title: LncRNA-miRNA-mRNA network interactions with clinicopathological outcomes in gastric cancer patients

city: Tehran

first: Ali Mohammad

last: Alizadeh

state: Tehran

address: Keshavarz Blvd, Cancer Institute, Imam Khomeini Hospital

department: Cancer institute

country: Iran

institute: Tehran University of Medical Sciences

summary:
To investigate lncRNA-miRNA-mRNA network interactions with clinicopathological outcomes in gastric cancer, microarray analysis was obtained by microRNA profiling from the patient samples. The potential target genes were then predicted by miRmap, targetscan, and miRWalk2.0. The candidate lncRNAs were collected by the LncRNA2target and TANRIC databases. The expression levels of candidate lncRNAs, miRNAs, and mRNAs were measured in tumor and normal samples using qRT-PCR and ELIZA techniques and compared with the clinicopathological outcomes.
We then performed gene expression profiling analysis using data obtained from RNA-seq of two tissue samples of gastric cancer patients.

overall_design: Comparative microRNA expression profiling analysis of RNA-seq data for differentially expressed microRNAs.

first: Zahra

last: Bagheri-Hosseinabadi

first: Solmaz

last: Khalighfard

first: Ali

first: Vahid

last: Khori

first: Sima

last: Sedighi

first: Taghi

last: Amiriani

first: Mohammad

last: Mirzaei

last: Hajizadeh


title: Genomic distribution of the cohesin subunit Stromalin (SA) in wild-type and Haspin knock-down Drosophila melanogaster Kc167 cells

status: Public on Jul 02 2022

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

summary:
Haspin is required for Drosophila SA binding to chromatin

Keywords: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq peak calling of SA  in WT and Haspin KD Drosophila melanogaster Kc167 cells

first: Ujué

last: Fresán

first: Maria

last: Rodríguez-Sánchez

last: Reina

first: M

middle: L

last: Espinàs


title: EZH2 and JARID2 change their binding profiles on RNA and DNA to promote hepatocellular carcinoma [CLIP-seq]

status: Public on Jul 04 2022

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

country: China

institute: ablife

type: Expression profiling by high throughput sequencing

summary: The molecular mechanisms of carcinogenesis have been deeply studied benefit from the highly developing biotechnologies. Here we used high throughput sequencing method to capture the global binding profiles on RNA and DNA of EZH2 and JARID2 in liver normal (THLE-2) and carcinoma (HepG2) cells, respectively. We found that EZH2 and JARID2 showed distinct binding profile in HepG2 and THLE-2 cells. By binding to the primary RNAs, bound transcripts of EZH2 and JARID2 in HepG2 showed significantly increased transcriptional level in hepatocellular carcinoma (HCC) patients. They bound transcripts were also highly related to the HCC development by performing gene set enrichment analysis (GSEA). By exploring the DNA binding profile, we also detected similar phenomena that EZH2 could increase the transcriptional level of bound genes in HepG2 cells, showing PRC2-independent functions in liver cancer cells. Integrating analysis of the RNA and DNA binding profile showed EZH2 could independent function at the transcriptional and post-transcriptional stages. In summary, we proposed that the novel regulatory functions of EZH2 and JARID2 that may promote the cancer development in carcinoma liver cells.

overall_design: We performed CLIP-seq experiment for EZH2 and JARID2 proteins in two liver cell lines, including HepG2 and THLE-2, respectively. Two biological replicates were obtained for each protein in each cell line with corresponding IgG controls.

first: Dong

last: Chen

first: Yi

last: Zhang


title: microRNA profile of extracellular vesicles derived from control vehicle- and LIPUS-induced stem cells from the apical papilla

city: Chongqing

first: Tingwei

address: 426# Songshibei Rd., Yubei District,

institute: Stomatological Hospital affiliated to Chongqing Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Low intensity pulsed ultrasound (LIPUS) is shown to promote osteogenic differentiation and antiinflammation of periodontal mesenchymal stromal cells. We found extracellular vesicles (EVs) derived from LIPUS-induced stem cells from apical papilla (SCAPs) also have stronger anti-inflammatory and osteogenic effects in vitro and in vivo. To obtain clues on whether microRNA (miR) of EVs contribute to stronger  anti-inflammatory and osteogenic effects, we analyzed miR expression in EVs from control- and LIPUS-induced SCAPs by deep sequencing. RNA-sequencing suggests that the LIPUS-EVs induce stronger osteogenic differentiation and antiinflammation by using their cargos, including upregulated osteogenic miRNAs to activate the PI3K/Akt and MAPK signaling pathways, and upregulated anti-inflammatory miRNAs to inhibit the TNF-α signaling pathways.

overall_design: EVs were isolated from control vehicle- and LIPUS-treated SCAPs (90mW/cm2, 0.5 h treatment). Equal number of EVs were subjected to microRNA analysis by deep-sequencing.

first: Ziqi

first: Jinlin

last: Song


title: DNA binding specificity for the bHLH-PAS transcription factor family

city: Adelaide

first: David

middle: C

last: Bersten

state: SA

address: Victoria Drive

department: Molecular and Biomedical Sciences

country: Australia

institute: The University of Adelaide

summary: Transcription factor-DNA interactions and their specificities have been described for many different classes of transcription factor families. However, heterodimeric transcription factor complexes still remain poorly characterised. The basic-Helix-Loop-Helix (bHLH) transcription factor family is one of the largest transcription factor families that typically bind DNA though a degenerate CANNTG elements as heterodimers or homodimers. Here we characterise the DNA binding of the bHLH - Per-Arnt-Sim (PAS) (bHLH-PAS) domain containing transcription factor family using SELEX-high-throughput sequencing coupled with quantitative computational modelling analysis. We show that most dimeric bHLH-PAS transcription factors bind to distinct core NNCGTG response elements but bind over a much larger footprint than previously characterised. Modelled DNA-protein interactions were found to correlate with structural analysis, DNA shape predictions and in vivo transcription factor occupancy.

overall_design: We determined the DNA binding specificity of the bHLH-PAS transcription factors by SELEX-seq and No-Read-Left Behind (NRLB) Protein-DNA Modelling. We purified full length human ARNT (1-774) or ARNT2 (1-717) homodimers from Expi293 cells, bHLH-PAS (PAS A and PAS B, N-terminus) heterdimers (human HIF1a(1-375)/ARNT(1-474), human HIF2a(1-353)/ARNT(1-474), human SIM1(1-348)/ARNT2(1-439) and mouse NPAS4(1-329)/ARNT2(1-481)) from baculovirus infected Sf9 insect cells or human AhR(1-287)/ARNT(1-364) from bacteria. Seven purified homo- or heterodimer complexes were incubated with SELEX libraries (Random 18mer or FixedCore (8N-CGTG-10N) 22mer) and bound DNA were separated by electrophoretic mobility assay (EMSA), followed by DNA isolation and PCR amplification. Random 18mer libraries were subjected to 3 rounds of SELEX, whereas FixedCore (8N-CGTG-10N) 22mer libraries were subjected to 1 or 2 rounds of SELEX. The Random 18mer initial library and round 3 were sequenced using a NextSeq500 1x75bp HighOutput mode yielding ~30million reads per sample. The FixedCore (8N-CGTG-10N) 22mer initial library, round 1 and round 2 were sequenced using a HighSeq2500 yielding ~30million reads per sample.

first: Murray

last: Whitelaw


title: RNASeq analysis for T-cell blasts from individuals with an AIOLOS Q402* mutation and healthy controls

status: Public on Jul 03 2022

city: Bethesda

first: Julie

middle: E

last: Niemela

state: MD

address: 10 Center Dr.

department: Dept. of Lab. Medicine

country: USA

institute: NIH Clinical center

summary: RNA-seq was performed using RNA extracted from enriched T-cell blasts for the following study groups: healthy controls (NC, n=5) and patients with AIOLOS Q402* (n=3 ). Illumina libraries were generated using the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian Components (Takara San Jose, CA). Libraries were sequenced on a Illumina HiSeq 2500 instrument using 2 x 75 bp paired-end reads, and alignment and mapping analyses were performed by the Takara Cogent NGS Analysis Pipeline v1.5.0 (also known as CogentAP). Differential gene expression analysis was performed by DESeq2 v1.32.0 [Bioconductor version: Release (3.15)].

overall_design: Comparative gene expression profiling analysis of RNA-seq data for T-cell blasts from individuals with an AIOLOS Q402* mutation and healthy controls

first: S

middle: D

last: Rosenzweig

first: H

middle: S

last: Kuehn

first: J

last: Stoddard


title: Human Transcriptomic Integrated Approach for Testing and Assessment Oral Reference Dose for Steatosis

city: apex

first: Lyle

last: Burgoon

state: nc

address: 216 kelly west dr

department: Environmental Laboratory

institute: US Army Engineer Research and Development Center

summary: Integrated Approaches to Testing and Assessment (IATA) are emerging as a means to strategically assess and test chemicals for toxicity, using existing information, and helping to identify potential data gaps. Adverse Outcome Pathways (AOPs) have recently been shown to be a good starting point for IATA development. Our interest in IATAs and AOP Networks (AOPNs) focuses on developing efficient testing and risk assessment strategies for new materials, new chemical entities, and setting environmental cleanup goals. We combine the maths logic of causality, specifically the notion of sufficiency to infer an adverse outcome, with AOPNs to develop Minimally Sufficient Sets of Key Events (MinSSKEs). These MinSSKEs represent a set of key events (can just be one key event) that taken together allow assessors to predict if an adverse outcome is likely or not. For our case study we use the military explosive trinitrotoluene (TNT). TNT is a relatively data rich chemical where the US Environmental Protection Agency has set a reference dose of 0.0005mg/kg-day, based on a point of departure for liver toxicity in dogs of 0.5mg/kg-day (a lowest observed adverse effect level; LOAEL) with uncertainty of 1,000X. Our IATA measures gene expression for genes in involved in our AOPN for energy metabolism, steatosis and oxidative stress in human induced pluripotent stem cells differentiated to hepatocytes exposed to TNT. We used a Bayesian statistical approach to identify differentially expressed genes, and a nonlinear data-driven dose-response modeling approach (Good Risk Assessment Values for Environmental Exposures; GRAVEE) to estimate points of departure for reference dose estimation. We obtained an RfD of 0.12mg/kg-day, with a 90% credible interval spanning from 0.02-0.19mg/kg-day using our IATA approach. Our RfD is based on a POD of 1.22mg/kg-day with a 90% credible interval spanning from 0.24-1.94mg/kg-day, and uncertainty of 10X after applying the IRIS uncertainty factors. Our PODs are highly comparable, with a difference of only 0.72mg/kg-day (or 2.44x). Our RfDs differ by 240x, owing to the fact that we have only a 10x uncertainty factor for human variability, whereas the IRIS assessment uses 1000x uncertainty for 10x animal-to-human extrapolation, 10x LOAEL-to-NOAEL extrapolation, and 10x for subchronic-to-chronic extrapolation. In this case study, our IATA resulted in a highly similar POD compared to the IRIS assessment, and an overall decrease in the uncertainty factors that needed to be applied. Our IATA approach worked well in this instance, and demonstrated several advantages by focusing on using a human-relevant in vitro model, data-driven POD modeling, and a net decrease in the overall risk assessment uncertainty factors, while maintaining the uncertainty associated with the data.

