title: Thioredoxin-interacting protein is essential for memory T cell formation via the regulation of the redox metabolism

status: Public on Dec 23 2022

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

summary: CD4+ memory T cells are central to long-lasting protective immunity and are involved in shaping the pathophysiology of chronic inflammation. While metabolic reprogramming is critical for the generation of memory T cells, the mechanisms controlling the redox metabolism in memory T cell formation remain unclear. We found that reactive oxygen species (ROS) metabolism changed dramatically in T helper-2 (Th2) cells during the contraction phase in the process of memory T cell formation. Thioredoxin-interacting protein (Txnip), a regulator of oxidoreductase, regulated apoptosis by scavenging ROS via the nuclear factor erythroid 2-related factor 2 (Nrf2)-biliverdin reductase B (Blvrb) pathway. Txnip regulated the pathology of chronic airway inflammation in the lung by controlling the generation of allergen-specific pathogenic memory Th2 cells in vivo. Thus, the Txnip-Nrf2-Blvrb axis directs ROS metabolic reprogramming in Th2 cells and is a potential therapeutic target for intractable chronic inflammatory diseases.

overall_design:
RNA-seq and ATAC-seq samples of Wild-type or Txnip KO mice that were immunized with 100 μg of OVA (Sigma-Aldrich) and 20% hydroxypropyl-β-cyclodextrin (HP-β-CD) (FUJIFILM, Tokyo, Japan) or 1×PBS administered intranasally (i.n.) and were collected on 0h and 48h in spleen. Th2 cells recovered from the spleen and sorted using a BD FACS Aria III (10,000 cells each, cell viability >98%) were encapsulated into droplets. Libraries were then prepared using Chromium Single Cell 3’ Reagent Kits v3.1 following the manufacturer’s protocol (10X Genomics; California, USA). The generated scRNA-seq libraries were sequenced using a total 127 cycle (paired-end reads) with a NovaSeq 6000 (Illumina). RNA sequencing (RNA-seq) was carried out as previously described. Total cellular RNA was extracted with TRIzol reagent (Invitrogen). For cDNA library construction, we used a SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (TaKaRa, Shiga, Japan) following the manufacturer’s protocol. Sequencing of library fragments was performed on an Illumina HiSeq 1500 System (Illumina, California, USA). ATAC-Seq was that 10,000 cells were used to extract the nuclei. The nuclei were treated with Tn5 transposase (15027865 and 15027866; Illumina) to tag and fragmentize the accessible chromatin. The fragmentized DNA was purified using a QIAGEN MinElute kit (QIAGEN, Venlo, Netherlands) and amplified with 14 PCR cycles, based on the amplification curve. The libraries were sequenced for 50 cycles.
The scRNA-seq samples of Th2 at day7 and day11 in vivo were that Naïve CD4+ cells were administered intravenously (i.v.) through the tail vein to BALB/c mice (1×10^6 cells per mouse, day 0). After cell transfer, OVA/Alum was administered intranasally (i.p.) on days 1 and 6, and were collected on day 7 and day11 in spleen. The scRNA-seq samples of Effector Th2 and transferred Th2 were that Th2 in vitro cells were administered intravenously (i.v.) through the tail vein to BALB/c mice (5×10^6 cells per mouse, day 0), and were collected Effector Th2 and transferred Th2 on 48h in spleen. The scRNA-seq , RNA-seq and ATAC-seq samples of Wild-type or Txnip KO mice were that these mice immunized with 100 ?g of OVA (Sigma-Aldrich) and 20% hydroxypropyl-?-cyclodextrin (HP-?-CD) (FUJIFILM, Tokyo, Japan) or 1×PBS administered intranasally (i.n.) , and were collected on 0h and 48h in spleen.Th2 cells recovered from the spleen and sorted using a BD FACS Aria III (10,000 cells each, cell viability >98%) were encapsulated into droplets. Libraries were then prepared using Chromium Single Cell 3? Reagent Kits v3.1 following the manufacturer?s protocol (10X Genomics; California, USA). The generated scRNA-seq libraries were sequenced using a total 127 cycle (paired-end reads) with a NovaSeq 6000 (Illumina). RNA sequencing (RNA-seq) was carried out as previously described (30). Total cellular RNA was extracted with TRIzol reagent (Invitrogen). For cDNA library construction, we used a SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (TaKaRa, Shiga, Japan) following the manufacturer?s protocol. Sequencing of library fragments was performed on an Illumina HiSeq 1500 System (Illumina, California, USA). ATAC-Seq was that 10,000 cells were used to extract the nuclei. The nuclei were treated with Tn5 transposase (15027865 and 15027866; Illumina) to tag and fragmentize the accessible chromatin. The fragmentized DNA was purified using a QIAGEN MinElute kit (QIAGEN, Venlo, Netherlands) and amplified with 14 PCR cycles, based on the amplification curve. The libraries were sequenced for 50 cycles.

first: Kota

last: Kokubo

first: Kiyoshi

last: Hirahara

first: Kaori

last: Tsuji

first: Yuki

last: Shimada

first: Yuri

last: Sonobe

first: Rie

last: Shinmi

first: Takahisa

last: Hishiya

first: Chiaki

last: Iwamura

first: Atsushi

last: Onodera

first: Toshinori

last: Nakayama


title: ZBTB12-HERVH-LncRNA axis is a molecular barrier for dedifferentiation of human stem cells [ChIP-seq]

status: Public on Dec 26 2022

city: Santa Barbara

first: Dasol

last: Han

state: California

address: University of California Santa Barbara

country: USA

institute: University of California Santa Barbara

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Development is generally viewed as one-way traffic of cell state transition from primitive to developmentally advanced states. However, molecular mechanisms that ensure the unidirectional transition remain largely unknown. NanoCAGE sequencing identified an evolutionarily conserved zinc finger repressor, ZBTB12, as a molecular barrier for dedifferentiation of human pluripotent stem cells (hPSCs). Single cell RNA sequencing revealed that ZBTB12 is essential for three germ layer differentiation by blocking hPSC dedifferentiation. Mechanistically, ZBTB12 cooperates with NANOG to fine-tune the expression of human endogenous retroviruses (HERVs). Active HERVH loci drive the expression of overlapping long non-coding RNAs (lncRNAs) whose downregulation by ZBTB12 is necessary for dedifferentiation blockage and pluripotency exit. Overall, we have identified a ZBTB12-HERVH-lncRNA axis as molecular machinery that safeguards the unidirectional transition of stem cell fates.

