title: Genome-wide maps of H3K4me3 and H3K9me3 in SUN-depleted macrophages

city: Shanghai

first: Shi

last: Jiao

address: 320 Yue Yang Road

institute: Shanghai Institutes of Biological Sciences

summary: We used chromatin immunoprecipitation-coupled to deep sequencing (ChIP-seq) to profile genome-wide locations of H3K4 trimethylation (H3K4me3) and H3K9 trimethylation (H3K9me3) epigenetic marks in SUN-depleted mouse peritoneal macrophages.

overall_design: Examination of 2 different histone modifications in mouse peritoneal macrophages.

first: Chuanchuan

last: Li


title: Effect of Snhg11 knockdown on gene expression in the murine adult dorsal hippocampus

status: Public on Oct 31 2022

city: Barcelona

first: Cesar

last: Sierra

address: C/ Dr Aiguader 88

country: Spain

institute: Centre for Genomic Regulation (CRG)

type: Expression profiling by high throughput sequencing

summary: To investigate the role of Snhg11 in brain gene expression regulation, we injected the dorsal DG of adult mice either with an ASO targeting Snhg11 or with a control ASO. RNA extraction of the dorsal hippocampus was done 3 days after injection

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3 dorsal hippocampi injected with a Control-ASO and 3 dorsal hippocampi injected with an ASO targeting Snhg11

first: Mara

last: Dierssen


title: Gene expression profile at single nuclei level of hippocampal neurons from WT and Ts65Dn mice

summary: In order to characterize the cellular and molecular alterations associated with DS hippocampal dysfunction, given the rich neural cell diversity of this brain region, we used single nucleus RNA sequencing to dissect transcriptional dysregulation associated with specific cell types in the DS mouse model Ts65Dn

overall_design: Neuronal hippocampal population from adult (4 month old) mice was isolated by  Fluorescence-activated nuclear sorting (FANS) according to the presence or absence of NeuN signal and analyzed using snRNAseq.


title: Comprehensive analysis of M2 macrophage-derived exosomes facilitating osteogenic differentiation of human periodontal ligament stem cells

city: Kunming

first: Jiang-Tian

last: Hu

state: Yunnan

address: No. 1088 Middle Haiyuan Road

country: China

institute: Yunnan Stomatology Hospital

summary: As the primary seed cells in periodontal tissue engineering, the role of periodontal ligament stem cells (PDLSCs) in periodontal tissue regeneration and bone remodeling during orthodontic tooth movement (OTM) has been well documented. Nevertheless, the impact of different polarization states of macrophages on the osteogenic differentiation of PDLSCs is poorly understood. M0, M1 and M2 macrophage-derived exosomes (M0-exo, M1-exo and M2-exo) were treated with primary cultured human PDLSCs, respectively. Identification of differentially expressed microRNAs (DE-miRNA) in M0-exo and M2-exo by miRNA microarray. In summary, we have indicated for the first time that M2-exo can promote osteogenic differentiation of human PDLSCs, and have revealed the functions and pathways involved in the DE-miRNAs of M0-exo and M2-exo and their downstream targets.

first: Jiang-tian

first: Xian-min

last: Liao


title: Gene expression Prurigo Nodularis

city: Muenster

first: Konstantin

last: Agelopoulos

address: Von-Esmarch-Str. 58

country: Germany

institute: Universitiy of Muenster

summary:
Prurigo nodularis is a debilitating skin condition that is characterized by chronic itch and a prolonged scratching behavior. Little is known of the underlying molecular mechanisms that initiate and maintain the desease.
Therefore, we analyzed gene expression in prurigo patients and matched healthy controls.

overall_design: Pruritic lesional and non pruritic non lesional skin from five PN patients and healthy skin from sex and age matched healthy volunteers were used to analyse gene expression by Affymetrix array hybridization.

first: Sonja

last: Ständer


title: DNA methylation in Prurigo Nodularis

type: Methylation profiling by genome tiling array

summary:
Prurigo nodularis is a debilitating skin condition that is characterized by chronic itch and a prolonged scratching behavior. Little is known of the underlying molecular mechanisms that initiate and maintain the desease.
Therefore, we analyzed DNA methylation in prurigo patients and matched healthy controls.

overall_design: Pruritic lesional and non pruritic non lesional skin from five PN patients and healthy skin from sex and age matched healthy volunteers were used to analyse DNA methylation by Illumina array hybridization.


title: Effect of STIM1 Knockout on gene expression in the Drosophila larval brain

city: Bangalore

first: Jsmine

last: Kaur

state: Karnatka

address: GKVK Campus

department: Biological Sciences

country: India

institute: NCBS

summary:
To investigate the function of STIM1 in the larval brain development, we established strains in which the target gene has been knocked out (Pathak et al., 2017)
We then performed gene expression profiling analysis using data obtained from RNA-Seq of brain lysates of 2 different genotypes CS and STIMKO at 58-62 hrs and 72-76hrs of larval development respectively with 4 biological replicates

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CS and STIM1 KO Drosophila larval brains

first: Gaiti

last: Hasan

first: K

last: Nandshree

first: Jasmine

middle: K

last: Dhall


title: circRNA-sequencing

city: Jinan

first: Dachuan

last: Wang

state: Shandong

address: Jingwu Weiqi Road NO.324

institute: Shandong provincial hospital

type: Methylation profiling by high throughput sequencing

summary: circRNA sequencing for 6 samples

overall_design: Examing 2 conditions, each with 3 replicates


title: FHL5 cofactor mediates vascular disease risk by regulating smooth muscle cell transcriptional networks

city: Charlottesville

first: Clint

middle: L

last: Miller

state: VA

department: Center for Public Health Genomics

country: USA

institute: University of Virginia

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Analysis of LPS stimulation on F480Hi CD11blo Macrophages from WT and PI3KδE1020K-B KI mice

status: Public on Nov 01 2022

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

summary: Single cell suspensions from WT or PI3KδE1020K-B KI mice were stimulated with LPS for 2 hours after which macrophages were sorted

overall_design: 4 WT mice and 4 PI3KδE1020K-B KI mice

first: J

middle: R

first: O

last: Suchanek

first: M

last: Clatworthy


title: RNA-seq analsis of control or knockout RN7SK in A549 cell line

first: Xin

last: Xu

address: West Huaihai Road No.241

institute: Shanghai Chest Hospital

summary: The goal of this experiment was to determine the effect of RN7SK knockout in A549 cell line.

overall_design: RNA-seq of A549 cell treated with knockout RN7SK or no treatment in three replicates


title: FHL5 cofactor mediates vascular disease risk by regulating smooth muscle cell transcriptional networks [CUT&RUN]

summary: Genome-wide association studies (GWAS) have identified hundreds of loci associated with vascular diseases such as coronary artery disease (CAD) and myocardial infarction (MI), and hypertension. However, the biological roles for many of these loci enriched in the vessel wall remains unknown. Among these, UFL1-FHL5 (chr6q16.1) emerged as a genome-wide significant locus in a recent CAD/MI meta-analysis. Here, we use an integrative approach leveraging human genetics, epigenomic profiling, and in vitro functional and ex vivo imaging analyses to prioritize FHL5 as the top candidate causal gene and reveal the molecular mechanisms of its pleiotropic genetic associations. Notably, FHL5 overexpression in coronary artery smooth muscle cells (SMC) increased vascular calcification and dysregulated processes related to extracellular matrix organization and calcium handling. Lastly, by mapping FHL5 binding sites genome-wide using CUT&RUN, we identified regulatory interactions with downstream disease loci having putative roles in SMC phenotypic modulation. Together, these trans-acting mechanisms may account for a portion of the heritable risk for CAD/MI and other complex vascular diseases.

overall_design: To identify FHL5 genome-wide binding sites, CUT&RUN experiments were performed using FHL5, CREB, H3K4me3, and H3K27ac antibodies using 250,000 HCASMC-hTERTs grown under basal conditions as input. The IgG and HCASMC-hTERT (with no FHL5 expression) samples were included as controls. We conducted at least 2 technical replicates per cell line for each antibody.  Next generation sequencing was performed on an Illumina NextSeq 2000 or Illumina NextSeq 500 instrument.

first: Doris

last: Wong


title: Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates [scRNA-Seq]

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: Longitudinal scRNA-seq  from LCMV-specific P14 CD8 T cells in LCMV-Armstrong and LCMV-Clone 13 infection

overall_design: LCMV-specific P14 cells were sorted from mice infected with LCMV-Arm or LCMV-Cl13 on days 8, 15, or 30 post infection. An additional group of mice was treated with anti-PDL1 every three days starting at day 16; cells were sorted at day 30. scRNA-seq  libraries were prepared using 10x Genomics kits.

first: Josephine

last: Giles

middle: J

last: Wherry


title: Next Generation Sequencing Facilitates Quantitative Analysis of WT and cry1cry2 mutant and cis1-1 mutant in dark and Blue light Transcriptomes

city: Shenzhen

first: Zhao

last: Zhiwei

state: Guangdong

address: 1066, Xueyuan Rd

department: College of Life Sciences and Oceanography

institute: Shenzhen univerisity

summary: Analysis of differential gene splicing and differential gene expression regulated by blue light. The hypothesis tested in the present study was that blue light regulated multiple genes splicing were mediated by CRY and CIS1

overall_design: mRNA profiles of 4 days of WT, cry1 cry2 and cis1-1 seedlings  grown in the dark and then exposed to continuous blue light (30 μmol·m-2·s-1) for 3 hours were generated by deep sequencing, in triplicate, using Illumina Hiseq4000

first: Zhiwei

last: Zhao

first: Hongtao

last: Liu


title: A satellite DNA array barcodes chromosome 7 and regulates totipotency via ZFP819

city: London

first: Helen

middle: M.

last: Rowe

state: --- Select a state ---

address: 4 Newark St, Whitechapel

department: Blizard Institute, Barts and The London School of Medicine and Dentistry

institute: Queen Mary University of London

summary: Mammalian genomes are a battleground for genetic conflict between repetitive elements (REs) and KRAB-zinc finger proteins (KZFPs). We explored whether KZFPs can regulate cell fate by employing Zfp819, which targets a satellite DNA array, ZP3AR. ZP3AR coats a megabase region of chromosome 7 that encompasses genes encoding ZSCAN4, a master transcription factor of totipotency. Depleting Zfp819 in mouse embryonic stem cells (mESCs) causes them to transition to a 2-cell (2C)-like state, whereby the ZP3AR array switches from a poised to an active enhancer state. This is accompanied by a global eviction of heterochromatin roadblocks, which we link to decreased SETDB1 stability. These events result in transcription of active LINE-1 elements and a block in differentiation. In sum, ZFP819 and TRIM28 partner up to close chromatin across Zscan4, allowing exit from totipotency. We propose that satellite DNAs may control developmental fate transitions through the barcoding and switching off of master transcription factor genes.

overall_design: Identification of how ZFP819 and its co-opted satellite repeat, ZP3AR, influence cell fate transitions through chromatin and gene expression changes.