overall_design: Total RNA was extracted from approximately 1.92x10^5 iPSC hepatocytes per replicate (4 replicates per TNT concentration and vehicle control, 1%DMSO).

first: Keri

last: Donohue

first: Anne

last: Mayo

first: Natalia

last: Vinas

first: Mitchell

last: Wilbanks

first: Edward

middle: J

last: Perkins


title: Reactive Oxygen Species promote Pyroptosis of Nucleus Pulposus Cells in Modic changes with disc herniation based on smart-RNA sequencing

city: Beijing

first: Lei

last: Yue

state: Beijing

address: 8th Xishiku AVe, Peking University First Hospital

department: Orthopaedics

institute: Peking University First Hospital

summary: We performed Smart-seq 2 and analyzed the differential expression of genes and pathways of Modic change to comparator group. Additionally, we detect the role of reactive oxygen species on pyroptosis of NP.

overall_design: NPs were isolated from 10 human herniated lumbar discs, including five with Modic change and five with degeneration, and then subjected to Smart-seq 2.

first: Haoyong

last: Fu

first: Yuetian

last: Wang

first: Haolin

last: Sun


title: Differential expression Profiles of microRNAs in PBMC specimen from tuberculosis patients and normal volunteers

city: ChongQing

first: min

last: xiao

address: xinqiao main street No.183

institute: XinQiao hospital

summary:
Purpose: To investigate the role and mechanism of microRNAs in tuberculosis.
Methods: microRNAs sequencing were performed to screen differential expressed microRNAs in PBMC specimen between tuberculosis patients and normal volunteers.
Results: A total of 1560 distinct microRNAs were identified in these samples, and 788 of these microRNAs were upregulated and 772 microRNAs were downregulated.
Overall design: Tuberculosis differential expression Profiles of microRNAs in PBMC were generated by high throughput sequencing, using Illumina Hiseq2000/2500.

overall_design: Human PBMC samples are analyzed,5 tuberculosis patients together with 5 normal volunteers are included.

first: Min

last: Xiao

first: Xu

first: Hui

last: Lin

first: Shiming

last: Yang


title: LncRNA expression in the formation of carotid plaque caused by atherosclerosis

status: Public on Jul 01 2022

city: Shanghai

first: Qu

last: LeFeng

address: Huangpu District Fengyang Road

department: Department of Vascular and Endovascular Surgery

institute: Second Affiliated Hospital of Naval Medical University

summary: Atherosclerotic plaques belong to the common vascular disease in the aged, which rupture will lead to acute thromboembolic diseases, the major reason for fatal cardiovascular events. Accumulating evidence indicates that lncRNAs exert critical functions in atherosclerosis. To identify novel astherosclerotic plaques-relevant lncRNAs,  four specimens of carotid atherosclerotic plaque were collected, and endovascular tissue one centimeter far from the carotid atherosclerotic plaque was taken as a control group, we performed lncRNA microarray analysis using Affymetrix Human OElncRNA

overall_design: LncRNA expression profiling analysis of 8 samples including 4 carotid atherosclerotic plaque tissues and endovascular tissue one centimeter far from the carotid atherosclerotic plaque tissues by Affymetrix Human OElncRNA.

first: Feng

last: Qu

first: Jin

last: Wu


title: NOTCH1 signaling during CD4+ T-cell activation alters transcription factor networks and enhances antigen responsiveness [CULTURED_NCT07]

city: Seattle

first: Scott

middle: N

last: Furlan

address: 1100 Fairview Ave N

institute: CRD

summary: Adoptive transfer of T cells expressing chimeric antigen receptors (CAR-T) effectively treats refractory hematologic malignancies in a subset of patients but can be limited by poor T-cell expansion and persistence in vivo. Less differentiated T-cell states correlate with the capacity of CAR-T to proliferate and mediate antitumor responses, and interventions that limit tumor-specific T-cell differentiation during ex vivo manufacturing enhance efficacy. NOTCH signaling is involved in fate decisions across diverse cell lineages and in memory CD8+ T cells was reported to upregulate the transcription factor FOXM1, attenuate differentiation, and enhance proliferation and antitumor efficacy in vivo. Here, we used a cell-free culture system to provide an agonistic NOTCH1 signal during naïve CD4+ T-cell activation and CAR-T production and studied the effects on differentiation, transcription factor expression, cytokine production, and responses to tumor. NOTCH1 agonism efficiently induced a stem cell memory phenotype in CAR-T derived from naïve but not memory CD4+ T cells and upregulated expression of AhR and c-MAF, driving heightened production of interleukin-22 (IL-22), IL-10, and granzyme B. NOTCH1-agonized CD4+ CAR-T demonstrated enhanced antigen responsiveness and proliferated to strikingly higher frequencies in mice bearing human lymphoma xenografts. NOTCH1-agonized CD4+ CAR-T also provided superior help to cotransferred CD8+ CAR-T, driving improved expansion and curative antitumor responses in vivo at low CAR-T doses. Our data expand the mechanisms by which NOTCH can shape CD4+ T-cell behavior and demonstrate that activating NOTCH1 signaling during genetic modification ex vivo is a potential strategy for enhancing the function of T cells engineered with tumor-targeting receptors.

overall_design: 18 samples (9 controls)

first: Alec

middle: B

last: Wilkens

first: Stanley

middle: R

last: Riddell


title: Allelic Polymorphism Gates Autoreactivity and Vaccine-Elicitation of Human Broadly Neutralizing Antibodies Against Influenza Virus

city: Cambridge

first: Maya

last: Sangesland

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT, and Harvard

summary: Human broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin stalk of group 1 influenza A viruses (IAVs) are biased for IGHV1-69 alleles that use phenylalanine (F54) but not leucine (L54) within their CDRH2 loops. Despite this, we demonstrate that both alleles encode for human IAV bnAbs that employ structurally convergent modes of contact to the same epitope. To resolve differences in lineage-expandability, we compared F54 vs L54 as substrate within humanized mice where antibodies develop with human-like CDRH3 diversity but are restricted to single VH-genes. While both alleles encoded for bnAb precursors, only F54 IGHV1-69 supported elicitation of heterosubtypic serum bnAbs following immunization with a stalk-only nanoparticle vaccine. L54 IGHV1-69 was unproductive, co-encoding for anergic B cells and autoreactive stalk antibodies that were cleared from B cell memory. Moreover, human stalk antibodies also demonstrated L54-dependent autoreactivity. IGHV1-69 polymorphism, which is skewed ethnically, therefore gates tolerance and vaccine-expandability of influenza bnAbs.

overall_design: Examination of antibody CDRH3 diversity within transgenic mice restricted to human IGHV1-69 F54 and L54 alleles.

first: Larance

last: Ronsard

first: Daniel

last: Lingwood


title: Combined MEK and JAK/STAT3 pathway inhibition effectively decreases medulloblastoma tumor progression.

city: Winnipeg

first: Tamra

last: Werbowetski-Ogilvie

state: Manitoba

address: 611-745 Bannatyne Avenue

department: Biochemistry & Medical Genetics

country: Canada

institute: University of Manitoba

summary: RNA sequencing was carried out to identify the signaling pathways and hallmarks that change following MEK and/or JAK/STAT3 pathway inhibition.

overall_design: (1) 2.5x10^5 UI226 cells were injected into the cerebellums of NOD SCID mice. Mice were treated with either vehicle controls of selumetinib twice daily (drug holiday on the weekend) via oral gavage. Tumor were extracted at endpoint and human cells were isolated by FACS with HLA. Human cells from vehicle and selumetinib treated xenografts were subject to RNA-seq. (2) We performed RNA sequencing on selumetinib and/or pacritinib treated UI226 tumorspheres (N=4-6 biological replicates for each condition) to characterize the sustained transcriptomic changes 5 days following treatment in vitro. Tumorspheres were treated with vehicle, selumetinib only, pacritinib only or selumetinib + pacritinib


title: Profiling of human monoclonal antibodies targeting SARS-CoV-2 Omicron variant

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

summary: We generated LNP-mRNA encoding B.1.1.529 SARS-CoV-2 spike, and intramuscularly administered it in a human IgG and IgK knock-in mouse. Single cell VDJ-seq unveiled the sequences of human monoclonal antibodies targeting the B.1.1.529 SARS-CoV-2 spike protein.

overall_design: Three sets of B cells were isolated and processed from the spleen, lymph nodes, bone marrows, or peripheral blood of the immunized mouse and then analyzed by scVDJ-seq.

first: Paul

middle: A

last: Renauer


title: Regional idiopathic pulmonary fibrosis airway epithelial cultures; Primary airway epithelial cells co-cultured with human lung fibroblasts

city: Aurora

first: Ivana

state: CO

address: 1635 Aurora Ct

institute: University of Colorado

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

overall_design: Refer to individual Series


title: Single cell sequencing of murine hepatic CD45+ cells from mice transplanted with Trem2-deficient or wild-type bone marrow with NASH

city: Vienna

first: Christoph

last: Binder

address: Lazarettgasse 14

department: Laboratory Medicine

country: Austria

institute: Medical University of Vienna

summary: We report the single cell transcriptome of CD45+ cells from the livers of bone marrow chimeric wildtype mice with NASH that had previously been transplanted with bone marrow from TREM2-deficient or wildtype littermate mice. We show that hematopoietic TREM2 deficiency is associated with alterations in the hepatic immune cell composition in the context of NASH.

overall_design: Male C57Bl6/J mice were lethally irradiated and transplanted with bone marrow from Trem2-/- or Trem2+/+ littermates. Following 6 weeks recovery, mice were placed on a methionine/choline-deficient (MCD) diet for 4 weeks to induce non-alcoholic steatohepatitis (NASH). Live (7AAD-) CD45+ cells were sorted from the livers of these mice and pooled in equal proportions from 4 mice per group, which were subsequently subjected to 5' single cell sequencing.

first: Tim

last: Hendrikx

first: Florentina

last: Porsch

first: Mate

middle: G

last: Kiss

first: Dragana

last: Rajcic

first: Nikolina

last: Papac-Milicevic

first: Constanze

last: Hoebinger

first: Laura

last: Goederle

first: Anastasiya

last: Hladik

first: Lisa

last: Shaw

first: Hauke

last: Horstmann

first: Sylvia

last: Knapp

first: Sophia

last: Derdak

first: Martin

last: Bilban

first: Lena

last: Heintz

first: Marcin

last: Krawczyk

first: Rafael

last: Paternostro

first: Michael

last: Trauner

first: Matthias

last: Farlik

first: Dennis

last: Wolf


title: Monocyte-derived alveolar macrophages autonomously determine severe outcome of respiratory viral infection

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

country: Switzerland

institute: ETH Zürich


title: Antigen presentation by B cells enables epitope spreading across an MHC barrier

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

summary: A progressive increase in the breadth and specificity of autoantibodies over time, termed epitope spreading, drives pathogenic targeting of an ever-widening repertoire of self-components in many autoimmune diseases. Ostensibly, this progressive inclusion of additional B cell clones into an ongoing autoreactive response can occur through linked recognition, whereby proto-autoreactive B cells recognize distinct antigenic epitopes, which carry shared T cell epitopes. In a murine model displaying epitope spreading resembling that observed in systemic lupus erythematosus, we find that the epitope spreading process is compartmentalized by MHC. Antigen presentation by B cells carrying two MHC haplotypes can bridge the MHC barrier between two compartments of B cells that do not share MHC haplotypes, by communicating with two separate pools of MHC-restricted T cells. This leads to inclusion of distinct and diverse B cell reactivities in germinal centers. Our findings demonstrate a formidable capacity of B cells to drive the autoreactive response.

overall_design: To better understand the immune landscape of the ‘no-bridge’ and ‘bridge’ chimeras, we leveraged the BD Rhapsody platform to perform linked single-cell Abseq, immune profiling and BCR/TCR analyses. We analyzed total splenocytes from two no-bridge chimeras, and total splenocytes enriched for GC B cells from a bridge chimera.

first: Søren

last: Degn


title: Mitochondria-targeted partial inhibiton of complex I increase health and lifespan in aged male and female mice.

