title: POINT technology illuminates the processing of polymerase-associated intact nascent transcripts

city: Lisboa

first: Rui

last: Sousa-Luís

address: Av. Professor Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular João Lobo Antunes

summary: Mammalian chromatin is the site of both RNA polymerase II (Pol II) transcription and coupled RNA processing. However, molecular details of such co-transcriptional mechanisms remain obscure, partly due to technical limitations in purifying authentic nascent transcripts. We present a new approach to purify and profile nascent RNA, called Polymerase Intact Nascent Transcript (POINT) technology. This three-pronged methodology maps nascent RNA 5’ends (POINT-5), establishes the kinetics of co-transcriptional splicing patterns (POINT-nano) and profiles whole transcription units (POINT-seq). In particular, we show by depletion of the nuclear exonuclease Xrn2 that this activity acts selectively on cleaved 5’P-RNA at polyadenylation sites. Furthermore, POINT-nano reveals that splicing occurs either immediately after splice site transcription or is delayed until Pol II transcribes downstream sequences. Finally, we connect RNA cleavage and splicing with either premature or full-length transcript termination. We anticipate that POINT technology will afford full dissection of the complexity of co-transcriptional RNA processing.

overall_design: POINT technology was employed over HeLa and HCT116 cells in order to reveal the RNA processing at the nascent level. Thus, POINT-nano, POINT-seq and PONT-5 samples were generated either untreated or with PlaB/DMSO in order to evaluate the splicing kinetics. Also, POINT technology was performed under XRN2 and CPSF73 KDs to study 3’end processing.

first: Gwendal

last: Dujardin

first: Carika

last: Weldon

first: Inna

last: Zukher

first: Hiroshi

last: Kimura

first: David

last: Buck

first: Maria

last: Carmo-Fonseca

first: Nick

last: Proudfoot

first: Takayuki

last: Nojima


title: Identification of age-related changes in gene expression and chromatin accessibility in T cells from thymus to periphery (60K)

status: Public on Mar 19 2021

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

country: USA

institute: NIH

summary: Aging of immune system is characterized by progressive decline of physiological and cellular function of T cells. Recent studies of naïve T cells from young and old mice have identified age-related altered gene expressions but the mechanisms underlying age associated changes of naïve T cells remain poorly understood. Here we compared the transcriptome and chromatin accessibility in mature CD4 and CD8 thymocytes and in naïve CD4 and CD8 T cells of spleen between young (6-8 weeks) and old (79-121 weeks) C57Bl/6 mice. We used Agilent microarray method and identified the age-related altering gene expressions 1) only in mature CD4 and CD8 T cell from thymus, 2) shared by both thymus and spleen naïve T cells, and 3) only in naïve T cells from spleen. The shared changes include increased chemokine and chemokine receptor expressions and decreased cell cycle regulator expression. We further analyzed the chromatin basis of altered gene expression using Assaying Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) between young and old mice. We have identified age-related changes of chromatin accessibility in T cells from thymus and spleen, and some correlated changes between gene expression and chromatin accessibility. Overall, we observedmore age-related alterations of gene expression and chromatin accessibility inthymus than in spleen, suggesting some age-related changes of T cells in thymus did not retain in periphery. Together, our findings have identified tissue specific altered gene expressions and chromatin status in T cells during aging and further study of these altered genes will shed new insights into the mechanisms underlying these age-related changes.

first: Achouak

last: Achour

first: Nan-ping

last: Weng


title: RNA-sequencing of lung tissues from Gprc5a-/- and Gprc5a-/-/Lcn2-/- mice at baseline and seven months post-NNK

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

type: Expression profiling by high throughput sequencing

summary: We have shown that Gprc5a-/- mice form Kras-mutant lung tumors spontaneously which is accelerated by  tobacco carcinogen (NNK) exposure. We found in these mice that Lcn2 was distinctively up-regulated along the spectrum of Kras-mutant lung cancer development. To understand the role of Lcn2 in lung cancer pathogenesis, we generated Gprc5a-/-/Lcn2-/- mice and found that these animals have increased lung tumor devleopment following NNK compared to Gprc5a-/- animals with intact Lcn2. To understand these effects, we performed RNA-sequencing (RNA-Seq) of lung tissues from Gprc5a-/-/Lcn2-/- and Gprc5a-/- mice at baseline (prior to NNK exposure) and of tumor-bearing lungs from both groups at seven months post-NNK exposure.

overall_design: Groups of 9-10 of each of Gprc5a-/- and Gprc5a-/-/Lcn2-/- mice (8 weeks old) were intraperitoneally administered 50 mg/kg body weight NNK three times per week for 8 weeks. After seven months following completion of NNK exposure, mice were sacrificed and portions of lung tissues were used for RNA isolation and subsequent RNA-Seq analysis. For comparison, lungs from  10 Gprc5a-/- and 10 Gprc5a-/-/Lcn2-/- mice (8 weeks old) were also studied at baseline (prior to NNK exposure) by RNA-Seq.

first: H

first: K

last: Chang


title: Aging ISCs and Polycomb KD ISCs

city: Warsaw

first: Michal

last: Pawlak

address: Domaniewska 39 B

country: Poland

institute: Roche Polska Sp. z o.o.

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: ChIP-seq analysis of genome-wide DNA-binding by STAT3 alternative spliceforms following Oncostatin M stimulation

city: Melbourne

first: Marie

last: Bogoyevitch

state: VIC

address: Medical Building, Grattan Street

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: The University of Melbourne

summary: Alternative splicing in the Signal Transducer and Activator of Transcription 3 (STAT3) transcription factor gene generates the STAT3α and STAT3β spliceforms that have identical DNA-binding domains but C-terminal transactivation domains that differ in both length and sequence. To delineate the impact that the different STAT3α and STAT3β transactivation domains have on cytokine-activated genome-wide DNA-binding, we measured STAT3α and STAT3β DNA-binding at identified STAT3 transcription factor binding sites within the mouse genome using cells engineered to express either the STAT3α or STAT3β spliceform only. The analyses show that ~40% of STAT3-bound genomic regions (2280 of 5343 regions) are commonly targeted by both STAT3 spliceforms. The remaining STAT3-bound genomic regions are preferentially targeted by either STAT3α or STAT3β (1450 and 1613 regions, respectively) and associated with genes enriched in unique biological functions. Motif enrichment analyses not only confirm the targeting of the canonical STAT3 target DNA motif by both spliceforms but reveal several co-occurring DNA motifs known to be targeted by transcription factors that can act cooperatively with STAT3 during target gene transcription regulation. Multiple additional co-occurring DNA motifs selectively enriched in STAT3α- or STAT3β-associated regions were also identified.

overall_design: NGS analysis of ChIP DNA prepared from STAT3-/- Mouse Embryonic Fibroblasts re-expressing only STAT3α and STAT3β following treatment with Oncostatin M

first: Vincent

last: Tano

middle: A


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Osmr-/- Epidermal keratinocytes Transcriptomes

status: Public on Mar 18 2021

city: Guangzhou

first: Jun

last: Liu

state: Guangdong

address: No.2 Lujing Road

department: Dermatology Hospital

country: China

institute: Southern Medical University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare epidermal keratinocytes transcriptome profiling (RNA-seq) between wild type and Osmr-/- mice
Methods: Epidermal keratinocytes mRNA profiles of wild-type (WT) and Oncostatin M receptor (Osmr−/−) mice were generated by deep sequencing, in triplicate. 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.

overall_design: Epidermal keratinocytes mRNA profiles of wild type (WT) and Osmr-/- mice

first: Zhili

last: Rong


title: RNA sequencing comparison of CXCR3+ and CX3CR1+ CD4+ epitope specific T cells from Se-infected mice.

city: Minneapolis

first: Marc

middle: Kevin

last: Jenkins

state: Minnesota

address: 2101 Sixth St. SE

department: Center for Immunology

institute: University of Minnesota

summary:
Interferon-γ (IFN-γ)-producing CD4+ T helper-1 (Th1) cells are critical for protection from microbes that infect the phagosomes of myeloid cells. We assessed Th1 cell generation in vivo by studying antigen-specific CD4+ T cells during infection with the phagosomal pathogen Salmonella enterica. We found that this infection induced two varieties of Th1 cells, one expressing CXCR3 and one expressing CX3CR1. We performed RNA sequencing on these two types of Th1 cells that were specific for the LpdAp:I-Ab epitope from B6 x 129 F1 mice 30 days after Salmonella enterica infection to gain information about the differences between these types of Th1 cells and how those differences might relate to protective immunity.
We report results for CXCR3+ CX3CR1- and CXCR3- CX3CR1+ LpdAp:I-Ab-tetramer binding cells.

overall_design: CXCR3+ CX3CR1- and CXCR3- CX3CR1+ LpdAp:I-Ab tetramer-binding CD4+ T cells were sorted from four B6 x 129 F1 mice on day 30 post Salmonella enterica infection.


title: Expression data from HER2 L755S, PIK3CA E545K, and co-cultured cells in the MCF-10A background

first: Ian

last: Waters

address: 1650 Orleans St

department: Oncology

institute: Johns Hopkins University

summary:
When co-cultured, HER2 L755S mutant cells are induced to proliferate when coming into close contact with PIK3CA E545K mutant cells
We used a microarray to compare transciptome-wide expression levels between HER2 L755S cells, PIK3CA E545K cells, and co-cultures containing both cell types.

overall_design: HER2 L755S and PIK3CA E545K mutant cells in the MCF-10A background were grown separately, and in co-cultures. When co-cultures reached ~75% HER2 L755S cells, all samples were harvested. Each single control and the co-cultures were grown in quadruplicate. The three experimental groups were HER2 L755S single controls, PIK3CA E545K single controls, and co-cultures containing ~75% HER2 L755S and 25% PIK3CA E545K.

middle: G


title: Identification of age-related changes in gene expression and chromatin accessibility in T cells from thymus to periphery


title: Age-related changes in Pc gene regulation disrupt lineage fidelity in intestinal stem cells

city: Novato

first: Tal

last: Ronnen Oron

state: CA

address: 8001 Redwood blvd.

department: Bioinformatics Core

institute: Buck Institute for Research on Aging

summary: Tissue homeostasis requires long-term lineage fidelity of somatic stem cells. Whether and how age-related changes in somatic stem cells impact the faithful execution of lineage decisions remains largely unknown. Here, we address this question using genome-wide chromatin accessibility and transcriptome analysis as well as single cell RNA-seq to explore stem cell-intrinsic changes in the aging Drosophila intestine. These studies indicate that in stem cells of old flies, promoters of Polycomb (Pc) target genes become differentially accessible, resulting in the increased expression of enteroendocrine (EE) cell specification genes. Consistently, we find age-related changes in the composition of the EE progenitor cell population in aging intestines, as well as a significant increase in the proportion of EE-specified ISCs and progenitors in aging flies. We further confirm that Pc-mediated chromatin regulation is a critical determinant of EE cell specification in the Drosophila intestine. Pc is required to maintain expression of stem cell genes while ensuring repression of differentiation and specification genes. Our results identify Pc group proteins as central regulators of lineage identity in the intestinal epithelium and highlight the impact of age-related decline in chromatin regulation on tissue homeostasis.

