title: Epigenetic analysis of hepatocyte-like cells from MSC-Ucs.

city: Shinjyuku-ku

first: Tomoki

last: Takashina

department: Department of Intractable Diseases

institute: National center for Global Health and Medicine

summary: Global DNA methylation profiling of hepatocyte-like cells. We established a protein-based artificial transcription system and successfully engineered human hepatocyte-like cells from human umbilical cord-derived mesenchymal stem cells (MSC-UCs). We utilized four artificial transcription factors (ATFs) that targeted hepatocyte nuclear factor (HNF)1α, HNF3γ, HNF4α and GATA4 (4F), and found that treatment with 4F for 3 (4Fd3) or 5 (4Fd5) days converted MSC-UCs to hepatocyte-like cells. We then examined global DNA methylation profiles of  4Fd3, 4Fd5, NTP-EGFP protein treated cells (NE) and non-treated cells (NC).

overall_design: Bisulphite converted DNA from the 4 samples were hybridised to the Illumina Infinium Methylation EPIC Beadchip.

first: Akihiro

last: Matsunaga

first: Yukiko

last: Shimizu

first: Tetsushi

last: Sakuma

first: Tadashi

last: Okamura

first: Kunie

last: Matsuoka

first: Takashi

last: Yamamoto

first: Yukihito

last: Ishizaka


title: Partial reprogramming restores youthful gene expression through transient suppression of cell identity

status: Public on Jun 10 2022

city: South San Francisco

first: Jacob

middle: Cameron

last: Kimmel

state: CA

address: 1170 Veterans Blvd

department: Computing

country: USA

institute: Calico Life Sciences, LLC

type: Expression profiling by high throughput sequencing

summary: Transient induction of pluripotent reprogramming factors has been reported to reverse some features of aging in mammalian cells and tissues. However, the impact of transient reprogramming on somatic cell identity programs and the necessity of individual pluripotency factors remain unknown. Here, we mapped trajectories of transient reprogramming in young and aged cells from multiple murine cell types using single cell transcriptomics to address these questions. We found that transient reprogramming restored youthful gene expression in adipogenic cells and mesenchymal stem cells but also temporarily suppressed somatic cell identity programs. We further screened Yamanaka Factor subsets and found that many combinations had an impact on aging gene expression and suppressed somatic identity, but that these effects were not tightly entangled. We also found that a transient reprogramming approach inspired by amphibian regeneration restored youthful gene expression in aged myogenic cells. Our results suggest that transient pluripotent reprogramming poses a neoplastic risk, but that restoration of youthful gene expression can be achieved with alternative strategies.

overall_design: Mouse adipogenic cells and mesenchymal stem cells (MSCs) were treated with inducible OSKM reprogramming factors delivered by lentivirus for 3 days followed by a 3 day chase and subsequently profiled by single cell RNA-seq. MSCs were treated with barcoded lentiviral vectors carrying each of the OSKM factors separately. Cells from young (2-4 months old) and aged (20-30 months old) animals were used for all experiments. Myogenic cells from aged animals were treated with transient Msx1 expression on an inducible lentivirus for 3 days followed by a 3-4 day chase period. Pooled screens were performed with barcoded S, O, K, M viruses in MSCs.

middle: C


title: Gene expression in glucose-grown P. putida KT2440 before and after 5 mM catechol addition

status: Public on Jun 09 2022

city: Saarbruecken

first: Michael

last: Kohlstedt

address: Campus A1.5

country: Germany

institute: Saarland University

summary: mRNA was sampled during exponential growth (OD600 = 2, Control), then an inhibitory dose of 5 mM catechol was added to the culture and samples were taken again after 1h (Stress)

overall_design: 3 biological replicates yielded one control and one stress sample each (total of 6 samples)

first: Anna

last: Weimer

first: Christoph

last: Wittmann


title: Transcriptomic Responses of Mycoplasma bovis upon Treatments of trans-Cinnamaldehyde, Carvacrol, and Eugenol

city: storrs

first: saurav

last: Ranjitkar

state: Connecticut (CT)

address: George White Building, Unit 4040, 17 Manter Road

department: Animal Science

institute: University of Connecticut

summary: Through RNA sequencing, we report here that Carvacrol (CAR) affected the expression of 153 genes which included the down-regulation of energy generation-related proteins, pentose phosphate pathway, and up-regulation of ribosomes and translation-related proteins. Few differentially expressed genes were found when M. bovis were treated with Trans-cinnamaldehyde (TC), Eugenol (EU), or Carvacrol (CAR) when the three PDAs were double or triple combined.  Our results suggest that, as opposed to the effect of CAR, the growth inhibitory effects of TC and EU at levels tested may be exerted through mechanisms other than gene expression regulations.

overall_design: Examining the effect of Trans-cinnamaldehyde, Carvacrol, and Eugenol on Mycoplasma bovis

first: Saurav

first: Jingyue

middle: E

last: Duan

first: Kanokwan

last: Srirattana

first: Fahad

last: Alqahtani

first: Edan

middle: R

last: Tulman

first: Ion

last: Mandoiu

first: Kumar

last: Venkitanarayanan

first: Xiuchun

last: Tian


title: Collateral lethality between HDAC1 and HDAC2 exploits cancer-specific NuRD complex vulnerabilities [ATAC-Seq]

city: La Jolla

first: Yuxiang

last: Zhang

address: 10550 N. Torrey Pines Rd.

department: Chemistry

institute: The Scripps Research Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcriptional coregulators have been widely pursued as targets for disrupting oncogenic gene regulatory programs. However, many proteins in this target class are universally essential for cell survival, which may limit the therapeutic window that can be achieved by drug candidates. By examining large collections of CRISPR/Cas9-based essentiality screens, we discovered a genetic interaction between histone deacetylase 1 (HDAC1) and HDAC2 wherein each paralog is synthetically lethal with hemizygous deletion of the other. This collateral synthetic lethality is caused by recurrent chromosomal translocations that occur in diverse solid and hematological malignancies, including neuroblastoma and multiple myeloma. Using genetic deletion or dTAG-mediated degradation, we show that HDAC2 disruption suppresses the growth of HDAC1-deficient neuroblastoma in vitro and in vivo. Mechanistically, we find that targeted degradation of HDAC2 in these cells prompts the degradation of several members of the nucleosome remodeling and deacetylase (NuRD) complex, leading to diminished chromatin accessibility at HDAC2/NuRD-bound sites of the genome and impaired control of enhancer-associated transcription. Furthermore, we reveal that several of the degraded NuRD complex subunits are dependencies in neuroblastoma and multiple myeloma, providing motivation to develop paralog-selective HDAC1 or HDAC2 degraders. Altogether, we identify HDAC1/2 collateral synthetic lethality as a new therapeutic target and reveal a novel mechanism for exploiting NuRD-associated cancer dependencies.

overall_design: Comparative chromatin accessibility profiling analysis by ATAC-seq for BE2C cells with HDAC2 degradation.

middle: A

last: Erb

first: Barbara

last: Karakyriakou


title: Collateral lethality between HDAC1 and HDAC2 exploits cancer-specific NuRD complex vulnerabilities [Cut & Run]

summary: Transcriptional coregulators have been widely pursued as targets for disrupting oncogenic gene regulatory programs. However, many proteins in this target class are universally essential for cell survival, which may limit the therapeutic window that can be achieved by drug candidates. By examining large collections of CRISPR/Cas9-based essentiality screens, we discovered a genetic interaction between histone deacetylase 1 (HDAC1) and HDAC2 wherein each paralog is synthetically lethal with hemizygous deletion of the other. This collateral synthetic lethality is caused by recurrent chromosomal translocations that occur in diverse solid and hematological malignancies, including neuroblastoma and lymphoid malignancies. Using genetic deletion or dTAG-mediated degradation, we show that HDAC2 disruption suppresses the growth of HDAC1-deficient neuroblastoma in vitro and in vivo. Mechanistically, we find that targeted degradation of HDAC2 in these cells prompts the turnover of several members of the nucleosome remodeling and deacetylase (NuRD) complex, leading to diminished chromatin accessibility at HDAC2/NuRD-bound sites of the genome and impaired control of enhancer-associated transcription. Several of the degraded NuRD complex subunits are themselves lineage-specific cancer dependencies, providing motivation to develop paralog-selective HDAC degraders. Altogether, we identify HDAC1/2 collateral synthetic lethality as a new therapeutic target and reveal a novel mechanism for exploiting NuRD-associated cancer dependencies.

overall_design: Profiling genomic localization of HDAC2, HDAC2-dTAG, MBD3, CHD4 in BE(2)-C wild-type cells at steady state and compare change of H3K9ac and H3K27ac with HDAC2 degradation in BE(2)-C-HDAC2-dTAG cells by CUT&RUN.


title: Network-based integrative analysis of lithium response in bipolar disorder using transcriptomic and GWAS data

first: John

last: Kelsoe

address: 9500 Gilman Dr

department: Psychiatry

institute: University of California, San Diego

summary:
Lithium is the gold standard treatment for bipolar disorder. The goal of this study was to identify gene expression networks associated with lithium response.
RNAseq data was obtained from IPSC derived neurons from lithium responders and non-responders. Focal adhesion was the network most associated with response.

overall_design: Hippocampal neurons were derived from IPSCs from 6 lithium responders, 6 non-responders, and 6 controls. All groups were treated with and without lithium in vitro and RNAseq data obtained.

first: Vipavee

last: Niemsiri

first: Fred

last: Gage


title: Severe congenital neutropenia with syndromic features in a patient with homozygous hypomorphic DBF4 mutation

city: Cambridge

first: Adrian

last: Liston

address: Babraham Research Campus

country: United Kingdom

institute: The Babraham Institute

summary: Accurate and efficient DNA synthesis is an essential function of replicating cells. Mutations in replisome components lead to a number of syndromic diseases including immunodeficiencies. Dumbbell former 4 (DBF4) is the regulatory subunit of the DBF4-dependent kinase (DDK) which is essential for the activation of replication origins. We here studied a patient with severe congenital neutropenia (SCN) and syndromic features without a genetic diagnosis.  We identified a private homozygous mutation in DBF4 (CADD 25.8 with a DBF4-specific MSC of 3.13) in a patient with SCN. The DBF4 mutant is normally expressed in stimulated PBMCs and dermal fibroblasts, but has a decreased CDC7-binding capacity in overexpression assays. DDK-specific phosphorylation of MCM2 was decreased in stimulated PBMCs with accumulation of CDK inhibitor p21, a G0 cell cycle arrest and impaired proliferation. Serum-starved fibroblasts showed a similar cell cycle phenotype but no p21 accumulation and normal MCM2 phosphorylation. In vitro differentiation of primary CD34+ cells recapitulated the SCN phenotype observed in vivo and was associated with a 4-fold increase in p21 gene expression. Single cell RNA sequencing of whole bone marrow revealed upregulation of p53 targets and activation of the PERK pathway of the unfolded protein response.   Autosomal recessive functional DBF4 deficiency causes SCN with syndromic features.

overall_design: Two RBC depleted whole bone marrow aspirates; one patient with severe congenital neutropenia with homozygous DBF4 mutation, one healthy gender-matched control

last: Barber

first: Erika

last: Van Nieuwenhove

first: Mathijs

last: Willemsen

first: Vasiliki

middle: I

last: Meyts

first: Stephanie

last: Humblet-Baron


city: London

first: Victoria

last: Male

state: Not Applicable (Outside of US and Canada)

address: Metabolism, Digestion and Reproduction, Imperial College London, Chelsea and Westminster Hospital Campus, 369 Fulham Road

institute: Imperial College London

summary: Mice that lack the transcriptional regulator Trerf1 lack ILC1 in the liver and immature ILC1 in the bone marrow. To determine which pathways are downstream of Trerf1, we sorted lineage-negative CD127+ bone marrow cells (which contain ILC progenitors) from 4 littermate pairs (wild type versus Trerf1 knockout) and examined them by RNAseq.