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

summary: We performed next-generation RNA sequencing (RNA-seq) using brain and fat tissue from 26 months old vehicle and CP2-treated (wild-type) WT mice.

overall_design: mRNA profiles of 26 months old Veh-treated and CP2 (mitochondrial complex I  inhibitor)-treated WT mice were generated by deep sequencing, using Illumina HiSeq 4000 with paired end 101-bp read length.

first: Eugenia

last: Trushina


title: Methylated RNA immunoprecipitation sequencing in the Kasumi-1 cell line treated with CoCl2 and echinomycin

first: Xiao-ning

last: Gao

address: 28 Fuxing Road

department: Department of Hematology

institute: Chinese PLA General Hospital

summary: To evaluate the role of HIF1α in modulating the m6A abundance, we conducted m6A sequencing in the Kasumi-1 cell line treated with CoCl2 and echinomycin. CoCl2 can mediate the stabilization of HIF1α protein. Echinomycin is a small-molecule inhibitor of HIF1α, which functions through sequence-specific binding to HRE to competitively inhibit HIF1α binding to its target genes. The m6A sequencing results  of the Kasumi-1 cell line treated with CoCl2 and non-treated control were uploaded previously (GSE168778). The differential m6A peaks analysis between CoCl2 + echinomycin group and CoCl2 group was performed.

overall_design: Kasumi-1 cells were treated with 100 uM CoCl2 and 10 nM echinomycin for 24 hours.  A total of 3 biological replicates were performed.


title: The shelterin-dependent recruitment of Stn1-Ten1 ensures replication of hard to replicate subtelomeric regions in fission yeast

city: Marseille

first: Karel

last: Naiman

address: BD Lei Roure

country: France

institute: CRCM

summary: Efficient replication of terminal sequences is crucial to maintain telomere stability. In fission yeast, the Taz1 protein, the TRF1-2 homolog, plays a prominent role in telomere replication. We and others have shown that the Stn1-Ten1 (ST) complex fulfills important function in telomeres and subtelomeres maintenance, however its function is not fully understood. Here, we analyzed genome-wide replication dynamics using the polymerase usage sequencing (PuSeq) allowing to assess polymerase usage across the genome. We show that the ST complex and Taz1 are crucial for the replication of the STE2-3 subtelomeric region. Both, the ST complex and Taz1, bind specifically to this region and the function of the ST complex relies on its association with the shelterin complex. Strikingly, when the ST complex is compromised, an HR-based fork restart mechanism becomes necessary to ensure replication of the STE2-3 region. Finally, we demonstrate that the firing of an origin, that is controlled by Rif1, within subtelomeric regions circumvents the replication defect of subtelomeres. Overall, we demonstrate that the ST complex is actively recruited at subtelomeres by the shelterin and this ensures replication of the STE2-3 region which exhibits specific features of a hard-to-replicate region.

overall_design: We mapped ribonucleotide-incorporation by the mutated DNA polymerase delta and epsilon at single-nucleotide resolution and used the data for following replication dynamics by subsequent informatics analysis.

first: Mélina

last: Vaurs

first: Chainez

last: Bouabboune

first: Rai

last: Sudhir

first: Katarzyna

last: Ptasinska

first: Marion

last: Rivers

first: Samah

last: Matmati

first: Antony

middle: M

last: Carr

first: Vincent

last: Géli

first: Stéphane

last: Coulon


title: RNA-Seq analysis of IL-23 induced skin transcriptome

city: Sacramento

first: Cuong

middle: T

last: Nguyen

state: CA

address: 2425 Stockton Blvd

department: Internal Medicine

institute: University of California, Davis

summary: We performed RNA-Seq analysis and compared three groups 1) WT+IL-23 v. WT+GFP (control), 2) Mdl1-/-+IL-23 v. WT+GFP (control), and 3) WT+IL-23 v. Mdl1-/-+IL-23. Sets of differentially expressed genes (DEG) were defined on the basis of standard thresholds i.e. a |log2FC|≥2 combined with an adjusted p-value≤0.01 against the control group. Differential expression analysis revealed 1171 (619 up-regulated and 552 down-regulated) DEGs in WT+IL-23 v. WT+GFP, 414 (303 up-regulated and 111 down-regulated) DEGs in Mdl1-/-+IL-23 v. WT+GFP, and 260 (122 up-regulated and 138 down-regulated) DEGs in WT+IL-23 v. Mdl1-/-+IL-23

overall_design: Define the transcriptomic profile of IL-23-induced skin inflammation regulated by MDL-1

first: Iannis

last: Adamopoulos


title: Loss of hepatic DRP1 exacerbates alcoholic hepatitis by inducing megamitochondria and mitochondrial maladaptation

city: Kansas City

first: Hong-Min

last: Ni

state: KS

address: 3901 Rainbow Blvd, MS-1018

department: Pharmacology, Toxicology and Therapeutics

institute: University of Kansas Medical Center

summary:
To investigate the function of mitochondrial fission protein DRP1 in the development of alcoholic liver disease, we generated liver-specific Dnm1l KO mice using Alb-Cre/loxP system. These mice were subjected to Gao-Binge alcohol model.
We then performed RNA sequensing analysis using the liver tissue. Gene expression profiling analysis was conducted using data obtained from RNA-seq of 4 different groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for L-DRP1 KO and its WT mice in both control and ethanol feeding conditions.

first: Wen-Xing

last: Ding

first: Xiaowen

last: Ma

first: Wanqing

last: Liu

first: Xiaokun

last: Wang


title: Effect of depletion of Smarca4 on gene expression of alcoholic liver disease

city: nanjing

first: li

state: Jiangsu

address: Longmian Avenue

department: Basic Medicine College

institute: nanjing medical university

summary: To investigate the  the role of Smarca4 in the regulation of alcoholic liver disease, we established Albcre,Smarca4fl/fl mice.

overall_design: We then performed gene expression profiling analysis using data obtained from  WT and KO livers

first: Li

first: Xu

last: Yong


title: Effects of knocking down RNP1A on gene expression in Dictyostelium discoideum

city: Baltimore

first: Yinan

address: 725 North Wolfe Street, Physiology Builiding Rm.100

department: Cell Biology

institute: Johns Hopkins University School of Medicine

summary: To investigate the function of RNP1A, an RNA-binding protein in Dictyostelium discoideum

overall_design: Comparative gene expression analysis of RNA-seq data from two independent rnp1A knockdowns (control + rnp1A knockdown cell lines)

first: Douglas

last: Robinson


title: Prognostic Liver Signature for NAFLD (PLS-NAFLD) profiles of cell-based PLS system treated with free fatty acids (FFA) and IDO1 inhibitor, epacadostat.

city: Tsu city

first: Naoto

last: Fujiwara

state: Mie

address: 2-174 Edobashi

country: Japan

institute: Mie University

summary: Non-alcoholic fatty liver disease (NAFLD), alongside the global obesity epidemic, is rapidly emerging as a dominant liver disease etiology that leads to progressive liver fibrosis, its terminal stage, cirrhosis, and hepatocellular carcinoma (HCC). We identified and validated a 133-gene signature (Prognostic Liver Signature for NAFLD [PLS-NAFLD]) to predict long-term HCC risk in patients with NAFLD. By analyzing PLS-NAFLD, IDO1 was identified as a potenial chemopreventive target for HCC from NAFLD. To test this hypothesis, we utilized our clinical-prognostic-signature-inducible cell culture model. We first confirmed that free fatty acid treatment (800 μM oleic acid and 400 μM palmitic acid) can induce PLS-NAFLD, then IDO1 inhibitor, epacadostat, can reverse the high-risk pattern in a dose-dependent manner.

overall_design: Co-cultuered DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif) and LX2 cell were exposed to FFA (800 μM oleic acid and 400 μM palmitic acid) or mock, then treated with IDO1 inhibitor, epacadostat, or DMSO to maesure modulation of Prognostic Liver Signature for NAFLD.

first: Emilie

last: Crouchet

first: Thomas

last: Baumert

first: Yujin

last: Hoshida


title: Transcriptome profiling reveals novel gene networks regulating tooth regeneration in sharks

city: Newcastle upon Tyne

first: Katherine

last: James

address: Urban Sciences Building

department: School of Computing

country: United Kingdom

institute: Newcastle University

summary: The dentition of elasmobranchs (sharks, skates and rays) is uniquely productive, capable of both rapid and continuous, lifelong regeneration. Elasmobranchs represent an important group of vertebrates with a deep evolutionary history, possessing several ancient and basal characters, i.e., the continuously regenerative dentition from a specialized dental lamina. The dental lamina is an expanded component of the oral epithelia that is responsible for initiating and producing new teeth among all toothed-vertebrates. In sharks, this dynamic epithelial unit is permanent and continuous – meaning it extends to cover the entirety of each jaw (jaw-wide) and develops early during embryogenesis and retained to produce teeth for the life of the shark. It is rare for a truly embryonic vertebrate tissue to be retained for its original function for the life of the organism. The dental lamina in sharks is unique and houses teeth in a developmental series from the deepest part, where teeth are initiated, through stages of tooth development in the form of a related, family of teeth to eruption and functionality of the advanced teeth at the jaw margin. How teeth are made and regenerated is an important question in vertebrate biology; here we investigated this question in the small spotted catshark (Scyliorhinus canicula), a new model in the field of developmental biology. Specifically, we divided the shark dental lamina into stage-compartments as follows: (i) the initiation site – the successional lamina (SL); (ii) the early developing teeth (ET); (iii) the late stage developing teeth (LT); (iv) the tooth-taste junction between the superficial oral and dental epithelium at the jaw margin that separates the taste territory and the dental lamina proper (TTJ); and basi-hyal oral epithelium that is strictly non-dental and only contains taste buds (BHTB). These 5 compartments each house both a shared and unique signature of gene transcripts. This study aims to understand the transcriptomic basis of continuous tooth regeneration in the shark. In this study we combine X-ray computed tomography, classic histology, insitu hybridization, immunohistochemistry, and functional assays of novel markers, and de novo and genome guided transcriptome assemblies for each of these 5 dental lamina compartments of the hatchling (stage 34) catshark (S. canicula).

overall_design: We produced both a de novo and genome-guided transcriptome assembly and expression analysis of the 5 dental lamina compartments (SL, ET, LT, TTJ and BHTB) of developing dentition in the hatching-stage (stage 34) small-spotted catshark (Scyliorhinus canicula).

