status: Public on Dec 18 2022

city: shanghai

first: xiaomeng

last: cheng

state: Shanghai

address: Jiangwan Campus of Fudan University, 2205 Songhu Road, Yangpu District, Shanghai, China

institute: Fudan University

summary: Knockdown LRRK1-CAPT in NCI-H1299 lung cancer cell line by two independent siRNAs, to investigate the mechanism of LRRK1-CAPT in regulation of cell proliferation.

first: Zhaozhao

last: Zhao

first: Ting

last: Ni


title: Effect of Smc and interaction with ParA on ParB binding to DNA in Pseudomonas aeruginosa

status: Public on Dec 17 2022

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In the majority of bacterial species, the tripartite ParAB-parS system, composed of an ATPase (ParA), a DNA-binding protein (ParB), and its target parS sequence(s), assists in the chromosome partitioning. ParB forms large nucleoprotein complexes at parS(s), located in the vicinity of oriC, which after replication are subsequently relocated by ParA to polar positions. It was shown that ParB-parS complexes are loading platforms for structural maintenance of chromosome (Smc) proteins, which juxtapose the two arms of the circular chromosome. In this work, we characterized the Pseudomonas aeruginosa ParB interactions with DNA in the absence of Smc and interaction with the cognate ParA using chromatin immunoprecipitation-sequencing (ChIPseq). We show that in strains lacking Smc or strains with disturbed ParB-ParA interactions  (ParA L84K or ParB G11A mutations) ParB is able to bind and spread around parS1-4 cluster and still binds to half-parS sites. Comparison of the ratio between the number of ChIP-seq reads mapping to region around parS1-4 with those mapping to ChIPseq peaks containing half-parSs indicate no major effect of the twod factors on the extent of  ParB spreading, thus suggesting that the mechanisms controlling ParB association with the DNA do not involve interaction with cognate ParA partner and Smc.

overall_design: Pseudomonas aeruginosa PAO1161 (leu-, r-, RifR) derivative of PAO1, was used in the experiment (Kawalek et al., 2020; BMC Genomics, 21:14). Chromatin immunoprecipitation and sequencing (ChIP-seq) analysis was performed on parental strain, Δsmc, parAstop Δsmc, and strains expressing ParB G11A or ParA L84K. A ΔparB strain was used as a background control. Cells were grown under in L broth until OD600 = 0.5. The immunoprecipitation was performed with polyclonal anti ParB antibodies, raised in rabbit and affinity purified (as in Reznekov et al., 1996, Genes Cells 1:529-542) and two replicates were performed for each strain (with the exception of ΔparB .

last: Kawalek

first: Aneta

middle: A

last: Bartosik

first: Jan

last: Gawor

first: Karolina

last: Zuchniewicz

first: Robert

last: Gromadka

first: Grazyna

last: Jagura-Burdzy


title: PfSET2 is involved in genome organization of var gene family in Plasmodium falciparum [ChIPseq_HP1]

status: Public on Dec 16 2022

city: Shanghai

first: Xuan

last: Cao

address: 320 Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health,  Chinese Academy of Sciences

summary: The three-dimensional (3D) genome structure of human malaria parasite Plasmodium falciparum is highly organized and plays important roles in regulating coordinated expression patterns of specific genes such as virulence genes which are involved in antigenic variation and immune escape. However, the molecular mechanisms that control 3D genome of the parasite remain elusive. Here by analyzing genome organization in P. falciparum, we identify high-interacting regions (HIRs) with strong chromatin interactions telomeres and virulence genes loci. Specifically, HIRs are highly enriched with repressive histone marks (H3K36me3 and H3K9me3) and form the transcriptional repressive center. Deletion of PfSETvs, which controls H3K36me3 level, results in marked reduction of both intra-chromosomal and inter-chromosomal interactions for HIRs. Importantly, such chromatin reorganization coordinates with dymamic changes in epigenetic feature in HIRs and specifically activation of var genes. Our results uncover a fundamental mechanism that the epigenetic factor PfSETvs controls the 3D organization of heterochromatin in regulating the transcription activities of var genes family in P. falciparum.

overall_design: ChIP-seq for wild-type and PfSETvs-KO samples at Ring stage in P.falciparum [ChIP-seq]

first: Gang

last: Wei


title: Next Generation Sequencing Facilitates Quantitative Analysis of  in 14-day-old wt and pkl seedlings.

status: Public on Dec 12 2022

city: Guangzhou

first: Liang

last: Zhenwei

state: Guangdong

address: Xingang West Road

department: School of Life Science

institute: Sun Yat-sen University

type: Expression profiling by high throughput sequencing

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: RNA from 14-day-old seedlings of wild-type and pkl was isolated using the RNAprep Pure Plant Kit as described above. RNAs from three biological replicates was sequenced separately at Novogene, using Illumina Hiseq X-Ten (Sequencing method: Hiseq-PE150).
Results: Reads were mapped to the TAIR10 Arabidopsis genome using TopHat (Galaxy V2.1.1 in usegalaxy.org) with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 5,000 bp were required (Paired-end). Then, mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks (version 2.1.1) with default settings. To analyze differential expression, the assembled transcripts from three independent biological replicates in Col and other mutants were included and compared using Cuffdiff (version 2.1.1) with default settings.
14-day-old seedling of WT and pkl were performed RNA-seq to analyzed their differential expression genes in Arabidopsis.

overall_design: Examination of global RNA expression in 14-day-old wt and pkl seedlings.

first: Zhenwei

last: Liang

first: Chenlong

last: Li


title: HexSDF are Required for Synthesis of a Novel Glycolipid that Mediates Daptomycin and Bacitracin Resistance in C. difficile

status: Public on Dec 10 2022

city: Iowa City

first: Anthony

last: Pannullo

state: IA

address: 431 Newton Road

country: USA

institute: University of Iowa

summary: Clostridioides difficile is a Gram-positive opportunistic pathogen that results in 250,000 infections, 12,000 deaths, and $1 billion in medical costs in the US each year. There has been recent interest in using a daptomycin analog, Surotomycin, to treat C. difficile infections. Daptomycin interacts with both phosphatidylglycerol and Lipid II to disrupt the membrane and halt peptidoglycan synthesis. C. difficile has an unusual lipid membrane composition as it has no phosphatidylserine or phosphatidylethanolamine, and ~50% of its membrane is composed of glycolipids, including the unique C. difficile lipid aminohexosyl-hexosyldiradylglycerol (HNHDRG). We identified a two-component system (TCS) HexRK that is required for C. difficile resistance to daptomycin. Using RNAseq we found that HexRK regulates a three gene operon of unknown function hexSDF. Based on bioinformatic predictions, hexS encodes a monogalactosyldiacylglycerol synthase, hexD encodes a polysaccharide deacetylase, and hexF encodes an MprF-like flippase. We find that deletion of hexRK leads to a 4-fold decrease in daptomycin MIC, and that deletion of hexSDF leads to an 8-16-fold decrease in daptomycin MIC. The ∆hexSDF mutant is also 4-fold less resistant to bacitracin but no other cell wall active antibiotics. Our data indicate that in the absence of HexSDF the phospholipid membrane composition is altered. In WT C. difficile the unique glycolipid, HNHDRG makes up ~17% of the lipids in the membrane. However, in a ∆hexSDF mutant, HNHDRG is completely absent. While it is unclear how HNHDRG contributes daptomycin resistance, the requirement for bacitracin resistance suggests it has a general role in cell membrane biogenesis.

overall_design: RNA-seq comparision of WT R20291 vs ∆hexRK

middle: G

first: Ziqiang

last: Guan

first: Howard

last: Goldfine

first: Craig

middle: D

last: Ellermeier


title: The identification of Dwg downstream targets using ChIP-seq

status: Public on Dec 14 2022

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: To study the autophagy related genes, we performed RNAi screens to identify new autophagic regulators. Dwg1 is one of new regulators of autophagy. We hypothesized that as an insulator, the Dwg protein might regulate autophagy through binding to insulator elements on chromatin and blocking enhancer functions. We therefore performed chromatin-immunoprecipitation followed by next-generation sequencing (ChIP-seq) to identify Dwg downstream targets. The results suggest that Dwg binds to the insulator elements present in/near the ATG genes, presumably suppressing their transcription.

overall_design: S2R+ cells expressing Flag-Dwg were subjected to ChIP assays using SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s protocol. DNA co-immunoprecipitation with either anti-Flag antibody or IgG control antibody was analyzed by deep DNA-sequencing or quantified by ChIP-qPCR.

first: Hong-Wen

last: Tang

first: Yifang

last: Liu

first: Norbert

last: Perrimon


title: PfSET2 is involved in genome organization of var gene family in Plasmodium falciparum [HiC]

overall_design: we generate Hi-C maps for wild-type and PfSETvs-KO samples at Ring stage in P.falciparum. Analysis of these datasets together with H3K9me3 and H3K36me3 and gene expression data allow us to uncover the changes in 3D genome with the epigenome changes and  regulation of antigenic variation in the parasite.


title: Single-cell sequencing of chicken spleen

status: Public on Dec 09 2022

city: Columbia

first: Wesley

middle: C

last: Warren

state: MO

address: 1201 Rollins St.

department: Bond Life Sciences Center

institute: University of Missouri

summary: We sequenced single cells with the 10x platform of chicken spleens from chickens genetically resistant and genetically susceptible to Marek's disease, with both infected individuals and uninfected controls from both lines

overall_design: A total of ten birds each from Marek's resistant and susceptible lines were incubated. Five from each line were infected with Marek's disease.

first: Edward

middle: S

last: Rice

first: Ashley

last: Meyer

first: Alec

last: Steep

first: Henry

last: Hunt

first: Melissa

last: Monson

first: Susan

middle: J

last: Lamont

first: Hans

middle: H

last: Cheng


title: Trans-cellular control of synapse properties by a cell type-specific splicing regulator

status: Public on Dec 08 2022

city: Basel

first: Peter

last: Scheiffele

state: Basel-Stadt

address: Spitalstrasse 41

country: Switzerland

institute: University of Basel

summary: The recognition of synaptic partners and specification of synaptic properties are fundamental for the function of neuronal circuits. 'Terminal selector' transcription factors coordinate the expression of terminal gene batteries that specify cell type-specific properties. Moreover, pan-neuronal alternative splicing regulators have been implicated in directing neuronal differentiation. However, the cellular logic of how splicing regulators instruct specific synaptic properties remains poorly understood. Here, we combine genome-wide mapping of mRNA targets and cell type-specific loss-of-function studies to uncover the contribution of the nuclear RNA binding protein SLM2 to hippocampal synapse specification. We find that SLM2 preferentially binds and regulates alternative splicing of transcripts encoding synaptic proteins, thereby generating cell type-specific isoforms. In the absence of SLM2, cell type-specification, differentiation, and viability are unaltered and neuronal populations exhibit normal intrinsic properties. By contrast, cell type-specific loss of SLM2 results in highly selective, non-cell autonomous synaptic phenotypes, altered synaptic transmission, and associated defects in a hippocampus-dependent memory task. Thus, alternative splicing provides a critical layer of gene regulation that instructs specification of neuronal connectivity in a trans-synaptic manner.