overall_design: RNA-seq analysis of Trerf1 knockout compared to wild type lineage-negative CD127+ bone marrow cells


title: Collateral lethality between HDAC1 and HDAC2 exploits cancer-specific NuRD complex vulnerabilities [RNA-Seq]

overall_design: Comparative gene expression profiling analysis of SLAM-seq and 3' end mRNA-seq data for BE2C cells with HDAC1/2 inhibition and HDAC2 degradation.

first: Michael


title: Epigenome-wide profiling uncovers novel pathway networks in human pulmonary arterial hypertension [pul35]

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

summary: Pulmonary arterial hypertension (PAH) is a progressive pulmonary vascular disease that culminates in right heart failure. Vascular pathology in PH is characterized by pulmonary vasoconstriction and progressive vascular remodeling processes that affects all layers of the vascular wall (intima, media and adventitia). Our objective was to profile and analyze the differential gene expression signatures between the cells isolated from normal and idiopathic PAH patients. We generated vascular cell-specific transcriptome profiles from the adventitial fibroblasts (PAAF) isolated ex vivo from the dissected human pulmonary arteries of normal donor and PAH lungs using paired-end RNA-sequencing.

overall_design: Transcriptome profiling of pulmonary artery adventitial fibroblasts (PAAF) isolated from 4 PAH afflicted patients treated with compound SGC-CBP30.

first: Prakash

last: Chelladurai

first: Alice

last: Bourgeois

first: Stefan

last: Günther

first: Chanil

last: Valasarajan

first: Anoop

middle: V

last: Cherian

first: Robbert

middle: J

last: Rottier

first: Charlotte

last: Romanet

first: Andreas

last: Weigert

first: Olivier

last: Boucherat

first: Christina

last: Eichstaedt

first: Clemens

last: Ruppert

last: Guenther

first: Thomas

last: Braun

first: Rajkumar

last: Savai

first: Mario

last: Looso

first: Werner

last: Seeger

first: Uta

middle: M

last: Bauer

first: Sébastien

last: Bonnet

first: Soni

middle: S

last: Pullamsetti


title: Lung function, airway and peripheral basophils and eosinophils are associated with molecular pharmacogenomic endotypes of steroid response in severe asthma.

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: Sputum airway cells transcriptome from 19 asthmatics from the Severe Asthma Research Program at baseline and 6-8 weeks follow-up after a 40mg dose of intramuscular corticosteroid triamcinolone acetonide.

overall_design: RNA-seq

middle: T

first: Michael

last: McGeachie

first: Jiang

last: Li

first: Deborah

last: Meyers

first: Eugene

last: Bleecker

first: Scott

last: Weiss

first: Kelan

middle: G

last: Tantisira


title: Epigenome-wide profiling uncovers novel pathway networks in human pulmonary arterial hypertension [pul28]

first: Carsten

last: Kuenne

overall_design: Transcriptome profiling of pulmonary artery adventitial fibroblasts (PAAF) isolated from 4 healthy donors and 4 PAH afflicted patients.

first: Prakash

last: Chelladurai

first: Alice

last: Bourgeois

first: Stefan

last: Günther

first: Chanil

last: Valasarajan

first: Anoop

last: Cherian

first: Robbert

last: Rottier

first: Charlotte

last: Romanet

first: Andreas

last: Weigert

first: Olivier

last: Boucherat

last: Eichstaedt


title: Structural basis for RNA capture and surveillance by the human Nuclear Exosome Targeting (NEXT) complex

city: New York

first: Christopher

middle: D

last: Lima

state: NY

address: 1275 York Ave RRL301A

department: Structural Biology

institute: Sloan Kettering Institute

summary: Abstract: RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation by ribonucleases such as the 3′ to 5′ ribonucleolytic RNA exosome. Here, we determined cryo-electron microscopy structures of human Nuclear Exosome Targeting (NEXT) complexes bound to RNA, that reveal mechanistic insights to substrate recognition and early steps that precede RNA handover to the exosome. The structures illuminate ZCCHC8 as a scaffold, mediating homodimerization while embracing the MTR4 helicase and flexibly anchoring RBM7 to the helicase core. All three subunits collaborate to bind the RNA, with RBM7 and ZCCHC8 engaging sequences upstream of the 3′ end that is bound by MTR4. ZCCHC8 obscures MTR4 surfaces that are important for RNA binding and extrusion as well as surfaces important for MPP6-dependent recruitment and docking onto the RNA exosome core, features of which might contribute to coordinating RNA translocation and extrusion from the helicase to exosome recruitment and decay.

overall_design: Total RNA seq comparing the transcriptomes of ZCCHC8 CRISPR knockout HAP1 cells stably transfected with GFP-tagged wild-type ZCCHC8 (WT) and ZCCHC8 with HD deleted (DM). Total RNA seq analysis of non-transfected ZCCHC8 CRISPR knockout HAP1 cells was also performed. Three biological replicates of each sample are included.

first: M

last: Puno

first: C


title: Epigenome-wide profiling uncovers novel pathway networks in human pulmonary arterial hypertension [pul31]

overall_design: Transcriptome profiling of lung tissue from healthy control or monocrotaline-induced PAH animals treated with vehicle or compound SGC-CBP30.

first: Christina

first: Clemens

last: Ruppert

last: Guenther

first: Thomas

last: Braun

first: Rajkumar

last: Savai

first: Mario

last: Looso

first: Werner

last: Seeger

first: Uta

last: Bauer

first: Sébastien

last: Bonnet

first: Soni

last: Pullamsetti


title: Compartment-specific and HuR-coordinated regulation of intronic polyadenylation isoforms by doxorubicin [total RNA-seq]

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

country: France

institute: Institut Curie

summary: We explored the regulation of intronic polyadenylation (IPA) isoforms by doxorubicin and HuR in breast cancer cells.

overall_design: We performed Total-RNA-seq analyses on breast cancer cells treated with doxorubcin and/or depleted of the RNA-binding protein HuR.

first: Martin

last: DUTERTRE

first: Alina

last: CHAKRABORTY

first: Mandy

last: CADIX

last: RELIER

first: Nicolò

last: TARICCO

first: Tina

last: ALAEITABAR

last: LABBE

first: Sylvain

last: MARTINEAU

first: Pierre

last: GESTRAUD

first: Nicolas

last: SERVANT

first: Stéphan

last: VAGNER


title: Compartment-specific and HuR-coordinated regulation of intronic polyadenylation isoforms by doxorubicin [3-seq]

summary: We explored the regulation of intronic polyadenylation (IPA) isoforms by doxorubicin and HuR in several subcellular compartments.

overall_design: We performed 3'-seq analyses on several subcellular compartments of breast cancer cells treated with doxorubcin and/or depleted of the RNA-binding protein HuR.


title: Compartment-specific and HuR-coordinated regulation of intronic polyadenylation isoforms by doxorubicin

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

overall_design: Refer to individual Series


title: Counteracting chromatin effects of a splicing-correcting antisense oligonucleotide improves its therapeutic efficacy in spinal muscular atrophy

city: Lisboa

first: Rui

last: Sousa-Luís

address: Av. Professor Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular João Lobo Antunes

summary: Spinal Muscular Atrophy (SMA) is a motor-neuron disease caused by mutations of the SMN1 gene. The human paralog SMN2, whose exon 7 (E7) is predominantly skipped cannot compensate for the lack of SMN1. Nusinersen is an antisense oligonucleotide that upregulates E7 inclusion and SMN protein levels by displacing the splicing repressors hnRNPA1/A2 from their target site in intron 7. We show that, by promoting transcriptional elongation, the histone deacetylase inhibitor VPA cooperates with nusinersen to promote E7 inclusion. Surprisingly, nusinersen promotes the deployment of the silencing histone mark H3K9me2 on the SMN2 gene, creating a roadblock to PolII elongation that inhibits E7 inclusion. By removing the roadblock, VPA counteracts the undesired chromatin effects of nusinersen, resulting in higher E7 inclusion, without large pleiotropic effects, as assessed by genome-wide analyses. Combined administration of nusinersen and VPA in SMA mice strongly synergized in SMN expression, growth, survival, and neuromuscular function.

overall_design: H3K9me2 ChIP-seq of HEK293T cells either untreated or treated with ASO1, VPA or a combination of both. Drosophila S2 was used as spike-in probes. RNA-seq of VPA and/or ASO1-treated cells. POINT-seq of VPA or ASO1-treated cells.

first: Luciano

last: Marasco

first: Gwendal

last: Dujardin

first: Ying

middle: H

last: Liu

first: José

last: Stigliano

first: Tomoki

last: Nomakuchi

first: Nick

last: Proudfoot

first: Adrian

last: Krainer

first: Alberto

last: Kornblihtt


title: Epigenome-wide profiling uncovers novel pathway networks in human pulmonary arterial hypertension

first: Carsten

last: Kuenne


title: Compartment-specific and HuR-coordinated regulation of intronic polyadenylation isoforms by doxorubicin [CLIP-seq]

first: Céline

last: Labbé

summary: We investigated the regulation by doxorubicin of HuR binding to RNA near intronic polyadenylation (IPA) sites in several subcellular compartments of breast cancer cells.

overall_design: We performed CLIP-seq (iCLIP) analyses for the RNA-binding protein, HuR on whole-cell, nuclear and cytosolic fractions of breast cancer cells treated or not with doxorubcin.

first: Martin

last: DUTERTRE

first: Alina

last: CHAKRABORTY

first: Mandy

last: CADIX

first: Sébastien

last: RELIER

last: TARICCO


title: Effect of Astragalus Polysaccharide Combined with Metformin on Liver mRNA expression profile in aging type 2 diabetic mice and functional analysis

status: Public on Jun 12 2022

city: Lanzhou

first: jiajia

last: liu

state: Gansu

address: Gansu university of traditional Chinese medicine

country: China

summary:
Objective:  To study the effect of astragalus polysaccharide combined with metformin on mRNA expression profile of type 2 diabetic mice, and to explore the molecular mechanism of astragalus polysaccharide combined with metformin in the treatment of type 2 aging diabetes.
Methods:  Natural aging mice were induced by high-sugar and high-fat diet combined with streptozotocin to prepare aging diabetes model. The experimental mice were divided into aging control group, aging diabetes model group, metformin treatment group, astragalus polysaccharide and metformin. The treatment group was treated with gavage for 60 consecutive days. Immunohistochemical detection of insulin levels in pancreatic tissue of each group of mice, serum insulin levels were measured by mouse insulin kit to observe the treatment of aging diabetes and astragalus polysaccharide combined with metformin; using Agilent mouse whole gene expression profile chip The mRNA expression changes of liver tissues in each group were analyzed, and the differential genes were screened by bioinformatics tools and the differential genes and signal pathways were enriched and analyzed.
Results: Compared with the aging group, the insulin and insulin antibody levels in the model group were significantly decreased (P<0.05). Compared with the model group, the insulin and insulin antibody levels in the two treatment groups increased (P<0.05), and jaundice The level of polysaccharide in combination with metformin was significantly higher than that in metformin group (P<0.05). The differential gene analysis of the chip showed that there were 5617 differential genes in the aging diabetes model group, 3131 were up-regulated, and 2486 were down-regulated; the Astragalus polysaccharide combined with metformin treatment group had 4767 differential genes, compared with the aging diabetes model group. 2143 up-regulated, 2624 down-regulated, genes with significant differences were mainly involved in protease activity and drug metabolism, and significantly enriched into 33 signaling pathways (P<0.01).
Conclusion: The gene regulatory network plays an important role in the intervention of Astragalus polysaccharides and metformin in the treatment of aging type 2 diabetes.

