title: Long Non-Coding RNAs MALAT1 and NEAT1 in Non-syndromic Cleft Lip and Palate

city: Lanzhou

first: Baoping

address: Donggang 199

department: School of Stomatology

institute: Lanzhou University

summary: The etiology and pathogenesis of non-syndromic cleft lip and palate (NSCL/P) are largely unknown. Long non-coding RNAs (lncRNA) are thought to play important roles in NSCL/P, but reports on the underlying processes are currently unavailable. Our study focused on children diagnosed with NSCL/P alone. Based on the morphology, patients were categorized as either cleft lip with or without cleft palate (CL/P) or cleft palate-only (CPO). When patients received surgery for NSCL/P, tissue excised from the trimmed wound edge was reserved to serve as experimental samples; adjacent normal tissue was used as a positive control. Target lncRNAs in the collected tissues were identified using microarray and quantitative reverse transcription PCR (RT-qPCR). Immunohistochemical (IHC) staining and RT-qPCR were used to verify the target mRNAs. Pathway, gene ontology (GO) enrichment, and TargetScan prediction were employed to construct endogenous RNA networks (ceRNA networks) and explore their potential functions. RNA-Seq analysis revealed 24 upregulated and 43 downregulated lncRNAs in the CL/P and CPO groups compared with those in the control group; of these, MALAT1and NEAT1 were screened and validated using RT-qPCR. Common NSCL/P risk factors positively correlated with MALAT1 and NEAT1 expression (ORMALAT1 = 28.111, 95% CI: 4.054-194.923; ORNEAT1 = 30.556, 95% CI: 4.422-211.142; P < 0.05). Bioinformatics predicted four ceRNA networks: MALAT1-hsa-miR-1224-3p-SP1, MALAT1-hsa-miR-6734-5p/hsa-miR-1224-3p-WNT10A, NEAT1-hsa-miR-140-3p.1-CXCR4, and NEAT1-hsa-miR-3129-5p/hsa-miR-199a-3p/hsa-miR-199b-3p-ZEB1. GO enrichment focused on the potential functions of ceRNA networks, including biosynthesis of organic cyclic compounds, formation of membrane-enclosed and organelle lumens, and Wnt-protein binding. The results of RT-qPCR were consistent with those of IHC staining with regard to expression of related mRNAs. MALAT1 and NEAT1, which are upregulated in NSCL/P, are associated with the severity of NSCL/P. This study provides a new insight into NSCL/P pathogenesis and suggests that MALAT1 and NEAT1 act as potential therapeutic targets and prognostic biomarkers for NSCL/P.

first: Errui

last: Wang

first: Yumeng

last: Guo

first: Shuting

last: Gao

first: Ying

last: Zhou

first: Bin

last: Liu

first: James

last: Tsoi

first: Yayuan

last: Zheng

first: Qiaozhen

first: Junkai

last: Zhai

first: Zhengkun

first: Kailiang

first: Ruimin


title: Protein binding profiles on chromatin in human AML cells

status: Public on Sep 06 2021

city: PHILADELPHIA

first: Zhendong

last: Cao

state: PA

address: BRB Rm620, 421 Curie Blvd

department: Cancer biology

country: USA

institute: university of pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cancer cell type-selective addiction of transcription-chromatin regulatory program provides opportunities for therapeutic interventions. Here, we uncovered an IRF8-MEF2D transcription factor (TF) regulatory circuit as an acute myeloid leukemia (AML)-biased dependency. Combining CRISPR-based genetic screens, transcriptional analysis, and chromatin profiling, we demonstrated that a chromatin regulator, ZMYND8, directly regulates IRF8 and MYC expression through occupying AML-specific enhancer regions. ZMYND8 was essential for AML proliferation both in vitro and in vivo. The ZMYND8-occupied IRF8 enhancer was further characterized using Circular Chromosome Conformation Capture and CRISPRi-based perturbation assays and was observed in  primary patient cells. Importantly, mutagenesis experiments revealed that the PHD/Bromodomain/PWWP reader module is required for ZMYND8 tethering to leukemia-essential co-activator BRD4 for enhancer-mediated gene regulation. Our results rationalize ZMYND8 as a potential selective therapeutic target for modulating the IRF8/MYC transcriptional networks in AML.

first: Hua

last: Huang

first: Junwei

last: Shi


title: tRNA overexpression rescues peripheral neuropathy caused by mutations in tRNA synthetase

status: Public on Sep 07 2021

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

country: Germany

institute: Universitaet Hamburg

summary: Heterozygous mutations in six tRNA synthetase genes cause Charcot-Marie-Tooth (CMT) peripheral neuropathy. CMT-mutant glycyl- or tyrosyl-tRNA synthetases inhibit global protein synthesis by an unknown mechanism, independent of aminoacylation activity. We report that tRNAGly overexpression rescues protein synthesis and peripheral neuropathy phenotypes in Drosophila and mouse models of CMT caused by glycyl-tRNA synthetase (GlyRS) mutations (CMT2D). Kinetic experiments revealed that CMT-mutant GlyRS  bind tRNAGly, but display markedly slow release rates. This tRNAGly sequestration may deplete the cellular tRNAGly pool, leading to insufficient glycyl-tRNAGly supply to the ribosome and translation deficit.

overall_design: Ribosomal sequencing of mouse spinal cord tissue to determine ribsome occupancy across Glycine codons in GARS mutant tissue

first: Robin

last: Thompson

first: Leonardo

middle: A

last: Santos

first: Amila

last: Zuko

first: Erik

last: Storkebaum


title: ATAC-seq on DHT treated/untreated prostate cell line RWPE1

city: London

first: Isabella

last: Barbutti

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

summary: Precise gene regulation is needed for the correct differentiation and function of cells. This is especially important when putting cells through stimuli that would change their characteristics. To understand the changes in chromatin accessibility of prostate cells when stimulating them with testosterone, we performed the ATAC-seq (Assay for Transposase Accessible Chromatin using sequencing). We have worked with the normal epithelial prostate cell line RWPE1, an heterogenous cell line composed of two subpopulations: WPE-stem (stem cell phenotype) and WPE-int (intermediate cellular subtype) and treated it with DHT. Our aim was to study haemoglobin gene regulation in prostate cells, and check whether changes in cell stimulus would lead to changes in chromatin accessibility in both haemoglobin loci. Nevertheless, the results obtained could be used to compare chromatin accessibility between DHT treated and untreated cells on any loci.

overall_design: ATAC-seq of the normal epithelial prostate cell line RWPE1 untreated (2 replicates) or treated with DHT (2 replicates)

first: Hernandes

middle: F

last: Carvalho


title: CaMKIIdelta is required for diabetic hyperglycemia but not nephropathy

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

type: Expression profiling by high throughput sequencing

summary: Type 2 diabetes is an increasing pandemic health problem and leads to several late diabetic complications of organs including kidney and eye. Lowering elevated blood glucose levels is the typical therapeutic goal in clinical medicine. However, it is possible that hyperglycemia is only a symptom of diabetes but not the correct target to monitor, in order to prevent late diabetic complications. Instead, other diabetes-related alterations could be primary causes for late diabetic complications. Here, we studied the role of CaM Kinase II δ (CaMKIIδ) that is activated through diabetic metabolism. CaMKIIδ is expressed ubiquitously and might therefore affect several different organ systems. We crossed diabetic leptin receptor mutant mice to mice lacking CaMKIIδ globally. Remarkably, CaMKIIδ-deficient diabetic mice did not develop hyperglycemia. As potential underlying mechanisms, we found evidence for improved insulin sensing and increased glucose transport into skeletal muscle. Despite normoglycemia CaMKIIδ-deficient diabetic mice developed the full picture of diabetic nephropathy. In contrast, diabetic retinopathy was prevented. These data challenge the clinical concept of normalizing elevated high glucose levels in diabetes as a causative treatment strategy for late diabetic complications and call for a more detailed analysis of intracellular metabolites in different organs.

overall_design: Retinal ("R") and renal ("K") mRNA profiles of 16week old Lepr(+/+) or Lepr(db/db) with a global CAMK2D knockout (4 groups per organ: WT_ndb; WT_db; KO_ndb; KO_db

first: Jessy

last: Chen

first: Johannes

last: Backs

first: Marco

last: Hagenmüller


title: IL-1β–driven osteoclastogenic Tregs accelerate bone erosion in arthritis

city: Paris

first: Anaïs

last: Levescot

address: 24 boulevard du Montparnasse

country: France

institute: INSERM Institut Imagine

summary:
Purpose: The goal of this study is to evaluate Il1rn-/- Tregs features by bulk RNA sequencing (RNA-seq) of Tregs from WT and Il1rn-/- lymph nodes.

Methods: mRNA profiles of isolated CD4+Foxp3eGFP+ from lymph nodes of three 35-day-old wild-type (WT) and three Il1rn-/- mice were generated by deep sequencing. RNA was extracted from sorted cells (5X10^4) using a Qiagen RNeasy Micro Kit. RNA-seq was performed using the Smart-Seq2 platform. Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Joint Biology Consortium– associated Broad Genomics Platform. Transcripts were quantified by the Broad computational pipeline using Cuffquant version 2.2.1.

Results: WT and Il1rn-/- Tregs showed similar expression of multiple genes associated with suppressor function, including Foxp3, Il2ra, Il7r, and Ebi3 (a component of the suppressive cytokine IL-35), and transcription factors including E_o_m_e_s_, Tbx21 (encoding Tbet), and Irf4. Tregs from WT and Il1rn-/- _mice showed similar expression of genes encoding molecules involved in Treg localization and trafficking, including CXCR6, CXCR3, and CCR10. However, gene set enrichment analysis (GSEA) identified enhanced expression of genes encoding proteins involved in fatty acid metabolism (for example, NTHL1 and GABARAPL1) in Il1rn-/- Tregs and oxidative phosphorylation (OxPhos; for example, ATP5H and NDUFB3) in WT Tregs.