overall_design: eCLIP-seq

first: Lisa

last: Traunmüller

first: Jan

last: Schulz

first: Raul

last: Ortiz

first: Huijuan

last: Feng

first: Elisabetta

last: Furlanis

first: Andrea

last: Gomez

first: Dietmar

last: Schreiner

first: Josef

last: Bischofberger

first: Chaolin

last: Zhang


title: Cross-Species Single-cell Comparative Analysis of Amygdala

status: Public on Dec 13 2022

city: Beijing

first: qian

middle: qian

last: zhang

address: Datun road, chaoyang district

department: State Key Laboratory of Brain and Cognitive Science

institute: Institute of Biophysics

summary: The amygdala or amygdala-like structure in the brain are found in all vertebrates, and plays a critical role for emotional processing. But the cellular architecture of amygdala and how they evolved are still elusive. Here, we generated single-nucleus RNA-sequencing data for more than 200,000 cells in human, macaque, mouse and chicken amygdala. Abundant neuronal cell types derived from different subnuclei of amygdala were identified in all datasets. Cross-species analyses revealed GABAergic neurons and GABAergic neuron-enriched subnuclei of amygdala were well-conserved in cellular composition and marker gene expression, whereas glutamatergic neuron-enriched subnuclei were relatively divergent. Furthermore, we discovered that LAMP5+ interneurons were much more numerous in primates, while DRD2+ GABAergic neurons, LAMP5+ and SATB2+ glutamatergic neurons were predominant in the human central amygdalar nucleus (CEA) and basolateral amygdala complex (BLA), respectively. In addition, we also identified GABAergic neuron-enriched subnuclei of amygdala in the chicken. Altogether, our study highlight extremely cell-type diversity in the amygdala across species and their species-specifc adaptations.

sample_organism:
Gallus gallus
Macaca mulatta
Homo sapiens
Mus musculus

overall_design: To transcriptomically characterize cell types of the amygdala in mammals and sauropsids, which have been the most diverse and successful group of land vertebrates, we applied snRNA-seq assays (Chromium v3) and focused on human, macaque, mouse and chicken. Human samples were from postmortem donors with very short postmortem interval (within 6 hours), and macaque, mouse and chicken amygdala were freshly dissected. We profiled a total of 17 specimens, including 3 human amygdala samples, 3 macaque amygdala samples, 2 chicken amygdala homolog samples, 4 mouse amygdala samples, 3 mouse basolateral amygdala complex (BLA; made up of the lateral (LA), basal (BA) and basomedial (BM) nucleus) samples, and 2 mouse central amygdalar nucleus (CEA) samples

first: Bin

last: Yu

first: Qianqian


title: Transcriptomics of colorectal cancer in Siriraj cohort, Thailand (RNA-Seq)

status: Public on Dec 07 2022

city: Bangkok-noi

first: Chandhanarat

last: Chandhanayingyong

state: Bangkok

address: 2 Wanglang road

department: Orthopaedic Surgery

country: Thailand

institute: Mahidol University

summary: To investigate the transcriptomes in colorectal cancer patients, who were diagnosed and treated at Siriraj Hospital, Thailand, we performed gene expression profiling analysis using data obtained from RNA-seq and Nanostring platforms.

overall_design: Total RNA was extracted from primary colorectal cancer tissues for comparative gene expression profiling analysis using RNA-seq and Nanostring platforms and then classifying consensus molecular subtypes.

first: Vitoon

last: Chinswangwatanakul

first: Pariyada

last: Tanjak

first: Amphun

last: Chaiboonchoe


title: Transcriptomics of colorectal cancer in Siriraj cohort, Thailand

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

overall_design: Refer to individual Series


title: Leveraging the pulmonary immune response and microbiome for improved lower respiratory tract infection diagnosis in critically ill children

status: Public on Dec 06 2022

city: San Francisco

first: Charles

last: Langelier

state: CA

address: HSE 401, 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

summary:
BACKGROUND. Lower respiratory tract infection (LRTI) is a leading cause of death in children worldwide. LRTI diagnosis is challenging since non-infectious respiratory illnesses appear clinically similar and existing microbiologic tests are often falsely negative or detect incidentally-carried microbes common in children. These challenges result in antimicrobial overuse and adverse patient outcomes. Lower airway metagenomics has the potential to detect host and microbial signatures of LRTI. Whether it can be applied at scale and in a pediatric population to enable improved diagnosis and precision treatment remains unclear.
METHODS. We used tracheal aspirate RNA-sequencing to profile host gene expression and respiratory microbiota in 261 children with acute respiratory failure. We developed a random forest gene expression classifier for LRTI by training on patients with an established diagnosis of LRTI (n=117) or of non-infectious respiratory failure (n=50). We then developed a classifier that integrates the: i) host LRTI probability, ii) abundance of respiratory viruses, and iii) dominance in the lung microbiome of bacteria/fungi considered pathogenic by a rules-based algorithm.
RESULTS. The host classifier achieved a median AUC of 0.967 by 5-fold cross-validation, driven by activation markers of T cells, alveolar macrophages and the interferon response. The integrated classifier achieved a median AUC of 0.986 and significantly increased the confidence of patient classifications. When applied to patients with an uncertain diagnosis (n=94), the integrated classifier indicated LRTI in 52% of cases and nominated likely causal pathogens in 98% of those.
CONCLUSIONS. Lower airway metagenomics enables accurate LRTI diagnosis and pathogen identification in a heterogeneous cohort of critically ill children through integration of host, pathogen, and microbiome features.

overall_design:
Metagenomic RNA-sequencing of tracheal aspirate samples from n=261 children (aged 31 days to 18 years) with respiratory failure requiring mechanical ventilation.
--------------------------------------
Authors state "Raw data not provided due to patient privacy concerns".

first: Eran

last: Mick

first: Alexandra

last: Tsitsiklis

first: Jack

last: Kamm

first: Peter

middle: M

last: Mourani

middle: R


title: Effect of Twist2 knockdown on the transcriptional profile of differentiating 3T3-L1 cells

status: Public on Dec 04 2022

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

summary: TWIST2 is a transcription factor heavily involved in proper development. We queried the role of TWIST2 in 3T3-L1 adipogenesis by silencing gene expression using a lentiviral-delivered shRNA and performed RNA-seq at various time points following initiation of differentiation. We found that previously identified TWIST2-target genes increase in transcription, suggesting that TWIST2 acts as a transcriptional repressor in this system.

overall_design: RNA was harvested from 3T3-L1 cells at 0, 1, 2, or 4 hours differentiation. Differentiation was induced by addition of 0.25 U/mL Insulin, 250 nM dexamethasone, and 0.5 mM 3-isobutyl-1-methylxanthine.

first: Arun

middle: B

last: Dutta

first: Daniel

last: Lank


title: Nascent transcriptional profiling of CEM-C7 ALL cells treated with dexamethasone

summary: The glucocorticoid receptor (GR) is a transcription factor that localizes to the nucleus and reuglates gene expression upon binding of  a glucocorticoid ligand such as dexamethasone. We perform nascent transcriptional profiling of C7 ALL cells following treatment with dexamethasone to evaluate the immediate transcriptional effects of GR. We find 51 dynamic genes (46 activated, 5 repressed) after 1 hour treatment and 141 dynamic genes (70 activated and 71 repressed) after 4 hour treatment. We input RNA polymerase density in pause and gene body regions into a mathematical model designed to quantify rate changes of individual transcriptional steps. We find that dexamethasone treatment primarily activates genes by inducing pause release rate.

overall_design: Nuclei of CEM-C7 ALL cells were harvested after treatment with dexamethasone or ethanol for 0, 1, or 4 hours

first: Anna

last: Cetnarowska


title: Activation of ISR/ATF4 signaling depletes HIV reservoir in CD4+ T cells

status: Public on Dec 05 2022

first: Jeremy

last: Simon

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

summary: Latent HIV reservoirs are extremely stable which pose a tremendous challenge to eradicate HIV. Here, we show that HIV explores the integrated stress response (ISR) signaling to establish its quiescent infection, refractory to the clearance for its persistence. HA15, a recently characterized specific ISR agonist, activates ATF4/CHOP signaling to not only disrupt HIV latency but also reduce HIV+ cells in the primary CD4+ T cell model of HIV latency without the induction of cell death in the HIV negative primary CD4+ T cells and the impact of viability in resting CD4+ T cells isolated from people living with HIV (PLWH). Mechanistically, the reduction of HIV+ cells by ISR/ATF4 activation is associated with the enhancement of cellular apoptosis. However, this mainly occurs in the HIV translation negative CD4+ T cells. In fact, ISR/ATF4 activation-induced cell death largely occurs in HIV transcription active (HIV gag-pol) CD4+ T cells. This is involved in HIV RNA-induced innate immune IFIT signaling. During the acute SIV infection in the rhesus macaques, the induction of ATF4 is associated with decrease of SIV reservoir in the intestine in vivo. When further tested in the resting CD4+ T cells isolated from PLWH on ART, the induction of ISR/ATF4 signaling by HA15 reduced HIV DNA reservoir. These findings support that inactivation of ISR/ATF4 signaling is associated with the maintenance of the stable and quiescent HIV reservoirs while enforced ISR/ATF4 signaling reduces translation quiescent HIV reservoirs in CD4+ T cells.

overall_design: Single-cell RNA-seq (10X 3' scRNA-seq) in control and HA15-treated primary CD4+ T cell model of HIV latency, in biological triplicate. Samples were run simultaneously via hashtag oligo (HTO).

first: Guochun

last: Jiang

first: Dajiang

last: Li


title: Effects of glutamate release inhibition on the transcriptome of BA-NAc neurons

status: Public on Dec 01 2022

city: Biberach an der Riss

first: Gregorio

last: Alanis-Lobato

address: Birkendorfer Str 65

department: Global Computational Biology and Digital Sciences

country: Germany

institute: Boehringer Ingelheim Pharma

summary: Reduced reward interest/learning and reward-to-effort valuation are distinct, common symptoms in   neuropsychiatric disorders for which chronic stress is a major aetiological factor. Pyramidal glutamate   neurons in the basal amygdala (BA) project to various brain regions including nucleus accumbens   (NAc). The BA-NAc neural pathway is activated by reward and aversion, with many neurons being   monovalent. In adult male mice, chronic social stress (CSS) led to both reduced discriminative reward  learning (DRL) associated with decreased BA-NAc Ca2+ activity, and reduced sucrose reward-to-effort   valuation (REV) associated, in contrast, with increased BA-NAc Ca2+ activity. Chronic tetanus toxin   inhibition of BA-NAc neurons replicated the CSS-DRL effect whilst causing only a mild REV reduction,   whilst chronic DREADDs activation of BA-NAc neurons replicated the CSS effect on REV without   affecting DRL. This study provides novel evidence that chronic stress disruption of reward processing   involves the BA-NAc neural pathway; the bi-directional effects implicate activity changes in BA-NAc   reward (learning) and aversion (effort) neurons, with the net overall direction of stress-induced   change in activity dependent on on-going stimulus processing and behaviour.

overall_design: Assessment of the effects of glutamate neurotransmission inhibition on the transcriptome of BA-NAc "reward-sensitive" glutamatergic neurons when compared to non-inhibited control BA-Nac glutamatergic neurons.