overall_design: Analysis of 4 samples, no repetition

first: Jiajia

first: Dandan

last: Li

first: Yi

last: Zhao

first: Yuhong

last: Wu

first: Jing

last: Wang


title: Epigenome-wide profiling uncovers novel pathway networks in human pulmonary arterial hypertension [RNA-seq]

summary: Pulmonary arterial hypertension (PAH) is a progressive pulmonary vascular disease that culminates in right heart failure. Vascular pathology in PH is characterized by pulmonary vasoconstriction and progressive vascular remodeling processes that affects all layers of the vascular wall (intima, media and adventitia). Our objective was to profile and analyze the differential gene expression signatures between the cells isolated from normal and idiopathic PAH patients. We generated vascular cell-specific transcriptome profiles from the adventitial fibroblasts (PAAF) isolated ex vivo from the dissected human pulmonary arteries of normal donor and PAH lungs  using paired-end RNA-sequencing.

overall_design: Transcriptome profiling of pulmonary artery adventital  fibroblasts (PAAF) isolated from 4 healthy donors and 4 PAH afflicted patients.

first: Prakash

last: Chelladurai

last: Künne

first: Christine

last: Weber

first: René

last: Nötzold

first: Mario

last: Schmoranzer

first: Stefan

last: Günther

last: Looso

first: Uta-Maria

last: Bauer

first: Werner

last: Seeger

first: Soni

last: Pullamsetti


title: PML-RARa induces dynamic changes in genome architecture during leukemic transformation

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: Acute Promyelocytic Leukemia (APL) is a fatal subtype of leukemia driven by the translocation between genes encoding the Promyelocytic Leukemia (PML) protein and the Retinoic Acid Receptor alpha (RARa) protein. We use mouse hematopoietic progenitor cells expressing PML-RARa and dissect the dynamic changes in the epigenome, transcriptome and genome architecture triggered by the expression of this oncogenic transcription factor during leukemic transformation. We find that PML-RARa induces a continuum of topologic and transcriptional alterations, mostly affecting distal regulatory elements. Furthermore, we identify Klf4 ― a master regulator of hematopoietic differentiation ― as an early mis-regulated gene during leukemogenesis, and deconstruct the dynamic alterations in long-range interactions, histone modifications and transcriptional output triggered by PML-RARa expression at the Klf4 locus. Our study provides a comprehensive overview of the dynamic genomic and transcriptomic alterations induced by PML-RARa, which ultimately block hematopoietic differentiation and induce leukemic transformation.

overall_design: ChIP-seq (29 samples), RNA-seq (12 samples), and Hi-C (10 samples) of Bone marrow lineage negative hematopoietic stem/progenitor cells. Stage 0 cells are GFP+ cells transformed with empty vector, Stage I cells are transformed with PML-RARa-3xFlag vector (both after sorting by FACS). Stage II cells are Stage I cells plated in methylcellulose supplemented with cytokines and stem cell factor, and serially re-plated for 2 weeks. Stage III are Stage I cells plated in methylcellulose supplemented with cytokines and stem cell factor, and serially re-plated for 4 weeks. Stage IV cells are bone marrow blasts from mice in which Stage I cells were transplanted via tail vein injection into lethally irradiated (9 Gy) syngeneic animals (129SvEv). (ChIP-seq) There is an specific Input for each experiment of H3K27ac, except in Stage IV, in which the Input for the rest of histone marks is applicable for H3K27ac too.

first: Gloria

last: Mas

first: Luciano

last: Di Croce

first: Cecilia

last: Ballare


title: NRF2 activator-treated human cardiac spheres have enhanced maturation and enable disease modeling

status: Public on Jun 08 2022

city: ATLANTA

first: Dong

last: Li

state: GEORGIA

address: 2015 UPPERGATE DR

department: Pediatrics

institute: Emory University

summary:
To investigate the functions of NRF2 activation on maturation of hiPSC derived cardiomyocytes, we treated 3D hiPSC derived cardiomyocytes with NRF2 activator CDDO-Me at 0.5 µM for 10 days.
Transcriptomic analyse was performed to identify molecular actions of NRF2 activation.

overall_design: RNA-sequencing analysis was performed to compare global gene expression profiles of hiPSC derived cardiomyocytes treated with NRF2 activator CDDO-Me at 0.5 µM (CDDO-Me)  vs. DMSO treatment (DMSO) vs. left ventricle tissue samples (LV).

first: Lawrence

last: Armand

first: Hyun

last: Hwang

first: Chunhui

last: Xu


title: Epigenome-wide profiling uncovers novel pathway networks in human pulmonary arterial hypertension [ChIP-seq]

first: Carsten

last: Kuenne

last: Chelladurai


title: BOD1 regulates the cerebellar IV/V lobe-fastigial nucleus circuit associated with motor coordination

city: Nanjing

first: chen

last: xiang

address: chunhua street

institute: nanjing medical university

summary: BOD1 plays an important role in  modulating of the cerebellar IV/V lobePCs→FNCaMKIIα+ circuit and provide therapeutic targets for the treatment of ataxia behaviors.

overall_design: Examination of BOD1f/f mice and L7-Cre;BOD1f/f mice cereberal IV/V lobe region different genes expression

first: Xiuxiu

last: Liu

first: Feng

last: Han

first: Yingmei

last: Lu


title: Collateral lethality between HDAC1 and HDAC2 exploits cancer-specific NuRD complex vulnerabilities

first: Yuxiang

last: Zhang


title: Transcriptional profiling of transport mechanisms and regulatory pathways in rat choroid plexus

city: Copenhagen

first: Søren

middle: Norge

last: Andreassen

state: Region Hovedstaden

address: Blegdamsvej 3

department: Department of Neuroscience

country: Denmark

institute: University of Copenhagen

summary: Transcriptomic profile of rat choroid plexus (whole tissue) of both male and female sex, epithelial cells captured by fluorescence-activated cell sorting (FACS), and compared to proximal tubules of the kidneys. The transcriptomic profile of choroid plexus displays high similarity between sex and choroid plexus epithelial cells, and lesser similarity to another secretory epithelium, the proximal tubules. The analysis provides an insight into transport mechanisms that could participate in CSF secretion and suggest regulatory candidates.

overall_design: mRNA profile analysis of whole tissue choroid plexus for both male and female, choroid plexus epithelial cells, and kidney proximal tubules in rats.

middle: N

first: Nanna

last: MacAulay


title: Single-cell antigen-specific landscape of CAR T infusion product identifies  determinants of CD19-positive relapse in patients with ALL

city: New Haven

first: Rong

last: Fan

state: Connecticut

address: 55 Prospect St.

department: Biomedical Engineering

institute: Yale University

summary: We report 101,326 single cell transcriptomes and surface protein landscape from the Chimeric antigen receptor-modified (CAR) T infusion  products of 12 pediatric ALL patients upon CAR antigen-specific stimulation in comparison with  TCR-mediated activation and controls.

overall_design: By combining scRNA-seq and CITE-seq, CAR T cells in infusion products were analyzed upon CARspecific  stimulation with human CD19-expressing antigen presenting cells (APCs), and compared  them to 3 additional conditions: TCR-mediated stimulation, non-target APC stimulation, and  unstimulated controls

first: Zhiliang

last: Bai

first: Steven

last: Woodhouse

first: Pablo

last: Camara

last: Melenhorst


title: Morphine  incubation craving-NAc_small RNA sequencing

city: Shijiazhuang

first: Bing

last: Xie

state: Hebei

address: Tiyubei street

institute: Hebei Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: The current study aimed at addressing two questions: 1) How the expression of key miRNAs is altered in the NAc during the cue-induced incubation of morphine craving? 2) Which is/are the target gene(s) and what is/are the regulatory mechanism(s) of gene(s) in response to the candidate miRNAs? To answer these two questions, the cue-induced incubation of the morphine craving model was first established by using the conditioned place preference (CPP) paradigm. Then, the aberrant expression of miRNAs was identified in the NAc tissue by RNA-sequencing.

overall_design: The NAc tissues from C57BL/6N mice from the two groups that were subjected to morphine induced CPP model test 1 (T1) and test 2 (T2) were harvested; three samples (6 mice) from each group were used for total RNA isolation. RNA-seq was performed by Novogene Co., LTD (Beijing, China). In short, following RNA quantification and qualification, RNA integrity was examined with the RNA Nano 6000 assay kit and Agilent Bioanalyzer 2100 library preparation for small RNA sequencing system (Agilent Technologies, CA, USA). Any library preparations in this study were sequenced on an Illumina HiSeq 2500 platform (Illumina, San Diego, CA, USA). We explored the occurrence of miRNA families identified from the samples in other species and used miFam.dat (http://www.mirbase.org/ftp.shtml) for known miRNAs to determine families. New miRNA precursors were submitted via the Rfam website (http://rfam.sanger.ac.uk/search/) for Rfam family identification.

first: Di

last: Wen

first: Chunling

last: Ma


title: Inactivation of YAP1 in human bladder cancer cell (UC3)

city: Yuseong-gu

first: Seung Woo

last: Baek

state: Daejeon

address: Gwahak-ro 125

country: South Korea

institute: Korea Research Institute Biology & Biotechnology

summary: transcriptomic data for UC3-siYAP1 were generated to observe changes in downstream genes in bladder cancer cells

overall_design: Total RNA was recorded 24 h after each transfection of control siRNA (siCON) or siYAP1 into the human bladder cancer cell line (UC3).

first: Seung-Woo

first: Sun-Hee

last: Leem


title: mRNA-sequencing data of Jurkat T cells with or without calcineurin inhibitors

city: Seoul

first: Sangho

last: Lee

address: College of Medicine, Biomedical Science Building 202, 103 Daehakro, Jongro-gu

department: MMBS

institute: Seoul National University

summary: In order to determine the calcineurin inhibitory effect of CABIN1 peptide, we performed RNA-sequencing in Jurkat T cells expressing negative contorl (HA-mCherry) or HA-mCherry-CABIN1 peptide. Jurkat T cells were activated by treatment 40 nM PMA and 1 μM Ionomycin for 8 hr. 0.5 μM FK506 (Tacrolimus, Tac) was pretreated for 1 hr before treatment with PMA and Ionomycin. Total RNA was extracted from these cells. Extracted RNA was used to prepare an mRNA sequencing library using TruSeq Stranded mRNA sample preparation kit. All samples were sequenced on Illumina NextSeq 500 with a 75 bp paired end read.

