title: Uncovering the role admixture in health disparities: Association of hepatocyte gene expression and DNA methylation to African Ancestry in African-Americans [RNA-seq]

first: Minoli

last: Perera

state: Illinois

address: 303 E. Chicago Avenue, Ward 9-188

department: Pharmacology

summary: In African Americans (AA), the proportion of West African ancestry (WAA) may explain the genetic drivers of health disparities in disease. Analysis of RNA sequencing data from sixty AA-derived primary hepatocytes identified 32 gene expression profiles associated with WAA (FDR <0.05) with enrichment in angiogenesis and inflammatory pathways (FDR <0.1). Association of DNA methylation to WAA identified 1037 differentially methylated regions (FDR <0.05), with hypomethylated genes enriched for drug response pathways. Within the PharmGKB pharmacogene, VDR, PTGIS, ALDH1A1, CYP2C19 and P2RY1 were associated with WAA (p <0.05) with replication of CYP2C19 and VDR in the GTEx liver cohort. For every 1% increment in WAA, P2RY1 gene expression increased by 1.6% and CYP2C19 gene expression decreased by 1.4%, suggesting effects on clopidogrel response and platelet aggregation. We conclude that WAA contributes to variablity in hepatic gene expression and DNA methylation with identified genes indicative of health disparities prevalent in AAs.

overall_design: RNA samples from cultured liver hepatocytes were used for RNA-Seq of 6 different drug treatments (Omeprazole, Phenobarbital, Dexamethasone, Carbamazepine, Phenytoin, and Rifampicine)

first: C

last: Park

first: T

last: De

first: Y

last: Zhong

first: E

last: Smithberger

last: Alarcon

last: Gamazon

first: M

middle: A


title: Chromatin accessibility analysis of  inducible HOTAIR overexpression mouse breast cancer cells

status: Public on Jan 10 2023

city: Shenzhen

first: Qing

last: Ma

address: 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, P.R.China

country: China

institute: Shenzhen Institutes of Advanced Technology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: HOTAIR is a 2.2 kb long noncoding RNA (lncRNA) whose dysregulation has been linked to oncogenesis, defects in pattern formation during early development, and irregularities during the process of epithelial-to-mesenchymal transition (EMT). However, the oncogenic transformation determined by HOTAIR in vivo and its impact on chromatin dynamics are incompletely understood. Here we generate a transgenic mouse model with doxycycline-inducible expression of human HOTAIR in the context of the MMTV-PyMT breast cancer-prone background (iHOT-PyMT mice) to systematically interrogate the cellular mechanisms by which human HOTAIR lncRNA acts to promote breast cancer progression. We isolated breast cancer cells from the primary tumors of iHOT-PyMT mice (named iHOT+ cells) and performed RNA-seq and ATAC-seq of iHOT+ cells treated with 3 conditions: Dox+, Dox- and DoxWD. We showed that HOTAIR overexpression altered both the cellular transcriptome and chromatin accessibility landscape of multiple metastasis-associated genes and promoted epithelial to mesenchymal transition. These alterations are abrogated within several cell cycles after HOTAIR expression is reverted to basal levels, indicating an erasable lncRNA-associated epigenetic memory. These results suggest that a continual role for HOTAIR in programming a metastatic gene regulatory program.

overall_design: The iHOT+ cells were treated with 3 conditions: Dox+ HOTAIR overexpressing cells which were consistently treated with Dox for several days; DoxWD cells which had been temporarily treated with Dox and later withdrawn from HOTAIR overexpression; and Dox- untreated control cells in which HOTAIR remained at baseline levels. Chromatin accessibility profiles in iHOT+ cells with different treatments were generated by ATAC-seq using the Illumina Genome Analyzer IIX platform.

first: Karen

last: Tolentino

first: Yang

last: Zhao

first: Lingjie

last: Li


title: Determination of the transposon insertion effect in Tn::Psrg mutant by RNA-seq

city: Grenoble

first: Manon

last: Janet-Maitre

address: 71 Avenue des Martyrs

country: France

institute: IBS

type: Expression profiling by high throughput sequencing

summary: Determination of the effect of transposon insertion in Tn::Psrg mutant by RNA-seq in Pseudomonas aeruginosa IHMA87

overall_design: RNA-seq analysis of Tn::Psrg mutant vs WT in Pseudomonas aeruginosa IHMA87, in liquid cultures grown to OD=1 at 37°C, in duplicates

first: Ina

last: Attrée


title: Inducible lncRNA transgenic mice reveal continual role of HOTAIR in promoting breast cancer metastasis

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

overall_design: Refer to individual Series


title: Expression data of S1M cells sorted high and low after ST2 antibody treatment

city: ChunCheon-si

first: Jun Won

address: Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Kangwondaehak-gil

country: South Korea

institute: kangwon national univercity

summary:
ST2 functions as a receptor for the cytokine IL-33. It has been implicated in carcinogenesis. In this study, we sought to mechanistically determine how ST2 and IL-33 function to support cancer stem cell (CSC) activity and drive gastric cancer (GC) pathogenesis.
We used microarrays to detail the global program of gene expression among S1M ST2 high and low cells and to identify distinct classes of genes upregulated in this process.

overall_design: ST2 high and low cells (2 samples) were successfully isolated using a Flow Cytometry Sorter and selected at a continuous stage of early development for RNA extraction and hybridization on Affymetrix microarrays.


title: Highly concentrated trehalose induces prohealing senescence-like state in fibroblasts via CDKN1A/p21

city: Toon

first: Jun

last: Muto

address: Shitsukawa 454

department: Department of Dermatology

country: Japan

institute: Ehime University Graduate School of Medicine

summary: Trehalose is the nonreducing disaccharide of glucose, evolutionarily conserved in invertebrates. The living skin equivalent (LSE) is an organotypic coculture containing keratinocytes cultivated on fibroblast-populated dermal substitutes. We demonstrated that human primary fibroblasts treated with highly concentrated trehalose promote significantly extensive spread of the epidermal layer of LSE without any deleterious effects. The RNA-seq analysis of trehalose-treated 2D and 3D fibroblasts at early time points revealed the involvement of the CDKN1A pathway, the knockdown of which significantly suppressed the upregulation of DPT, ANGPT2, VEGFA, EREG, and FGF2. The trehalose-treated fibroblasts were positive for senescence-associated β-galactosidase. Finally, transplantation of the dermal substitute with trehalose-treated fibroblasts accelerated wound closure and increased capillary formation significantly in the experimental mouse wounds in vivo, which was canceled by the CDKN1A knockdown. These data indicate that high-concentration trehalose can induce the senescence-like state in fibroblasts via CDKN1A/p21, which may be therapeutically useful for optimal wound repair.

overall_design: RNA-seq analysis of human primary fibroblasts and keratinocytes treated with or without trehalose.

first: Shinji

last: Fukuda

first: Kenji

last: Watanabe

first: Xiuju

last: Dai

first: Teruko

last: Tsuda

first: Takeshi

last: Kiyoi

last: Kameda

first: Ryosuke

last: Kawakami

first: Hideki

last: Mori

first: Ken

last: Shiraishi

first: Masamoto

last: Murakami

last: Imamura

first: Shigeki

last: Higashiyama

first: Yasuhiro

last: Fujisawa

first: Yoichi

last: Mizukami

first: Koji

last: Sayama


title: RSPO4 is a potential risk gene of stages III–IV, grade C periodontitis through effects on innate immune response and oral barrier integrity

status: Public on Jan 09 2023

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health, Charité Medical University of Berlin

summary: Aim  R-spondin 4 (RSPO4) is a suggestive risk gene of stage III–IV, grade C periodontitis and upregulated in gingiva of mice resistant to bacteria-induced alveolar bone loss. We aimed to replicate the association, identify and characterize the putative causal variant(s) and molecular effects, and understand the downstream effects of RSPO4 upregulation.    Materials and Methods  We performed a two-step association study for RSPO4 with imputed genotypes of a German–Dutch (896 stage III–IV, grade C periodontitis cases, 7104 controls) and Spanish sample (441 cases and 1141 controls). We analysed the allelic effects on transcription factor binding sites with reporter gene and antibody electrophoretic mobility shift assays. We used CRISPR/dCas9 activation and RNA sequencing to pinpoint RSPO4 as the target gene and to analyse downstream effects.    Results  RSPO4 was associated with periodontitis (rs6056178, pmeta = 4.6 × 10−5). rs6056178 contains a GATA-binding motif. The rs6056178 T-allele abolished reporter activity (p = .004) and reduced GATA binding (−14.5%). CRISPRa of the associated region increased RSPO4 expression (25.8 ± 6.5-fold, p = .003). RSPO4 activation showed strongest induction of Gliomedin (439-fold) and Mucin 21 (178-fold) and of the gene set “response to interferon-alpha” (area under the curve [AUC] = 0.8, p < 5 × 10−6). The most repressed gene set was “extracellular matrix interactions” (AUC = 0.8, padj = .00016).    Conclusion  RSPO4 is a potential periodontitis risk gene and modifies host defence and barrier integrity.

overall_design: Differences in gene expression between control HeLa cells and HeLA cells with overexpressed RSPO4 after CRISPR-dCas9 activation

first: Arne

last: Schaefer

first: Avneesh

last: Chopra


title: Single cell RNA-seq data for studying human intervertebral discs and the mechanism of discogenic low back pain

city: Los Angeles

first: Wensen

last: Jiang

state: CA

address: 127 S San Vicente Blvd

department: Board of Governors Regenerative Medicine Institute

country: USA

institute: Cedars-Sinai Medical Center

summary: We report the single cell RNA-seq (scRNA-seq) data for human intervertebral discs.

overall_design: Examining single-cell atlases and transcriptomes of human intervertebral discs (IVDs), including the asymptomatic group (aIVD) and back pain group (bpIVD), another group harvested from human IVDs followed by in vitro culture with stressors (sIVD), and another group harvested from human IVDs followed by in vitro culture with no stressor (nsIVD)

first: Dmitriy

last: Sheyn


title: Chromatin-associated OGT promotes hepatocellular carcinoma malignancy via activating ZNF263 [RNA-seq]

city: Panjin

first: Yubo

last: Liu

address: Dagong Lu

institute: Dalian University of Technology

summary: The reversible and dynamic O-GlcNAcylation regulates vast networks of highly coordinated cellular and nuclear processes. Despite the dysregulation of the sole enzyme O-GlcNAc transferase (OGT), is showed to associated with the progression of hepatocellular carcinoma (HCC), the mechanisms by which OGT controls the cis-regulatory elements in the genome and achieves transcriptional functions remain unclear. Here, we demonstrate that the elevated OGT increases HCC proliferation and metastasis by orchestrating the transcription of numerous malignant regulators in vitro and in vivo. Diverse transcriptional regulators are recruited by OGT in HCC cells with progressive malignancy, which shapes the genome-wide OGT chromatin cis-elements occupation. Further, an unrecognized cooperation between ZNF263 and OGT is crucial for activating downstream transcriptomics. We reveal that the O-GlcNAcylation site Ser662 is responsible for ZNF263 chromatin association at candidate gene promoters and OGT facilitated HCC the malignant phenotypes. Our data establish the importance of aberrant OGT and ZNF263 O-GlcNAcylation in HCC malignant progression, and represents the pursuit of OGT as a target for HCC therapy.