first: Gareth

last: Fraser

first: Zerina

last: Johanson


title: hPSC-derived Sacral Neural Crest Enables Rescue in a Severe Model of Hirschsprung’s Disease [RNA-seq]

city: New York

first: YUJIE

last: FAN

state: New York

address: 430 E 67th St

institute: Memorial Sloan Kettering Cancer Center; Weill Graduate School of Medical Sciences of Cornell University

summary: The enteric nervous system (ENS) is derived from both the vagal and sacral component of the neural crest (NC). Here, we present the derivation of sacral ENS precursors from human PSCs via timed exposure to FGF, WNT and to GDF11 to enable posterior patterning and transition from posterior trunk to sacral NC identity respectively. Using a SOX2::H2B-tdTomato/ T::H2B-GFP dual reporter hPSC line, we demonstrate that both trunk and sacral NC emerge from a double-positive neuro-mesodermal progenitor (NMP). Vagal and sacral NC precursors yield distinct neuronal subtypes and migratory behaviors in vitro and in vivo. Remarkably, xenografting of both vagal and sacral NC lineages is required to rescue a mouse model of total aganglionosis, suggesting novel opportunities in the treatment of severe forms of Hirschsprung’s disease.

overall_design: RNA seq data and ATAC seq data of a series of samples collected at different time points, comparing cells treated with or without GDF11

first: Yujie

last: Fan


title: Electronic vaping preferentially target respiratory bronchioles leading to severe bronchiolitis in experimentally-exposed macaques

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

summary: Electronic cigarette use has increased dramatically over the past three years, despite numerous reports of acute lung injury and even death.   In this report we provide evidence from a nonhuman primate model for Electronic Vapor-Induced Lung Injury (EVALI), demonstrating significant lung pathology from electronic vaping (EV).  Here we characterized the particle size and pathogenic effects induced by EV exposure of nonhuman primates using the commercial nicotine JUUL® pod modular devices.  Vaping aerosols appear to preferentially and exclusively target the bronchioles while bypassing larger bronchi.  We demonstrate a significantly smaller particle size, generated by the EV device relative to combustion product aerosols produced by conventional cigarettes.   Histopathologically, vaping aerosols appear to preferentially and exclusively target the bronchioles while bypassing larger bronchi which is consistent with a significanlty smaller particle size compared to cigarette smoke.   Our immunohistochemical and RNAseq studies provide further evidence for severe small airway inflammation and dysregulation of gene expression within immune cells derived from bronchial lavage, respectively.  Our findings raise major concerns regarding the safety of e-cigarettes, and provide a mechanism for the preferential induction of lung injury by EV.  Our results, in a species whose lung architecture is the closest possible approximation of that of a human adolescent, suggest the danger of the EV device itself and resultant small particulate aerosols produced, preferentially entering and damaging a highly susceptible part of the respiratory system.

overall_design: RNA-seq

first: Chad

last: Roy

middle: K


title: RNA-seq of THP-1 cells stimulated with CpG-c and Hydroxychloroquine intervention

city: hefei

last: zhou

state: anhui

address: NO.17 lujiang road

department: the first affiliated hospitail of USTC

institute: University of Science and Technology of China

summary:
Purpose: To investigate the inhibition of inflammatoty cytokines of Hydroxychloroquine to phagocytic THP-1 cells.
Methods: we established a cell model of  hemophagocytosis by simulating THP-1 cells with CpG-c for 24h in vitro to produce macrophages, and then coculture the cells with human RBCs. RNA sequencing analysis of THP-1 cells were performed to find  Gene changed with CpG-c stimulation and Hydroxychloroquine intervention.
Results:CpG-c sitimulation significantly altered gene expression of THP-1 cells. Cytokine genes were upregulated, especially a significant increase in IL-6 level from scratch. HCQ significantly inhibited the expression of inflammatory cytokines and decreased IL-6 gene level to baseline.
Conclusions:Hydroxychloroquine can inhibite cytokine genes, especially IL-6 Gene level of THP-1 cells caused by CpG-c sitimulation.

overall_design: THP-1 cells (5 × 10e5 cells) were cultured with 3 μM CpG-c (ODN-2395)  or PBS for 24 h to produce macrophages(CpG-c group) or control THP-1 cells(control group). Human RBCs (1 × 10^7 cells) were added to the system to perform haemophagocytosis for 3 h. Hydroxychloroquine  (10 mg/μL) was administered to inhibit phagocytosis for 3 h(CpG-HCQ group).

last: Zhou

first: Huiru

first: Haiming

last: Wei


title: The effect of Bailing Capsule on gene expression in rat kidney

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

overall_design: We performed microarray analyses of Bailing Capsule-treated rats kidney

first: Xinhua

last: Xiao

first: Jia

last: Zheng

first: Ming

last: Li

first: Miao

last: Yu

first: Fan

last: Ping

first: Tong

last: Wang

first: Xiaojing


title: Redefining electrical stimulation safety using spatial transcriptomics

city: East Lansing

first: Quentin

middle: Alexander

last: Whitsitt

state: Michigan

address: 775 Woodlot Dr.

department: Biomedical Engineering

institute: Michigan State University

summary: Current standards for safe delivery of electrical stimulation to the central nervous system are based on foundational studies which examined post-mortem tissue for histological signs of damage. This set of observations and the subsequently proposed limits to safe stimulation, termed the “Shannon limits,” allow for a simple calculation (using charge per phase and charge density) to determine the intensity of electrical stimulation that can be delivered safely to brain tissue. In the three decades since the Shannon limits were reported, advances in molecular biology have allowed for more nuanced and detailed approaches to be used to expand current understanding of the physiological effects of stimulation. Here, we investigated spatial transcriptomics as a new approach to assess the safety and efficacy of electrical stimulation in the brain. Electrical stimulation was delivered to the rat visual cortex with either acute or chronic electrode implantation procedures (acute: tissue collection 3 hours post-stimulation on the day of surgery; chronic: stimulation delivered 1-month post-implantation, and tissue collection 24 hours later). To explore the influence of device type and stimulation parameters, we used carbon fiber ultramicroelectrode arrays (7 µm diameter) and microwire electrode arrays (50 µm diameter) delivering charge and charge density levels selected above and below reported tissue damage thresholds (range: 2-20 nC, 0.1-1 mC/cm2). Spatial transcriptomics was performed using Visium Spatial Gene Expression Slides (10x Genomics), which enabled simultaneous immunohistochemistry and spatial transcriptomics to directly compare traditional histological metrics to transcriptional profiles within each tissue sample. Our data revealed unique spatial patterns of differentially expressed genes that are related to cellular processes including inflammation, cell cycle progression, and plasticity. Effects were dependent on stimulation parameters and were localized to both traditional and ultra-small device locations. The abundance of data gathered using this approach allows for sophisticated analysis that can be used to generate new hypotheses while also revealing novel potential biomarkers of neurostimulation.

overall_design: 10 micron tissue section from Long-evans rat visual cortex ~600 microns deep

first: Beomseo

last: Koo

first: Mahmut

last: Celik

first: Blake

last: Evans

first: Erin

last: Purcell

first: James

last: Weiland


title: Metabolic reprogramming of skeletal muscle by resident macrophages points to CSF1R inhibitors as muscular dystrophy therapeutics

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

institute: University of British Columbia

overall_design: Refer to individual Series


title: Monocyte-derived alveolar macrophages autonomously determine severe outcome of respiratory viral infection [scRNA-seq]

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

institute: ETH Zürich

summary: Various lung insults can result in replacement of resident alveolar macrophages (AM) by blood monocyte-derived (BMo)-AM. However, the dynamics of this process and its long-term consequences for respiratory viral infections remain unclear. Using several mouse models and a marker to unambiguously track fetal monocyte-derived (FeMo)-AM and BMo-AM, we established the kinetics and extent of replenishment and their function to recurrent influenza virus (IAV) infection. Massive loss of FeMo-AM resulted in rapid replenishment by self-renewal of survivors followed by generation of BMo-AM, which progressively outcompeted FeMo-AM over several months due to increased glycolytic and proliferative capacity. The presence of both naïve and experienced BMo-AM conferred severe pathology to IAV infection, which was associated with a pro-inflammatory phenotype. Furthermore, upon aging of naïve mice, FeMo-AM are gradually replaced by BMo-AM, which contribute to IAV disease severity in a cell autonomous manner. Taken together, our results suggest that origin rather than training of AM determines long-term function to respiratory viral infection and provide an explanation for increased severity in elderly.

overall_design: Monocytes and macrophages were sorted from lung of mice infected with influneza A virus at different timepoint. ScRNAseq was performed to trace fate of different cell over time using trajectory analysis.

first: Fenqqi

first: Federica

last: Piattini

first: Lea

last: Pohlmeier

last: Feng

first: Hubert

last: Rehrauer


title: Genome-wide maps of H3K36me3 ChIP-seq state in lung smooth muscle cells

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To examine the effects of Tet3-inactivation on genome-wide transcriptional fidelity, we determined the binding profiles of H3K36me3, a specific form of H3K36me3 that marks transcriptional elongation sites, by ChIP-seq analysis.

overall_design: Examination of control and Tet3-inactivation smooth muscle cells.

last: Wu

first: Stefan

last: Guenther

first: Thomas

last: Braun


title: Effect of IL-1a-deficiency on neutrophil gene expression during P. aeruginosa infection of the corneas

city: Irvine

first: Morgan

last: Dragan

address: D288 Medical Sciences I

department: Biological Chemistry

institute: UC Irvine

summary: We found enhanced bacterial killing and less disease in Il1a-/- corneas compared to WT when infected with PAO1. To investigate the mechanism downstream of IL-1R1, we compared the transcriptomic profile of neutrophils isolated from WT or Il1a-/- infected corneas.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and Il1a-/- neutrophils FACS isolated from PAO1-infected corneas at 24 hours post infection.

first: Eric

last: Pearlman

first: Bridget

last: Ratitong


title: Transcriptome profile of liver biopsy tissues from patients with non-alcoholic fatty liver disease (derivation set).

first: Naoto

last: Fujiwara

summary: Non-alcoholic fatty liver disease (NAFLD) is a major global health problem with its high prevalence and risk of developing lethal complications, progressive liver fibrosis and hepatocellular carcinoma (HCC), the only rising cancer mortality in the U.S. For early HCC detection to improve the dismal prognosis, there is an urgent unmet need to identify a subset of NAFLD patients with elevated risk of HCC. Herein, we derived a hepatic-transcriptome-based NAFLD-specific HCC risk biomarker, PLS-NAFLD, and validated it in two independent cohorts of HCC-naive and experienced NAFLD patients..

overall_design: Liver biopsy tissues were obtained at the time of ablating NAFLD-related HCC tumors and subjected for RNA isolation and genome-wide transcriptome profiling with RNA-Seq.

first: Shijia

last: Zhu

first: Yujin

last: Hoshida


title: Transcriptome analysis of primary airway epithelial cells co-cultured with human lung fibroblasts

city: Aurora

first: Ivana

last: Yang

address: 1635 Aurora Ct

institute: University of Colorado

summary: To determine the effects of fibroblast crosstalk on healthy airway epithelial cells, we performed RNA sequencing on isolates from airway epithelial cells co-cultured with control and idiopathic pulmonary fibrosis (IPF) fibroblasts.