overall_design: mRNA profiles of negative control and CABIN1 peptide expressing Jurkat T cells under the treatment with PMA and Ionomycin

first: Hong-Duk

last: Youn


title: Plasmodium falciparum HRP2-induced damage to brain cortical organoids damage is Toll-Like Receptor dependent and is attenuated via Neuregulin-1/ErbB4 signaling

city: Atlanta

first: Adriana

last: Harbuzariu

state: Georgia

address: 615 Michael Street, Room 425, Department of Cell Biology

institute: Atlanta

summary:
Human cerebral malaria (HCM) is a severe complication of Plasmodium falciparum (P.f.) infection that is characterized by capillary occlusions, rupture of the blood-brain barrier (BBB) and perivascular cellular injury. P.f. histidine-rich protein 2 (HRP2), a byproduct of parasitized red blood cell (pRBC) lysis, crosses the BBB when compromised to cause brain injury. We hypothesized that HRP2-induced neuronal damage can be attenuated by Neuregulin 1 (NRG1), an anti-inflammatory neuroprotective factor. Using brain cortical organoids, we determined that HRP2 upregulated cell death and inflammatory markers and disorganized brain organoid tissue. We identified Toll Like Receptors (TLR1 and 2) as potential mediators of HRP2-induced cellular damage and inflammation.  Exogenous treatment of organoids with NRG1 attenuated HRP2 effects. The results indicate that HRP2 mediates malaria-associated HRP2-induced brain injury and inflammation and that NRG1 may be an effective therapy against HRP2 effects in the brain.
In the study presented here, we assessed the inflammatory genes induced by HRP2 using the Immunology Panel on the nCounter system (NanoString) and results were analyzed using nSolver softaware.

overall_design: We treated 50 days old cortical organoids (n=3) for 26 hours with 4.2 μg/ml HRP2 with or without 100 ng/ml NRG1, while untreated (n=3) organoids were used as control.

first: Annette

last: Nti

first: Keri Oxxendine

middle: O

last: Harp

first: Juan Carlos

middle: C

last: Cespedes

first: Adel

last: Dris

first: Jonathan

middle: K

last: Stiles


title: Spatial and temporal development of Müller glial cells in hiPSC-derived retinal organoids facilitating the cell enrichment and transcriptome analysis

city: Guangzhou

first: Xiufeng

last: Zhong

address: 54 xianlie Rd

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: Müller glial cells (MGs) play important roles in human retina during physiological and pathological conditions. However, there are still many obstacles to obtain large numbers of human MGs in vitro so far, which hinder the further study of MGs. Human induced pluripotent stem cells (hiPSCs) have capacity to differentiate into almost all body cells, even develop complex, organized tissues, including retinal organoids (ROs) with all cell subtypes, providing many opportunities in study of retinal development and disorders. This study explored the development of MGs within hiPSC-derived ROs and the approach to isolate and expand these MGs. In ROs, MG precursors expressing SOX9 and Ki67 appeared since differentiation day 60 (D60), while SOX9+ CRALBP+ GS+ and Ki67- mature MGs developed from D150. MGs isolated from ROs aged older than 120 days could be expanded and exhibited a spindle-like morphology under adherent culture conditions. These expanded cells expressed MG specific markers SOX9, vimentin, nestin, CRALBP and GS, and responded to L-glutamate stimuli revealed by whole-cell patch-clamp recordings. They could be passaged several times, yielding large numbers of cells in a short period. In addition, they did not transdifferentiate into other types of retinal cells after subretinal transplantation in NOD/SCID mice. This study firstly clarified the timecourse of human MG development in ROs, and established a simple approach to expand and enrich these cells from ROs, paving the way for downstream investigation and application of human MGs.

overall_design: hiPSCs (N>1×10^5 cells per experiment, 2 independent experiments), different stage ROs (N=3~5 ROs per experiment, 2 independent experiments), different passage MGs from D150-ROs (n>1X10^6 cells per experiment, 3 independent experiments) were collected and sent to Novogene Biotechnology Co. (Beijing, China) and Gene Denovo Biotechnology Co. (Guangzhou, China) for RNA extraction, library construction, sequencing and data analyses. Total RNA was extracted using Trizol reagent kit (Invitrogen) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Oligo (dT) beads were used to isolate the poly mRNA from the total RNA. The enriched mRNA was fragmented and reverse transcribed into cDNA using random primers. After synthesis of the second strand, the cDNA was purified, end-repaired and ligated to Illumina sequencing adapters. The ligation products were size selected, amplified, and sequenced. Raw reads were filtered and the clean reads were obtained. Afterwards, an index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. The mapped reads of each sample were assembled by using StringTie. Gene expression levels were quantified, and for each transcription region, a fragment per kilobase of transcript per million mapped reads (FPKM) value was calculated to quantify its expression abundance and variations. Differential expression analysis was performed by DESeq2 software between two different groups. The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 was considered differentially expressed genes/transcripts. Co-analyses of these data were performed by Gene Denovo Biotechnology Co. (Guangzhou, China) using a quarter median correction approach to reduce the error from different batches of data.

first: Rong

last: Ning

first: Dandan

last: Zheng

first: Bingbing

first: Guanjie

last: Gao

first: Ping

last: Xu

first: Yuan

last: Wang

first: Fuhua

last: Peng

first: Bin

last: Jiang

first: Jian

last: Ge

first: Jinhai


title: RNA-seq analyses of effects of Alpinetin and Zingiberone on hair follicle regeneration

city: Hangzhou

first: Ying

last: Xiao

address: Qingchun East Road

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University

summary: The aim of this study was to determine the effects of Alpinetin (AP) on transcriptome profiles of hair follicle regeneration. Depilation was performed on mice back skin. After 24 hours, the depilated area was treated with 3 mg/ml Alpinetin that were dissolved in 65% ethanol once a day. At day 4 post depilation, skin samples without interfollicular epidermis were obtained for RNAseq. We identified 1567 different expression genes between AP and VC group by using an optimized data analysis workflow.

overall_design: We separate the back skin of depilated and AP treated mice, which removed epidermics, and identified the genome-wide expression level of each group.

last: Wei

first: Xiaojiao

last: Fan

first: Jing

last: Chen

first: Yajun

last: Zhang

first: Siyi

first: Wenqian

first: Chaochen

first: Xia

last: Wu


title: VEGFA-derived hsa_circ_0076611 promotes proliferation by regulating translation initiation rate in triple-negative breast cancer

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

summary: Hsa_circ_0076611 is a circular RNA derived from back splicing of VEGFA exon 7 and expressed in triple-negative breast cancer (TNBC) cells and tissues. Through RNAseq analysis of hsa_circ_0076611-interacting RNAs, recovered by ChIRP assays, we here identified target mRNAs potentially controlled by hsa_circ_0076611 in MDA-MB-468 TNBC cells. Validation experiments confirmed that hsa_circ_0076611 interacts with and controls the expression of proliferation- and differentiation-related genes.

overall_design: RNA samples from 2 biological replicates of ChIRP assays performed in MDA-MB-468 cells to recover hsa_circ_0076611-interacting RNAs have been pulled and subjected to RNAseq, along with relative Input samples used as reference

first: Chiara

last: Turco

first: Frauke

last: Goeman

first: Giulia

last: Fontemaggi


title: Transcriptional effects of IL-10 neutralization on LPS-activated M-CSF-derived macrophages

city: Madrid

first: Angel

middle: L

last: Corbí

state: Madrid

address: Ramiro de Maeztu 9

department: Molecular Microbiology and Infection Biology

institute: Consejo Superior de Investigaciones Científicas

summary: Analysis of the role of IL-10 on the transcriptional signature of LPS-activated human M-CSF-dependent monocyte-derived macrophages.   Methods: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes from three independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO2 and 21% O2 for 7 days in the presence of 1000 U/ml M-CSF, with cytokine addition every two days. Then, monocyte-derived macrophages were treated with an anti-IL-10 blocking antibody (anti-IL10) or an isotype-matched antibody (IgG2b) at 2.5 micrograms/ml for 1 hour, and exposed to LPS (10 ng/ml). After 4 hours of LPS treatment, cells were lysed and RNA isolated for transcriptional analysis.

overall_design: mRNA profiles of human M-CSF-derived macrophages activated with LPS in the presence of an anti-IL-10 blocking antibody

first: Miriam

last: Simón Fuentes

first: Ángeles

last: Domínguez Soto

first: Miguel

middle: A

last: Vega


title: The prostate cancer androgen receptor cistrome in African American men differs from White men and associates with upregulation of lipid metabolism [EA]

city: Boston

first: Elio

last: Adib

address: 20 Shattuck Street

institute: Brigham and Women's Hospital

summary: We use androgen receptor chromatin immunoprecipitation (AR ChIP) on frozen prostate adenocarcinoma samples and normal prostate counterparts in men of European ancestry as well as men of African (AA) ancestry and derive a model whereby increased androgen signaling drives higher levels of lipogenesis in AA prostate tumors.

overall_design: Examination of the androgen receptor cistrome in prostate adenocarcinomas and normal prostate tissue derived men of European ancestry

first: Matthew

last: Freedman

first: Salma

last: Kaochar


title: Transcriptional effects of siRNA-mediated STAT3 knockdown on LPS-activated M-CSF-derived macrophages

summary: Analysis of the role of STAT3 on the transcriptional signature of LPS-activated human M-CSF-dependentmonocyte-derived macrophages.   Methods: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures.monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells).monocytes from three independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO2 and 21% O2 for 5 days in the presence of 1000 U/ml M-CSF, with cytokine addition every two days. Then,monocyte-derived macrophages were transfected with STAT3-specific siRNA or control siRNA, kept in culture for 48 hours, and then stimulated (or not) with LPS (10 ng/ml). After 4 hours, cells were lysed and RNA isolated for transcriptional analysis.

overall_design: mRNA profiles of human M-CSF-derived macrophages activated with LPS after downregulation of STAT3 expession

last: Fuentes

last: Soto


title: The prostate cancer androgen receptor cistrome in African American men differs from White men and associates with upregulation of lipid metabolism [AA]

overall_design: Examination of the androgen receptor cistrome in prostate adenocarcinomas and normal prostate tissue derived men of African ancestry


title: Chronic allergic asthma alters m6A epitranscriptomic tagging of mRNAs and lncRNAs  in the lung

city: Huai'an

first: Xiuqin

last: Ni

address: No.4 Mei Cheng Road, Higher Education Park

institute: Jiangsu Food and Pharmaceutical Science College

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

summary:
Chronic allergic asthma alters the lung m6A epitranscriptome, suggesting functional implications in the pathophysiology of refractory asthma.
Methylated IL17RB mRNA possibly become a new therapeutic target for chronic allergic asthma.

overall_design: m6A epitranscriptome of mRNAs and lncRNAs in lung of mice was measured at control (C1,C2,C3) and asthma (T1,T2,T3) group.  Three independent experiments were performed in control and asthma mice for each experiment.

first: Xing

last: Li


title: Spatiotemporal dynamics of Bach2 orchestrates B cell responses and fate decision II

city: shanghai

first: Qianwen

last: Hu

address: 重庆南路280号

institute: Shanghai Jiao Tong University School of Medicine

summary: The molecular circuits that direct early T-dependent B cell responses and alternative cell-fate decisions remain poorly understood. Here, we show that either B cell receptor (BCR) or CD40 signals promoted mTORC1-dependent translation of the transcription factor Bach2. Transient up-regulation of Bach2 protein restrained activated B cell expansion and differentiation into plasma cell while promoting the germinal center (GC) and memory B cell fates at the pre-GC stage. However, enforced Bach2 expression facilitated memory B cell generation versus other cell fates. Mechanistically, Bach2 limited access of AP-1 factors and formed a reciprocal repression loop with IRF4. BCR and CD40 signals also down-regulated Bach2 transcript in antigen-activated B cells, and diversified its abundance in various effector populations, predisposing Bach2 protein expression and subsequent cell-fate choices during memory recall and GC reaction. Thus signaling-induced differential dynamics of Bach2 protein and mRNA in activated B cell control their cell-fate outcomes and imprint the fate of their descendant effector cells.