overall_design: We performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using anti-Flag magnetic beads in Flag-OGT stably expressed MHCC-97H and MHCC-97L cells. ZNF263 ChIP-seq was performed using anti-ZNF263 antibody in the above cells. Next, ZNF263 was knockdown by shRNA in 97H/OGT and 97L/OGT cells. HA-ZNF263-WT and HA-ZNF263-S662A ChIP-seq were performed using anti-HA magnetic beads in ZNF263 knockdown cells. Next-generation sequencing libraries were generated and amplified for 15 cycles. 100-300 bp DNA fragments were gel-purified and sequenced with an Illumina NovaSeq 6000 instrument by Novogene Technology (Beijing, China). Two biological replicates of each ChIP-seq were performed. We also analyzed gene expression in Flag-OGT expressed cells by RNA-seq.

first: Lingyan

last: Wang

first: Yajie


title: Chromatin-associated OGT promotes hepatocellular carcinoma malignancy via activating ZNF263.


title: Gene expression alterations in the cell lines Jurkat, THP1, and KHYG-1 upon treatment with glycodelin from non-small-cell lung cancer cell line supernatant

city: Heidelberg

first: Sarah

last: Richtmann

address: Roentgenstr. 1

department: Translational Research Unit

institute: Thoraxklinik Heidelberg

summary: The function of glycodelin A in the endometrium, during the menstrual cycle, and before or during pregnancy is well characterized. Numerous studies have investigated the highly pleiotropic effects and the modulation of different leukocytes upon glycodelin interaction.  In NSCLC, the function of glycodelin is not known, yet. While it was shown to be highly expressed in lung tumor tissue compared to normal lung, the functionality and possible immunomodulating characteristics remain to be described.

overall_design: The three different immune cell lines Jurkat, THP1, and KHYG-1 were treated with glycodelin containing cell culture supernatant derived from a NSCLC cell line. Differential expression upon glycodelin treatment was assessed and further pathway analyses were performed.

first: Elisabeth

middle: X

last: Meister

first: Marc

last: Schneider


title: RNA-seq analysis of L1 arrest linc-133(aqz 3) and WT worms

city: Kaifeng

first: Shanqing

last: Zheng

address: 1 Jinming Avenue North, Longting District,  School of Basic Medical Sciences, Henan University

institute: Henan university

summary: We used RNA-seq analysis to identify changes in gene expression occurring in linc-133 (aqz 3) mutants comparing with that in wild type (N2) worms during L1 arrest stage.  Basing on these sequencing data, genes which were up-regulated or down-regulated by at least 2 times( |log2(FoldChange)| ≥ 1 and padj ≤ 0.05) subsequent to WT worms were analyzed. These differentially expressed genes were analyzed for pathway and gene ontology (GO) enrichment, which indicated that the genes influenced by aqz 3 mutation of linc-133 gene were enriched in several significant signaling pathways, including longevity, protein degradation in endoplasmic reticulum pathway, and fat metabolism pathways.

overall_design: mRNA profiles of linc-133(aqz 3) and wild type (WT)  were generated by deep sequencing. using Illumina GAllx


title: Single cell transcriptome of mouse aortas underlying Apoe−/− mice and EC-iDKO/Apoe−/− mics.

city: Nanjing

first: Mulong

last: Du

state: Jiangsu

address: 101 Longmian Avenue

institute: Nanjing Medical University

summary: To investigate whether epsins play a role in EndoMT, we performed scRNAseq analysis in atherosclerotic Apoe−/− mouse model.

overall_design: Apoe−/− and EC-iDKO/ Apoe−/− mice were fed western diet (WD) for 12 weeks, followed by the isolation of aortas and enzymatic digestion and scRNA seq.

first: Yunzhou

last: Dong

first: Hong

last: Chen


title: Chromatin organization drives the exploration strategy of nuclear factors

city: Milan

first: Davide

last: Mazza

address: via Olgettina 58

country: Italy

institute: Università Vita-Salute San Raffaele

summary: The transcription factor p53 is activated in response to DNA damage. To identify the genes that are directly and indirectly regulated by p53 in the U2OS-derived DIvA cells, we performed RNAseq analysis following DNA damage. We induce DNA damage by using 4OHT, which activates the endonuclease AsiSI in this cell line leading to the formation of DNA double strand breaks. We compared p53 wild-type cells to p53 knock-out cells.

overall_design: RNAseq analysis of p53 WT and p53 KO DIvA cells treated with 300nM 4-OHT for 5 hours.

first: Matteo

last: Mazzocca

first: Emanuele

last: Monteleone


title: Effects of nitric oxide and NCX4040 on the reversal of drug resistance in human tumor cells

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Ovarian tumor cells (OVCA-8 and its reistant variant) were treated with NCX4040 for different times in 10% FBS and RNA was isolated by triazol method

overall_design: OVCAR and NCI/ADR-RES cells were treated with NCX at 4 hr, 24hr, and 48hr.  Each treatment group has three replicates.

first: Birandra

middle: K

last: Sinha


title: Direct TLR2 signaling through mTOR and TBK1 induces C/EBPβ and IRF7-dependent macrophage differentiation in hematopoietic stem and progenitor cells

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

country: Spain

institute: Universitat de Valencia

summary: During an infection, hematopoiesis is altered to increase the output of mature myeloid cells to fight off the pathogen. Despite convincing evidence that hematopoietic stem and progenitor cells (HSPCs) can sense pathogens directly, more mechanistic studies are needed to reveal whether pattern recognition receptor (PRR) signaling initiates myeloid development directly, or indirectly through the production of cytokines by HSPCs that can act in an autocrine/paracrine manner, or by a combination of both direct and indirect mechanisms. In this study, we have used an in vitro model of murine HSPCs to study myeloid differentiation in response to the TLR2 ligand Pam3CSK4 and showed that, besides indirect mechanisms, TLR2 stimulation of HSPCs promotes myelopoiesis directly by initiating a MyD88-dependent signaling. This direct differentiation program involves a combined activation of the transcription factors PU.1, C/EBPβ and IRF7 driven by TBK1 and PI3K/mTOR. Notably, downstream of MyD88, the activated TBK1 kinase can activate mTOR directly and IRF7 induction is mediated by both TBK1 and mTOR. TLR2 signaling also induces NF-κB dependent IL-6 production that may further induce indirect myeloid differentiation. Our results have identified the direct signaling pathways and the transcription factors involved in macrophage development from HSPCs in response to TLR2 engagement, a critical process to trigger a rapid immune response during infection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Pam3CSK4 treated vs control hematopoietic stem and progenitor cells.

first: C

last: Bono

first: P

last: Guerrero

first: A

last: Jordán-Pla

last: Yáñez

first: M

middle: L

last: Gil


title: Longitudinal Profiling in Patients Undergoing Cardiac Surgery Reveals Postoperative Changes in DNA Methylation

first: Matthew

last: Fischer

address: 650 Charles Young Dr

department: Anesthesiology and Perioperative Medicine

institute: University of California, Los Angeles

type: Methylation profiling by high throughput sequencing

summary: Cardiac surgery and cardiopulmonary bypass induce a substantial immune and inflammatory response, the overactivation of which is associated with significant complications. Longitudinal DNA methylation profiling allows the potential to identify changes in gene regulatory mechanisms that are secondary to surgery and to identify molecular processes that predict and/or cause postoperative complications. In this study, we measure DNA methylation in preoperative and postoperative whole blood samples from 96 patients undergoing cardiac surgery on cardiopulmonary bypass. We identify several loci with statistically significant postoperative changes in methylation. Additionally, two of these loci are associated with new-onset postoperative atrial fibrillation, a significant complication after cardiac surgery. This research establishes that there are statistically significant changes in DNA methylation that occur immediately after cardiac surgery and that these acute alterations in DNA methylation have the granularity to identify processes associated with major postoperative complications.

overall_design: Identify changes in DNA methylation after cardiac surgery

first: Douglas

middle: J

last: Chapski

first: Elizabeth

last: Soehalim

first: Dennis

last: Montoya

first: Tristan

last: Grogan

last: Pellegrini

first: Hua

last: Cai

first: Richard

last: Shemin

first: Thomas

middle: M

last: Vondriska


title: Comparison of single-nuclei 5’ versus 3’-RNA-seq approaches: utility for somatic variant detection

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

summary: Somatic mosaic variants are a major cause of human disease, including cancer and focal epilepsies, but can be challenging to study due to their mosaicism in bulk tissue biopsies. Coupling single-cell genotype and transcriptomic data has potential to provide insight into the role somatic variants play in disease etiology, such as by determining what cell types are affected or how the mutations affect gene expression. Here, we asked whether commonly used single-cell 3’- or 5’-RNA-sequencing assays can be used to derive single-cell genotype data for a priori known variants that are located near to either end of a transcript. To that end, we compared performance of commercially available single-cell 3’- and 5’- gene expression kits using resected brain samples from three pediatric patients with focal epilepsy. We quantified the ability to detect genetic variants in single-cell datasets depending on distance from the transcript end. Finally, we demonstrated the ability to identify affected cell types in a patient with a RHEB somatic variant causing an epilepsy-associated cortical malformation. Our results demonstrate that native single-cell 3’ or 5’-RNA-sequencing data can be used successfully to genotype single-cells for somatic variants that are expressed within proximity to a transcript end.

overall_design: We established a workflow to compare performance between the 10x Genomics Chromium NextGEM Single-Cell 3’ and 5’ gene expression kits and evaluate detection of known germline and somatic variants in the resulting datasets (Fig. 1). For these analyses, we obtained frozen resected brain tissue from three pediatric patients treated for focal epilepsy and enrolled in an IRB-approved research protocol. In a previous study, germline and somatic variants were identified in bulk tissue samples via exome sequencing analysis [7]. In this study, we performed single-nuclei RNA-sequencing (snRNA-seq) on remaining material cut from the same tissue section (Fig. 1a). To evaluate performance of the 3’ vs. 5’ gene expression kits, we compared QC metrics, gene expression, cell type clustering, and marker gene efficacy. For variant analysis we evaluated the detection rate of both germline and somatic variants depending on distance from the transcript end and expression level of each gene of interest (Fig. 1b). Finally, as a proof-of-concept, we identified cell types expressing a disease-causing RHEB variant using single-nuclei 5’-RNA-seq data (Fig. 1c).