overall_design: We used ATAC-seq to compare the chromatin accessibility profiles of sorted intestinal stem cells from young, middle-aged and old Drosophila adults.

first: Helen

last: Tauc

last: Ronnen-Oron


title: RNA helicase-mediated regulation of snoRNP dynamics on pre-ribosomes and rRNA 2’-O-methylation

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: RNA helicases play important roles in diverse aspects of RNA metabolism through their functions in remodelling ribonucleoprotein complexes (RNPs), such as pre-ribosomes. Here, we show that the DEAD box helicase Dbp3 is required for efficient processing of the U18 and U24 intron-encoded snoRNAs and 2'-O-methylation of various sites within the 25S ribosomal RNA (rRNA) sequence. Furthermore, numerous box C/D snoRNPs accumulate on pre-ribosomes in the absence of Dbp3. Many snoRNAs guiding Dbp3-dependent rRNA modifications have overlapping pre-rRNA basepairing sites and therefore form mutually exclusive interactions with pre-ribosomes. Analysis of the distribution of these snoRNAs between pre-ribosome-associated and 'free' pools demonstrated that many are almost exclusively associated with pre-ribosomal complexes. Our data suggest that retention of such snoRNPs on pre-ribosomes when Dbp3 is lacking may impede rRNA 2'-O-methylation by reducing the recycling efficiency of snoRNPs and by inhibiting snoRNP access to proximal target sites. The observation of substoichiometric rRNA modification at adjacent sites suggests that the snoRNPs guiding such modifications likely interact stochastically rather than hierarchically with their pre-rRNA target sites. Together, our data provide new insights into the dynamics of snoRNPs on pre-ribosomal complexes and the remodelling events occurring during the early stages of ribosome assembly.

overall_design: All samples were analyzed in biological dublicates.

first: Gerald

middle: R

last: Aquino

first: Philipp

last: Hackert

first: Roman

last: Martin

first: Jimena

last: Davila Gallesio

first: Robert

middle: W

last: van Nues

first: Claudia

last: Schneider

first: Nicholas

middle: J

last: Watkins

first: Henrik

last: Nielsen

first: Markus

middle: T

last: Bohnsack

first: Katherine

middle: E


title: Transcriptional profiling of Caco2 cells infected with Encephalitizoon intestinalis

city: Newark

last: Gao

state: NJ

address: 195 University Avenue

department: Biological Sciences

institute: Rutgers, the State University of New Jersey

summary: Encephalitizoon intestinalis infection occurs in immunocompromised individuals and has relatively few treatment options due to the lack of understanding of impact of microsporidia life cycle on host molecular effects.  We profiled transcriptome of a physiologically relevant intestinal epithelial cell line to understand what cellular processes are most impacted.

overall_design: Cells were grown to confluency and then infected with 100 μl of ∼10^6 spores/ml solution and maintained for 14 days.

first: Juan

last: Flores


title: Whole-transcriptome analysis using RNA sequencing in OTUD5-wild type, OTUD5-null, and GDC0349-treated HEK293 cells

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Whole-transcriptome analysis was performed on RNA from OTUD5-wild type, OTUD5-null, and GDC0349-treated HEK293 cells to identify the cellular processes regulated by OTUD5 and mTOR simultaneously.

overall_design: mRNA profiles of OTUD5-wild type, OTUD5-null, and GDC0349-treated HEK293 cells were generated by RNA-sequencing, in duplicate, using illumina HiSeq2000 platform.

first: JinHwa

last: Cho

first: Jeong-Hoon

first: Sunhong

first: Jong-Hwan

first: Seon-Young


title: circRNA in cervical cancer tissue

city: Foshan

first: Chenglai

last: Xia

address: Renming Xi  11#

institute: Affiliated Foshan Maternity & Chlid Healthcare Hospital, Southern Medical University

summary: The sample library was built using ILUMIMA recommended kit, and the original data was sequenced using HiSeq 4000. The simple procedure is as follows: the sample RNA is reverse-transcribed into a cDNA, then a poly A is added at the 3’ End, then the sample is connected to the sequencing connector of the kit, and then PCR amplification is performed. Finally, HiSeq 4000 was used to detect the fault.

overall_design: Examination of different circRNA in normal cervical tissue and cervical cancer tissue.


title: Next Generation Sequencing Facilitates Quantitative Analysis of HaCaT and OSM-treated HaCaT Transcriptomes

first: Jun

last: Liu

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) between HaCaT cell and OSM-treated HaCaT cells
Methods: mRNA profiles of HaCaT cells and OSM-treated HaCaT cells were generated by deep sequencing, in triplicate, using Illumina GAIIx. 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.

first: Zhili

last: Rong


title: Development of diagnosis method for LTBI with circulating miRNA

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

country: Japan

institute: Chuo University

type: Non-coding RNA profiling by high throughput sequencing

summary:
When exposed to M. tuberculosis, 25-50% become infected, of which 10-20% having several symptoms. Currently, there is no marker for judging the efficacy of M tuberculosis (Mtb) treatment, and it is judged based on the appearance of subjective symptoms and radiological findings. In this study, we attempted to establish a marker to distinguish patients who relapsed after TB treatment from patients who had recurrence after TB treatment using the information of circulating miRNA expression.
Thirty two patients with tuberculosis infection aged 18 years or older were enrolled. 16 patients had onset or recurrence of TB and 16 patients with latent tuberculosis infection (LTBI) with positive test for Interferon gamma release assays (IGRA) and no chest X-ray examination. Total RNA from serum in exosome-rich fraction was extracted and then miRNA expression analysis was performed using a next-generation sequencer and NGS data analyzed using miRDeep2.
Using expression information of nine miRNAs, TB and LTBI could be separated with 71.8% accuracy. The odds ratio also was 6.16, and the p-value was 3.20e-02, respectively. The expression of hsa-miR-122-5p was significantly different between TB and LTBI (p <0.05).
Here we established a novel method to efficiently differentiate LTBI from patients with tuberculosis infection. Since this method can be performed in a low invasive manner such as blood sampling, it is promising tool for utilizing follow-up of TB treatment.

overall_design: Examination of circulating miRNA in tuberculosis and latent tuberculosis infection

first: Shoji

last: Hashimoto

first: Hong

last: Zhao

first: Michiyo

last: Hayakawa

first: Koichi

last: Nakajima

first: Y

middle: H

first: Yoshiki

last: Murakami


title: Gene expression profiles of LN-1 cells with IGFBP3 knockdown

city: Miaoli County

first: Ya-Wen

last: Chen

address: 35, Keyan Rd, Zhunan Town

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

summary:
To understand the signal pathways involved in IGFBP3 expression, LN1-1 cells were infected with lentivirus expressing IGFBP3 shRNA and confirmed the IGFBP3 expression by Western blot.
Total RNA was extracted from LN1-1 pLKO-GFP and LN1-1 IGFBP3 sh5 cells and used for array analysis.

overall_design: Gene expression profiles of LN-1 pLKO-GFP and LN1-1 IGFBP3 cells.

first: S

last: Wang


title: Single cell atlas of the healthy breast

status: Public on Mar 17 2021

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

summary: The study involved breast biopsies of 11 healthy donors. No replicates

overall_design: These are normal human breast tissues. The cells from the tissue were extracted using Tumor Dissociation kit human, cat# 130-095-929 from Miltenyl Biotec. Cells were extracted from either freshly collected tissues or cryopreserved using a procedure described in PMID: 26311223


title: Profiling non-human primate germline RNA to understand the legacy of early life stress

city: Los Angeles

first: Dias

last: Brian

address: 4640 West Sunset Boulevard

institute: Children's Hospital Los Angeles

summary: Validation of the methodology for extracting and demonstrating the quality of the ability to profile RNA in sperm of rhesus macaques.

overall_design: Total RNA sequencing: Monkey sperm - Control and Monkey sperm - Maltreated

first: Brian

last: Dias


title: Next Generation Sequencing Facilitates Quantitative Analysis of Primary Keratinocytes and OSM-treated Primary Keratinocytes Transcriptomes

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) between Primary Keratinocytes and OSM-treated Primary Keratinocytes
Methods: mRNA profiles of Primary Keratinocytes and OSM-treated Primary Keratinocytes were generated by deep sequencing, in triplicate, using Illumina GAIIx. 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.


title: Survey of Functional Genes in the Arctic Soil of Pond Inlet

city: Tachikawa-shi,

first: Shu-Kuan

last: Wong

state: Tokyo

address: 10-3, Midori-cho,

institute: National Polar Research Institute

type:
Expression profiling by array
Other

summary: The objective of this study was to identify the different functional genes involved in key biogeochemical cycles in thehigh Arctic regions. Understanding the microbial diversity in the Arctic region is an important step to determine the effects of climate change on these areas.

overall_design: Soil samples were collected from high Arctic region of Pond Inlet. At each sampling site five biological replicates were collected and DNA and RNA were subsequently extracted. The DNA and cDNA (synthesized from RNA samples) samples were shipped to the University of Oklahoma, where it was analyzed with the GeoChip microarray.

first: M

last: Uchida

first: S-K


title: Transcriptomic analysis of primed synovial fibroblasts from monosodium urate crystal-induced arthritis in the mouse

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

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


title: scRNA-Seq analysis of primed synovial fibroblasts

summary: scRNA-Seq analysis of FACS sorted CD45-CD31- cells from naive and MSU crystals injected mouse paws.

overall_design: scRNA-Seq of FACS sorted CD45-CD3- cells from collagenase-digested paws of uninjected BALB/ mouse paws (-/-) or BALB/c mouse paws 9 days after the first (-/MSU) or second (MSU/MSU) injection of monosodium urate (MSU) crystals, respectively.

first: Markus

last: Hoffmann

first: Arif

middle: B

last: Ekici


title: Analysis of EPS structure and transcriptome expression difference of Bifidobacterium longum W13 and W13R

city: Tianjin

first: Tang

last: jiao

address: Binhai new area

institute: Tianjin University Of Science and Technology

summary: The purpose of this course is to study the relationship between the primary structure of exopolysaccharides and the gene expression level of Bifidobacterium longum W13 and W13R, and to better explain the differences between different strains from the level of gene transcription.

overall_design: We analyzed two samples, one is Bifidobacterium longum W13 and the other is Bifidobacterium longum W13R

first: Wei

middle: t

last: Geng

first: Jiao

last: Tang

first: Ting

last: Xu


title: Innate immune signatures to a partially-efficacious HIV vaccine predict correlates of HIV-1 infection risk

city: Seattle

first: Lamar

last: Ballweber Fleming

state: WA

address: 1100 Fairview Ave N

department: VIDD

institute: Fred Hutchinson Cancer Res Ctr

summary: Using specimens from a phase 1b trial of the RV144 regimen in HIV-1-uninfected South Africans (HVTN 097), we profiled innate responses to the first ALVAC-HIV immunization. PBMC transcriptional responses peaked 1 day post-vaccination. Type I and II interferon signaling pathways were activated, as were innate pathways critical for adaptive immune priming.