Conclusions: Il1rn-/- Foxp3+ Tregs exhibited greater glycolytic capacity and reserve that WT Tregs. This finding is consistent with the superiority of Il1rn-/- Tregs with respect to suppression of T cell proliferation, a capacity associated with glycolysis

overall_design: Lymph node mRNA profiles of 35-day old wild type (WT) and Il1rn-/- mice

first: Peter

last: Nigrovic


title: IRF8 binding profiles in human AML cells


title: Gene expression change after inactivation of ZMYND8 by CRISPR-Cas9

overall_design: mRNA profiles of Cas9 sgRNA-expressing human cell lines


title: PrbP modulates biofilm formation in Liberibacter crescens

city: Gainesville

first: Kaylie

last: Padgett-Pagliai

state: Florida

address: 2033 Mowry Road, Lab 325 CGRC

institute: University of Florida

summary: RNA sequencing of L. crescens grown with tolfenamic acid and a DMSO vehicle control.

overall_design: L. crescens BT-1 cells were grown with 10 μM tolfenamic acid (in 0.05% dimethyl sulfoxide) while the control was grown with 0.05% DMSO. L. crescens BT-1 cells were collected at OD600= 0.3 (mid-exponential phase) by centrifugation at 8000 rpm, at 4 °C. Total RNA was extracted with the RiboPure-Bacteria (Life Technologies) kit following the manufacturer’s protocol. The quality of isolated RNA samples was examined in an Agilent 2100 Bioanalyzer. The rRNA was depleted using the MICROBExpress Bacterial mRNA enrichment kit (Life Technologies) according to the manufacturer’s instructions. Single end RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and followed by sequencing using a HiSeq2500 system. RNA sequencing was performed by the Genome Sciences Facility at Penn State University in Hershey, PA. The assays were performed in duplicates, and approximately 2million reads were obtained for each library.

first: Lei

last: Pan

first: Christopher

last: Gardner

first: Reagan

last: Beliakoff

first: Danilo

last: da Silva

first: Ran

last: Zuo

first: Fernando

last: Pagliai

first: Marcelo

last: Merli

first: Erol

last: Bahadiroglu

first: Claudio

last: Gonzalez

first: Graciela

last: Lorca


title: Single-cell analysis of non-myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA-seq]

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

country: China

institute: Sun Yat-sen University

summary: Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes, yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes, but also non-cardiomyocytes (nonCMs). However, the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single-cell datasets, we analyzed the transcriptome dynamics of 61,977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single-cell analysis and in situ hybridization, we identified major nonCM cell types, including multiple novel subpopulations with unique tempo-spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly, genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single-cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration.

overall_design: Single-cell RNA-seq profiles of cardiac non-cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.

first: Hong

last: Ma

first: Jiandong

last: Liu


title: A genome-scale antibiotic screen in Serratia marcescens identifies YdgH as a conserved modifier of cephalosporin and detergent susceptibility

city: Boston

first: Jacob

middle: Eric

last: Lazarus

address: 55 Fruit St

institute: Massachusetts General Hospital

summary: Serratia marcescens, a member of the order Enterobacterales, is adept at colonizing healthcare environments and an important cause of invasive infections. Antibiotic resistance is a daunting problem in S. marcescens because in addition to plasmid-mediated mechanisms, most isolates have considerable intrinsic resistance to multiple antibiotic classes. To discover endogenous modifiers of antibiotic susceptibility in S. marcescens, a high-density transposon insertion library was subjected to sub-minimal inhibitory concentrations of two cephalosporins, cefoxitin and cefepime, as well as the fluoroquinolone ciprofloxacin. Comparisons of transposon insertion abundance before and after antibiotic exposure identified hundreds of potential modifiers of susceptibility to these agents. Using single gene deletions, we validated several candidate modifiers of cefoxitin susceptibility and chose ydgH, a gene of unknown function, for further characterization. In addition to cefoxitin, deletion of ydgH in S. marcescens resulted in decreased susceptibility to multiple 3rd generation cephalosporins, and in contrast, to increased susceptibility to both cationic and anionic detergents. YdgH is highly conserved throughout the Enterobacterales, and we observed similar phenotypes in Escherichia coli O157:H7 and Enterobacter cloacae mutants. YdgH is predicted to localize to the periplasm and we speculate that it may be involved there in cell envelope homeostasis. Collectively, our findings provide insight into chromosomal mediators of antibiotic resistance in S. marcescens and will serve as a resource for further investigations of this important pathogen.

sample_organism: Serratia marcescens subsp. marcescens ATCC 13880

overall_design: We performed transposon-insertion sequencing on transposon mutagenized libraries in S. marcescens ATCC 13880 and in libraries exposed to clinically used antibiotics

middle: E

first: Alyson

middle: R

last: Warr

first: Katherine

last: Westervelt

first: David

middle: C

last: Hooper

first: Matthew

middle: K

last: Waldor


title: Beyond the protoplast: isolating and analyzing fixed cells for plant single-cell research

city: Stanford

first: D.

middle: Blaine

last: Marchant

state: California

address: Gilbert Biological Sciences Building, 371 Serra Mall

department: Biology

institute: Stanford University

summary: We isolated fixed maize anther cells for single-cell RNA-seq. All anthers were 2.0 mm from the W23 inbred line.

overall_design: Fixed single-cell RNA-sequencing of early meiotic maize anther cells. Libraries were constructed using a modified version of CEL-Seq2.

first: D

middle: B

first: B

last: Nelms

first: V

last: Walbot


title: Genome wide analysis of cis-regulatory elements reveals gene regulatory networks in metabolic adaptation of cavefish

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

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

overall_design: Refer to individual Series


title: Cortical transcriptome analysis of Cyfip2 mutant mice

city: Seoul

first: Kihoon

last: Han

address: 73, Inchon-ro, Seongbuk-gu

department: Neuroscience

country: South Korea

institute: Korea University College of Medicine

summary: CYFIP2 is a component of the WAVE regulatory complex which regulates actin polymerization and branching in diverse cellular compartments. Recent molecular genetic studies identified mutations of CYFIP2 in patients with early-onset epileptic encephalopathy and microcephaly, suggesting that CYFIP2 may have some roles in embryonic brain development. To understand its functions in vivo at the molecular level, we performed RNA-seq analysis in embryonic Cyfip2 mutant mice.

overall_design: Cortical transcriptome of embryonic day 18.5 wild-type and Cyfip2 mutant mice.

first: Yinhua

last: Zhang

first: Hyojin

last: Kang


title: Discovery of Dual targeting PEGylated BG-P1600-TAT to Norepinephrin Transporter (NET) and Thyrointegrin αvβ3 in the Treatment of Neuroblastoma cancer cellline

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: Molecular mechanisms of anti-cancer activities of BG-P1600-TAT were explored employing genome-wide expression profiling experiments. Human neuroblastoma cell line SK-N-FI and primary cells SKNAS were treated with 30µM of the BG-P1600-TAT for 48 hours, harvested, and total RNA was immediately isolated from three biological replicates of control (vehicle-treated) and BG-P1600-TAT-treated cells. Gene expression profiling experiments identified 14-gene BG-P1600-TAT molecular interference signature captured most biologically important significantly enriched records reflecting the putative molecular mechanisms of anti-cancer activities of the BG-P1600-TAT. In  BG-P1600-TAT  treated SK-N-FI cells, 753 differentially expressed genes (DEGs) were identified compared to control vehicle-treated cells. Among 753 DEGs, 427 genes were down-regulated and 326 genes were up-regulated. In SKNAS cells, BG-P1600-TAT showed a significant effects on signal transduction pathways activated during cellular responses to IL-1alpha, TNF-alpha, EGF, TGF, PDGF, and AR. Further BG-P1600-TAT also showed a significant effect on multiprotein complexes of potential biological and therapeutic significance, including several complexes engaged during apoptosis (BCL-2 family protein complex; Survivin complex; BAX complex; Caspase complex), angiogenesis (VEGF-A complex; Thrombospondin complex), and cell adhesion (Galectin complex; Integrin alpha/beta complexes).

overall_design: Genome-wide expression profiling experiments were carried out to gain insights into biological and molecular functions of genes expression of which was significantly affected in neuroblastoma cells by the BG-P1600-TAT treatment. RNA isolation from three biological replicates of control SK-N-FI cells compared with SK-N-FI cells treated with BG-P1600-TAT (30 µM) for 48 h. Further neuroblastoma primary cells SKNAS (control) compared with SKNAS cells treated with BG-P1600-TAT (30 µM) for 48 h

first: Gennadi

last: Glinsky

first: Kavitha

last: Godugu

first: Karakus

last: Ozlem

first: Shaker

last: Mousa


title: Karrikins control seedling photomorphogenesis through the HY5-BBX transcriptional module.

city: Berlin

first: Henrik

last: Johansson

address: Albrecht-Thaer-Weg 6

institute: Freie Universität Berlin

summary: Karrikins (KARs) are a class of butenolide molecules found in the smoke of burned plant material that can induce germination of many plant species that emerge after fire. Intriguingly, KAR perception is widely conserved and not limited to fire-followers. For example, germination of dormant Arabidopsis thaliana seeds can also be stimulated by KARs. Additionally, KAR treatment enhances responses of seedlings to light. These responses include inhibition of hypocotyl elongation, enhancement of cotyledon expansion, and transcriptional upregulation of light-responsive genes not only in Arabidopsis but also in Brassica tournefortii.   Although the core KAR signaling mechanism, consisting of KAI2-SCF/MAX2-mediated degradation of SMAX1 and SMXL2, is well described, it remains elusive how SMXL degradation leads to downstream growth responses. In this study, we analyse the role of BBX20 in the KAR signaling pathway through both chemical and genetic approaches using knock-out mutants. We find that BBX20, together with its close homologue BBX21, is essential for KAR-induced inhibition of hypocotyl elongation and anthocyanin accumulation. Our detailed genetic analysis suggests that BBX20 and BBX21 act in a HY5-dependent transcriptional module downstream of SMAX1 and SMXL2. While RNA-seq analysis revealed large-scale transcriptional changes in the smax1 smxl2 mutant, our results clearly suggest that BBX20 and BBX21 are required for a subset of SMAX1/SMXL2-dependent transcriptional regulation. Overall, our data suggest that the KAR signaling pathway promotes the activity of the HY5-BBX transcriptional module and that this module represents a point of convergence between KAR and light signaling.

overall_design: RNA-seq analysis of bbx2021 and smax1 smxl2 Arabidopsis seedlings grown for 4 days in red light, in triplicate, using RNA-seq analysis

first: Katharina

last: Bursch


title: Regulatory elements in a Transcriptional Network Orchestrating Regional Patterning of Cortical Progenitors

city: San Francisco

first: Kenneth

last: Lim

state: CA

department: Psychiatry

institute: UCSF

summary: To map enhancers involved in regional patterning of cortical progenitors, we performed TF ChIP for patterning transcription factors as well as assays for epigenomic marks and DNA accessibility in VZ cells purified from wild-type and patterning mutant mice. This integrated approach identified a cortical Regionalization TF network and VZ enhancers involved in cortical regional patterning.

overall_design: TF (EMX2, LHX2, NR2F1, PAX6, PBX1) and histone ChIP-Seq (H3K27ac and H3k27me3) and ATAC-Seq were conducted on mouse cortex at E12.5.TF ChIP-seq was conducted on microdissected cortex. Histone ChIP-Seq and ATAC-Seq was conducted on VZ purified cells (using FlashTag methods) in WT and patterning mutant mice (Emx2 KO, Pax6 KO, Nr2f1 KO).

first: Athena

last: Ypsilanti

first: Susan

middle: L

last: Lindtner

first: Olga

last: Golonzhka

first: Rinaldo

last: Catta-Preta

first: John

last: Rubenstein


title: TIPE1 regulation on macrophage polarization

status: Public on Sep 05 2021

city: Jinan

first: xiao

middle: lei

last: Ren

address: 44 Wenhua  Xi Road

department: School of Basic Medical Science

institute: Shandong University

summary: Macrophages perform key and distinct functions in maintaining tissue homeostasis through finely tuning their polarization state.Here, we found that tumor necrosis factor-α-induced protein 8-like 1 (TIPE1) was highly expressed in macrophages and Tipe1 depletion impeded M2 polarization of macrophages.  The goals of this study are to compare BMDMs from LyzM-Cre; Tipe1f/f or Tipe1f/f mice to have a further view of the potential difference.