overall_design: Chromatin immunoprecipitation, H9 hESCs transduced with shGFP or shZBTB12 lentivirus, Antibodies: HDAC1 and H3K27ac (Active Motif, cat # 40967 and cat# 39133, respectively).

first: Guojing

last: Liu


title: Exploring the binding motif in genome wide for p53, Pygo2 and H3K4-Me3 in mouse (Pten/Smad4 KO) PS cell line

city: South Bend

first: Xin

middle: Lu

last: Lu

state: Indiana

address: 113 Galvin Life Science Center

department: Biological Department

institute: University of notre dame

summary: Since our data support that Pygo2 function is p53 Wild type status dependent and the interaction of Pygo2 with H3K4-Me3 is needed for the c-Kit regulation by Pygo2, however, neither Pygo2 nor p53 bind at c-Kit promoter region. To find out the potential co-binding locia for Pygo2, p53 and H3K4-Me3, we performed a Cut&Run assay followed by Miseq Sequencing.

overall_design: Examination of Pygo2, p53 and H3K4-Me3 binding locia in mouse genome, the fragmented input was used as control.

first: Yini

last: Zhu


title: Prenatal and postnatal exposure to acetaminophen and mouse neurodevelopment

city: Seattle

first: Brennan

middle: H

last: Baker

state: WA

institute: Columbia University Mailman School of Public Health

type: Expression profiling by high throughput sequencing

summary: Abstract pending

overall_design: Pregnant mice (n=12/group) were randomly assigned to receive either acetaminophen (150 mg/kg/day) or no acetaminophen (vehicle control) via palatable gelatin tablets, once a day from embryonic day 10 through postnatal day 21 (weening). At birth, 12 offspring per group, half male and half female, were removed from their litters for tissue harvesting. Prefrontal corticies were harvested, and RNA was extracted with Qigen RNeasy kits. RNA sequencing was performed with the Illumina HiSeq 4000 platform. FASTQ files were preprocessed with fastp using the default settings to filter bad reads, trim low quality bases, and cut adaptors. (https://academic.oup.com/bioinformatics/article/34/17/i884/5093234). Reads were mapped to the GRCM38(mm10) mouse genome using BWA-MEM (https://arxiv.org/abs/1303.3997) and assigned to exons using featureCounts (https://academic.oup.com/bioinformatics/article/30/7/923/232889) before performing differential expression analysis using DESeq2 (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8). Gene expression fold-changes compared acetaminophen treated to control offspring, accounting for sex. Normalized counts from DESeq2 were input into EGSEA (https://academic.oup.com/bioinformatics/article/33/3/414/2875813) to determine enrichment for MSigDB hallmark gene sets (https://www.pnas.org/content/102/43/15545.abstract) (https://www.cell.com/fulltext/S2405-4712(15)00218-5) and KEGG Pathways (https://scholar.google.com/scholar?hl=en&as_sdt=0%2C33&q=KEGG%3A+integrating+viruses+and+cellular+organisms&btnG=). We examined the top 20 EGSEA enrichments sorted by median ranking score and considered pathways significant if FDR-adjusted P<0.05.

first: Brandon

middle: L

last: Pearson


title: Recycling of parental histones preserves the epigenetic landscape during embryonic development (CUTAC)

status: Public on Dec 27 2022

city: Göttingen

first: Ufuk

last: Günesdogan

address: Justus-von-Liebig Weg 11

country: Germany

institute: University of Göttingen

summary: Epigenetic inheritance during DNA replication requires an orchestrated assembly of nucleosomes from parental and newly synthesized histones. We analyzed Drosophila HisC mutant embryos harboring a deletion of all canonical histone genes, in which nucleosome assembly relies on parental histones from cell cycle 14 onwards. Lack of new histone synthesis and parental histone recycling leads to more accessible chromatin and reduced nucleosome occupancy. This leads to upregulated and spurious transcription, whereas the control of the developmental transcriptional program is partially maintained. Importantly, the genomic positions of modified parental H2A, H2B, and H3 are restored during DNA replication. Therefore, the results suggest that parental histones with active or repressive marks are recycled to preserve the epigenetic landscape during DNA replication in vivo.

overall_design: Profiling of chromatin accessibility in whole Drosophila melanogaster embryos between 4.5 to 6 hours after egg laying. Wild type embryos (w1118) are compared with mutant embryos (Df(2L)HisC) lacking newly synthesized histones. Each experiment was analyzed in dublicates.

first: Herbert

last: Jäckle

first: Xiaojuan

last: Li

first: Oleksandr

last: Dovgusha

first: Dominik

last: Mühlen


title: Bacteria hijack a neuro-immune axis in meninges to facilitate brain invasion

city: St Louis

first: Felipe

last: Almeida de Pinho Ribeiro

state: MO

address: 4515 McKinley Ave

institute: Washington University in St Louis

summary: The meninges are densely innervated by nociceptive sensory neurons that mediate pain and headache. How pain and neuro-immune interactions impact meningeal host defenses is unclear. Bacterial meningitis causes life-threatening infections of the meninges and central nervous system (CNS), affecting over one million people a year. Here we find that Nav1.8+ neuron signaling to immune cells in the meninges via the neuropeptide calcitonin gene-related peptide (CGRP) exacerbates bacterial meningitis. Nociceptor ablation reduced meningeal and brain invasion by two bacterial pathogens: Streptococcus pneumoniae and Streptococcus agalactiae. S. pneumoniae activated nociceptors via Pneumolysin to release CGRP, which acts   through its receptor RAMP1 on meningeal macrophages to inhibit chemokine expression, neutrophil recruitment and antimicrobial defenses. Macrophage-specific RAMP1 deficiency or blockade of RAMP1 signaling enhanced immune responses and bacterial clearance in meninges and brain. Therefore, targeting a neuro-immune axis in the meninges can enhance host defenses and may be a potential treatment for bacterial meningitis.