overall_design: NP-specific naïve B cell（CD19+IgD+）was sorted at day0,and NP-specific plasma cell(IgD-CD19-CD138+),memory B cell(CD19+IgD-GL7-CD38+),germianl center B cell(CD19+IgD-GL7+CD38-) and active precursor B cell(CD19+IgD-GL7+CD38+) were sorted at day 5 after immunization and subjected for transcriptional profile analysis

first: Tingting

last: Xu


title: Modification of gene expression in prostate cancer cells treated with Perfluorooctanoic acid

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: DU145 (human prostate cancer cell line) were treated with different concentrations of Perfluorooctanoic acid (PFOA) : 10-6,  10-9 and 10-12M for 48h and modifications of gene expression were analyzed.

overall_design: The experiement includes the treatment with three concentrations of PFOA (10-6, 10-9, 10-12 M) and a control condition (treatment with EtOH, solvent). Each conditions are in duplicate.

first: Stéphan

last: Clavel

first: Aurélie

last: Charazac

first: Charlotte

last: Hinault

first: Bastien

last: Dolfi

first: Solène

last: Hautier

first: Célia

last: Decondé Le Butor

first: Frédéric

last: Bost

first: Nicolas

last: Chevalier


title: Single cell RNA-seq analysis of human glioma

first: Hongyi

last: Liu

state: Jiangsu

address: 264 Guangzhou Road

department: Neurosurgery

institute: Nanjing Brain Hospital Affiliated to Nanjing Medical University

summary: To understand the diversity of expression states within human gliomas, we obtained eleven freshly resected glioma-related samples, profiled ~3000 cells from each sample and examined their diversity.

overall_design: One low-grade glioma, 8 high-grade primary gliomas, 1 recurrent glioma and 2 paratumor tissues were collected immediately during operation. Microwell arrays were used as the platform for isolating single cells, and those samples were profiled by Smart-seq2.

first: Yong

last: Xiao

first: Mengjie

last: Zhao

first: zhen

last: Wang

first: Xianglong

last: Tang

first: Hong


title: Transcriptome profiling data of THP-1 cells upon Huh7 cell-derived ectosomes incubation

city: Xiamen

first: Peipei

last: Hou

state: Fujian

address: Xiangan South Road, Xiangan District

department: School of Life Sciences

institute: Xiamen University

summary: Analysis of the transcriptome of THP-1 cells upon Huh7 cell-derived ectosomes incubation. Monocytic THP-1 cells were incubated with or without ectosomes (10 mg/ml) derived from scramble sequence transfection (Scramble Ecto) or PKM2 knocking down (PKM2 KD Ecto) Huh7 cells for 24 h. Results provide a novel insight into monocyte differentiation.

overall_design: Total RNA was extracted from THP-1 cells by Trizol method and processed for RNA-seq.

first: Hangzi

last: Chen

first: Qiao

last: Wu


title: Alterations in the gene expression profile in SKOV3 cells exposed to elaiophylin

status: Public on Jun 07 2022

city: Wuhan

first: Guannan

last: Li

state: Hubei

address: 1095 Jiefang Avenue

department: Department of Gynecological Oncology

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary:
Elaiophylin was screened and identified as a novel autophagy inhibitor, with significant antitumor efficacy as a single agent. To explore the mechanisms by which elaiophylin kills cancer cells, NimbleGen 12x135K microarrays were used to find the gene expression changes in SKOV3 cells treated with elaiophylin for indicated time points.
The gene expression microarray data were also analyzed and described in our previous study. Zhao, X., Fang, Y., Yang, Y., Qin, Y., Wu, P., Wang, T., Lai, H., Meng, L., Wang, D., Zheng, Z., Lu, X., Zhang, H., Gao, Q., Zhou, J., & Ma, D. (2015). Elaiophylin, a novel autophagy inhibitor, exerts antitumor activity as a single agent in ovarian cancer cells. Autophagy, 11(10), 1849–1863 (PMID: 25893854).

overall_design: Total RNA was extracted from SKOV3 cells exposed to 0.5 μM of elaiophylin for 0, 3, 6, or 12 h, and was subsequently subjected to microarray analysis. The Roche NimbleGen Human Genome 12×135K Array was used.

first: Xuejiao


title: Genome-wide screen unveils the synthetic lethality targets of mitomycin C

city: Shanghai

first: Jingyu

last: Lang

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

summary: To dig out the synthetic lethality targets of mitomycin C, we we performed Genome-scale CRISPR-Cas9 knockout screening in SNU-1 with 0.1% DMSO or 0.3 µM MMC for 14 days. We found that BRCA2 is a synthetic lethality target of mitomycin C.

overall_design: GeCKO Library screen in SNU-1 with vehicle or MMC for 14 days.

first: Xiaomin

first: Jing-Yu


title: Ethylene modulates the dynamics of translation via GCN2 and EIN2 in Arabidopsis under submergence

city: Taipei

first: Hsing Yi

last: Cho

state: Select One

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: ABRC

country: Taiwan

institute: Academia sinica, Taiwan

summary: General translational repression is predicted as a key process to reduce energy consumption under hypoxia. We have previously showed that mRNA loading onto polysome is reduced in Arabidopsis under submergence. Here, we showed that plant stress activated GCN2 (general control nonderepressible 2) can phosphorylate eIF2a (Eukaryotic Initiation Factor 2a) in Arabidopsis under submergence, and this process is reversible after desubmergence. Compared to the wild-type, the reduction in polysome loading during submergence was less severe in the gcn2 mutant. Transgenic lines overexpressing GCN2 had more ATP and conferred better tolerance under submergence, suggesting that GCN2 might modulate the dynamics of translation to adjust the energy homeostasis under hypoxia. Interestingly, GCN2-eIF2a signaling was activated by ethylene under submergence. However, GCN2 activity was not affected in ein2-5 and eil1ein3 under submergence, suggesting that GCN2 activity was regulated by noncanonical ethylene signaling. In addition, the polysome loading was retained in both ein2-5 and etr1-1 under submergence, implying that ethylene modulated the dynamic translation under submergence via EIN2 and GCN2. Notably, our NGS analysis also demonstrated that EIN2 and GCN2 regulated the translation of 23 core hypoxia genes as well as 53% translational repressed genes under submergence. On the other hand, EIN2 and GCN2 also affected the expression of genes involved in hypoxic response, ethylene response, biotic stress and negative regulation of cytokinin signaling. Taken together, these demonstrated that entrapped ethylene triggers GCN2 and EIN2 to ensure the translation of stress required proteins under submergence and also provide a step stone for future investigation how eukaryotic cells modulate the translation to response for the changeable environments.

overall_design: 64 samples were analyzed. 4 plants lines were included to build up the trasciptome and translatome under submergence. Col-0 without treatment was used as control.Two biological independent replicates

first: Hsing

middle: Y

first: Mei

last: Chuo

first: Hsiu-Yin

last: Ho

first: Wan-Chieh

first: Ming-Che

last: Shih


title: Analysis of EHF Regulated Network in HNSCC Cell Lines

city: Buffalo

first: Rose-Anne

last: Romano

address: 3435 Main Street

department: Oral Biology

institute: State University of New York at Buffalo

summary: We evaluated the gene expression changes upon the loss and gain of EHF in HNSCC cells

overall_design: 1. NGS sequencing of HNSCC cell lines with EHF overexpression and EHF Knockdown. 2. EHF ChIP-Sequencing of CAL27 cells (a representative EHF expressing HNSCC cell line)

first: Akinsola

last: Oyelakin

first: Satrajit

last: Sinha


title: Integrative analysis of expression profile in the glioma-related epilepsy

city: ChangSha

first: ZhaoQian

last: Liu

state: China

address: xiangya road 110

institute: Xiangya Hospital, Central South University

summary: To investigate the potential pathogenic mechanism of glioma-related epilepsy (GRE), we have employed analyzing of the dynamic expression profiles of microRNA/ mRNA/ lncRNA in brain tissues of glioma patients. Brain tissues of 16 patients with GRE and nine patients with glioma without epilepsy (GNE) were collected. The total RNA was dephosphorylated, labeled, and hybridized to the Agilent Human miRNA Microarray, Release 19.0, 8x60K. The cDNA was labeled and hybridized to the Agilent LncRNA+mRNA Human Gene Expression Microarray V3.0, 4x180K. The raw data was extracted from hybridized images using Agilent Feature Extraction, and quantile normalization was performed using the Agilent GeneSpring. We found that three differentially expressed miRNAs (miR-10a-5p, miR-10b-5p, miR-629-3p), six differentially expressed lncRNAs (TTN-AS1, LINC00641, SNHG14, LINC00894, SNHG1, OIP5-AS1), and 49 differentially expressed mRNAs may play a vitally critical role in developing GRE.

overall_design: Brain tissues of 25 glioma patients with or without epilepsy were retrospectively obtained from the Affiliated Cancer Hospital of Xiangya School of Medicine (Changsha, Hunan, China) with informed consent.

first: Zhi-Bin

first: Jian

last: Qu

first: Pan

last: Xie

first: Chen-Xue

last: Mao

first: Ying

last: Zhang

first: Zheng-Wen

last: He

first: Xiao-Yuan

first: Zhao-Qian


title: RNA high-throughput sequencing in synovium of human temporomandibular joint osteoarthritis.

first: Chuyao

last: Wang

address: The Ninth People's Hospital, No. 639, Zhizaoju Road, Huangpu District, Shanghai

institute: shanghai ninth people hospital

summary:
To investigate differentially expressed lncRNAs,circRNAs,miRNAs and mRNAs in synovium of human temporomandibular joint osteoarthritis (TMJOA), we performed RNA high-throughput sequencing in synovium of human TMJOA.
We then performed gene expression profiling analysis using data obtained from RNA-seq .

overall_design: Patients with reducible anterior disc displacement were  used as control groups and patients with TMJOA were used as experimental group.

first: Dongmei


title: A TET1-PSPC1-Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency [ChIRP-Seq]

city: New York

first: Jianlong

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: The mammalian Ten-eleven translocation (TET) family proteins regulate the epigenome through catalytic activity (CA)-dependent and -independent functions. While catalytic activity of TETs has been intensely studied as DNA demethylation enzymes, little is known about their CA-independent function in early embryo development. Here we defined the CA-independent function of TET1 in naïve-to-formative pluripotent states transition. Using a proteomics method, we mapped the TET1 interactome and identified Paraspeckle component 1 (PSPC1) as a partner of TET1 for transcriptional repression at the bivalent genes in early development. Genome-wide location analysis revealed that PSPC1-bound regions largely overlap with TET1 and Polycomb repressive complex 2 (PRC2) subunits. Functional studies with genetic methods indicated that PSPC1 and TET1 repress, while lncRNA Neat1 activates the bivalent genes during their transcriptional activation. In embryonic stem cell (ESC) state, Neat1 tethers TET1, PSPC1, and PRC2 at promoters. During the ESCs to formative Epiblast like stem cells (EpiLCs) differentiation, PSPC1 and TET1 repress the PRC2 affinity to nascent mRNA transcripts of bivalent genes, while Neat1 facilitates PRC2 binding to those transcripts. Our study reveals a molecular mechanism by which proteins TET1 and PSPC1, and lncRNA Neat1 dynamically regulate gene transcription by modulating the PRC2 activity in pluripotent states transition.

overall_design: Neat1 ChIRP-seq analysis in WT and Neat1KO ESCs and EpiLCs

first: Xin

last: Huang


title: Genomic profiles of oxidative stress-induced renal cell carcinomas developed in wild-type and BRCA1+/- SD rats

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

summary: Fenton reaction-based repeated oxidative stress via ferric nitrilotriacetate (Fe-NTA) causes renal cell carcinoma (RCC) with genetic alterations similar to those in humans. We conducted high-resolution microarray comparative genomic hybridization with Fe-NTA induced RCC obtained from both wild-type and BRCA1+/- rats to evaluate the involvement of BRCA1 haploinsufficiency in carcinogenesis.