first: Sydney

last: Townsend

first: Tracy

last: Bedrosian


title: Chromatin-associated OGT promotes hepatocellular carcinoma malignancy via activating ZNF263 [ChIP-seq]

first: Yubo

last: Liu

overall_design:
We performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using anti-Flag magnetic beads in Flag-OGT stably expressed MHCC-97H and MHCC-97L cells. ZNF263 ChIP-seq was performed using anti-ZNF263 antibody in the above cells. Next, ZNF263 was knockdown by shRNA in 97H/OGT and 97L/OGT cells. HA-ZNF263-WT and HA-ZNF263-S662A ChIP-seq were performed using anti-HA magnetic beads in ZNF263 knockdown cells. Next-generation sequencing libraries were generated and amplified for 15 cycles. 100-300 bp DNA fragments were gel-purified and sequenced with an Illumina NovaSeq 6000 instrument by Novogene Technology (Beijing, China). Two biological replicates of each ChIP-seq were performed. We also analyzed gene expression in Flag-OGT expressed cells by RNA-seq.
Antibody used for the study:
anti-Flag magnetic beads (Bimake, #B26102), anti-HA-magnetic beads (Bimake, #B26202), anti-ZNF263 antibody (Invitrogen, #PA5-95772, 1:50, added with protein A/G-magnetic beads), anti-H3K27ac antibody (CST, #8173, 1:50, added with protein A/G-magnetic beads), and anti-H3K4me3 antibody (CST, #9751, 1:50, added with protein A/G-magnetic beads) in this study.

first: Lingyan

last: Wang

first: Yajie


title: Modulation of radiation biomarkers in a randomized phase II study of 131I-MIBG with or without radiation sensitizers for relapsed or refractory neuroblastoma

city: Livermore

last: Coleman

address: 7000 East Avenue

institute: Lawrence Livermore National Laboratory

summary: Background  131I-metaiodobenzylguanidine (131I-MIBG) has demonstrated efficacy as a single agent in neuroblastoma.  Recent trials have focused on 131I-MIBG combination strategies, though little is known about the impact of combination agents on markers of radiation exposure.      Methods   Trial NANT11-01 (NCT02035137) evaluated 131I-MIBG therapy alone (Arm A) or in combination with vincristine/irinotecan (Arm B) or vorinostat (Arm C) for patients with relapsed or refractory neuroblastoma.  We collected blood samples before and after 131I-MIBG infusion and determined levels of radiation-associated biomarkers. We evaluated marker association with treatment arm, clinical response, and toxicity.    Results   The cohort included 99 patients who had at least one biomarker available for analysis. We observed significant modulation in most biomarkers between baseline, 72 hours, and 96 hours following 131I-MIBG. Patients in Arm C had the lowest degree of modulation in FLT3 ligand. Lower baseline BCL2 levels were associated with higher overall response.  Patients with greater increases in FLT3 ligand at 96 hours after 131I-MIBG therapy were significantly more likely to have grade 4 thrombocytopenia.  Peripheral blood gene expression of the BCL2 family of apoptotic markers (BCL2/L1 and BAX) was significantly associated with grade 4 hematologic toxicity.  RNA sequencing demonstrated little overlap in the top modulated peripheral blood transcripts between randomized arms.       Conclusions   Peripheral blood biomarkers relevant to radiation exposure demonstrate significant modulation after 131I-MIBG and concomitant radiation sensitizers impact extent of modulation. Biomarkers related to hematopoietic damage and apoptosis were associated with hematologic toxicity.

overall_design: Comparative study of human peripherlal blood samples (clinical trial NANT11-01 (NCT02035137)) evaluating 131I-MIBG therapy alone (Arm A) or in combination with vincristine/irinotecan (Arm B) or vorinostat (Arm C) for patients with relapsed or refractory neuroblastoma.

first: Kevin

last: Campbell

first: Susan

last: Groshen

first: Angela

last: Evans

first: Stephen

last: Wilson

first: Aimy

last: Sebastian

first: Gaby

last: Loots

first: Araz

last: Marachelian

first: Myriam

last: Armant

first: Sharmistha

last: Pal

first: Daphne

last: Haas-Kogan

first: Julie

middle: R

last: Park

first: Meaghan

last: Granger

last: Matthay

first: Steven

middle: G

last: DuBois


title: A multiplexed in vivo gene knockout approach to identify cancer drivers in small cell lung cancer [RNAseq]

city: Stanford

first: Myung Chang

last: Lee

address: 265 Campus Drive, G2065

department: Pediatrics and Genetics

institute: Stanford University

summary: We generated a model of lentivirus-initiated mouse small cell lung cancer (SCLC) combined with CRISPR/Cas9 knockout and barcoding. We analyzed tumor suppressive functions of 39 gene candidates using these in vivo CRISPR screening approaches and found Tsc1 to be one of the top tumor suppressor genes in SCLC.

overall_design: mRNA profiles of tumors initiated from Rb/p53/Rbl2-mutant (RPR2) mouse model using adenoviral and lentiviral vectors, with or without naphthalene treatment.

first: Myung

middle: C

first: Julien

last: Sage


title: A multiplexed in vivo gene knockout approach to identify cancer drivers in small cell lung cancer [LCM Tuba-seq]

overall_design: mRNA profiles of tumors initiated from Rb/p53/Rbl2-mutant (RPR2) mouse model using adenoviral and lentiviral vectors, as well as sequencing of sgRNA identifier-barcode (sgID-BC) amplicons from genomic DNA extracted from whole mouse lung or laser capture microdissected sections.


title: A multiplexed in vivo gene knockout approach to identify cancer drivers in small cell lung cancer [SCLC Tuba-seq]


title: Expression data from C. elegans harboring type 1-like and type 2-like calreticulin mutations of MPN patients

city: Pamplona

first: José Luis

last: Vizmanos

state: Navarra

address: Irunlarrea, 1

department: Department of Biochemistry and Genetics

institute: University of Navarra

summary:
There is growing evidence that Ph-negative myeloproliferative neoplasms (MPNs) are blood cancers in which multiple molecular mechanisms are significantly disturbed. Since their discovery in 2016, CALR (calreticulin) type 1 and type 2 driver mutations have been demonstrated to trigger pathogenic mechanisms apart from the well-documented activation of JAK2/MPL-related pathways affecting these diseases. C. elegans seems to be a suitable model for the study of these mechanisms since they have a CALR ortholog (crt-1) but have no JAK or MPL ortholog.
We used microarrays in C. elegans strains harboring patient-like calreticulin mutations to identify JAK/MPL-independent molecular mechanisms derived from mutant calreticulin and identified a significant disruption of some of the typically altered biological processes in cancer and Ph-negative MPN patients. Finally, we compared the expression of the genes participating in these processes with a calreticulin knockout strain in order to examine if the alteration of these processes is a consequence of a gain or a loss of function of the mutant protein.

overall_design: C. elegans calreticulin-mutated strains and the wild-type strain (N2 Bristol) were synchronized and selected at the late L4 developmental stage for RNA extraction and hybridization of Affymetrix microarrays. Three samples per strain were analyzed in all cases, except for type 1 mutants and the knockout strain.

first: Ana

last: Guijarro-Hernández

first: Laura

last: Eder-Azanza

first: Cristina

last: Hurtado

first: José


title: RNA-seq of WT and p27KO

first: Antonio

last: Jordan

summary: Cell differentiation involves profound changes in global gene expression that often have to occur in coordination with cell cycle exit. Because cyclin-dependent kinase inhibitor p27 reportedly regulates proliferation of neural progenitor cells in the subependymal neurogenic niche of the adult mouse brain, but can also have effects on gene expression, we decided to molecularly analyze its role in adult neurogenesis and oligodendrogenesis. At the cell level, we show that p27 restricts residual cyclin-dependent kinase activity after mitogen withdrawal to antagonize cycling, but is not essential for cell cycle exit. Contrasting gene expression with chromatin accessibility, we find that p27 is coincidentally necessary to globally repress many genes involved in the transit from multipotentiality to differentiation, including those coding for neural progenitor transcription factors SOX2, OLIG2, and ASCL1. Our data reveal both direct association of p27 with regulatory sequences in the three genes and an additional hierarchical relationship where p27 repression of the Sox2 gene leads to reduced levels of SOX2-downstream targets Olig2 and Ascl1. In vivo, p27 is also required for the regulation of the proper level of SOX2 necessary for neuroblasts and oligodendroglial progenitor cells to timely exit cell cycle in a lineage-dependent manner.

overall_design: 3 DIV proliferating WT and p27KO neurospheres and WT and p27KO NPs at the onset of differentiation (2+1 DIV) were harvested for RNA extraction. Between 2 and 3 biological replicates per condition and genotype.

last: Domingo-Muelas

first: Jose

last: Morante-Redolat

first: Verónica

last: Moncho-Amor

last: Jordán-Pla

first: Robin

last: Lovell-Badge

first: Isabel

last: Farinas


title: ATAC-seq of WT and p27KO

overall_design: Nuclei from 3 DIV proliferating WT and p27KO neurospheres and WT and p27KO NPs at the onset of differentiation (2+1 DIV) were harvested for ATAC preparaton. Between 2 and 3 biological replicates per condition and genotype.


title: WT and p27KO

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

overall_design: Refer to individual Series


summary:
RNA-seq, LCM sequencing, and Tuba-seq data for the article titled, "A multiplexed in vivo gene knockout approach to identify cancer drivers in small cell lung cancer."
This SuperSeries is composed of the SubSeries listed below.


title: Selective autophagic degradation of ATP citrate lyase maintains citrate homeostasis and promotes oocyte maturation

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

summary: Autophagy is a cellular and energy homeostatic mechanism that contributes to maintain the number of primordial follicles, germ cell survival, and anti-ovarian aging. However, it remains unknown whether autophagy in granulosa cells affects the oocyte maturation. Here, we show a clear tendency of reduced autophagy level in human granulosa cell from women of advanced maternal age, implying a potential negative correlation between autophagy level and oocyte quality. We therefore established a co-culture system and show that either pharmacological inhibition or genetic ablation of autophagy in granulosa cells negatively affect the oocyte quality and fertilization ability. Moreover, our metabolomics analysis indicates that the adverse impact of autophagy impairment on oocyte quality is mediated by downregulated citrate levels, while exogenous supplementation of citrate can significantly restore the oocyte maturation. In molecular level, we found ATP citrate lyase (Acly), which is a crucial enzyme catalyzing the cleavage of citrate, was preferentially associated with K63-linked ubiquitin chains and recognized by the autophagy receptor protein SQSTM1/p62 for the selective autophagic degradation. In human follicles, autophagy levels in granulosa cells was downregulated with maternal aging, accompanied by decreased citrate in the follicular fluid, implying a potential correlation between citrate metabolism and oocyte quality. We also show that elevated citrate levels in porcine follicular fluid promote oocyte maturation. Collectively, our data reveal that autophagy in granulosa cells is a beneficial mechanism to maintain a certain degree of citrate by selectively targeting Acly during oocyte maturation.

overall_design: The RNA-Seq experiments of the control and Atg5 KD cumulus granulosa cells.

first: Hainan

last: He

first: Junling

last: Wang

first: Jilong

last: Zhou

first: Yi-Liang

last: Miao


title: Next Generation Sequencing Facilitates Quantitative Analysis of over-expression of Wild Type TEAD4 and K178R mutant in HCT116 CELL

city: shanghai

first: Zhenyu

last: Huang

address: NO. 1665 kongjiang RD.

institute: Colorectal Cancer Research Center of Shanghai

summary: To investigate the Gene expression profiles of the HCT116 stable cells of TEAD4 and its mutant .

overall_design: Examination   mRNA profiles of the HCT116 stable cells of wild type TEAD4 and its mutant.