overall_design: Examination of 2 different bone marrow derived macrophages from LyzM-Cre; Tipe1f/f or Tipe1f/f mice respectively

first: Xiaohong

last: Liang

first: Yang

last: Cheng


title: Delineating Chromatin Accessibility Re-patterning at Single Cell Level during Early Stage of Direct Cardiac Reprogramming

first: Yuchen

last: Yang

summary: Direct conversion of cardiac fibroblast into functional induced cardiomyocytes by forced expression of three cardiac transcription factors, Mef2c, Gata4, and Tbx5, holds great promise for regenerative medicine. Cardiac reprogramming consists of waves of transcription remodeling events, including the fast acquisition of cardiac program and the gradual loss of fibroblast program. However, how this transcription remodeling was driven by the upstream chromatin landscape is still unclear. In this study, we performed single-cell ATAC-seq on Day 3 cardiac reprogramming cells and unveiled networks of transcription factors (TFs) playing a pivotal role in the shift of chromatin accessibility during the early stage of cardiac reprogramming. Moreover, integration analysis of scRNA-seq and scATAC-seq lead to the identification of active TFs function as barriers to cardiac reprogramming.

overall_design: Single-cell ATAC-seq profiles of Day 3 cardiac fibroblast undergoing cardiac reprogramming  were generated by 10x Genomics Chromium System.

first: Haofei

last: Wang

first: Li

last: Qian


title: Diurnal gene expression in the retina of a mouse model of diabetic retinopathy

first: Carsten

last: Sticht

summary:
The mammalian retina contains an endogenous circadian clock system, located in various cell types. This system enables timing of a broad range of essential retinal functions to anticipate daily changes in environmental lighting conditions. Furthermore, the circadian clocks appear to promote retinal health. A leading cause of blindness in developed countries is diabetic retinopathy. While it is clear that diabetes affects the master clock and its circadian output in the SCN, the effect of diabetic retinopathy on the retinal clock system is unknown.
To investigate the influence of diabetic retinopathy on circadian regulation of the retina at a genome-wide level, microarray analysis was used to compare retinal transcriptomes between light- and dark-adapted non-diabetic and diabetic mice.

overall_design: Retinae of adult non-diabetic (db/+) and diabetic (db/db) mice (BKS.Cq-Dock7m +/+ Leprdb/J) were sampled at two different zeitgeber times (ZTs) during the 24-hour light/dark-cycle namely 6 hours after lights-on (ZT6) and 6 hours after lights-off (ZT18) for RNA extraction and hybridization on Affymetrix microarrays. 3 mice were used for each genotype and time-point.

first: Patrick

last: Vancura

first: Rainer

last: Spessert


title: Chromatin Immunoprecipitation(ChIP)-seq of Flag-USP39 in ovarian cancer cells

city: jinan

first: Shourong

address: 44 Wenhua Xi Road

summary: High-grade serous ovarian carcinoma is the most lethal type of gynecologic malignancy.Emerging evidences have suggested the vital roles of splicing factor in the human cancers. RNA splicing pathways was found excessive activated in HGSOC. USP39 was one of overexpressed splicing factor in HGSOC. However, the biological function and concrete regulatory mechanism of USP39 in ovarian cancer remain unclear. In this study, we investigate the oncogenic roles of the splicing factor USP39 in HGSOC through facilitated the growth speed and invasion of ovarian cancer cells.Elevated USP39 expression levels, based on immunohistochemistry staining, were associated with poor survival in HGSOC patients. Since many RNA-binding proteins showed DNA-binding ability , we performed ChIP-seq in A2780 cells with Flag-USP39 overexpression in order to detect the bindng of USP39 to DNA and POLR2A was used as a positive control.

overall_design: The assay was performed in A2780 cells with Flag-USP39 using anti-Flag antibody.POLR2A was used as a positive control.10% of gemonic DNA was used as input.

first: Zhaojina

last: Liu


title: Role of TGFb1 and Wnt6 in FGF2 and BMP4-driven endothelial differentiation of murine embryonic stem cells

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

country: Italy

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute


title: Role of TGFb1 and Wnt6 in FGF2 and BMP4-driven endothelial differentiation of murine embryonic stem cells [3h]

summary:
In this work we investigated the molecular mechanisms that sustain the endothelial differentiation of murine embryonic stem cells (ES). When ES cells are co-cultured with the stromal PA6 cells in serum-free medium they differentiate mainly into neurons, thanks to the neural inducing activity exerted by the stroma. The addition of exogenous FGF2 allows also the differentiation of endothelial cells whereas, in presence of exogenous BMP4, ES cells differentiate exclusively into endothelium. A pivotal role in ES cells differentiation is played by the stromal PA6 cells.To analyze the early signals released by PA6 cells in the medium of the co-cultures in response to FGF2 and BMP4,  monolayers of PA6 cells were treated with recombinant FGF2 or BMP4 for 3 hours and the gene expression analysis of treated PA6 cultures versus the untreated ones was performed.
In this work we investigated the molecular mechanisms that sustain the endothelial differentiation of murine embryonic stem cells (ES). When ES cells are co-cultured with the stromal PA6 cells in serum-free medium they differentiate mainly into neurons, thanks to the neural inducing activity exerted by the stroma. The addition of exogenous FGF2 allows also the differentiation of endothelial cells whereas, in presence of exogenous BMP4, ES cells differentiate exclusively into endothelium. A pivotal role in ES cells differentiation is played by the stromal PA6 cells.To analyze the early signals released by PA6 cells in the medium of the co-cultures in response to FGF2 and BMP4,  monolayers of PA6 cells were treated with recombinant FGF2 or BMP4 for 3 hours and the gene expression analysis of treated PA6 cultures versus the untreated ones was performed.

overall_design: PA6 cell monolayers were cultured for 3 hours in serum-free medium in absence of growth factors (-GFs), in presence of FGF2 (+FGF2) or in presence of BMP4 (+BMP4)


title: Overexpression of wild type IL-7Rα promotes T-cell acute lymphoblastic leukemia/lymphoma

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

summary: Tight regulation of IL-7Rα expression is essential for normal T-cell development. IL-7Rα gain-of-function mutations are known drivers of T-cell acute lymphoblastic leukemia (T-ALL). Although a subset of T-ALL patients display very high IL7R mRNA levels and cases with IL7R gains have been reported, the impact of IL-7Rα overexpression, rather than mutational activation, on leukemogenesis remains unclear. Here, we show that overexpression of IL-7Rα in tetracycline-inducible Il7r transgenic and Rosa26 IL7R knock-in mice drives thymus hyperplasia due to increased proliferation of T-cell precursors, which subsequently infiltrate lymph nodes, spleen and bone marrow, ultimately leading to fatal leukemia. The tumors mimic key features of human T-ALL, including heterogeneity in immunophenotype and genetic subtype between cases, frequent hyperactivation of PI3K/Akt pathway that is paralleled by downregulation of p27Kip1 and upregulation of Bcl-2, and gene expression signatures evidencing JAK/STAT, PI3K/Akt/mTOR and Notch signaling activation. Notably, we also find that established tumors no longer require high levels of IL-7R expression upon secondary transplantation and can progress even in the absence of IL-7, but remain sensitive to the Bcl-2 inhibitor Venetoclax. The relevance of these findings for human disease are highlighted by the fact that T-ALL patient samples with high wild type IL7R expression display a transcriptional signature resembling that from IL-7-stimulated pro-T cells and, critically, from IL7R mutant T-ALL cases. Overall, our studies demonstrate that high expression of IL-7Rα can promote T-cell tumorigenesis even in the absence of IL-7Rα mutational activation.

overall_design: T-ALL tumors developing in mice with tetracycline-inducible expression of IL-7Rα were compared with control tissue from healthy mice

last: Silva

first: Mafalda

last: Matos

first: Benedict

last: Seddon

first: João

middle: T

last: Barata


title: Gene expression in primary AML patients

city: PHILADELPHIA

first: Zhendong

last: Cao

institute: university of pennsylvania

summary: Cancer cell type-selective addiction of transcription-chromatin regulatory program provides opportunities for therapeutic interventions. Here, we uncovered an IRF8-MEF2D transcription factor (TF) regulatory circuit as an acute myeloid leukemia (AML)-biased dependency. Combining CRISPR-based genetic screens, transcriptional analysis, and chromatin profiling, we demonstrated that a chromatin regulator, ZMYND8, directly regulates IRF8 and MYC expression through occupying AML-specific enhancer regions. ZMYND8 was essential for AML proliferation both in vitro and in vivo. The ZMYND8-occupied IRF8 enhancer was further characterized using Circular Chromosome Conformation Capture and CRISPRi-based perturbation assays and was observed in  primary patient cells. Importantly, mutagenesis experiments revealed that the PHD/Bromodomain/PWWP reader module is required for ZMYND8 tethering to leukemia-essential co-activator BRD4 for enhancer-mediated gene regulation. Our results rationalize ZMYND8 as a potential selective therapeutic target for modulating the IRF8/MYC transcriptional networks in AML.

overall_design: mRNA profiles of primary AML blasts

first: Junwei

last: Shi


title: Role of TGFb1 and Wnt6 in FGF2 and BMP4-driven endothelial differentiation of murine embryonic stem cells [3d]

summary:
In this work we investigated the molecular mechanisms that sustain the endothelial differentiation of murine embryonic stem cells (ES). When ES cells are co-cultured with the stromal PA6 cells in serum-free medium they differentiate mainly into neurons, thanks to the neural inducing activity exerted by the stroma. The addition of exogenous FGF2 allows also the differentiation of endothelial cells whereas, in presence of exogenous BMP4, ES cells differentiate exclusively into endothelium. The purpose of the gene expression analysis of FGF2 and BMP4 treated co-cultures versus the untreated ones was to profile the transcriptomes of FGF2 and BMP4-driven endothelial differentiation in order to detect molecules and pathways involved upon each of the two exogenous signals. In parallel we also performed transcriptome analysis of single monocultures of stromal PA6 cells to investigate the signals released by the stroma in response to FGF2 and BMP4. We found that TGFb1 is involved in the differentiation of ES cells into endothelium in response to FGF2 while Wnt6 and Wnt pathway sustain the endothelial differentiation of ES cells in response to BMP4.
In this work we investigated the molecular mechanisms that sustain the endothelial differentiation of murine embryonic stem cells (ES). When ES cells are co-cultured with the stromal PA6 cells in serum-free medium they differentiate mainly into neurons, thanks to the neural inducing activity exerted by the stroma. The addition of exogenous FGF2 allows also the differentiation of endothelial cells whereas, in presence of exogenous BMP4, ES cells differentiate exclusively into endothelium. The purpose of the gene expression analysis of FGF2 and BMP4 treated co-cultures versus the untreated ones was to profile the transcriptomes of FGF2 and BMP4-driven endothelial differentiation in order to detect molecules and pathways involved upon each of the two exogenous signals. In parallel we also performed transcriptome analysis of single monocultures of stromal PA6 cells to investigate the signals released by the stroma in response to FGF2 and BMP4. We found that TGFb1 is involved in the differentiation of ES cells into endothelium in response to FGF2 while Wnt6 and Wnt pathway sustain the endothelial differentiation of ES cells in response to BMP4.

