bladder. Further, we developed a novel mouse anti-IFN-γ DNA aptamer and observed that intravesical instillation of the aptamer significantly ameliorated bladder inflammation, pelvic pain and voiding dysfunction in a recently developed novel murine HIC mouse model with little migration into the blood. Our study provides the plausible basis for clinical translation of the anti-IFN-γ DNA aptamer in the treatment of human HIC.

overall_design: For 25 patients with HIC, paired cold-cup biopsy samples, one from a Hunner lesion and one from a background mucosal area without Hunner lesion, were obtained. For 13 patients with BCG, one cold-cup biopsy sample was obtained from a reddened mucosal flat lesion resembling a Hunner lesion. Biopsy samples were immediately frozen in liquid nitrogen and stored at -80°C for RNA extraction. We performed RNA-seq using these samples for comparative gene expression analyses of Hunner-type interstitial cystitis (lesion and non-lesion) and BCG cystitis.

last: Akiyama

first: Yi

last: Luo

first: Miyuki

last: Hori


title: The Downregulated ADAMTS1 Incorporating with A2M Contributes to Tumorigenesis and Alters Tumor Immune Microenvironment in Lung Adenocarcinoma

status: Public on Jul 12 2023

city: Kaohsiung City

first: Ying-Ming

last: Tsai

address: No.100, Shih-Chuan 1st Road, Sanmin Dist.

country: Taiwan

institute: Kaohsiung Medical University

summary: Lung cancer is the most dreadful cancer type and has the worst cancer-related clinical outcomes. This study used specimens from the in-house lung cancer cohort and public cohort to verify the roles of downregulated ADAMTS1, a protease remodeling extracellular matrix, to facilitate cancer promotion and progress. Based on the clinical specimens, cell and animal study with the aid of the public databases, we concluded that downregulated expression of ADAMTS1 might promote tumor progression and metastasis and modify the tumor microenvironment in lung cancer. Further investigation would be required for its application in treating lung cancer.

overall_design:
Compare ADAMTS1 gene expression in normal tissue and cancer tissues
Submitter states that raw data are not available.


title: The Tox gene encodes two proteins with distinct and shared roles in gene regulation

status: Public on Jul 10 2023

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

summary: Here we report that the murine Tox gene encodes two proteins from a single mRNA and investigate the mechanism of production and function of these proteoforms. The annotated TOX coding sequence is predicted to produce a 526 amino acid protein (TOXFL). However, western blots reveal two bands. We found that the lower band consists of an N-terminally truncated variant of TOX (TOXDN), while the slower migrating band is TOXFL. The TOXDN proteoform is alternatively translated via leaky ribosomal scanning from an evolutionarily conserved translation initiation site downstream of the annotated translation initiation site. When expressed exogenously from a cDNA in murine CD8 T cells or HEK cells, or endogenously from the murine Tox locus, both forms are translated, although the ratio of TOXFL: TOXDN significantly varies with cellular context. This includes regulation of proteoform production during development of murine CD4 T cells in the thymus, where the positive selection of CD4+8+ cells and subsequent differentiation to CD4+8lo transitional and CD4SP cell subsets is associated with both an increase in total TOX protein and increased TOXDN production relative to TOXFL. Finally, we found that sole expression of TOXFL had a greater effect on gene regulation during chronic stimulation of murine CD8 T cells in culture mimicking exhaustion, than did TOXDN, including uniquely regulated cell cycle and other genes.

overall_design: Naïve CD3+CD8+ splenocytes were isolated from OTI mice and stimulated with OVA peptide for 3 days and transduced to express TOXFL or TOXdeltaN (and IRES-GFP) at 24 hours after initiation of culture. Cells were FACS sorted on day 5 and GFP- (exogenous TOX-) and the top 20% of GFP+ (exogenous TOX+) populations were analyzed by RNA-seq.

first: Alyson

last: Yeckes

first: Andrew

last: Victor

first: Zheng

last: Zhu

first: Meena

last: Narayanan

first: Bharani

last: Srinivasan

first: Bethany

last: Bruce

first: Jonathan

last: Kaye


title: Gene expression signatures of MDCK-pTR GFP-RasV12 cells cultured alone or mixed with MDCK cells

status: Public on Jul 11 2023

city: Noda-shi

first: Shunsuke

last: Kon

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

institute: Tokyo University of Science

summary: Newly emerging transformed cells carrying genetic defects, including the active Ras mutant, are apicall extruded when surrounded by normal epithelial cells. This biological phenomenon is termed as cell competition. It remains elusive which factors prime RasV12-transformed cells to be expelled via cell competition. Here, We performe microarray analysis to search for molecules whose expression is changed in RasV12 cells surrounded by normal cells.