overall_design: NGS transcriptome profiling using RNA-seq  of PBMC speciments from a phase 1b trial in HIV-1 uninfected South Africans (HVTN 097), at baseline and days 1,3, and 7 post vaccination.

first: Erica

last: Andersen-Nissen

first: Andrew

last: Fiore-Gartland

last: Fleming

first: Lindsay

middle: N

last: Carpp

first: Anneta

middle: F

last: Naidoo

first: Michael

middle: S

last: Harper

first: Valentin

last: Voillet

first: Nicole

last: Grunenberg

first: Fatima

last: Laher

first: Craig

last: Innes

first: Linda-Gail

last: Bekker

first: James

last: Kublin

first: Ying

last: Huang

first: Guido

last: Ferrari

first: Georgia

middle: D

last: Tomaras

first: Glenda

last: Gray

first: Peter

last: Gilbert

last: McElrath


title: FGFR2 fusion protein-driven mouse models of intrahepatic cholangiocarcinoma unveil a necessary role for Erk signaling

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

summary: Four structurally different FFs were expressed in Tp53-/- mouse liver organoids. The tumorigenic properties of genetically-modified liver organoids were assessed by intrahepatic or subcutaneous transplantation in immuno-deficient mice. RNA was extracted from tumors and subjected to RNAseq. Transcriptional profiling identified up/down-regulated signatures shared between human and mouse cholangiocarcinomas driven by FGFR2 fusion proteins.

overall_design: Tumors diagnosed as cholangiocarcinoma, obtained upon s.c. or intra-hepatic transplantation of Tp53 null liver organoids engineered to express either FGFR2-BICC1 or FGFR2-TACC3, were excised and subjected to RNAseq. RNAseq data were analyzed in order to discover transcriptional similarities between human and mouse cholangiocarcinomas driven by oncogenic FGFR2 fusion proteins.

first: Giulia

last: Cristinziano

first: Oreste

last: Segatto

first: Cristina

last: Cristofoletti


title: Unique human beta-cell senescence-associated secretory phenotype (SASP) reveal conserved signaling pathways and heterogeneous factors

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: The aging of pancreatic beta-cells may undermine their ability to compensate for insulin resistance, leading to the development of type 2 diabetes (T2D). Aging beta-cells acquire markers of cellular senescence and develop a senescence-associated secretory phenotype (SASP) that can lead to senescence and dysfunction of neighboring cells through paracrine actions, contributing to beta-cell failure. Herein, we defined the beta-cell SASP signature based on unbiased proteomic analysis of conditioned media of cells obtained from human senescent beta-cells. These experiments revealed that the beta-cell SASP is enriched for factors associated with inflammation, cellular stress response, and extracellular matrix remodeling across species.

overall_design: After FACS-sorting, beta-Gal-positive and negative primary beta-cells were plated in 96-well plates and incubated in serum-free islet media to generate conditioned media. Conditioned media were analyzed using SomaScan at the Genomics Proteomics Core at Beth Israel Deaconess Medical Center.

first: Ayush

last: Midha

last: Aguayo-Mazzucato


title: Transcriptomic analysis of primed synovial fibroblasts from monosodium urate crystal-induced arthritis in the mouse [RNA-seq]

first: Steffen

last: Uebe

summary: Repeated challenge of synovial fibroblasts with MSU crystals in vivo induced inflammatory priming.

overall_design:
Differential gene expression analysis of cultured synovial fibroblasts derived from non-injected BALB/c mouse joints (-/-) or mouse joints 9 days after the first (-/MSU) or the second (MSU/MSU) injection of MSU crystals.
The primed and non-primed samples were extracted from different paws, but not necessarily different mice. The numbering (1 to 3) also does not necessarily identify a particular mouse.

first: Markus

last: Hoffmann

first: Arif

last: Ekici


title: Multi-influential interactions controls behaviour and cognition through a limited number of pathways in Down syndrome mouse models (RNA-Seq reanalysis II)

city: Strasbourg

first: maria

middle: del mar

last: muñiz moreno

state: Alsace

address: 1 Rue Laurent Fries

department: Translational medicine and neurogenetics

country: France

institute: IGBMC

summary: Down syndrome (DS) is the most common genetic form of intellectual disability with additional clinical features, caused by the presence of an additional copy of human chromosome 21 (Hsa21). A few number of patients with DS features, carry partial duplication of Hsa21 and their study provided novel insights into genotype–phenotype correlations. Despite the progress of genome analysis, the rareness of patients with partial duplication, and the human genetic heterogeneity, makes difficult to achieve a more detailed phenotypic map at present. As a complementary approach, we screened the in vivo DS mouse library with highly standardized behavioural tests, magnetic resonance imaging (MRI) and digged into hippocampal gene expression to go further in dissecting the genotype–phenotype correlations and in deciphering misregulated genes, functional pathways and biological cascades in DS models. Altogether this approach bring novel insights into the field. First, we unravelled the complexity of the genetic interactions between different regions of the chromosome 21 and how they play an important role in modulating the outcome of the behavioural and molecular phenotypes. Then, in depth analysis of misregulated expressed genes involved in synaptic dysfunction highlitghed six biological cascades centered around DYRK1A, GSK3beta, NPY, RHOA, NPAS4 and the SNARE complex. Finally, we provide a novel vision of the existing altered gene-gene crosstalk and molecular mechanisms that could be at play for both the DS clinical features and the rescue mechanisms by targeting specific hubs or well connected nodes that may be central to advance in our understanding of DS  and therapies development.

relation:
Reanalysis of: GSM1338311
Reanalysis of: GSM1338312
Reanalysis of: GSM1338313
Reanalysis of: GSM1338314
Reanalysis of: GSM1338315
Reanalysis of: GSM1338316
Reanalysis of: GSM1338317
Reanalysis of: GSM1338318
SubSeries of: GSE149470

overall_design: I downloaded and re-analysed the gene expression profile of human foetal fibroblast derived datasets published by Letourneau et al., (2014) and  adult fibroblast published by Prandini et al., 2007 with GEO accession number GSE55426. We re-analysed the expression of 3 biological replicates + 1 technical replicate of foetal cultured fibroblasts from monozygotic twins  discordant for Down syndrome and adult cultured fibroblasts samples from 8 Down syndrome and Euploid adults. The re-analysis was performed using our bioinformatics pipeline, developed over the R environment. As a brief sumup, the pipeline consisted in eight major steps: Alignment & counts generation, Quality control (QC), pre-processing and normalization of the raw data, analysis of the structure and homogenicity of the data, differential expression analysis (DEA), differential functional analysis (DFA), Network connectivity analyses of pathways and genes and finally network topology and centrality analyses.Alignment & counts generation: To perform the aligning I downloaded from ENSEMBL the human genome assembly version GRCh38 release 96 together with the corresponding gene location file in .gtf format files. The alignment was performed using HISAT2 with the options -p 8 –dta, -t –summary-file –no-unal, --no-hd. Samtools version 1.9 was used to generate the bam file and index and the counts were generated using HTSeq-Count 0.9.1 with the options –mode=intersection-nonempty ---type=exon --idattr=gene_id –aditional-attr=gene_name. Data quality control: I performed an initial quality control analysis (QC) of the raw .fastq files using fastQC. I also checked that there were none overrepresented sequences matching to any other organism, the levels of GC content, the duplication levels were good, and no residual adapters sequences were identified. Then, DESeq2 was chosen for the normalization and both DESeq2 and FCROS for the differential expression analysis (DEA). Ultimately, we decided to carry on all downstream analyses using FCROS68results although we maintained the DEGs annotations identified by  DESeq2 (RNA-Seq) for the purpose of maintained the results of one of the DEA method most widely used by the community for RNA-Seq analyses.FCROS is a fold change (FC) rank based method that works well with noisy datasets and gives strong reproducible results. FCROS computes for each pair of test/control samples (K pairs), a statistic associated with the k ranks of the FC values for each gene, and the obtained probability (f-value) is used to identify the differential expressed genes (DEGs) within an error level fixed by the analyst. Our fixed error level corresponds to a 5% False Discovery Rate (FDR), and is attained by setting the Ɑ parameter within this range 0.025<Ɑ>0.975.Differential functional analysis (DFA): To identify the altered functions due to the changes in gene expression and possibly get new insights into the mechanistic changes along the pathways between the two conditions trisomic vs. wild type on each model we used the generally applicable gene set enrichment for pathway analysis (GAGE, Luo et al., 2009) R package  to carry on the functional expression analysis.The main aim of re-analysing this data was to get new insights into DS gene deregulation first in humans applying a more updated computational pipeline and  secondly, by applying a comparative genomic approach with rodent Down syndrome datasets identify the conserved gene and functional deregulated profiles.

first: Maria

middle: M

last: Muñiz Moreno


title: Next Generation Sequencing Facilitates Quantitative Analysis of GlyTranscriptomes

city: Da lian

first: zelong

last: li

address: Ling shui

department: Environmental Science and Engineering

institute: Dalian University of Technology

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived consortium GLY transcriptome profiling (RNA-seq) and to evaluate protocols for optimal high-throughput data analysis

overall_design: mRNA profiles of consortium GLY were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Miaomiao

last: Du

first: Zelong

last: Li


title: Genome-wide shifts in histone modification patterns at early stage of rice infection with root-knot nematode Meloidogyne graminicola

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

summary: Epigenetic processes play a crucial role in the regulation of plant stress responses, but their role in plant-pathogen interactions remains poorly understood. Although histone modifying enzymes are deregulated in galls induced by root-knot nematode (RKN, Meloidogyne graminicola) in rice, their influence on plant defence and their genome-wide impact has not been comprehensively investigated. At genome-wide level, three histone marks, H3K9ac, H3K9me2 and H3K27me3 were studied by chromatin-immunoprecipitation (ChIP)-sequencing on RKN-induced galls at 3 days post inoculation. While levels of H3K9ac and H3K27me3 were strongly enriched, H3K9me2 was generally depleted in galls versus control root tips. Differential histone peaks were generally associated with plant defence related genes. Total RNA sequencing was performed to assess the effect of histone modification changes on gene expression.

overall_design: Total RNA sequencing was done on RNA extracted from rice roots under two eperimental conditions: infection with Meloidogyne graminicola and mock infection (three replicates per condition).