overall_design: ES/PA6 co-cultures or PA6 cell monocultures were cultured for 3 days in serum-free medium in absence of growth factors (-GFs), in presence of FGF2 (+FGF2) or in presence of BMP4 (+BMP4)

first: Anna

last: Gualandris

first: D

last: Corà

first: Federico

last: Bussolino


title: 14q32 recombinations deregulating BCL11B mark a distinct Mixed Phenotype Leukemia

city: Perugia

first: Danika

last: Di Giacomo

address: Piazzale Menghini 0

department: Medicine

institute: University of Perugia

type: Genome variation profiling by high throughput sequencing


title: RNA-seq analysis of 12 cases with BCL11B rearrangement

summary: This study identified a cytogenetic-molecular entity, we named BCL11B-R, that showed a typical constellation of genomic features, namely BCL11B activation via chromosome translocations at 14q32, a distinct transcriptome profile, and FLT3 mutations.

overall_design: Expression analysis by RNAseq of 12 cases bearing a 14q32/BCL11B rearrangement

first: Cristina

last: Mecucci

first: Rocco

last: Piazza


title: Symmetry breaking in gastruloid development

status: Public on Sep 04 2021

first: Marietta

last: Zinner

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: We use single cell RNA sequencing to describe the transcriptional changes during gastruloid development from 24 to 84 hours with 12 hours intervals.

overall_design: Examination of transcriptional profiles of gastruloids cultured in N2B27 at 24, 36, 48, 60, 72, and 84 hours post-seeding.

first: Ilya

last: Lukonin

first: Simon

last: Suppinger

first: Giovanni

last: Palla

first: Raphael

last: Ortiz

first: Chiara

last: Azzi

first: Ludivine

last: Challet-Meylan

first: Michael

last: Stadler

first: Stefano

last: Vianello

first: Fabian

middle: J

last: Theis

first: Matthias

middle: P

last: Lutolf

first: Prisca

last: Liberali


title: Role of TGFb1 and Wnt6 in FGF2 and BMP4-driven endothelial differentiation of murine embryonic stem cells [7d]

first: Davide

last: Cora'

overall_design: ES/PA6 co-cultures or PA6 cell mono-cultures were cultured for 7 days in serum-free medium in absence of growth factors (-GFs), in presence of FGF2 (+FGF2) or in presence of BMP4 (+BMP4)


title: RNA Profiles of the Korat Chicken Breast Muscle with Increased Carnosine Content Produced through Dietary Supplementation with β-Alanine or L-Histidine

city: Muang District

first: Satoshi

last: Kubota

state: Nakhon Ratchasima

address: 111 University Avenue, Suranaree Sub-District,

country: Thailand

institute: Suranaree University of Technology

summary: Carnosine is a bioactive food component with several potential health benefits for humans due to its physiological functions. Dietary　supplementation with β-alanine or L-histidine can increase the carnosine content of skeletal muscles in chickens. Dietary supplementation with β-alanine or L-histidine has produced a slow-growing chicken variety　with high carnosine content in the breast meat; however, the　supplementation with L-histidine alone softens the meat toughness, which may affect consumers’ willingness to buy the meat. Gene　expression is a key factor that influences meat quality. Understanding the molecular mechanisms that affect carnosine content and meat toughness would allow the production of more value-added slow-growing chickens. We compared global gene expression in chicken breast muscles with differing carnosine contents and meat toughness produced through dietary supplementation with β-alanine or L-histidine. We identified differentially expressed genes involved in regulating myosin, collagen, intramuscular fat, and calpain—factors that may affect meat tenderness. Pathway enrichment analysis indicated that the insulin-related and adipocytokine signaling pathways were altered by dietary supplementation with β-alanine or L-histidine. These data will be useful for future studies on carnosine content and meat toughness in slow-growing chickens.

overall_design: A total of 15 samples consisting of five biological replicates of three feed trials: non-supplementation (control), β-alanine supplementation, and L-histidine supplementation.

first: Kasarat

last: Promkhun

first: Panpradub

last: Sinpru

first: Chanadda

last: Suwanvichanee

first: Wittawat

last: Molee

first: Amonrat


title: Single-cell analysis of non-myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [bulk RNA-seq]

first: Yuchen

last: Yang

summary: Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes, yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes, but also non-cardiomyocytes (nonCMs). However, the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single-cell datasets, we analyzed the transcriptome dynamics of 61,977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single-cell analysis and in situ hybridization, we identified major nonCM cell types, including multiple novel subpopulations with unique tempo-spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly, genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single-cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration.

overall_design: To assess the proliferation defect of kit (aka, c-kit) mutant CMs, we conducted transcriptome-wide bulk RNA-seq of control and mutant cardiomyocytes

first: Hong

last: Ma

first: Jiandong

last: Liu


title: Enriched Alternative Splicing in Islets of Diabetes-Susceptible Mice

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

summary: Mouse strains like NZO and B6-ob/ob differ in their susceptibility to diet-induced diabetes. Comparison of the islet transcriptomes already revealed different biological processes, here we focused on alternative splicing events as one possible mechanism.

overall_design: Male NZO and B6-ob/ob mice were kept on a carbohydrate-free high-fat diet until the age of 18 wks. Afterwards, diet was switched to a carbohydrate-containing diet to induce glucolipotoxic stress.

first: Annette

last: Schürmann

first: Meriem

last: Ouni

first: Ilka

last: Wilhelmi

first: Alexander

last: Neumann

first: Markus

last: Jähnert


title: Single-cell analysis revealed the role of CD8+ effector T cells in preventing cardioprotective macrophage differentiation in the early phase of heart failure

city: Shinjuku

first: Kyoko

last: Komai

state: Tokyo

address: 35 Shinanomachi

department: Department of Microbiology and Immunology

country: Japan

institute: Keio University school f medecine

summary: In this study, we explore a dynamic interplay between cardiac CD8+T cells and macrophages that is necessary for adaptation to cardiac stress, highlighting the homeostatic functions of resident and infiltrated macrophages in the heart. To understand transcriptomic differences of the heart, we performed single-cell RNA sequencing (scRNA-seq) analysis on cardiomyocytes.

overall_design: WT mice or mice without Tcells were pressure over loaded, and CD45＋cells were harvested from the heart 1 week later for single-cell RNA sequencing (scRNA-seq) analysis.

first: Minako

last: Ito

first: Seitaro

last: Nomura

first: Shigeyuki

last: Shichino

first: Manami

last: Katoh

first: Shintaro

last: Yamada

first: Toshiyuki

last: Ko

first: Mana

last: Iizuka-Koga

first: Hiroko

last: Nakatsukasa

first: Akihiko

last: Yoshimura


title: Affymetrix SNP array data for acute leukemias with a 14q32/BCL11B rearrangement

first: Danika

last: Di Giacomo

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

overall_design: Copy number analysis of Affymetrix 200K SNP arrays was performed for 15 BCL11B-R cases

first: Silvia

last: Arniani

first: Valentina

last: Pierini

first: Cristina

last: Mecucci


title: 4C-seq on MYC/IRF8

first: Zhendong

last: Cao

address: BRB Rm620, 421 Curie Blvd

overall_design: 4C-seq using MYC or IRF8 as viewpoint

first: Yeqiao

last: Zhou

first: Junwei

last: Shi


title: Comprehensive analysis on the signaling pathway of Norrie disease protein (Ndp)

first: Yushi

last: Hayashi

state: MA

address: 243 Charles St

department: Department of Otolaryngology

institute: Harvard Medical School

summary: Mutations in the gene for Norrie disease protein (Ndp) cause syndromic deafness and blindness. We show that cochlear function in an Ndp knockout (KO) mouse deteriorated with age: at P3-P4, hair cells (HCs) showed progressive loss of Pou4f3 and Gfi1, key transcription factors for HC maturation, and Myo7a, a specialized myosin required for normal function of HC stereocilia. Loss of expression of these genes correlated to increasing HC loss and profound hearing loss by 2 months of age. We show that overexpression of the Ndp gene in neonatal supporting cells or, remarkably, upregulation of canonical Wnt signaling in HCs rescued HCs and cochlear function. We conclude that Ndp secreted from supporting cells orchestrates a transcription factor network for the maintenance and survival of HCs and that increasing the level of b-catenin, the intracellular effector of Wnt signaling, is sufficient to replace the functional requirement for Ndp in the cochlea.

overall_design: Examination of sorted cochlear hair cells of wildtype and Norrie disease protein (Ndp) knockout mice

first: Albert

middle: S

last: Edge


title: Functional genomic analysis of the SPL9 gene in Arabidopsis thaliana under low phosphate conditions

status: Public on Sep 03 2021

city: Kaifeng

first: Lisa

last: Lei

address: Jinming Xi Street

institute: Henan University

summary: Inorganic phosphate (Pi) is an essential nutrient, which is often served as a limiting factor in plant growth. It has been reported that SPL family members, such as SPL3, regulate Pi deficiency responses by controlling the expression of Pi deficiency responsive genes. To elucidate whether SPL9 respond to low phosphorus stress, we investigated the phenotypes and conduct RNA sequencing analysis in transgenic Arabidopsis thaliana with overexpressing SPL9 (R9) under conditions of both normal and low Pi availability. Compared with wild-type plants, R9 showed decreased anthocyanin accumulation and increased Pi contents in shoots under Pi deficiency. Through RNA-seq analysis compared with wild-type plants, we detected 217 genes significantly differentially expressed in conditions of Pi sufficiency, and 121 genes differentially expressed in conditions of Pi deficiency in R9 plants. Under Pi deficiency, these genes included multiple protein kinases, jasmonic acid response genes and genes related to salt stress responses. Genes associated with hydrolase and transferase activity were also differentially regulated by Pi deficiency, such as cytochrome P450 monooxygenases. Of particular note, the transcription factor AP2-EREBP and members of the bHLH family were among the most significantly differentially regulated genes identified under both Pi sufficient and Pi deficient conditions.

overall_design: RNA sequence profiles of 21-day old of Pi-sufficient and Pi-deficient treatment of wild type (WT) and R9 seedlings were generated using Illumina NovaSeq 6000 platform in triple.