overall_design: For in vitro bulk RNA-seq experiments, there are 24 samples total, representing 4 biological replicates, two technical replicates, of 3 conditions at 1 time point. For in vivo scRNA-seq experiments, there are 40 samples total, representing 10 biological replicates of 4 conditions at 1 time point.

middle: A

last: Pinho-Ribeiro

first: Liwen

last: Deng

first: Dylan

middle: V

last: Neel

first: Ozge

last: Erdogan

first: Himanish

last: Basu

first: Daping

last: Yang

first: Samantha

last: Choi

first: Alec

middle: J

last: Walker

first: Simone

last: Carneiro-Nascimento

first: Kathleen

last: He

first: Glendon

last: Wu

first: Beth

last: Stevens

first: Kelly

last: Doran

first: Dan

last: Levy

first: Isaac

last: Chiu


title: The tetraspanin CD53 protects stressed hematopoietic stem cells via promotion of DREAM complex-mediated quiescence

status: Public on Dec 22 2022

city: Saint Louis

first: laura

last: schuettpelz

address: 660 S. Euclid

institute: washington university

summary: Hematopoietic stem cells (HSCs) cycle in response to inflammatory and other proliferative stressors; however, they must quickly return to quiescence to avoid exhaustion and maintain their functional integrity. The mechanisms that regulate this return to quiescence are not well understood. Here we show that the tetraspanin CD53 is markedly upregulated in HSCs in response to a variety of inflammatory and proliferative stimuli, and loss of CD53 is associated with prolonged cycling and reduced HSC function in the context of inflammatory stress. Mechanistically, CD53 promotes the activity of the DREAM transcriptional repressor complex, which downregulates genes associated with cycling and division. Proximity labeling and confocal fluorescent microscopy studies show that CD53 interacts with DREAM-associated proteins, specifically promoting the interaction between Rbl2/p130 and its phosphatase, PP2A, effectively stabilizing p130 protein availability for DREAM binding. Together, these data identify a novel mechanism by which stressed HSCs resist continued cycling.

overall_design: We profiled HSCs (KSL CD48- CD150+) from the bone marrow and spleen of Cd53 KO mice and their WT littermates treated with G-CSF x 7 days or saline control

first: Zev

last: Greenberg

first: Laura

last: Schuettpelz


title: Expression data from nDKO and nTKO Tumor cells

first: Xin

last: Lu

summary:
To investigate how Pygo2 regulate the downstream moleculars in vivo to affct the progression of prostate tumor using prostate specific GEMM model
We used microarrays to find out the differetial expression gene between nDKO and nTKO to study the molecular mechanism of Pygo2 in prostate cancer progression

overall_design: nDKO and nTKO tumor were dissociated  into single cell suspension and the tumor cells were  isolated  using Epicam Beads and then extract the total RNA of isolated tumor cells for Microarray analysis

first: Yini

last: Zhu


title: Recycling of parental histones preserves the epigenetic landscape during embryonic development (CUT&Tag)

first: Ufuk

last: Günesdogan

overall_design: Profiling of histone PTMs in whole Drosophila melanogaster embryos between 3.5 to 6 hours after egg laying. Wild type embryos (w1118) are compared with mutant embryos (Df(2L)HisC) lacking newly synthesized histones. Each PTM at the respective timepoint and genotype was analyzed in dublicates or triplicates.

first: Herbert

last: Jäckle

first: Xiaojuan

last: Li

first: Oleksandr

last: Dovgusha

first: Dominik

last: Mühlen


title: Genome-wide CRISPR screen for regulators of SARS-CoV-2 programmed ribosomal frameshifting

city: Dallas

first: Joshua

last: Mendell

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: Genome-wide CRISPR-Cas9 knockout screens were performed in dual-fluorescent frameshifting reporter cell lines to identify human host factors for SARS-CoV-2 programmed ribosomal frameshfiting.

overall_design: Two independent clones for PRF-1 and PRF0 were used for the screen and 1.4x10^8 cells were infected with the Brunello pooled lentiviral CRISPR library (Addgene #73179) in the presence of 5 μg/ml polybrene at a multiplicity of infection between 0.3 to 0.5. Two days after transduction, the cells were selected in medium containing 1 μg/ml puromycin. After 10 days of puromycin selection, the top 1% eGFP/mCherry population and bottom 0.75% eGFP/mCherry population were sorted on an FACS Aria 2 cell sorter (BD Biosciences). gDNA from sorted pools was isolated by phenol-chloroform extraction. gDNA from 6x10^7 unsorted cells, was isolated with the Masterpure DNA isolation kit (Lucigen). Sequencing libraries were generated from the isolated gDNA through two sequential PCR reactions using the Herculase II DNA polymerase (Agilent). After 18 rounds of initial PCR amplification, 5% of the reaction product was used for a second round of PCR (11-13 cycles) with primers that introduced Illumina sequencing adapters and barcodes. The final PCR products were purified using AMPure XP beads (Beckman Coulter). Libraries were sequenced on a NextSeq500 (Illumina) with 75 bp single-end reads at an average sequencing depth of ~2x10^7 reads per sample. sgRNAs sequences were extracted from fastq files through an in-house Galaxy script and normalized reads counts were calculated.

first: Frederick

last: Rehfeld

first: Jennifer

last: Eitson

first: John

middle: W

last: Schoggins

middle: T


title: Mechanistic insights into the role of the canonical poly(A) polymerase Pla1 in RNA surveillance by the fission yeast MTREC complex

city: Melbourne

first: Attila

last: Horvath

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

summary: In this study we analysed the functional relevance of the interaction between Pla1 and the MTREC complex core component Red1 using various high throughput sequencing analyses performed on different Pla1-Red1 interaction mutants.Our analyses revealed that as part of MTREC complex, Pla1 hyper-adenylates Cryptic Unstable Transcripts (CUTs) for their efficient degradation. Interestingly, our H3K9(me)2 ChIP seq. data analysis also showed us that a functional Red1-Pla1 interaction was also required for the efficient assembly of the fission yeast facultative heterochromatic islands. Together, our data suggest a complex interplay between the RNA surveillance and 3’-end processing machineries.