overall_design: 1.2×10^7 of 10:1 mix culture of MDCK and MDCK-pTR GFP-RasV12 cells or a single culture of MDCK-pTR GFP-RasV12 cells were cultured in collagen type I-coated dishes. After incubation with tetracycline for 24 h, GFP-positive cells were collected by an analytical flow cytometer, and total RNA was extracted from the isolated cells.

first: Kojiro

last: Ishibashi


title: An injury responsive enhancer promotes heart regeneration in zebrafish

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

summary: we profiled chromatin accessibility of zebrafish endothelial cells after amputation injury and identify an mmp14b endothelial enhancer induced by heart injury in zebrafish. We show that the enhancer is required for mmp14b expression and regeneration in response to heart injury. Moreover, the enhancer depends on a consensus TEAD-binding motif, suggesting a role for Hippo signaling upstream of mmp14b.

overall_design: After cardiac injury, Fli1+ cells are purified for ATAC-seq profiling.

first: Fei

last: Sun

first: Jianhong

last: Ou

first: Alexis

last: Safi

first: Gregory

last: Crowford

first: Kenneth

middle: D

last: Poss


title: Effect of overexpression of A3B and RNA editing calling in mouse tissues [RNA-seq]

first: Alicia

last: Alonso de la Vega

address: Im Neuenheimer Feld 280

institute: Deutsches Krebsforschungszentrum, DKFZ

summary:
To test if A3B has RNA editng activity we performed SNV calling from RNA-seq of 6 mouse lungs (Samples 7-12), 8 mouse livers (Samples 14-20) and 8 pancreas (Samples 21-28)
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 mouse livers (Samples 1-6), 6 mouse lungs (Samples 7-12), 8 mouse livers (Samples 14-20) and 8 pancreas (Samples 21-28)

overall_design: Comparative gene expression profiling analysis and SNV calling of RNA-seq data for A3B overexpressing mice

first: Nuri

last: Alpay Temiz


title: C99R mutation in IRF4 drives a novel gain of function binding and gene upregulation in classical Hodgkin lymphoma [DNase-Seq]

city: Freiburg

first: Pierre

last: Cauchy

overall_design: DNase-Seq from IRF4WT NHL and IRF4WT, IRF4C99R HL-derived cell lines

first: Nikolai

last: Schleußner

first: Vedran

last: Franke

first: Oriol

last: Crespo

first: Benjamin

last: Edginton-White

first: Salam

last: Assi

first: Lionel

last: Huber

first: Nadine

last: Obier

first: Thomas

last: Bukur

first: Peter

last: Cockerill

first: Ralph

last: Küppers

first: Sylvia

last: Hartmann

first: Martin

last: Hansmann

first: Rudolf

last: Grosschedl

first: Constanze

last: Bonifer

first: Stephan

last: Mathas


title: C99R mutation in IRF4 drives a novel gain of function binding and gene upregulation in classical Hodgkin lymphoma [RNA-Seq]

overall_design: RNA-Seq from IRF4WT NHL and IRF4WT, IRF4C99R HL-derived cell lines


title: Genome-wide expression profiling of nematode-trapping fungus Arthrobotrys oligospora TWF154 upon nematode exposure

status: Public on Jul 01 2023

city: Nankang, Taipei

first: Hung-Che

last: Lin

address: 128 Academia Road, Section 2

institute: Academia sinica

summary: We report the transcriptomic comparisions between key processes required for various stages of fungal carnivory in nematode-trapping fungus Arthrobotrys oligospora when induced with nematodes. The reference assembly used for remapping is A. oligospora TWF154 (GenBank assembly accession: GCA_004768765.1)

overall_design: Profiling of the transcriptional response upon nematode contact in Arthrobotrys oligospora

first: Yen-Ping

last: Hsueh

first: Guillermo

last: Vidal-Diez de Ulzurrun


title: Hyaluronic Acid Induction Promotes the Differentiation of Human Neural Crest-like Cells into Periodontal Ligament Stem-like Cells