overall_design:
Primary airway epithelial cells from healthy control donors were cultured at air-liquid interface with human fibroblasts isolated from either control or IPF lungs. Mono-cultures of control and IPF airway epithelial cells were used for comparison. RNA was isolated from epithelial cells only at various timepoints. Illumina TruSeq library prep was performed on 500 ng from each sample and ran on the NovaSEQ 6000 with 80 million reads per sample.
Raw data not provided due to patient privacy concerns.

first: Jacob

last: Michalski

first: Ian

last: Stancil

middle: V

first: David

last: Schwartz


title: SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression [ATAC-seq]

city: Vienna

last: Kubicek

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: We have found that loss of SMNDC1 (Survival Motor Neuron Domain Containing 1), a component of the spliceosome complex, in both murine alpha cells and human islets is capable of inducing an overall increase in beta cell markers and activating insulin transcription.

overall_design: ATAC-seqs in alphaTC1 cells (murine alpha cell line) 5 days after transduction with either an Smndc1 or Atrx-targeting shRNA.

first: Tamara

last: Casteels

first: Jiri

last: Reinis


title: Transcriptome profile of liver biopsy tissues from patients with non-alcoholic fatty liver disease (tissue validation set 1).

city: Dallas

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Non-alcoholic fatty liver disease (NAFLD) is a major global health problem with its high prevalence and risk of developing lethal complications, progressive liver fibrosis and hepatocellular carcinoma (HCC), the only rising cancer mortality in the U.S. For early HCC detection to improve the dismal prognosis, there is an urgent unmet need to identify a subset of NAFLD patients with elevated risk of HCC. Herein, we derived a hepatic-transcriptome-based NAFLD-specific HCC risk biomarker, PLS-NAFLD, and validated it in two independent cohorts of HCC-naive and experienced NAFLD patients.

overall_design: Liver biopsy tissues were obtained from 106 HCC-naive NAFLD patients (164 biopsy tissues, including 1st biopsy for all patients and 2nd follow-up biopsy for 58 PLS-NAFLD high-risk patients), and used for RNA isolation and genome-wide transcriptome profiling by RNA-Seq.


title: Iron limitation in M. tuberculosis has broad impact on bacterial metabolism revealing alternative routes to novel therapeutics

city: Ithaca

first: Monique

last: Theriault

state: NY

address: 930 Campus Rd C5-105 VMC, Cornell University

department: Microbiology and Immunology

institute: Cornell University

summary: Mycobacterium tuberculosis (Mtb), the cause of the human pulmonary disease tuberculosis (TB), contributes to approximately 1.5 million deaths every year. Prior work has established that lipids serve as the primary carbon and energy source for Mtb in vivo and fulfill major roles in Mtb physiology and pathogenesis. We conducted a high-throughput screen to identify novel inhibitors of Mtb survival in its host macrophage. One of the hit compounds identified in this screen, sAEL057, demonstrated highest activity on Mtb grown in conditions where cholesterol was the primary carbon source. Transcriptional and functional data indicate that sAEL057 limits Mtb’s access to iron by acting as an iron chelator. Furthermore, pharmacological and genetic inhibition of iron acquisition led to dysregulation of cholesterol catabolism, revealing a previously unappreciated linkage between these pathways. These results identify a vulnerability in Mtb’s metabolic programming and physiology that could be targeted for therapeutic purposes.

sample_organism:
Mycobacterium tuberculosis
Homo sapiens

platform_organism:
Mycobacterium tuberculosis
Homo sapiens

overall_design: Examination of transcriptional profile of Mtb grown in primary macrophages or cholesteterol media. Dual Seq: three biological replicates. Cholesterol RNA-seq: two biological replicates

first: Davide

last: Pisu

first: Kaley

last: Wilburn

first: Gabrielle

last: Le-Bury

first: Case

middle: W

last: MacNamara

first: Michael

middle: H

last: Petrassi

first: Jeremy

last: Rock

first: Brian

last: VancerVen

last: Russell


title: Genome-wide maps of ESR2 chromatin state in Mantle cell lymphoma cells

city: Stockholm

first: Dan

last: Huang

address: Neo, Department of Biosciences and Nutrition, Huddinge, Stockholm.

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary: In order to elucidate chromatin binding regions of ESR2 in Mantle cell lymphoma, we used ESR2 antibodies, opti-mized chromatin-immunoprecipitation (ChIP), and performed ChIP-Seq of ESR2 over-expressed Granta-519 cells and Granta519-mock cells.We present for the first time, the cistrome of nuclear receptor ESR2 in Mantle cell lymphoma cell line.

overall_design: Examination of ESR2 chromatin binding in ESR2 over-expressed Granta-519 cells and Granta519-mock cells. Each ChIP was performed twice.

first: Sam

last: Okret


title: Next Generation Sequencing of Mantle cell lymphoma Granta-519 Transcriptomes

summary:
Purpose: The goal of this study is to get a deeper insight of whole transcriptome changes and of signaling pathways involved in eliciting the DPN-mediated effects on Granta-519 tumor progression in vivo.
Methods: Mantle cell lymphoma cell line Granta-519 cells were grafted to male NSG mice, followed by treated with ESR2 selective agonist DPN or vehicle. When tumor size reached around 1300 mm3, RNA was extracted with RNeasy Plus Mini Kit (Qiagen) for sequencing.
Results: ESR2 selective agonist DPN could inhibit cell adhesion, EMT and angiogenesis in vivo which likely involves regulation of VEGFA, FOS, FOSB, CXCR4, MALAT1 and NEAT1.
Conclusions: Our study represents the detailed analysis of Granta-519 transcriptomes in vivo experiment after DPN treatment, with biologic replicates, generated by RNA-seq technology.

overall_design: Male NSG mice were subcutaneously grafted with human Granta-519 cells, followed by treatment with vehicle or ESR2 selective agonist DPN to a predefined size (1.3 cm3)


title: SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression [ChIP-seq]

first: Stefan

overall_design: H3K9me3 ChIP-seqs in alphaTC1 cells (murine alpha cell line) 5 days after transduction with an Smndc1 shRNA and in betaTC3 cells (murine beta cell line).

last: Schuster


title: Transcriptomic profiling of wild-type and Bmal1-/- myoblasts under normoxia or actue hypoxia conditions

city: Chicago

first: Pei

last: Zhu

state: IL

address: 1111 S Laflin Street, Apt314

department: Department of Biochemistry and Molecular Genetics

institute: university of illinois at chicago

summary:
Purpose: The goal of this study is to investigate the role of interplay between circadian clock and oxygen-sensing pathways in determining myogenic progenitor cell fate.
Methods:  Total RNAs were extracted from wild-type and Bmal1-/- myoblasts following exposure to normoxia (21% O2) or hypoxia (1% O2) for 6 hours, and subjected to RNA-sequencing.
Results: There were significantly up-regulated (443 in normoxia versus 477 in hypoxia) and down-regulated (745 in normoxia versus 796 in hypoxia) genes in Bmal1-/- cells compared to wild-type, with a large degree of overlap between hypoxia and normoxia, although the fold change of differential gene expression was generally greater under hypoxia versus normoxia.
Conclusion: Loss of Bmal1 in myoblasts leads to a premature differentiation-prone transcriptome, which was exaggerated following exposure to hypoxia.

overall_design: Primary myoblasts obtained from TA muscle tissues of wild-type and Bmal1-/- C57b6/J mice were exposed to normoxia (21% O2) or hypoxia (1% O2) for 6 hours, and then immediately total RNA extraction. Whole genome-wide transcriptom was characterized by RNA sequencing.

first: Noah

last: Hamlish

first: Clara

last: Peek


title: Single-cell RNA sequencing analysis of adult murine lung, kidney and spleen by TAS-Seq

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

institute: Tokyo University of Science

summary: Single-cell RNA-sequencing (scRNA-seq) is valuable for analyzing cellular heterogeneity. Cell composition accuracy is critical for analyzing cell-cell interaction networks from scRNA-seq data because cell abundancy might affect to the network. We developed terminator-assisted solid-phase cDNA amplification and sequencing (TAS-Seq), a scRNA-seq method that relied on terminator, terminal transferase, and nanowell/beads-based scRNA-seq platform, that could acquire scRNA-seq data with higher correlation with flow-cytometric data, gene-detection sensitivity, and robustness than widely-used methods.

overall_design: To clarify performance of TAS-Seq, we analyzed 8-week-old C57BL/6J female mouse lung, kidney, and spleen by TAS-Seq. For mouse spleen cells, we also analyzed the cells by using random priming-based BD Rhapsody WTA kit.

first: Tatsuro

last: Ogawa

first: Bin

last: Wu

first: Satoshi

last: Ueha

first: Kouji

last: Matsushima


title: Defining the Transcriptional and Epigenetic Basis of Organotypic Endothelial Diversity in the Developing and Adult Mouse

city: Houston

first: Manuel

middle: Eliezer

last: Cantu Gutierrez

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: The transport of gases, nutrients, metabolites and cells -  a prerequisite for proper organogenesis and tissue homeostasis - requires a functional circulatory system consisting of arteries and veins, separated by intervening capillary networks. Despite their shared origin and some common functions, endothelial cells (ECs), which line every blood vessel, display profound structural and functional heterogeneity unique to the organ and tissue that they reside in. The diversity of phenotypes that ECs can adopt suggest substantial plasticity and indicates that heterogeneity is a core endothelial property that allows ECs to fulfill their multiple tasks. While the anatomical heterogeneity of blood vessels across different organs has been appreciated for centuries, the molecular basis of the variation within the vertebrate vascular tree is poorly understood.   To decipher the transcriptional and epigenetic basis of endothelial heterogeneity across organs, and to determine how ECs mature during development, we surveyed the transcriptional and accessible chromatin landscape of ECs from the brain, retina, heart, liver, lung, and kidney of E12.5, P6, and adult mice. Through analysis of differential gene expression signatures, as well as chromatin accessibility, we have identified unique transcripts, as well as regulatory regions, that define each organ bed and developmental time point. Additionally, through single cell RNA-seq profiling of the embryonic and adult mouse we have determined that the endothelium of a single organ - in this case the brain - uses a diverse set of gene regulatory networks to mature and create a functional blood brain barrier.

overall_design: Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) and RNA-seq of endothelial cells (Ecs) or input nuclei of trunk, heart and brain at embryonic day 12.5 and brain, retina, heart, lung, liver and kidney at postnatal day 6 and adult (2 month old) mice; single cell RNA-seq of ECs at embryonic day 9.5, 12.5, 16.5, postnatal day 8 and adult (2 month old) mouse brain.

middle: E

first: Matthew

middle: C

last: Hill

last: Largoza

first: James

middle: F

last: Martin

first: Joshua

last: Wythe


title: hPSC-derived Sacral Neural Crest Enables Rescue in a Severe Model of Hirschsprung’s Disease

first: YUJIE

last: FAN

address: 430 E 67th St

institute: Memorial Sloan Kettering Cancer Center; Weill Graduate School of Medical Sciences of Cornell University

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


title: Comprehensive identification of RNA transcripts and construction of RNA networks in coronary arterial calcification

city: Hefei

first: Liang

last: Chen

state: Anhui

address: NO. 443 Huangshan Road

summary: Here, we report a comprehensive analysis of dysregulated mRNAs, lncRNAs, miRNAs and circRNAs in peripheral blood of CAC patients with high-throughput RNA sequencing. We mapped about 50 million sequence reads per sample to the human genome. GSEA analysis showed that these dysregulated RNAs correlate with several critical biological processes such as RNA modification, and RNA metabolism. RT-qPCR (SYBR Green assays) with more clinical CAC samples were used for the validation of some dysregulated RNAs. We have also constructed the co-expression network between lncRNA and mRNA, and established the circRNA-miRNA-mRNA in CAC based on this data. This study provides valuable insights to understand the RNA involvement and regulation in CAC, assisting future CAC investigations.