overall_design: Detailed analysis of two Pla1-Red1 interaction mutants namely red1W298A/F305A and red1△288-345 with WT and total red1△ control strains using high throughput poly(A)+ RNA sequencing, total RNA sequencing, RNA-immunoprecipitation (RIP) followed direct RNA sequencing and ChIP seq. analysis.

first: Anusree

last: Lakshmi Sivadas

first: Tamas

last: Fischer


title: CircRNA, lncRNA and mRNA expression profiles in normal and LPS-induced septic cardiomyopathy mice

status: Public on Dec 24 2022

first: Yingzhou

last: Shi

address: 余杭塘路866号浙江大学紫金港校区白沙4舍111

country: China

institute: 浙江大学

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

summary: To further explore the expression of circRNA, lncRNA and mRNA in mice with septic cardiomyopathy, we have employed microarray analysis as a discovery platform to identify circRNAs and lncRNAs with the potential to play role in the pathophysiology process of LPS-induced septic cardiomyopathy in mice. Six hours after intraperitoneal injection of LPS(10mg/kg) or saline solution, eight mice (LPS group, n=4; Cont group, n=4) were anesthetized and the heart were collected.  And then total RNA was extracted and used for microarray detection.

first: Mingzhi

last: Zheng


title: Igh repertoire analysis in primary pro-B cells from  WT and NE1-/- mice (VDJ-seq)

city: Chicago

first: Amy

last: Kenter

state: IL

address: 835 S Wolcott

institute: UIC

summary: Analysis of the antibody repertoire composition is now possible using VDJ-seq.  We used this recently developed method for unbiased amplification from genomic DNA (gDNA) to directly compare the Igh repertoire of C57Bl/6 (WT) and NE1-/- pro-B cells. We find that a group of contiguous proximal and intermediate VH genes are under-utilized in V->DJ rearrangement in the absence of NE1 revealing a NE1 zone of influence.  We report the VH gene usage profile from WT and NE1-/-  primary pro-B cells from the VDJ-seq data.

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus

overall_design: VDJ-seq of WT and NE1-/-  primary pro-B cells

first: Eden

last: Kleiman

first: Xue

last: Lei

first: Sarah

last: Naiyer

first: Khalid

last: Bhat

first: Ann

last: Feeney


title: HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia

city: Cambridge

last: Horton

state: Cambridgeshire

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute - Department of Haematology

country: United Kingdom

institute: University of Cambridge

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

overall_design: Refer to individual Series


title: A modular CRISPR screen identifies individual and combination pathways contributing to HIV-1 latency

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Transcriptional silencing of latent HIV-1 proviruses entails complex and overlapping mechanisms and are a major barrier to in vivo elimination of HIV-1. We developed a new latency CRISPR screening strategy, called Latency HIV-CRISPR, which uses the packaging of guideRNA-encoding lentiviral vector genomes into the supernatant of budding virions as a direct readout of factors involved in the maintenance of HIV-1 latency. We developed a custom guideRNA library targeting epigenetic regulatory genes and paired the screen with and without a latency reversal agent – AZD5582, an activator of the non-canonical NFkB pathway – to examine a combination of mechanisms controlling HIV-1 latency. A component of the Nucleosome Acetyltransferase of H4 histone acetylation (NuA4 HAT) complex, ING3, acts in concert with AZD5582 to activate proviruses in J-Lat cell lines and in a primary CD4+ T cell model of HIV-1 latency. We found that the knockout of ING3 reduces acetylation of the H4 histone tail and BRD4 occupancy on the HIV-1 LTR, and the combination of ING3 knockout with the activation of non-canonical NFkB via AZD5582 act together to dramatically increase initiation and elongation of RNA Polymerase II on the HIV-1 provirus in a manner that is nearly unique among all cellular promoters.

overall_design: We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.

first: Emily

last: Hsieh

first: Derek

last: Janssens

first: Patrick

last: Paddison

first: Edward

middle: P

last: Browne

first: Molly

last: OhAinle

first: Steven

first: Michael

last: Emerman


title: Targeting neural cell senescence reverses neuropsychiatric disorders

city: Nice

first: Melanie

last: Pousse

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

country: France

institute: IRCAN

summary: The accumulation of senescent cells behaves as a key driver of several age-related cancers and degenerative diseases of the general population. Whether cellular senescence also contributes to psychiatric diseases is still elusive.  We report here the characterization of a zebrafish model of psychiatric disorder resulting from the invalidation of the ppp2r2c gene known to be involved in various psychiatric pathologies in human and encoding a neural specific regulatory subunit of the Protein Phosphatase 2A (PP2A). We found that the behavioral abnormalities of adult ppp2r2c-defficient fish were associated to neural cell senescence and that they can be reversed by invalidating the tp53 gene or by treating the fish with a drug that eliminates senescent cells. A molecule commonly used to treat ADHD patients, the methylphenidate, decreases the number of senescent neural cells both in adult PPP2R2C-defficient fish and in wild-type old fish. At the molecular level, methylphenidate attenuates the DNA damage response. We propose that some of the drugs commonly used in neuropsychiatry such as methylphenidate can prevent the appearance of senescent neural cells and that general strategies to clear senescent cells are promising therapies for common psychiatric disorders.

overall_design: RNA-Seq of zebrafish brain was performed using HiSeq X Ten, in two biological replicates for vehicle groups (a4 and WT) and three biological replicates for treated groups (MpH and Val).

first: Jing

last: YE


title: Hi-C analyses of pro-B lymphocytes

first: Hammad

last: Farooq

address: 835 S Wolcot

department: Microbiology and Immunology

institute: University of Illinois Chicago, College of Medicine

summary: We report the application of in situ Hi-C for analysis of progenitor (pro)-B cells. We generated genome-wide Hi-C heatmaps for pro-B cells from Rag1-/- and Rag1-/-NE1-/- mice.

overall_design: Hi-C

last: Hussain Bhat

first: Jie

last: Liang


title: A CpG island-encoded mechanism protects genes from premature transcription termination [SET1_ChIPseq]

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

institute: University of Oxford

summary: Transcription must be highly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, we reveal that actively transcribed CpG island-associated gene promoters recruit SET1 chromatin modifying complexes to enable gene expression. Counterintuitively, this effect is independent of SET1 complex histone modifying activity, and instead relies on the capacity of these complexes to interact with the RNA Polymerase II-binding protein, WDR82. Unexpectedly, we discover that SET1 complexes sustain gene transcription by counteracting the activity of the ZC3H4/WDR82 protein complex, which we show can pervasively terminate both genic and extragenic transcription. Therefore, we discover a new gene regulatory mechanism whereby CpG island elements nucleate a protein complex that protects genic transcription from premature termination, effectively distinguishing genic from non-genic transcription to enable gene expression.