first: Huang

last: zhenyu

first: Liu

last: chen-ying


title: Next Generation Sequencing of Exosomal and Cellular miRNAs Between hCEp and Siha

city: Guangzhou

first: Chenfei

state: Guangdong

address: No.151, Yanjiang Road, Yuexiu District, Guangzhou

department: Obstetrics and Gynecology

institute: The First Affiliated Hospital of Guangzhou Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the differences in miRNA profiles, exosomal and cellular miRNA profiles between hCEp (Human Cervical Epithelia Cells) and Siha cells were generated by deep sequencing, in triplicate, using Illumina GAIIx. qRT–PCR validation was performed using TaqMan and SYBR Green assays

overall_design: Exosomal and cellular miRNA profiles between hCEp (Human Cervical Epithelia Cells) and Siha cells were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Wei

first: Sha

last: Wu


title: A cost effective process development for enhanced expression of antibody fragment in microbial cells, its impact on cellular physiology and transcriptome

city: NEW DELHI

first: Anurag

middle: Singh

last: Rathore

state: DELHI

address: Lab no. 356, Block III

department: Chemical Engineering

country: India

institute: Indian Institute of Technology

summary: A process for manufacturing the recombinant Ranibizumab has been developed with overall productivity of 0.72±0.02 mg/ml. Initially this study was attempted to find critical medium components based on literature. Among all the additives, glutamine, proline, arginine and ethanol showed increase in protein production compared to control. There was approximately 2 fold increase in Ranibizumab production in all the four additives analyzed using RP HPLC. Addition of glutamine, arginine and proline amino acids resulted in enhanced protein production however, the pH of the medium changed variably (pH 3.5-6.0). Since economic considerations decides the longevity of the process, as it plays a major role when large-scale operations are considered. Therefore, after economical potential analysis ethanol was finalized as the medium additive. Later, its effect was checked on cell size (control 1.82 µm and optimized 2µm), cellular physiology (no cell swelling or shrinkage was observed, cell width and length came out almost same in both the cases) and cellular viability (was found even better in optimized). Later, RNAseq was also performed to find out the underlying mechanism. Based on the literature as well as transcriptomic analysis and RT-qPCR validation, changes in membrane properties and DNA synthesis resulting in gene amplification that may have enhanced the synthesis of inducible proteins in case of optimized medium. The transcriptome studies always generates a huge dataset that can act as valuable resource for future studies to perform host cell engineering with the aim of improving heterologous protein expression.

overall_design: Examination of differential genes expression postinduction (control and test) of E. coli

first: Priyanka

last: Priyanka

first: Rucha

middle: S

last: Patil

first: Pradnya

last: Meshram

first: Jaya

last: Gupta

first: Manidipa

last: Banerjee


title: Gene and protein sequence features augment HLA class I ligand predictions.

status: Public on Jan 08 2023

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

country: Netherlands

institute: Sanquin


title: Gene and protein sequence features augment HLA class I ligand predictions (mRNA sequencing)

summary: The sensitivity of malignant tissues to T cell-based cancer immunotherapies is dependent on the presence of targetable HLA class I ligands on the tumor cell surface. Peptide intrinsic factors, such as HLA class I affinity, likelihood of proteasomal processing, and transport into the ER lumen have all been established as determinants of HLA ligand presentation. However, the role of sequence features at the gene and protein level as determinants of epitope presentation has not been systematically evaluated. To address this, we performed HLA ligandome mass spectrometry on patient-derived melanoma lines and used this data-set to evaluate the contribution of 7,124 gene and protein sequence features to HLA sampling. This analysis reveals that a number of predicted modifiers of mRNA and protein abundance and turn-over, including predicted mRNA methylation and protein ubiquitination sites, inform on the presence of HLA ligands. Importantly, integration of gene and protein sequence features into a machine learning approach augments HLA ligand predictions to a comparable degree as predictive models that include experimental measures of gene expression. Our study highlights the value of gene and protein features to HLA ligand predictions.

overall_design:
Three different melanoma cell lines were cultered by an approximate density of 80%, harvested and snap frozen. mRNA was extracted and used for mRNA sequencing.
Please note that each processed data was generated from both replicates and is linked to the corresponding 'replicate 1' sample records.

first: Ton

last: Schumacher


title: Chromatin epimutations in transgenerational epigenetic inheritance

city: London

first: Rachel

last: Wilson

address: Du Cane Road

country: United Kingdom

institute: Imperial College

summary: Epigenetic inheritance is the transmission of altered gene expression states across dividing cells without DNA sequence variation. Induced epigenetic changes (epimutations) have been extensively studied, but importantly, epimutations also occur spontaneously in a manner reminiscent of DNA sequence change. Small RNAs are established as a source of spontaneous epimutations which transmit gene expression changes over multiple generations in C.elegans. These changes are generally short lived, but rarely long-lived changes occur. Given that chromatin state is a critical regulator of gene expression, we explored whether chromatin states also undergo spontaneous change and whether this could be a potential alternative mechanism for transgenerational epigenetic inheritance.  We compared the chromatin profiles and gene expression profiles at matched time points from a twenty generation bottlenecked lineage of C.elegans. We found that heritable changes in gene expression arose at a higher rate than the estimate for DNA sequence variation, indicating that these were true epigenetic events. In addition to recapitulating the known role for small RNAs, we provide evidence for chromatin mediated epimutations as an alternative mechanism driving epigenetic inheritance. Chromatin epimutations were heritable, enriched in the germline and synchronised with inherited gene expression changes. As with small RNA mediated epimutations, they were generally short lived with a tendency to resolve to baseline after 2-3 generations. A subset of chromatin epimutations however were long lasting, and these were uniquely enriched in piRNA clusters. Genes with long lived epimutations were implicated in multiple components of xenobiotic response pathways. This points to a mechanism for epigenetic ‘anticipation’ of environmental stressors.  Adaptive traits driven by epimutations may be selected for under adverse conditions and lost on return to normal conditions, enabling soft adaptation in the absence of genetic sequence change.

overall_design: Examination of time matched RNA, ATAC and small RNA from 10 time points across 3 independent lineages of C.elegans

first: Peter

last: Sarkies


title: Gene and protein sequence features augment HLA class I ligand predictions (ribosome profiling)

overall_design:
Three different melanoma cell lines were cultered by an approximate density of 80%, subsequently treated with cycloheximide, harvested and snap frozen. Ribosome profling was performed.
Please note that each processed data was generated from both replicates and is linked to the corresponding 'replicate 1' sample records.


title: Increased PXR and suppressed T-cell signaling are associated with malignant degeneration of Barrett’s esophagus

first: Sanne

last: Hoefnagel

state: Noord-Holland

address: Meibergdreef 9

department: Gastroenterology

institute: Academic Medical Centre Amsterdam

summary: Barrett’s esophagus (BE) is the precursor lesion for esophageal adenocarcinoma (EAC). To detect EAC in early stage, patients with BE undergo endoscopic surveillance. Surveillance cohorts largely consist of non-dysplastic Barrett’s esophagus (NDBE) patients with a low annual progression risk  (<0.5%). Predictive biomarkers for malignant progression of NDBE could improve efficacy of surveillance. Biomarker research has mostly focused on aberrant protein expression on BE epithelial cells. Moreover, insight in cell signaling driving malignant transformation is unknown. This study uses a data-driven approach to analyze tumor-stroma interaction in NDBE which progressed to high grade dysplasia (HGD) or EAC.

overall_design: In this case control study, we performed RNA sequencing analysis on index NDBE biopsies from six patients who during long term follow-up progressed and seven who not progressed to HGD/EAC. For control samples, squamous and duodenum tissues from BE patients were analysed. For validation we used qPCR.


title: Integrative single-cell analysis of transcriptional and epigenetic regulatory features in the human clear cell renal cell carcinoma

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

summary: Clear cell renal cell carcinoma (ccRCC) is a disease with a potentially high level of tumour heterogeneity and inherited predisposition. Although many studies performed comprehensive molecular characterisation of ccRCC, the DNA regulatory mechanism is still unknown, especially at the single-cell level. Single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) were performed on 19 ccRCC samples. A total of 102,723 high-quality single-cell transcriptome information, 61,693 high-quality nuclei and 190,916 unique peaks were captured. We used whole-exome sequencing to understand the heterogeneity between individuals, validate the function of long noncoding RNAs (lncRNAs) in vitro and identify protein interactions by protein mass spectrometry. Single-cell transcriptome and chromatin accessibility maps of ccRCC were constructed. We found the gene expression characteristics of different tumour cell subtypes in ccRCC and predicted their sensitivity to targeted and conventional drugs. Interestingly, we discovered that two lncRNAs (RP11-661C8.2 and CTB-164N12.1) promoted the invasion and migration of ccRCC, which were verified by in vitro experiments. Taken together, this study demonstrated the comprehensive gene expression and DNA regulation information of ccRCC and discovered and validated lncRNAs that promote tumour cell invasion and migration, which will provide new insights into the treatment of ccRCC.

overall_design: ccRCC samples from 19 patients were used for both single-cell RNA sequencing and single-cell ATAC sequencing by 10X Genomics.

first: Yufang

last: Lv

first: Cheng

last: Su

first: Wenhao

last: Lu

first: RuiRui

last: Zhang

first: Jiaping

last: Li

first: Bingqian

last: Guo

first: Haibiao

last: Yan

first: Deyun

last: Liu

first: Zhanbin

last: Yang

first: Hua

last: Mi

first: Linjian

last: Mo

first: Yi

first: Wenyu

last: Feng

first: Haotian

last: Xu

first: Wenyi

last: Peng

first: Jiwen

last: Cheng

first: Aruo

first: Zengnan


title: Identification of novel molecular subgroups in esophageal adenocarcinoma to predict response to neo-adjuvant therapies

first: Sanne

last: Hoefnagel

summary: Esophageal adenocarcinoma (EAC) is a highly aggressive cancer and its response to chemo-, and radiotherapy is unpredictable. EAC are highly heterogeneous at the molecular level. The aim of this study was to perform gene expression analysis of EAC to identify distinct molecular subgroups and to investigate expression signatures in relation to treatment response.

overall_design: In this prospective observational study, RNA sequencing was performed on pre-treatment endoscopic EAC biopsies from a discovery cohort included between 2012 and 2017 in one Dutch Academic Center. Four additional cohorts were analyzed for validation purposes. Unsupervised clustering was performed on 107 patients to identify biological EAC subgroups. Specific cell signaling profiles were identified and evaluated with respect to predicting response to neoadjuvant chemo(radio)therapy.

first: K

last: Krishnadath


title: Chip-seq data of BV2 cells by anti-Nr4a2 antibody

city: chengdu

first: huang

last: liang

address: No.24, South First Section, First Ring Road, Wuhou District, Chengdu City

institute: sicuan university

summary: Glioma is the most common type of intracranial tumor and  accounts for 75% of malignant brain tumors. Glioblastoma (GBM)  is the most malignant form of glioma, with strong invasive  capabilities and a high relapse rate even after treatment. Here, our RNA seqencing analysis of BV2 cells treated by H2O2 and si-Nr4a2  reveal the effect of oxdiative stress and Nr4a2-knockdown on phenotype of microglia. Chip-seqencing andlysis of BV2 cells by anti-Nr4a2 antibody is to find the target genes regulated by Nr4a2. Overall, our results reveal that Nr4a2 as the major transcription factors for microglia involved in immunosuppression of glioma.