first: Liane

middle: P

last: Fernandes

first: Rocio

last: Enriquez-Gasca

first: Poppy

middle: A

last: Gould

first: James

middle: H

last: Holt

first: Lucia

last: Conde

first: Javier

last: Herrero

first: Didier

last: Trono

first: George

last: Kassiotis

middle: M


title: Mammalian CDC14 phosphatases control bivalent promoters and exit from stemness in pluripotent cells [snATAC-Seq]

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

summary: CDC14 phosphatases are critical components of the cell cycle machinery that drives exit from mitosis in yeast. However, the two mammalian paralogs, CDC14A and CDC14B, are dispensable for cell cycle progression or exit, and their function remains unclear. By generating a double Cdc14a; Cdc14b -null mouse model, we report here that CDC14 phosphatases control cell differentiation in pluripotent cells, and their absence results in deficient development of the neural system. Lack of CDC14 impairs neural differentiation from embryonic stem cells (ESCs) accompanied by deficient induction of genes controlled by bivalent promoters. CDC14 directly dephosphorylates and destabilizes Undifferentiated embryonic Transcription Factor 1 (UTF1) during the exit from stemness. Multiomic single-cell analysis of differentiating ESCs suggest that increased UTF1 levels in the absence of CDC14 prevent the firing of bivalent promoters required for differentiation. These results, along recent data suggesting a critical role for cell cycle kinases in pluripotency, suggest that cell cycle kinase-phosphatase modules such as CDK-CDC14 are critical for linking cell cycle regulation and self-renewal, with a specific function for CDC14 phosphatases modulating key epigenetic regulators during the terminal exit from pluripotency.

overall_design: Wild-type and Cdc14ab KO mESC at day 0 (LIF-containing medium) and day 5 of the neural differentiation protocol were subjected to single-cell ATACseq coupled to single-cell RNAseq in the same cell

first: Carolina

last: Villarroya

last: Graña-Castro

first: Marcos

last: Malumbres


title: Mammalian CDC14 phosphatases control bivalent promoters and exit from stemness in pluripotent cells


title: Transcriptome analysis of in-vitro differentiated myotubes from Emery-Dreifuss Muscular Dystrophy patients.

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

institute: University of Edinburgh

summary: Emery-Dreifuss muscular dystrophy (EDMD) is a genetically and clinically variable disorder. Here we performed transcriptome analysis on 10 EDMD patients covering mutations in 7 EDMD-linked genes, compared to 2 healthy controls. Myoblasts were isolated from muscle biopsies and differentiated in-vitro for 6 days. Differentiated myotubes were isolated, total RNA extracted, and mRNA sequenced. The genes and mutations included were: patient 1 (TMEM214, p.R179H), patient 2 (PLPP7/NET39, p.M92K), patient 3 (SUN1, p.G68D, p.G388S), patient 4 (SYNE1, p.6869*, p.6869*), patient 5 (EMD, p.S58Sfs*1), patient 6 (FHL1, c.688+1G>A), patient 7 (FHL1, p.C224W), patient 8 (FHL1, p.V280M), patient 9 (LMNA, p.T528K), patient 10 (LMNA, p.R571S). The patients were found to segregate into 3 subgroups, defined as: gp1 = patients 1,2,5,7 and 10; gp2 = patients 3,6, and 8; gp3 = patients 4 and 9.

overall_design: Transcriptome analysis was performed comparing in-vitro differentiated EDMD patients against healthy controls. All samples were analysed in triplicate (separate in-vitro differentiation experiments). Four types of comparisons were considered: G1 = all EDMD patients as a single group compared to the controls; G10 = each individual patient, in triplicate, compared to the controls; G3 = each patient subgroup against the controls; G3x = each patient subgroup against all other patients.

middle: I

first: Eric

middle: C

last: Schirmer


title: Evaluation of chromatin accessibility during prostate cancer progression

first: Fei

last: Li

address: 320 Yue-Yang Road Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

summary: We performed ATAC-seq analyses of freshly dissociated epithelial tumor cells at the early stage (W2) or the late stage (M6) of NEPC progression.

overall_design: Chromatin accessibility of prostate tumor cells at the early stage (W2) or the late stage (M6) of NEPC progression.


title: Next Generation Sequencing Facilitates Quantitative Analysis of hepatic macrophages Transcriptomes in  dnTGFβRII(TG) cholangitis model

city: High Education Mega Center, SCUT, Building B2, Room 404

first: min

last: ma

state: guangzhou

address: Panyu Square

department: medical division

institute: south china university of technology

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare  two hepatic macrophage subsets in wild-type (WT) mice with TG mice  transcriptome profiling (RNA-seq).

overall_design: Two hepatic macrophage subsets  mRNA profiles of TG mice and WT mice

first: Liang

first: Pan-Yue

last: Luo

first: Min

last: Ma


title: Prurigo Nodularis

first: Konstantin

last: Agelopoulos


title: Profiling of Nf-e2 binding in primary erythroid cells by CUT&RUN

city: Oxford

first: Robert

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

institute: MRC Weatherall Institute of Molecular Medicine

summary: The chromatin landscape of developing erythroblasts changes dramatically during differentiation. We have profiled the change in Nf-e2 binding in primary erythroid cells entering terminal differentiation using CUT&RUN.

overall_design: This series contains CUT&RUN datasets for Nf-e2 binding in FACS sorted primary erythroid cells. There are multiple biological replicates for each progenitor population, plus IgG control datasets.

first: Douglas

last: Higgs


title: Regulatory cistrome landscape of Foxa1 and Foxa2 during prostate cancer progression [ChIP-seq]

summary: To characterize the genome-wide regulatory cistrome of Foxa1 and Foxa2, we performed both Foxa1 and Foxa2 chromatin immunoprecipitation followed by sequencing (ChIP-seq) on freshly dissociated prostate tumor cells at the early stage (2 weeks post tamoxifen administration) and the late stage (6 months post tamoxifen administration) of NEPC progression, respectively.

overall_design: Characterisation of the genome-wide regulatory cistrome of Foxa1 and Foxa2


title: Profiling of H3K4me1 positioning in primary erythroid cells by CUT&RUN

summary: The chromatin landscape of developing erythroblasts changes dramatically during differentiation. We have profiled the localisation of H3K4me1 in primary erythroid cells entering terminal differentiation using CUT&RUN.

overall_design: This series contains CUT&RUN datasets for H3K4me1 in FACS sorted primary erythroid cells. There are multiple biological replicates for each progenitor population.

first: Ruxandra

last: Tesloianu


title: PICH promotes reprogramming of somatic cells to iPSCs by alleviating DNA replication stress-induced genomic instability

city: Hangzhou

first: Xinwei

last: Geng

address: 866 Yuhangtang Rd., Zijingang Campus, Zhejiang University, Hangzhou, China

institute: Zhejiang University School of Medicine

summary: ATAC-seq of MEF cells reprogrammed by expression of defined exogenous factors (OCT4, SOX2, KLF4 and c-MYC (OSKM))

overall_design: ATAC-seq of day-6 reprogrammed WT and PICH-KO MEF cells.

first: Fengjiao

last: Zhang


title: Profiling of H3K27ac positioning in primary erythroid cells by CUT&RUN

summary: For identifying the specific expressed genes in PDAC, we constructed sequencing libraries from polyadenylated-RNA extracted from 6 PDAC specimens and 6 non-tumor adjacent tissues.

overall_design: This series contains CUT&RUN datasets for H3K27ac in FACS sorted primary erythroid cells. There are multiple biological replicates for each progenitor population, plus IgG control datasets.


title: Profiling of H3K27me3 positioning in primary erythroid cells by CUT&RUN

summary: The chromatin landscape of developing erythroblasts changes dramatically during differentiation. We have profiled the localisation of H3K27me3 in primary erythroid cells entering terminal differentiation using CUT&RUN.

overall_design: This series contains CUT&RUN datasets for H3K27me3 in FACS sorted primary erythroid cells. There are multiple biological replicates for each progenitor population, plus IgG control datasets.


title: Profiling of H3K4me3 positioning in primary erythroid cells by CUT&RUN

summary: The chromatin landscape of developing erythroblasts changes dramatically during differentiation. We have profiled the localisation of H3K4me3 in primary erythroid cells entering terminal differentiation using CUT&RUN.

overall_design: This series contains CUT&RUN datasets for H3K4me3 in FACS sorted primary erythroid cells. There are multiple biological replicates for each progenitor population.


title: CFDP1 is a neuroblastoma susceptibility gene that regulates transcription factors of the noradrenergic cell identity

status: Public on Oct 30 2022

city: Napoli

first: Mario

last: Capasso

address: Via Gaetano Salvatore, 486

department: Dept. of  Molecular Medicine and Medical Biotechnology

country: Italy

institute: University of Napoli "Federico II" - CEINGE Biotecnologie Avanzate Scarl

summary: Pleiotropic genetic factors (e.g., DNA polymorphisms) may be involved in the initiation of neuroblastoma (NB) and coronary artery disease (CAD) given their common origin from defects in neural crest development.  To discover novel NB susceptibility genes, we conducted a three-stage survey including a meta-analysis of NB and CAD genome-wide association data, prioritization of NB causal variants, and validation in an independent case-controls cohort.  The lead SNP, rs13337397 at the 16q23.1 locus, associated with both diseases in the meta-analysis and with NB in the validation study. All the SNPs in linkage disequilibrium with rs13337397 were annotated using the H3K27ac epigenetic marker of neural crest cells (NCC) and NB cell lines. Indeed, we identified the functional SNP rs13337017, mapping within an enhancer of NCCs and NB cell lines and showing long-range interactions with CFDP1 by Hi-C analysis. Luciferase assays indicated that the risk allele of rs13337017 increased CFDP1 expression in NB cell lines. Of note, CFDP1 high expression associated with unfavorable prognostic markers in an analysis including 498 NB transcriptomes. Moreover, depletion of CFDP1 markedly decreased viability and migration and increased apoptotic rates in NB cell lines. Finally, transcriptome and qPCR analyses revealed that the depletion of CFDP1 may affect noradrenergic neuron differentiation by downregulating master regulators of sympathetic noradrenergic identity, including PHOX2B, HAND2 and GATA3.  Our data strongly suggest that CFDP1 acts as oncogene in NB. Additionally, we provide evidence that genetic predisposition to NB can be mediated by the alteration of noradrenergic lineage-specific gene expression.

overall_design: To elucidate the molecular mechanisms involved in CFDP1, we sequenced the whole transcriptome (bulk RNA-Seq) of the SK-N-AS NB cell lines under siCFDP1 and siScrambled experimental conditions (silenced and control, respectively) and performed differential gene expression analysis of biological duplicates.

first: Daniela

last: Formicola

first: Vito

last: Lasorsa


title: The effect of human gingival fibroblast-conditioned medium (HGF-CM) on pulp regeneration

status: Public on Oct 29 2022

city: Cheonansi

first: Ji-Young

last: Yoon

state: Chungnam

address: Dandaero 119

department: Nanbiomedical science

country: South Korea

institute: Dankook University

summary: HGF-CM increases the proliferation and migration ability of DPSC (Dental pulp stem cells) in a dosage dependent manner, and facilitates the mineralization of DPSC by upregulating odotogenic genes. Although lack of in vitro evidence, DPSC and hGF-CM could be a promising combination for pulp regeneration in the future.