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: The genomic distribution of SET1A was profiled in dTAG-SET1A ESCs, in which SET1A can be conditionally depleted. The genomic distribution of H3K4me3 and RNA Pol II was profiled in dTAG-SET1A/B ESCs, in which both SET1A and SET1B can be conditionally depleted. The genomic distribution of ZC3H4 was profiled in untreated ESCs.

first: Amy

last: Hughes

first: Robert

last: Klose


title: Pathways linking aging and atheroprotection in Mif-deficient atherosclerotic mice

status: Public on Dec 21 2022

city: Munich

first: Jürgen

last: Bernhagen

address: Feodor-Lynen-Straße 17

department: Division of Vascular Biology

institute: Institute for Stroke and Dementia Research (ISD), LMU University Hospital, Ludwig-Maximilians-University (LMU) Munich

summary: Atherosclerosis is a chronic inflammatory condition of our arteries and the main underlying pathology of myocardial infarction and stroke. The pathogenesis is age-dependent, but the links between disease progression, age, and atherogenic cytokines and chemokines are incompletely understood. Here, we studied the chemokine-like inflammatory cytokine macrophage migration inhibitory factor (MIF) in atherogenic Apoe–/– mice across different stages of aging and cholesterol-rich high-fat diet (HFD). MIF promotes atherosclerosis by mediating leukocyte recruitment, lesional inflammation, and suppressing atheroprotective B- cells. However, links between MIF and advanced atherosclerosis across aging have not been systematically explored. We compared effects of global Mif-gene deficiency in 30-, 42-, and 48-week-old Apoe–/– mice on HFD for 24, 36, or 42 weeks, respectively, and in 52-week- old mice on a 6-week HFD. Mif-deficient mice exhibited reduced atherosclerotic lesions in the 30/24- and 42/36-week-old groups, but atheroprotection, which in the applied Apoe–/– model was limited to lesions in the brachiocephalic artery and abdominal aorta, was not detected in the 48/42- and 52/6-week-old groups. This suggested that atheroprotection afforded by global Mif-gene deletion differs across aging stages and atherogenic diet duration. To characterize this phenotype and study the underlying mechanisms, we determined immune cells in the periphery and vascular lesions, obtained a multiplex cytokine/chemokine profile, and compared the transcriptome between the age-related phenotypes. We found that Mif- deficiency promotes lesional macrophage and T cell counts in younger but not aged mice, with sub-group analysis pointing towards a role for Trem2+ macrophage. The transcriptomic analysis identified MIF- and aging-dependent changes in lipid, cell respiration, and inflammation pathways, and key enriched genes such as Cpne7, Cd6, Plin1, Cd274 hinting towards effects on lesional T cells, lipids, and foamy macrophages. Moreover, Mif-deficient aged mice exhibited a distinct plasma cytokine/chemokine signature consistent with the notion that mediators known to drive inflamm’aging are either not down-regulated or even up- regulated in Mif-deficient aged mice compared to the corresponding younger ones. Lastly, Mif-deficiency favored formation of lymphocyte-rich peri-adventitial leukocyte clusters. While the causative contributions of these mechanistic pillars and their interplay will be subject to future scrutiny, our study suggests that atheroprotection due to global Mif-gene deficiency in atherogenic Apoe–/– mice is reduced upon advanced aging and identifies previously unrecognized cellular and molecular targets that could explain this phenotype shift. These observations enhance our understanding of inflamm’aging and MIF pathways in atherosclerosis and may have implications for translational MIF-directed strategies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from braciocephalic artery tissue sections from Apoe–/– and Apoe–/–Mif–/– mice on a 24- and 42-week hyperlipidemic diet (HFD)

first: Simon

last: Besson-Girard

first: Hao

last: Ji

first: Bishan

last: Yang

first: Christine

last: Krammer

first: Özgün

last: Gökçe


title: Differential Expression of Long Non-Coding RNAs and mRNAs in the active tuberculosis patients, multidrug-resistant tuberculosis patients, cured tuberculosis subjects and healthy controls

city: Hangzhou

first: Zhi-Bin

last: Li

address: 866 Yuhangtang Road

institute: Zhejiang University School of Medicine

summary:
The expression of the long non-coding RNAs (lncRNAs) in the active tuberculosis patients,multidrug-resistant tuberculosis patients,cured tuberculosis subjects and healthy controls were scanned using lncRNA microarray.The Arraystar Human LncRNA Microarray version 4.0 (Agilent Technologies) was used,containing 40173 lncRNA probes and 20730 mRNA probes for the detection of lncRNAs and mRNAs in the sample.
Non-coding RNAs and mRNAs profiling by array

overall_design: Plasma samples from active tuberculosis  patients,multidrug-resistant tuberculosis patients,cured tuberculosis subjects,healthy controls were collected.

first: Yu-Ting

last: Hu

first: Yu-Shuai

last: Han

last: Chen

first: Li-Liang

last: Wei

first: Li-Ying

last: Shi

first: Wen-Jing

last: Yi

first: Huai

last: Huang

first: Hui-Hui

last: Tu

first: Ting-Ting

last: Jiang

first: Ji-Cheng


title: Prolidase deficiency causes spontaneous T cell activation and lupus-like autoimmunity