overall_design: ChIP-seq experiments were performed in BV2 cell lines against Nr4a2. Input samples was used as control.

first: Zengpanpan

last: Ye

first: Xiaolin

last: Ai

first: Linjie

last: Zhao

first: Shengtao

last: Zhou


title: Identification of mechanism of cancer-cell-specific reactivation of hTERT offers therapeutic opportunities for blocking telomerase specifically in human colorectal cancer

city: Singapore

first: Vinay

last: Tergaonkar

address: 61 Biopolis Drive,  Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology


title: Transcriptomic profiles of melanin pigmentation in a plumage ornament

city: Bloomington

first: Ellen

middle: D

last: Ketterson

state: IN

address: 1001 E. Third Street

institute: Indiana University

summary: Feather coloration is one of the most extraordinary examples of phenotypic diversity. This diversity results both from the variation in hue as well as from the presence/absence of pigment in distinct feather regions. The mechanisms that drive presence/absence of pigmentation in feathers are not yet fully understood. Here we characterize the gene expression profiles associated with differential melanin pigmentation in Dark-eyed junco (Junco hyemalis) tails, a social feather ornament used in courtship and male-male competition. Junco tail feathers contain both white apigmented regions as well as dark melanin-pigmented regions.  We compared the transcriptome-wide gene expression in developing white and dark regions of tail feathers to understand the regulatory pathways that may regulate the development of this feather ornament. We show that both white and dark feathers express melanocyte markers, indicating that white feathers contain cells capable of producing pigment. However, only dark cells express genes associated with melanin synthesis. We identify differences in expression of genes that may regulate melanocyte activation in dark feathers. Future studies should experimentally test the role of these genes in driving differences in feather pigmentation.

overall_design: We analyzed gene expression in developing feathers from 7 Dark-eyed junco (Junco hyemalis) individuals, sampling 3 to 8 feathers from each bird. Specifically, we contrast gene expression in the completely white outer tail feathers (6th rectrix), completely dark inner feathers (2nd rectrix), and the white and dark developing portions of the intermediate 4th rectrix.

first: Mikus

last: Abolins-Abols

first: Douglas

middle: B

last: Rusch


title: Genome-wide chromatin accessibility analysis in T-INT2 WT and KO isogenic HCT116 cells (ATAC-seq)

summary: Transcriptional re-activation of hTERT is the limiting step in tumorigenesis. While mutations in hTERT promoter seen in 19% of all cancers are recognized as key drivers of hTERT reactivation, mechanisms by which the wildtype hTERT (WT-hTERT) promoter is reactivated, as observed in the majority of cancers, remain unknown. We report that unlike with the mutant-hTERT promoters, a T-INT2 (Tert INTeracting region 2) region located ~120kb upstream of the hTERT proximal promoter is essential to uniquely reactivate the WT-hTERT promoter, via long-range chromatin interactions. Unlike mutant-hTERT promoters, which are driven by GABPa/b tetramers tethered between T-INT1 (Tert-INTeracting-region 1) and de-novo ETS sites created by promoter mutations, WT-hTERT promoter firing is initiated by 2 events a) elevated JunD mediated recruitment of CTCF and b) β-catenin and CBP mediated recruitment of Sp1 tetramers between T-INT2 and WT-hTERT proximal-promoter, leading to chromatin-openness, pol2 recruitment and productive transcription.

overall_design: The Sp1 cluster in T-INT2 region has been deleted using Crispr-Cas9 editing (450bp deletion). WT and KO HCT116 isogenic cell lines were analyzed for ATAC-seq. 2 clones were used for WT and KO cells with 2 technical replicates.

first: Semih

last: AKINCILAR

first: Luay

last: Aswad

first: Kaijing

last: Chen


title: Genome-wide chromatin accessibility analysis in Tert promoter WT and mutant isogenic BLM  cells (ATAC-seq)

overall_design: The BLM melanoma cell line which originally harbors TERT promoter mutation was corrected to WT using Crispr editing. Furthermore, mutant Tert promoter specific chromatin interaction region (T-INT1) was knocked out by CRISPR-cas9 method. Tert promoter WT/mutant isogenic lines with or without the T-INT1 region were analyzed for ATAC-seq. Two replicates were used for each clones.


title: Genome-wide chromatin accessibility analysis in colorectal cancer PDC (ATAC-Seq)

summary: Transcriptional reactivation of hTERT is the limiting step in tumorigenesis. While mutations in hTERT promoter in 19% of cancers are recognized as key drivers of hTERT reactivation, mechanisms by which wildtype hTERT (WT-hTERT) promoter is reactivated, in majority of human cancers, remain unknown. Using primary colorectal cancers (CRC) we identify, Tert INTeracting region 2 (T-INT2), the critical chromatin region essential for reactivating WT-hTERT promoter in CRCs. T-INT2 is essential for the formation of a unique chromatin architecture needed for the reactivation of WT-hTERT. This cancer-cell-specific WT-hTERT reactivation is mediated by -catenin and JunD signalling via T-INT2. Pharmacological screens uncovered Salinomycin, which inhibits WT-hTERT reactivation by blocking T-INT2 mediated formation of chromatin architecture essential for WT-hTERT promoter reactivation. Our results provide a framework for therapeutic targeting of WT-hTERT, specifically in cancer cells and explain, for the first time how known CRC alterations, such as APC lead to WT-hTERT promoter reactivation during oncogene-induced  stepwise-transformation.

overall_design: 6 Primary colon cancer cells were analyzed using ATAC-seq. Each cells include 2 replicates.

first: Joelle

last: Chua


title: Antibody-Free and Fast Profiling of Transcription Factor Binding Sites Using Aptamer-Guided Chromatin Cleavage with Sequencing (AptaChC-seq)

status: Public on Jan 07 2023

city: Hefei

first: Xucong

last: Teng

address: No. 96, Jinzhai Road

department: Hefei National Laboratory of Physical Science at Microscale

institute: University of Science and Technology of China

summary: A large number of transcription factors are enriched at specific DNA sites in the nuclear, playing an important role in the regulation of gene expression. Chromatin immunoprecipitation sequencing (ChIP seq) is the classic method for the detection of chromatin transcription factor landscape. This method is limited by the complexity of steps, low signal to noise ratio, large number of cells required, high cost, and heavy reliance on high-purity high-performance antibodies. In recent years, based on MNase and Tn5 transposase, CUT&RUN, CUT&Tag, ChIL-seq, itChIP-seq have been developed and widely used, but they still rely on antibodies and take a long time. Here, we develop an antibody-free and fast method for profiling transcription factor binding sites, called Aptamer-Guided Chromatin Cleavage with Sequencing (AptaChC-seq). AptaChC-seq has the advantages of high signal to noise ratio, low cost, good reproducibility.

overall_design: The Transcription Factor Binding Sites of human FOXM1 was detected by AptaChC-seq and CUT&Tag in HEK293FT cells. ATAC-seq was also conducted for comparation. AptaChC-seq of human FOXM1 was further tested in human MCF-7 and MCF-10A cells. AptaChC-seq of human RELA and RBPJ was also tested in HEK293FT cells.

first: Yicong

last: Dai

first: Yuncong

last: Wu

first: Jinghong

last: Li


title: Human Mesenchymal Stem / Stromal Cells (hMSCs) treated with Eltrombopag show increase of the hematopoietic supporting ability

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

institute: Cancer Research Center (CiC-IBMCC)

summary: Eltrombopag (EP) is a small molecule that acts on hematopoietic cells and megakaryocytes to stimulate the hematopoiesis. Mesenchymal stem/stromal cells (MSCs) are key hematopoietic niche regulators. In the current work we aimed to assess if EP exert any effect on MSCs function, especially on their hematopoietic-supporting ability, and if so, what are the changes (including transcriptomic) induced in MSCs after EP treatment. For this purpose, MSCs were isolated from 12 healthy donors and treated with 15 uM and 50 uM of EP for 24 hours. The toxicity of the drug on MSCs and their differentiation ability were analyzed, as well as the transcriptomic profile, ROS and DNA damage and finally the changes induced in the clonogenic capacity of HSC. We observed that EP acts on MSCs decreasing their adipogenic differentiation, increasing the expression of genes involved in hypoxia and other pathways and enhancing their ability to support hematopoiesis. We used high density oligo microarrays (Affymetrix Clariom_S_Human) to obtain the global programme of gene expression underlying the effect of the Eltrombopag (EP) and Thrombopoietin (TPO) in human MSCs (derived from bone marrow) and identify the genes activity.

overall_design: Mesenchymal Stem / Stromal Cells (MSCs) isolated from human bone marrow were treated with EP at concentrations 15 uM and 50 uM for 24 hours and then RNA extraction and hybridization on Affymetrix genome-wide expression microarrays (Clariom S) was performed. The aim was to evaluate the toxicity of the drug EP in two different concentrations and the differentiation ability of the mesenchymal stem cells treated. To achieve this we analyzed the genome-wide expression profile of MSC samples prepared from four independent donors (i.e., using four biological replicates 1,2,3,4) and studied in four treatment conditions: (i) MSCs control with no drug addition, 0 micromolar; (ii) MSCs with Eltrombopag at concentration 15 micromolar: Eltrombopag_15uM; (iii) MSCs with Eltrombopag concentration 50 micromolar: Eltrombopag_50uM; and (iv) MSCs treated with Thrombopoietin.

first: Sandra

last: Muntión

first: Silvia

last: Preciado

first: Elena

last: Sánchez-Luis

first: Luis

last: Corchete

first: María

last: Díez-Campelo

first: Lika

last: Osugui

first: Gerardo-Javier

last: Martí-Chillón

first: María-Belén

last: Vidriales

first: Almudena

last: Navarro-Bailón

first: Fermín

last: Sánchez-Guijo


title: Nr4a2 as a transcription factor sustaining immunosuprssion in glioma

first: huang

last: liang

overall_design: scRNA-seq experiments were performed to cluster CD45+ cells in glioma

first: Zengpanpan

last: Ye

first: Xiaolin

last: Ai

first: Linjie

last: Zhao

first: Shengtao

last: Zhou


title: Specification of human germ cell fate with enhanced progression capability

city: Cambridge

first: Walfred

last: Tang

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: Human primordial germ cells (hPGCs) are the embryonic precursors of sperm and eggs. While the exact temporal window of hPGC specification and the cellular identity of their precursors remains unclear, few studies on ex vivo and in vitro cultured human embryos reported plausible hPGCs on embryonic day (E) 12−13, and in a E16−17 gastrulating embryo. In vitro, hPGC-like cells (hPGCLCs) can be specified from intermediary pluripotent stage or peri-gastrulation precursors. Nevertheless, it remains unclear the extent of the spectrum of precursors for hPGCLC specification and how these different cellular identities impact hPGCLC development. Here we show that capacitating and resetting precursors respond to BMP and induce resetting hPGCLCs (rhPGCLCs). Strikingly, rhPGCLC in the human hindgut organoid co-cultures show progression at a pace reminiscent of in vivo timing, demonstrating their higher potential for progression compared to those derived from peri-gastrulation precursors. Notably, EOMES and TBXT act synergistically during rhPGCLC specification, while only EOMES is necessary for peri-gastrulation hPGCLC specification. Our results emphasize the notion that the function of a cell identity can be largely influenced by features of their precursors rather than their convergent identity. Importantly, our study provides the foundation for refined and efficient in vitro models of human gametogenesis, which may contribute to design new therapeutic approaches for human infertility.