overall_design: Examination of mRNAs, lncRNAs, miRNAs and circRNAs in peripheral blood of CAC patients

first: Yucong

last: Wang


title: MLID imprinting disorders

city: Vitoria-Gasteiz

first: Guiomar

last: Perez de Nanclares

state: Araba

address: Jose Atxotegi sn

department: (Epi)Genetics Lab

institute: Bioaraba Health Research Institute

summary: Genomic imprinting is the parent-of-origin-specific allelic transcriptional silencing observed in mammals, which is governed by DNA methylation established in the gametes and maintained throughout the development. The frequency and extent of epimutations associated with the nine reported imprinting syndromes varies because it is evident that aberrant preimplantation maintenance of imprinted differentially methylated regions (DMRs) may affect multiple loci. Using a custom Illumina GoldenGate array targeting 27 imprinted DMRs, we profiled allelic methylation in 8 imprinting defect patients.

overall_design: DNA samples extracted from peripheral blood were subjected to methylation profile analysis using a custom Illumina Veracode GoldenGate Methylation array. We include 15 patients and 28 individuals as control samples, ages between 1-35 years.

first: Franck

last: Court

first: Alex

last: Martin-Trujillo

first: Valeria

last: Romanelli

first: Intza

last: Garin

first: Isabel

last: Iglesias-Platas

first: Arrate

last: Pereda

first: David

last: Monk


title: Loss of Cdx2 drives direct trophoblast differentiation into trophoblast giant cells via TFAP2C (ChIP-Seq)

city: London

first: Kayleigh

last: Bozon

address: 1 Midland Road

institute: The Francis Crick Institute

summary: In this experiment, the binding of CDX2 to chromatin in trophoblast stem cells was assayed using ChIP-seq.

overall_design: Duplicate chromatin immunoprecipitations from independent biological replicates were performed.

first: K

first: H

last: Patel

first: F

last: Cooper

first: C

last: Bouissou

first: J

last: Smith

first: A

middle: S

last: Bernardo


title: Loss of Cdx2 drives direct trophoblast differentiation into trophoblast giant cells via TFAP2C (RNA-Seq)

summary: In this experiment, the effect of reduced CDX2 expression on the trophoblast stem cells (TSCs) transcriptome was assayed.

overall_design: Transcriptional profiles were generated from three independent biological replicates in four experimental conditions. shRNA vectors containing a constitutively active mCherry cassette to visualise and isolate transfected and non-transfected populations. Positively transfected CDX2 knockdown TSCs were compared with control transfected and untransfected TSC populations.


title: Transcriptome analysis of regional idiopathic pulmonary fibrosis airway epithelial cultures

first: Ivana

last: Yang

summary: We performed RNA sequencing of idiopathic pulmonary fibrosis (IPF) epithelia obtained from different regions of the disease lung and cultured at air-liquid interface. We analyzed cultures from large airways (>10 mm), small airways (<2 mm), non-fibrotic distal airways, fibrotic distal airways, and honeycombed regions.

overall_design:
Epithelial cells were isolated individual IPF donor lungs from each region and cultured at air-liquid interface. RNA was isolated from cultures at various timepoints. Illumina TruSeq library prep was performed on 500 ng from each sample (1 per donor, per timepoint) and ran on the NovaSEQ 6000 with 80 million reads per sample.
Raw data not provided due to patient privacy concerns.

first: Ian

last: Stancil

first: Jacob

last: Michalski

last: Schwartz


title: hPSC-derived Sacral Neural Crest Enables Rescue in a Severe Model of Hirschsprung’s Disease [ATAC-seq]

city: New York

first: YUJIE

last: FAN

summary: The enteric nervous system (ENS) is derived from both the vagal and sacral component of the neural crest (NC). Here, we present the derivation of sacral ENS precursors from human PSCs via timed exposure to FGF, WNT and to GDF11 to enable posterior patterning and transition from posterior trunk to sacral NC identity respectively. Using a SOX2::H2B-tdTomato/ T::H2B-GFP dual reporter hPSC line, we demonstrate that both trunk and sacral NC emerge from a double-positive neuro-mesodermal progenitor (NMP). Vagal and sacral NC precursors yield distinct neuronal subtypes and migratory behaviors in vitro and in vivo. Remarkably, xenografting of both vagal and sacral NC lineages is required to rescue a mouse model of total aganglionosis, suggesting novel opportunities in the treatment of severe forms of Hirschsprung’s disease.

overall_design: RNA seq data and ATAC seq data of a series of samples collected at different time points, comparing cells treated with or without GDF11

first: Yujie

last: Fan


title: Loss of Cdx2 drives direct trophoblast differentiation into trophoblast giant cells via TFAP2C (ATAC-Seq)

summary: In this experiment, the effect of reduced CDX2 expression on chromatin accessibility in trophoblast stem cells (TSCs) was assayed using ATAC-seq.

overall_design: High read depth transposase accessible chromatin profiles were generated using 50,000 cells. shRNA vectors containing a constitutively active mCherry cassette to visualise and isolate transfected and non-transfected populations. Positively transfected CDX2 knockdown TSCs were compared with control transfected and untransfected TSC populations.


title: Loss of Cdx2 drives direct trophoblast differentiation into trophoblast giant cells via TFAP2C

overall_design: Refer to individual Series


title: Anticancer Agent Fb-Pmt Links The Thyroid Hormone Receptor On Integrin Αvβ3 To Cancer Cell Metabolism/Atp Generation [Suit2-fbPMT]

city: Rensselaer

first: Sridar

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: Microarray analysis was carried out on human SUIT2 cells, cells exposed to fb-PMT (10-6 M tetrac equivalent) for 24 h. fb-PMT significantly downregulated electron transport chain genes ATP5A1 (ATP synthase A1), ATP51, ATP5G2, COX6B1 (cytochrome c oxidase subunit 6B1), NDUFA8 (NADH dehydrogenase [ubiquinone] FA8), NDUFV2 and other NDUF genes, SLC25A6 (solute carrier group 2), UCP2 ([mitochondrial] uncoupling protein 2) and COX5A. The NDUF and ATP genes are also relevant to control of oxidative phosphorylation and transcription. Six additional NDUF genes linked to oxidative phosphorylation were affected. Conclusions. fb-PMT caused downregulation of expression of a panel of genes involved in electron transport, oxidative phosphorylation, and cytoplasmic ribosomal protein generation in SUIT2 cells, cells. A key component of the anticancer activity of fb-PMT relates to disordering of ATP generation mechanisms in tumor cells.

overall_design: Studied the anticancer functions of fb-PMT in SUIT2 cells, cells in terms of modulation of transcription by the drug of genes essential to cancer cell mitochondrial function. Compared with duplicate SUIT2 cells, cells with SUIT2 cells, cells treated with fb-PMT (30 µM) for 24 h.

first: Gennadi

last: Glinsky

first: Thangirala

last: Sudha

first: Godugu

last: Kavitha

first: Shaker

last: Mousa

first: Paul

middle: J

last: Davis


title: SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression [BSA_0337_Smndc1_KD]

first: Stefan

last: Kubicek

summary: We have found that loss of SMNDC1 (Survival Motor Neuron Domain Containing 1), a component of the spliceosome complex, in both murine alpha cells and human islets is capable of inducing an overall increase in beta cell markers and activating insulin transcription.

overall_design: Paired-end RNAseq results of bulk pancreatic human islets 5 days after transduction with two SMNDC1 shRNAs.

first: Tamara

last: Casteels

first: Michael

last: Schuster


title: Single cell analyses reveals a non-canonical EZH2 activity as main driver of RA resistance in PLZF/RARA leukemia [RNA-seq]

city: Marseille

first: Estelle

last: Duprez

address: 27 Boulevard Lei Roure

institute: CRCM

summary: Resistance to treatment is due to the heterogeneity of the tumor which contains a subset of cancer cells that escape treatment and are responsible for the relapse. We took advantage of the PLZF/RARA retinoic acid (RA) resistant acute promyelocytic leukemia (APL) model to catch relapse-initiating cell features and their vulnerabilities. By developing an integrative single-cell multi-omics analysis (scRNA-seq and scATAC-seq), we uncovered transcriptional and chromatin heterogeneity of the PLZF/RARA APL blasts. We highlighted a subset of cells insensitive to RA-induced differentiation with a strong DNA repair signature ("Rep" cluster) and exhibiting a fine tuned transcriptional network targeting the histone methyltransferase Ezh2. Combining epigenomic profiling with mouse-derived models for Ezh2 catalytic inhibition or total KO, we revealed an independent methyltransferase Ezh2 activity linked to RA resistance. These findings demonstrate the power of single-cell multi-omics integration to highlight paths to sensitize therapy-resistant leukemia cells

overall_design:
RNAseq was performed on total RNA purified from U937 MT (parental cells) and U937 B412 (PLZF/RARA expressing cells) exposed to GSK126, an inhibitor of Ezh2 catalytic activity.
Please note that each processed data file was generated from all replicates and is linked to the corresponding *Repicate1 sample records.

first: Mathilde

last: Poplineau

first: Mazuel

last: Adrien


title: Design, synthesis, and bio-evaluation of 9-(pyrimidin-2-yl)-9H-carbazole derivatives that disrupt mitochondrial homeostasis in human lung adenocarcinoma

city: Guangzhou

first: Xiaoxuan

last: Su

address: 132 East Outer Ring Road

department: School of Pharmaceutical Sciences

institute: Sun Yat-Sen University

summary:
Purpose:To further explore the possible molecular mechanism by which compound 5n induces A549 cell apoptosis, we analyzed global transcriptome alterations of A549 cells at certain time points (48 h) after compound 5n treatment using RNA-seq analysis.
Methods: Differential expression analysis for mRNA was performed using R package edgeR. Differentially expressed RNAs with |log2(FC)| value >1 and q value <0.05, considered as significantly modulated, were retained for further analysis. This choice is motivated by the decision to maximize the sensitivity of this analysis, in order to perform a massive screening and identify candidate genes to be validated with a wider sample population with real-time PCR analysis
Results: The quantity of gene expression was calculated by FPKM (Fragments Per Kilobase of transcript per Million fragments mapped). Genes with log2 (Fold change) >1 and P value < 0.05 were considered as differentially expressed genes (DEGs).  There were 146 upregulated genes and 158 downregulated genes for a total of 304 DEGs that were results are shown in Fig. 8A. Furthermore, the enriched KEGG pathways were analyzed and the top 30 pathways involved in these 304 DEGs between the two groups are shown in Figure SI. Among the top 30 pathways, 9 pathways related to mitochondrial function had significant effects. 37 DEGs in KEGG pathway associated with mitochondrial function was conducted and analyzed.
Conclusions: Metabolism-related pathways was affected by compound 5n according the RNA-seq analysis

overall_design: Retinal mRNA profiles of A549 cells (ctrl) and A549 cells (treated by compound 5n, S541)

first: Xiao-xuan


title: Transcriptomic Profiling and Pathway Analysis of Cultured Human Lung Microvascular Endothelial Cells following Ionizing Radiation Exposure

city: Bethesda

first: Anthony

middle: Robert

last: Soltis

state: MD

address: 4301 Jones Bridge Road

department: Anatomy, Physiology and Genetics

institute: Uniformed Services University

summary: Using RNA-seq we report changes in gene expression, over a 24 hour time course, in human lung microvascular endothelial cells subjected to 10 Gy X-irradiation.