first: Lorraine

last: Madur

first: Coralie

last: Viollet

first: Christopher

last: Pryce


title: The combination of XAGE-1 expression and tertiary lymphoid structures predicts prognosis in cutaneous angiosarcoma (Targeted RNA-Seq)

status: Public on Dec 03 2022

city: Nagoya

first: Tetsuya

last: Magara

address: 1 kawasumi, mizuho-tyo, mizuho-ku, Nagoya

country: Japan

institute: Nagoya City University

summary: To investigate tumor immune microenvironment in cutaneous angiosarcoma, we performed comprehensive RNA sequencing using Next-generation sequencer

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  FFPE biopsy samples obtained from patients with cutaneous angiosarcoma

first: Motoki

last: Nakamura

first: Maki

last: Yoshimitsu

first: Shinji

last: Kano

first: Yuka

last: Nojiri

first: Akihiro

last: Matsubara

first: Hiroshi

last: Kato

first: Akimichi

last: Morita


title: Effects of Chronic Social Stress on the transcriptome of BA-NAc neurons

overall_design: Assessment of the effects of chronic social stress on the transcriptome of BA-NAc "reward-sensitive" glutamatergic neurons when compared to BA-Nac glutamatergic neurons from control non-stressed animals.


title: Longitudinal liver sampling in patients with chronic hepatitis B starting antiviral therapy reveals hepatotoxic CD8+ T cells

city: Toronto

first: Adam

last: Gehring

state: ON

address: 101 College St

country: Canada

institute: UHN

summary: The objective of this study is to identify immunological mechanisms that contribute to normalization of liver inflammation in chronic hepatitis B (CHB) patients starting the antiviral nucleoside analogue, Tenofovir alafenamide (TAF).

overall_design:
Investigator-initiated, phase 4 study in which recruited patients received TAF 25mg once daily for 48 weeks. The total duration of the study to End of Follow-up was 48 weeks. After Week 48, participants were offered 2 years of TAF therapy. Sample collection 0, 12, 24 w was chosen to analyze immune responses based on ALT normalization rates. This mono-center study was conducted at Toronto Centre for Liver Disease, Canada.
***Raw data for human samples not available due to patient privacy concerns***

first: Shirin

last: Nkongolo

first: Deeqa

last: Mahamed

first: Adrian

last: Kuipery

first: Juan

last: Sanchez Vasquez

first: Samuel

last: Kim

first: Aman

last: Mehrotra

first: Anjali

last: Patel

first: Christine

last: Hu

first: Ian

last: McGilvray

first: Jordan

last: Feld

first: Scott

last: Fung

first: Diana

last: Chen

first: Jeffrey

last: Wallin

first: Anuj

last: Gaggar

first: Harry

middle: L

last: Janssen


title: Porphyromonas gingivalis outer membrane vesicles promote apoptosis via msRNA-regulated DNA methylation in periodontitis

status: Public on Nov 30 2022

city: Nanjing

first: Ruyi

last: Fan

state: Jinngsu

address: 1 Shanghai Road

department: Department of Periodontics

institute: Nanjing Medical University

summary:
The outer membrane vesicles (OMVs) produced by Porphyromonas gingivalis (P. gingivalis) contain a variety of bioactive molecules that may be involved in the progression of periodontitis. However, the participation of P. gingivalis OMVs in the development of periodontitis has not been elucidated. Here we isolated P. gingivalis OMVs and confirmed their participation in periodontitis both in vivo and in vitro. Microcomputed Tomography (micro-CT) and histological analysis showed that under the stimulation of P. gingivalis OMVs, the alveolar bone of rats was significantly resorbed in vivo. We found that P. gingivalis OMVs were taken up by hPDLCs (human Periodontal Ligament Cells, hPDLCs) in vitro, then subsequently resulting in apoptosis and inflammatory cytokines releasing which was accomplished by the microRNA-size small RNAs (msRNAs) sRNA45033 in the P. gingivalis OMVs.
Through bioinformatics analysis and screening of target genes, Chromobox 5 (CBX5) was identified as the downstream target of screened-out small RNA s45033. Using dual-luciferase reporter assay, overexpression, and knockdown methods, s45033 was confirmed to target CBX5 to regulate hPDLCs apoptosis. In addition, Cleavage Under Targets and Tagmentation (Cut&Tag) analysis confirmed the mechanism that CBX5 regulates apoptosis through the methylation of p53 DNA. Collectively, these findings indicate that the role of P. gingivalis OMVs is immunologically relevant and related to bacterial virulence in the development of periodontitis.

overall_design: hPDLCs were treated with  LPS,  P. gingivalis 33277 OMVs,  P. gingivalis W83 OMVs

first: Yan

last: Xu

first: Yi

last: Zhou

first: Xu

first: Fanzhen

last: He

first: Wenzao

last: Peng

first: Lu

last: Li

first: Xiaoqian

last: Wang


title: NGF-induced gene expression in silent nociceptors

city: Hamburg

first: Stefan

last: Lechner

address: Martinistrasse 52

department: Anaesthesiology

institute: University Medical Center Hamburg-Eppendorf

summary: Silent nociceptors are sensory afferents that are insensitive to noxious mechanical stimuli under normal conditions but become sensitized to such stimuli during inflammation. We had previously shown that mouse silent nociceptors express the nicotinic acetylcholine receptor alpha-3 subunit (CHRNA3) and can thus readily be identified in Tg(Chrna3-EGFP)BZ135Gsat reporter mice (Prato et al. Cell Reports 2017). Most importantly, we had shown that CHRNA3+ slient nociceptors acquire mechanosensitivity upon treatment with the inflammatory mediator nerve growth factor and demonstrated that this process requires de-novo gene transcription. Here, we performed paired-end RNA-sequencing to identify transcripts that might be involved in the acquisition of mechanosenstivity in mouse silent nociceptors.

overall_design: 3 Controls and 3 NGF-treated samples from three different animals were analyzed

first: Timo

last: Nees


title: USP1 modulates hepatocellular carcinoma progression via Hippo/TAZ axis

status: Public on Nov 23 2022

city: xinxing

first: huijie

last: yang

address: Hongqi District, Xinxiang City

institute: Xinxiang Medical University

summary: To investigate the  function of USP1  in the HCC.

overall_design: HLF cell mRNA samples were summarized in six samples, divided into two groups, siControl and siUSP1. Comparative gene expression profiling analysis of RNA-seq data for HLF cells treated with siControl and siUSP1.

first: Ding

last: Yinlu

first: Huijie

last: Yang

first: Dongyi

last: Liu

first: Quanhui


title: Eosinophilic esophagitis-associated epithelial remodeling may limit esophageal carcinogenesis

status: Public on Nov 21 2022

city: Philadelphia

first: Kelly

last: Whelan

state: PA

address: 3307 N Broad St. PAHB Rm 203

department: Fels Institute

institute: Temple University

summary: Eosinophilic esophagitis and esophageal squamous cell carcinoma both feature epithelial remodeling in the form of hyperplasia. We used scRNA-Seq to examine the cellular and molecular alterations between these distinct pathologies.

overall_design: C57B6 animals were chemically induced with EoE or ESCC. Esophageal epithelium was isolated and analyzed via scRNA-Seq.

first: Adam

last: Karami

first: Annie

last: Fuller


title: Effect of potato tuber bruising on gene expression 2h after mechanical shock in tetraploid potato genotypes

status: Public on Nov 29 2022

city: Lincoln

first: Susan

last: Thomson

address: 74 Gerald Street

department: New Cultivar Innovation

country: New Zealand

institute: The New Zealand Institute for Plant & Food Research LTD

summary: Tuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economical importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still a lot to learn about this complex phenotype. Here, we used genotype by sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis for tuber bruising. In addition, we collected transcriptomics data to enrich the GWAS results, by performing a differential expression analysis between samples with high- and low-bruising susceptibility.

overall_design: Differential expression analysis of samples taken at the bruising site 2h after mechanical impact between genotypes with low and high bruising

first: Olivia

last: Angelin-Bonnet

first: Matthieu

last: Vignes

first: Patrick

last: Biggs

first: Katrina

last: Monaghan

first: Rebecca

last: Bloomer

first: Samantha

last: Baldwin


title: Developmental effects of neonatal exposure to NOAEL-dose of neonicotinoid clothianidin on the gene expression profiles of hippocampus in male mice

city: Toyama

first: Tetsushi

last: Hirano

state: Toyama

address: 2630 sugitani

department: Life Science Research Center

institute: University of Toyama

summary:
The mechanisms of developmental neurotoxicity of neonicotinoid pesticides were not fully understood.
We examined the effects of neonatal exposure to a neonicotinoid pesticide, clothianidin (CLO) on gene expression profiles of the hippocampus in male mice at 3 or 10 weeks of age.

overall_design: Dams were orally administrated no-observed adverse effect level (NOAEL; 65 mg/kg/day) of CLO or vehicle during postnatal day 1 to 4.

first: Asuka

last: Shoda

first: Nobuhiko

last: Hoshi

first: Yoshiaki

last: Tabuchi


title: IGF1 treatment of developing mouse molar

status: Public on Nov 19 2022

city: Helsinki

first: Jukka

last: Jernvall

address: P.O. Box 56 (Viikinkaari 9)

country: Finland

institute: University of Helsinki

summary: When evolution leads to differences in body size, organs generally scale along. A well-known example of the tight relationship between organ and body size is the scaling of mammalian molar teeth. To investigate how teeth scale during development and evolution, we compared mouse and rat molar development from initiation through final size. Whereas the linear dimensions of the rat first lower molar are twice that of the mouse molar, their shapes are largely the same. We found that scaling of the molars starts early, and that the rat molar is patterned equally as fast but in a larger size than the mouse molar. Using transcriptomics, we discovered that a known regulator of body size, insulin-like growth factor 1 (Igf1), is more highly expressed in the rat molars compared to the mouse molars. Ex vivo and in vivo mouse models demonstrated that modulation of the IGF pathway reproduces several aspects of the observed scaling process. Furthermore, analysis of IGF1-treated mouse molars and computational modeling indicate that IGF signalling scales teeth by simultaneously inhibiting the cusp patterning programme and by enhancing growth, thereby providing a relatively simple mechanism for scaling teeth during development and evolution. Finally, comparative data from shrews to elephants suggest that this scaling of patterning mechanism regulates the minimum tooth size possible, as well as the patterning potential of large teeth.

overall_design: Embryonic day 14 (E14) mouse molars were dissected and cultured in a hanging drop culture (Närhi & Thesleff, 2010) for 6 hours pairwise so that from each embryo one tooth was treated with IGF1-containing media (750ng/ml in 1x PBS + 0.1% BSA ) or control media (same volume of 1x PBS + 0.1% BSA as was added to treatment samples). Right and left sides were balanced, n = 5 for both the treatments and controls. Tissue was stored in RNAlater (Qiagen, Düsseldorf, Germany) at −80°C for RNAseq. For RNAseq, each tooth was handled individually. Samples were homogenized using Precellys 24 homogenizer (Bertin instruments). RNA was extracted using guanidium thiocyanate-phenol-chloroform method and purified using RNeasy Plus micro kit (Qiagen GmbH) following manufacturer's protocol. The putiry of RNA was measured using Nanodrop microvolume spectrophotometer (Thermo Fisher Scientific). The complementary DNA (cDNA) libraries were prepared using Ovation Mouse RNAseq System (Tecan).