status: Public on Jun 27 2023

first: Atsushi

last: Tomokiyo

state: Hokkaido

address: Kita13 Nishi7, Kita-ku

summary: Periodontal ligament (PDL) stem-like cells (PDLSCs) are considered to be promising for the regeneration of periodontium because they demonstrate multipotency, high proliferative capacity, and potential to regenerate bone, cementum, and PDL tissue. However, the transplantation of autologous PDLSCs is restricted by limited availability and the need for tooth extraction to isolate these cells. PDLSCs are derived from neural crest cells (NCs) in early vertebrate development and NCs persist in adult PDL tissue. Therefore, we devised to promote the regeneration of periodontium by activating NCs to differentiate into PDLSCs and increasing their total number. SK-N-SH cells cultured on the extracellular matrix derived of human PDL cells (SK-PDLSCs) strongly expressed PDL-related marker genes and highly differentiated into mesenchymal lineage cells compared to untreated SK-N-SH cells. Expression levels of various hyaluronic acid (HA)-related genes were upregulated in induced pluripotent stem cells (iPSCs)-derived PDLSCs and SK-PDLSCs compared to iPSCs-derived NCs and SK-N-SH cells, respectively. Magnetic-activated cell sorting-assisted CD44-positive enrichment population of SK-N-SH cells showed higher expression of PDL-related marker genes after SK-PDLSCs induction than the CD44-negative population. Knockdown of CD44 in SK-N-SH cells significantly inhibited their ability to differentiate into SK-PDLSCs, while lower molecular HA (LHA) induction enhanced SK-PDLSC differentiation. LHA-containing electrospun nanofibrous membranes also promoted their SK-PDLSC differentiation. Our findings suggest that SK-N-SH cells are applied as a new model to induce the differentiation of NCs into PDLSCs. The LHA-CD44 relation is important for the differentiation of NCs into PDLSCs. LHA-containing electrospun nanofibrous membranes would promote the regeneration of periodontium by activating NCs in PDL tissue and increasing the total number of PDLSCs.

overall_design: Control: iPS cells-derived neural crest-like cells, experiment: iPS cells-derived periodontal ligament stem cell-like cells

first: Muhammad

last: Alhaasn

first: Sayuri

last: Hamano

first: Hideki

last: Sugii

first: Taiga

last: Ono

first: Keita

last: Ipposhi

first: Kozue

last: Yamashita

first: Fumiko

last: Minowa

first: Hidefumi

last: Maeda


title: Contrasting genes conferring short and long-term biofilm adaptation in Listeria

status: Public on Jun 28 2023

city: Bath

first: William

last: Monteith

address: Claverton Down

institute: University of Bath

summary: Listeria monocytogenes is an opportunistic food-borne bacterium that is capable of infecting humans with high rates of hospitalisation and mortality. Natural populations are genotypically and phenotypically variable, with some lineages being responsible for most human infections. The success of L. monocytogenes is linked to its capacity to persist on food and in the environment. Biofilms are an important feature that allow these bacteria to persist and infect humans, therefore, understanding the genetic basis of biofilm formation is key to understanding transmission. We sought to investigate the biofilm forming ability of L. monocytogenes by identifying genetic variation that underlies biofilm formation in natural populations using genome-wide association studies. Changes in gene expression of specific strains during biofilm formation were then investigated using RNAseq. Genetic variation associated with enhanced biofilm formation was identified in 273 genes by GWAS and differential expression in 220 genes by RNAseq. Statistical analyses show that number of overlapping genes flagged by either type of experiment is less than expected by random sampling. This is consistent with an evolutionary scenario where rapid adaptation is driven by variation in gene expression of pioneer genes, and this is followed by slower adaptation driven by nucleotide changes within the core genome.

overall_design: To investigate gene expression under biofilm formation in L. monocytogenes we established cultures for L. monocytogenes strains Lm0132 and Lm0134. Two replicates were grown for each strain. Each replicate was grown under two conditions, shaken media and stationary media. We then performed a differential gene expression analysis on Illumina sequence reads containing expression data under the two conditions. Reads from each strain were taken from the shaken media at 0 hours, 24 hours and 48 hours and were compared with reads taken from 24 hours stationary growth.

first: Ben

last: Pascoe

first: Evangelos

last: Mourkas

first: Jack

last: Clark

first: Maliha

last: Hakim

first: Matthew

last: Hitchings

first: Noel

last: McCarthy

first: Koji

last: Yahara

first: Hiroshi

last: Asakura

first: Samuel

middle: K

last: Sheppard


title: Neurodevelopmental Defects in Human Cortical Organoids with N-acetylneuraminic Acid Synthase Mutation

status: Public on Jun 26 2023

city: chengdu

first: Qian

last: Bu

state: Sichuan

address: 28 Gaopeng Street, High-tech District

institute: Chengdu  West China-Frontier PharmaTech Co.,Ltd

summary: Biallelic genetic variants in N-acetylneuraminic acid synthase (NANS), a critical enzyme in endogenous sialic acid biosynthesis, are clinically associated with neurodevelopmental disorders. However, the mechanism underlying the neuropathological consequences has remained elusive. Here, we discovered that NANS mutation resulted in absence of both sialic acid and protein polysialylation in the cortical organoids and significantly reduced the proliferation and expansion of neural progenitors. NANS mutation dysregulated neural migration and differentiation, disturbed synapse formation, and weakened neuronal activity. Single-cell RNA sequencing revealed that NANS loss-of-function markedly altered transcriptional programs involved in neuronal differentiation and ribosomal biogenesis in various neuronal cell types. Similarly, Nans heterozygous mice exhibited impaired cortical neurogenesis and neurobehavioral deficits. Collectively, our findings reveal a crucial role of NANS-mediated endogenous sialic acid biosynthesis in regulating multiple features of human cortical development, thus linking NANS mutation with its clinically relevant neurodevelopmental disorders.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Control cerebral organoids and  NANS-KO cerebral organoids in 4 time points (3 samples per group)


title: Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing

city: shanghai

first: di

last: sun

address: pujian road 160

department: institute of molecular medicine

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Here, we report a dendrimeric DNA coordinate barcoding design for spatial RNA sequencing (Decoder-seq) offering both high sensitivity and high resolution.