overall_design: HGF-CM was collected from their cultivation in serum free media after 48 hours, and basal media was used as a control media. DPSC proliferation and survival rate were assessed and the migration test was performed to confirm the ability of hGF-CM in cell recruitment.  Odontogenic differentiation on DPSC was administered under HGF-CM diluted ostegenic medium at a 1:1 ratio. The level of odontoblast differentiation genes expression, alkaline phosphatase assays and Alizarin red S were conducted on the different time points throughout the 21 day study.

first: Huong

middle: T

last: Vu

first: Jung-Hwan

last: Lee


title: Gene expression profile of healthy individuals phenotyped based on Prakriti types (Vadu cohort)

city: New Delhi

first: Mitali

last: Mukerji

state: Delhi

address: Near Mathura Road, Sukhdev Vihar

department: CSIR TRISUTRA UNIT

institute: CSIR-Institute of Genomics and Integrative Biology

summary: Gene expression profiles of healthy individuals ascribed as Prakriti types based on principles of Ayurveda (TRIDOSHA)

overall_design: PBMCs were obtained from healthy individuals. RNA was extracted. Labeled cRNA was hybridized to Illumina Human HT-12 V4 Beadchips.

first: Shilpi

last: Aggarwal

first: Rintu

last: Kutum

first: Bhavana

last: Prasher


city: Tokyo

first: Harumi

last: Yamada

address: 2-4-41 Ebara Shinagawa-ku

department: Department of Epigenomics

country: Japan

institute: Hoshi University

summary:
The CpG island methylator phenotype (CIMP) is associated with prognosis and drug sensitivity in multiple cancer types.  In gastric cancer, the CIMP is closely associated with Epstein-Barr virus (EBV) infection and AT-rich interactive domain 1A (ARID1A) mutations, a component of the SWI/SNF chromatin remodeling complex.  However, the involvement of SWI/SNF defects in CIMP induction has been unclear.  In this study, we demonstrate a causal role of ARID1A loss-of-function in CIMP induction.  Mutations of SWI/SNF components, especially ARID1A, was associated with the CIMP, as well as EBV infection, in gastric cancers, and also in uterine endometrial and colorectal cancers, which are not affected by EBV infection.  Genome-wide DNA methylation analysis showed that ARID1A knockout (KO) in cultured 293FT cells and gastric epithelial cells, GES1, induced aberrant DNA methylation of a substantial number of CpG sites.  DNA methylation was induced at genomic regions with high levels of pre-existing histone H3 lysine 27 trimethylation (H3K27me3) and those with acquired H3K27me3 by ARID1A KO.  These results showed that the ARID1A mutation induced aberrant DNA methylation, and this is likely to be one of the potential mechanisms of CIMP induction.
(See GSE188293 for data of GES1 with ARID1A KO.)

overall_design: DNA methylation statuses in ARID1A KO cells were analyzed using Infinium MethylationEPIC.

first: Toshikazu

last: Ushijima

first: Hideyuki

last: Takeshima


title: Non-redundant functions of group 2 innate lymphoid cells

status: Public on Oct 28 2022

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

summary: Here, we report the generation of a new mouse model based on the Nmur1 promoter as a driver for simultaneous expression of Cre recombinase and green fluorescent protein (GFP), which allows gene targeting in ILC2 without affecting other innate and adaptive immune cells. By removing Id2 and Gata-3 using Cre-mediated gene deletion in Nmur1-expressing cells, we have generated mice with selective and specific deficiency in ILC2. ILC2-deficient mice have decreased eosinophil counts in steady state and are unable to recruit eosinophils in the airways in models of allergic asthma. Further, ILC2-deficient mice fail to mount an appropriate immune and epithelial type 2 response resulting in a profound defect in worm control and a non-protective type 3 immune response. In total, our data establish non-redundant functions for ILC2s in the presence of adaptive immune cells at steady state and during diseases and argue for a multilayered organization of the immune system based on a spatiotemporal division of labor.

overall_design: RNA-Sequencing of Eosinophils from the Lung after papain treatment (day7) comparing cKO mice (Nmur1Cre-T2A-GFPId2flox/flox) and littermate controls (Id2flox/flox)

first: Katja

last: Jarick

first: Patrycja

last: Topczewska

first: Manuel

middle: O

last: Jakob

first: Christoph

middle: S

last: Klose


title: Genome-wide analysis of long noncoding RNA and mRNA expression profile in A549 CSCs and non-CSCs

city: Changsha

first: Jun

last: Wang

address: No. 87, Xiangya Road

institute: Xiangya Hospital, Central South University

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

summary: Lung cancer is the malignant tumor with the highest incidence in the world. Cancer stem cells (CSCs) has the characteristics of immortal proliferation, self-renewal, differentiation of stem cells and high invasion and migration capabilities. In recent years,  the function of non-coding RNA (ncRNA) that is regarded as transcription noise has been gradually discovered which  can participate in the occurrence and development of tumors by regulating the stemness of cancer stem cells. Herein, we detected the differential expressed lncRNAs in A549 NANOG+ (CSCs) and A549 NANOG- (non-CSCs) cells. Our finding suggest the profiles of lncRNAs changed in CSCs compared with non-CSCs and provide new insight into molecular mechanism that may account for the lung  adenocarcinoma.

overall_design: Microarray expression profiling of lncRNAs and mRNAs were conducted using RNA extracted from three A549 Nanog+ (CSCs)samples and three A549 Nanog- (non-CSCs) samples

first: Chaojun

last: Duan


title: SLC35F2 is Essential for Proliferation and Osteogenic Differentiation of Bone Marrow-Derived Human Mesenchymal Stem Cells

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary: We compared the gene expression at each passage stage in two cell lines.

overall_design: Human mesenchymal stem cells, hMSC, was cultured in MesenPRO RS medium (Gibco, 12746012) supplemented with 2 mM L-glutamine (Gibco, 25030-81) and 1 % Penicillin-Streptomycin (Gibco, 15140-122) at 37 ℃ in a humidified atmosphere of 5 % CO2. Total RNA was extracted from cell samples using ISOGEN (Nippon gene).DNA microarray was performed by using a SurePrint G3 Human GE 8 × 60 K Microarray Kit (G4851A) and a Low Input Quick Amp Labeling Kit, 1 color (Agilent).

first: Tomoko

last: Watanabe


title: ILC2 promote type 2 immunity in colonic epithelial cells during N. brasiliensis infection.

summary: ILC2 contribute to tissue immunity by secreting large amounts of cytokines upon activation. However, their specific contribution to worm infection and epithelial remodeling remains incompletely understood. We tested the impact of ILC2 on tissue immunity in the colon of mice infected with the nematode Nippostronylus brasiliensis. We performed scRNA sequencing of colon epithelial cells from mice specifically lacking ILC2 (Nmur1-Cre Id2 fl/fl). Transcripts typically associated with type 2 immunity were reduced in ILC2-deficient mice, indicating a non-redundant role of ILC2 for type 2 tissue immunity in worm protection that cannot be compensated by other cell types. These findings highlight the importance of ILC2 for nematode control and type 2 tissue immunity.

overall_design: Sequencing of RNA was performed from flow cytometry-sorted colon epithelial cells (CD45lo/- EpCAM+) of Nmur1-Cre Id2fl/fl mice and littermate controls, using the 10X Genomics platform with the 10X Chromium Next GEM Single Cell 3’ Reagent kit (v3.1 Chemistry Dual Index).

first: Caroline

last: Braeuning

first: Thomas

last: Conrad

first: Dieter

last: Beule


title: Transcriptome analysis of the cranial dura of neonatal C57 BL/6 mice

city: Beijing

first: Tao

last: Zou

address: 27, Taipingroad

institute: Beijing Institute of Basic Medical Sciences

summary: To investigate the possible changes of meningeal gene expression during neonatal stage, we performed gene expression profiling analysis using data obtained from bulk RNA-seq of the cranial dura of C57 BL/6 mice on postnatal day1,day7, and day14.

overall_design: Bulk RNA-seq of the cranial dura from neonatal C57 BL/6 mice.

first: Jiyan

last: Zhang

first: Chunxiao

last: Niu

first: Jijun

last: Yu


title: Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [TRIBE_STAMP]

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

department: Biochemistry

institute: Duke University School of Medicine

summary: N6-methyladenosine (m6A) plays critical roles in gene expression control by recruiting the cytoplasmic reader proteins YTHDF1,2 and 3. Recently, the function of YTHDF proteins and whether they bind to shared or distinct sets of methylated mRNAs in cells has been the subject of debate. Here, we developed TRIBE-STAMP, an approach for single-molecule detection of the target RNAs of two RNA binding proteins simultaneously in cells. Applying TRIBE-STAMP to the YTHDF proteins revealed that most target mRNAs are shared among the three YTHDF proteins. Surprisingly, we also found that individual mRNA molecules can be bound by more than one YTHDF protein throughout their lifetime. Furthermore, we show that YTHDF proteins bind sequentially to target methylated mRNAs, with YTHDF1 binding before YTHDF2 or YTHDF3. Our data reveal shared molecular interactions among the YTHDF proteins and support a model in which YTHDF1 and YTHDF3 are unlikely to promote rapid mRNA decay.

overall_design: YTHDF1, YTHDF2 and YTHDF3 TRIBE-STAMP in HEK293T cells. YTHDF-ADAR expressing plasmids were transfected in cells stably expressing YTHDF-APOBEC1 proteins for 24h. Total RNA was extracted, and libraries prepared in triplicates for cells transfected with YTHDF1- or YTHDF2-ADAR or in duplicates for cells transfected with YTHDF3-ADAR. cDNA was sequenced in paired end mode using read lengths of 150bp and 250bp. For identification of editing sites by each protein, cells transfected with plasmids expressing APOBEC1 or ADAR alone were used as controls.

first: Mathieu

middle: N

last: Flamand

first: Ke

last: Ke

middle: D


title: Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [Polysome]

overall_design: YTHDF1, 2 and 3 TRIBE in polysome-associated RNAs.


title: The hallmarks of circRNA expression throughout the circadian cycle.

first: Andranik

last: Ivanov

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNAs (circRNAs) are a large class of highly stable RNA molecules with abundant expression in blood and different brain regions.  CircRNA deregulation has been linked to psychiatric, neurodegenerative and neurodevelopmental disorders. Many of these brain conditions occur in parallel or arguably due to aberrant wake/sleep cycle, which is why it is necessary study circRNA expression in the context of circadian rhythm. Here we study the hallmarks of circRNA expression in different brain regions and identify potential regulators of synaptic signaling and light entrainment.

overall_design: The hippocampus and frontal cortex were investigated during 6 different time points of the 24 hour light-dark cycle: ZT1 (07:00), ZT5 (11:00), ZT9 (15:00), ZT13 (19:00), ZT17 (23:00), ZT21 (03:00). Each group consists of 3 biological replicates. Overall (2 tissues * 6 time points * 3 replicates =) 36 samples

first: Daniele

last: Mattei

first: Urs


title: Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules.