first: Mona

last: Christensen

first: Outi

last: Hallikas

first: Rishi

last: Das Roy


title: Lin28b augments protein synthesis to control B cell positive selection early in life.

status: Public on Nov 16 2022

city: Lund

first: Joan

last: Yuan

address: Klinikgatan 17

country: Sweden

institute: Lund University


title: Lin28b augments protein synthesis to control B cell positive selection early in life [RNA-seq]

summary:
In this study, we identify elevated protein synthesis as a defining characteristic of early life B cell development and a determinant for the qualitative switch in B cell output whereby self-reactive CD5+ B-1 cells becomes censored in postnatal mice
This is in part mediated by the heterochronic RNA binding protein LIN28B.
To identify Lin28b-dependent, stage specific effects, B cell progenitors at different developmental stages were sorted and analyzed by RNA-seq

overall_design: Large Pro-B, large Pre-B, and small Pre-B were sorted from tet-Lin28b and littermate control mice before their transcriptome were analyzed by RNA-sequencing

first: Hugo

last: Åkerstrand

first: Giorgia

last: Montano

first: Stijn

last: Vanhee

first: Jonas

last: Ungerbäck


title: Lin28b augments protein synthesis to control B cell positive selection early in life [RIP-seq]

overall_design: B cell progenitors from whole bone marrow was expanded for five days under saturating concentration of IL-7 (20 ng/mL) before subjected to immunoprecipitation and poly-A targeted sequencing of co-IP RNA


title: Disease-specific exhaustion features and PD-1 immunotherapy responsiveness of antigen-specific CD8+ T cells at single-cell resolution [scRNA-seq]

city: Chicago

first: Jun

last: Huang

state: IL

address: Eckhardt, 5640 S Ellis Ave

department: Institute for Molecular Engineering

institute: University of Chicago

summary: We reported the CD8+ T cell exhaustion differences between chronic viral infection and tumor regarding their transcriptomic and epigenetic landscapes, immune checkpoint blockade responsiveness and underlying molecular mechanisms by using bulk RNA-seq, single-cell RNA-seq and single-cell ATAC-seq.

overall_design: Exhausted P14 CD8+ T cells bearing a same TCR recognizing a same epitope presented in either chronic viral infection (LCMV-Cl13) or tumor (B16F10-GP) were harvested and performed with RNA- and ATAC-sequencing. Exhausted P14 CD8+ T cells were obtained from the spleens or lungs of chronic virus-infected mice and from the subcutaneous tumor tissues or metastatic lungs of tumor-engrafted mice. The chronic virus-infected or tumor-engrafted mice were treated with either anti-PD-L1 antibody or isotype antibody. As control, P14 CD8+ T cells from the spleens of acute virus-infected mice were also performed with RNA-sequencing.

first: Lilin

last: Ye

first: Guoshuai

last: Cao

first: Xiangyu

last: Chen


title: Effects of gene transcription profiles of Streptococcus suis between planktonic and biofilm states

status: Public on Nov 15 2022

city: Luoyang

first: Yang

last: Wang

address: Ancient city street

institute: College of Animal Science and Technology, Henan University of Science and Technology

summary: To investigate the gene transcription profiles of Streptococcus suis in the planktonic state and biofilm state, we provided samples cultured for 8 h in the planktonic state and samples cultured for 24 h in vitro biofilm. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different samples at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Streptococcus suis in the planktonic state and Streptococcus suis in the biofilm state.

first: Li

last: Yi

first: Qingying

last: Fan

first: Haikun


title: Suppression of endogenous CBS promotes Ferroptosis.

city: Xiamen

first: yongyou

last: zhang

state: Fujian

address: Xiang'an South Road

institute: Xiamen University

summary:
To identify the gene profile change caused by cystine depletion, we compared the whole-genome transcriptional profiling of colorectal cancer cells in the full medium (FM) or cystine-restricted medium (CR).
We analyzed the early regulatory events in the course of ferroptosis via whole-genome transcriptional analysis of gene expression of cells under FM or CR mediums

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for SW480 cells and its KD derivatives shCBS.
Comparative gene expression profiling analysis of RNA-seq data for SW480 cells under the full medium (FM) or cystine-restricted medium (CR) mediums for 6 hrs.

first: Liu

last: Junjia


title: Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization

status: Public on Nov 14 2022

city: New York

first: Jennifer

last: Zagelbaum

address: 1130 Saint Nicholas

institute: Columbia

summary:
Purpose: Evaluate how ARP2/3-coupled DSB mobility affects chromatin organization (Hi-C) and translocation frequency (HTGTS) in mouse embryonic fibroblasts (MEFs) harboring an inducible AsiSI restriction enzyme.
MEF Hi-C Methods: Damaged samples were treated with 3 ug/mL doxycycline for 24 hours. For the last 6 hours of doxycycline treatment, 1 ug/mL 4-OHT was used to induce AsiSI translocation to the nucleus, triggering DSBs. Cells were co-treated with DMSO, 100 μM CK-666, or 10 μM NU7441. For DNA-PKcs inhibitor experiments, cells were pretreated with 10 μM NU7441 for 1 hour prior to induction of damage with 4OHT. 2 biological replicates were performed for each experimental condition.
MEF HTGTS Methods: WT MEFs and AsiSI MEFs were treated as above. Following 6 hours treatment with dox and 4OHT, cells were lysed. For WASP inhibition, cells were treated with 3 μM wiskostatin following induction of damage. For flag-actin experiments, AsiSI-MEF cells were transfected with Flag–actinR62D–NLS 24 hours prior to induction of AsiSI expression. For cas9 experiments, WT MEF cells were transfected with sgRNA targeting Chr2 48 hours prior to cell lysis.

overall_design: Hi-C and HTGTS analysis in MEF cells harboring inducible restriction endonuclease.

first: Allana

last: Schooley

first: Junfei

last: Zhao

first: Benjamin

last: Schrank

first: Elsa

last: Callen

first: Shan

last: Zha

first: Max

middle: E

last: Gottesman

first: Andre

last: Nussenzweig

first: Raul

last: Rabadan

first: Job

last: Dekker

first: Jean

last: Gautier


title: Control of white mold (Sclerotinia sclerotiorum) through plant mediated RNA interference

status: Public on Nov 11 2022

city: Winnipeg

first: Philip

last: Walker

state: Manitoba

address: 104 Dunrobin Avenue

institute: Agriculture and AgriFood Canada

summary: In this study, we developed transgenic Arabidopsis thaliana (AT1703) expressing double-stranded (ds)RNA to silence S. sclerotiorum ABHYDROLASE-3 and slow infection through host induced gene silencing (HIGS). Leaf infection assays show reduced S. sclerotiorum lesion size, fungal load, and ABHYDROLASE-3 transcript abundance in AT1703 lines compared to wild-type Col-0. To better understand how HIGS influences host-pathogen interactions, we performed global RNA sequencing on AT1703 and wild-type Col-0 lines directly at the site of S. sclerotiorum infection. Together, these results demonstrate the utility of HIGS technology in slowing S. sclerotiorum infection and provides insight into the role of ABHYDROLASE-3 gene activity in the A. thaliana – S. sclerotiorum pathosystem.

overall_design: Arabidopsis thaliana expressing dsRNA targeting Sclerotinia sclerotiorum ABHYDROLASE-3 (AT1703) and background wildtype Col-0 A. thaliana leaves at 0, 2 and 3 days post inoculation with S. sclerotiorum

first: Mark

middle: F

last: Belmonte


title: Genome‑wide analysis  of sex‑specifc diferences  in the mother–child  PELAGIE cohort exposed  to organophosphate metabolites

status: Public on Nov 10 2022

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

summary: In this project exposuere to DiethylPhosphate (DE)  metabolites has been monitored in the usine of pregnant women of the French mother-child cohort PELAGIE. We performed ChIPs against H3K4me3 from male or female  newborns' placenta in order to identify whether exposure to DE can affect their epigenetic landscape. Representing samples from each group were selected for genome-wide ChIP-seq analysis. Exposure and epigenetic data are compared and associated with potential effects on developmental processes.

overall_design:
We provided 18 libraries (17 ChIPs + 1 input) for single-end sequencing (1x50bp). ChIP was performed from chromatin obtained from placenta of human male new borns.
We provided 14 libraries (14 ChIPs) for single-end sequencing (1x50bp). ChIP was performed from chromatin obtained from placenta of human female new borns.

last: Smagulova


title: ATF3-CBS axis regulates ferroptosis and tumorigenesis via targeting mitochondrial homeostasis

last: zhang

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

overall_design: Refer to individual Series


title: Microbiota-host crosstalk mechanism in the newborn and adult rumen at single-cell resolution

status: Public on Nov 17 2022

city: Hangzhou

first: Jiajin

last: Wu

state: Zhejiang

address: Yuhangtang road

institute: Zhejiang University

summary: As the unique organ, rumen plays vital roles in providing products for humans, however, the underlying cell composition and interactions with epithelium-attached microbes remain largely unknown. Herein, we performed an integrated analysis in single-cell transcriptome, epithelial microbiome, and metabolome of rumen tissues to explore the differences of microbiota-host crosstalk between newborn and adult cattle models. We found that fewer epithelial cell subtypes and more abundant immune cells (e.g., Th17 cells) in the rumen tissue of adult cattle. Metabolism-related functions and oxidation-reduction process were significantly upregulated in the adult rumen epithelial cell subtypes. The epithelial Desulfovibrio was significantly enriched in the adult cattle. To further clarify the role of Desulfovibrio in host’s oxidation-reduction process, we performed metabolomics analysis of rumen tissues and found that Desulfovibrio showed a high co-occurrence probability with the pyridoxal in the adult cattle compared with newborn ones. The adult rumen epithelial cell subtypes also showed stronger ability of pyridoxal binding. These indicates that Desulfovibrio and pyridoxal likely play important roles in maintaining redox balance in adult rumen. The integrated analysis provides novel insights into the understanding of rumen function and facilitate the future precision improvement of rumen function and milk/meat production in cattle.

overall_design: Single-cell RNA sequencing of 3 samples from rumen tissues of dairy cattle.