overall_design: RNA-seq of hESC-derived cell types (2-4 biological replicates for each cell type)

first: João

middle: P

last: Alves-Lopes

middle: W

first: Wolfram

middle: H

last: Gruhn


title: Identification of genes associated with Periodontal pathogens induced endothelial dysfunction using RNA-seq data

city: Yangsan-si

first: Yeongjoo

last: Kim

institute: Pusan National University

summary: Periodontal pathogens (Porphyromonas gingivalis, Fusobacterium nucleatum) are known as one of several important bacterial pathogens associated with sporadic Alzheimer's disease (AD). It is suggested that the entry of Periodontal pathogens into the brain is due to the disruption of the tight junctions of endothelial cells by Periodontal pathogens. However, genomic alterations that occur as a result of Periodontal pathogens infection in endothelial cells are not well understood. Our goal was to identify genes associated with Periodontal pathogens infection-induced endothelial dysfunction by integrating gene expression data.

overall_design: Nine samples, 3 controls, 3 F. nucleatum infected, 3 P. gingivalis infected.

first: Hae

last: Park

first: Hyeon

last: Hwang

first: Seon


title: Novel targets in renal fibrosis based on bioinformatic analysis I

status: Public on Jan 06 2023

first: xi

last: xiong

state: Hubei Province

address: No.241, Pengliuyang Road

department: Department of Urology

institute: Wuhan Third Hospital

summary: Renal fibrosis is a widely used pathological indicator of progressive chronic kidney disease (CKD), and renal fibrosis mediates most progressive renal diseases as a final pathway. Nevertheless, the key genes related to the host response are still unclear. In this study, the potential gene network, signaling pathways, and key genes under UUO model in mouse kidneys were investigated by integrating two transcriptional data profiles.

overall_design: The mice were exposed to UUO surgery in two dependent experiments. After seven days, two datasets were sequenced from mice kidney tissues, respectively, and the transcriptome data were analyzed to identify the differentially expressed genes (DEGs). Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were executed. A Protein-Protein Interaction (PPI) network was constructed based on an online database STRING. Additionally, hub genes were identified and shown, and their expression levels were investigated in dataset GSE36496 and confirmed by utilizing the quantitative real time-PCR (qRT-PCR) in vivo.

first: Xi

last: Xiong

first: Yuan

last: Yuan


title: Notch Activation Commits Mesoderm Cells to the Cardiac Lineage [embryo]

city: NYC

first: Nicole

last: Dubois

state: NY

address: 1740 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: During early development multiple progenitor populations contribute to the formation of the four-chambered heart and its diverse lineages. However, the underlying mechanisms that result in the specification of these progenitor populations are not yet fully understood. We have recently identified a population of cells that gives rise selectively to cardiovascular cells of the heart ventricles. Here, we have used this knowledge to isolate and profile subsets of cardiac mesoderm cells from the mouse embryo and have identified an enrichment for the Notch signaling pathway in ventricular cardiac mesoderm. Using the pluripotent stem cell differentiation system to investigate the role of Notch in a temporally controlled manner, we show that Notch induction increases cardiomyocyte differentiation efficiency. This is due to the enhanced specification of mesoderm to the cardiac lineage. Finally, our data suggests that Notch interacts with WNT signaling to enhance commitment to the cardiac lineage. Overall, our findings support the notion that key signaling events during early heart development are critical for proper lineage specification and segregation and provide additional detail into these processes in mouse and human cardiogenesis.

overall_design: Examination of global gene expression in four different cell types

first: Evan

last: Bardot

first: Bharati

last: Jadhav

first: Nadeera

last: Wickramasinghe

first: Amélie

last: Rezza

first: Michael

last: Rendl

first: Andrew

last: Sharp


title: Notch Activation Commits Mesoderm Cells to the Cardiac Lineage [cardiomyocytes]

overall_design: Examination of global gene expression in day 30 cardiomyocytes from control, Notch-induced, and Notch-inhibited cardiac mesoderm cultures.


title: Lactoferrin attenuated deoxynivalenol induced malfunction in mouse testis

city: Yangzhou

first: Demin

last: Cai

address: Daxue South Road 88

institute: Yangzhou University

summary: DON impaired the male spermatogenesis and induced oxidative stress, testicular apoptosis and disruption of blood-testis barrier (BTB). The milk protein lactoferrin (LF) is an iron-binding glycogenprotein with multifunctions including anti-inflammation and antioxidant. The current study was aimed to investigate the beneficial effects of LF on spermatogenesis and integray of BTB of mice treated with diet DON.

overall_design: Sexually mature male mice were fed diet inclusion of DON,and oral administration of LF for 35 days, a 2×2 factorial arrangement.

first: Zhaojian

last: Li

first: Ping

last: Hu


title: Machine learning multi-omics analysis reveals cancer driver dysregulation in pan-cancer cell lines compared to primary tumors

city: Little Rock

first: Analiz

last: Rodriguez

state: AR

address: 4301 W. Markham St Slot 507

department: College of Medicine, Department of Neurosurgery

institute: University of Arkansas for Medical Sciences

summary: Cancer cell lines have been widely used for decades to study biological processes driving cancer development, and to identify biomarkers of response to therapeutic agents. Advances in genomic sequencing have made possible large-scale genomic characterizations of collections of cancer cell lines and primary tumors, such as the Cancer Cell Line Encyclopedia (CCLE) and The Cancer Genome Atlas (TCGA). These studies allow for the first time a comprehensive evaluation of the comparability of cancer cell lines and primary tumors on the genomic and proteomic level. Here we employ bulk mRNA and micro-RNA sequencing data from thousands of samples in CCLE and TCGA, and proteomic data from partner studies in the MD Anderson Cell Line Project (MCLP) and The Cancer Proteome Atlas (TCPA), to characterize the extent to which cancer cell lines recapitulate tumors. We identify dysregulation of a long non-coding RNA and microRNA regulatory network in cancer cell lines, associated with differential expression between cell lines and primary tumors in four key cancer driver pathways: KRAS signaling, NFKB signaling, IL2/STAT5 signaling and TP53 signaling. Our results emphasize the necessity for careful interpretation of cancer cell line experiments, particularly with respect to therapeutic treatments targeting these important cancer pathways.

overall_design: Primary patient-derived melanoma brain metastasis tissue and cell lines derived from those primary tumor samples were analyzed using scRNAseq

first: Annick

last: De Loose

first: Grace

last: Guzman

first: Emilie

last: Darrigues


title: SARS-CoV-2-associated ssRNAs activate human neutrophils in a TLR8-dependent fashion

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

institute: University of Verona

summary:
COVID-19 disease is characterized by a dysregulation of the innate arm of the immune system. However, the mechanisms whereby innate immune cells, including neutrophils, become activated in patients are not completely understood. Recently, we showed that a GU-rich RNA sequence from SARS-CoV-2 genome (i.e., SCV2-RNA2) activates dendritic cells. To clarify whether human neutrophils may also represent targets of SCV2-RNA2, neutrophils were treated with either SCV2-RNA2 or, as control, R848 (a TLR7/8 ligand), and then analysed for several functional assays and also subjected to RNA-seq experiments.
Results highlight a remarkable response of neutrophils to SCV2-RNA2 in terms of TNFa, IL1ra, CXCL8 production, apoptosis delay, modulation of CD11b and CD62L expression and release of neutrophil extracellular traps. By RNA-seq experiments, we observed that SCV2-RNA2 promotes a transcriptional reprogramming of neutrophils, characterized by the induction of thousands of proinflammatory genes, similarly to that promoted by R848. Furthermore, by using CU-CPT9a, a TLR8-specific inhibitor, we found that SCV2-RNA2 stimulates neutrophils exclusively via TLR8-dependent pathways. In sum, our study proves that single-strand RNAs from the SARS-CoV-2 genome potently activate human neutrophils via TLR8, thus uncovering a potential mechanism whereby neutrophils may contribute to the pathogenesis of severe COVID-19 disease.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data from human neutrophils treated with SCV2-RNA2 or R848, in presence or absence of the TLR8 specific inhibitor CU-CPT9a

first: Elisa

last: Gardiman

first: Sara

last: Gasperini

first: Marco

middle: A

last: Cassatella

first: Nicola

last: Tamassia


title: Differential lncRNA expression in human ovarian tumors from depressed and non-depressed nude mice

city: Changsha

first: fang

last: zhou

address: 283 Tongzipo Road, Yuelu District,

institute: hunan cancer hospital

summary: Comparison of stressed nude mice ovarian tumor tissue and epithelial ovarian cancer.

overall_design: We injected untreated human SKOV3 ovarian cancer cells into nude mice peritoneal cavity. Tumor tissues with good growth were obtained from nude mice, including 3 non-stressed malignant ovarian tumor tissue samples and 3 stressed malignant ovarian tissue samples. This series includes only the tissues from the stressed mice. High-throughput profiling of protein-coding RNA and lncRNA from the collected ovarian tissue samples.

first: Jie

last: Tang

first: Le

last: Chen

first: Xiaofang

last: Zhou


title: Structural and functional distinctions of co-resident microglia and monocyte-derived macrophages after retinal degeneration

city: Davis

first: Marie

last: Burns

address: 1 Shields Ave

institute: University of California Davis

summary: Both resident microglia and invading peripheral immune cells can respond to injury and degeneration in the central nervous system. However, after dead and dying neurons have been cleared and homeostasis is re-established, it is unknown whether resident immune cells fully resume normal functions and to what degree the peripheral immune cells take up residence. Using flow cytometry, in vivo retinal imaging, immunohistochemistry, and single-cell mRNA sequencing, we assess resident microglia and monocyte-derived macrophages in the retina during and after the loss of photoreceptors in the Arr1-/- mouse model of inducible degeneration. We find that photoreceptor loss results in a small, sustained increase in mononuclear phagocytes and, after degeneration wanes, these cells re-establish a spatial mosaic reminiscent of healthy retinas. Transcriptomic analysis revealed the population remained unusually heterogeneous, with several subpopulations expressing gene patterns consistent with mildly activated phenotypes. Roughly a third of “new resident” cells expressed markers traditionally associated with both microglial and monocytic lineages, making their etiology ambiguous. Using an inducible Cre-based fluorescent lineage tracing paradigm to confirm the origins of new resident immune cells, we found approximately equal numbers of microglia and monocyte-derived macrophages after degeneration had subsided. In vivo retinal imaging and immunohistochemical analysis showed that both subpopulations remained functionally responsive to sites of local damage, though on average the monocyte-derived cells had less morphological complexity, expressed higher levels of MHCII, and had less migratory activity than the native resident population. Monocytic cells that infiltrate the retina during degeneration differentiate into monocyte-derived macrophages that can remain in the retina long-term. These monocyte-derived macrophages adopt ramified morphologies and microglia-like gene expression. However, they remain distinguishable in morphology and gene expression from resident microglia and appear to differ functionally, showing less responsiveness to subsequent retinal injuries. These findings support the idea that persistent changes in the local immune population in response to cell loss in aging and progressive retinal diseases may include subpopulations of bone marrow derived cells whose ability to respond to subsequent insults wanes over time.