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

overall_design: Refer to individual Series


title: Blockage of PPARg T166 phosphorylation enhances the inducibility of beige adipocytes and improves metabolic dysfunctions

city: Nanjing

first: Yuxin

address: 163 Xianlin Road

institute: Nanjing University

summary: Beige adipocytes in mammalian white adipose tissue (WAT) can reinforce fat catabolism and energy expenditure. Promoting beige adipocyte biogenesis is a tantalizing tactic for combating obesity and its associated metabolic disorders. Here, we report that a previously unidentified phosphorylation pattern (Thr166) in the DNA-binding domain of PPARg regulates the inducibility of beige adipocytes. This unique posttranslational modification (PTM) pattern influences allosteric communication between PPARg and DNA or coactivators, which impedes the PPARg-mediated transactivation of beige cell-related gene expression in WAT. The genetic mutation mimicking T166 phosphorylation (p-T166) hinders the inducibility of beige adipocytes. In contrast, genetic or chemical intervention in this PTM pattern favors beige cell formation. Moreover, inhibition of p-T166 attenuates metabolic dysfunction in obese mice. Our results uncover a mechanism involved in beige cell fate determination. Moreover, our discoveries provide a promising strategy for guiding the development of novel PPARg agonists for the treatment of obesity and related metabolic disorders.

overall_design: mRNA profiling of SVF differentiated adipocytes from PPARg WT, T166A and T166D mutant mice.

first: Nanfei

last: Yang

first: Pingping

last: Shen


title: Variation in Ubiquitin System Genes Creates Substrate-Specific Effects on Proteasomal Protein Degradation

status: Public on Oct 26 2022

city: Minneapolis

first: Mahlon

last: Collins

state: MN

address: 6-160 Jackson Hall, 321 Church St SE

department: Genetics, Cell Biology, and Development

institute: University of Minnesota

summary: Ubiquitin-proteasome system (UPS) protein degradation regulates protein abundance and eliminates misfolded and damaged proteins from eukaryotic cells. Variation in UPS activity influences numerous cellular and organismal phenotypes. However, to what extent such variation results from individual genetic differences is almost entirely unknown. Here, we developed a statistically powerful mapping approach to characterize the genetic basis of variation in UPS activity. Using the yeast Saccharomyces cerevisiae, we systematically mapped genetic influences on the N-end rule, a UPS pathway that recognizes N-degrons, degradation-promoting signals in protein N-termini. We identified 149 genomic loci that influence UPS activity across the complete set of N-degrons. Resolving four loci to individual causal nucleotides identified regulatory and missense variants in ubiquitin system genes whose products process (NTA1), recognize (UBR1 and DOA10), and ubiquitinate (UBC6) cellular proteins. Each of these genes contained multiple causal variants and several individual variants had substrate-specific effects on UPS activity. A cis-acting promoter variant that modulates UPS activity by altering UBR1 expression also alters the abundance of 36 proteins without affecting levels of the corresponding mRNAs. Our results demonstrate that natural genetic variation shapes the full sequence of molecular events in protein ubiquitination and implicate genetic influences on the UPS as a prominent source of post-translational variation in gene expression.

overall_design: Comparative gene expression analysis by RNA-seq in the yeast Saccharomyces cerevisiae strain BY4741 using 5 biological replicates with UBR1 wild-type and 5 biological replicates with UBR1 -469A>T

first: Gemechu

last: Mekonnen

first: Frank

middle: W

last: Albert


title: Effect of depletion of the gne gene in Zebrafish

city: Jerusalem

first: Stella

last: Mitrani-Rosenbaum

address: Ein Karem

country: Israel

institute: Hadassah -The Hebrew University Medical Center

summary: GNE Myopathy is a rare, recessively inherited neuromuscular worldwide disorder, caused by a spectrum of bi-allelic mutations in  the human GNE gene. GNE encodes a bi-functional enzyme responsible for the rate-limiting step of sialic acid biosynthesis pathway.  However, the process in which GNE mutations lead to the development of a muscle pathology is not clear yet. Cellular and mouse  models for GNE Myopathy established to date have not been informative. Further, additional GNE functions in muscle have been  hypothesized. In these studies, we aimed to investigate gne functions using zebrafish genetic and transgenic models, and  characterized them using macroscopic, microscopic, and molecular approaches.  We first established transgenic zebrafish lineages expressing the human GNE cDNA carrying the M743T mutation, driven by the  zebrafish gne promoter. These fish developed entirely normally. Then, we generated a gne knock-out (KO) fish using the CRISPR/Cas9 methodology. These fish died 8-10 days post-fertilization (dpf), but a phenotype appeared less than 24 hours before  death and included progressive body axis curving, deflation of the swim bladder and decreasing movement and heart rate. However, muscle histology uncovered severe defects, already at 5 dpf, with compromised fiber organization. Sialic acid  supplementation did not rescue the larvae from this phenotype nor prolonged their lifespan. To have deeper insights into the potential functions of gne in zebrafish, RNA sequencing was performed at 3 time points (3, 5, and 7 dpf). Genotype clustering was  progressive, with only 5 genes differentially expressed in gne KO compared to gne WT siblings at 3 dpf. Enrichment analyses of the  primary processes affected by the lack of gne also at 5 and 7 dpf point to the involvement of cell cycle and DNA damage/repair  processes in the gne KO zebrafish. Thus, we have established a gne KO zebrafish lineage and obtained new insights into gne  functions. This is the only model where GNE can be related to clear muscle defects, thus the only animal model relevant to GNE  Myopathy to date. Further elucidation of gne precise mechanism-of-action in these processes could be relevant to GNE Myopathy  and allow the identification of novel therapeutic targets.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  homozygote gne KO zebrafish, heterozygote gneKO zf and gne WT zebrafish.

first: Hagay

last: Livne

first: Alon

last: Daya

first: Shmuel

last: Ruppo


title: Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis

status: Public on Oct 27 2022

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: Histone chaperones and chromatin remodelers control nucleosome dynamics, which are essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated replication-dependent H3.1 deposition and HIRA-mediated replication-independent H3.3 deposition in yeast and metazoans. Whether ASF1 function is evolutionarily conserved in plants is unknown. Here, we show that Arabidopsis ASF1 proteins display a preference for the HIRA complex. Simultaneous mutation of both Arabidopsis ASF1 genes caused a decrease in chromatin density and ectopic H3.1 occupancy at loci typically enriched with H3.3. Genetic, transcriptomic, and proteomic data indicate that ASF1 proteins strongly prefers the HIRA complex over CAF-1. asf1 mutants also displayed an increase in spurious Pol II transcriptional initiation and showed defects in the maintenance of gene body CG DNA methylation and in the distribution of histone modifications. Furthermore, ectopic targeting of ASF1 caused excessive histone deposition, less accessible chromatin, and gene silencing. These findings reveal the importance of ASF1-mediated histone deposition for proper epigenetic regulation of the genome.

overall_design: This dataset includes ChIP-seq, RNA-seq and BS-seq to understand the molecular mechanism of Arabidopsis histone chaperone ASF1 proteins.


title: Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [RIP-Seq]

first: Kate

overall_design: YTHDF1, YTHDF2 and YTHDF3 RIP-TRIBE in HEK293T cells expressing YTHDF-ADAR proteins.


title: Comparison of toxicological effects and exposure levels between triclosan and its structurally similar chemicals using in vitro tests for read-across case study

city: Tochigi

first: shota

last: Nakagawa

address: 2606, Akabane, Ichikai-Machi, Haga-Gun

institute: Kao Corporation

summary: To improve prediction accuracy of read-across, we compared biological similarities between triclosan and its structurally similar chemicals including diclosan and 1-chloro-3-(4-chlorophenoxy) benzene. To elucidate and compare the potential mechanisms between them, we performed in vitro toxicogenomics with rat primary hepatocytes.

overall_design: We performed in vitro toxicogenomics with Sprague Dawley rat primary hepatocytes exposed by triclosan, diclosan, 1-chloro-3-(4-chlorophenoxy) benzene. After 24 h pre-culture, the cells were exposed to each chemical at 30 µM for 24 h. Three independent experiments were performed at each condition.

first: Shota


title: Cas9 off-target binding to the promoter of bacterial genes leads to silencing and toxicity [RNA-Seq]

status: Public on Oct 25 2022

city: Paris

first: David

last: Bikard

address: 28 rue du Dr Roux

country: France

institute: Institut Pasteur

summary: Over the last decade, gene-silencing mediated by dCas9 binding to transcribed regions or their promoters, a strategy referred to as CRISPRi, has emerged as a powerful tool in bacterial genetics. While this strategy has already been broadly adopted, several studies have reported experimental setups in which dCas9 expression was toxic. In particular, guide RNAs that share specific PAM-proximal sequence motifs were shown to be toxic to E. coli. Here we demonstrate that this toxicity is caused by off-target binding of dCas9 to the promoter of essential genes. Silencing of off-target genes can occur with as little as 4nt of identity between the PAM-proximal sequence and the off-target position. This phenomenon only occurs in some promoter sequences but does not appear to be constrained to any specific PAM-proximal sequence. Accordingly, screens performed in various strains of E. coli and related species shows that the nature of toxic guide RNAs changes together with the evolution of the sequence of off-target positions. These results highlight the importance of relying on several guide RNAs targeting the same gene when performing CRISPRi experiments in bacteria in order to avoid any possible confounding results due to off-target binding.

overall_design: Samples were prepared from E. coli LC-E18 harbouring psgRNAcos plasmids with 3 different guides (control guide, AGGAA_non1 and ACCCA_non1). Samples were harvested 3 hours after aTc induction.

first: Lun

last: Cui


title: WES data from 286 diffuse gliomas under the 2021 WHO Classification of Tumors of the Central Nervous System

first: changlin

last: yang

address: No. 119 South Fourth Ring Road West

department: Department of Molecular Neuropathology

institute: Beijing Neurosurgical Institute, Capital Medical University

summary: Diffuse gliomas (DGs) are the most common and lethal primary neoplasms in the central nervous system. The latest 2021 WHO Classification of Tumors of the Central Nervous System (CNS) was published in 2021, immensely changing the approach to diagnosis and decision making. As a part of the Chinese Glioma Genome Atlas (CGGA) project, our aim was to provide genomic profiling of gliomas in a Chinese cohort. Two hundred eighty six gliomas with different grades were collected over the last decade. Using the Illumina HiSeq platform, over 75.8 million high-quality 150 bp paired-end reads were generated per sample, yielding a total of 43.4 billion reads. We also collected each patient’s clinical and pathological information and used it to annotate their genetic data. This dataset provides an important reference for researchers and will significantly advance our understanding of gliomas.