first: Mohammad

last: Reza Atighi

first: Tim

last: De Meyer

first: Tina

last: Kyndt


title: Transcriptomic and Functional Analyses of Mitochondrial Dysfunction in Pressure Overload-induced Right Ventricular Failure

city: Stanford

first: Hyun Tae

middle: V

last: Hwang

address: 300 Pasteur Dr. S242

institute: Stanford University

summary: Background: In complex congenital heart disease patients such as those with tetralogy of Fallot, the right ventricle (RV) is subject to pressure overload, leading to RV hypertrophy and eventually RV failure. The mechanisms that promote the transition from stable RV hypertrophy to RV failure are unknown. We evaluated the role of mitochondrial bioenergetics in the development of RV failure. Methods: We created a murine model of RV pressure overload by pulmonary artery banding and compared with sham-operated controls. Gene expression by RNA-sequencing, oxidative stress, mitochondrial respiration, dynamics, and structure were assessed in pressure overload-induced RV failure. Results: RV failure was characterized by decreased expression of electron transport chain genes and mitochondrial antioxidant genes (aldehyde dehydrogenase 2 and superoxide dismutase 2) and increased expression of oxidant stress markers (heme oxygenase, 4-hydroxynonenal). The activities of all electron transport chain complexes decreased with RV hypertrophy and further with RV failure (oxidative phosphorylation: sham 552.3±43.07 vs. RV hypertrophy 334.3±30.65 vs. RV failure 165.4±36.72 pmol/(sec*ml), p<0.0001). Mitochondrial fission protein DRP1 did not change, while MFF decreased and fusion protein OPA1 decreased. In contrast, transcription of electron transport chain genes increased in the left ventricle of RV failure. Conclusion: Pressure overload-induced RV failure is characterized by decreased transcription and activity of electron transport chain complexes and increased oxidative stress which are associated with decreased energy generation. An improved understanding of the complex processes of energy generation could aid in developing novel therapies to mitigate mitochondrial dysfunction and delay the onset of RV failure.

overall_design: The left and right ventricles from FVB mice were used for RNA-sequencing. Control and right ventricular failure samples, achieved through pulmonary artery banding, were compared. N is 4 for each group.

first: HyunTae

first: Nefthi

last: Sandeep

first: Ramesh

last: Nair

first: Dong-Qing

last: Hu

first: Mingming

last: Zhao

first: Ingrid

last: Lan

first: Giovanni

last: Fajardo

first: Scot

last: Matkovich

first: Daniel

last: Bernstein

first: Sushma

last: Reddy


title: Transcriptomics analysis of mouse tumor sample

city: Nanjing

first: Fei

middle: jun

last: Gu

address: 138 Xianlin Avenue

institute: Nanjing University of traditional Chinese Medicine

summary: A total of 30 differential genes were callbacked in colon tumor samples after AC(Astragalus zedoary extract) treatment.

overall_design:
Colon tumors were induced by injecting CT26 cells into syngeneic BALB/c mice
9 Samples in total; 3 samples per condition (Sham, model and AC treated), the colon tumor samples were isolated and transcriptomics testing  was performed

first: Junfei

first: Qiaohan

last: Wang


title: Sciatic Nerve Injury Triggered Inflammation: Insights into Conditioning-Lesion Induced Axon Regeneration [bulk RNA-seq]

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: Sciatic nerve crush (SNC) triggers sterile inflammation within the distal nerve and deafferented dorsal root ganglia (DRGs). Granulocytes and pro-inflammatory Ly6Chigh monocytes infiltrate the nerve first, and rapidly give way to Ly6C- inflammation-resolving macrophages. Inflammation in DRGs is dominated by tissue resident macrophages, with little contribution from hematogenous leukocytes. Single-cell transcriptomics analysis of injured nerve identified six macrophage subpopulations, repair Schwann cells, and mesenchymal cells as the main cell types. Macrophages at the nerve crush site are distinct from macrophages associated with degenerating nerve fibers. Monocytes and macrophages in the injured nerve “eat” cell corpses of apoptotic leukocytes and thereby promote an anti-inflammatory milieu. Myeloid cells in the injured nerve, but not DRGs, strongly express the receptor for the chemokine GM-CSF. In the absence of GM-CSF, conditioning-lesion induced regeneration of DRG neuron central projections is abolished. Thus, a carefully orchestrated immune response in the nerve is required for conditioning-lesion induced neurorepair.

overall_design: Comparative analysis of transciptomic changes in the sciatic nerve and lumbar (L) 3-5 DRGs following sciatic nerve crush

first: Ashley

middle: L

last: Kalinski

first: Choya

last: Yoon

first: Lucas

last: Huffman

first: Patrick

middle: C

last: Duncker

first: Rafi

last: Kohen

first: Ryan

last: Passino

first: Hannah

last: Havner

first: Craig

last: Johnson

first: Kevin

last: Carbajal

first: Sebastian

last: Rojas

first: Edmond

last: Hollis

last: Geschwind

first: Benjamin

last: Segal

first: Roman

last: Giger


title: Expression data from adult mouse heart

first: Zhongzhou

last: Yang

state: Jiangsu

address: 12 Xuefu Road

department: Model Animal Research Center

institute: Nanjing University

summary: We isolated mRNA from adult mouse (C57BL/6J background) hearts and performed mRNA micro-array analysis to compare gene expression profiles between control and Rhau-deletion mice (inducible deletion by tamoxifen).

overall_design: Total RNA was isolated from the hearts of mice (CAAG-ERT2-Cre;Rhau F/F and Rhau F/F mice) at 2 months after tamoxifen administration. Then, RNA samples were applied for microarray analysis (Affymetrix Mouse 430 2.0 Array, Shanghai Biotechnology Co. Ltd.).

first: Mingyang

last: Jiang


title: Multi-influential interactions controls behaviour and cognition through a limited number of pathways in Down syndrome mouse models (Dp3Yah)

first: maria

last: muñiz moreno

overall_design: The gene expression profile of the hippocampus of five male controls littermates and five male mutant trisomic mice from the following Down Syndrome models: Dp1Yey, Dp3Yah, Ts65Dn, Dp5Yah.Dp1Rhr (also noted Dp5/Dp1), Dp5Yah, Dp1Rhr and Tg(Dyrk1a) was analyzed using the Affymetrix GeneChip® Gene 1.0 ST Array System for Mouse   We analyzed the differences in gene expression between each mutant trisomic mice model and their respective control littermates independently as they were independent experiments. The only exception is for Dp5/Dp1, Dp5Yah and Dp1Rhr, as these animals  were gen-erated using the same breeding by crossing Dp5Yah/ control mice Dp1Rhr/ control mice mice they share the same control littermates and are all part of the same independent experiment.   Then the differences and similarities in gene expression and functional dysregulation in all the models were assessed.

first: Arnaud

last: Duchon

first: Maria

last: Muñiz Moreno

first: Claire

last: Chevalier

first: Valérie

last: Nalesso

first: Veronique

last: Brault

first: Yann

last: Herault


title: Multi-influential interactions controls behaviour and cognition through a limited number of pathways in Down syndrome mouse models (Dp1Yey)


title: Multi-influential interactions controls behaviour and cognition through a limited number of pathways in Down syndrome mouse models (Ts65Dn)


title: The expression of circRNA in rheumatic valvular heart disease (RVHD) and healthy controls plasma samples

status: Public on Mar 16 2021

city: Ningbo

first: Linwen

last: Zhu

address: 57 Xingning Road, Yinzhou District

institute: Ningbo Medical Treatment Center Lihuili Hospital

summary: To determine the circRNA expression profile in RVHD and healthy controls plasma samples, we uesed circRNA microArray analysis form Arraystar to examine the expression of circRNAs in RVHD and healthy controls plasma samples.

overall_design: RVHD and healthy controls plasma samples were distributed into two experimental groups: RVHD plasma group and healthy controls plasma group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar)

first: Guofeng

last: Shao


title: Gene expression profiles of LMNA-V6 silencing or overexpression in HCT116 cells

city: Toskushima

first: Yuki

last: Kuwano

address: Kuramoto-cho

department: Pathophysiology

institute: The University of Tokushima Graduate School

summary: Lamin A/C proteins, major components of the nuclear lamina, are encoded by the LMNA gene. These proteins have multiple cellular functions. LMNA has implications in cancer; however, its mechanisms of dysregulation in cancer cells are not yet fully understood. Among the LMNA transcript variants, we focused on a spliced variant 6 (termed LMNA-V6), which contains unique 3 exons upstream of exon 1 of LMNA. In this study, after LMNA-V6 levels were modulated by overexpression or silencing in colon cancer HCT116 cells, gene expression profiles were measured using microarray analysis.

overall_design: One of mRNA variants of the LMNA gene, LMNA-V6, was overexpressed in colon cancer cells. After we overexpressed or reduced LMNA-V6 levels in colon cancer HCT116 cells, total RNA was extracted from cells using a RNeasy kit (Qiagen) and purified RNAs were labeled using a Low RNA Input Liner Amplification Kit and a succinimide-containing fluorescent dye (Cy3)-CTP according to the manufacturer’s protocol (Agilent). Expression profiles were measured using a whole human genome microarray (SurePrint G3 Human GE v3 8x60K; Agilent).


title: Multi-influential interactions controls behaviour and cognition through a limited number of pathways in Down syndrome mouse models

overall_design: Refer to individual Series


title: Comparison of transcriptomic adjustments to availability of sugar, cellular energy, and oxygen in germinating rice embryos

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

institute: GreenGene Biotech Inc.

summary: During germination, the availability of sugars, oxygen, or cellular energy fluctuates under dynamic environmental conditions, and the global RNA profile of rice genes can be affected by their availabilities. In the aerobically germinating rice embryos, most sugar-regulated genes are responsive to low energy and anaerobic conditions, indicating that sugar-regulation is closely associated with energy and anaerobic signaling. The interference pattern of sugar-regulation by either anaerobic or low energy conditions indicates that induction is likely the more prevalent regulatory mechanism than repression for the alteration in the expression of sugar-regulated genes in aerobically germinating rice embryos. Among the aerobically sugar-regulated genes, limited genes exhibit sugar regulation under anaerobic conditions, indicating that anaerobic conditions strongly influence sugar-regulated gene expression. Anaerobically responsive genes are highly overlapped with low-energy responsive genes. In particular, the expression levels of anaerobically downregulated genes are consistent with those induced by low energy-conditions, suggesting that anaerobic downregulation results from the prevention of aerobic respiration due to the absence of the final electron acceptor, i.e., molecular oxygen. It was noted that abscisic acid (ABA)-responsive genes were over-representative of the genes upregulated under low energy conditions, in contrast to the downregulated genes. This suggests that either ABA itself or upstream signaling components of the ABA signaling pathway are likely to be involved in the signaling pathways activated by low energy conditions.

overall_design: To test sugar-responsive gene expression in germinating rice embryos under either aerobic or anaerobic conditions, we analyzed saliva from 6 rice samples the Affymetrix RJpGene-1_1-st-v1. Data was processed by Affymetrix Gene Expression Array Computational Tool. Two techinical replicates were performed.

first: Mi-na

last: Lim

first: Yong-sic

last: Hwang


title: Multi-influential interactions controls behaviour and cognition through a limited number of pathways in Down syndrome mouse models (RNA-Seq reanalysis I)

relation:
Reanalysis of: GSM1338325
Reanalysis of: GSM1338326
Reanalysis of: GSM1338327
Reanalysis of: GSM1338328
Reanalysis of: GSM1338329
Reanalysis of: GSM1338330
Reanalysis of: GSM1338331
Reanalysis of: GSM1338332
Reanalysis of: GSM1338333
Reanalysis of: GSM1338334
Reanalysis of: GSM1338335
Reanalysis of: GSM1338336
Reanalysis of: GSM1338337
Reanalysis of: GSM1338338
Reanalysis of: GSM1338339
Reanalysis of: GSM1338340
SubSeries of: GSE149470


title: Examination of gene expression in S. mediterranea transitioning from recirculation to static culture in the presence or absence of Gentamycin at 0, 1, 2, 3, or 4 days