overall_design:
Decoder-seq offers exceptional flexibility and precision in spatial resolution with spot widths of 50, 25, and 15 μm and various capture areas of spatially barcoded arrays. It was employed to mouse hippocampus, olfactory bulb and hemibrain, and human renal cancers.

Please note that [1] the records have been updated with additional HE image files and coordinate file information on Nov 16, 2023 [2] the processed data for GSM7585162 has been updated on Dec 8, 2023.

first: Jiao

last: Cao

first: Di

last: Sun


title: Combined CDK4/6 and ERK1/2 inhibition enhances anti-tumor activity in NF1-associated plexiform neurofibroma [sciatic nerve]

city: Indianapolis

first: Steven

last: Rhodes

state: IN

address: 1044 W. Walnut St.; Bldg R4, Rm 325

institute: Indiana University

summary:
Purpose: Plexiform neurofibromas (PNF) are peripheral nerve sheath tumors that cause significant morbidity in persons with neurofibromatosis type 1 (NF1), yet treatment options remain limited. To identify novel therapeutic targets for PNF, we applied an integrated multi-omics approach to quantitatively profile kinome activation in a mouse model that has predicted therapeutic responses in clinical trials for NF1-associated PNF with high fidelity.
Experimental Design: Utilizing RNA sequencing combined with chemical proteomic profiling of the functionally enriched kinome using multiplexed inhibitor beads coupled with mass spectrometry, we identified molecular signatures predictive of response to CDK4/6 and RAS/MAPK pathway inhibition in PNF. Informed by these results, we evaluated the effectivity of the CDK4/6 inhibitor, abemaciclib, and the ERK1/2 inhibitor (LY3214996) alone and in combination to reduce PNF tumor burden in Nf1flox/flox;PostnCre mice.
Results: Converging signatures of CDK4/6 and RAS/MAPK pathway activation were identified within the transcriptome and kinome that were conserved in both murine and human PNF. We observed robust synergism of the CDK4/6 inhibitor, abemaciclib, in combination with the ERK1/2 inhibitor (LY3214996) in primary Nf1-/- Schwann cell cultures. Consistent with these findings, the combination of abemaciclib (CDK4/6i) and LY3214996 (ERK1/2i) synergized to suppress molecular signatures of MAPK activation and exhibited enhanced anti-tumor activity in Nf1flox/flox;PostnCre mice in vivo.
Conclusion: These findings provide rationale for the clinical translation of CDK4/6 inhibitors alone and in combination with therapies targeting the RAS/MAPK pathway for the treatment of PNF and other peripheral nerve sheath tumors in persons with NF1.

overall_design:
RNAseq of sciatic nerve from Nf1 flox/flox PostnCre+ (Nf1) mice treated with Vehicle, abemaciclib (CDK4/6i), LY3214996 (ERK1/2i), or abemaciclib (CDK4/6i) and LY3214996 (ERK1/2i) for 1 week
24 experimental samples

middle: P

last: Angus


title: GDF15 gene suppression by BET inhibition and gene signature based personalized chemotherapy to counteract cachexia [RNA-seq]