overall_design: Analysis of DNA methylation from 5 human glioma tissues

first: Zheng

last: Zhao

first: Ke-Nan

last: Zhang

first: Zhiyan

last: Sun

first: Changlin

first: Wenping

last: Ma

first: Fan

last: Wu

first: Tao

last: Jiang


title: Time-course  tracking of physical proximity and its effect on gene expression for elucidating single NK and cancer cell interactions using a microfluidic platform

first: Smriti

last: Chawla

address: Okhla Industrial Estate, Phase III, near Govind Puri Metro Station

institute: Indraprastha Institute of Information Technology,

summary: We report a platform that combines the capture, co-incubation, time-lapse imaging, and gene expression profiling of doublets using the microfluidic integrated fluidic circuit (IFC) which could be used for real-time physical and transcriptional cell-cell interaction quantification. The temporal variations in natural killer (NK) - triple-negative breast cancer (TNBC) cell distances were tracked and compared with terminally-profiled cellular transcriptomes. The results showed the time-bound activities of regulatory modules and alluded to the existence of transcriptional memory. Our experimental and bioinformatic approaches serve as a proof of concept for interrogating cell interactions at doublet resolution, which can be applicable across different cancer types.

overall_design: Effect of physical proximity on transcriptomic signatures during single NK and cancer cell interactions on a microfluidic platform

first: Debarka

last: Sengupta

first: Stefanie

last: Jeffrey

first: Naveen

last: Ramalingam


title: Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways (SU2C nasal brushings)

city: Boston

first: Adam

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary: SARS-CoV-2 infection and disease severity are influenced by viral entry (VE) gene expression patterns in the airway epithelium. The similarities and differences of VE gene expression (ACE2, TMPRSS2, and CTSL) across nasal and bronchial compartments have not been fully characterized using matched samples from large cohorts. Gene expression data from 793 nasal and 1673 bronchial brushes obtained from individuals participating in lung cancer screening or diagnostic workup revealed that smoking status (current versus former) was the only clinical factor significantly and reproducibly associated with VE gene expression. The expression of ACE2 and TMPRSS2 was higher in smokers in the bronchus but not in the nose. AQ1 scRNA-seq of nasal brushings indicated that ACE2 co-expressed genes were highly expressed in club and C15orf48 secretory cells while TMPRSS2 co-expressed genes were highly expressed in keratinizing epithelial cells. In contrast, these ACE2 and TMPRSS2 modules were highly expressed in goblet cells in scRNA-seq from bronchial brushings. Cell-type deconvolution of the gene expression data confirmed that smoking increased the abundance of several secretory cell populations in the bronchus, but only goblet cells in the nose. The association of ACE2 and TMPRSS2 with smoking in the bronchus is due to their high expression in goblet cells which increase in abundance in current smoker airways. In contrast, in the nose, these genes are not predominantly expressed in cell populations modulated by smoking. In individuals with elevated lung cancer risk, smokinginduced VE gene expression changes in the nose likely have minimal impact on SARS-CoV-2 infection, but in the bronchus, smoking may lead to higher viral loads and more severe disease.

overall_design: Cells from the inferior turbinate of the nose were collected as part of a study involving participants with indeterminate pulmonary nodules undergoing lung cancer screening at Boston Medical Center and Lahey Hospital Medical Center.

first: Ke

last: Xu

first: Xingyi

last: Shi

first: Joshua

last: Campbell

first: Jennifer

last: Beane


title: nCounter analysis of mRNAs associated with muscle invasive urothelial bladder carcinoma (MIBC) using a Nanostring custom assay

city: Houston

first: Sreyashi

last: Basu

address: 7455 Fannin Street

institute: MDACC

summary: Gene profiling analysis to evaluate pre- and post-immune checkpoint therapy with tremelimumab (anti-CTLA-4) plus durvalumab (anti-PD-L1) as neoadjuvant treatment prior to radical cystectomy in MICB were analyzed using customized 749- gene Nanostring panel

overall_design: 21 pretreatment and 13 tremelimumab (anti-CTLA-4) plus durvalumab (anti-PD-L1) treated patient samples were analyzed


title: Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways (BCLHS bronchial brushings)

summary: RNA was isolated from bronchial brushings obtained from current and former smokers with and without COPD. mRNA expression was profiled using Affymetrix Human Gene 1.0 ST Arrays.

overall_design: RNA isolated from bronchial brushings was processed and hybridized to Affymetrix Human Gene 1.0 ST Arrays. A total of 269 arrays from 267 subjects were hybridized. Data from the 269 microarrays were used for RMA normalization. Data from 238 subjects was used in the analysis to determine the association of gene expression with COPD-related phenotypes.


title: Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways (DECAMP bronchial brushings)

overall_design: Bronchial brushings were obtained from subjects enrolled in the DECAMP (Detection of Early lung Cancer Among Military Personnel) cohorts.


title: A Role for Orphan Nuclear Receptor Liver Receptor Homolog-1 (LRH-1, NR5A2) in Primordial Follicle Activation

status: Public on Oct 24 2022

city: University Park

first: Camilla

middle: H. K.

last: Hughes

address: 439 Shortlidge Rd

department: Animal Science

institute: Penn State University

summary: The ovarian reserve of follicles comprises all oocytes for lifetime fertility and is depleted by progressive activation. The orphan nuclear receptor liver receptor homolog 1 (LRH-1; Nr5a2) is essential for ovulation, but its role in the early stages of follicular development is not known. We therefore developed a model of conditional depletion of LRH-1 from early postnatal ovaries (postnatal day 4) and performed RNAsequencing to identify LRH-1 regulated genes during the earliest stages of follicular activation.

overall_design: Mice with ovarian knockout of  liver receptor homolog 1 (LRH-1) were generated using Amhr2-cre (LRH-1 cKO; Nr5a2 f/f, Amhr2-cre Tg/+) and compared to littermate controls with intact LRH-1 expression(Con; Nr5a2 f/f, Amhr2-cre +/+). Ovaries were collected from mice on postnatal day (PND) 4.

first: Marie-Charlotte

last: Meinsohn

first: Anthony

last: Estienne

first: Hatice

last: Saatcioglu

first: David

last: Pépin

first: Raj

last: Duggavathi

first: Bruce

last: Murphy


title: The CIC-ERF co-deletion underlies fusion independent activation of ETS family member, ETV1, to drive prostate cancer progression.

city: San Francisco

first: Hanbing

last: Song

state: CA

address: 513 Parnassus Ave.

institute: UCSF

summary:
Methods: To characterize the expression profile of ERF-CIC deleted prostate cells, we performed single-cell RNA-sequencing of PNT2 ERF knock down and CIC knockout cell line.
Results: We found that CIC and ERF loss were significantly associated with the ETV1-regulated gene set but was anti-correlated with the TMPRSS2-ERG fusion signature gene set. The enrichment gene signature of ERF-CIC dual loss was similar to ERF loss alone and ETV1-regulated gene set signature.
Conclusions: Our results provide relevant insights about a new subtype of prostate cancer with ERF and CIC codeletion

overall_design: RNA sequencing of CIC-ERF codeletion in PNT2, CICKO and ERF KD in PNT2 cells

first: Nehal

last: Gupta

first: Wei

first: Rovingaile

middle: K

last: Ponce

first: Yone

last: Lin

first: Ji

last: Kim

first: Eric

last: Small

first: Felix

middle: Y

last: Feng

first: Franklin

last: Huang

first: Ross

last: Okimoto


title: Gene expression profile of Leishmania major infected THP1 cell lines

city: Izmir

first: Mayda

last: Gursel

address: Dokuz Eylül Üniversitesi İnciraltı Yerleşkesi

department: Basic and Translational Research Program

country: Turkey

institute: Izmir Biomedicine and Genome Center

summary: Nanostring nCounter gene expression analysis on L. major infected wild type versus knockout THP1 cells was performed based on 784 genes with nCounter PanCancer Immune Profiling CS Kit (no MK).

overall_design:
In the study presented here, total RNA was extracted from 3 biological replicates per cell line were analyzed using internal positive, negative and housekeeping controls of nCounter PanCancer Immune Profiling CS Kit (no MK).
Fold changes were calculated by nSolver Analysis software (v4.) and nCounter® Advanced Analysis Software (v2.)

first: Ismail

last: Yilmaz

first: Emre

last: Dunuroglu

first: Ihsan

last: Ayanoglu

last: Ipekoglu

first: Muzaffer

last: Yildirim

first: Nogay

last: Girginkardesler

first: Yusuf

last: Ozbel

first: Seray

last: Toz

first: Ahmet

last: Ozbilgin

first: Gamze

last: Aykut


title: Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways (IDA bronchial brushings)

first: Adam

last: Gower

overall_design: Cells from the main stem bronchus were brushed as part of a study involving participants undergoing diagnostic bronchoscopy for suspected lung cancer at Boston Medical Center.

first: Ke

last: Xu

first: Xingyi

last: Shi

first: Joshua

last: Campbell

first: Jennifer

last: Beane


title: The Heterochromatin protein 1 is a regulator in RNA splicing precision deficient in ulcerative colitis

first: Laurence

last: Arbibe

address: 156 rue de Vaugirard

department: Immunology, microbiology and hematology

institute: INEM

summary: Total RNA was extracted from mouse Villin-creERT2:Cbx3-/- mice epithelial cells from the small intestine crypt, villi and colon epithelia

overall_design: 18 samples


title: mRNA-seq of thymic epithelial cells from PBS or IL-33 treated thymus

status: Public on Oct 23 2022

first: Lei

address: longmian avenue

institute: Nanjing Medical University

summary: Severe infection commonly results in T cell aging, which leads to impaired pathogen clearance or increased secondary infection in both humans and animals. However, the exact mechanisms remain poorly understood. Here, we demonstrated that severe infection-induced IL-33 production resulted in acute thymic involution-mediated naive T cell aging and impaired host control of infection in mouse disease models of schistosomiasis or sepsis. Furthermore, we illustrated that IL-33 triggered excessive generation of medullary thymic epithelial cell (mTEC) IV (thymic tuft cells) in a Pou2f3-dependent manner, as a consequence, disturbed mTEC/cortical TEC (cTEC) compartment and caused acute thymic involution during severe infection. More importantly, IL-33 deficiency or IL-33 receptor ST2 deficient thymus transplantation rescued T-cell immunity to better control infection in mice. Our findings not only uncover a novel link between severe infection-induced IL-33 and thymic involution-mediated naive T cell aging, but also suggest that targeting IL-33 or ST2 is a promising strategy to rejuvenate T cell immunity to better control severe infection.

first: Chuan

last: Wei

first: Xiaojun

last: Chen

last: Su


title: Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways (DECAMP nasal brushings)

overall_design: Nasal brushings were obtained from subjects enrolled in the DECAMP (Detection of Early lung Cancer Among Military Personnel) cohorts.


title: little skate motor neuron

city: Seoul

first: DongAhn

last: Yoo

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

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

sample_organism:
Leucoraja erinaceus
Gallus gallus
Mus musculus

overall_design: Refer to individual Series


title: Inter-species comparison of little skate motor neuron gene expression with chick and mouse

summary: The little skate, a cartilaginous fish evolutionarily distal from tetrapods, displays walking-like behavior and has conserved genetic programs and neuronal substrates for land-walking. Studies on little skate have been limited due to lack of high-quality genome assembly. Here, we generated an improved genome assembly of little skate reflecting precise gene annotation and structures and performed integrated analysis of gene expression and chromatin accessibility to investigate molecular mechanisms of fin motor neuron development. Through interspecies comparison of RNA expression, common and species-specific genes expressed in fin/limb/wing level motor neurons were identified. Moreover, by performing chromatin accessibility analysis with a pure fin motor neuron population the potential regulators controlling the gene expression in fin motor neurons were identified. Interspecies comparison of genomic data, gene expression, and chromatin accessibility assay suggest that the little skate has highly conserved gene regulatory mechanisms controlling tetrapod locomotion, which was not previously expected.