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: The interrelationship between endogenous microbiota, the immune system, and tissue regeneration is an area of intense research due to its potential therapeutic applications. In this study, we investigated the relationship between endogenous microbiota, host response, and regeneration in Schmidtea mediterranea, a model organism capable of regenerating any and all of its adult tissues. We performed deep sequencing of bacterial 16s rDNA under various perturbations to elucidate the composition and dynamics of the planarian microbiome. Microbiome characterization revealed a high Bacteroidetes to Proteobacteria ratio in healthy animals. Perturbations eliciting an expansion of Proteobacteria coincided with ectopic lesions and tissue degeneration. The culture of these bacteria yielded a strain of Pseudomonas capable of inducing progressive tissue degeneration. RNAi screening uncovered a TAK1 innate immune signaling module underlying compromised tissue homeostasis and regeneration during infection. TAK1/MKK/p38 signaling mediated opposing regulation of apoptosis during infection versus normal tissue regeneration. Given the complex role of inflammation in either hindering or supporting reparative wound healing and regeneration, this invertebrate model provides a basis for dissecting the duality of evolutionarily conserved inflammatory signaling in complex, multi-organ adult tissue regeneration.

overall_design: Whole worms transitioning from aseptic to septic conditions at 0, 1, 2, 3, or 4 days with or without Gentamycin were assayed for gene expression by RNA-Seq, in quadruplicate for a total of 36 samples.

first: Christopher

middle: P

last: Arnold

first: M

last: Merryman

first: Aleishia

last: Harris-Arnold

first: Sean

middle: A

last: McKinney

first: Sydney

last: Loethen

first: Kylie

last: Proctor

first: Longhua

last: Guo

first: Alejandro

last: Alvarado


title: Multi-influential interactions controls behaviour and cognition through a limited number of pathways in Down syndrome mouse models (Dp5Dp1)

first: maria

last: muñiz moreno

first: Arnaud

last: Duchon

first: Maria

last: Muñiz Moreno

first: Claire

last: Chevalier

first: Valérie

last: Nalesso

first: Veronique

last: Brault


title: scRNA-seq of E14 Bax null, Atoh7 null, and Bax null/Atoh7 null retinas

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

summary: Single Cell RNA sequencing using 10x Genomics 3' v2 chemistry assessing the consequence of Bax/Atoh7 loss of function on retinal ganglion cell development and retinal development

overall_design: RNA expression from 93,128 individual retinal cells at E14 of mouse development. Characterization of the gene expression changes in Bax mutant, Atoh7 mutant, or Bax/Atoh7 double mutant cells

first: Justin

last: Brodie-Kommit

first: Samer

last: Hattar


title: The mRNA-LNP platform’s lipid nanoparticle component used in preclinical vaccine studies is highly inflammatory

city: PHILADELPHIA

first: Botond

middle: Z

last: Igyártó

state: PA

address: 233 South 10th Street, Bluemle Life Science Building, Suite 620

department: Microbiology and Immunology

institute: Thomas Jefferson University

summary: Vaccines based on mRNA-containing lipid nanoparticles (LNPs) are a promising new platform used by two leading vaccines against coronavirus disease in 2019 (COVID-19). Clinical trials and ongoing vaccinations present with very high protection levels with varying degrees of side effects. However, the nature of the reported side effects remains poorly defined. Here we present evidence that LNPs used in many preclinical studies are highly inflammatory in mice. Intradermal injection of these LNPs led to rapid and robust inflammatory responses, characterized by massive neutrophil infiltration, activation of diverse inflammatory pathways, and production of various inflammatory cytokines and chemokines. The same dose of LNP delivered intranasally led to similar inflammatory responses in the lung and resulted in a high mortality rate.   In summary, here we show that the LNPs used for many preclinical studies are highly inflammatory.  Thus, their potent adjuvant activity and reported superiority comparing to other adjuvants in supporting the induction of adaptive immune responses could stem from their inflammatory nature. Furthermore, the preclinical LNPs are similar to the ones used for human vaccines, which could also explain the observed side effects in humans using this platform.

overall_design: A total of 8 samples are included in this study with 4 replicates each for naive and immunized mice.

last: Igyarto

first: Sonia

last: Ndeupen


title: Expression data from the cortex after middle cerebral artery occlusion (MCAO) between young and aged rats

city: Chengdu

first: Yingjia

state: Sichuan

address: 1 Keyuan 4 Road, Gaopeng Avenue

department: West China Hospital

institute: Sichuan University

summary:
Elderly patients suffer more brain damage in comparison with young patients from the same ischemic stroke. In that regard, it is imperative to investigate the factors responsible for decreased resistance to anti-ischemic/hypoxic injury in the aged brain.
We conducted analysis of the gene expression pattern on our samples (Transient MCAO for 60 minutes established acute ischemic stroke followed by 3 days reperfusion) by the Affymetrix rat 230 2.0 chip.

overall_design: First, differences between MCAO-subjected young and aged rats were determined, and then differential expression between sham-operated young and aged rats was then subtracted. Thus, differentially expressed genes between MCAO-subjected young and aged rats obtained using the above calculation were only due to the ischemia model.

first: Y

middle: J

last: Kang


title: Multi-influential interactions controls behaviour and cognition through a limited number of pathways in Down syndrome mouse models (Dp1Rhr)

first: Yann

last: Herault


title: Single-cell sequencing of human lacrimal gland tissue and organoids

city: Utrecht

first: Marie

last: Bannier-Hélaouët

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Human lacrimal gland tissue and organoids, cultured in expansion or differentiation, were FAC sorted into plates to follow the SORTseq protocol (Muraro et al., 2016).

overall_design: Human lacrimal gland tissue was obtained from the UMC Utrecht. Tissue was dissociated into single-cell and stained for EpCAM, NGFR or nothing. Then cells were sorted into plates. For human organoids, cells were cultured in expansion medium for 7 or 9 days and, to differentiate them, they were first split into expansion medium for 2 days then switched to differentiation medium for 7 days, as described before. Then, organoids were dissociated and FAC sorted.

first: Yorick

last: Post

first: Jeroen

last: Korving

first: Marc

last: Trani Bustos

first: Helmuth

last: Gehart

first: Harry

last: Beghtel

first: Yotam

middle: E

last: Bar-Ephraim

first: Jelte

last: van der Vaart

first: Rachel

last: Kalmann

first: Saskia

last: Imhoff

first: Hans

last: Clevers


title: Multi-influential interactions controls behaviour and cognition through a limited number of pathways in Down syndrome mouse models (TgDyrk1a)

first: maria

last: muñiz moreno

first: Arnaud

last: Duchon

first: Maria

last: Muñiz Moreno

first: Claire

last: Chevalier

first: Valérie

last: Nalesso

first: Veronique

last: Brault


title: Multi-influential interactions controls behaviour and cognition through a limited number of pathways in Down syndrome mouse models (Dp5Yah)

first: Yann

last: Herault


title: SIRT6 maintains redox homeostasis to promote porcine oocyte maturation

first: Li

last: Yu

address: No. 1 Weigang, Nanjing City, Jiangsu Province

institute: College of Animal Science and Technology, Nanjing Agricultural University

summary: SIRT6, the sixth member of sirtuin family proteins, has been identified as a crucial regulator in multiple molecular pathways related to aging, including genome stability, DNA damage repair, telomere maintenance and inflammation. However, the exact roles of SIRT6 during mammalian oocyte meiosis have not yet fully clarified. Here, we investigated the critical events during porcine oocyte meiotic maturation with the treatment of SIRT6 specific inhibitor SIRT6-IN-1. We found that SIRT6 inhibition resulted in oocyte meiotic failure by displaying the poor expansion of cumulus cells and reduced rate of polar body extrusion. Meanwhile, the compromised spindle assembly, chromosome alignment and actin dynamics were also observed in SIRT6-inhibited oocytes. Moreover, inhibition of SIRT6 led to the defective cytoplasmic maturation by showing the abnormal distribution of cortical granules and their component ovastacin. Notably, we identified that expression of genes related to oocyte meiosis, oxidative phosphorylation and cellular senescence was remarkably altered in SIRT6-inhibited oocytes by transcriptome analysis, and validated that the meiotic defects caused by SIRT6 inhibition resulted from the excessive ROS-induced early apoptosis in oocytes. Taken together, our findings demonstrate that SIRT6 promotes the porcine oocyte meiotic maturation via maintaining the organelle dynamics.

overall_design: Transcriptomic analysis of oocytes at M II stage was carried out using a protocol for RNA-Seq. The constructed library was sequenced with Illumina platform.

first: Bo

last: Xiong


title: Gene Expression Signature Predicts Relapse in Adult Patients with Cytogenetically Normal Acute Myeloid Leukemia

city: Columbus

first: Christopher

last: Walker

state: Ohio

address: 1276 Eastwood Ave

institute: Ohio State

summary: Although approximately 80% of adult patients with cytogenetically normal acute myeloid leukemia (CN-AML) achieve a complete remission (CR), over half of them relapse. Better identification of patients who are likely to relapse can help inform clinical decisions. We performed RNA sequencing on pretreatment samples from 268 adults with de novo CN-AML younger than 60 years who achieved a CR after induction treatment with standard “7+3” chemotherapy. After filtering for genes whose expressions were associated with gene mutations known to impact on outcome (i.e., CEBPA, NPM1, and FLT3-internal tandem duplication [FLT3-ITD]), we identified a 10-gene signature strongly predictive of patient relapse (area under the curve [AUC]=0.81). The signature consisted of seven coding genes: GAS6, PSD3, PLCB4, DEXI, JMY, NRP1, C10orf55, and three long non-coding RNAs. In multivariable analysis, the 10-gene signature was strongly associated with relapse (P<.001), after adjustment for the FLT3-ITD, CEBPA and NPM1 mutational status. Validation of the expression signature in an independent patient set from The Cancer Genome Atlas showed the signature’s strong predictive value with AUC=0.78. Implementation of the 10-gene signature into clinical prognostic stratification could be useful for identifying patients likely to relapse.

overall_design:
Total transcriptome RNA sequencing (RNAseq) was performed using pretreatment blood or bone marrow samples from 268 adult CN-AML patients younger than 60 years, who were similarly treated with intensive chemotherapy on Cancer and Leukemia Group B (CALGB) (now part of Alliance for Clinical Trials in Oncology [Alliance]) therapeutic trials (see Supplementary Methods), and who achieved a CR. The patient cohort did not include patients with AML secondary to antecedent hematologic disorder or patients with therapy-related AML. RNAseq reads were aligned to hg38 using HISAT2, and gene counts were obtained using featureCounts. Normalization was performed with DeSeq2, which divides counts by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene.
Note from submitter: we were advised that submission of fastq or bam files would raise concerns about the privacy of these patients and their consent.