first: Huan

last: Dong

first: Kaijian


title: Quantitative Analysis of Cerebral Cortex Transcriptomes of BrapcKO Mice and their Wildtype-like Control Mice by Next-Generation Sequencing

city: Bethesda

first: Yuanyi

last: Feng

state: MD

address: 4301 Jones Bridge Road

institute: UNIFORMED SERVICES UNIVERSITY OF THE HEALTH SCIENCES

summary:
Purpose: Transcriptome profiling (RNA-seq) was performed in this study in order to assess differential gene expressions resulting from Brap loss of function in murine cerebral cortex.
Methods: Cerebral cortical mRNA profiles of 3-month-old Emx1-Cre-mediated Brap conditional knockout mice (BrapcKO) and their Cre-negative control littermates (Brap flox Cre-) were generated by next-generation sequencing, using Illumina HiSeq4000. Five BrapcKO and five control samples were analyzed. The quality of raw sequencing data was assessed using FastQC. Sequence reads that passed quality filters were analyzed by several methods, including DESeq2, edgeR, and Iimma, to discover differentially expressed genes.
Results: We obtained more than 30 million sequence reads per sample that are uniquely mapped to the mouse reference genome (build mm10). After alignment of reads, expression levels of individual genes were quantified and estimated using subread::featureCounts. With the removal of lowly expressed genes using the threshold at least 10 raw read counts, 14,276 out of 21,969 annotated, valid mouse genes were retained for further analysis. Data were analyzed using several state-of-the-art tools, including DESeq2, edgeR, and Iimma, with a fold change ≥1.5 and FDR < 0.1. We collected overlapped differentially expressed mRNA genes detected with more than one method, and identified 811 differentially expressed genes between BrapcKO and control group.
Conclusions: Our study represents detailed analysis of transcriptomes, with biologic replicates, generated by RNA-seq technology. The data provide insight into the neurological defects of BrapcKO mice.

overall_design: Cerebral cortical mRNA profiles of 3-month BrapcKO mice and their wildtype-like control littermates.


title: Single-cell analysis of non-myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations.

city: Guangzhou

first: Yuchen

last: Yang

address: Xingangxi Road 135

institute: Sun Yat-sen University

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

overall_design: Refer to individual Series


title: Differential DNA methylation profiles of HS ILAE type 1 in human temporal lobe epilepsy

city: Harbin

first: wang

last: zhang

state: Heilongjiang

address: No.23, Postal street, Nangang distric

department: Neurosurgery

institute: First Affiliated hospital of Harbin Medical Univesity

type: Methylation profiling by high throughput sequencing

summary:
Purpose:To provide new perspectives for molecular diagnosis of HS subtypes and find new therapeutic targets for the TLE patients with HS ILAE type 1.
Methods:DNA methylation was detected by Whole Genome Bisulfite Sequencing (WGBS). The distribution of differentially methylated regions (DMRs) in the whole genome and different functional regions of genes was comprehensively analyzed.
Results:A total of 3708 DMRs, including 1171 highly methylated DMRs and 2537 low methylated DMRs. Distinctions were found in the distributions of DMRs in different regions of genes as well. Six hundred and thirty-two DMGs were found in the promoter region. The results of functional enrichment analysis showed that DMR-related genes were mainly enriched in some signal pathways related to axonal growth, neuronal cytoskeleton, neurotransmitter release, synapse reorganization, epileptogenesis, excess synchronization, and hyperexcitability of neurons.
Conclusions:This study preliminarily identified the differential DNA methylation profiles of HS ILAE type 1 in patients with TLE, which provides a theoretical basis for further understanding the molecular mechanism and novel biomarkers for subtypes of HS.

overall_design: Examination of 3 temporal lobe epilepsy patients with hippocampal sclerosis and 3 temporal lobe epilepsy patients without hippocampal sclerosis.

first: Wang

last: Zhang

first: Meng

first: Zhiguo

last: Lin


title: Transcriptome modulation combined with morpho-physiological analyses of Sinapis alba L in response to cadmium challenge

city: Gui'yang

first: hu

middle: li

last: juan

address: 116 Baoshan North Road, Guiyang City, Guizhou Province, China

institute: Guizhou Normal University

summary: The purpose of this study is to explore the influence of the morpho-physiological of Sinapis alba L in response to cadmium challenge

overall_design: Transcriptome analysis of Sinapis alba L treated with cadmium


title: Glioblastoma stem cells after treatment with sulconazole.

city: Singapore

first: Roberto

last: Tirado-Magallanes

email: e0056363@nus.edu.sg, rtmag4@gmail.com

state: Singapore

address: 14 Medical Dr

country: Singapore

institute: Cancer Science Institute of Singapore

summary: Glioblastoma (GBM) is a uniformly lethal disease that is driven by GBM stem cells (GSCs). However, methods that selectively eradicate the GSCs remain limited. Here, we employed a chemical biology approach to identify novel compounds and strategies that target GSC proliferation, invasiveness and stemness. We studied the effect of sulconazole (SN) previously reportedly known as an antifungal drug.  In GSCs SN inhibited multiple biotin-dependent carboxylases by competing with biotin, an important co-factor for these enzymes. Consequently, there was reduced carbon flux into the cholesterol biosynthesis and TCA cycle pathways, depleting intracellular cholesterol and impairing oxidative phosphorylation, resulting in impaired GSC proliferation. Notably, these metabolic changes were GSC-specific and undetected in SN treated mouse astrocytes. Thus, the pharmacologic inhibition of biotin-dependent carboxylases represents a viable therapy for GBM.

overall_design: RNA-seq from glioblastoma stem cell specimens (TS-543) following treatment ether with DMSO or sulconazole nitrate.

first: Jeehyun

last: Yoon

first: Oleg

last: Grinchuk

first: Derrick

last: Ong


title: Genome expression profile for CD3+ T cells treated by nimodipine in EAU model

first: Guanyu

last: Chen

address: Xianlienan Road NO. 54

department: Zhongshan Ophthalmic Center

summary: Uveitis is a severe autoimmune disease characereized by retinal inflammation, whicn brings harms to the visual function of the patients. We found that nimodipine could protect annimals from experimental autoimmune uveitis. To further clarify the possible mechanism through which nimodipine exerted effect, we  performed genomic expression profiling of CD3+ T cells in EAU model and nimodipine treated group.

overall_design: Gene expression profiling was performed in CD3+ T cells sorted from draining lymph node of two control mouse, three EAU model mouse and three EAU + nimodipine mouse.

first: Yunwei

last: Hu

first: Jun

last: Huang

first: Zhuang

last: Li

first: Zuoyi

first: Yanyan

last: Xie

first: Yuxi

first: He

first: Wenru

last: Su

first: Xiaoqing

first: Dan

last: Liang


title: Chd4 ensures stem cell lineage fidelity during skeletal muscle regeneration

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

summary: The chromatin remodeler Chd4, a member of the nucleosome remodeling and deacetylase (NuRD) repressive complex, is essential for the expansion and regenerative functions of satellite cells.

overall_design: Dissection of fore and hind limb muscles was done with a scalpel and retrieved in cold DMEM (Dulbecco's Modified Eagle Medium, Gibco). Muscle tissues were finely minced and digested with Liberase 5 mg/mL (Roche/Sigma Aldrich), 0.03% Dispase II (Sigma), DMEM, 1% penicillin/streptomycin, BSA 0.2% (Sigma), 1 M CaCl2, and 1 M MgCl2 at 37ºC. Samples were then centrifuged 10 min at 50g at 4ºC. Supernatant was filtered through 100-µm and then a 70-µm cell strainers filters and then centrifuged at 1700 rpm for 15 min. Pellets were then resuspended in Lysis Buffer 1 (BD) and incubated for 10 min. Samples were resuspended in cold DMEM, filtered through 40-µm cell strainer filters, and centrifuged again for 15 min at 1700 rpm. Cells were resuspended in PBS, and 2.5% of goat serum (FACS buffer). Samples were incubated 30 min at 4ºC with the following antibodies: anti-CD45 PE-Cy7 (Biolegend), anti-Sca1 PE-Cy7 (Biolegend), anti-α7-integrin PE (Ablab.ca), and anti-CD34 Alexa-647 (BDPharmingen). Samples were centrifuged at 1700 rpm for 15 min and finally resuspended in FACS buffer with 1 μg/mL DAPI. After antibody labelling, SCA1–/CD45–/α7-integrin+/CD34+ cells were sorted by fluorescence-activated cell sorting (FACS) in the BD Influx cell sorter, and processed for RNA-seq and ATAC-seq. Sets are indicated in the sample and file names (Invitro and Invivo).

first: Pura

last: Munoz-Canoves


title: Single-cell transcriptome and cell-specific network analysis reveal the reparative effect of NT-4 supplementation in preantral follicles grown in vitro

status: Public on Sep 08 2021

first: Ying-chun

last: Guo

address: NO.17, Shougouling Rd.

institute: Sixth Affiliated Hospital of Sun Yat-sen University


title: Development of an exosomal gene signature to detect residual disease in dogs with osteosarcoma using a novel xenograft platform and machine learning

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

sample_organism:
Canis lupus familiaris
Mus musculus

platform_organism:
Canis lupus familiaris
Mus musculus


title: Development of an exosomal gene signature to detect residual disease in dogs with osteosarcoma using a novel xenograft platform and machine learning [mouse data]

summary: We developed a method using canine osteosarcoma in mouse xenografts to distinguish tumor-derived from host-response exosomal mRNAs. The model allows for the identification of canine osteosarcoma-specific gene signatures by RNA sequencing and a species-differentiating bioinformatics pipeline. An osteosarcoma-associated signature consisting of five gene transcripts was validated in dogs with osteosarcoma. Serum/plasma exosomes were isolated from 53 dogs in distinct clinical groups (“healthy”, “osteosarcoma”, “other bone tumor”, or “non-neoplastic disease”). Pre-treatment samples from osteosarcoma cases were used as the training set and a validation set from post-treatment samples was used for testing, classifying as “osteosarcoma–detected” or “osteosarcoma–NOT detected”. Dogs in a validation set whose post-treatment samples were classified as “osteosarcoma–NOT detected” had longer remissions, up to 15 months after treatment. In conclusion, we identified a gene signature predictive of molecular remissions with potential applications in the early detection and minimal residual disease settings. These results provide proof-of-concept for our discovery platform and its utilization in future studies to inform cancer risk, diagnosis, prognosis, and therapeutic response.

overall_design:
Development of an exosomal gene signature in dogs with osteosarcoma using RNA sequencing and machine learning
[Mouse data]

first: Kelly

middle: M

last: Makielski

first: Alicia

last: Donnelly

first: Ali

last: Khammanivong

first: Milcah

last: Scott

first: Andrea

last: Ortiz

first: Dana

last: Galvan

first: Hirotake

last: Tomiyasu

first: Clarissa

last: Amaya

first: Kristi

last: Ward

first: Alexa

last: Montoya

first: John

last: Garbe

first: Gary

last: Cutter

first: Joelle

last: Fenger

first: William

last: Kisseberth

first: Timothy

middle: D

last: O'Brien

first: Brenda

last: Weigel

first: Logan

middle: G

last: Spector

first: Brad

middle: A

last: Bryan

first: Subbaya

last: Subramanian

first: Jaime

middle: F

last: Modiano


title: Profiling histone modifications in clinical archived formalin fixed paraffin embedded samples

city: Uppsala

first: xingqi

last: chen

address: Uppsala Biomedical Center C10:2, Husargatan 3

department: IGP

country: Sweden

institute: Uppsala University

summary: Here, we present FACT-Seq, a highly sensitive method to decode the histone modifications in FFPE tissues. The FACT-Seq generates the high-quality chromatin profiles from both active and silent histone modifications with 1000 nuclei purified from a single FFPE tissue section, and reveals the disease-specific super enhancers in the FFPE archived human colorectal and human glioblastoma multiforme cancer tissue. In summary, the approach allows decoding the histone modifications that regulate gene expression in archival FFPE tissues with high sensitivity, in order to better understand epigenetic regulation in cancer and precision medicine.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: FACT-Seq of mouse FFPE kidney and clinical archived CRC and GBM.