city: London

first: Rose

last: Hodgson

address: 2 Monnery Road

institute: MiNA Therapeutics

summary: Prolidase Deficiency (PD) is a multi-system disorder caused by mutations in the PEPD gene, which encodes a ubiquitously-expressed metallopeptidase essential for the hydrolysis of dipeptides containing C-terminal proline or hydroxyproline. PD typically presents in childhood with developmental delay, skin ulcers, recurrent infections and in some patients, autoimmune features which can mimic systemic lupus erythematosus (SLE). The basis for the autoimmune association is uncertain, but might be due to self-antigen exposure with tissue damage, or indirectly driven by chronic infection and microbial burden. Here we address the question of causation and show that Pepd null mice have increased anti-nuclear autoantibodies and raised serum IgA, accompanied by kidney immune complex deposition, consistent with an SLE-like disease. These features are associated with an accumulation of CD4 and CD8 effector T cells in the spleen and liver. Pepd deficiency leads to spontaneous T cell activation and proliferation into the effector subset, which is cell intrinsic and independent of antigen receptor specificity or antigenic stimulation. However, an increase in KLRG1+ effector CD8 cells is not observed in mixed chimeras, in which the autoimmune phenotype is also absent. Our findings link autoimmune susceptibility in PD to spontaneous T cell dysfunction, likely to be acting in combination with immune activators that lie outside the haemopoietic system but result from the abnormal metabolism or loss of non-enzymatic prolidase function. This knowledge provides insight into the role of prolidase in the maintenance of self-tolerance and highlights the importance of treatment to control T cell activation.

overall_design: Splenic T cells from 3 WT or 3 Pepd-/- mice were subjected to 3' scRNAseq in combination with ADT T cell markers. Samples were multiplexed together by hashtagging, WT are B0301-B0303, Pepd-/- are B0304-B0306.

first: Katherine

last: Bull


title: PS19 brain lysate transfection changing ER stress gene expression in Biosensor cell

city: Palo Alto

first: Goonho

last: Park

state: CA

address: 3801 Miranda Avenue

department: Pathology

institute: Stanford University

summary: To investigate whether PS19 brain lysate transfection changes ER stress gene expression in Biosensor cell

overall_design: We performed bulk RNA-seq analysis using Biosensor cells transiently transfected with WT and PS19 brain lysate. As a positive control for ER stress induction, we tested thapsigargin treatment. This is a comparative gene expression profiling analysis of RNA-seq data for PS19 brain lysate and control brain lysate transfections

first: Jonathan

last: Lin


title: Vertical and horizontal gene transfer tradeoffs direct plasmid fitness

city: Durham

first: Lingchong

last: You

state: NC

address: 101 Science Drive

institute: Duke University

summary: Plasmid fitness is directed by two orthogonal processes—vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical E. coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.

overall_design: 5 plasmid-carrying E. coli strains (ESBL41T, ESBL92T, GN02560T, GN05243T, and pCU1T) were preapred for plasmid transfer in 2 media conditions (M9, TB), then harvested for RNA to compare gene expression to conjugation efficiency and between media

last: Bethke


title: Identification of miRNA information related to different skin color of golden-backed crucin carp

city: Wuxi

first: Mingkun

last: Luo

state: Jiangsu

address: East Shanshui Road 9

department: Wuxi Fisheries College

institute: Nanjing Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: In order to explore the regulatory information of the two different color associations in crucian carp, we identified the differential miRNAs of gold and greenish grey by smallRNA sequencing, and analyzed their functional and pathway enrichment.

overall_design: Comparative miRNA expression profiling analysis of RNA-seq data for gold and greenish grey skin of crucian carp.

first: Xianbo

last: Zhang

first: Webin

last: Zhu

first: Zaijie

last: Dong


title: Engineering an inhibitor resistant human CSF1R variant for microglia replacement [InVitro_RNA]

city: Irvine

first: Mathew

last: Blurton-Jones

address: 845 Health Sciences Road

department: Neurobiology and Behavior

institute: University of California, Irvine

summary:
iPSC-derived microglia expressing the wildtype, G795A, or G795C CSF1R variants were generated in vitro and treated with either DMSO or Plexxicon 5622 in order to
compare the gene expression differences exising between genotypes at baseline or following CSF1R inhibtion.

overall_design: Gene expression comparisons between in vitro iPSC-derived microglia expressing either the wildtype, G795A, or G795C CSF1R variants and treated with either DMSO or Plexxicon 5622

first: Blurton-Jones

last: Mathew

first: Hasselmann

last: Jonathan

first: Chadarevian

last: Jean Paul


title: DNA methyltransferase inhibition induces dynamic gene expression changes in lung CD4+ T cells of neonatal mice with E. coli pneumonia

city: Philadelphia

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

type: Methylation profiling by high throughput sequencing


title: SMARCB1 Loss in Poorly-differentiated Chordomas Drives Tumor Progression

city: Chapel Hill

first: Austin

last: Hepperla

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Poorly-differentiated (PD) chordoma, a tumor found mainly in children, adolescents and young adults is a rare, aggressive tumor originating from notochordal tissue, with limited therapeutic options. SMARCB1, a core component of the BAF and PBAF chromatin remodeling complexes, is the most frequently mutated gene in PD chordomas, the most aggressive form of this cancer. In this study, we employed cellular models of SMARCB1-negative PD chordomas to characterize expression of SWI/SNF complex members and determine the impact of SMARCB1 re-expression on cell growth as well as the transcriptional landscape by RNA-seq. We generated 2 SMARCB1-negative PD chordoma cell lines, CH22 and UM-Chor5, with an inducible SMARCB1 expression system. After 72 hours of induction of SMARCB1 re-expression, we observed continued growth of both SMARCB1-negative PD chordoma cell lines. This is in striking contrast to SMARCB1-deficient rhabdoid cell lines, where we found SMARCB1 re-expression inhibits growth completely. We also found the lack of growth inhibition may arise from the loss of CDKN2A/p16INK4A expression in all poorly differentiated chordoma cell lines which correlated well with the gene expression data. SMARCB1 re-expression in both CH22 and UM-Chor5 cells showed downregulation for rRNA and RNA processing as well as metabolic processing. Upregulated differentially expressed genes included those involved in cell adhesion, cell migration, and development. Taken together, our data establish SMARCB1 re-expression in PD chordomas alters the repertoire of SWI/SNF complexes, perhaps restoring those associated with cellular differentiation. Our findings support a model where SMARCB1 inactivation blocks the conversion of growth-promoting SWI/SNF complexes to differentiation-inducing ones.

overall_design: RNA-seq of various chordoma and malignant rhabdoid tumor (MRT) cell lines with and without the addition of SNF5 (SMARCB1).