overall_design: Myeloid (CD11b+CD45+) cells were collected from dissociated mouse retinas using fluorescence-activated cell sorting before, immediately after, and well after photorecetor degeneration (Arr1-/- mouse model, 0, 7, and 20 days of approximately 200 lux light exposure, respectively). ScRNAseq was performed using 10x Genomics.

first: Kaitryn

last: Ronning

first: Sarah

last: Karlen


title: Notch Activation Commits Mesoderm Cells to the Cardiac Lineage

first: Nicole

last: Dubois

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Novel targets in renal fibrosis based on bioinformatic analysis II

city: Wuhan

first: xi

last: xiong

first: Xi

last: Xiong

first: Yuan

last: Yuan


title: RNA-seq analysis of gene expression in Helicobacter pylori expressing either WT Fur or a Fur variant (Fur-R88H).

city: Nashville

first: John

last: Loh

state: TN

address: A2320 MCN VUMC

department: Infectious Diseases

institute: Vanderbilt University

summary: Purpose: Next-generation sequencing (NGS) was used to analyze gene expression in H. pylori strains expressing either WT Fur or a Fur variant (i.e. Fur-R88H). The goals of this study are to examine the role that WT Fur and Fur-R88H play in affecting salt-responsive gene expression in the 2 different strains. The H. pylori strains were grown in the presence of routine salt (0.5% added NaCl) or high salt (1.0% added NaCl).

overall_design: Analysis of transcriptional changes in H. pylori grown for 15 h in medium containing either 0.5% or 1.0% added NaCl.

first: Timothy

last: Cover


title: Target enrichment sequencing of head and neck cell lines

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

summary: We analysed HPV integration sites of UPCI-SCC-090 and UM-SCC-104.

overall_design: Validation of HPV integration sites using target enrichment sequencing

first: Masato

last: Mima

first: Atsushi

last: Okabe

first: Takayuki

last: Hoshii

first: Takuya

last: Nakagawa

first: Tomoya

last: Kurokawa

first: Satoru

last: Kondo

first: Harue

last: Mizokami

first: Ryoji

last: Fujiki

first: Bahityar

last: Rahmutulla

first: Tomokazu

last: Yoshizaki

first: Toyoyuki

last: Hanazawa

first: Kiyoshi

last: Misawa

last: Kaneda


title: miRNA sequencing data of normal glucose tolerant (NGT) and gestational diabetes (GDM) pregnant women

city: Shanghai

first: Liying

last: Jiang

address: 279 zhouzhugong road

institute: Shanghai University of Medicine and Health Sciences

summary: Total RNA was isolated from lymphocyte. We compared the miRNA expression profiles between healthy and GDM women by RNA sequencing, and determined the signaling pathways associated with the changes. Our study offers new insights into circulating biomarkers of GDM and thus provides a valuable resource for future investigations.

overall_design: Sample from 12 pregnant women (6 from normal controls and 6 from GDM patients) were used for miRNA sequencing analysis.


title: Genome-wide analysis of histone modification in UPCI-SCC-090, UM-SCC-104, FaDu and NP69SV40T.

summary: We analysed active enhancers in UPCI-SCC-090, UM-SCC-104, FaDu and NP69SV40T by performing ChIP-seq on H3K4me3, H3K4me1 and H3K27ac.

overall_design: Examination of active enhancers.


title: RNA-seq of head and neck cell lines

summary: Two HPV(+) head and neck cancer cell lines (UPCI-SCC-090, UM-SCC-104), one HPV(–) head and neck cancer cell line (FaDu) and one nasopharyngeal epithelial cell line (NP69SV40T) were subjected to RNA-seq analysis.

overall_design: Transcriptome analysis


title: Tumorigenic activation around HPV integrated sites in head and neck squamous cell carcinoma


title: Hi-C of head and neck cell lines

summary: We comprehensively analysed chromatin interactions in UPCI-SCC-090, UM-SCC-47, UM-SCC-104, FaDu and NP69SV40T by performing Hi-C.

overall_design: Comprehensive chromatin conformational analysis using Hi-C


title: 4C-seq of HPV(+) head and neck cancer cell lines

summary: To identify HPV interaction region, two cell lines (UPCI-SCC-090, UM-SCC-104) were subjected to 4C-seq analysis.

overall_design: Examination of HPV interaction region.


title: Identification of a novel GR-ARID1a-P53BP1 protein complex involved in DNA damage repair and cell cycle regulation [ChIP-seq]

city: Bristol

first: Felicity

last: Stubbs

address: Whitson St

institute: University of Bristol

summary: ARID1a (BAF250), a component of human SWI/SNF chromatin remodeling complexes, is frequently mutated across numerous cancers, and its loss of function has been putatively linked to glucocorticoid resistance. Here, we interrogate the impact of siRNA knockdown of ARID1a compared to a functional interference approach, both in the HeLa human cervical cancer cell line.  We report that ARID1a knockdown resulted in a significant global decrease in chromatin accessibility in ATAC-seq analysis, as well as affecting a subset of genome-wide GR binding sites in GR ChIP-seq analysis. Interestingly, the specific effects on gene expression were limited to a relatively small subset of glucocorticoid-regulated genes, notably those involved in cell cycle regulation and DNA repair. The vast majority of glucocorticoid-regulated genes were largely unaffected by ARID1a knockdown or functional interference, consistent with a more specific role for ARID1a in glucocorticoid function than previously speculated. Using liquid chromatography mass spectrometry, we have identified a chromatin-associated protein complex comprising GR, ARID1a, the cell cycle regulating P53 binding protein P53BP1, DNA repair proteins including Poly(ADP-Ribose) Polymerase 1 (PARP1), DNA damage-binding protein 1 (DDB1), DNA mismatch repair protein MSH6 and splicing factor proline and glutamine rich protein (SFPQ), as well as the histone acetyl transferase KAT7, an epigenetic regulator of steroid-dependent transcription, DNA damage repair and cell cycle regulation. Not only was this protein complex ablated with both ARID1a knockdown and functional interference, but DNA damage repair was also significantly impaired. Recovery from dexamethasone-dependent cell cycle arrest was also significantly impaired. Taken together, our data demonstrates that although glucocorticoids can still promote cell cycle arrest in the absence of ARID1a, the purpose of this arrest to allow time for DNA damage repair is hindered.

overall_design: ChIP-SEQ following ARID1a KNOCKDOWN and Dex treatment

first: Becky

last: Conway-Campbell


title: Identification of a novel GR-ARID1a-P53BP1 protein complex involved in DNA damage repair and cell cycle regulation [ATAC-seq]

overall_design: ATAC-SEQ following ARID1a knockdown and Dex treatment

first: Songjoon

last: Baek


title: Identification of a novel GR-ARID1a-P53BP1 protein complex involved in DNA damage repair and cell cycle regulation [RNA-SEQ ARID1A KNOCKDOWN]

overall_design: RNA-SEQ following ARID1a knockdown and Dex treatment


title: Identification of a novel GR-ARID1a-P53BP1 protein complex involved in DNA damage repair and cell cycle regulation [C_terminal ARID1a RNA-seq]

overall_design: RNA-SEQ following ARID1a C-terminal Overexpression and Dex treatment


title: Grape berry response to heatwaves in a climate change scenario: a physiological, transcriptional, and metabolic overview

city: Legnaro

first: Giovanni Battista

last: Tornielli

state: Padova

address: Viale dell'Università, 16

department: DAFNAE

institute: University of Padova

summary: Grapevines cv Sauvignon Blanc were subjected to different stress regimes by simulating the most common extreme weather events occurring within the current climate change scenario. During spring, just before bud break, the vines were either flooded or kept under normal conditions. Both vines were then split in two groups and put in differnt tunnels, either undergoing a simulated heatwave or not. Berry samples were collected from the four groups of plants (control, only flooded, only heatwave, flooded + heatwave) at different timepoints before, during and after the stress. Transcriptomic analyses were carried out on these samples along with some metabolomic assessments to characterize the response to stress in the different samples and the effect of the combined stresses.

overall_design: The vines have been divided into two distinct tunnels. In the first, the control ones were posed: C (control, plants that have never undergone stress) and F (flooded, plants that have undergone to a submersion stress in pre-bud break, for more details consult Ruperti et al. 2019). In the second tunnel the plants stressed during the summer period were posed: DHW (drought+heat wave, or rather, plants that have undergone only the combined summer stresses) and DHW + F (drought+heat wave+spring flooding, so, plants that have suffered the combined summer stresses after being subjected to submersion stress in spring).

first: Alessandro

last: Botton

first: Benedetto

last: Ruperti

first: Francesco

last: Girardi

first: Matteo

last: Brilli

first: Veronica

last: Tijero

first: Giulia

last: Eccher

first: Francesca

last: Populin

first: Angela

last: Rasori

first: Valerio

last: Cardillo

first: Elisabetta

last: Schievano

first: Tobia

last: Riello

first: Monica

last: Canton

first: Franco

last: Meggio


title: Ablating Lgr5-expressing prostatic stromal cells activates the ERK-mediated mechanosensory signaling and disrupts prostate tissue homeostasis

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: The heterogeneity of the prostate stromal cells is widely appreciated but the functional implication remains incompletely understood. Using genetic lineage tracing and light-sheet imaging, we show that some fibroblast cells near the junction of the mouse proximal prostatic ducts and prostatic urethra highly express Lgr5. Genetic ablation of these anatomically restricted stromal cells, but not nonselective ablation of prostatic stromal cells, rapidly induces prostate epithelial turnover and dedifferentiation that are reversed following spontaneous restoration of the Lgr5+ stromal cells. These changes are not mediated via endocrine or nervous regulation but can be phenocopied by physical disruption of prostatic lumen integrity. RNA-Seq analysis implies that ablating the Lgr5+ stromal cells activates a mechanosensory response, which is supported by increased prostate tissue stiffness and activation of the mitogen-activated protein kinase (MAPK). Suppressing MAPK overrides the increased epithelial proliferation. This study demonstrates that the Lgr5+ stromal cells regulate tissue homeostasis in a long-distance manner by maintaining anatomic integrity and implies that the cells near the transitional regions between organs likely control organ homeostasis by sustaining a balanced mechanoforce.

overall_design: To understand the molecular changes induced by the ablation of the Lgr5+ stromal cells, we FACS-isolated the basal, luminal, and stromal cells from anterior prostates of DT-treated Lgr5-DTR-eGFP and control wild type mice and compared their gene expression profiles by RNA-seq.