overall_design: Comparison of gene expression in non-irradiated cells with that of cells 2, 4, 6, 8, and 24 hours post 10 Gy irradiation.

first: Roxane

last: Bouten

first: Clifton

middle: L

last: Dalgard

middle: R

first: John

last: Slaven

first: Regina

last: Day


title: SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: E-cadherin regulates the stability and transcriptional activity of beta-catenin in mouse embryonic stem cells

city: Pune

first: Deepa

last: Subramanyam

state: Maharashtra

address: National Centre For Cell Science, Sp Pune University, Ganeshkhind Road

country: India

institute: National Centre for Cell Science, SP Pune University Campus, Ganeshkhind, Pune - 411007, India

summary: E-CADHERIN is abundantly expressed in embryonic stem cells (ESCs) and plays an important role in the maintenance of cell-cell adhesions. However, the exact function of this molecule beyond cell adhesion, in the context of cell fate decisions is largely unknown. Using mouse ESCs (mESCs), we report that E-CADHERIN and -CATENIN interact at the membrane and continue to do so upon internalization within the cell. Knockout of Cdh1 in mouse ESCs resulted in a failure to form tight colonies, with altered expression of differentiation markers, including retention of pluripotency factor expression. Interestingly, these Cdh1-/- mESCs showed a dramatic reduction in the amount of -CATENIN present, and its associated transcriptional activity. Transcriptional profiling of Cdh1-/- mESCs displayed a significant alteration in the expression of a subset of -CATENIN targets, in a cell-state dependent manner. While treatment with a pharmacological inhibitor against GSK3 could rescue levels of -CATENIN in Cdh1-/- mESCs, expression of downstream targets remained largely unaffected, indicating an additional layer of regulation within this subset. Together, our results reveal the existence of a cell-state-dependent regulation of -CATENIN and its transcriptional targets in an E-CADHERIN dependent manner. Our findings further hint at hitherto unknown roles played by E-CADHERIN in regulating the activity of -CATENIN.

overall_design: 3 replicates of WT V6.5 mESCs vs Cdh1-/- V6.5 cells

first: Jacob

last: Freimer

first: Sinjini

last: Bhattacharyya

first: Ridim

middle: D

last: Mote

first: Surya

middle: B

last: Singh

first: Sandhya

last: Arumugam

first: YV

last: Narayana

first: Raghav

last: Rajan


title: Anticancer Agent Fb-Pmt Links The Thyroid Hormone Receptor On Integrin Αvβ3 To Cancer Cell Metabolism/Atp Generation [MOH-fbPMT]

first: Sridar

last: Chittur

summary: Microarray analysis was carried out on human MOH cells exposed to fb-PMT (10e-6 M tetrac equivalent) for 24 h. fb-PMT significantly downregulated electron transport chain genes ATP5A1 (ATP synthase A1), ATP51, ATP5G2, COX6B1 (cytochrome c oxidase subunit 6B1), NDUFA8 (NADH dehydrogenase [ubiquinone] FA8), NDUFV2 and other NDUF genes, SLC25A6 (solute carrier group 2), UCP2 ([mitochondrial] uncoupling protein 2) and COX5A. The NDUF and ATP genes are also relevant to control of oxidative phosphorylation and transcription. Six additional NDUF genes linked to oxidative phosphorylation were affected. Conclusions. fb-PMT caused downregulation of expression of a panel of genes involved in electron transport, oxidative phosphorylation, and cytoplasmic ribosomal protein generation in MOH cells. A key component of the anticancer activity of fb-PMT relates to disordering of ATP generation mechanisms in tumor cells.

overall_design: Studied the anticancer functions of fb-PMT in MOH cells in terms of modulation of transcription by the drug of genes essential to cancer cell mitochondrial function. Compared duplicate MOH cells with MOH cells treated with fb-PMT (30 µM) for 24 h.

first: Gennadi

last: Glinsky

first: Thangirala

last: Sudha

first: Godugu

last: Kavitha

first: Shaker

middle: A

last: Mousa

first: Paul

last: Davis


title: Next-generation Sequencing contributes to Quantitative Analysis of Transcriptomes in circBNC2-KO L-02 cells

city: guangzhou

first: peng

last: wang

address: 1838 North Guangzhou Avenue

institute: Southern Medical University

summary: Purpose: We idenficied a circRNA, circBNC2, that was downregulated during hepatocytes injury. To study the function of circBNC2, we performed CRISPR-Cas9 to knock out circBNC2 in L-02 (a well recognized human hepatocytes) cells.  Next-generation Sequencing was used to identified the differentially expressed mRNA between circBNC2-KO L-02 cells and wild-type L-02 cells.

overall_design: Methods:  mRNA profiles of circBNC2-KO cells or wild-type cells were generated by deep sequencing, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.  qRT–PCR validation was performed using SYBR Green assays.

first: Peng

last: Wang


title: Effects of maternal nutrient restriction during pregnancy on the adult offspring longissimus dorsi transcriptome in cattle

city: College Station

first: Michael

middle: Carey

last: Satterfield

address: 2471 TAMUS

department: Animals Science

institute: Texas A&M University

summary: Maternal undernutrition during pregnancy followed by ad libitum access to nutrients during postnatal life induces postnatal metabolic disruptions in multiple species. As skeletal muscle is a major metabolic organ, RNAseq was performed on the longissimus dorsi muscles of slaughter-weight adult females that had been exposed to nutrient-restriction in utero.

overall_design: Dams received either 100% (control; n=7) or 70% (restricted; n=7) of their NRC nutritional requirements from gestational day 158 to parturition. After birth all female calves were treated equally according to standard production practices with an ad libitum diet being provided from post natal day 301 to slaughter at post natal day 485.


title: The methylation level alterations from cardiac-specific NPRA-deficient mice.

city: 西安

first: Jun

last: Yu

state: Shaanxi

address: North of Wei 32nd Road, and east of Xitai Road, High-tech Zone

department: Clinical Experimental Center

institute: Xi'an International Medical Center Hospital

summary: To investigate the altered methylation cardiac-specific NPRA-deficient mice compares to wild type, methylation level alterations were detected by Arraystar Mouse m6A Single Nucleotide resolution microarray analysis (mazF-RIP) using the myocardium from NPRA-deficient (NPRA-/-) mice and wild-type (NPRA+/+) mice as control.

overall_design: Detected m6A modification from myocardium of NPRA-deficient mice and wild type mice by Arraystar Mouse m6A Single Nucleotide resolution microarray analysis.

first: Shen

last: Xi

first: Yu

last: Jun


title: SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression [BSA_0275_SMNDC1]

city: Vienna

first: Stefan

last: Kubicek

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

overall_design: Paired-end RNAseq results of alphaTC1 cells (murine alpha cell line) 5 days after transduction with an Smndc1 shRNA. Additionally, to further study the subpopulation of alpha cells that robustly induce insulin expression, we co-transduced the cells with a Rat Insulin Promoter and sorted for the positive and negative populations post-knockdown.

first: Tamara

last: Casteels

last: Schuster


title: Exploration of differentially-expressed exosomal mRNAs, lncRNAs and circRNAs from serum samples of gallbladder cancer and xantho-granulomatous cholecystitis patients

city: Shanghai

first: Qiang

last: Cai

address: 197 Ruijin No.2 Road

department: Department of General Surgery

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

summary: Gallbladder cancer (GBC) is the most common biliary tract malignancy worldwide. Although a growing number of studies have been devoted to the mechanism’s exploration of GBC, few molecules can be utilized as a specific biomarker for GBC early diagnosis and therapeutic treatment. Recent studies have shown that exosomes not only participate in the progression of tumors, but also carry the specific information which can define multiple cancer types. The present study was carried out to investigate the expression profile of coding and non-coding RNAs (lncRNAs and circRNAs) in the plasma-derived exosomes from GBC patients. By using high-throughput RNA sequencing and subsequently bioinformatic analysis, we identified a number of differentially expressed (DE) mRNAs, lncRNAs and circRNAs in GBC-exosomes comparing to xantho-granulomatous cholecystitis (XGC)-exosomes. Then we applied Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) analysis to investigate the potential function of these DE RNAs. Furthermore, we explored the interaction networks and competing endogenous RNA networks of these DE RNAs and their targeted genes, which revealed a complex regulatory network among coding and non-coding RNAs. In summary, this study will give evidence on the diagnostic worth of plasma-derived exosomes in GBC and provide a new perspective on the novel mechanism of GBC.

overall_design: Examination of 5 serum exosomal samples of gallbladder cancer and xantho-granulomatous cholecystitis patients.

first: Yongjun

last: Chen


title: The differencial expression of cardiac-specific NPRA-deficient mice compares to wild type.


title: RNA sequencing of MCF7 cells after vinigrol 6 hours treatment

city: Shenzhen

first: Yan

last: Zhao

address: No. 1088,Xueyuandadao

department: BIology

institute: Southern University of Science and Technology

summary: This study compares the gene expression level in four cancer cell lines before and after vinigrol treatment. The Lexogen QuantSeq 3'mRNA-seq library kit or Hieff NGS MaxUp II Dual-mode mRNA Library Prep Kit for Illumina MaxUp II was used to prepare the RNA-seq libraries in this study. We identified the dysregulated genes during this progress and explored the potential mechanism of vinigrol induced cell death in breast cancer cells. Overall design: MCF7-ADR, ,MDA-MB-231 and T47D cells treated with vinigrol (50 micromoles) for 6 hours compared with the DMSO group.

overall_design: Examination of gene expression level change after vinigrol 6 hours treatment

first: Wencheng

last: Wei

first: Yuhui

last: Hu


title: Rip3 effect on mouse articular chondrocytes

city: Suwon

first: Jimin

last: Jeon

address: 206, World cup-ro, Yeongtong-gu

department: Biomedical Sciences

country: South Korea

institute: Ajou University Graduate School of Medicine

summary:
Gene expression profiling of mouse articular chondrocytes infected with Ad-C or Ad-Rip3
In this study, we have attempted to explore the effects of Rip3 and have identified numerous genes which are involved in osteoarthritis pathogenesis.

overall_design: mouse articular chondrocytes were isolated from mouse femoral condyles and tibial plateaus cartilage tissue and infected with Ad-C(control) or Ad-Rip3 for 36 hours. Total RNA was extracted from primary mouse articular chondrocytes cultured with Ad-C (2 biological replicates) or Ad-Rip3 for 36 hours (2 biological replicates) and subjected to microarray analysis.

first: Siyoung

last: Yang

first: You-sun

last: Kim


title: Next-generation Sequencing contributes to Quantitative Analysis of Transcriptomes in circBNC2-KO HK2 cells

last: wang

summary: Purpose: We idenficied a circRNA, circBNC2, that was downregulated during tubular epithelial cell (TEC) injury. To study the function of circBNC2, we performed CRISPR-Cas9 to knock out circBNC2 in HK2 (a well recognized TEC) cells.  Next-generation Sequencing was used to identified the differentially expressed mRNA between circBNC2-KO HK2 cells and wild-type HK2 cells.