first: Chen

last: Xingqi

first: Zhao

last: Linxuan

first: Xing

last: Pengwei

first: Vamsi

middle: K

last: Polavarapu


title: Targeted Sequencing of BCL11B-R patients

first: Danika

last: Di Giacomo

address: Piazzale Menghini 0

summary: This study identified a cytogenetic-molecular entity, we named BCL11B-R, that showed a typical constellation of genomic features, namely BCL11B activation via chromosome translocations at 14q32, a distinct transcriptome profile, and FLT3 mutations.

first: Fabrizia

last: Pellanera

first: Caterina

last: Matteucci

first: Cristina

last: Mecucci


title: Gene expression change after targeted degradation of ZMYND8 or IRF8

first: Zhendong

last: Cao

department: Cancer biology

institute: university of pennsylvania

summary: Cancer cell type-selective addiction of transcription-chromatin regulatory program provides opportunities for therapeutic interventions. Here, we uncovered an IRF8-MEF2D transcription factor (TF) regulatory circuit as an acute myeloid leukemia (AML)-biased dependency. Combining CRISPR-based genetic screens, transcriptional analysis, and chromatin profiling, we demonstrated that a chromatin regulator, ZMYND8, directly regulates IRF8 and MYC expression through occupying AML-specific enhancer regions. ZMYND8 was essential for AML proliferation both in vitro and in vivo. The ZMYND8-occupied IRF8 enhancer was further characterized using Circular Chromosome Conformation Capture and CRISPRi-based perturbation assays and was observed in  primary patient cells. Importantly, mutagenesis experiments revealed that the PHD/Bromodomain/PWWP reader module is required for ZMYND8 tethering to leukemia-essential co-activator BRD4 for enhancer-mediated gene regulation. Our results rationalize ZMYND8 as a potential selective therapeutic target for modulating the IRF8/MYC transcriptional networks in AML.

first: Junwei

last: Shi


title: Biop-C: A Method for Chromatin Interactome Analysis of Solid Cancer Needle Biopsy Samples

first: Melissa

middle: Jane

last: Fullwood

address: Centre for Translational Medicine,14 Medical Drive

department: School of Biological Sciences

institute: Nanyang Technological University

summary: Our results demonstrate the utility of our Biop-C method in investigating the 3D genome organization in solid cancers, and the importance of 3D genome organization in regulating oncogenes in nasopharyngeal cancer.

overall_design:
We have analysed 3 nasopharyngeal cancer biopsy samples using our novel Biop-C method as well as 2 replicates of NPC cell line HK1 using arima Hi-C kit protocol. To test the reproducibility of the method, we performed Biop-C on 2 replicates of a biopsy samples. For comparision with healthy tissue, we performed hic on near normal epithelial cell line NP-69.

>>>Raw data not provided for human biopsy samples due to patient privacy concerns<<<

first: Sambhavi

last: Animesh

first: Ruchi

last: Choudhary


title: Gene expression in Atlantic salmon cell culture in response to infectious salmon anaemia virus (ISAV) and polyinosinic-polycytidylic acid - poly(I:C)

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: ISAV is one of the most dangerous pathogens causing high mortality of farmed Atlantic salmon. In this study, transcriptome responses to the virus were examined in vitro in Atlantic salmon head kidney cells culture (ASK). Poly(I:C), synthetic double-stranded RNA stimulating antiviral responses was used as a positive control.

overall_design: Viral infection was performed at 15° C in 75cm2 flasks and cells were harvested after 1 and 5 days. Cells cultivated with added poly(I:C) were sampled at 5 days. Analyses were performed in two replicates.


title: Applying of transcriptomics to screen the significantly altered genes, cell function and signal transduction pathway of chicken trachea exposed to hydrogen sulfide

first: ziwei

last: zhang

address: No. 600, Changjiang Road, Xiangfang District

institute: Northeast Agricultural University

summary: Hydrogen sulfide (H2S) is well known to cause irritation and damage to airway following inhalation, but the mechanism by which H2S contributes to airway toxicity is unclear. We apply  transcriptomics  to demonstrate the possible effects, obtain valuable information about adverse health effects following H2S exposure and to study the molecular mechanisms of the gas toxicity in trachea.

overall_design: Trachea mRNA profiles of 42-day old normal and hydrogen sulfide exposed chicken were generated by deep sequencing, in duplicate.

first: Menghao

last: Chen

first: Ziwei

last: Zhang

first: Shiwen

last: Xu


title: Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV (RNA-Seq)

city: Montreal

first: Erwin

last: Schurr

address: 1001 boulevard Decarie

country: Canada

institute: McGill University Health Centre

summary: Persons living with HIV (PLWH) are at increased risk of tuberculosis (TB). HIV-associated TB is mainly the result of recent infection with Mycobacterium tuberculosis (Mtb) followed by rapid progression to disease. Alveolar macrophages (AM) are the first cells of the innate immune system that engage Mtb, but how HIV and antiretroviral therapy (ART) impact on the anti-mycobacterial response of AM is not known. In this study AM were challenged in vitro with Mtb, and their epigenetic and transcriptomic responses were determined for PLWH receiving ART, control subjects who were HIV-free (HC) and subjects who received pre-exposure prophylaxis (PrEP) with ART to prevent HIV infection. Compared to HC subjects’ response to Mtb, we showed that AM isolated from PLWH and PrEP subjects displayed substantially weaker transcriptomic response and no significant changes in their chromatin state. These findings revealed a previously unknown adverse effect of ART.

overall_design: AM cells were challenged with Mtb at a multiplicity of infection (MOI) of 5:1 or kept in sterile medium for 18-20hrs. Cells were then processed to perform RNA-seq, ATAC-seq and ChIP-seq

first: Wilian

last: Correa-Macedo

first: Vinicius

last: Fava


title: Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

summary: Acute myeloid leukemia patients refractory to induction therapy or relapsed within one year have poor outcomes.  Autocrine production of hepatocyte growth factor by myeloid blasts drives leukemogenesis in pre-clinical models.  A phase Ib trial evaluated ficlatuzumab, a first-in-class anti-HGF antibody, in combination with cytarabine in this high-risk population.  Dose-limiting toxicities were not observed, and 20 mg/kg was established as the recommended phase II dose.  The most frequent treatment-related adverse event was febrile neutropenia.  Among 17 evaluable patients, the overall response rate was 53%, all complete remissions.  Phospho-proteomic mass cytometry showed potent on-target suppression of p-MET after ficlatuzumab and that attenuation of p-S6 was associated with clinical response.  Multiplexed single cell RNA sequencing using longitudinally collected patient specimens identified interferon and MYC target genes as adverse predictive factors.  The ficlatuzumab and cytarabine combination is well-tolerated with favorable efficacy.  High-dimensional analyses at single-cell resolution represent promising approaches for identifying biomarkers of response and mechanisms of resistance in prospective clinical studies.

overall_design: 10x Chromium based single cell RNA sequencing was performed on samples from 11 patients with refractory AML treated with ficlatuzumab and one normal control.  57 samples collected prospectively over 5 timepoints were pooled and run in 10 separate reactions.  Samples were demultiplexed based on expressed genetic variants using freemuxlet.

first: Victoria

middle: E

last: Wang

middle: W

first: Ravi

last: Patel

first: Gregory

last: Behbehani

first: Arjun

last: Rao

first: Blythe

last: Durbin-Johnson

first: Tommy

last: Jiang

first: Aaron

middle: C

last: Logan

first: Matthew

last: Settles

first: Gabriel

middle: N

last: Mannis

first: Rebecca

last: Olin

first: Lloyd

last: Damon

first: Thomas

last: Martin

first: Peter

last: Sayre

first: Karin

last: Gaensler

first: Emma

last: McMahon

first: Michael

last: Flanders

first: Vivian

last: Weinberg

first: Chun

last: Ye

first: David

last: Carbone

first: Pamela

last: Munster

first: Gabriela

last: Fragiadakis

first: Frank

last: McCormick

first: Charalambos

last: Andreadis


title: Development of gene expression signatures for In-stent Restenosis

city: China

first: Liu

last: longbin

state: Zhejiang province

address: 568 Zhongxing N Rd, Yuecheng District, Shaoxing, Zhejiang, China575 Pingjiang Rd, Yuecheng District, Shaoxing, Zhejiang, China

institute: Affiliated Hospital of Shaoxing University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To further development of our gene expression approach to Restenosis, we have employed lncRNA microarray expression profiling.

overall_design: In-stent Restenosis induced lncRNA and mRNA expression in human serum was measured .Three independent experiments were performed at each group. using different donors for each experiment.


title: BG-P400TAT, A Dual Targeting of Norepinephrine Transporter Function and Thyrointegrin  αvβ3 receptors to Treat Neuroblastoma cancer

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: To explore molecular mechanisms of anti-cancer activities of BG-P400-TAT, genome-wide expression profiling experiments were carried out . Human neuroblastoma SKNAS cells were treated with 30µM of the BG-P400-TAT for 48 hours, harvested, and immediately processed for RNA isolation from three biological replicates of control and drug-treated cells. BG-P400-TAT targets among intracellular multiprotein complexes NF-kB complex, Survivin complex, Bcl-2 complex, and VEGF-A complex and integrated with signal transduction pathways of EGF, FGF1, AR, estradiol, TNF, and IL-1

overall_design: To evaluate the anticancer functions of BG-P400-TAT in SK-N-AS cells, igenome-wide expression profiling experiments were carried out.  RNA isolation from two biological replicates of control SK-N-AS cells compared with SK-N-AS cells treated with BG-P400-TAT (30 µM) for 48 h.