first: Tara

last: Walhart

first: Bryanna

last: Vacca

first: Samera

last: Hamad

first: James

last: Petrongelli

first: Yemin

last: Wang

first: Erin

last: McKean

first: Stephen

last: Yip

first: Martin

last: Hirst

first: Bernard

middle: E

last: Weissman


title: Effect of ZBTB18 on gene expression and chromatin organization [ATAC-seq]

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

summary: This study set out to delineate gene expression programs that are differentially modulated in metastatic breast cancer cells with high versus low ability to further metastasize. To this end, the gene expression profiles of E0771GFP cells, M11GFP and M12GFP cells were determined. Analysis of these data sets identified ZBTB18 as a transcriptional repressor with lower activity in tumor cells that retain a high metastatic potential. To determine how ZBTB18 affects gene expression and chromatin organization, ZBTB18 was overexpressed in E0771GFP breast cancer cells. Gene expression profiles and differentially accessible DNA regions analyses were performed and identified Tgfbr2 as one of the genes most significantly repressed by ZBTB18. To determine the contribution of the TGFb1 -TGFBR2 signaling axis towards ZBTB18-mediated effects, E0771GFP cells overexpressing ZBTB18 were transduced with a doxycycline-inducible Tgfbr2 construct. These cells were then treated with doxycycline and recombinant TGFb1 or vehicle control and gene expression profiles were determined. These studies revealed that inhibition of ZBTB18 activity in tumor cells promotes metastasis by increasing chromatin accessibility and by enabling pro-metastatic TGFb1-TGFBR2-driven changes.

overall_design: This project aims at identifying the global changes in gene expression and open chromatin regions between ZBTB18-overexpressing and control mouse cancer cell lines.

first: Ruishan

first: Beisi

last: Xu

first: Myriam

last: Labelle


title: a4b7 engagement triggers CD4+ T cell differentiation into TRM cells that are susceptible to HIV infection

city: Bethesda

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

summary: We report that MAdCAM and retinoic acid (RA), two constituents of gut tissues, together with TGF-b, promote the differentiation of CD4+ T cells into a distinct subset a4b7+ CD69+ CD103+ TRMs. These findings provide a framework to better understand the contribution of CD4+ TRMs to persistent viral reservoirs and HIV pathogenesis.

overall_design:
CD4+ T cells from 6 healthy donors were subjected to 8 different treatments with 5 reagents (i.e. anti-CD3 Ab, anti-CD30 Ab, cV2, MadCAM, RA). The mRNA was extracted from approximately 2 million human T-cells for each sample, and subjected to 75-bp RNA-Seq sequencing by Illumina NextSeq. The Genome-wide gene expression profile was further analyzed as described in the manuscript.
----------------------------------------
Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns.

first: Claudia

last: Cicala

last: Arthos


title: Single-Cell Transcriptomic Profiling of the Mouse Testicular Germ Cells Reveals Important Role of Phosphorylated GRTH/DDX25 in Round Spermatid Differentiation and Acrosome Biogenesis during Spermiogenesis

city: BETHESDA

first: Veronica

last: Gomez-Lobo

state: MD

address: 10 Central Dr. Bldg10, Rm 8N248

institute: NIH

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the gene expression dynamics of germ cell development during spermatogenesis in the testis.

overall_design: Testicular cells were isolated from mouse seminferous tubules using 2 step enzymatic digestion followed by filteration using 100 µm and 40 µm cell strainer and analyzed using scRNAseq.

first: Raghuveer

last: Kavarthapu

first: Rajakumar

last: Anbazhagan

first: Soumitra

last: Pal

first: Maria

last: Dufau


title: A CpG island-encoded mechanism protects genes from premature transcription termination [SET1_TTseq]

first: Emilia

last: Dimitrova

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: Transcription profiling using spike-in calibrated transient transcriptome-seq of embryonic stem cells in which dTAG-SET1A/B, ZC3H4-dTAG or dTAG-SET1A/B/ZC3H4 can be conditionally depleted upon addition of dTAG13.

first: Amy

last: Hughes

first: Robert

last: Klose


title: A Novel Approach to Interrogating the Effects of Chemical Warfare Agent Exposure Using Organ-on-a-Chip Technology and Multiomic Analysis

city: Aberdeen Proving Ground

first: Jennifer

last: Sekowski

address: 5183 Blackhawk Rd.

department: BioSciences Division

institute: US Army DEVCOM Chemical Biological Center

summary: Organ-on-a-chip platforms are utilized in global bioanalytical and toxicological studies as a way to reduce materials and increase throughput as compared to in vivo based experiments. These platforms bridge the infrastructure and regulatory gaps between in vivo animal work and human systems, with models that exemplify active biological pathways. In conjunction with the advent of increased capabilities associated with next generation sequencing and mass spectrometry based ‘-omic’ technologies, organ-on-a-chip platforms provide an excellent opportunity to investigate the global changes at multiple biological levels, including the transcriptome, proteome and metabolome. When investigated concurrently, a complete profile of cellular and regulatory perturbations can be characterized following treatment with specific agonists. In this study, global effects were observed and analyzed following liver chip exposure to the chemical warfare agent, VX. Even though the primary mechanism of action of VX (i.e. acetylcholinesterase inhibition) is well characterized, recent in vivo studies suggest additional protein binding partners that are implicated in metabolism and cellular energetic pathways. Also, secondary toxicity associated with peripheral organ systems, especially in human tissues, is not well defined.  Our results demonstrate the efficacy of utilizing an organ-on-a-chip platform as a surrogate system to traditional in vivo studies. This is realized by specifically indicating significant dysregulation of a number of cellular processes in response to VX exposure including but not limited to amino acid synthesis, drug metabolism, and energetics pathways.

overall_design: Gene expression profiling analysis of RNA-seq data for primary liver cells grown in the Emulate MPS system comparing VX-exposed (three concentrations) to Control media -exposed cultures at Day 1 (24 hrs) and Day 7 (168 hrs) post-exposure.