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus

overall_design: Gene expression data of mouse and chick were generated to examine conservation of candidate genes for motor neuron development in little skate

first: Chul

last: Lee

first: Yeongho

first: JunHee

last: Park

first: Adriana

last: Heguy

first: Jeremy

last: Dasen

first: Heebal

last: Kim

first: Myungin

last: Baek


title: Genome-wide screening of gene regulation of little skate motor neuron

overall_design: Examination of chromatin accessibility of little skate motor neuron compared with tail region spinal cord.


title: Gene expression profile of bone marrow cells from leukemic mice by transduction of synonymous mutant of MLL-AF4

status: Public on Oct 20 2022

city: Yokohama

first: Hiroshi

last: Okuda

state: Kanagawa

address: 3-9 Fukuura, kanazawa-ku

department: Immunology

institute: Yokohama city university school of medicine

summary: The establishment of a murine disease model of MLL-AF4 via retroviral transduction has been difficult due to a lack of understanding of its unknown regulatory mechanisms. We showed that MLL-AF4 protein is post-transcriptionally regulated, and its synonymous mutant is able to induce myeloid leukemia by retroviral transduction. To validate synonymous mutant of MLL-AF4 is phenotypically similar to the MLL-mAf4, we analyzed the gene expression profiles by RNA-seq.

overall_design: We purified RNA from bone marrow cells when the sign of leukemia is observed and performed gene expression profiling analysis by RNA-seq.


title: Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways

first: Adam

last: Gower


title: Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways (AEGIS nasal brushings)

summary: Nasal epithelial brushings were prospectively collected from current and former smokers with pulmonary lesions suspicious for lung cancer in the AEGIS-1 (n=375) and AEGIS-2 (n=130) clinical trials and gene expression profiled using microarrays.

overall_design: mRNA gene expression from 505 nasal epithelial brushings was profiled using Affymetrix Gene 1.0 ST microarrays. Samples were collected from patients in the Airway Epithelial Gene Expression in the Diagnosis of Lung Cancer (AEGIS) trials (AEGIS-1 and AEGIS-2), two independent, prospective, multicenter, observational studies. 375 nasal samples (243 with lung cancer, 132 with benign lung disease) were patients in the AEGIS-1 trial and 130 nasal samples (66 with lung cancer, 64 with benign lung disease) were from patients in the AEGIS-2 trial.

first: Ke

last: Xu

first: Xingyi


status: Public on Oct 19 2022

city: Philadelphia

first: Patrick

middle: M.

last: Schaefer

address: 3501 Civic Center Blvd

department: CMEM

institute: Children's Hospital of Philadelphia

summary: RNA Sequencing of transmitochondrial cybrids revealed a downregulation of oxidative phosphorylation and nicotinamide metabolism in cybrids with patient mitochondria

overall_design: We report RNA Sequencing of transmitochondrial cybrids (143B(TK-) ρ0 osteosarcoma cells) fused with mitochondria either from a haplogroup H7 control (399-2) or from a patient with the ND5 m.13708G>A mutation on haplogroup H7 (2 clones, 370-1 and 370-5).

first: Komal

last: Rathi


title: Specification of the Germline in Monozygotic Twins with Discordant Primary Ovarian Insufficiency

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

summary: Women diagnosed with primary ovarian insufficiency (POI) cannot produce oocytes and therefore are not candidates for the majority of current assisted reproductive technology treatments. POI can in some cases arise due to errors in primordial germ cell (PGC) specification and PGC differentiation into oogonia and oocytes. To address the ability to reverse germ cell loss in infertile women through induced reprogramming followed by germ cell differentiation, we derived hiPSCs from monozygotic (MZ) twins discordant for POI. hiPSC lines derived from all research participants successfully differentiated into primordial germ cell-like cells (hPGCLCs), as determined by flow cytometry, immunofluorescence, and 10x single-cell RNA sequencing. Therefore, we demonstrate that after epigenetic reprogramming, infertile women with POI can re-specify germ cells. The research presented here advances efforts of fertility restoration and understanding of the germ cell lineage.

overall_design: hPGCLC aggregates differentiated from five hiPSC sublines were sequenced for 10X single cell-RNA seq. Three replicates per sample.

first: Erica

last: Pandolfi

first: Amander

last: Clark


title: mRNA-seq of naïve CD4+ T cells from uninfected or schistosome-infected mice

first: Lei

overall_design: mRNA sequence of naïve CD4+T cells from uninfected or schistosome-infected mice

first: Chuan

last: Wei

first: Xiaojun

last: Chen


title: Single cell RNA-seq in small intestine

first: Jonathan

last: Moody

address: 1-7-22 Suehiro-cho

institute: RIKEN Center for Integrative Medical Sciences

summary: Identify cytotoxic CD4+ T cells in human intestine and analyze characteristics of the population in IBD patients by using single cell RNA-seq

overall_design: CD4+CD8A+ T cells in human intestine of IBD patients are extracted and compared with control samples and with mouse CD4CTLs

first: Shun

last: Tanemoto

first: Tomohisa

last: Sujino

first: Kentaro

last: Miyamoto

first: Yusuke

last: Yoshimatsu

first: Yoshinari

last: Ando

first: Ikuko

last: Koya

first: Yosuke

last: Harada

first: Anna

last: Tojo

first: Keiko

last: Ono

first: Yukie

last: Hayashi

first: Kaoru

last: Takabayashi

first: Takeshi

last: Okabayashi

first: Toshiaki

last: Teratani

first: Yohei

last: Mikami

first: Nobuhiro

last: Nakamoto

first: Naoki

last: Hosoe

first: Haruhiko

last: Ogata

first: Chung-Chau

last: Hon

first: Jay

last: Shin

first: Takanori

last: Kanai


title: Genome-wide identification of target genes for the transcription factor Klf13 in differentiated primary mouse oligodendrocytes.

status: Public on Oct 21 2022

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

summary: To identify target genes of the Klf13 transcription factor in oligodendroglia in a genome-wide and unbiased approach, we cultured primary mouse oligodendroglia of wild type and Klf13-knockout mice, kept them under differentiating conditions, and isolated total RNA which was followed by RNA-Seq studies. Among others we detected substantial changes in the expression of genes associated with differentiation and myelination of oligodendrocytes.

overall_design: We generated mRNA profiles of wild type (ctrl) and Klf13-kockout cells (Klf13_ko) using the Illumina NovaSeq 6000, PE 2x150 platform.

first: Celine

last: Bernhardt

first: Franziska

last: Fröb


title: RNA profiles of primary AML cells engrafted in xenograft mouse model

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: RNA-seq analysis of RNAs isolated from primary FLT3-ITD+ AML cells in the spleen and bone marrow from xenograft mouse model after 16 hours of treatment with FLT3 inhibitor AC220 (quizartinib)

overall_design: FLT3-ITD+ AML cells were engrafted in NRG-S mice. After engraftment (2-5% of leukemic burden in the blood), mice were treated with vehicle or 2.5mg/kg AC220 (quizartinib) for 16 hours, followed by harvest of spleen and bone marrow. Human AML cells were isolated from each compartment. Using RNAs isolated from human AML cells in each compartment, we performed transcriptome analysis.

first: H

last: Park

first: V

last: Zaberezhnyy

first: A

first: J

last: DeGregori


title: Investigation of bone marrow mediated therapeutic resistance to FLT3 inhibition in acute myeloid leukemia cells


title: The transcriptional regulator Prdm1 is a master gene for the early development of the sensory whisker follicle and is wired to the Lef1 circuitry.

city: Milan

first: Pierluigi Giuseppe

last: Manti

address: Via Festa del Perdono 7

institute: University of Milan


title: The transcriptional regulator Prdm1 is a master gene for the early development of the sensory whisker follicle and is wired to the Lef1 circuitry [4C-seq]

summary: Prdm1 encodes the transcriptional repressor PRDM1/BLIMP1 and Prdm1 mutant mice are one of the rare mutant strains that do not develop whisker hair follicles while still displaying a pelage. We demonstrate that Lef1, a key mediator of the Wnt/Beta Catenin pathway, acts upstream of Prdm1 and identify a primate specific deletion of a Lef1 enhancer, Leaf. This loss may have been significant in the evolutionary process, leading to the progressive defunctionalization and disappearance of vibrissae in primates.

overall_design: 120 whisker pads from e12.5 embryos were microdissected and digested to a single cell suspension and processed with the 4C-Seq protocol per condition. The murine adult kidneys were used as control.

first: Manti

last: Pierluigi

first: Darbellay

last: Fabrice

first: Leleu

last: Marion

first: Barrandon

last: Yann


title: The transcriptional regulator Prdm1 is a master gene for the early development of the sensory whisker follicle and is wired to the Lef1 circuitry [CUT&TAG]

overall_design: 3 whisker pads from e12 whisker pads were microdissected, digested to a single cell suspension and processed with the CUT&Tag protocol.

first: Pierluigi

first: Aisling

last: Coughlan

first: Marion

last: Leleu

first: Giuseppe

last: Testa


title: RNA profiles of polysomes from MOLM-13 cells treated with FLT3 inhibitor and/or mTOR inhibitor in the presence of conditioned media of bone marrow stomal cells

summary: RNA-seq analysis of MOLM13 cells to compare mRNAs enriched in heavy polysomes post FLT3 inhibition and/or mTOR inhibition in the presence or absence of conditioned media of bone marrow stromal cells HS-5 (hBMSC-CM)

overall_design: MOLM-13 cells were treated with FLT3 inhibitor AC220 (quizartinib) and/or mTOR inhibitor everolimus in the presence or absence of hBMSC-CM for 12 hours. Post drug treatments, cells were harvested for polysome profiling. Using input RNAs and mRNAs enriched in heavy polysomes, we performed transcriptome analysis.