first: Senlin

last: Zhu

first: Fengfei

last: Gu

first: Huizeng

last: Sun


title: Comprehensive microRNA analysis across genome-edited colorectal cancer organoid models reveals miR-24 as a candidate regulator of cell survival

city: Ithaca

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

department: Biomedical Science

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

summary: Colorectal cancer (CRC) is the third most diagnosed cancer and the second leading cause of cancer-related death worldwide Unique mutational combinations can result in distinct changes to gene regulatory mechanisms leading to variability in the efficacy of available therapeutics. To work toward novel therapeutic strategies, it is important to understand the mechanisms by which unique combinations of mutations affect gene regulatory mechanisms. To that end, in this study, we generated RNA- and small RNA-seq data from Apc (A; n=3), Apc/Kras/p53 (AKP; n=1), B-catenin (B; n=5), B-catenin/Kras/p53 (BKP; n=1), Kras/Rspo3/p53 (KRP; n=2), Kras/Rspo3/p53/Smad4 (KRPS; n=4), Kras/Rspo3/Smad4 (KRS; n=3), Rspo3 (R; n=2) mutant mouse enteroids, and wild-type (WT; n=2) controls. From this analysis, we found that miR-24-3p is upregulated master miRNA regulator across mutational contexts. Functional studies identified miR-24-3p as a regulator of cell survival. Utilizing RNA- and leChRO-seq from HCT116 cells treated with a miR-24-3p inhibitor (n=3) or scramble control (n=3), we identified HMOX1 and PRSS8 as candidate miR-24-3p targets subject to post-transcriptional regulation by miR-24-3p.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA- and small RNA-seq comparison between genetically modified mouse enteroid models and WT control. RNA- and ChRO-seq comparison between HCT116 cells treated with a miR-24-3p inhibitor or scramble control.

first: Jonathan

middle: W

last: Villanueva


title: ChIP-seq of E13.5 Mouse Incisors

city: Farmington

first: Emma

middle: Wentworth

last: Winchester

state: Connecticut

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

summary: Chromatin state profiling using multiple histone modifications in isolated wild type E13.5 mandibular mouse incisors. Imputed files were generated using these files and data obtained from ENCODE embryonic and postnatal mouse ChIP samples.

overall_design: Examination of 6 different histone modifications (plus input) for E13.5 mandibular mouse incisor.

first: Alexis

last: Hardy

first: Justin

last: Cotney

first: Mina

last: Mina


title: Single cell seq from: A circular RNA expressed from the FAT3 locus regulates neural development

status: Public on Nov 07 2022

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

summary: Circular RNAs (circRNAs) are key regulators of cellular processes, are abundant in the nervous system, and have putative regulatory roles during neural differentiation. However, the knowledge about circRNA functions in brain development is limited. Here, using RNA-sequencing, we show that circRNA levels increase substantially over the course of differentiation of human embryonic stem cells into rostral and caudal neural progenitor cells (NPCs), including three of the most abundant circRNAs, ciRS-7, circRMST, and circFAT3. Knockdown of circFAT3 during early neural differentiation resulted in alterations in the expression of genes involved in insulin signaling and resistance. Single-cell transcriptomic analysis of 30 and 90 days differentiated cerebral organoids deficient in circFAT3 showed a loss of telencephalic radial glial cells and mature cortical neurons, respectively. Furthermore, non-telencephalic NPCs in cerebral organoids showed changes in the expression of genes involved in neural differentiation and migration, including FAT4, ERBB4, UNC5C, and DCC. In vivo depletion of circFat3 in mouse prefrontal cortex using in utero electroporation led to alterations in the positioning of the electroporated cells within the neocortex. Overall, these findings suggest a conserved role for circFAT3 in neural development involving the formation of anterior cell types, neuronal differentiation, and migration.

overall_design: Loss-of-function study for circFAT3 (scRNA-seq) in H9 human embryonic stem cells (hESCs) using AGO-dependent short hairpin RNAs (agoshRNAs) targeting the circRNA backsplicing junction or an empty vector control (CTRL). After transduction with lentiviral vectors encoding the agoshRNAs or empty control vectors, hESCc were differentiated for 30 and 90 days to cerebral organoids and subsequently subjected to scRNAseq.

first: Sabine

last: Seeler

first: Maria

last: Andersen

first: Tamas

last: Sztanka-Toth

first: Mateja

last: Rybiczka-Tešulov

first: Chi-Chih

last: Chang

first: Muyesier

last: Maimaitili

last: Venø

first: Thomas

last: Hansen

first: R

last: Pasterkamp

last: Denham

first: Agnieszka

last: Rybak-Wolf

first: Nikolaus

last: Rajewsky

first: Lasse

last: Kristensen

first: Jørgen

last: Kjems


title: A circular RNA expressed from the FAT3 locus regulates neural development.


title: Targeted modulation of chicken genes in vitro using CRISPRa and CRISPRi toolkit

city: University Park

first: Tae Hyun

last: Kim

address: 317 AVBS

institute: Penn State University

summary: To investigate the effectiveness of CRISPR based gene modulation, IRF7 was repressed in dCas9-KRAB DF1 cell line or activated in dCas9-VPR DF1 cell line followed by whole transcriptome analysis

overall_design:
a. Differntiall gene expression analysis between mock (non-targeting) and IRF7 targeting gRNAs transfected dCas9-KRAB DF1 cells for assessing the endogenous targeted gene knockdown
b. Differntiall gene expression analysis between mock (non-targeting) and IRF7 targeting gRNAs transfected dCas9-VPR DF1 cells for assessing the endogenous targeted gene activation

first: Brittany

last: Chapman

first: Jeong

last: Han

first: Hong

last: Lee

first: Isabella

last: Rudd

first: Tae


title: ChIP-seq of PHF8 and c-MYC in 786-O cell line

status: Public on Nov 06 2022

city: Chongqing

first: Jun

last: Jiang

state: Chongqing

address: 10#, Changjiang Zhilu, Yuzhong District

department: Department of Urology

institute: Daping Hospital, Army Medical University

summary: Genome-wide ChIP-Seq of PHF8 and c-MYC in 786-O cell line was performed to assess  the presence of common target genes.

overall_design: ChIP-seq of PHF8 and c-MYC

first: Song

last: Peng

first: QiuLi

last: Liu


title: Human DUX4 and mouse Dux interact with STAT1 and broadly inhibit interferon-stimulated gene induction

status: Public on Nov 01 2022

city: Seattle

first: Stephen

last: Tapscott

state: Washington

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

summary: DUX4 activates the first wave of zygotic gene expression in the early embryo. Mis-expression of DUX4 in skeletal muscle causes facioscapulohumeral dystrophy (FSHD), whereas expression in cancers suppresses IFNg-induction of MHC Class I and contributes to immune evasion. We show that the DUX4 protein broadly suppresses immune signaling pathways—including IFNg, IFNb, DDX58, IFIH1 and cGAS mediated pathways. A conserved region containing (L)LxxL(L) motifs in the DUX4 carboxyterminal domain (CTD) was necessary to suppress interferon stimulated genes (ISGs). Co-immunoprecipitation identified DUX4-CTD interaction with multiple immune signaling factors, including STAT1. The DUX4-CTD (L)LxxL(L) region interacts with phosphorylated STAT1, sequesters it in the nucleus, modestly reduces its DNA binding, and prevents STAT1 from inducing ISG transcription. Mouse Dux similarly interacted with STAT1 and suppressed IFNg induction of ISGs. These findings identify an evolved role of the DUXC family in modulating immune signaling pathways with implications for development, cancers, and FSHD.

overall_design: Examination of mRNA expression in two DUX4 mutants, F67A and aa154-424

first: Amy

last: Spens

first: Sean

last: Bennett


title: MeRIP sequencing analysis of PK15 cell line infected with PRV

status: Public on Nov 02 2022

city: Chengdu

first: Pei-Lun

last: Yu

address: No. 211, Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

type: Methylation profiling by high throughput sequencing

summary: Purpose: Evaluation of the m6A modification of PRV and PK15 transcripts during PRV infection  Methods: Porcine kidney cell line PK15 was uninfected or infected with PRV for 24 hours. Total RNA from each sample were extracted. Intact mRNA was isolated from total RNA samples and then chemically fragmented to 300-nucleoside-long fragments. Fragmented mRNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody (a part of the fragmented mRNAs was kept as input). Both m6A enriched mRNAs and input mRNAs were concentrated for RNA-seq libraries construction. The libraries were  forwarded to sequencing run on  Illumina NovaSeq 6000.  Results:  PRV transcripts were m6A modified during PRV infection and PRV infection changed m6A modification profiles of PK15 transcripts.

overall_design: Conduct three independent biological repetitions to infect  or uninfect with PRV in parallel, and collect the total RNA samples obtained from three biological repetitions as Mock group and PRV group.

first: Qi-Gui

last: Yan


title: Total RNA seq from: A circular RNA expressed from the FAT3 locus regulates neural development

first: Morten

last: Veno

overall_design: Total RNA-seq of H9 human embryonic stem cells (hESCs) differentiated into neuroepithelial or -mesodermal progenitor cells (NEPs/NMPS) and further into rostral and caudal neural progenitor cells (rNPCs and cNPCs, respectively). Total RNA from three biological replicates from day 0, 4, and 11 of differentiation.

first: Sabine

last: Seeler

first: Maria

last: Andersen

first: Tamas

last: Sztanka-Toth

first: Mateja

last: Rybiczka-Tešulov

first: Chi-Chih

last: Chang

first: Muyesier

last: Maimaitili

last: Venø

first: Thomas

last: Hansen

first: R

last: Pasterkamp

first: Mark

last: Denham

first: Agnieszka

last: Rybak-Wolf

first: Nikolaus


title: Comparison of gene profiles of human bone marrow stromal stem cell (hBMSCs) transfected by siRNA-Control and siRNA-KIAA1199

status: Public on Oct 31 2022

city: 桂林市

first: 陈琍

last: 陈

address: 临桂区临桂镇致远路

institute: 桂林医学院

summary:
human bone marrow stromal stem cells were transfected by siRNA-control (non-target) and siRNA-KIAA1199, after 72 hours, gene profiles were compared
We used microarrays to detail the global programme of gene expression underlying cellularization and identified distinct classes of up-regulated genes during this process.

overall_design: human bone marrow stromal stem cell line (hBMSC-T4) were transfected by siRNA-control (non-target) and siRNA-KIAA1199, after 72 hours,  RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain most-up and down regulated genes by KIAA1199 knockdown

first: Li

last: Chen


title: Quantseq from: A circular RNA expressed from the FAT3 locus regulates neural development

overall_design: Loss-of-function studies of ciRS-7, circRMST, and circFAT3 in H9 human embryonic stem cells (hESCs) differentiation into rostral and caudal neural progenitor cells (rNPCs and cNPCs, respectively) using AGO-dependent short hairpin RNAs (agoshRNAs) targeting the circRNA backsplicing junction. Five days prior to the 11 days of differentiation into rNPCs and cNPCs, H9 hESCs were transduced with lentiviral vectors encoding the agoshRNAs or empty control vectors (A244).