overall_design: Methods:  mRNA profiles of circBNC2-KO cells or wild-type cells were generated by deep sequencing, in duplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.  qRT–PCR validation was performed using SYBR Green assays.

first: Fan

last: Hou


title: Cell-free DNA as biomarker for sepsis by integration of microbial and host information

city: Hong Kong

first: Qiuyu

last: JING

state: Hong Kong

address: Room 6202C, Academic Building, The Hong Kong University of Science and Technology

department: Division of Life Science

country: Hong Kong

summary: We report that blood cell-free DNA as a promising biomarker for the diagnosis of sepsis and for the prediction of 28-day mortality of ICU patients by integrating both human and microbial cfDNA components.

sample_organism:
Homo sapiens
blank sample

platform_organism:
Homo sapiens
blank sample

overall_design: Comparison of human cfDNA fragmentation patterns and blood microbial features profiled by cfDNA between septic patients and non-septic ICU patients

first: Chi

last: Leung

first: Angela

last: Wu


title: Transcriptional profiling of EGFR variants in mouse Glioblastoma model

city: Houston

first: Brittney

last: Lozzi

address: 1 Baylor Plaza

department: Cell & Gene Therapy

summary: The RTK/PI3K/MAPK pathway is one of the most frequently altered pathways in Glioblastoma (GBM) with EGFR mutations and/or amplifications present in 57% of all samples. It remains the most frequently mutated oncogene in GBM. We utilized an established in vivo competition screening assay to identify and validate bona fide, driver mutations in GBM. The screen nominated A298I, T263P, and R108G mutations as potential drivers. We also analyzed R108K and R222C which were not identified by the screen. The goal of this study is to characterize the transcriptional changes of GBM when driven by different EGFR variants. Using in utero electroporation (IUE) and CRISPR/Cas9 constructs we knocked out Tp53 and Pten in developing glial cells. Each EGFR variant was overexpressed in this model and tumors were collected at end stage for RNA-sequencing analysis.

overall_design: Bulk tumor was collected from 3-5 mice for each variant on post-natal day 70 and the effect of EGFR variants on GBM was determined through RNA-seq transcriptomic profiling.

first: Kwanha

last: Yu

first: Benjamin

last: Deneen


title: ISR pathway activation signatures in MEFs: GCN2 and PERK

city: South San Francisco

first: Mengshu

last: Xu

state: CA

address: 561 Eccles Ave

institute: RAPT Therapeutics

summary: In response to different cellular stressors, the ISR kinases, PERK, PKR, HRI and GCN2, activate downstream transcriptional programs. While the core ISR transcription program is well characterized, markers that are specific to each individual ISR kinase activation pathway are not known. To identify markers that are induced by PERK or GCN2, but not the other ISR kinases, we subjected WT, GCN2-/-, and PERK-/- MEFs to amino acid starvation (RPMI 1640 SILAC -Lys -Arg) or Thapsigargin (200nM) treatment for 6 hours to activate the GCN2 and PERK pathways, respectively and performed RNA sequencing.

overall_design: To identify markers that are induced by PERK or GCN2, but not the other ISR kinases, we subjected WT, GCN2-/-, and PERK-/- MEFs to amino acid starvation for 6 hours to activate the GCN2 and PERK pathways, respectively and performed RNA sequencing and differential analysis.

first: George

last: Katibah

first: Raashi

last: Sreenivasan

first: Buvana

last: Ravishankar

first: Paul

last: Kassner


title: GCB subtype DLBCL with BCL2 translocation

first: Weili

last: Zhao

address: 197 Rui Jin Er Road

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: RNA-seq data for 6 de novo GCB subtype DLBCL patients with BCL2 translocation

first: Di

last: Fu


title: Targeting integrated metabolic and epigenetic pathways in lethal childhood ependymomas

city: Ann Arbor

first: Sriram

last: Venneti

state: MI

address: 3520E MSRB 1, 1150 W. Medical Center Dr.

institute: University of Michigan

summary: Childhood Posterior Fossa-A ependymomas (PFAs) have limited treatment options. Integrated metabolic/epigenetic analyses performed to discover therapeutic targets in PFAs demonstrated enhanced glycolysis and TCA-cycle metabolism. PFAs exhibit low H3K27me3, as in H3K27M gliomas. Therefore, we subjected them to panobinostat which kills H3K27M cells, along with the metabolic inhibitor metformin. Combined treatment increased H3K27me3, suppressed metabolism and demonstrated potent therapeutic efficacy in vitro and in vivo, suggesting promising therapeutic strategies.

overall_design: H3K27ac ChIP sequencing was performed on 3 posterior fossa (PF) and 3 supratentorial (ST) ependymoma samples

first: S


title: Evaluating the anti-metastatic potential of curcumin against TGFβ induced EMT process in A549 cells using systems biology tools

city: shimoga

first: Shivananda

last: Kandagalla

state: Karnataka

address: Jnana sahyadri shankaraghatta

department: Biotechnology

institute: Kuvempu University

summary: Curcumin (diferuloylmethane) is the bioactive phenolic compound, and the mechanism by which curcumin exerts its anti-metastatic effects was comprehensive and diverse. Several studies reported the anti-metastasis effect of curcumin by its ability to modulate the epithelial-to-mesenchymal transition (EMT) process in different cancers, and the underlying molecular mechanism is poorly understood. EMT is a highly conserved biological process in which epithelial cells acquire mesenchymal-like characteristics by losing their cell-cell junctions and polarity deviating cellular mechanism towards cancer metastasis triggering cancer cells to escape from a primary site to distant locations causing spread of cancer to the entire system ultimately leading to death. In this perspective, we explored the anti-metastatic potential and mechanism of curcumin on the EMT process by establishing in-vitro EMT model using A549 cells induced by TGF-β1. Our results showed that curcumin inhibited EMT by regulating the expression of crucial mesenchymal markers such as MMP2, vimentin, and N-Cadherin. Besides, the transcriptional analysis revealed that curcumin treatment differentially regulated the expression of 75 genes in the NanoString n-counter platform. Further PPI (Protein-protein interaction) network and clusters analysis of differentially expressed genes (DEGs) revealed their involvement in essential biological processes. Altogether, the analysis gives a comprehensive overview of the anti-metastatic effect of curcumin in inhibiting TGF-β1 induced EMT in A549 cells.

overall_design: The present study consists of two samples from human derived A549 cell lines. The present study does not contain replicates. The samples include both control and treated samples.


title: CircRNA expression profile analysis of myocardial reperfusion injury in rats

status: Public on Jun 30 2022

city: JIAMUSI

first: Rao

last: Hongyu

address: 348 Dexiang Street, Jiamusi City, Heilongjiang Province, China

institute: First Affiliated Hospital of Jiamusi University

summary: To explore the differences in the expression of circRNA in myocardial ischemia-reperfusion injury and the potential effects of these differences in circRNA. Methods 6 SPF male SD rats were randomly divided into two groups, including 3 in Myocardial ischemia reperfusion group and 3 threading without ligation in control group by ligating the left anteriors branch for 40 minutes and reperfusing for 2 hours to establish a model of myocardial ischemia reperfusion injury. The myocardial specimens from the infarct area were taken for high-throughput sequencing analysis to obtain differently expressed circRNA. After that, GO and KEGG analysis were performed to speculate on the biological functions and possible biological pathways involved. RT-qPCR was used to verify the sequencing results of differential circRNA, and bioinformatics analysis predicted that circRNA could combine with miRNA to construct a visual network diagram and their interaction. Results Analyzing of 13576 circRNAs detected in 6 rats from MIRI group and control group, A total of 132 circRNAs showed significant differential expression, of which 82 were up-regulated and 50 were down-regulated. The results of GO and KEGG analysis suggest that differential circRNA is closely related to myocardial ischemia reperfusion injury, and KEGG analysis suggests that differential circRNA is involved in calcium, AMPK, mTOR and adrenaline signal pathways. 4 circRNAs were extracted from the up-regulated circRNA for RT-qPCR verification, and the results of 2 were consistent with the high-throughput sequencing results. circRNA-miRNA interaction analysis shows that circRNA interacts with a variety of miRNAs. Conclusions The expression of circRNA in myocardial reperfusion injury rats is significantly different, which may be involved in the occurrence and development of myocardial ischemia-reperfusion injury through miRNA sponge action of circRNA.

last: HongYu

first: Gao

last: Shan


title: the role of SMN complex in tissue regeneration

first: zelin

last: chen

address: 50 South Dr.

department: NHGRI

institute: NIH

summary: we conducted RNA-Seq and MiRNA-Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members

overall_design: we compared the 3 regeneration gene mutants to the 4 non-regeneration gene mutants.

first: Wuhong

last: Pe

first: Zelin

last: Chen

first: Shawn

middle: M

last: Burgess


title: Colonic CD8 T Cell Topography in IBD revealed by Single-Cell Profiling

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: 10x Chromium 5' single cell RNA-Seq and VDJ sequencing of colonic CD8+ T cell cell populations in health and Ulcerative Colitis in human patients.

overall_design: CD8+ T cells were isolated from colonic biopsies of 3 healthy donors and 3 patients with active Ulcerative Colitis. Cells have been characterized by performing 5' single cell RNA-seq and VDJ sequencing.

first: Daniele

last: Corridoni

first: Agne

last: Antanaviciute

first: Tarun

last: Gupta

first: David

last: Fawkner-Corbett

first: Marta

last: Jagielowicz

first: Kaushal

last: Parikh

first: Emmanouela

last: Repapi

first: Steve

last: Taylor

first: Dai

last: Ishikawa

first: Ryo

last: Hatano

first: Wei

last: Xin

first: Hubert

last: Slawinki

first: Rory

last: Bowden

first: Giorgio

last: Napolitani

first: Chikao

last: Morimoto

first: Hashem

last: Koohy


title: Expression of telomerase prevents ALT and maintains telomeric heterochromatin in juvenile brain tumors.

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

summary: The up-regulation of a telomere maintenance mechanism (TMM) is an essential step in cancer progression to escape dysfunctional telomeres, senescence and apoptosis. Paediatric brain tumors frequently exhibit Alternative Lengthening of Telomere (ALT) as active TMM,  but the mechanisms involved in the induction of ALT in brain tumor cells are not clear.  Here, we report a model of juvenile zebrafish brain tumor that progressively develops ALT. We discovered that reduced expression of tert and increase in Terra expression precedes ALT development. Additionally, tumors show persistent telomeric DNA damage and loss of heterochromatin marks. Comparative analysis of gene expression after the rescue of ALT with telomerase and analysis of telomerase positive paediatric brain cancers showed normalization of telomeric heterochromatin and maintenance of telomere length, with reduced expression of genes of the pre-replicative complex as hallmark. Thus our study identifies telomere maintenance mechanisms as major drivers of DNA replication and chromatin status at telomeres in brain cancers.

overall_design: In order to identify the genes involved in the development of alternative lenghtening of telomeres in juvenile brain cancer, we performed RNA sequencing analysis (RNA-Seq), of the transcriptome of two zebrafish models of brain cancer, one ALT+ and the other telomerase+.

first: Aurora

last: Idilli

first: Emilio

last: Cusanelli

first: Emanuela

last: Kerschbamer

first: Maria

last: Mione