last: Kieft


title: Dynamics of leaf transcriptome during cold acclimation in wheat

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

summary:
This dataset is associated with two publications
1.	Elucidating the biochemical basis of trans-16:1 fatty acid change in leaves during cold acclimation in wheat. http://doi.org/10.1002/pei3.10044
In this study, comparative RNA-seq analyses with leaf tissues undergoing cold acclimation reveal concerted transcriptome shifts indicating a reduced chloroplast lipid pathway activity and increased cytosolic ER membrane lipid synthesis. To explore the underlying metabolic and transcriptional mechanisms responsible for the reduction of the t16:1 under cold, a detailed lipid analysis and comparative transcriptome study were conducted with four wheat cultivars during cold treatment. The RNA-seq dataset includes four wheat cultivars (Manitou, Winter Manitou, Norstar and Spring Norstar) treated with cold paired with control. The data as a whole show that leaf tissues experience a gradual decrease in chloroplast lipid pathway activity and the variation in the decline of chloroplast lipid synthesis in different cultivars manifest in the rate of decrease in t16:1decrease in leaf tissues. Future efforts are required to determine if and how the down regulation of the chloroplast lipid pathway is related to the development of winter hardiness.
2.	Computational genomics insights into cold acclimation in wheat. https://doi.org/10.3389/fgene.2022.1015673
In this study, integrated computational approaches was employed to investigate the transcriptomics and lipidomics data associated with cold acclimation and vernalization in the four wheat genotypes of distinct cold tolerance. Differential expression was investigated between cold treated and control samples and between the winter-habit and spring-habit wheat genotypes. Collectively, 12,676 differentially expressed genes (DEGs) were identified. Principal component analysis of these DEGs indicated that the first, second, and third principal components (PC1, PC2, and PC3) explained the variance in cold treatment, vernalization and cold hardiness, respectively. Differential expression feature extraction (DEFE) analysis revealed that the winter-habit wheat genotype Norstar had high number of unique DEGs (1884 up and 672 down) and 63 winter-habit genes, which were clearly distinctive from the 64 spring-habit genes based on PC1, PC2 and PC3. Correlation analysis revealed 64 cold hardy genes and 39 anti-hardy genes. Cold acclimation encompasses a wide spectrum of biological processes and the involved genes work cohesively as revealed through network propagation and collective association strength of local subnetworks. Integration of transcriptome and lipidomics data revealed that the winter-habit genes, such as COR413-TM1, CIPKs and MYB20, together with the phosphatidylglycerol lipids, PG(34:3) and PG(36:6), played a pivotal role in cold acclimation and coordinated cohesively associated subnetworks to confer cold tolerance.

Citations:
http://doi.org/10.1002/pei3.10044
https://doi.org/10.3389/fgene.2022.1015673

overall_design: RNA-seq data were collected from leaf tissues of the four wheat varieties (Manitou, Winter Manitou, Norstar and Winter Norstar) respectively at normal condition and cold treatment condition. There are three biological replicates for each sample, total 24 RNA-seq samples.

first: Qiang

last: Li

first: Yifeng

first: Youlian

last: Pan

first: Jitao

last: Zou


title: RNA profiles of MOLM-13 cells treated with FLT3 inhibitor in the presence of conditioned media of bone marrow stromal cells

first: Andrew

last: Goodspeed

summary: RNA-seq analysis of MOLM-13 cells to compare the gene expression profiles post FLT3 inhibition and/or ATM inhibition in the presence or absence of conditioned media of bone marrow stromal cell HS-5

overall_design: MOLM-13 cells were treated with 3nM FLT3 inhibitor quizartinib and/or 3uM ATM inhibitor AZD1056 for 15 hours in the presence of either RPMI (regular media) or hBMSC-CM (conditioned media of human bone marrow stromal cell line HS-5). Using RNAs isolated from each treatment condition, we performed transcriptome analysis.

first: H


title: Clinical and immunological signatures of severe COVID-19 in previously healthy patients with clonal hematopoiesis

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

institute: KAIST

summary: Many clinical risk factors for severe COVID-19, such as diabetes, hypertension, and high body mass index have been reported. However, searching for additional risk factors should be continued to predict the progression of severe COVID-19 more accurately. We suppose that clonal hematopoiesis of indeterminate potential (CHIP) can also be regarded as one of risk factors. To identify the influence of CHIP in COVID-19 pathogenesis, we performed single-cell RNA-seq using peripheral blood mononuclear cells (PBMCs) obtained from severe COVID-19 patient with CHIP and integrate the data with other published COVID-19 scRNA seq data (GSE149689). After clustering and annotating cell types, we compare the expression profiles between CHIP vs non-CHIP COVID-19 severe patient.

overall_design: Single-cell RNA sequencing performed with PBMC of 3 COVID-19 patients carrying clonal hematopoesis of intermediate potential, CHIP. nCoV_CHIP_1_1[SW202] and nCoV_CHIP_1_2[SW205] are double sampled from one patient.  nCoV_CHIP_1_1[SW202] were sampled in day 17 and nCoV_CHIP_1_2[SW205] were sampled in day 30 after hospitalization.  For the control group, COVID-19 severe patient who doesn't carry CHIP were selected from other published COVID-19 scRNA seq data (GSE149689).

first: Changkyung

last: Kang

first: Seongwan

last: Park

first: Baekgyu

last: Choi

first: Youngil

last: Koh


title: Transcriptional effects of KLF15 deletion in brown adipose tissue in response to fasting and cold

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: We report bulk RNA-sequencing of brown adipose tissue (BAT) harvested from K15flox/flox and BAT specific KLF15 knockout (K15-BKO) mice in response to cold challenge and fasting

overall_design: BAT were isolated from K15F/F or K15-BKO mice (n=3-4) according to standard protocols and transcriptional sequencing was performed.

first: Liyan

last: Fan

first: Mukesh

last: Jain

first: Vinesh

last: Vinayachandran


title: Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish

city: Poznan

first: Barbara

last: Uszczyńska-Ratajczak

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry, Polish Academy of Sciences

summary: Analysis of subcellular location of mitochondrial gene products using two distinct cell fractions: membrane-bound (MB) and high speed (HS) obtained via biochemical fractionation from wild type individuals and mia40a zebrafish mutants, respectively.

overall_design: Identification and characterization of membrane associated (MB) mitochondrial transcripts that are likely to be translated on the surface of mitochondria and those that seem to be synthesized by the free cytosolic polysomes (HS).  Additionally, we noticed that proteostatic stress response triggered by the mia40a mutation in zebrafish causes accumulation of mRNAs encoding mitochondrial proteins in HS.

last: Uszczynska-Ratajczak

first: Sreedevi

last: Sugunan

first: Monika

last: Kwiatkowska

first: Silvia

last: Carbonell-Sala

first: Maciej

last: Migdał

first: Roderic

last: Guigo

first: Cecilia

middle: L

last: Winata

first: Agnieszka

last: Chacinska


title: A novel risk score based on immune-related genes for hepatocellular carcinoma as a reliable prognostic biomarker and correlated with immune infiltration

status: Public on Oct 18 2022

city: Nanning

first: Meiying

last: Long

state: Guangxi

address: Guangxi nanning of China

institute: Guangxi Medical University

summary:
Our study aimed to develop an IRG-based survival prediction model for hepatocellular carcinoma (HCC) patients. To validate the expression levels of the model signature genes, we then performed gene expression profiling analysis using data obtained from RNA-seq of 65 HCC patients.
Finally, we confirmed the 5-IRG signature has good predictive power by RNA-seq data from tumor tissues and paired adjacent normal tissues.

overall_design: Comparative the 5-IRG signature gene expression profiling analysis of RNA-seq data for tumor tissues and paired adjacent normal tissues.

first: Zihan

last: Zhou

first: Xueyan

last: Wei

first: Qiuling

last: Lin

first: Moqin

last: Qiu

first: Yunxiang

first: Peiqin

last: Chen

first: Yanji

last: Jiang

first: Qiuping

last: Wen

first: Yingchun

last: Liu

first: Runwei

last: Li

first: Xianguo

first: Hongping

last: Yu


title: Immunostimulatory effect of senescence in B16F10 melanoma cells

city: Huddinge

first: Federico

last: Pietrocola

address: Halsovagen 7C

country: Sweden

institute: Karolinska Institute

summary: To investigate the effect of senescence induction on immunogical signatures in immunosuppresive B16F10 cells treated with the senescence inducer Doxorubicin

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3 untreated B16F10 cells versus 3 Doxorubicin-treated B16F10 cells.

first: Pietrocola

last: Federico

first: Castoldi

last: Francesca


title: Folliculin-interacting protein FNIP2 impacts on overweight and obesity through a polymorphism in a conserved 3’ untranslated region (SNP array)

city: Madrid

first: Lara

last: Fernández

state: Madrid

address: Carretera Cantoblanco 8

institute: IMDEA Food

summary: SNPs in metabolic genes functionally associated with the mechanistic target of rapamycin (mTOR) pathway were analysed in healthy volunteers.

overall_design: 48 manually-curated SNPs in metabolic genes functionally associated with mTOR pathway were analysed in a cohort of 790 healthy volunteers.

middle: P

first: Nerea

last: Deleyto-Seldas

first: Gonzalo

last: Colmenarejo

first: Alba

last: Sanz

first: Sonia

last: Wagner

first: Ana

middle: B

last: Plata-Gómez

first: Mónica

last: Gómez-Patiño

first: Susana

last: Molina

first: Isabel

last: Espinosa-Salinas

first: Elena

last: Aguilar-Aguilar

first: Sagrario

last: Ortega

first: Osvaldo

last: Graña-Castro

first: Viviana

last: Loria-Kohen

first: Pablo

middle: J

last: Fernández-Marcos

first: Alejo

last: Efeyan

last: RamírezdeMolina


title: Targeting polyamines catabolism to counteract the detrimental effects of cellular senescence

first: Federico

last: Pietrocola

summary: To investigate the effect of pharmacological targeting of polyamines catabolic enzymes in the establishment and reversion of the senescent phenotype

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3 untreated IMR90 cells versus 3 Doxorubicin-treated IMR90 cells (senescent) versus 3 Doxorubicin +MDL72527 treated IMR90 cells

first: Francesca

last: Castoldi


title: Expression data of hypothalamus from the BACHD and HTT overexpression mouse models of Huntington's disease (HD)

city: Lund

first: Rana

last: Soylu-Kucharz

address: Sölvegatan 19

institute: Lund University

summary:
We used microarrays to investigate whether transcriptional dysregulation in hypothalamus is caused by expression of the huntingtin (HTT) protein
We used two different Huntington's disease mouse models: BACHD mice with ubiquitous full-length mutant HTT expression (97 CAG repeats) and wild-type mice with targeted bilateral injections of wild-type or mutant HTT (853 amino acids length, wild-type HTT: 18 CAG repeats, mutant HTT: 79 CAG repeats) in hypothalamus.

overall_design: BACHD mice were analyzed at 2 months of age (early disease progression) and at 10 months of age (late disease progression).  Wild-type mice with targeted overexpression of 18 CAG or 79 CAG HTT in hypothalamus were analyzed at 4 weeks post-injection (12 weeks of age). All mice in the study were females, and age-matched littermate wild-type mice were used as control groups for each mouse model and timepoint.

first: Elna

last: Dickson

first: Amoolya

last: Sai Dwijesha

first: Natalie

last: Andersson

first: Sofia

last: Lundh

first: Maria

last: Björkqvist

first: Åsa

last: Petersén


title: A hierarchical transcription factor cascade regulates enteroendocrine cell diversity and plasticity in Drosophila

city: Beijing

first: xi

last: rongwen

address: No. 7 Science Park Road, zhongguancun Life Science Park, Changping District,

institute: National Institute of Biological Sciences, Beijing

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

overall_design: Refer to individual Series


title: Activity and rational combinations of a novel, engineered chimeric, TRAIL-based ligand in diffuse large B-cell lymphoma