last: Rajewsky

first: Lasse

last: Kristensen

first: Jørgen

last: Kjems


title: T6SS effector induces B. subtilis sporulation mediated by σW

status: Public on Nov 03 2022

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

summary: We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of Bacillus subtilis growing in the presence of Tse1, a T6SS effector of Pseudomonas chlororaphis

sample_organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

overall_design: B. subtilis mRNA profiles comparing their growth in presence of Tse1 or control buffer after 3 h of treatment

first: A

middle: I

last: Pérez-Lorente

first: C

last: Molina-Santiago

first: D

last: Romero


title: RRBS in XX and XO Xmas ES cells

city: Royal Parade

first: Andrew

last: Keniry

state: Victoria

department: Molecular Medicine

country: Australia

institute: The Waler and Eliza Hall Institute of Medical Research

summary: This experiment is designed to test if our new culture protocol affects DNA methylation of XX mESCs

overall_design: n=1. Xmas mESCs are FACS sorted into XX and XO using the X-linked reporter alleles

first: Marnie

last: Blewitt


title: RNA-seq in male ES cells cultured by either standard ES cell culture or our improved culture conditions [Male RNA-seq]

summary:
Major complications with in vitro culture of female embryonic stem cells (ESC) have impeded study of sex-specific pluripotency; however, from the published work female pluripotency significantly differs to male. We report a replenishable female ESC system that has enabled us to optimise a protocol for preserving the XX karyotype. Our protocol also improves male ESC fitness. To demonstrate the utility of the system, we screened for regulators of the female-specific process of X chromosome inactivation, revealing a new role for chromatin remodellers Smarcc1 and Smarca4 in establishment of X inactivation. The remodellers create a nucleosome depleted region at gene promotors on the inactive X during exit from pluripotency, without which gene silencing fails. Our female ESC system provides a tractable model for XX ESC culture that will expedite study of female pluripotency and has enabled us to discover new features of the female-specific process of X inactivation.
This experiment is designed to test the effect of our improved ES culture conditions on the male ES cell transciptome.

overall_design: n=2  for male cells cultured in standard culture conditions and n=2 for male ES cells cultured in our improved conditions. Samples taken at passages 0, 10 and 20 of ES cell maintenance in 2i media.


title: A method of mESC culture that helps preserve the XX karyotype


title: RNA-seq in mouse embryonic stem cells treated with or without Adriamycin

status: Public on Oct 29 2022

city: Guangzhou city

first: Mangmang

last: Li

state: Guangdong province

address: 1838 N Guangzhou Ave

department: Department of Cell Biology School of Basic Medical Sciences

institute: Southern Medical University

summary: The tumor suppressor p53 is a well-recognized transcription factor that directly regulates transcriptional activation through sequence-specific DNA binding. However, whether p53 functions as a direct transcriptional repressor has long been debatable.

first: M


title: Sall4 guides p53-mediated enhancer interference upon DNA damage in mouse embryonic stem cells

overall_design: Here, we conducted RNA-seq and chromatin-immunoprecipitation followed by deep sequencing (ChIP-seq) for p53 and two histone modifications (H3K4me3 and H3K27ac) in mouse embryonic stem cells treated with or without Adriamycin to identify enhancer-targeting of p53 for transcriptional repression.


title: ChIP-Seq of p53, H3K4me3 and H3K27ac in mouse embryonic stem cells with or without DNA damage.

summary: To study the association between p53 occupancy and promoters and putative enhancers genome-widely, we performed ChIP-seq of p53, H3K3me3 (histone mark for promoter), and H3K27ac (histone mark for active enhancer) in mouse embryonic stem cells with or without DNA damage.

overall_design: Total seven samples: one input (mixed DNA from ES cells untreated and treated with Adriamycin) and six ChIP samples (p53_Ctr, p53_Adr8h, H3K4me3_Ctr, H3K4me3_Adr8h, H3K27ac_Ctr, and H3K27ac_Adr8h).


title: DNA-seq in male ES cells cultured by either standard ES cell culture or our improved culture conditions [Male DNA-seq]

summary:
Major complications with in vitro culture of female embryonic stem cells (ESC) have impeded study of sex-specific pluripotency; however, from the published work female pluripotency significantly differs to male. We report a replenishable female ESC system that has enabled us to optimise a protocol for preserving the XX karyotype. Our protocol also improves male ESC fitness. To demonstrate the utility of the system, we screened for regulators of the female-specific process of X chromosome inactivation, revealing a new role for chromatin remodellers Smarcc1 and Smarca4 in establishment of X inactivation. The remodellers create a nucleosome depleted region at gene promotors on the inactive X during exit from pluripotency, without which gene silencing fails. Our female ESC system provides a tractable model for XX ESC culture that will expedite study of female pluripotency and has enabled us to discover new features of the female-specific process of X inactivation.
This experiment is designed to test the effect of our improved ES culture conditions on the male ES cell karyotype.


title: Dose-dependent disruption of hepatic zonation by 2,3,7,8-tetrachlorodibenzo-p-dioxin in mice: integration of single-nuclei RNA sequencing and spatial transcriptomics

status: Public on Oct 21 2022

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

summary: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) dose-dependently induces the development of hepatic fat accumulation and inflammation with fibrosis in mice initially in the portal region. Conversely, differential gene and protein expression is first detected in the central region. To further investigate cell-specific and spatially resolved dose-dependent changes in gene expression elicited by TCDD, single-nuclei RNA sequencing and spatial transcriptomics were used for livers of male mice gavaged with TCDD every 4 days for 28 days. The proportion of 11 cell (sub)types across 131,613 nuclei dose-dependently changed with 68% of all portal and central hepatocyte nuclei in control mice being overtaken by macrophages following TCDD treatment. We identified 368 (portal fibroblasts) to 1,339 (macrophages) differentially expressed genes. Spatial analyses revealed initial loss of portal identity that eventually spanned the entire liver lobule with increasing dose. Induction of R-spondin 3 (Rspo3) and pericentral Apc, suggested dysregulation of the Wnt/β-catenin signaling cascade in zonally resolved steatosis. Collectively, the integrated results suggest disruption of zonation contributes to the pattern of TCDD-elicited NAFLD pathologies.

overall_design: Male C57BL/6 mice were received from Charles Rivers Laboratories at postnatal day (PND) 25 and acclimated until PND 28. Mice were randomly assigned to Innocages (Innovive, San Diego, CA) with ALPHA-dri bedding (Shepherd Specialty Papers, Chicago, IL) at 30-40% humidity and a 12-hour light/dark cycle. Mice had free access to Harlan Teklad 22/5 Rodent Diet 8940 (Envigo, Indianapolis, IN) and Aquavive water (Innovive). On PND 28 and every 4 days thereafter, for a total of 7 administrations (24 days), mice were orally gavaged with sesame oil vehicle (Sigma-Aldrich, St. Louis, MO), 0.3, 3, or 30 µg/kg TCDD (AccuStandard, New Haven, CT) between ZT00 and ZT01. On PND 56, 28 days after the initial gavage, mice were euthanized by CO2 asphyxiation and livers were immediately collected, snap frozen in liquid nitrogen and stored at -80°C. All procedures were approved by the Michigan State University Institutional Animal Care and Use Committee. Spatial transcriptomics was performed using the Resolve BioScience Molecular Cartography system. Two biological replicates for each dose group were examined by placing 10 µm thick frozen liver sections in O.C.T compound (Sakura, Torrance, CA) in one of 8 designated custom slide regions. Frozen slides were shipped to Resolve BioSciences for analysis following manufacturer’s instructions (protocol version 3.0).

first: Tim

last: Zacharewski


title: The transcriptomic and physiological basis of desiccation stress response in natural European D. melanogaster populations

city: Lund

first: Vivien

last: Horvath

address: Sölvegatan 17

institute: Lund University

summary: Climate change is one of the main factors shaping the distribution and biodiversity of organisms, among others by greatly altering water availability, thus exposing species and ecosystems to harsh desiccation conditions. Insects are especially threatened by these challenging dry environments, because of their small size and thus large surface area to volume ratio. Drosophila melanogaster is a great model to study the response of populations to rapidly changing conditions, because of its southern-central African origin and recent worldwide colonization. Desiccation stress response is a complex and extensively studied trait, however the natural variation in tolerance, and the underlying transcriptomic and physiological mechanisms are still not clear. Here we subjected to desiccation stress 74 natural D. melanogaster European strains, belonging to five different climate zones. We found that the strains from cold semi-arid climates are more tolerant compared with the ones from hot summer mediterranean climate zones. Moreover, the variance in the tolerance of the strains correlates with the interaction of altitude and evaporation. We found that the tolerant strains had a lower level of initial water content and lose less water during desiccation stress. The reduction in the water loss is probably due to the decrease in the respiration rate in desiccation stress conditions, and to the cuticular hydrocarbon composition found in tolerant strains. Moreover, we found that the genes related to response to stimulus and environmental sensing are up-regulated only in the tolerant strains. Furthermore, we identified several desiccation candidate genes unique for the tolerant strains that can be targeted by tRNA derived fragments, known to be important in post-transcriptional gene regulation in several stress responses. We also looked for transposable element insertions possibly affecting the expression of genes relevant in desiccation tolerance, however, except for four insertions, there is no clear association between the presence of the TE insertions and the tolerance level of the strains. Overall, our study for the first time described the physiological and transcriptomic changes underlying the desiccation tolerance of natural European D. melanogaster strains and puts tRFs in the scope of desiccation related studies as possible regulators of desiccation tolerance.

overall_design: Six Drosophila melanogaster strains (three  tolerant to desiccation stress: ES_GIM_15_12 (GIM-012), ES_GIM_15_24 (GIM-024),ES_COR_15_23 (COR-023) and three sensitive to desiccation stress ES_TOM_15_8 (TOM-08), LUN_15_7 (LUN-07) and MUN_15_13 (MUN-013)) were chosen for small RNA sequencing. For each of the six strains, three replicates were subjected to desiccation stress (treated samples) and other three acted as control. In treated conditions,  flies were placed in empty vials and between the cotton and the parafilm, three grams of silica gel (Merck) were placed, so they were starved and desiccated. Control vials were prepared similarly, except that it contained 1mL of 1% agar on the bottom of the vial to prevent desiccation. Agar in the tubes provides hydration but not food source for the control flies (Sinclair et al 2007).

first: Sara

last: Guirao-Rico

first: Judit

last: Salces-Ortiz

first: Gabriel

last: Rech

first: Eugenio

last: Aprea

first: Mirco

last: Rodeghiero

first: Gianfranco

last: Anfora

first: Josefa

last: Gonzalez


title: RNA-sequencing of Endothelial Cell Lines Expressing GNAQ WT or Mutant Q209L

status: Public on Oct 25 2022

city: Cincinnati

first: Sandra

last: Schrenk

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

summary: To investigate the transcriptional effects of GNAQ p.Q209L mutation on endothelial cells, bulk RNA-sequencing was performed on endothelial cells lines expressing GNAQ wildtype or mutant Q209L. Cells were also treated with Trametinib or vehicle control to elucidate the specific effects of MAPK/ERK signaling on these cells.

overall_design: An endothelial cell line (endothelial colony forming cells) was transduced with doxycycline-inducible GNAQ-WT or GNAQ-Q209L constructs. For these experiments, cells were grown in low-serum media (2% FBS in EGM2). To induce gene expression prior to RNA collection, cells were treated with 1µg/mL doxycycline for 18 hours, followed by an additional 6 hours of DMSO (vehicle control) or 10nM Trametinib treatment. Four conditions were analyzed: 1) WT (no dox) – vehicle; 2) WT (dox) – vehicle; 3) Q209L (dox) – vehicle; 4) Q209L (dox) – Trametinib. For each condition, we performed four biological replicates.