first: Gennadi

last: Glinsky

first: Kavitha

last: Godugu

first: Karakus

last: Ozlem

first: Shaker

last: Mousa


title: Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV (ChIP-Seq)

first: Erwin

last: Schurr

first: Vinicius

last: Fava

first: Wilian

last: Correa-Macedo


title: Development of an exosomal gene signature to detect residual disease in dogs with osteosarcoma using a novel xenograft platform and machine learning [canine data]

first: Lauren

last: Mills

overall_design:
Development of an exosomal gene signature in dogs with osteosarcoma using RNA sequencing and machine learning
[Canine Data]

first: Kelly

last: Makielski

first: Alicia

middle: J

last: Donnelly

first: Ali

last: Khammanivong

first: Milcah

last: Scott

first: Andrea

middle: R

last: Ortiz

first: Dana

last: Galvan

first: Hirotake

last: Tomiyasu

first: Clarissa

last: Amaya

first: Kristi

last: Ward

first: Alexa

last: Montoya

first: John

last: Garbe

first: Gary

last: Cutter

first: Joelle

last: Fenger

first: William

last: Kisseberth

first: Timothy

last: O'Brien

first: Brenda

last: Weigel

first: Logan

last: Spector

first: Brad

last: Bryan

first: Subbaya

last: Subramanian

first: Jaime

last: Modiano


title: Airway epithelial cells prime plasmacytoid dendritic cells to respond to pathogens via secretion of growth factors

city: Irvine

first: Farah

last: Rahmatpanah

address: Medical sciences C

department: Pathology

institute: UCI

summary: Plasmacytoid dendritic cells (PDCs) are thought to play a role in mucosal tolerance as well as in defense against respiratory viruses because of their propensity to secrete high levels of type I interferons (IFN). The functions of PDCs in the lung can be influenced by airway epithelial cells (AECs) because of their close proximity. We examined the effect of human primary AECs on PDC functions by performing RNA-sequencing of PDCs after co-culture with air liquid interphase differentiated AECs. Co-culture led to the upregulation of transcripts included those encoding cytosolic sensors of DNA, ZBP-1,IRF-3 and NFkB as well as genes involved in amplification of the type 1 IFN response, such as IFNAR1, JAK/STAT, ISG15. These data highlight possible mechanisms to enhance the production of type-I IFN in the airways, which is critical for host defense against respiratory infections

overall_design:
We examined the effect of human airway epithelial cells on plasmacytoid dendritic cell (PDC) functions by performing RNA-sequencing of PDCs after co-culture with air liquid interface differentiated bronchial epithelial cells (PBEC)
Each Sample was cultured with and without Epithelial cells in the culture.

first: Rahmatpanah

last: Farah

first: Agrawal

last: Anshu


title: Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV

first: Erwin

last: Schurr

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of the hypothalamic paraventricular and the arcuate nucleus of NNAT null mice

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: Neuronatin (Nnat) has previously been reported to be part of a network of imprinted genes. Disruption of  neuronatin results in an unusual phenotype of a bimodal body weight.In order to understand at the molecular level how the Nnat deficiency could contribute to the hypervariable phenotypes seen, we performed RNA sequencing from laser-capture micro dissected paraventricular nucleus (PVN) and arcuate nucleus (ARC) and compared the transcriptome between Nnat+/-p mice and their Nnat+/+ littermates in different feeding conditions. We performed an analysis of three subgroups: Nnat+/+ (all non-obese), Nnat+/-p non-obese, and Nnat+/-p obese mice and combined two approaches to identify differences in hypothalamic gene expression between subgroups

overall_design: Gene expression analysis between wild-type and NNAT null mice

first: Irene

last: Cimino

first: Katherine

last: Lawler

first: Anthony

last: Coll

first: Stephen

last: O'Rahilly


title: Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV (ATAC-Seq)

first: Vinicius

last: Fava

first: Wilian

last: Correa-Macedo


title: Dual expression of Atoh1 and Ikzf2 promotes transformation of adult cochlear supporting cells into outer hair cells

city: Beijing

first: Zhiyong

last: Liu

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

summary: Mammalian cochlear outer hair cells (OHCs) are essential for hearing. Severe hearing impairment follows OHC degeneration. Previous attempts at regenerating new OHCs from cochlear supporting cells (SCs) have been unsuccessful, notably lacking expression of the key OHC motor protein, Prestin. Thus, regeneration of Prestin+ OHCs represented a barrier to restoring auditory function in vivo. Here, we reported the successful in vivo conversion of adult mouse cochlear SCs into Prestin+ OHC-like cells through the concurrent induction of two key transcriptional factors known to be necessary for OHC development: Atoh1 and Ikzf2. Single cell RNA sequencing reveals the upregulation of 729 OHC genes and downregulation of 331 SC genes in OHC-like cells. The resulting differentiation status of these OHC-like cells was much more advanced than previously achieved. This study thus established an efficient approach to induce the regeneration of Prestin+ OHCs, paving the way for in vivo cochlear repair via SC transdifferentiation.

overall_design:
Determining the similarity and difference between OHC-like cells regenerated from adult cochlear SCs and wild type OHCs at adult ages

Please note that sample titles have been updated on Sep 10, 2021.

first: Suhong

last: Sun

first: Shuting

last: Li

first: Zhengnan

last: Luo

first: Minhui

last: Ren

first: Shunji

last: He

first: Guangqin

last: Wang


title: Longitudinal single cell RNA-seq of the inflamed colon

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka university

summary: We demonstrate single-cell RNA sequencing with time course study on DSS-induced colitis mouse model to reveal the overall cellular status during colon inflammation. Based on single cell transcriptome analysis in inflamed colon, we showed that the stromal cell population of colon functions as a hub to coordinate dynamic change with other cell type. We also found the Serpina3n, a serine protease inhibitor is specific up-regulation in the stromal cells during the resolution phase of colon inflammation. Furthermore, we found that systemic administration of Serpina3n promoted the recovery of resolution phase and ameliorated colitis-related symptoms. This study provides a comprehensive understanding of cell-cell interactions during colorectal inflammation at the single-cell level and reveals a potential therapeutic target by hijacking the endogenous inflammation resolution mechanism.

overall_design: Mice were treated with 1.5%DSS for 6 days then switched to drinking water. Colon from each time points (Day 0, 3, 6, 9, 12 and 15) or treatment (PBS or Serpina3n) were collected. To limit mouse-to-mouse biased, three biological replicates from each group were pooled and analyzed using FACS-based, smart-seq2 method. The sequencing libraries were sequenced on the Illumina NextSeq500 platform.


title: Identification of anoctamin 1 (ANO1) as a key driver of esophageal epithelial proliferation in eosinophilic esophagitis

status: Public on Sep 02 2021

city: Ann Arbor

first: Sunil

last: Tomar

address: 109 Zina Pitcher Place

institute: University of Michigan

summary: In this study we performed H3K4me3 and STAT6 ChIP seq analyses on hTERT immortalized human esophageal keratinocytes (hTERT-EPC2) under air-liquid interface conditions following IL-13 (100ng/ml) 30 minutes and 4 hours stimulation

overall_design: Examination of H3K4me3 and STAT6 ChIP-seq in EPC2 cells after treatment of IL13

first: Simone

last: Vanoni

first: Chang

last: Zeng

first: Simon

middle: P

last: Hogan


title: Differential expression of long noncoding RNAs of dental pulp stem cells in the SDF-1α induced

city: shaanxi,xi'an

first: min

last: xiao

address: Fourth Military Medical University

institute: Fourth Military Medical University

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: We triggered the involvement of lncRNAs in odontogenic differentiation of DPSCs by incubation with SDF-1α. By LncRNA microarray, alterations in lncRNA expression at odontogenic differentiation inducted by 100ng/Ml SDF-1α were identified. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to validate several random upregulated and downregulated LncRNAs in the odontogenic differentiation of DPSCs. In addition, Gene ontology (GO) analysis and coding-noncoding gene coexpression (CNC) analysis were conducted to predict the interactions of coding and noncoding RNA and identify core regulatory factors in odontogenic differentiation of DPSCs.

overall_design: SDF-1α induced lncRNAs expression in human dental pulp stem cells was measured at 7 days after exposure to doses of 100ng/mL. Three independent experiments were performed at each group (with or without SDF-1α) for each experiment.

first: Min

last: Xiao


title: Bone marrow dendritic cell and exosome RNA profiling

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: In this study, we sought to identify differentially RNAs found in mouse bone marrow-derived dendritic cells and their exosomes. As a secondary aim, we sought to determine whether deletion of the Sidt1 and Sidt2 genes affects the RNA content of exosomes.

overall_design: Dendritic cells and exosomes were harvested from the bone marrow of 6 mice. 3 of the mice were wild type, and 3 were Sidt1/Sidt2 double knock-outs. Differential expression analyses were performed between all experimental groups.

middle: L

first: Marilou

last: Barrios

first: Ken

last: Pang


title: Single-cell RNA sequencing analysis reveals Greater Epithelial Ridge cells degeneration during postnatal development of cochlea in Rats

city: Shanghai

first: Jianyong

last: Chen

state: Yangpu

address: 1665 Kongjiang Rd

department: Otorhinolaryngology Head and Neck Surgery

institute: Xinhua Hospital, Shanghai Jiaotong University School of Medicine

summary: Greater epithelial ridge cells, a transient neonatal cell group in the cochlear duct, which plays a crucial role in the functional maturation of hair cell, structural development of tectorial membrane, and refinement of audio localization before hearing. Greater epithelial ridge cells are methodologically homogeneous, while whether different cell subtypes are existence in this intriguing region and the degeneration mechanism during postnatal cochlear development are poorly understood. In the present study, single-cell RNA sequencing was performed on the cochlear duct of postnatal rats at day 1 (P1) and day 7 (P7) to identify subsets of greater epithelial ridge cell and progression. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were used to examine genes enriched biological processes in these clusters. We identified a total of 26 clusters at P1 and P7 rats and found that the cell number of five cell clusters decreased significantly, while four clusters had similar gene expression patterns and biological properties. The genes of these four cell populations were mainly enriched in Ribosome and P13K-Akt signal pathway. Among them, Rps16, Rpsa, Col4a2, Col6a2, Ctsk, and Jun are particularly interesting as their expression might contribute to the greater epithelial ridge cells degeneration. In conclusion, our study provides an important reference resource of greater epithelial ridge cells landscape and mechanism insights for further understanding greater epithelial ridge cells degeneration during postnatal rat cochlear development

first: Dekun

last: Gao

first: Junmin

first: Jun

last: Yang


title: Integrated miRNA-genomic analysis of sunitinib resistance in clear cell renal cell carcinoma (CCRCC) cell lines

city: Donsotia-San Sebastian

first: charles

last: lawrie

address: Paseo Mikeletegi, 83- planta 3

department: Oncology

institute: Biodonostia Research Institute

summary:
clariom D and miRNA v4.0 microarray analyses of 786-O, A498 and Caki-1 cells suntinib resistant cell lines and originator cell lines
we used intergrated pathway network analysis to identify miRNA-target gene pairs involved in sunitinib resistance.