first: Yiqun

last: Zhang

first: Li

last: Xin


title: Single cell analysis of activated iNKT cells from murine epididymal adipose tissue and spleen

city: Dublin

first: Lydia

last: Lynch

address: Trinity Biomedical Sciences Institute 152-160 Pearse St

country: Ireland

institute: Trinity College Dublin

summary: We show that iNKT cells undergo rapid and extensive transcriptional remodeling after activation with the lipid antigen αGalactosylceramide (αGalCer). A common transcriptional framework underpins the activation of heterogeneous iNKT cell populations, including NKT1, NKT2 and NKT17 cells. We show that regulatory iNKT cell populations, including iNKT cells from epididymal adipose tissue, undergo blunted activation and show reduced transcriptional remodeling after αGalCer. We find that regulatory iNKT cell populations are enriched for memory-like KLRG1+ and cMAF+ iNKT subsets, and express gene signatures associated with adaptive Tr1 cells. IL-10 producing NKT10 cells express cMAF, and show enrichment for a cMAF-associated gene network. We also show that NKT10 cells are also phenotypically similar to adaptive Tr1 cells and NKTFH cells.

overall_design: Unbiased single cell sequencing of sorted whole murine iNKT cells from epididymal adipose tissue (three samples) and spleen (three samples). Mice were treated with 1μg αGalCer and iNKT cells were isolated after 4 hours or 72 hours, or mice were treated with 4μg αGalCer and iNKT cells were isolated after 4 weeks without further activation, or after reactivation for 4 hours with 1μg αGalCer in vivo. This data was generated in association with the data in GSE142845.

first: Harry

last: Kane

first: Nelson

last: LaMarche

first: Áine

last: Ní Scannail

first: Michael

last: Brenner


title: Gene expression profiles of  METTL5-Wild type(WT) knockout(KO) in HCC cells

city: wuhan

first: xia

last: peng

state: hubei

address: zhongnan hospital

institute: wuhan university

summary: HCC cell line, Huh-7 cells and HCC-LM3 cells, was transfected with METTL5 sgRNA to knockout METTL5 expression., and check the downstream mRNA changes.

overall_design: Comparison of transcriptomes from METTL5-WT and METTL5-KO  in HCC cells

first: Peng

last: Xia

first: Hao


title: The application of a reverse transcriptase inhibitor suppresses LTR retrotransposon mobilization in plants [RNA-seq]

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

summary: Recently developed methods applied to plant material, for example tissue culture during plant transformation, can induce genome instability by activating uncontrolled mobilization of LTR retrotransposons (LTR-TEs), the most abundant class of mobile genetic elements in plant genomes. Here we tested the use of Reverse Transcriptase inhibitors to avoid LTR-TE mobilization in plants. We demonstrated that the application of the drug Tenofovir in systems with high LTR-TE activity, like Arabidopsis and rice, allows generation of plants free from LTR-TE insertions without interfering with their development. We propose the use of Tenofovir as a new tool to both study LTR-TE transposition and to regenerate more genetically stable plant lines from tissue culture.

overall_design: Transcriptional profile of Arabidopsis thaliana seedlings germinated in presence and absence of Tenofovir, analysed before stress, after heat stress and three days after recovery from the stress. Each condition has three biological replicates.


title: The application of a reverse transcriptase inhibitor suppresses LTR retrotransposon mobilization in plants [ALE-seq]

overall_design: Mobilome profile sequenced with ALEseq (DOI:10.1038/s41477-018-0320-9) of rice (Oryza sativa cv. Nipponbare) calli in presence and absence of Tenofovir, with leaves tissue used as control

first: Jungnam

last: Cho


title: comparative cellular and transcriptomic analyses reveal differential gene networks regulating pollen development in synthetic haploid and tetraploid Brassica carinata

city: Zhengzhou

first: Shen

last: xiaohan

address: 100 Science Avenue

institute: Zhengzhou University

summary:
Purpose:Comparative cellular and transcriptome analyses was applied to characterize gene expression during male gametophytic development in Brassica carinata.
Methods:  floral buds (contain two developmental progress,1.1-1.6 mm and 1.8-6.5 long floral buds) were collected, then Separated male organs were kept in liquid nitrogen immediately until use. Total RNA was extracted using the TRIzol reagent (Invitrogen, Waltham, MA, USA). DNase (Promega, USA) was used to remove potential DNA contamination. For the quantitative real-time polymerase chain reaction (qRT-PCR) analysis
Results: In this study, Up-regulated expression of DNA methylation probably affected pollen abortion in synthetic allohaploid B. carinata,and Down-regulated expression of cytokinin may affect pollen division and growth in synthetic allohaploid B. carinata
Conclusions: Genes  were shown male-preferred implies the dynamic changes of DNA methylation during the development of male gametes.  The DEGs, related to CK signaling pathway and BR synthesis pathway were highly enriched in developmental male gametes, suggesting that CK played pivotal roles in male gamete development.

overall_design: mRNA profiles of male gametophytes

first: Xiaohan

last: Shen

first: Fang

last: Wei


title: Mouse thymic lymphomas arising after irradiation between with or without calorie restriction

first: Masaaki

last: Sunaoshi

state: Chiba

address: 4-9-1 Anagawa, Inage-ku

department: Department of Radiation Effects Research, Institute for Radiological Science

institute: National Institutes for Quantum Science and Technology

type: Genome variation profiling by genome tiling array

summary: Calorie restriction (CR) is known to decrease not only spontaneous but also chemical carcinogen and radiation-induced carcinogenesis. However, the biological mechanisms for the anti-cancer effect of CR remain unclear. In this study, analyzed and compared with genomic alterations in thymic lymphoma (TL) arising after irradiation between with or without CR. The frequency of point mutations at Pten locus on chromosome 19 was not different between 95 kcal and 65 kcal groups, but the frequency of LOH with DNA copy number change in 65 kcal group tended to be higher than 95 kcal group. On chromosome 4 and 11, the LOH frequency was not different between 95 kcal and 65kcal groups, but the LOH mechanism was different. In 65 kcal group, the frequency of LOH without DNA copy number change by chromosome mis-segregation or mitotic recombination was lower than 95 kcal group, but then the frequency of LOH with DNA copy number change by deletion was higher than 95 kcal group. The frequency of genomic alterations such as LOH and point mutation at Ikaros on chromosome 11 were observed as high as 70% (19 / 27) in 95 kcal group and 76% (16 / 21) in 65 kcal group. However, the mechanisms of LOH and Ikaros inactivation are different between 95 kcal and 65 kcal group.

overall_design: Mice were irradiated with 3.8 Gy X-rays at 1 week of age, and calorie restriction started at 7 weeks of age. Forty-eight thymic lymphomas were analyzed consisted of 27 samples obtained from normal diet group, 95 kcal/week, and 21 samples obtained from the calorie restriction group, 65 kcal/week.

first: Takafumi

last: Nakayama

first: Shizuko

last: Kakinuma


title: Identification of a novel GR-ARID1a-P53BP1 protein complex involved in DNA damage repair and cell cycle regulation

first: Felicity

last: Stubbs

overall_design: Refer to individual Series


title: Changes in neutrophil gene expression in psoriatic arthritis patients in response to sekukinumab

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

institute: University of Liverpool

summary: We report changes in gene expression in human peripheral blood neutrophils from patients with psoriatic arthritis (PsA) before and 12-weeks after treatment with Secukinumab (SKB, 150mg). All patients achieved a good PSARC (Psoriatic Arthritis Response Criteria) and PASI 90 (Psoriasis Area and Severity Index) response to treatment. We also report gene expression in healthy control neutrophils compared to patients wth psoriatic arthritis.

overall_design: Human neutrophils were isolated from peripheral blood samples (5 PsA pre- and post-SKB, 5 healthy controls) using Ficoll-Paque (neutrophil purity >95%). RNA was isolated uisng Trizol. RNA was sequenced using DNBseq PE100 protocols. Sequencing data was mapped to the human genome (hg38) using Tophat2 (v2.1.1). Count data were generated using featureCounts (Rsubread v2.0). Statistical analysis was carried out using edgeR (v3.28.1) with sva (v3.34) batch correction, TMM normalisation and a false-discovery rate cut-off of 0.05.

first: Andrew

last: Cross

first: Jennifer

last: Hawkes

last: Frankland

first: Ayren

last: Mediana

first: Nicola

last: Goodson

first: Steven

last: Edwards

first: Robert

last: Moots


title: Cytological and transcriptome analysis at meiosis and mitosis reveals insights into pollen fertility in synthetic Brassica allohaploid by crosses between B. nigra and B. rapa

first: liang

middle: nian

last: nian

summary:
Purpose:The molecular mechanism of pollen abortion in interspecific hybrids of B.rapa and B.nigra was revealed by cytological and transcriptional analysis
Methods:floral buds (contain two developmental progress,1.1-1.5 mm and 1.5-6.0 long floral buds) were collected, then Separated male organs were kept in liquid nitrogen immediately until use. Total RNA was extracted using the TRIzol reagent (Invitrogen, Waltham, MA, USA). DNase (Promega, USA) was used to remove potential DNA contamination. For the quantitative real-time polymerase chain reaction (qRT-PCR) analysis
Results:In this study, there were extensive variations in gene expression patterns of this hybrid, and down-regulated expression of key genes for pollen development, such as meiosis of pollen mother cells, DNA damage repair and pollen sperm cell differentiation, may lead to pollen abortion. Styrene-propyl synthesis and wax biosynthesis pathway were blocked, which affected pollen wall formation.
Conclusions:The wide variation of genes showed that the expression of A and B genomes were affected differently. B genome tended to downregulate the expression of key genes during meiosis and mitosis, while A genome tended to downregulate the expression of genes related to stress and pollen wall formation. The results showed that the development of male gametophyte was seriously affected after synthesis.

sample_organism:
Brassica nigra
Brassica rapa
Brassica rapa x Brassica nigra

first: Niannian

last: Liang


title: Essential role of Jab1 in mouse chondrocyte differentiation.

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: RNA sequencing was performed at the Genomics Core - Case Western Reserve University

overall_design: Three WT controls and three Jab1-conditional knockout primary chondrocytes samples were analysed for RNA-sequencing analysis.

first: Murali

middle: K

last: Mamidi

first: William

last: Samsa

first: E

first: Guang

last: Zhou


title: RNA Sequencing Quantitative Analysis of control and knockdown ZBTB7A.

city: Taipei

first: LIYIN

last: YEH

address: No.155, Sec.2, Linong Street, Taipei, 112 Taiwan (ROC)

country: Taiwan

institute: National Yang-ming university

summary: The aim of the study is to compare the RNA-sequencing data to protein array and qRT-PCR and to clarify the effect of ZBTB7A on apoptosis.

overall_design: HNSCC cell line SAS were infected with control (sh.con) and knockdown ZBTB7A (sh.ZBTB7A).  Total RNA was subjected to mRNA enrichment, fragmentation, reverse transcription, library construction and sequencing (Genomics Co., Taipei, Taiwan). The transcriptome was then aligned according to the various genes' FPKM (Fragments Per Kb of transcript per Million mapped reads) values in order to detect discrepancies in the transcript levels within the various cells.

first: Li-Yin

last: Yeh

first: Kuo-Wei

last: Chang