status: Public on Jul 07 2023

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary: Elevation of growth differentiation factor 15 (GDF15) has recently emerged as a key driver of cancer cachexia, a syndrome of extreme weight loss that affects patients with various types of cancer. Chemotherapy, as well as the tumour itself have been reported to contribute to increased GDF15 secretion in both cancer and host tissues. Bromodomain and extraterminal (BET) domain proteins have been shown to regulate GDF15 expression in pancreatic cancer cells. With currently neither preventive strategies nor specific therapeutic options for cachexia available, antibodies targeting GDF15 or its receptor are being developed. However, the mechanism of chemotherapy-induced GDF15 upregulation in tumour and host cells is still unknown, leaving uncertainty about safety and efficacy of therapies targeting retrospective reduction of GDF15 in cancer cachexia. We tested various cardiotoxic drugs for their effect on GDF15 regulation in cardiomyocyte cell culture and analysed gene expression, mutational status, and pathway activities of the NCI-60 cancer cell line panels to get further insights into the regulation of GDF15 expression in both cancer and host cells upon treatment with anticancer drugs. To investigate the regulatory effect of BET inhibition on GDF expression more extensively, we screened BET inhibitors in doxorubicin treated human cardiomyocyte cell culture as well as in 21 cancer cell lines and performed differential analysis of gene expression, metabolites, and pathway activities. Our results reveal that DNA interacting compounds induce GDF15 expression in human cardiomyocytes up to 20-fold, whereas cardiotoxic drugs with other modes of action led, if at all, to less than 3-fold induction. We discovered that BET inhibitors suppress doxorubicin-induced GDF15 overexpression in human cardiomyocytes up to 7.4-fold (p=0.0051). In cancer cell lines, we identified compound-specific gene signatures that correlate with the extent of GDF15 induction upon treatment in the espective cell line. BET inhibition also reduces GDF15 expression in a defined subset of cancer cell lines that differentiate from the other tested cell lines in a less active PI3K/Akt axis and significantly higher extracellular pantothenate concentration (p=0.00095). We identified compound- and cell-line-specific gene signatures that predict GDF15 upregulation upon treatment, providing indication that the risk for drug-induced GDF15 overexpression and concomitant cachexia can be reduced by a biomarker-driven selection of patient-specific anticancer agents. Our results suggest that BET inhibitors could counteract cachexia at the transcriptional level in tumour and host tissues by reducing GDF15 expression. We identified characteristic gene and metabolite expressions of responsive cancer cell lines that can serve as biomarkers for patient selection.

overall_design: Small cell lung cell lines were grown in media and treated with either DMSO (control) or compound. BI 894999 (WO2014076237) is the clinical compound synthesized by Boehringer Ingelheim. The experiment was performed in biological duplicates per condition/cell lines. Information about sampling time points, compounds, compound concentrations, and replicates are detailed out in the respective sample descriptions. All samples were subjected to RNA isolation, followed by library preparation (TruSeq RNA Library Preparation Kit v2), and messenger RNA sequencing on an Illumina NextSeq 500 system.

first: Ulrike

last: Tontsch-Grunt

first: Schweifer

last: Norbert


title: GDF15 gene suppression by BET inhibition and gene signature based personalized chemotherapy to counteract cachexia

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

overall_design: Refer to individual Series


title: Nutritional and metabolic control of germ cell fate through O-GlcNAc regulation

status: Public on Jun 22 2023

city: Sendai

first: Yohei

last: Hayashi

state: Miyagi

address: 4-1 Seiryo-machi, Aobaku

department: Institute of Development, Aging and Cancer

institute: Tohoku University

summary: Fate determination of primordial germ cells (PGCs) is regulated in a multi-layered manner, involving signaling pathways, epigenetic mechanisms and transcriptional control. Epigenetic mechanisms are expected to be closely related with metabolic mechanisms but the detailed molecular machinery linking these two layers remain poorly understood. Here, we show that the hexosamine biosynthetic pathway controls PGC fate determination via O-linked -N-acetylglucosamine (O-GlcNAc) modification. Consistent with this model, reduction of carbohydrate metabolism via a maternal ketogenic diet that decreases O-GlcNAcylation levels causes repression of PGC formation in vivo. Further, the effect of maternal ketogenic diet intake until mid-gestation affected the number of ovarian germ cells in newborn pups. Taken together, we show that nutritional and metabolic mechanisms play a previously unappreciated role in PGC fate determination.

overall_design: To ivestigate the role of glucose and its metabolic pathways in germ cell formation, we  prepared the primordial germ cell-like cells (PGCLCs) cultured with or without glucose/ Further we preprared the PGCLCs cultured with OSMI-1, an O-GlcNAc transferase (OGT) inhibitor, to examine the contribution of O-GlcNAcylation in PGCLC induction. We then performed RNA-seq analysis of 4 different conditions with 2 biological replicates.


title: Spatiotemporal trajectory analysis and validation of microglia activation in traumatic brain injury

status: Public on Jul 03 2023

city: Spring Hill

first: Duy

middle: Truong

last: Pham

state: Queensland

address: 391 Wichkham Terrace

country: Australia

institute: The University of Queensland

summary: Spatial transcriptomics (ST) is an innovative technology that holds tremendous potential for transforming the field of tissue biology research. By simultaneously capturing multiple types of spatial data, including gene expression values, spatial distance information, and tissue morphology, ST enables a comprehensive understanding of biological samples. However, the effective integration of these diverse data types remains a challenge. In this study, we present stLearn, a collection of three computational-statistical algorithms specifically designed to exploit the combined power of gene expression, spatial distance, and tissue morphology data. Our aim is to unlock novel insights into tissue maintenance, development, and disease. The first algorithm, known as pseudo-time-space (PSTS), employs a spatial-graph-based approach to uncover the spatial relationships between cells' transcriptional states in dynamic tissue contexts. To demonstrate the effectiveness of stLearn, we utilize traumatic brain injury datasets to investigate the spatio-temporal dynamics of microglia activation. By applying the PSTS algorithm to a well-established mouse model of acquired brain injury, we successfully reconstruct the spatial trajectory of microglia activation following insult, thereby validating this key component of stLearn.