first: Krzysztof

last: Mrózek

first: Hatice

middle: G

last: Ozer

first: Deedra

last: Nicolet

first: Jessica

last: Kohlschmidt

first: Dimitrios

last: Papaioannou

first: Luke

middle: K

last: Genutis

first: Marius

last: Bill

first: Bayard

last: Powell

first: Geoffrey

last: Uy

first: Jonathan

last: Kolitz

first: Andrew

last: Carroll

first: Richard

last: Stone

first: Ramiro

last: Garzon

first: John

last: Byrd

first: Ann-Kathrin

last: Eisfeld

first: Albert

last: de la Chapelle

first: Clara

last: Bloomfield


title: Harnessing Features of Adaptive NK Cells to Generate iPSC-Derived NK Cells for Enhanced Immunotherapy

city: Minneapolis

first: Frank

middle: Martin

last: Cichocki

address: 420 Delaware Street SE

department: Department of Medicine

institute: University of Minnesota

summary: Cell-based immunotherapy can control bulky tumors, but effector cell persistence, tumor resistance, inconsistencies of the manufactured product, and treatment cost continue to pose challenges. To address these limitations, we developed a triple gene-edited induced pluripotent stem cell (iPSC) platform for broad patient-based adoptive cell therapy. iPSCs were engineered to express a high affinity, non-cleavable version of the Fc receptor CD16a to augment antibody-mediated activity and a membrane-bound IL-15/IL-15R fusion (IL-15RF) protein to promote survival and maturation. The third edit was knockout of the ecto-enzyme CD38 that hydrolyzes NAD+ and is the target of the therapeutic antibody daratumumab. Natural killer (NK) cells derived from these iPSCs displayed metabolic features and gene expression profiles similar to those of adaptive NK cells that arise in response to cytomegalovirus (CMV) infection. These engineered iPSC-derived NK cells, termed iADAPT, persisted in vivo in the absence of exogenous cytokine and could be combined with daratumumab for efficient killing of multiple myeloma and acute myeloid leukemia cells both in vitro and in vivo. This strategy has broad off-the-shelf potential for the treatment of patients with advanced cancer.

overall_design: 10,000 cells of each sample was submitted for sequencing to target at least 50,000 reads per cell

first: Karrune

last: Woan

first: Hansol

last: Kim

first: Ryan

last: Bjordahl

first: Zachary

middle: B

last: Davis

first: Svetlana

last: Gaidarova

first: Sajid

last: Mahmood

first: Ramzey

last: Abujarour

first: Hongbo

last: Wang

first: Katie

last: Tuininga

first: Bin

last: Zhang

first: Cheng-Ying

last: Wu

first: Behiye

last: Kodal

first: Melissa

last: Khaw

first: Laura

last: Bendzick

first: Paul

last: Rogers

first: Moyar

middle: Q

last: Ge

first: Greg

last: Bonello

first: Miguel

last: Meza

first: Martin

last: Felices

first: Janel

last: Huffman

first: Thomas

last: Dailey

first: Tom

middle: T

last: Lee

first: Bruce

last: Walcheck

middle: R

last: Blazar

first: Yenan

last: Bryceson

first: Bahram

last: Valamehr

first: Jeffrey

middle: S

last: Miller


title: H3K4 methylation buffers the effects of metabolic adaptation on replication initiation

city: Taipei

first: Cheng-Fu

last: Kao

address: 128, Academia Rd., Sec. 2, Nankang

department: Institute of Cellular and Organismic Biology

institute: Academia Sinica

summary: In this study, we unravel a previously unknown function of H3K4 methylation (H3K4me; a universal marker of actively transcribed genes that also accumulates around replication origins) as a capacitor that masks the adverse effects of metabolic adaptation by facilitating initiation of replication.

overall_design: 20 Samples of  Rpb3, Mcm4 ChIP-Seq or ATAC-seq for S.cerevisiae in wild type and relevant mutant conditions.

first: Chia-Ling

last: Hsu

first: Wei-Chun

last: Hsiao

first: Hsin-Yi

last: Tseng

first: Chen-Yi

last: Wang

first: Ya-Ling

last: Chen

first: Chung-Shu

last: Yeh

first: Chun-Mei

last: Hu

first: Tien-Hsien

last: Chang


title: TBL1XR1 ensures balanced neural developmental through NCOR complex-mediated regulation of the MAPK pathway

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: TBL1XR1 gene is associated with multiple developmental disorders presenting several neurological  aspects. The relative protein is involved in regulation of important cellular pathways and master  regulators of transcriptional output including nuclear receptor repressors, Wnt signaling, and MECP2  protein. However, TBL1XR1 mutations (including complete loss of its functions) have not been  experimentally studied in neurological context, leaving a lack of knowledge in the mechanisms at the  basis of the diseases. We show that Tbl1xr1 knock-out mice exhibit behavioral and neuronal  abnormalities. Either the absence of TBL1XR1, or point mutations interfering with  stability/regulation of NCOR complex induced decreased proliferation and increased differentiation  in neural progenitors. We suggest that this developmental unbalance is due to the failure in the  regulation of MAPK cascade. Together, our results broaden the molecular and functional aftermath  of TBL1XR1 deficiency associated with human disorders.

overall_design: 3x Tbl1xr1 flox/flox NSCs infected with Cre, 3x Tbl1xr1 flox/flox NSCs infected with GFP

first: Alessandro

last: Sessa

first: Mattia

last: Zaghi

first: Vania

last: Broccoli


title: EKLF/Klf1 expression specifies a unique macrophage subset during mouse erythropoiesis

city: New York

first: Kaustav

last: Mukherjee

state: NY

address: 1 Gustave Levy Place

department: Cell, Developmental and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

summary:
Purpose: We characterized the role of EKLF in erythroblast island macrophages in E13.5 mouse fetal liver by analysing the transcriptomes of F4/80+ macrophages from WT and EKLF-/- by RNA-Seq. In addition we analyzed the transcriptomes of F4/80+ fetal liver macrophages from an EKLF/GFP mouse, where GFP acts as a surrogate for EKLF expression, to determine the genes enriched in EKLF/GFP+ macrophages compared to EKLF/GFP- macrophages where EKLF is not expressed. Finally, we used single cell RNA sequencing to resolve the heterogeneous population of F4/80+ macrophages from WT.
Methods: For RNA-Seq from WT and EKLF-/- F4/80+ macrophages were FACS sorted from primary E13.5 mouse fetal livers and RNA was isolated using the Trizol method. F4/80+ macrophages were also FACS sorted from the EKLF/GFP mouse and the GFP+ and GFP- populations were collected. The GFP+ population had low cell numbers and therefore RNA was isolated using an Agilent RNA Nanoprep kit. For single cell sequencing, E13.5 fetal livers were stained with F4/80-PE antibody and the F4/80-PE+ cells were purified using an EZ-Sep PE selection kit (mouse). 25,000 cells were submitted for single cell sequencing for the Chromium V3 platform. Library preparation was done using the standard Illumina Truseq workflow, and libraries were sequenced in a Hiseq 2500 for WT and EKLF-/-, or Novaseq for EKLF/GFP and single cell sequencing.
Results: We found that 1954 genes are differentially expressed in EKLF-/- F4/80+ macrophages vs WT and 2330 genes are differentially enriched in EKLF/GFP+ F4/80+ macrophages using DESeq2. Of these, 504 are common and constitute the EKLF-dependent gene expression program in F4/80+ fetal liver macrophages. We resolved the F4/80+ WT macrophages into 13 clusters based on gene expression and find that 23% of the total F4/80+ cells express EKLF.
Conclusions: We find that the F4/80+ fetal liver macrophage are a unique cell type. We identify the EKLF-dependent gene expression program in these macrophages and determine an important transcription circuit governed by EKLF that constitute cell cycle and other Klf and Sp family transcription factors. Single cell sequencing showed a highly heterogeneous population of macrophages with activated macrophage as well as erythro-myeloid characteristics. Based on the expression of EKLF, we identified specific cell surface markers for EKLF+ F4/80+ macrophages.

overall_design: Bulk RNA-Seq: EKLF+/+ F4/80+ vs EKLF-/- F4/80+ E13.5 fetal liver.  Bulk RNA-Seq: EKLF/GFP+ F4/80+ vs EKLF/GFP- F4/80+ E13.5 fetal liver. Single cell RNA-Seq F4/80+ EKLF+/+ E13.5 fetal liver.

first: Antanas

last: Planutis

first: Xue

last: Li

first: James

last: Bieker


title: CD81 marks immature and dedifferentiated pancreatic β-cells

city: Garching

first: Maren

last: Büttner

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

summary: We performed 3 single-cell RNAseq experiments to dissect the postnatal islet heterogeneity. In order to reach our goal, we used the Fltp lineage tracing (FltpiCre mTmG) mouse line. Thus we used mice at the age of 16 days, isolated islets of Langerhans from them and sorted via flow cytometry the three Fltp subpopulations.

overall_design: 3 single-cell RNA-seq experiments were performed using 10X Genomics technology to generate single cell transcriptomic profiles of pancreatic islets of Langherans. Cells were sorted to according to the fluorescence of our lineage tracing mouse model and processed separately.

first: Ciro

last: Salinno

first: Perla

last: Cota

first: Sophie

last: Tritschler

first: Marta

last: Tarquis-Medina

first: Aimee

last: Bastidas-Ponce

first: Katharina

last: Scheibner

first: Ingo

last: Burtscher

first: Anika

last: Böttcher

first: Fabian

last: Theis

first: Mostafa

last: Bakhti

first: Heiko

last: Lickert


title: Transcriptomic analysis of the RNA-binding RsmA proteins in Pseudomonas syringae

city: Urbana

first: Frank

last: Zhao

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: This RNA-seq analysis examined the global effect of the RNA binding RsmA proteins in P. syringae under the T3SS-inducing condition and in KB medium.  The results showed differential expression of more than 50% genes in the genome, which include significant down-regulation of T3SS genes.

overall_design: Differential gene expression of the rsmA2 and rsmA2/A3 mutants versus wild type grown in the T3SS-inducing condition at 18 °C and KB medium at 28 °C.

first: Jun

last: Liu

first: Menghao

last: Yu

first: Youfu


title: Deregulated Expression of Circular RNAs in Acute Myeloid Leukemia

city: Ulm

first: Susanne

last: Lux

address: Albert-Einstein-Allee 23

institute: University Hospital Ulm

summary: Circular RNAs (circRNAs) are dynamically regulated during differentiation and show cell-type specific expression, which is altered in cancer and can have a direct impact on various hallmarks of cancer. In accordance, we hypothesized that circRNA expression is deregulated in acute myeloid leukemia (AML), and that circRNA candidates might contribute to the pathogenesis of the disease. To identify leukemia-specific and differentiation-independent changes in circRNA expression, we determined the whole circular RNAome of 61 AML patients and 16 healthy hematopoietic stem and progenitor cell (HSPC) samples using ribosomal RNA-depleted RNA sequencing. We found hundreds of circRNAs that were differentially expressed between AML and healthy HSPCs. Gene set analysis found that many of these circRNAs were transcribed from genes implicated in leukemia biology. We discovered a circRNA derived from the T cell transcription factor gene BCL11B, circBCL11B, which was exclusively expressed in AML patients and associated with a T cell-like gene expression signature. We were able to validate this finding in an independent cohort of 332 AML patients, and knockdown of circBCL11B had a negative effect on leukemic cell proliferation, thereby suggesting circBCL11B as a novel functionally relevant candidate in AML pathogenesis. In summary, our study enables comprehensive insights into circRNA expression changes upon leukemic transformation, and provides valuable information on the biology of leukemic cells and potential novel pathway dependencies relevant for AML therapy.