overall_design: The carcinogenesis protocol was started with 20 wildtype and 19 BRCA1+/- male Jcl: SD rats. 17 of each genptype of rats developed a renal cell carcinoma in total. Genomes of 8 samples from RCCs for each genotype (16 in total) were profiled on Agilent 180K rat genome CGH microarrays.

first: Yingyi

last: Kong

last: Akatsuka


title: Transcriptome analysis of subacute injured kidney by intraperitoneal injections of Fe-NTA in wildtype and BRCA1+/- rats

summary: Fenton reaction-based repeated oxidative stress via ferric nitrilotriacetate (Fe-NTA) causes renal cell carcinoma (RCC), which was found to be promoted in BRCA1 haploinsufficiency rats.To elucidate the molecular mechanism, we performed a subacute study of repeated ip administration of Fe-NTA for 1 or 3 weeks to understand the early events. We compared the microarray gene expression profiles of rat kidney cortex tissues of wild-type and BRCA1+/- rats from the study.

overall_design: The subacute kidney injury protocol was started with 17 wildtype and 18 BRCA1+/- male Jcl: SD rats. A total of 16 microarrays (Whole Rat Genome Microarray) were used for screening purpose: 8 microarrays for wildtype SD rats, and 8 for BRCA1+/- SD rats.


title: A TET1-PSPC1-Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency [H3 ChIP-Seq]

overall_design: ChIP-seq analysis of H3K4me3 and H3K27me3 in ESCs and EpiLCs


title: Gut microbial metabolite trimethylamine N-oxide aggravates pulmonary hypertension

first: Ruidi

last: Tang

state: Guangdong

address: 151 Yanjiang Road, Guangzhou, Guangdong, China

institute: State  Key  Laboratory  of  Respiratory  Diseases

summary: Trimethylamine N-oxide (TMAO), a metabolite derived from intestine microbial flora, enhances vascular inflammation in a variety of cardiovascular disease, and the bacterial communities associated with trimethylamine N-oxide (TMAO) metabolism is higher in pulmonary hypertension (PH) patients. The effects of TMAO on PH, however, has not been elucidated. In the present study, we found that circulating TMAO is elevated in intermediate to high-risk PH patients when compared to healthy control or low-risk PH patients. In monocrotaline-induced rat PH models, circulating TMAO is elevated; and reduction of TMAO using 3,3-dimethyl-1-butanol (DMB) significantly decreased right ventricle systolic pressure, pulmonary vascular muscularization in both monocrotaline-induced rat PH and hypoxia induced mice PH models. RNA sequencing of rat lungs on DMB revealed significant suppression of pathways involved in cytokine-cytokine receptor interaction, and cytokine and chemokine signaling. Protein-protein interaction analysis of the differentially expressed transcripts regulated by DMB showed 5 hub genes with a strong connectivity of proinflammatory cytokines and chemokines including Kng1, Cxcl1, Cxcl2, CxcL6 and Il6. In vivo, TMAO significantly increased the expression of Kng1, Cxcl1, Cxcl2, CxcL6 and Il6 in bone marrow derived macrophage. And TMAO-treated conditioned medium from macrophage increased the proliferation and migration of pulmonary artery smooth muscle cells; but TMAO treatment did not change the proliferation or migration of pulmonary artery smooth muscle cells. In conclusion, our study demonstrates that TMAO is increased in severe PH, and the reduction of TMAO using DMB reduces pulmonary vascular muscularization and alleviates PH via suppressing the macrophage production of chemokines and cytokines.

overall_design: RNA-seq of lung tissue of MCT-PH rats with or without 3,3-dimethyl-1-butanol treatment

first: Yuhang

first: Tao

first: Wenju

last: Lu

first: Fanjie

last: Lin

first: Changlei

last: Bao


title: Epiblast inducers capture mouse Trophectoderm Stem Cells in vitro and pattern blastoids for implantation in utero.

city: Vienna

first: Giovanni

last: Sestini

address: Dr.-Bohr-Gasse 3, 1030 Wien

country: Austria

institute: IMBA - Institute of Molecular Biotechnology

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

overall_design: Refer to individual Series


title: Comparative Transcriptomic Profiles of Adipocyte in Differentiation Process Provide Insights into Different Mechanisms of Adipogenesis between Subcutaneous and Intramuscular Fat Tissues in Pig [mRNA-seq]

city: Beijing

first: Pan

address: No. 2, Yuanmingyuan West Road, Beijing

institute: China Agricultural University

summary:
Purpose: In this study, RNA-Seq was performed on intramuscular adipocytes and subcutaneous adipocytes at 0, 2, 4, and 8 days of differentiation to find genes and miRNAs that regulate the differentiation of two types of adipocytes.
Methods: High-throughput sequencing was performed with NovaSeq 6000, and 150 paired-end reads were generated.Clean reads were filtered  using HISAT2. The StringTie  was used to assemble the transcript and calculate fragments per kilobase million mapped reads (FPKM) value.
Results: We found 30 genes that mainly regulate the differentiation of subcutaneous adipocytes and 22 genes that mainly regulate the differentiation of subcutaneous intramuscular adipocytes. A total of 17 important candidate differential miRNAs were found, of which 4 miRNAs are believed to play a regulatory role in both types of cells, and 10 and 3 act on lipid deposition in subcutaneous and intramuscular adipocytes, respectively.

first: Bo

first: Hao


title: Comparative Transcriptomic Profiles of Adipocyte in Differentiation Process Provide Insights into Different Mechanisms of Adipogenesis between Subcutaneous and Intramuscular Fat Tissues in Pig [miRNA-seq]

summary:
Purpose: In this study, RNA-Seq was performed on intramuscular adipocytes and subcutaneous adipocytes at 0, 2, 4, and 8 days of differentiation to find genes and miRNAs that regulate the differentiation of two types of adipocytes.
Method:The clean reads were mapped to the pig reference genome (scrofa. Sscrofa11.1) with perfect matches using Bowtie software. Annotated tRNA, rRNA, snoRNA, and snRNA sequences were filtered out, and conserved miRNAs were identified by the BLAST method against miRBase. The miRDeep2 software was used to predict new miRNAs based on the characteristics of the miRNA precursor hairpin structure. Differential expression analysis of two groups was performed using the DESeq2 R package. Differentially expressed miRNAs (DE-miRNAs) were screened with criterion of fold change > 1.5 and FDR < 0.05 using DESeq2. Target genes of DE-miRNAs were predicted by miRanda and targetscan.
Results: We found 30 genes that mainly regulate the differentiation of subcutaneous adipocytes and 22 genes that mainly regulate the differentiation of subcutaneous intramuscular adipocytes. A total of 17 important candidate differential miRNAs were found, of which 4 miRNAs are believed to play a regulatory role in both types of cells, and 10 and 3 act on lipid deposition in subcutaneous and intramuscular adipocytes, respectively.


title: Epigenome-wide profiling uncovers novel pathway networks in human pulmonary arterial hypertension [pul36]

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

summary: Pulmonary arterial hypertension (PAH) is a progressive pulmonary vascular disease that culminates in right heart failure. Vascular pathology in PH is characterized by pulmonary vasoconstriction and progressive vascular remodeling processes that affects all layers of the vascular wall (intima, media and adventitia).

overall_design: Transcriptome profiling on pulmonary artery adventitial fibroblasts (PAAF) isolated from 4 PAH afflicted patients were treated with gene-specific siRNAs or scrambled siRNAs.

first: Prakash

last: Chelladurai

first: Alice

last: Bourgeois

first: Stefan

last: Günther

first: Chanil

last: Valasarajan

first: Anoop

middle: V

last: Cherian

first: Robbert

middle: J

last: Rottier

first: Charlotte

last: Romanet

first: Andreas

last: Weigert

first: Olivier

last: Boucherat

first: Christina

last: Eichstaedt

first: Clemens

last: Ruppert

last: Guenther

first: Thomas

last: Braun

first: Rajkumar

last: Savai

first: Mario

last: Looso

first: Werner

last: Seeger

first: Uta

last: Bauer

first: Sébastien

last: Bonnet

first: Soni

last: Pullamsetti


title: Comparative Transcriptomic Profiles of Adipocyte in Differentiation Process Provide Insights into Different Mechanisms of Adipogenesis between Subcutaneous and Intramuscular Fat Tissues in Pig

first: Pan

last: Zhang


title: A TET1-PSPC1-Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency [ChIP-seq]

first: Jianlong

last: Wang

overall_design: ChIP-seq analysis of PSPC1 and SUZ12 in ESCs and EpiLCs

first: Xin

last: Huang


title: A TET1-PSPC1-Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency [RNA-seq]

overall_design: RNA-seq analysis of Pspc1KO and Neat1KO in ESCs and EpiLCs


title: Rhabdomyosarcomas are oncogene addicted to the activation of AVIL

city: Charlottesville

first: Zhongqiu

last: Xie

state: VA

address: 345 Crispell Dr,  Charlottesville

institute: University of Virginia

summary: Rhabdomyosarcoma (RMS) is one of the most common pediatric soft-tissue cancer. Previously, we discovered a gene fusion, MARS-AVIL formed by chromosomal inversion in RMS. Suspecting that forming a fusion with a housekeeping gene may be one of the mechanisms to dysregulate an oncogene, we investigated AVIL expression and its role in RMS. We first showed that MARS-AVIL translates into an in-frame fusion protein, which is critical for the RMS cell tumorigenesis. Besides forming a gene fusion with the housekeeping gene, MARS, the AVIL locus is often amplified, and its RNA and protein expression is overexpressed in the majority of RMSs. Tumors with AVIL dysregulation exhibit evidence of oncogene addiction: silencing MARS-AVIL in cells harboring the fusion, or silencing AVIL in cells with AVIL overexpression, nearly eradicated the cells in culture, as well as inhibited in vivo xenograft growth in mice. Conversely, gain-of-function manipulations of AVIL led to increased cell growth and migration, enhanced foci formation in mouse fibroblasts, and most importantly transformed mesenchymal stem cells in vitro and in vivo. Mechanistically, AVIL seems to serve as a converging node functioning upstream of two oncogenic pathways, PAX3-FOXO1 and RAS, thus connecting two types of RMS associated with these pathways. Interestingly, AVIL is overexpressed in other sarcoma cells as well, and its expression correlates with clinical outcomes, with higher levels of AVIL expression being associated with worse prognosis. AVIL is a bona fide oncogene in RMS, and RMS cells are addicted to its activity.

overall_design: Transcriptome examination of overexpresses AVIL in MSC and control cells.

first: Hui

last: Li


title: Cell and chromatin transitions in intestinal stem cell regeneration

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: The progeny of intestinal stem cells (ISCs) dedifferentiate in response to ISC attrition. The precise cell sources, transitional states, and chromatin remodeling behind this activity remain unclear. In the skin, stem cell recovery after injury preserves an epigenetic memory of the damage response; whether similar memories arise and persist in regenerated ISCs is not known. We address these questions by examining gene activity and open chromatin at the resolution of single Neurog3-labeled mouse intestinal crypt cells, hence deconstructing forward and reverse differentiation of the intestinal secretory (Sec) lineage. We show that goblet, Paneth, and enteroendocrine cells arise by multilineage priming in common precursors, followed by selective access at thousands of cell-restricted cis-elements. Selective ablation of the ISC compartment elicits speedy reversal of chromatin and transcriptional features in large fractions of precursor and mature crypt Sec cells without obligate cell cycle re-entry. ISC programs decay and reappear along a cellular continuum lacking discernible discrete interim states. In the absence of gross tissue damage, Sec cells simply reverse their forward trajectories, without invoking developmental or other extrinsic programs, and starting chromatin identities are effectively erased. These findings identify strikingly plastic molecular frameworks in assembly and regeneration of a self-renewing tissue.