overall_design: We conducted an experimental study to investigate the spatio-temporal dynamics of microglia in the mouse brain following injury. The Visium ST data were acquired from the mouse brain at 3 days post-injury. To segment the brain regions, we employed stSME-based clustering, fine-tuning the clustering parameters using the Allen Mouse Brain Atlas. Next, we identified microglia-containing spots by examining the expression of marker genes, specifically Fcrls and Tmem119. To analyze the transcriptional dissimilarity between the injury site and different brain regions, we applied the PSeudo-Time-Space (PSTS) algorithm, which assigned a PTS score. Our analysis revealed that the hypothalamus region exhibited the greatest transcriptional dissimilarity compared to the injury site. To visualize the spatial trajectory of microglia activation, we utilized the PSTS algorithm to predict the minimum spanning tree connecting the damaged site and the hypothalamus. The resulting trajectory displayed the activation of microglia along the dorsoventral axis of the injured brain, with the directionality of transcriptional changes indicated by the arrows. Additionally, we compared the results with the mouse naive brain as a control to provide evidence for the spatio-temporal dynamics of microglia.

first: Quan

last: Nguyen

first: Xiao

last: Tan

first: Brad

last: Balderson

first: Jun

last: Xu

first: Laura

middle: F

last: Grice

first: Sohye

last: Yoon

first: Emily

last: Willis

first: Minh

last: Tran

first: Pui

middle: Y

last: Lam

first: Arti

last: Raghubar

first: Priyakshi

last: Kalita de Croft

first: Sunil

last: Lakhani

first: Jana

last: Vukovic

first: Marc

middle: J

last: Ruitenberg


title: Modeling Diabetic Endothelial Dysfunction with Patient-Specific Induced Pluripotent Stem Cells

status: Public on Jul 05 2023

city: Chicago

first: Yogesh

last: Goyal

state: IL

address: 303 E Superior St

institute: Northwestern University

summary: Diabetes is a known risk factor for various cardiovascular complications, mediated by endothelial dysfunction. Despite the high prevalence of this metabolic disorder, there is a lack of in vitro models that recapitulate the complexity of genetic and environmental factors associated with diabetic endothelial dysfunction. Here, we utilized human induced pluripotent stem cell (iPSC)-derived endothelial cells (ECs) to develop in vitro models of diabetic endothelial dysfunction. We found that the diabetic phenotype was recapitulated in diabetic patient-derived iPSC-ECs, even in the absence of a diabetogenic environment. Subsequent exposure with culture conditions that mimic the diabetic clinical chemistry induced a diabetic phenotype in healthy iPSC-ECs but did not affect the already dysfunctional diabetic iPSC-ECs. RNA-seq analysis revealed extensive transcriptome-wide differences between cells derived from healthy individuals and diabetic patients. The in vitro disease models were used as a screening platform which identified angiotensin receptor blockers (ARBs) that improved endothelial function in vitro for each patient. In summary, we present in vitro models of diabetic endothelial dysfunction using iPSC technology, taking into account the complexity of genetic and environmental factors in the metabolic disorder. Our study provides novel insights into the pathophysiology of diabetic endothelial dysfunction and highlights the potential of iPSC-based models for drug discovery and personalized medicine.

overall_design: Bulk paired end (61:8:8:61) RNA sequencing was done using MiRNeasy Micro Kit (Qiagen 217084) for extraction, NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490L), NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (E7770L), and NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (E7600S), as described previously (1,2). Prior to library preparation, the samples were randomized to avoid experimental and human biases. We started our experiments with a total of 24 samples (iPSCs and differentiated iPSCs-ECs) from healthy and disease patients. During library preparation, 2 DiPSC and 2 HiPSC-EC patient samples were excluded from sequencing due to insufficient RNA isolation. RNA-seq reads were pseudo-aligned to the human transcriptome (GRCH38 cDNA) utilizing Kallisto v0.48.0 to generate estimated gene count matrices(3). Count matrices were normalized and differential gene expression analyses were done with DESeq2 v1.38.3 using R v4.2.3 for each subgrouping comparison (4). The count matrix was further filtered for low expression counts such that any gene less than a total of 10 counts across samples cutoff were removed from downstream analysis. To compare between samples, differential gene expression data was extracted. The top 50 most up and down regulated genes (total 100, unless the number of differentially expressed genes were <100) were filtered utilizing an ordered Log2FC gene list and then used to generate corresponding comparisons within heat maps. GO analysis was performed using clusterProfiler in R. Scripts for all extraction and downstream differential expression analysis are provided at the Goyal laboratory GitHub: https://github.com/GoyalLab/Bulk-RNA-Jiang-Analysis.git .