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: sunitinib resistant renal cell lines (786-O, A498 and Caki-1) were produced using increasing quantities of sunitinib over many weeks until lines were resistant to >10uM. Two clones for each cell lines were independently produced in this manner. Resistant cells and parental (sensitive) cells were harvested and RNA extracted. Affymetrix miRNA (v4.0) and gene (Clariom D) microarrays were carried out on all the cell lines in technical triplicates

first: Charles

last: Lawrie

first: Maria

last: Armesto


title: Brd2 inhibitor ABBV-744 inhibits SARS-CoV-2 infection in Syrian Hamsters

city: Shenzhen

first: Ruilin

last: Tian

address: 1088 Xueyuan Avenue

institute: SUSTech

summary: We tested if Brd2 inhibitor ABBV-744 could reduce SARS-CoV-2 infection in Syrian Hamsters. Three days post-infection, the lungs of hamsters were harvested and subjected to RNA-seq. Infected, but untreated, hamsters showed marked up-regulation of a number of genes including ISGs when compared to uninfected controls. In contrast, hamsters treated with ABBV-744 showed a down-regulation of ISG levels, confirming ABBV-744 activity. Thus, Brd2 inhibition can decrease SARS-CoV-2 infection in Syrian Hamsters.

overall_design: To determine gene expression changes induced by SARS-COV-2 infection, 4 lung tissue samples from hamsters infected with SARS-COV-2 and 4 samples from uninfected hamsters were harvested and subjected to RNA-seq. To determine the effect of ABBV-744, hamsters were treated with ABBV-744 or vehicle, followed by SARS-COV-2 infection. 8 lung tissue samples from ABBV-744 treated group and 8 samples from vehicle treated group were harvested and subjected to RNA-seq

first: Avi

last: Samelson

first: Lucia

last: Carrau

first: Benjamin

last: TenOever

first: Martin

last: Kampmann


title: RNA-Seq in WT and KO liver tumor tissues

city: Nanjing

first: Anliang

last: Xia

address: 321 Zhongshan Road

institute: The Affiliated Drum Tower Hospital of Nanjing University Medical School

summary: Total RNA was extracted from WT or KO liver tumor tissues. RNA samples were analyzed by RNA sequencing based on the manufacturer’s protocols. Briefly, Illumina HiSeq 2500 platform was used to sequence the RNA samples for the subsequent generation of raw data. KEGG pathway and GSEA enrichment analysis were used for functional pathway analysis.

overall_design: mRNA profiles of WT and KO liver tumor tissues


title: Identification differentially expressed genes in the mouse testis caused by Prss37 deficiency

first: Wenfeng

last: Xiong

state: Shanghai

address: Ruijin er road

department: Research Center for Experimental Medicine

institute: Ruijin hospital

summary: Testes from three wt and three Prss37-/- mice were used for gene expression analysis using whole mouse genome 4 × 44 k microarray (Agilent Technologies). A total of 31 genes were identified to be differentially expressed significantly (p < 0.05, fc ≥ 2). Fold changes of ten genes (seven up-regulated genes and three down-regulated genes) were examined by qRT-PCR for data validation.

overall_design: Total RNAs were extracted from testes of wt and Prss37-/- mice (n = 3 each genotype, 6-8 weeks old).

first: Chunling

last: Shen

first: Zhugang

last: Wang


title: Excessive Branched Chain Amino Acid Accumulation Creates an Unfavourable Myocardial Milieu that Inhibits the Cardioprotective Effects of Implanted Mesenchymal Stem Cells in Ischemic Heart Injury [RNA-Seq]

city: Xi'an

first: Fuyang

last: Zhang

state: Shaanxi

address: 127 West Changle Rd

department: Cardiology

institute: Xijing hospital

summary: Myocardial infarction (MI) causes cardiac metabolic reprogramming and results in  robust changes in intramyocardial metabolite composition, but little is known about how these metabolic changes influence the fate of implanted stem cells. We found that  excessive branched chain amino acid (BCAA) accumulation, a metabolic signature of  the post-infarcted heart, created an unfavorable milieu inhibiting the retention and  cardioprotection of intramyocardially-delivered mesenchymal stem cells (MSCs). BCAA  at pathological levels sensitized MSCs to the acquisition of a injured phenotype by  suppressing the histone H3K9 trimethylation (H3K9me3) modification. Furthermore, a  novel mTORC1/DUX4/KDM4E axis was identified as the cause of the H3K9me3 loss  and adverse phenotype acquisition induced by BCAA. Enhancing BCAA catabolism in  MSCs via genetic or pharmacological approaches improved their adaptation to the  extracellular BCAA milieu and strengthened their cardioprotective efficacy. These  findings reveal a critical role of myocardial metabolic reprogramming in regulating the  fate and cardioprotection of implanted MSCs after MI.

overall_design: RNA-Seq of ADSCs treated with vehicle or BCAA

first: Guangyu

last: Hu

first: Xiyao

first: Ling

last: Tao


title: Excessive Branched Chain Amino Acid Accumulation Creates an Unfavourable Myocardial Milieu that Inhibits the Cardioprotective Effects of Implanted Mesenchymal Stem Cells in Ischemic Heart Injury [CUT&Tag]

overall_design: CUT&Tag (H3K9me3) of ADSCs treated with vehicle or BCAA

last: Chen


title: BRD2 CUT & RUN in Calu-3 cells

summary: we performed CUT&RUN to comprehensively map genomic loci bound to BRD2 in control and BRD2 knockdown Calu-3 cells. We also included H2A.Z, H3K4me3 and IgG antibodies.

overall_design: The CUT&RUN experiment was performed with BRD2 antibody as well as the H2A.Z,  IgG and H3K4Me control antibodies with 1 million control or BRD2 knockdown cells.


title: Expression of lncRNAs in children with pancreaticobiliary maljunction: functional analysis and potential biomarkers

city: Suzhou

first: Wan-liang

last: Guo

address: 92 Zhongnan Street

institute: Children's Hospital of Soochow University

summary:
Background: The present study was aimed to investigate the expression profile of long non-coding RNAs (lncRNAs) and its potential as biomarker for pancreaticobiliary maljunction (PBM).
Methods: The differential expression of lncRNA and messenger RNA (mRNA) from 15 pediatric patients with PBM and 15 control subjects were analyzed with microArray and validated with quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Gene Ontology enrichment and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis were used to investigate the biological functions of these genes. The area under curve (AUC) of receiver operating characteristic (ROC) curve was used to predict the biomarker of lncRNA in PBM.
Results: There were 2915 mRNAs and 173 lncRNAs upregulated, 2121 mRNAs and 316 lncRNAs downregulated in PBM cases, respectively. The enriched GO associated with differentially expressed mRNA were extracellular matrix, extracellular region and kinetochore. The most enriched pathway of Protein digestion and absorption was associated with cancer and PI3K-Akt signaling. Cis- and Trans-target gene analysis indicated that mRNAs were predicted to be regulated by one lncRNA and one mRNA corresponded to several lncRNAs. The results showed that the expression trends of NR_110876, NR_132344, XR_946886 and XR_002956345 were consistent with the microarray results, and the difference was statistically significant NR_132344, XR_946886 and XR_002956345 (P < 0.05).The AUC of ROC curve was significant only for XR_946886 (0.837, P<0.001).
Conclusion: The present study indicated that lncRNAs were involved the pathogenesis of common bile duct in PBM and XR_946886 would be biomarkers for PMB.

first: Lian

last: Zhao

first: San-li

last: Shi


title: Transcriptomic analysis of antigen experienced Mariyln (TCR-transgenic) CD4 T cells  proliferation during an ongoing immune response in vivo

city: Paris

first: Aurélien

last: Sutra del Galy

address: 26 rue d'Ulm

institute: Institut Curie

summary: The study explore the intrinisic inhibitors of antigen experienced Marilyn CD4 T cells (TCR-Tg) expansion after footpad vaccinations in vivo and in the presence of a first cohort of expanded Marilyn cells to mimick an ongoing immune response

overall_design: C57BL6 mice are intravenously injected with either naive or antigen experienced Marilyn cells and restimulated via footpad vaccinations (DC+peptide) in the presence of the first cohort of Marilyn cells, mimicking an ongoing CD4 immune response. CD4 T cells are sorted from draining lymph node, 7 days after transfer.

first: Laurie

last: Menger

last: Sutra Del Galy


title: SOCS1


title: RNA-Seq in Hep3B-shNC and Hep3B-shlnc-CTHCC cells

summary: Total RNA was extracted from Hep3B cells with sh-NC (n = 3) or sh-lnc-CTHCC (n = 3). RNA samples were analyzed by RNA sequencing based on the manufacturer’s protocols. Briefly, Illumina HiSeq 4000 platform was used to sequence the RNA samples for the subsequent generation of raw data. R package was utilized to select genes with significantly differential expression based on fold change ≥2.0 and P≤0.05 between sh-NC and sh-lnc-CTHCC cells. KEGG pathway and GSEA enrichment analysis were used for functional pathway analysis.

overall_design: mRNA profiles of Hep3B-shNC and Hep3B-shlnc-CTHCC cells


title: Low transcriptomic plasticity of the Antarctic giant isopod Glyptonotus antarcticus to acute thermal stress

status: Public on Sep 01 2021

city: Punta Arenas

first: Alejandro

last: Font

state: Punta Arenas

address: Plaza Muñoz Gamero 1055

country: Chile

institute: Instituto Antartico Chileno

summary: The Western Antarctic Peninsula (WAP) is among the areas of the planet showing some of the most significant increases in air and water temperature. It is projected that increasing temperature will modulate communities of coastal ecosystems at species ecological performance and molecular composition. The main way that the organisms can cope with large thermal variation is by having a reversible phenotypic plasticity, which provides the organisms with a compensatory physiological response when facing challenging conditions. However, since Antarctic organisms have evolved in a very cold and stable environment. The giant Antarctic isopod Glyptonotus antarcticus is one of the most abundant in Antarctic waters. This species has a larval development inside of maternal marsupium, where juveniles have a short period to acclimate to environmental conditions after birth. In this sense, we hypothesize that juveniles exposed to unusual temperature increases even for short periods, would not respond adequately showing a narrow phenotypic plasticity. We assessed if early juveniles of G. antarcticus have the molecular plasticity when exposed to increased temperature at 5¡C during 1, 6, 12, and 24 hours in comparison to control 0¡C. Sequenced HIseq2000 libraries were compared between control and each treatment to detect differentially expressed transcripts. The main molecular pathways affected by thermal stress were antioxidants, proteases, endopeptidases, and ubiquitination transcripts which were up-regulated, and mitochondrial respiratory chain, cuticle, cytoskeleton, and a molt transcript which were down-regulated. Considering HSP transcript, only 3 were up-regulated at least in two points of the stress kinetic, without classical HSP70 and HSP90 transcripts. This study shows that juveniles of G. antarcticus do not show molecular phenotypic plasticity to cope with acute short-term heat stress, even for one or few hours of exposure without an eco-physiological capacity to respond. This may have consequences at the ecological population level, showing a reduced individual ability to survive decreasing population recruitment.

overall_design: Transcriptomic plasticity in Glyptonotus antarcticus juveniles

first: Rodolfo

last: Rondon


title: The STAT3-MYC Axis Promotes Survival of Leukemia Stem Cells by Regulating SLC1A5 and Oxidative Phosphorylation

city: Aurora

first: Shanshan

last: Pei

state: CO

country: USA

institute: University of Colorado

summary: Transcriptome comparison between leukemia stem cells treated with a STAT3 inhibitor versus vehicle control

overall_design: Leukemia stem cells were isolated from human bulk leukemia cells. mRNAs were extracted for RNA-seq.

first: Craig

middle: T

last: Jordan

first: Maria

last: Amaya