first: Lindsay

last: Bischoff

first: Elisa

last: Boscolo


title: A chemokine trail laid down by migratory dendritic cells directs antigen-presenting monocytes into draining lymph nodes

status: Public on Oct 17 2022

city: Lebanon

first: Claudia

middle: V

last: Jakubzick

state: NH

address: 1 Medical Center Drive, Rm 626 W Borwell, PO#1250960

department: Microbiology and Immunology

institute: Dartmouth College

summary: Antigen presenting dendritic cells (DCs) and monocytes capture and transport antigens from barrier tissues for presentation to antigen-specific T cells in the draining-lymph nodes (LNs). While DCs enter LNs through afferent lymphatics in a CCR7-dependent manner, how exactly antigen-carrying monocytes reach LNs is less clear since monocytes do not express CCR7 and can also enter LNs via the bloodstream. In steady state, and following injection of several PAMPs, scRNA-seq data on LN mononuclear phagocytes identified LN resident versus migratory type 1 and type 2 conventional (c)DCs despite downregulation of DC subset-defining transcripts, such as Xcr1, Clec9a, H2-Ab1, Sirpa, and Clec10a on migratory cDCs. Migratory cDCs gained expression of transcripts controlling cellular migration such as Ccr7, Ccl17, Ccl22, and Ccl5, while migratory monocytes expressed Ccr5 without Ccr7. Using two tracking methods and a gating strategy that clearly distinguishes migratory CD88hiCD26lo monocytes from CD88-CD26hi cDCs, we found that both captured antigens in the lung and migrated to lung-draining LNs. Using global and mixed-chimeric Ccl5-, Ccr2-, Ccr5-, Ccr7-, and Batf3-deficient mice, we found that CCR5+ monocytes follow CCL5-secreting migratory cDCs to reach the draining LN via lymphatic vessels. In a model of asthma, such recruited monocytes regulated the induction of type 2 immunity. Overall, our data suggest that CCL5-secreting migratory cDCs lay down the chemokine trail for CCR5+ antigen-presenting monocytes to reach draining lymph nodes and regulate adaptive immunity.

overall_design: Five groups of mice (n=4) were immunized as described before without TLR adjuvant or with individual different TLR adjuvants: Poly:IC, LPS, CpG, R848 in 40 μl sterile PBS 24 hours before harvest. The LLNs were harvested and single cell suspensions were prepared. Cells were stained with flow cytometry antibodies and different TotalSeq A antibodies (BioLegend) according to the different TLR adjuvant treatment. After the staining, single cells suspensions were washed 3 times by resuspension in 4.5 ml HBSS plus 0.5% BSA, followed by centrifugation at 300g for 5 min at 4°C. After the final wash, cells from different treatment groups were resuspended and mixed. Myeloid cells were sorted as shown in Supplementary Figure 1A with the exclusion of Ly6G neutrophils. Sorted cells were centrifugated at 300g for 5 min at 4°C. Supernatants were aspirated, and pellets were resuspended with HBSS plus 0.5% BSA at an approximate concentration of 2.5 × 105 cells/ml.

first: Kavita

last: Rawat

first: Anita

last: Tewari

first: Xin

first: Arlind

last: Mara

first: William

last: King

first: Sophie

last: Gibbings

first: Chinaza

last: Nnam

first: Fred

last: Kolling

first: Bart

middle: N

last: Lambrecht


title: Disruption of the tumor suppressor-like activity of aryl hydrocarbon receptor by arsenic in epithelial cells and human lung cancer

status: Public on Oct 08 2022

city: Stony Brook

first: Fei

last: Chen

state: New York

address: 100 Nicolls Road

institute: Stony Brook University

summary: As3+ will disrupt the tumor suppressor-like activity of AHR, either through preventing the formation of repressive complexes or the binding of the repressive complexes to these oncogenic genes. Meanwhile, the reduced AHR binding to the DNA may also enhance the nuclear translocation and transcriptional regulation of these oncogenic transcription factors, such as Nrf2 and HIF1α, leading to active transcription and expression of oncogenes and genes in the TGF and Nrf2 signaling pathways, which promotes carcinogenesis or tumorigenesis.

overall_design: Genome-wide ChIP-seq analysis of the global binding of AhR (Enzo) on the genome in the cells treated with As3+ (1 μM for 6 hrs) and RNA-seq analysis of differential expression between control cells and AHR KO cells.

first: Yao

last: Fu

first: Zhuoyue

last: Bi


title: Activation of XBP1 but not ATF6α rescues heart failure induced by persistent ER stress in medaka fish

status: Public on Oct 14 2022

city: Kyoto

first: Byungseok

last: Jin

state: Sakyo-ku

address: Kitashirakawa-oiwake

department: Biophysics

institute: Kyoto University

summary:
To investigate contribution of different UPR pathways to ER stress-induced abnormal heart phenotype in medaka, we generated constitutive XBP1(S) or ATF6(N) expression medaka lines.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different genotype medaka hearts.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AXER+/+, AXER-/-, AXER-/- +XBP1(S), and AXER-/- +ATF6(N)

first: Tokiro

last: Ishikawa

first: Makoto

last: Kashima

first: Rei

last: Komurai

first: Hiromi

last: Hirata

first: Tetsuya

last: Okada

first: Kazutoshi

last: Mori


title: Short-term transcriptomic changes in the mouse neural tube induced by an acute alcohol exposure

status: Public on Oct 19 2022

city: Boston

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

summary: Alcohol exposure during the formation and closure of the neural tube, or neurulation (embryonic day [E] 8-10 in mice; ∼4th week of human pregnancy), perturbs development of midline brain structures and significantly disrupts gene expression in the rostroventral neural tube (RVNT). Previously, alcohol exposure during neurulation was found to alter gene pathways related to cell proliferation, p53 signaling, ribosome biogenesis, immune signaling, organogenesis, and cell migration 6 or 24 hours after administration. Our current study expands upon this work by investigating short-term gene expression changes in the RVNT following a single binge-like alcohol exposure during neurulation. Female C57BL/6J mice were administered a single dose of 2.9 g/kg alcohol or vehicle on E9.0 to target mid-neurulation. The RVNTs of stage-matched embryos were collected 2 or 4 hours after exposure and processed for RNA-seq. Functional profiling was performed with g:Profiler, as well as the CiliaCarta and DisGeNet databases. Two hours following E9.0 alcohol exposure, 650 genes in the RVNT were differentially expressed. Functional enrichment analysis revealed that pathways related to cellular metabolism, gene expression, cell cycle, organogenesis, and Hedgehog signaling were down-regulated and pathways related to cellular stress response, p53 signaling, and hypoxia were up-regulated by alcohol. Four hours after alcohol, 225 genes were differentially expressed. Biological processes related to metabolism, RNA binding, ribosome biogenesis, and methylation were down-regulated, while protein localization and binding, autophagy, and intracellular signaling pathways were up-regulated. Two hr after alcohol, the differentially expressed genes were associated with disease terms related to eye and craniofacial development and anoxia. These data provide further information regarding the biological functions targeted by alcohol exposure during neurulation in regions of the neural tube that give rise to alcohol-sensitive midline brain structures. Disruption of these gene pathways contributes to the craniofacial and brain malformations associated with prenatal alcohol exposure.

overall_design: RNA-seq at 2 or 4 hours after alcohol exposure in E9.0 gastrulation-stage embryos of C57BL6/J mice

first: Karen

last: Boschen

first: Scott

last: Parnell


title: Multiomic analysis reveals conservation of cancer associated fibroblast phenotypes across species and tissue of origin

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

institute: Stanford University

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

overall_design: Refer to individual Series


title: Single cell RNA sequencing analysis of purified MAIT and Vdelta2 (Vd2) subset of gamma delta T cells in allo-HCT patients and healthy controls

status: Public on Oct 24 2022

city: Duarte

first: Anastasia

last: Kousa

address: 1500 E Duarte Rd

department: Hematology / HCT

institute: City of Hope

summary: We report the transcriptional changes of MAIT and Vd2 cells in the patients receiving allogeneic stem cell transplantation with good outcome compared to MAIT and Vdelta2 cells of healthy volunteers

overall_design: Comparison of MAIT and Vd2 cells collected from 5 patients and 5 healthy control subjects

first: Hana

last: Andrlová

first: Ronan

last: Chaligne

first: Ignas

last: Masilionis

first: Marcel

last: van den Brink

first: Kate

middle: A

last: Markey


title: Mitochondrial double-stranded RNAs as a pivotal mediator in the pathogenesis of Sjogren’s syndrome

status: Public on Oct 05 2022

city: Daejeon

first: Yoosik

last: Kim

address: 291 Daehak-ro

department: Department of Chemical and Biomolecular Engineering

country: South Korea

institute: KAIST

summary: Sjogren’s syndrome (SS) is a systemic autoimmune disease that targets the exocrine glands, resulting in impaired saliva and tear secretion. To date, type I interferons (I-IFNs) are increasingly recognized as pivotal mediators in SS, but their endogenous drivers have not been elucidated. Here, we investigate the role of mitochondrial double-stranded RNAs (mt-dsRNAs) in regulating I-IFNs and other glandular phenotypes of SS. We find that mt-dsRNAs are elevated in the saliva and tear of SS patients (n=73 for saliva and n=16 for tear) and in salivary glands of non-obese diabetic mice with salivary dysfunction. Using the in-house-developed 3D culture of immortalized human salivary gland cells, we show that stimulation by exogenous dsRNAs increase mt-dsRNAs, activate the innate immune system, trigger I-IFNs, and promote glandular phenotypes. These responses are mediated via the JAK1/STAT pathway. Indeed, a small chemical inhibitor of JAK1 attenuates mtRNA elevation and immune activation. We further show that muscarinic receptor ligand acetylcholine ameliorates autoimmune characteristics by preventing mt-dsRNA-mediated immune activation. Lastly, direct suppression of mt-dsRNAs reverses the glandular phenotypes of SS. Altogether, our study underscores the significance of mt-dsRNA upregulation in the pathogenesis of SS and suggests mt-dsRNAs as propagators of a pseudo-viral signal in the SS target tissue.

overall_design: mRNA-sequencing was performed in NS-SV-AC after 14 h-long poly I:C administration with different chemical treatment in vitro (i.e. 2-C'-Methyladenosine, Resveratrol, and DMSO as control). Two replicates were used for each sample.

first: Jimin

last: Yoon

first: Namseok

last: Lee


title: Single-cell RNA sequencing reveals distinct transcriptional features of the purinergic signaling in mouse trigeminal ganglion

status: Public on Oct 12 2022

city: GuangZhou

first: Jia

last: Shilin

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Institute of Stomatological Research, Sun Yat-sen University

summary: Trigeminal ganglion (TG) is the first station of sensory pathways in the orofacial region. The TG neurons communicate with satellite glial cells (SGCs), macrophages and other cells forming a functional unit that is responsible for processing of orofacial sensory information. Purinergic signaling, one of the most widespread autocrine and paracrine pathways, plays a crucial role in intercellular communication. The multidirectional action of purinergic signaling in different cell types contributes to the neuromodulation and orofacial sensation. To fully understand the purinergic signaling in these processes, it is essential to determine the shared and unique expression patterns of genes associated with purinergic signaling in different cell types. Here, we performed single-cell RNA sequencing of 22,969 cells isolated from normal mouse TGs. We identified 18 distinct cell populations, including 6 neuron subpopulations, 3 glial subpopulations, 7 immune cell subpopulations, fibroblasts, and endothelial cells. We also revealed the transcriptional features of genes associated with purinergic signaling, including purinergic receptors, extracellular adenosine triphosphate (eATP) release channels, eATP metabolism-associated enzymes, and eATP transporters) in each cell type. Our results have important implications for understanding and predicting the cell type-specific roles of the purinergic signaling in orofacial signal processing in the trigeminal primary sensory system.