first: Rayyan

last: Gorashi


title: Leveraging RNA-seq of bread wheat transcriptome to reveal diversity of RSA-related transcripts and their expression in contrasting environments

status: Public on Jun 29 2023

city: Islamabad

first: Saman

last: Maqbool

address: Shahdra Road

department: Plant Sciences

country: Pakistan

institute: Quaid-i-Azam University, Islamabad

summary: Root traits are significant targets for breeding stress-resilient and high-yielding wheat genotypes under climatic fluctuations. However, root transcriptome analysis is usually obscured due to challenges in root research. We performed transcriptome analysis of thirty bread wheat cultivars using RNA-seq to investigate the diversity and expression of root system architecture (RSA) related transcripts. We examined the expression patterns of these transcripts in both root and leaf tissues and found that various transcripts are root-specific which could be manipulated for desirable root traits.The presented RNA-seq datasets provide valueable source for identification of genes involved in various biological processes under varying climatic conditions.

overall_design: Thirty spring wheat cultivars with three biological replicates under optimum growth conditions

first: Awais

last: Rasheed


title: Dynamics of m6A RNA methylome during leukemogenesis reveals a role of IGF2BP2-PRMT6-MFSD2A signaling axis in maintaining AML stem cells

status: Public on Jun 20 2023

city: Wuhan

first: Haojian

last: Zhang

address: Donghu Rd.

institute: Wuhan University


title: Expression data from murine adipose tissue endothelial cells during pre-cachexia

status: Public on Jun 19 2023

city: Heidelberg

first: Andreas

last: Fischer

institute: DKFZ

summary:
Endothelial cells form a barrier between the contents of the blood and adipocytes. We hypothesized that during cancer cachexia development, transcriptomic changes alter angiocrine signals to contribute to adipose tissue remodelling.
We used microarrays to observe changes in gene expression in endothelial cells isolated from subcutaneous fat of mice during pre-cachexia.

overall_design: Adipose tissue endothelial cells were isolated from inguinal adipose tissue of KPC mice during pre-cachexia. RNA was extracted and subjected to hybridization on Affymetrix microarrays.

first: Jacqueline

last: Taylor


title: RNA-sequencing comparison of adipose tissue endothelial cells with Notch1 ICD overexpression

summary: RNA-sequencing was used to compare the transcriptome in white adipose tissue endothelial cells from humans which overexpressed N1ICD or GFP.

overall_design: Human adipose tissue endothelial cells from 6 patients were isolated and pooled. Samples were derived from either visceral (vWAT) or subcutaneous (sWAT) white adipose tissue. Adenoviruses were used to overexpress Notch1 ICD (NICD) or GFP.


title: Restoring Tumor Immunogenicity with Dendritic Cell Reprogramming [human RNA-Seq]

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

summary: Decreased antigen presentation contributes to the ability of cancer cells to evade the immune system. We used the minimal gene regulatory network of type 1 conventional dendritic cells (cDC1) to reprogram cancer cells into professional antigen- presenting cells (tumor-APCs). Enforced expression of the transcription factors PU.1, IRF8, and BATF3 (PIB) was sufficient to induce cDC1 phenotype in 36 cell lines derived from human and mouse hematological and solid tumors. Within 9 days of reprogramming, tumor-APCs acquired transcriptional and epigenetic programs associated with cDC1 cells. Reprogramming restored the expression of antigen presentation complexes and costimulatory molecules on the surface of tumor cells, allowing the presentation of endogenous tumor antigens on MHC-I, and facilitating targeted killing by CD8+ T cells. Functionally, tumor-APCs engulfed and processed proteins and dead cells, secreted inflammatory cytokines, and cross- presented antigens to naïve CD8+ T cells. Human primary tumor cells could also be reprogrammed to increase their capability to present antigen and to activate patient-specific tumor-infiltrating lymphocytes. In addition to acquiring improved antigen presentation, tumor-APCs had impaired tumorigenicity in vitro and in vivo. Injection of in vitro generated melanoma-derived tumor-APCs into subcutaneous melanoma tumors delayed tumor growth and increased survival in mice. Antitumor immunity elicited by tumor-APCs was synergistic with immune checkpoint inhibitors. Our approach serves as a platform for the development of immunotherapies that endow cancer cells with the capability to process and present endogenous tumor antigens.

overall_design: Population mRNAseq profiling of 17 human cancer cell lines and human embryonic fibroblasts (HEFs) after transduction with polycystronic vectors encoding PU.1, IRF8 and BATF3 at day 3, 5, 7 and 9. mRNA profilling of eGFP-transduced human cell lines and freshly isolated peripheral blood Dendritic cells type 1 (HLA-DR+CD11C+CD141+), Dendritic cells type 2 (HLA-DR+CD11C+CD141-CD1C+) and plasmacytoid dendritic cells (HLA-DR+CD11C-CD123+) were used as controls.