overall_design: Ribosomal RNA-depleted RNAseq of 61 AML patient samples (including NPM1mut, t(8;21), inv(16), U2AF1mut, SF3B1mut, SRSF2mut) and 16 healthy samples of mobilized CD34+ HSPCs

first: Lars

last: Bullinger


title: Transcriptome sequencing analysis for NCI-H209 lung tumor cells conditioned by human brain microvascular endothelial cells

city: shengyang

first: Bo

last: Li

state: Liaoning

address: shengyang puhe road 77

department: Department of Developmental Cell Biology

institute: China medical university

summary: Endothelial cells of blood vessel playing a key role in the metastasis of tumor cells particularly the brain microvascular endothelial cells in the brain-tropic metastasis of lung tumor cells. Currently, studies towards the influence contributed by tumor cells to the alteration of endothelial cells have been extensively conducted by contrast studies for the alteration of gene-expression signature of tumor cells under the influence of endothelial cells remains poorly characterized, thus in this study the transcriptome of the human small-cell lung cancer cell NCI-H209 was sequenced via RNA-Seq after conditioned by human brain microvascular endothelial cell (HBMEC) for characterizing the alteration of gene-expression signature.

overall_design: mRNA expression signatures of 5 samples of tumor cells were profiled, among of which three samples belonging to control group and the other two making up the experiment group conditioned by human brain microvascular endothelial cells

first: Xuge

last: Wei

first: Kewei

last: Bi


title: The m6A reader CPSF30-L regulates alternative polyadenylation affecting nitrate signaling in Arabidopsis

city: Beijing

first: Jing

last: Sun

address: No. 1 West Beichen Road

department: IGDB

institute: Chinese Academy of Sciences

summary: As the most ubiquitous internal modification of eukaryotic mRNA, m6A (N6-methyladenosine) modification plays a vital role in almost every aspect of mRNA metabolism. However, the evidence of m6A in regulating the alternative polyadenylation (APA) is limited. APA is controlled by a large protein-RNA complex with many components including CPSF30. Arabidopsis CPSF30 has two isoforms, the longer one named CPSF30-L containing an additional YTH (YT512-B Homology)-domain in the C terminus, which is unique in plant. In this study, we revealed that m6A modification directly regulated APA, by proving the capability of Arabidopsis CPSF30-L YTH domain binding to m6A substrate by using in vitro assay and structural studies. We observed that extensive genes shifted their poly(A) sites in cpsf30-2 and found that numerous genes altered polyadenylation site (PAS) that correlated well with previously identified m6A peaks, indicating that genes carry m6A modification are prone to be regulated by APA. Moreover, we found that several important genes involved in nitrate metabolism are amongst those genes with APA site alteration in cpsf30-2.And we could rescue these APA and nitrate metabolism defects by introducing the wild-type CPSF30-L, but not by m6A-binding defective mutants (W259A, W310A or Y319A), which explained the nitrogen signaling defects of cpsf30-2 discovered previously. Taken together, our results demonstrated that m6A modification could directly regulate APA in Arabidopsis and revealed the function of m6A reader CPSF30-L in nitrate signaling by controlling APA regulation. This study will shed new lights on the roles of m6A modification during RNA 3’-end processing in plant development.

overall_design: Investigate the role of AtCPSF30 in Alternative Polyadenylation

first: Yifeng

last: Hou

first: Xiaofeng

last: Cao


title: Bromodomain and extra-terminal (BET) inhibitors regulate NK cell biology by inhibiting BRD2 mediated NK cytolytic activity and BRD2/BRD4 mediated inflammatory function

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary: Natural killer cells are innate lymphocytes that play a pivotal role in the immune surveillance and elimination of transformed or virally infected cells. Using a combined chemico-genetic approach, we have identified that BET bromodomains BRD2 and BRD4 are central regulators of NK cell responses. We show that both BRD2 and BRD4 play a key regulatory function in controlling NK cell specific inflammatory responses. However, knockdown of BRD2 but not BRD4 impairs NK cell cytolytic response, highlighting a redundant role for BRD4 in regulating NK cell killing. We further show that the prototypic monovalent BET inhibitor impairs in vitro NK cell mediated killing of cancer target cells, while the bivalent BET bromodomain AZD5153 does not. We ascribe these differences to the preferential affinity of JQ1(+) to BRD2, while AZD5153 has a higher affinity for BRD4. Our work suggests that inhibiting BET bromodomains may be an effective therapeutic strategy for controlling inflammatory function. Given that BRD2 but not BRD4 inhibition can impair NK cell mediated killing, our findings also have clinical significance in light of the ongoing clinical application of BET bromodomains in oncology.

overall_design: Examination of JQ1 and AZD5153 treated NK, CD4, CD8 and monocytes from peripheral blood


title: Evaluation of differential gene expression in placental tissues exposed to the trichloroethylene metabolite S-(1,2-dichlorovinyl)-L-cysteine (DCVC)

city: San Diego

first: Elana

last: Elkin

state: CA

address: 5500 Campanile Drive

department: School of Public Health

institute: San Diego State University

summary: Trichloroethylene (TCE) is an industrial solvent and widespread environmental contaminant. Human TCE exposure is prevalent, though epidemiological studies testing TCE exposure and adverse birth outcomes are inconclusive. The TCE metabolite S-(1,2-dichlorovinyl)-L-cysteine (DCVC) exhibits toxicity at human-relevant concentrations in a placental cell line. To date, DCVC cytotoxicity mechanistic studies have been limited to single molecular signaling pathways and biological responses. In the current study, genome-wide gene expression and gene set enrichment analyses (GSEA) were used to identify novel genes and pathways altered by human exposure-relevant DCVC concentrations in human placental villous explant tissues. The results of this study were compared to a parallel study using the placental cell line HTR-8/SVneo.

overall_design: Placental villous explants were exposed in five independent experiments to 0 or 20 µM DCVC for 12 h in vitro; 10 samples in total.  Villous explants used for non-treated and treated groups, respectively within each experiment, were sourced and matched from the same placenta. Gene specific gene expression levels were compared between non-treated samples (controls) and samples treated with 20 µM DCVC for 12 h.

first: Kelly

middle: M

last: Bakulski

first: Justin

last: Colacino

first: Dave

last: Bridges

first: Brian

last: Kilburn

first: D

last: Armant

first: Rita

last: Loch-Caruso


title: Evaluation of differential gene expression in a placental cell line exposed to the trichloroethylene metabolite S-(1,2-dichlorovinyl)-L-cysteine (DCVC)

summary: Trichloroethylene (TCE) is an industrial solvent and widespread environmental contaminant. Human TCE exposure is prevalent, though epidemiological studies testing TCE exposure and adverse birth outcomes are inconclusive. The TCE metabolite S-(1,2-dichlorovinyl)-L-cysteine (DCVC) exhibits toxicity at human-relevant concentrations in a placental cell line. To date, DCVC cytotoxicity mechanistic studies have been limited to single molecular signaling pathways and biological responses. In the current study, genome-wide gene expression and gene set enrichment analyses (GSEA) were used to identify novel genes and pathways altered by human exposure-relevant DCVC concentrations in the human placental cell line HTR-8/SVneo. The results of this study were compared to a parallel study using placental villous exlant tissues.

overall_design: HTR-8/SVneo cells were exposed in four independent experiments to 0, 10 or 20 µM DCVC for 6 or 12 h in vitro; 24 samples in total. Gene specific gene expression levels were compared between non-treated samples (controls) and samples treated with 10 or 20 µM DCVC, with separate comparisons made for 6 h or 12 h treatments.


title: Creb5 establishes the competence for Prg4 expression in articular cartilage

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: Zhang et al. identify Creb5 as a transcription factor that is required for induction of Prg4 expression by TGFbeta and EGFR ligands. They show that Creb5 directly binds to two Prg4 promoter-proximal regulatory elements, working together with a more distal regulatory element to drive induction of Prg4 by TGFbeta. These findings provide new insight into the molecular regulation of Prg4 expression in superficial zone articular chondrocytes.

overall_design: We conducted RNA-seq, ATAC-seq, experiments using bovine superficial zone articular chondrocytes (SZC) and deep zone articular chondrocytes (DZC).

first: Cheng-Hai

last: Zhang

first: Yao

last: Gao

first: Unmesh

last: Jadhav

first: Han-Hwa

last: Hung

first: Alan

last: Grodzinsky

first: Andrew

last: Lassar


title: RNA-seq analysis of de larval ventral nerve cord (VNC) from kdm5[L854F] and enzymatically inactive kdm5[JmjC*]

city: Bronx

first: Julie

last: Secombe

address: 1300 Morris park ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: We performed a transcriptome analysis of the larval VNC in kdm5 WT, kdm5[L854F] and enzymatically inactive kdm5[JmjC] in order to identify genes contributing to the phenotypes observed in the mutants' neuromuscular junction (NMJ). We found that inactivation of the catalytic activity in kdm5[JmjC] causes dysregulation of genes related to glutamate metabolism while the mutation L854F leads to dysregulation of genes involved in microtubule cytoskeleton dynamics. We also found a group of genes dysregulated in both mutants that likely explain a common NMJ phenotype.

overall_design: VNC mRNA profiles of third instar larvae of wildtype (kdm5 140 rescued by a gKDM5 transgene), kdm5[L854F] homozygotes and  kdm5[JmjC*] homozygotes, in quadruplicate.

first: Helen

last: Belalcazar

first: Sumaira

last: Zamurrad

first: Emily

last: Hendricks

first: Faith

last: Leibl


title: DNMT3L is crucial for the osteogenesis ability of mesenchymal stem cells

first: Pao-Yang

last: Chen

address: 128 Academia Road, Section 2, Nankang

department: Institute of Plant and Microbial biology

summary: DNA methyltransferase 3-like (DNMT3L), an epigenetic modulating factor known to participate in facilitating de novo DNA methylation with DNMT3A and DNMT3B, is mainly expressed in pluripotent stem cells and germ cells. We observed that Dnmt3l deficiency imped mesenchymal stem cells (MSCs) self-renewal and proliferation by colony forming unit – fibroblast (CFU-F) assay and growth curve test. Furthermore, calcium precipitation is dramatically decreased after 14 days of osteogenic induction in Dnmt3l KO mice derived MSCs. We further investigated the gene expression pattern in undifferentiated and day 3 of osteogenic induction MSCs derived from wild type and Dnmt3l KO mice respectively by RNA-sequencing, and found that differentially expressed genes (DEGs) before osteogenesis are highlighted in various pathways related to bone and the DEGs from day 3 of osteogenic induction MSCs are associated with proliferation and differentiation. Collectively, these results indicate that Dnmt3l deficiency abrogated MSCs property and may play role in MSC differentiation potential. By these results, we suggested that transiently expressed DNMT3L in pluripotent stem cells contribute to mediation of epigenetic mark establishment and have a lasting effect in mesenchymal stem cells.