overall_design: ScRNA-seq and scATAC-seq profiles of Neurog3 traced tomato positive cells, after two daily doses of TAM, at 12h, 24h, 48h, 72h from Ngn3CreERT2;R26tdtomato;Lgr5-DTRGFP mice and Neurog3 traced cells after stem cell ablation, via DT injection,  at 12h, 24h, 48h and 72h from Ngn3CreERT2;R26tdtomato;Lgr5-DTRGFP mice

first: Pratik

last: Singh

first: Shariq

last: Madha

first: Andrew

middle: B

last: Leiter


title: MIA-PaCa2 cells transfected with silencer RNA against HuR and YAP1

city: Portland

first: Jonathan

last: Brody

state: OR

address: 2730 S. Moody Ave CL6JB

institute: Oregon Health & Science University

summary: Purpose: To determine biological impact between silencing HuR and YAP1, in MIA-PaCa2.  Methods: Expression profiling of MIA-PaCa2 cells knocked-down for HuR and YAP1 and control cells transfected with scramble siRNA.

overall_design: MIA-PaCa2 cells transfected with siRNA (siCTRL, siHuR, siYAP1) in quadruplicate (n=3 for siYAP1) were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Samantha

middle: Z

last: Brown

middle: R

first: Carl

last: Pelz


title: Glutaminase 2 Knockdown Reduces Hyperammonemia and Associated Lethality of Urea Cycle Disorder Mouse Model

city: Tarrytown

first: Xiping

last: Cheng

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

summary: Urea cycle disorders with hyperammonemia remain difficult to treat and eventually necessitate liver transplantation. An ornithine transcarbamylase defect (Otcspf-ash) mouse model, a model of urea cycle disorder, was used to test whether knockdown of a key glutamine metabolism enzyme glutaminase 2 (Gls2) or glutamine dehydrogenase 1 (Glud1) could rescue the hyperammonemia and associated lethality induced by a high protein diet. Reduced hepatic expression of Gls2, but not Glud1, by AAV8-mediated delivery of a short hairpin RNA in Otcspf-ash mice diminished hyperammonemia, reduced body weight loss, and reduced lethality. These data suggest that Gls2 hepatic knockdown could help alleviate risk for hyperammonemia and other clinical manifestations of patients suffering from defects in the urea cycle.

overall_design: Wildtype (B6EiC3SnF1/J, The Jackson Laboratory Stock No. 001875, abbr: WT) and Otcspf-ash (B6EiC3Sn a/A-Otcspf-ash/J, The Jackson Laboratory Stock No. 001811, abbr: OTC) mice at 4 months old were randomized into 3 groups of shRNA-scramble (abbr: control), shRNA-Gls2 (abbr: sh-Gls2) and shRNA-Glud1 (abbr: sh-Glud1) (n=12-13 for each group). IV injection delivery of AAV were applied at week 0. Mice were switched from chow diet to 40% high protein diet at week 2 until the end of the study at week 5. Liver samples were collected at week 5 for RNA sequencing.

first: Xia

last: Mao

first: Helen

last: Chen

first: Allen

last: Lin

first: Sun

last: Kim

first: Erqian

first: Gabor

last: Halasz

first: Mark

middle: W

last: Sleeman

last: Murphy

first: Haruka

last: Okamoto


title: An artificial host system enables the obligate parasitic plant Cuscuta campestris to grow and complete its life cycle in vitro

city: BLACKSBURG

first: James

last: Westwood

address: 401 Latham Hall (0390)

department: School of Plant and Environmental Sciences

institute: Virginia Tech

summary: Cuscuta campestris is an obligate parasitic plant that requires a host to complete its lifecycle. Parasite-host connections occur via an haustorium, a unique organ that acts as a bridge for the uptake of water, nutrients and macromolecules. Research on Cuscuta is often complicated by host influences, but comparable systems for growing the parasite in the absence of a host do not exist. We developed an axenic method to grow C. campestris on an Artificial Host System (AHS). We evaluated the effects of nutrients and phytohormones on parasite haustoria development and growth. Haustorium morphology and gene expression were characterized. The AHS consists of an inert, fibrous stick that mimics a host stem, wicking water and nutrients to the parasite. It enables C. campestris to exhibit a parasitic habit and develop through all stages of its lifecycle, including production of new shoots and viable seeds. Phytohormones NAA and BA affect haustoria morphology, and increase parasite fresh weight and biomass. Gene expression in AHS haustoria reflect process similar to those in haustoria on actual host plants. The AHS is a methodological improvement for studying Cuscuta biology by avoiding specific host effects on parasite and giving researchers full control of the parasite environment.

overall_design:
Two types of tissue were compared: haustorial regions and shoots. Four different replicates were used for each type of tissue. Plant material from 3 or 4 different plants were pooled to get each of the replicates.
Haustorial region without visible meristems collected from a plant grown on artificial host
Shoot includes stem tissue and meristems collected from a plant grown on artificial host

first: Vivian

last: Bernal-Galeano


title: Expression data from lesional (LP) and non-lesional (NP) skin in patients with psoriasis.

city: Aarhus

first: Kirsten

last: Rønholt

address: Palle Juul-Jensens Boulevard

department: Department of Dermatology

institute: Aarhus University Hospital

summary: We used microarry to charactarize differences in gene expression between lesional and non-lesional psoriasis skin. Our hypothethis was that IL-37 is downregulated in psoriasis.

overall_design: Nine adult patients with psoriasis vulgaris were included. Excisional biopsies (2.5 cm x 1 cm) from non-involved (NP) and involved tissue (LP) were obtained using a local anesthetic containing 1% Lidocaine. Subcutis was removed and biopsies were snap frozen in liquid nitrogen and used for RNA isolation.

first: K

last: Ronholt

first: A

last: Langkilde

first: C

last: Johansen

last: Vestergaard

last: Fauerbye

first: R

last: López-Vales

last: Dinarello

first: L

last: Iversen


title: Chromatin recruitment of Rad6 determines H3K4me3 in Saccharomyces cerevisiae

city: Chuncheon

first: Junsoo

last: Oh

institute: Kangwon National University

summary: Project abstract : The trimethylation of histone H3 lysine 4 (H3K4me3) is a crucial factor in defining the promoter regions of active genes in all eukaryotes ranging from Saccharomyces cerevisiae (yeast) to humans. In budding yeast, this trimethylation process facilitated by the Set1 complex results in H3K4me3 requiring a prior mono-ubiquitination at the histone H2BK123 residue (H2Bub) by E2 enzyme Rad6 and E3 enzyme Bre1. A previous in vitro study suggested that ubiquitinated H2B directly facilitates H3K4me3. However, even low levels of global H2Bub is sufficient for the required H3K4me3 in yeast cells, thereby indicating that other factors resulting in the H2Bub-dependent H3K4me3 remain unknown. This study revealed the high level of correlation of H3K4me3 with chromatin recruitment of Rad6 at the genome-wide level.  Rad6 is confirmd to interact and co-localize with Swd2/Cps35, a key factor for the H2Bub-dependent H3K4me3 in genes with high levels of H3K4me3 and intronic genes rather than non-intronic genes. This study therefore provides a mechanistic insight of the H2Bub-Rad6- Swd2/Cps35-H3K4me3 axis and its potential role in RNA biogenesis.

overall_design: To define the global binding sites of Rad6 and to identify whether chromatin recruitment of Rad6 is affected by catalytic activity or phosphorylation status of Rad6, chromatin immunoprecipitation (ChIP) sequencing against 9myc antibody is performed with yeast strains endogenously tagged with 9myc at Rad6 locus in WT, Rad6 C88A catalytically dead mutant, Rad6S120A phosphorylation site mutant background. To confirm if H2B ubiquitination contributes to chromatin recruitment of Rad6, ChIP with 9myc antibody is performed to endogenously expressed Rad6-9myc at H2B WT and H2B K123R strain. 9myc ChIPseq is carried out with no tag WT strain as control. To define the chromatin binding sites of Swd2 and to compare with chromatin binding of Rad6 and H3K4me3, ChIP against 3HA tag of endogenously tagged Swd2-3HA WT strain is performed.

first: Jung-Shin

last: Lee

first: Shinae

last: Park

first: Jueun

first: Yong-Joon

last: Cho


title: Methods for Culturing Adult CNS Neurons Reveal a CNS Conditioning Effect

status: Public on Jun 06 2022

city: La Jolla

first: Erna

last: van Niekerk

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

summary:
To develop a successful, reliable and scalable method for establishing primary cultures of adult neurons from all regions of the brain.
Using adult motor cortex cultures, we identify a CNS "conditioning" effect after spinal cord injury.  In vivo conditioning was administered 24hrs prior to cultures.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary cortical neurons that received an in-vivo conditioning lesion 24hrs prior to plating.

last: Tuszynski


title: A TET1-PSPC1-Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency

first: Jianlong

last: Wang


title: Toxics effects of NX and 3ANX toxins compared to DON in intestinal explants

city: Toulouse

first: Philippe

last: Pinton

address: 180 Chemin de Tournefeuille

department: TOXALIM

institute: INRAE

summary: To investigate the possible toxics effects of newly discovered mycotoxins NX and 3ANX and compare with the known effects of DON, we performed a microarray to study their effects on expression profile of intestinal explants

overall_design: Pigs jejunal explants of 6 animals were exposed 4 hours at 10 µM of DON, NX, 3ANX or a control medium.

first: Manon

last: Neves

first: Alix

last: Pierron

first: Isabelle

last: Oswald

first: Joelle

last: Laffitte

first: Sylvie

last: Puel

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: ARID1B, a molecular suppressor of erythropoiesis, is essential for the  prevention of Monge’s disease

first: Shankar

last: Subramaniam

department: Department of Bioengineering

summary: In this work, we used genomic and molecular functional  assays to understand the role of ARID1B in regulating red blood cells under hypoxia using iPS cells derived from non-CMS adapted individuals and comparing the non-CMS wild type cells to non-CMS cells with ARID1B-KD using in-vitro iPSC-derived model system.

overall_design: hiPSC-derived cell erythroid cells were generated from the adapted non-CMS individuals (referred to as non-CMS) and cell line was created in which ARID1B was knocked down (using shRNA lentivirus) in these non-CMS cells (Referred to as ARID1B-KD).  For ATAC-Seq, transposition reactions were performed on 50,000 non-CMS and non-CMS with ARID1B KD (replicates, n = 3) hiPSC-derived erythroid cells grown under hypoxic and normoxic conditions for two weeks as previously described Buenrostro et al., 2013 (52). Briefly Cells were washed with PBS followed by lysis with cold lysis buffer. Cells were then suspended in 50 μl 1X reaction buffer. Transposase reactions were carried out at 37°C for 30 minutes and DNA was purified using ChIP DNA Clean & Concentrator kits. DNA was amplified using the dual barcoded primers (Illumina) using NEBNext High-Fidelity 2XPCR Master Mix for 14 cycles. Resulting libraires were sequenced on an Illumina  Novaseq platform  generating Paired-End, 50bp (PE50) reads with an average of over 100 million reads per sample.