first: Olga

last: Zimmermannova

first: Carlos-Filipe

last: Pereira


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

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: H3R2me2a ChIP-seq of Prmt6-/- and Igf2bp2-/- leukemia cells

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: Dynamics of m6A RNA methylome during leukemogenesis reveals a role of IGF2BP2-PRMT6-MFSD2A signaling axis in maintaining AML stem cells [MeRIP-seq]

first: Haojian

last: Zhang

summary: Our data reveal that RNA m6A displays a sharp transition during leukemogenesis and involves in acquiring stem cell properties of leukemia stem cells (LSCs). We find that m6A reader IGF2BP2 and protein arginine methyltransferase PRMT6 play key roles in the acquisition of LSCs properties. Genetical deletion and pharmacological inhibition of PRMT6 delayed AML development. Mechanistically, IGF2BP2 regulates PRMT6 expression by stabilizing its mRNA in an m6A-dependent manner. PRMT6 further suppresses the expression of lipid transporter MFSD2A by establishing inactive H3R2me2a in its promoter region. Loss of PRMT6 and IGF2BP2 upregulates the expression of MFSD2A that increases the uptake of docosahexaenoic acid. Collectively, our findings uncover a critical role of IGF2BP2-PRMT6-MFSD2A signaling axis in AML development, and provide a promising therapeutic strategy for targeting LSCs.

overall_design: MeRIP-seq of LIC and BLAST cells sorted from WT mice BM leukemia cells.

first: Ying

first: Zhuying

first: Tiantian

first: Yuhua

first: Guoqiang


title: H3K27ac changes upon overexpression of the active NOTCH1 intracellular domain (N1ICD) in human adipose tissue endothelial cells.

status: Public on Jun 16 2023

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

summary: The Notch signaling pathway regulates several differentiation and developmental processes, and is involved in the development of a multitude of diseases. Here we investigate by ChIP-Seq the effects of overexpression of the active NOTCH1 intracellular domain (N1ICD) on H3K27ac in human adipose tissue endothelial cells.

overall_design: Human adipose tissue endothelial cells were infected with adenoviruses expressing either the active NOTCH1 intracellular domain (N1ICD) or green fluorescent protein (GFP) as a control. Effects on H3K27ac were investigated by ChIP-Seq.

first: Benedetto

last: Giaimo

first: Jacqueline

last: Taylor


title: AR/miR-221/IGF-1 pathway mediates the pathogenesis of androgenetic alopecia

city: Guangzhou

first: Yang

last: Sun

address: Nanfang Hospital

institute: Nanfang Hospital, Southern Medical University

summary: Our data showed that miR-221 had a profound effect on the biological function of dermal papilla cells (DPCs) and dermal sheath cells (DSCs) of hair follicle. Overexpression of miR-221 affected the MAPK signaling in DPCs, and PI3K/AKT signaling in DSCs.

overall_design: The effect of miR-221 overexpression on gene expression profile in cultured DPCs and DSCs

first: Kaitao

first: Zhiqi

first: Yong

last: Miao


title: Dynamics of m6A RNA methylome during leukemogenesis reveals a role of IGF2BP2-PRMT6-MFSD2A signaling axis in maintaining AML stem cells [Prmt6 RNA-seq]

overall_design: RNAseq of mice L-GMP cells sorted from WT and Prmt6-/- BM leukemia cells.

last: Cheng

last: Gao

last: Wang

last: Han

first: Yashu

last: Li

first: Peipei

first: Jin

last: Hu

first: Tong

first: Chengli

first: Jihua

first: Jing

first: Manman

first: Kexin

first: Weidong

first: Shuxin

first: Pengbo

first: Ziyan


title: Dynamics of m6A RNA methylome during leukemogenesis reveals a role of IGF2BP2-PRMT6-MFSD2A signaling axis in maintaining AML stem cells [IGF2BP2 RNA-seq]

first: Haojian

overall_design: RNAseq of AML leukemia cell line (Molm13).

first: Ying

first: Zhuying

first: Tiantian

first: Yuhua

first: Guoqiang

last: Guo

last: Chai

last: Cui

last: Liu

last: Yao

last: Lu

first: Yanbing

first: Jiwei

first: Rong


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

status: Public on Jun 14 2023

city: La Jolla

first: Jesse

middle: R

last: Dixon

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: Investigation of 3D chromatin architecture using Hi-C experiments during mouse T-cell maturation, with a focus on T-reg development in both wild-type and mutant T-regs


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

last: Zhang


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

status: Public on Jun 13 2023

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

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: HiChIP assays of H3K4me3 in wild-type zebrafish whole embryos, at developmental stage 80% epiboly, 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

last: Gómez-Skarmeta

first: Juan

last: Tena