overall_design: gene expression analysis in undifferentiated and after 3 days of osteogenic induction of  MSCs which respectively derived from wild type and Dnmt3l KO mice,  two replicate

first: Jui-Hsien

last: Lu

first: Chih-Yi

last: Yang

first: Ming-Kang

last: Lee

first: Felix

last: Hsiao

first: Ya-Ping

last: Yen

first: Chun-Chun

last: Cheng

first: Hung-Fu

last: Liao

first: I-Hsiun

last: Liu

first: Yi-Jing

first: Shau-Ping

last: Lin


title: Bulk RNA sequencing of WT and Pax6-KO mouse lacrimal gland organoids under expansion and differentiation conditions

first: Marie

last: Bannier-Hélaouët

address: Uppsalalaan 8

summary: First, we determined the gene expression profile of WT mouse lacrimal gland tissue and organoids in expansion and in differentiation. Then, we sought the differences between WT and Pax6-KO mouse lacrimal gland organoids in expansion and in differentiation.

overall_design: Mouse lacrimal gland tissue (n = 3), mouse lacrimal gland organoids cultured in expansion for 7 days (EM, n = 3) and cultured in expansion for 2 days then in differentiation for 5 days (DM, n = 3). To determine the effect of Pax6-KO, we established 2 WT and 2 Pax6-KO clonal lines, that were each exposed to EM and to DM for 7 days before being subjected to bulk RNA sequencing.

first: Yorick

last: Post

first: Jeroen

last: Korving

first: Marc

last: Bustos

first: Helmuth

last: Gehart

first: Harry

last: Beghtel

first: Yotam

last: Bar-Ephraim

first: Jelte

last: van der Vaart

first: Rachel

last: Kalmann

first: Saskia

last: Imhoff

first: Hans

last: Clevers


title: Ventricular, Atrial and Outflow Tract heart progenitors arise from spatially and molecularly distinct regions of the primitive streak

city: London

first: Kenzo

last: Ivanovitch

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Molecular characterisation of the primitive streak cells and cardiac progenitors

overall_design: Single cell RNA sequencing analysis on MS/LS -E6+21h-, OB/EB-E+3h- and EHF E7+14h mouse embryos  from tamoxifen treated TnEGP-CreERT2/+; R26Rtdtomato/R26Rtdtomato  animals at E6+5h, E6+21h and E7+7h respectively.

first: Pablo

last: Soro Barrio

first: Probir

last: Chakravarty

first: Jim

last: Smith


title: CRISPR/Cas9 screening of RNA binding proteins (RBPs) that regulate RUNX1 isoform production

city: La Jolla

first: Dong-Er

last: Zhang

address: 3855 Health Sciences Drive #0815

institute: UC San Diego Moores Cancer Center

summary: The proper balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for normal hematopoiesis and disrupted in hematologic malignancy. Among regulators of HSC fate, transcription factors have a well-defined, central role and mutations promote malignant transformation. More recently, studies have illuminated the importance of post-transcriptional regulation by RNA-binding proteins (RBPs) in hematopoiesis and leukemia development. However, the RBPs involved and breadth of regulation are only beginning to be elucidated. Furthermore, the intersection between post-transcriptional regulation and hematopoietic transcription factor function is poorly understood. Here, we studied the post-transcriptional regulation of RUNX1, a key hematopoietic transcription factor.  Alternative polyadenylation (APA) of RUNX1 produces functionally antagonistic protein isoforms (RUNX1a versus RUNX1b/c) that mediate HSC self-renewal versus differentiation, an RNA-processing event that is dysregulated in malignancy. Consequently, RBPs that regulate this event directly contribute to healthy and aberrant hematopoiesis. We modeled RUNX1 APA using a split GFP minigene reporter and confirmed the sensitivity of our model to detecting changes in RNA-processing. We utilized this reporter in a CRISPR screen consisting of single guide-RNAs exclusively targeting RBPs and uncovered HNRNPA1 and KHDRBS1 as antagonistic regulators of RUNX1a isoform generation. Overall, our study provides mechanistic insight into the post-transcriptional regulation of a key hematopoietic transcription factor and identifies RBPs which may have a widespread, important function in hematopoiesis.

overall_design: CRISPR screen of enriched sgRNAs targeting RBPs in GFP high and low cell populations compared to the bulk cell population at day 21, by sequencing of gDNA in biological duplicates. Day 0 gDNA sequencing in biological duplicates was also compared to day 21. Also included are 3'RNA sequencing data from three biological replicates of healthy, human common myeloid progenitors (CMPs) isolated from leukapheresis products. Bigwig files were generated to visualize poly(A) site usage of the RUNX1 gene.

first: Amanda

last: Davis


title: DROSHA is recruited to DNA damage sites by the MRN complex to promote non-homologous end-joining

status: Public on Mar 15 2021

city: Pavia

first: Sofia

last: Francia

address: Via Abbiategrasso, 207

institute: Istituto di Genetica Molecolare - Consiglio Nazionale delle Ricerche (IGM-CNR)

summary: The DNA damage response (DDR) is the signaling cascade that recognizes DNA double-strand breaks (DSB) and promotes their resolution via the DNA repair pathways of Non-Homologous End Joining (NHEJ) or Homologous Recombination (HR). We and others have shown that DDR activation requires DROSHA. However, whether DROSHA exerts its functions by associating with damage sites, what controls its recruitment and how DROSHA influences DNA repair, remains poorly understood. Here we show that DROSHA associates to DSBs independently from transcription.  Neither H2AX, nor ATM nor DNA-PK kinase activities are required for its recruitment to break site. Rather, DROSHA interacts with RAD50 and inhibition of MRN by Mirin treatment abolishes this interaction. MRN inactivation by RAD50 knockdown or mirin treatment prevents DROSHA recruitment to DSB and, as a consequence, also 53BP1 recruitment. During DNA repair, DROSHA inactivation reduces NHEJ and boosts HR frequency. Indeed, DROSHA knockdown also increase the association of downstream HR factors such as RAD51 to DNA ends. Overall, our results demonstrate that DROSHA is recruited at DSBs by the MRN complex and direct DNA repair toward NHEJ.

overall_design: gH2AX ChIP-seq, 1 replicate per condition, 2 conditions (Induced and Uninduced)  DROSHA ChIP-seq, 1 replicate per condition, 2 conditions (Induced and Uninduced)

first: Matteo

last: Cabrini

first: Marco

last: Roncador

first: Alessandro

last: Galbiati

first: Lina

last: Cipolla

first: Antonio

last: Maffia

first: Fabio

last: Iannelli

first: Simone

last: Sabbioneda

first: Fabrizio

last: d'Adda di Fagagna


title: Expression data from adult mouse adrenal tissue.

city: Riyadh

first: Katharine

middle: Sara

last: Collison

state: Central

address: Riyadh, Saudi Arabia

department: Cell Biology

country: Saudi Arabia

institute: King Faisal Specialist Hospital and Research Center

summary:
Two strains of rodent C57Bl/6J and KK/HIJ were compared to find the most suitable rodent model of obesity and type 2 diabetes. KK/HIJ become larger and glucose intolerant on standard chow but are not as well characterized as the C67Bl/6J model which has a more defined behavioral phenotype. The present study is to asses and determie the most suitable mouse model for our research.
We used microarray analysis to examine differences in gene expression in C57Bl/6J and KK/HIJ , male and female adult rodent mice

overall_design: Total of 12 samples analyzed, in replicates of 3.

first: Kate

first: Angela

last: Inglis

first: Sarah

last: Farooq


title: Expression data from adult mouse pancreas.

summary:
Two strains of rodent C57Bl/6J and KK/HIJ were compared to find the most suitable rodent model of obesity and type 2 diabetes. KK/HIJ become larger and glucose intolerant on standard chow but are not as well characterized as the C67Bl/6J model which has a more defined behavioral phenotype. The present study is to asses and determie the most suitable mouse model for our research.
We used microarray analysis to examine changes in adult rodent pancreatic gene expression.


title: EphA2-SE-KO RNA-seq

city: Harbin

first: Qiong

last: Wu

address: No.92, Xidazhi Street

institute: Harbin Institute of Technology

summary: We used Crispr/Cas9 technology to establish a homozygous clone of EphA2-SE deletion in tumor cells. Wild-type cells (WT) and homozygous cloned cells (EphA2-SE-/-) were selected for high-throughput data detection.

overall_design: mRNA profiles of WT and EphA2-SE-/- cells.

first: Shuang

last: Cui


title: Transcriptional changes in alveolar macrophages from adults with asthma after intrabronchial allergen challenge.

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

summary: In recent years, alveolar macrophages (AM) have been shown to play an important role in environmental allergen-induced airway inflammation in asthma. In this study, we investigated the effect of house dust mite (HDM) and lipopolysaccharide  (LPS) challenge on the transcriptome of AM from patients with mild asthma. We have shown previously that intrabronchial HDM/LPS challenge induces a mixed eosinophilic and neutrophil airways inflammation in asthma patients(5). Therefore, we hypothesize that exposure of AM to HDM/LPS would upregulate genes associated with eosinophil and neutrophil signaling. AM were harvested from the bronchoalveolar fluid of 8 asthma patients who were challenged with either saline in one lung segment or HDM/LPS in the contralateral lung segment. We performed RNA sequencing and found over 1000 significantly different expressed genes following HDM/LPS challenge. To the best of our knowledge, this is the first investigation to examine gene expression profiles in AM from asthma patients challenged with HDM and LPS in vivo. Using a well-controlled study design allowing paired analysis of saline and HDM/LPS effects in the same patient, we identified different transcriptional profiles in AM as consequence of local exposure to HDM and LPS. These findings may provide a better understanding of AM functions in (exacerbations of) allergic asthma.

overall_design: House dust mite (HDM) and lipopolysaccharide  (LPS) challenged alveolar macrophages (n=8); saline control alveolar macrophages (n=8)

first: Jack

last: Yang

first: Tom

last: van der Poll


title: Differential gene expression analysis of Wildtype and NMD deficient mutants grown at 16 and 27°C Long day condition

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

institute: Korea University

summary: We sequenced mRNA of WT, upf1-5, upf3-1 and their double mutant seedlings grown at 16C and 27°C, day 8 after germination, ZT 16

overall_design: Examination of mRNA level in WT and NMD deficient mutant seedling grown at 16 and 27°C

first: Nasim

last: Zeeshan

first: Fahim

last: Muhammad

first: Ji-Hoon

last: Ahn