first: Priti

last: Azad

first: Andrew

last: Caldwell

first: Srinivasan

last: Ramachandran

first: Orit

last: Poulsen

first: Dan

last: Zhou

first: Gabriel

last: Haddad


title: Feb2017_GenderPoolPlasmaRNA

city: Boston

first: Ionita

middle: Calin

last: Ghiran

address: 3 Blackfan Circle

department: Medicine

institute: Beth Israel Deaconess Medical Center

summary: exRNAs profiles by gender in healthy individuals

overall_design: 2 pooled plasma samples by gender from 5 males and 3 female subjects

first: Shulin

last: Lu


title: Ribosomal RNA-depletion provides an efficient method for successful dual RNA-Seq expression profiling of a marine sponge holobiont

city: Brisbane

first: Xue Yan

last: Xiang

address: St Lucia

department: Biological Sciences

country: Australia

institute: The University of Queensland

summary: To determine the optimal RNA-Seq approach for animal host-bacterial symbiont analysis, we compared transcriptome bias, depth and coverage achieved by two different mRNA capture and sequencing strategies applied to the marine demosponge Amphimedon queenslandica holobiont, for which genomes of the animal host and three most abundant bacterial symbionts are available.

overall_design:
The two strategies were: (i) poly(A) captured mRNA-Seq (Poly(A)-RNA-Seq); and (ii) ribosomal RNA depleted RNA-Seq (rRNA-depleted-RNA-Seq).
Please note that each processed data was generated from all three replicates and is linked to the *A and *D sample records.

first: Xueyan

first: Davide

last: Poli

first: Bernard

middle: M

last: Degnan

first: Sandie


title: Satellite repeat RNA expression in epithelial ovarian cancer is linked to a tumor immunosuppressive phenotype

city: Saugus

first: Michael

last: Raabe

address: 3214 Founders Way

institute: Massachusetts General Hospital

summary: Repeatome profiling across ovarian, pancreatic, and colorectal cell lines identifies distinct clustering that is independent of tissue of origin highlighting differences in repeat co-expression patterns.  Deeper analysis of ovarian cancer cell lines demonstrated that HSATII satellite repeat expression was highly associated with epithelial mesenchymal transition (EMT) and anti-correlated with interferon (IFN) response genes indicative of a more aggressive phenotype.

overall_design: Different cell lines and extracellular vesicles were subjected to total RNA-seq using the Clontech-Takara Smarter Stranded Total RNA-Seq kit v2 (Cat No#634413).  RNA-seq across a panel of cell lines and extracellular vesicles was done as a single sample.  When cell lines were treated, the cell lines were collected at different time points after treatment (HSATII LNA, HDAC inhibitor, DNMT inhibitor).

first: Rebecca

last: Porter

first: Siyu

last: Sun

first: Micayla

last: Flores

first: Emily

last: Berzolla

first: Eunae

last: You

first: Ildiko

middle: E

last: Phillips

first: Neelima

last: KC

first: Niyati

last: Desai

first: Eric

last: Tai

first: Annamaria

last: Szabolcs

first: Evan

last: Lang

first: Amaya

last: Pankaj

first: Vishal

last: Thapar

first: Katherine

middle: H

last: Xu

first: Linda

middle: T

last: Nieman

first: Daniel

last: Rabe

first: David

last: Kolin

first: Elizabeth

last: Stover

last: Peppin

first: Shannon

last: Stott

first: Vikram

last: Deshpande

first: Joyce

middle: F

last: Liu

first: Alexander

last: Solovyov

first: Ursula

last: Matulonis

first: Benjamin

middle: D

last: Greenbaum

last: Ting


title: Nov2016_AnticoagulantPlasmaRNA

first: Ionita

last: Ghiran

summary: Impact of different anticoagulants in obtaining reference profiles of exRNAs in healthy individuals

overall_design: 23 samples from 6 subjects, 3 anticoagulants (C-Citrate, E-EDTA, H-Heparin) were used for each subject, and serum (S) was also collected

first: Shulin

last: Lu


title: Microarray analysis of hub genes, non-coding RNAs and pathways in lung after whole body irradiation in a mouse model

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary:
Objective:Biomarkers of radiation injury are needed in planning therapeutic measures for cancer patients receiving radiation therapy and civilians exposed to nuclear events. Previous research has highlighted the impact of radiation damage, with cancer patients developing acute disorders including radiation induced pneumonitis or chronic disorders including pulmonary fibrosis months after radiation therapy ends. Discovery of biomarkers that predict these injuries will offer the potential to treat people proactively to mitigate this damage and improve quality of life. Recent research has highlighted the potential for messenger RNA (mRNA), microRNA (miRNA), and long non-coding RNA (lncRNA) to be used as radiation biomarkers. Our study focused on the changes in these RNAs at 48h after radiation exposure of mouse lung tissue to define biological pathway changes and determine potential biomarkers.
Result: We observed sustained dysregulation of specific mRNAs, lncRNAs, and miRNAs across all doses. We observed gene dysregulation which can be used to develop both markers to identify no-exposure vs radiation exposure including Hba and Hbb mRNA which were dysregulated even at 1 Gy. We also observed genes which can indicate high dose exposure including Cpt1c and Pdk4.  Gdf15, and Eda2r, mRNA markers of senescence and fibrosis, were the most significantly upregulated.  Only three miRNAs were significantly dysregulated across all radiation doses, with miRNA-142-3p and miRNA-142-5p downregulated and miRNA-34a-5p upregulated. IPA analysis indicated that numerous pathways relevant to immune function, cell proliferation and survival decreased with increasing doses of radiation. This data highlighted early pathways of dysregulation depending on dose of exposure. This data will help with development of treatments and in medical decision-making.  Further experiments are planned to develop medical countermeasures based on this early dysregulation.

overall_design: Six- to 8-week old female C57BL/6 J mice were given total-body irradiation (TBI) with X-rays using the Small Animal Radiation Research Platform (SARRP Xstrahl Ltd.). Mice were placed in plastic containers and exposed to a single surface dose of 1, 2, 4, 8, or 12 Gy at a dose rate of 1.05 Gy/min. Control mice (0 Gy) were placed in the same type of plastic container and sham irradiated. Three animals per dose were included in the study. Hearts of irradiated and control animals were harvested 48 h after TBI. Organs were snap frozen in liquid nitrogen and stored at − 80 °C until processed for RNA isolation. All animal experiments were performed at the Department of Pathology at New York University (NYU) Langone Medical Center under an approved IACUC protocol as part of a collaborative study.

first: Molykutty

last: Aryankalayil

first: Michelle

last: Bylicky

last: Martello

first: Sunita

last: Chopra

first: Mary

last: Sproull

first: Jared

last: May

first: Aman

last: Shankardass

first: Laurel

last: MacMillan

first: Claire

last: Vanpouille-Box

first: Iris

last: Eke

first: Kevin

last: Scott

first: Juan

last: Dalo

first: C

middle: N

last: Coleman


title: Murine follicular helper T cells

city: manhasset

first: kyungwoo

last: lee

address: 350 community drive

institute: Feinstein Institute

summary: Goal of the experiment is to compare the transcriptome of splenic Tfh cells from female DC-specific Blimp-1 deficient mice and age/gender matched littermate controls.

overall_design: Comparative gene expression profiling of Tfh cells (CXCR5+PD1+) from spleens were isolated by cell sorter

first: Su

last: Jang

last: Lee

first: Sun

last: Kim

first: Vera


title: Salt-inducible kinase 3 protects tumor cells from cytotoxic T cell attack by promoting TNF-induced NF-κB activation

city: REGENSBURG

first: Claudia

last: GEBHARD

address: FRANZ-JOSEF-STRAUSS ALLEE 11

institute: UNIVERSITY HOSPITAL REGENSBURG

summary: Background: Cancer immunotherapeutic strategies showed unprecedented results in the clinic. However, many patients do not respond to immuno-oncological treatments due to the occurrence of a plethora of immunological obstacles, including tumor intrinsic mechanisms of resistance to cytotoxic T cell attack. Thus, a deeper understanding of these mechanisms is needed to develop successful immunotherapies.  Methods: To identify novel genes that protect tumor cells from effective T cell-mediated cytotoxicity, we performed a genetic screening in pancreatic cancer cells challenged with TILs and antigen-specific T cells.  Results: The screening revealed 108 potential genes that protected tumor cells from T cell attack. Among them, salt-inducible kinase 3 (SIK3) was one of the strongest hits identified in the screening. Both genetic and pharmacological inhibition of SIK3 in tumor cells dramatically increased T cell-mediated cytotoxicity in several in vitro co-culture models, using different sources of tumor and T cells. Consistently, adoptive T cell transfer of TILs led to tumor growth inhibition of SIK3 depleted cancer cells in vivo. Mechanistic analysis revealed that SIK3 rendered tumor cells susceptible to TNF secreted by tumor-activated T cells. SIK3 promoted NF-ΚB nuclear translocation and inhibited Caspase-8 and -9 after TNF stimulation. Chromatin accessibility and transcriptome analyses showed that SIK3 knockdown profoundly impaired the expression of pro-survival genes under the TNF-NF-ΚB axis. TNF stimulation led to SIK3-dependent phosphorylation of the NF-κB upstream regulators inhibitory-κB kinase (IKK) and NF-kappa-B inhibitor alpha (IκBα) on the one side, and to inhibition of histone deacetylase 4 (HDAC4) on the other side, thus sustaining NF-κB activation and nuclear stabilization. A SIK3 dependent gene signature of TNF-mediated NF-κB activation was found in a majority of pancreatic cancers where it correlated with increased cytotoxic T cell activity and poor prognosis.

overall_design: ATAC-seq of PANC1 cell line with shRNA mediated SIK3 knockdown was treated with human TNF or vehicle control

first: Antonio

last: Sorrentino

first: Christian

last: Schmidl

first: Ayse

last: Nur Menevse


title: FIBP interacts with transcriptional factor STAT3 to induce Eme1 expression and drives radioresistance in lung cancer

city: wuhan

first: Xu

last: YunHong

state: hubei

address: xinhua road

department: Union Hospital

institute: Huazhong University of Science and Technology

summary:
Background: Cancer cells inevitably develop resistance to radiation in lung cancer radiotherapy. However, the underlying mechanisms remain to be fully clarified. This study aimed to explore the roles and mechanisms of FGF1 intracellular binding protein (FIBP)?in lung cancer radioresistance.
Methods: Expression levels of FIBP in human lung cancer and adjacent tissues were analyzed by immunohistochemical (IHC) staining. Cell growth and proliferation, EdU and CFSE assays, Neutral comet and clonogenic survival analysis as well as mouse xenograft model were performed to explore the functions of FIBP in vitro and in vivo. The underlying mechanisms were investigated by RNA sequencing, co-immunoprecipitation and dual luciferase reporter assays.
Results: The expression levels of FIBP in lung cancer tissues were significantly upregulated compared with adjacent normal tissues and associated with worse overall survival. Functionally, we found that depletion of FIBP impairs lung cancer progression and radioresistance in vitro and in vivo. Mechanistically, we uncovered that FIBP interacts with STAT3 to enhance the transcriptional activity of STAT3, thereby inducing the expression of downstream target gene Eme1. Importantly, we also demonstrated that the biological effects of FIBP were partially dependent on Eme1 in lung cancer.
Conclusions: These results reveal that FIBP modulates STAT3/Eme1 axis to drive lung cancer progression and radioresistance, indicating targeting FIBP may be a novel intervention strategy for lung cancer radiotherapy.

overall_design: mRNA profiles of H1299 cells and FIBP depleted cells from 3 independent samples each.

first: Yunhong

last: Xu

first: Jun

last: Li

first: Kuikui

last: Zhu

first: Sheng

last: Zhang

first: Shuangbing

first: Gang

last: Wu