overall_design: Bilateral TGs of 5 normal mouse were harvested (n=10) and performed scRNA-seq. We aimed to identify distinct cellular populations in TG and describe the transcriptional features of the genes associated with the purinergic signaling in each cell type using scRNA-seq.

first: Lijia

last: Mai

first: Shilin

last: Jia

first: Qing

last: Liu

first: Yanhao

last: Chu

first: Jinyue

first: Shengyan

last: Yang

first: Fang

last: Huang

first: Hongwen

last: He

first: Wenguo

last: Fan


title: Dual specificity and target gene selection by the MADS domain protein FRUITFULL

status: Public on Oct 04 2022

city: Berlin

first: Jose

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

institute: German Federal Institute for Risk Assessment

summary: How transcription factors of a single family confer different functional specificities in vivo, is an important question in molecular biology. Even more intriguingly, a single transcription factor can regulate context- or tissue-specific target genes to achieve distinct functions. Here we show, using a variety of genome-wide techniques, that gene regulation and DNA binding site selection by the MADS domain protein FRUITFULL (FUL) is tissue-specific. FUL has a dual role in regulating floral transition and fruit development.

overall_design: SELEX-seq experiments of several Arabidopsis MADS-domain transcription factor dimers.

first: Hilda

last: van Mourik

first: Marian

last: Bemer

first: Gerco

last: Angenent


title: Crotonylation of GAPDH regulates human embryonic stem cell endodermal lineage differentiation and metabolic switch

status: Public on Oct 03 2022

city: Guangzhou

first: Pang

last: Junjie

address: 132 Waihuan East Road, Beigang Village, Xiaoguwei Street, Panyu District, Guangzhou, Guangdong

institute: Sun Yat-sen University

summary: Post-translational modifications of proteins are crucial to the regulation of their activity and function. As a newly discovered acylation modification, crotonylation of non-histone proteins remains largely unexplored, particularly in human embryonic stem cells (hESCs). Here we report the investigation of induced crotonylation in hESCs, which resulted in hESCs of different pluripotency states differentiating into the endodermal lineage. We showed that increased protein crotonylation in hESCs was accompanied by transcriptomic shifts and decreased glycolysis. Through large-scale profiling of non-histone protein crotonylation, we showed that metabolic enzymes were major targets of inducible crotonylation in hESCs. We further discovered GAPDH as a key glycolytic enzyme regulated by crotonylation during endodermal differentiation from hESCs, where crotonylation of GAPDH decreased its enzymatic activity thereby leading to reduced glycolysis. Our study demonstrates that crotonylation of glycolytic enzymes may be crucial to metabolic switching and cell fate determination in hESCs.

overall_design: Compare transcriptome profiling (RNA-seq) of crotonate treated primed human embryonic stem cell H9 and EPS cells with untreated primed H9 cells, EPS cells and endodermal cells.

first: Jingran

last: Zhang

first: Guang

last: Shi

first: Junjie

last: Pang


overall_design: mRNA profiles of Arabidopsis pistils/siliques and for inflorescence/flower meristem tissues in WT and ful mutants were analyzed for 3 biological replicates.

first: Kerstin

last: Kaufmann


title: Next Generation Sequencing Facilitates Quantitative Analysis of Mock/ZIKV Infected AG6 Mice Olfactory Mucosa and Olfactory Bulb Transcriptomes

city: Beijing

first: Rui-Ting

last: Li

state: Beijing

address: No.20 Dongda Street, Fengtai District

department: State Key Laboratory of Pathogen and Biosecurity

institute: Beijing Institute of Microbiology and Epidemiology

summary: In this work, we demonstrate that neonatal mice infected with ZIKV via intracranial injection suffers from transient olfactory dysfunction when they grow up to puberty. Moreover, ZIKV exhibits broad cellular tropism and mainly targets the olfactory ensheathing cells (OECs) in the olfactory mucosa (OM) of mice. To decipher the underlying mechanism of the observed olfactory dysfunction in ZIKV infected mice at the molecular level, RNA-Seq analyses of the OM and OB samples from ZIKV infected mice were performed in comparison with that from the control animals.

overall_design: To investigate the comprehensive cellular response induced by ZIKV infection in olfactory tissues at the molecular level, we carried out global transcriptome analyses of mouse OM and OB infected  (3- and 5- dpi) with ZIKV in comparison with the mock-treated group.

first: Cheng-Feng

last: Qin

first: Jia

last: Zhou


title: A robust and efficient microvascular isolation method for multimodal characterization of the mouse brain vasculature

status: Public on Oct 01 2022

city: Stockholm

first: Michael

last: Vanlandewijck

address: Blickagången 6

department: Department of Medicine

institute: Karolinska Institute

summary: Studying disease related changes in the brain vasculature is pivotal due to its crucial role in supplying oxygen and nutrients, and removing waste. To study the vascular cells in detail, improved techniques for isolation of the vascular components are warranted. In this study, 22,515 cells were isolated using CD31 coupled magnetic beads and analyzed using single cell RNA sequencing. Their transcriptomes separated into 23 clusters corresponding to all known vascular and perivascular cell types. Western blot analysis using markers for these cell types confirmed their presence in the isolate and suggests that the protocol is suitable also for proteomic analysis. Finally, we adapted the protocol to accommodate primary culture. In conclusion, this method can successfully isolate murine brain microvasculature independent of cell sorting, alleviating the need for reporter mouse lines. The protocol is suitable for several testing modalities, including single-cell analyses, WB, and primary cell culture.

overall_design: The samples are mouse brain vasculature, freshly isolated and digested into single cell suspensions. These were subjected to the 10x Genomics Gene expression v3.1 chemistry and sequenced on a NextSeq platform as per manufacturers' recommendations.

first: Katrine

last: Dahl-Bjørnholm

first: Francesca

last: Del Gaudio

first: Hao

first: Weihan

first: Elisa

last: Vazquez-Liebanas

first: Maarja

last: Mäe

first: Urban

last: Lendahl

first: Christer

last: Betsholtz

first: Per

last: Nilsson

first: Helena

last: Karlström


title: Next-generation sequencing of cTEC and mTEC isolated from non-pregnant and pregnant females lacking the expression of Klf4 (KO) or not (LOX)

status: Public on Sep 30 2022

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: Stress-induced thymic involution is defined by profound damage to thymic epithelial cells (TECs), resulting in an acute and transient reduction of thymopoietic capacity. During pregnancy, thymic involution is not associated with TEC loss but rather with TEC quality modifications. Study of the mechanisms of TEC maintenance during pregnancy may be of critical importance for identifying new players for thymic regeneration in other models of thymic involution. We report a strong enrichment for motifs recognized by KLF4 based on genes differentially expressed in TECs of pregnant females. Therefore, we studied the impact of Klf4 deletion in TECs during pregnancy by analyzing thymus composition and TEC transcriptome. Conditional Klf4 deletion in homeostatic conditions does not injure thymic integrity. However, pregnant females lacking Klf4 show a disrupted thymus with substantial loss of thymic epithelial cells. Klf4 maintains cTEC number during pregnancy by maintaining cell survival and inhibiting the transition to a mesenchymal state. Our study reveals Klf4 as a protective factor for TECs during pregnancy-associated thymic involution and represents a potential study subject for other models of stress-induced thymic involution.

overall_design: mRNA sequencing was performed on cortical and medullary thymic epithelial cells (cTECs and mTECs) extracted from 12 weeks aged non-pregnant and pregnant female mice (2 days before delivery), which are either expressing Klf4 (LOX) or not (KO). The conditional deletion of Klf4 in TECs was performed using a Cre/lox system. cTECs (EpCAM+, CD45-, UEA1-) and mTECs (EpCAM+, CD45-, UEA1+) were purified by cell sorting after the enzymatic digestion of the stroma.

first: Lucyle

last: Depoërs

first: Maude

last: Dumont-Lagacé

first: Chloé

last: Houques

first: Sylvie

last: Brochu

first: Jean

middle: D

last: Larouche


title: Exploring the microbiome of oral epithelial dysplasia as a predictor of malignant progression

city: Vancouver

first: Wan

last: Lam

address: 675 West 10th Ave

institute: BC Cancer Research Centre

summary: The objectives of this study were to establish a microbiome profile for oral epithelial dysplasia using archival lesion swab samples to characterize the community variations and the functional potential of the microbiome using 16S rRNA gene sequencing

overall_design: Retrospective case-control study

first: Erin

last: Marshall

first: Michelle

last: Pewarchuk

first: Miriam

middle: P

last: Rosin

first: Denise

middle: M

last: Laronde

first: Lewei

last: Zhang

first: Morgan

middle: G

last: Langille

first: Leigha

last: Rock


title: 3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice [ChIP-seq]

status: Public on Sep 28 2022

city: Wuhan

first: yue

last: li

address: Shizishan Street

institute: HUAZHONG Agriculture University

summary: Repressive epigenetic modification histone H3 lysine 27 tri-methylation (H3K27me3) marks many agronomically important genes in plants. However, H3K27me3-associated three-dimensional (3D) genome architecture and its regulatory functions in rice flowering time remain unclear. In this study, we map H3K27me3-associated genome topology using long-read ChIA-PET and reveal extensive chromatin loops among H3K27me3-marked regions in different rice varieties and tissues. Multiple H3K27me3-associated chromatin loops usually tether together and further form repressive chromatin interacting domains (RIDs), which provide structural bases for the regulation of the co-modification and co-expression of interacting genes. Surprisingly, we identified extensive chromatin loops between the rice florigen genes Hd3a and RFT1, and frequent chromatin interactions between the positive flowering regulator Ehd1 on the chromosome 10 and Hd3a/ RFT1 loci on the chromosome 6. These results suggest that flowering genes might form a Ehd1-Hd3a/RFT1-centered spatial gene cluster in rice. We also demonstrate the flowering regulator protein complexes comprising Ghd7, Ghd8, and Hd1 could bind to the Ehd1-Hd3a/RFT1 spatial gene cluster. In addition, liquid-liquid phase separation of Ghd7 and Hd1, as well as the essentially synchronous expression of Ehd1 and Hd3a suggest that this spatial gene cluster acts as a regulatory hub to coordinately regulates the expression of Ehd1-Hd3a. This work uncovers the frame of integrated cis and trans molecular mechanism underlying transcriptional regulation of florigen genes in rice.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: H3K27me3 modification of DJ and osemf2b; Different Ghd8 binding sites in Ghd8:GFP NILs (ZS-ghd7/Ghd8:GFP/Hd1, ZS-Ghd7/Ghd8:GFP/Hd1, ZS-Ghd7/Ghd8:GFP/hd1), ZS-ghd7/ghd8/Hd1 as control

first: Yue

last: Li

first: Zhanyi


title: 3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice

platform_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group