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

institute: Maria Skłodowska-Curie National Research Institute of Oncology

summary: Background: TRAIL (TNF-related apoptosis inducing ligand) exhibits selective proapoptotic activity in multiple tumor types, while sparing normal cells. This selectivity makes TRAIL an attractive therapeutic candidate for cancer patients. However, despite encouraging activity in preclinical models, clinical trials with TRAIL mimetics/death receptor agonists demonstrated insufficient activity, largely due to emerging resistance to these agents. Herein, we investigated the cytotoxic activity of a novel, TRAIL-based chimeric protein AD-051.4 combining TRAIL and VEGFA-derived peptide sequences, in hematological malignancies. We characterize key molecular mechanisms leading to resistance and propose rational pharmacological combinations sensitizing cells to AD-051.4.  Methods: Sensitivity of DLBCL, classical Hodgkin lymphoma, (cHL), Burkitt lymphoma (BL) and acute myeloid leukemia (AML) to AD-051.4 was assessed in vitro with MTS assay and apoptosis tests (Annexin V/PI staining). Markers of apoptosis were assessed using immunoblotting, flow cytometry, or fluorogenic caspase cleavage assays. Resistant cell lines were obtained by incubation with increasing doses of AD-O51. Transcriptomic analyses were performed by RNA sequencing. Sensitizing effects of selected pathway modulators (BCL2, dynamin and HDAC inhibitors) were assessed using MTS/apoptosis assays.  Results: AD-051.4 exhibited low-nanomolar cytotoxic activity in DLBCL cells, but not in other lymphoid or AML cell lines. AD-051.4 induced death-receptor (DR) mediated, caspase-dependent apoptosis in sensitive DLBCL cells, but not in primary resistant cells. The presence of DRs and caspase 8 in cancer cells was crucial for AD-O51.4-driven apoptosis. To understand the potential mechanisms of resistance in an unbiased way, we engineered AD-051.4-resistant cells and evaluated resistance-associated transcriptomic changes. Resistant cells exhibited changes in the expression of multiple genes and pathways associated with apoptosis, endocytosis and HDAC-dependent epigenetic reprogramming, suggesting potential therapeutic strategies of sensitization to AD-051.4. In subsequent analyses, we demonstrated that HDAC inhibitors, BCL2 inhibitors and endocytosis/dynamin inhibitors sensitized primary resistant DLBCL cells to AD-051.4   Conclusions: Taken together, we identified rational pharmacologic strategies sensitizing cells to AD-051.4, including BCL2, histone deacetylase inhibitors and dynamin modulators. Since AD-051.4 exhibits favorable pharmacokinetics and an acceptable safety profile, further clinical development is expected. Identification of resistance mechanisms in a clinical setting might indicate a personalized pharmacological approach to override the resistance.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for parental LY7 and RIVA cell lines  and its AD-051.4-resistant derivatives (LY7res; RIVAres).

first: Karolina

last: Piechna

first: Aleksandra

last: Matrejek

first: Ewa

last: Jabłońska

first: Monika

last: Noyszewska-Kania

first: Maciej

last: Szydłowski

first: Bartłomiej

last: Żerek

last: Kulecka

first: Izabela

last: Rumienczyk

first: Michał

first: Przemysław

last: Juszczyński


title: A hierarchical transcription factor cascade regulates enteroendocrine cell diversity and plasticity in Drosophila [RNA-Seq]

summary: Enteroendocrine cells (EEs) represent a heterogeneous cell population in intestine and exert endocrine functions by secreting a diverse array of neuropeptides. Although many transcription factors (TFs) required for specification of EEs have been identified in both mammals and Drosophila, it is not understood how these TFs work together to generate this considerable subtype diversity. Here we show that EE diversity in adult Drosophila is generated via an “additive hierarchical TF cascade”. Specifically, a combination of a master TF, a secondary-level TF and a tertiary-level TF constitute a “TF code” for generating EE diversity. We also discover a high degree of post-specification plasticity of EEs, as changes in the code—including as few as one distinct TF—allow efficient switching of subtype identities. Our study thus reveals a hierarchically-organized TF code that underlies EE diversity and plasticity in Drosophila, which can guide investigations of EEs in mammals and inform their application in medicine.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of normal and pros-depleted EE cells of adult drosophila midgut, three replicates for each group.

first: Xingting

last: Guo

first: Yongchao

last: Zhang

first: Huanwei

last: Huang

first: Rongwen

last: Xi


title: A hierarchical transcription factor cascade regulates enteroendocrine cell diversity and plasticity in Drosophila [DamID-Seq]

overall_design: We performed a targeted DNA Adenine Methyltransferase Identification (DamID) by specifically expressing optimized Dam (oDam) alone (control group) or oDam-Pros fusion transgene in EEs to profile potential Pros targets, and  oDam-Fer1 fusion transgene in EEs to profile potential Fer1 targets


title: Mucociliary epidermis RNA-seq data from controls and after manipulation of cell fates by Notch (suh-dbm, nicd) and cell type controlers (Foxa1MO, dnMCIDAS)

city: Freiburg

first: Peter

last: Walentek

state: BW

address: Breisacherstr. 113

department: Internal Medicine IV & IMITATE

institute: University Freiburg Medical Center

summary: This study was conducted to investigate the effects of enriching or depleting cell types in mucociliary organoids in Xenopus laevis. (1) Uninjected control embryos were compared to (2) inhibition of Notch signaling (suh-dbm) which enriches ionocytes and multiciliated cells, (3) inhibition of Notch and suppression of MCIDAS (suh-dbm + dnMCIDAS) which enriches ionocytes and depletes multiciliated cells, (4) overactivation of Notch (nicd) which suppresses ionocytes and multiciliated cells and promotes small secretory cells and basal cells, (5) knockdown of foxa1 (foxa1MO) which depletes small secretory cells.    Embryos were injected at 2-4 cell stage and were used to generate animal cap explants at embryonic stage 8. Explants were grown into mucociliary organoids and collected at embryonic stages 10.5, 16, 25, and 32 for total RNA extraction.

overall_design: The experiment was conducted in two biological replicates (embryos were derived from two different females and fertilizations). Control samples remained uninjected, embryos were injected with either suh-dbm (loss of Notch), suh-dbm and dnmcidas (loss of Notch and dominant-negative multicilin), nicd (gain of Notch by intracellular domain), or foxa1 morpholino oligonucleotides targeting the start condon of foxa1 and resulted in protein knockdown (loss-of-function). Sequencing was performed in two seperate paired-end runs to increase sequencing depth, with each run containing all samples.


title: Titanium nanoparticles activate a transcriptional response in Arabidopsis that enhances tolerance to low phosphate, osmotic stress and pathogen infection

status: Public on Oct 17 2022

city: Irapuato

first: Luis

middle: Herrera

last: Estrella

state: Guanajuato

address: Libr. Norte carr. León Km 9.6

department: UGA/Langebio

country: Mexico

institute: Centro de Investigacion y de Estudios avanzados del IPN

summary: Titanium is a ubiquitous element with a wide variety of beneficial effects in plants, including enhanced nutrient uptake and resistance to pathogens and abiotic stresses. While there is numerous evidence supporting the beneficial effects that Ti fertilization give to plants, there is little information on which genetic signaling pathways the Ti application activate in plant tissues.  In this study, we utilize RNA-seq and ionomics technologies to unravel the molecular signals that Arabidopsis plants unleash when treated with Ti. RNA-seq analysis showed that Ti activates abscisic acid and salicylic acid signaling pathways and the expression of NUCLEOTIDE BINDING SITE-LEUCINE RICH REPEAT receptors likely by acting as a chemical priming molecule. This activation results in enhanced resistance to drought, high salinity, and infection with Botrytis cinerea in Arabidopsis. Ti also grants an enhanced nutritional state by upregulating the expression of multiple nutrient and membrane transporters and by modifying or increasing the production root exudates. Our results suggest that Ti might act similarly to the beneficial element Silicon in other plant species.

overall_design: Comparative gene expression profiling analysis using data obtained from RNA-seq of Ti-treated and untreated plants of Arabidopsis thalina Col-0 from, roots and shoots were sampled at two time points.

first: Francisco

middle: G

last: Pérez-Zavala

first: Karina

last: Atriztán-Hernández

first: Paulina

last: Martínez-Irastorza

first: Araceli

last: Oropeza-Aburto

first: Damar

last: López-Arredondo

last: Herrera-Estrella


title: A dual functions of autism-related chromatin remodeler CHD8 in developmental and adult neurogenesis

city: Cincinnati

first: Richard

last: Lu

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

summary: The loss-of-function mutations in the chromatin remodeler CHD8, a high-risk factor in autism spectrum disorder (ASD), lead to severe developmental delay, however, the underlying mechanisms remains elusive. Here, we use transcriptome and genomic occupancy reveal that CHD8 regulates chromatin accessibility and activates neurogenesis-related genes for cortical neurogenesis.

overall_design: 9 samples

first: Chen

last: Dong

first: Qing


title: SYK coordinates neuroprotective microglial responses in neurodegenerative disease

status: Public on Oct 15 2022

city: Charlottesville

first: Daniel

last: Shapiro

state: VA

address: 1340 Jefferson Park Ave

department: Neuroscience

institute: University of Virginia School of Medicine


title: SYK coordinates neuroprotective microglial responses in neurodegenerative disease [scRNA-seq]

summary: Many neurodegenerative diseases are thought to be caused by impaired containment and/or disposal of neurotoxic material such as amyloid beta (Ab) and myelin debris. Indeed, recent human genome-wide association studies (GWAS) and animal model studies have begun to reveal critical roles for the brain’s professional phagocytes, microglia, as well as various innate immune receptors expressed by microglia in the control of neurotoxic material and subsequent neurodegenerative disease pathogenesis. Yet, the critical intracellular molecules that orchestrate the neuroprotective functions of microglia in degenerative disorders remain poorly understood. In our studies, we have identified the innate immune signaling molecule spleen tyrosine kinase (SYK) as a key regulator of microglial phagocytosis in neurodegenerative disease. We find that targeted deletion of SYK in microglia leads to exacerbated Ab deposition, aggravated neuropathology, and cognitive defects in the 5xFAD mouse model of Alzheimer’s disease (AD). Furthermore, disruption of SYK signaling in this AD model was also shown to impede the development of disease-associated microglia (DAMs), alter AKT/GSK3b-signaling in microglia, and to cause severe deficits in the ability of microglia to phagocytose Ab. Importantly, these critical neuroprotective functions of SYK in microglia were not only restricted to Ab-driven models of neurodegeneration, as we found that SYK is also a critical regulator of microglial phagocytosis and DAM phenotype acquisition in demyelinating disease. Collectively, these results help to break new ground in our understanding of the key innate immune signaling molecules that instruct beneficial microglial functions in response to neurotoxic material. Moreover, these findings suggest that targeting SYK may offer a therapeutic strategy to treat a spectrum of neurodegenerative disorders.

overall_design: Comparison of EAE severity and microglial response with or without SYK function. Using SYK +/+ pooled samples as baseline control to compare with SYK fl/fl microglia.

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