first: Brooke

last: Simmons

first: Alvin

last: Liem

first: Pierce

last: Roth

first: Jessica

last: Hill

first: Mark

last: Karavis


title: Differential transcriptional responses to BIRC6 depletion between BIRC6-dependent and -nondependent cells

first: Tsukasa

last: Shibue

state: MA

department: Cancer Program

institute: Broad Institute of MIT and Harvard

summary: To investigate the mechanism underlying the differing responses of cancer cells to BIRC6 depletion, we knocked out BIRC6 in a series of  BIRC6-dependent and -nondependent cell lines. We subsequently profiled the effect of BIRC6 depletion on gene expression using RNA-sequencing.

overall_design: Comparative gene expression profiling of three BIRC6-dependent (HCC202, SNU503, HCC95) and three BIRC6-nondependent (JIMT1, SW837, HCC15) cell lines that were transduced with an sgRNA against BIRC6 (sgBIRC6-1, -4; two different sgRNA sequences against BIRC6 were tested) or a control sgRNA (sgCh2-2). Two biological replicates were analyzed for each sample.

first: Lisa

middle: D

last: Cervia

first: Francisca

last: Vazquez

first: William

middle: C

last: Hahn


title: JNK pathway blockade promotes HER2-driven breast cancer [RNA-seq_primary_mammary_tumor_cell_lines]

city: Worcester

first: Zeynep

last: Itah

address: 373 Plantation St. Suite 309

department: Program in Molecular Medicine

institute: UMass Medical School

summary: JNK deletion in MMTV-NIC mouse model promotes mammary gland tumor formation.

overall_design: mRNA expression of WT and JNKKO primary mammary tumor cell lines.

first: Shanzah

last: Chaudhry

first: Sithara

middle: R

last: Ponny

first: Ozkan

last: Aydemir

first: Alexandra

last: Lee

first: Julie

last: Cvanagh-Kyros

first: Wiliam

last: Muller

first: Roger

last: Davis


title: JNK pathway blockade promotes HER2-driven breast cancer [RNA-seq]

summary: JNK knockout cells proliferate more and forms bigger mulit acinar sturctures under normal conditions on 3D culture.

overall_design: mRNA expression of WT and JNKKO during trasformation on the 3D culture

first: SitharaRaju


title: Absolute Scaling of Single-Cell Transcriptomes Reveals Pervasive Hypertranscription in Adult Stem and Progenitor Cells

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

summary: Hypertranscription facilitates biosynthetically demanding cellular state transitions through global upregulation of the nascent transcriptome. Despite its potential widespread relevance, documented examples of hypertranscription remain few and limited predominantly to early development. This limitation is in large part due to the fact that modern sequencing approaches, including single-cell RNA sequencing (scRNA-seq), generally assume similar levels of transcriptional output per cell. Here, we use molecule counting and spike-in normalization to develop absolute scaling of single-cell RNA sequencing data. Absolute scaling enables an estimation of total transcript abundances per cell, which we validate in embryonic stem cell (ESC) and germline data and apply to adult mouse organs at steady-state or during regeneration.

overall_design: scRNA-seq

first: Yun-Kyo

last: Kim

first: Miguel

last: Ramalho-Santos


title: DDX5 RNA interactome in cultured T cells

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary:
RAR-related orphan receptor gamma (ROR  t)-expressing regulatory T (ROR  t+ Treg) cells play pivotal roles in preventing T cell hyperactivation and maintaining tissue homeostasis, in part, by secreting the anti-inflammation cytokine interleukin 10 (IL-10). Here, we report that Hypoxia Induced Factor 1a (HIF1alpha) is the master transcription factor for *Il10* in ROR  t+ Tregs.
Interestingly, this critical anti-inflammatory pathway is negatively regulated by an RNA-binding protein DEAD box helicase 5 (DDX5). As a transcriptional corepressor, DDX5 restricts the expression of HIF1   and its downstream target gene *Il10* in ROR  t+ Tregs. T cell specific *Ddx5* knockout (DDX5  T) mice have augmented ROR  t+ Treg suppressor activities and are better protected from intestinal inflammation. Genetic ablation or pharmacologic inhibition of HIF1a restores enteropathy susceptibility in DDX5  T mice. The DDX5-HIF1  -IL-10 pathway is conserved in mice and humans. These findings reveal potential therapeutic targets for intestinal inflammatory diseases.

overall_design: Primary cultured Th17 from two 8-10 weeks old wild-type (C57BL/6) female mice were subjected to UV- mediated crosslinking, lysis, and treatment with RNases, followed by immunoprecipitation (IP) of the DDX5-containing RNA complexes.

first: Shengyun

last: Ma

first: Benjamin

middle: S

last: Cho

first: Yuxin

last: Li

first: Nazia

last: Abbasi

first: Brian

last: Yee

first: Ge

last: Sun

first: Claire

last: Luo

first: Bing

last: Zhou

first: Xiang-dong

last: Fu

first: Wendy

last: Huang


title: Engineering an inhibitor resistant human CSF1R variant for microglia replacement

first: Mathew

last: Blurton-Jones

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

overall_design: Refer to individual Series


title: JNK pathway blockade promotes HER2-driven breast cancer

first: Zeynep

last: Itah

overall_design: small RNA expression of WT and JNKKO during transformation on the 3D culture

first: Shanzah

last: Chaudhry

last: Ponny

first: Ozkan

last: Aydemir

first: Alexandra

last: Lee

first: Julie

last: Cvanagh-Kyros

first: Wiliam

last: Muller

first: Roger


title: Next Generation Sequencing Facilitates Quantitative Analysis of wild-type (WT) and ERF4 tansgenic plants (OE) Transcriptomes

city: Qingdao

first: Anming

last: Ding

state: Shandong

address: No.11 Keyuanjingsi Rd.

institute: Tobacco Research Institute of CAAS

summary: Analysis of gene expression level. The hypothesis tested in the present study was that ERF4 overexpression affects cell cycle-related genes expression which promotes endoreduplication in Arabidopsis.

overall_design: mRNA profiles from rosette leaves of 28-d-old plants of WT and OE (overexpression of ERF4 driven by the CaMV 35S promoter, Pro35S:ERF4) were generated by deep sequencing, in duplicate, using Illumina NovaSeq 6000.

first: A


title: Genetic Association study of Autism in Saudi Females using SNP array

city: Dammam

first: Noor

middle: B

last: Almandil

address: C1 West Campus

department: Department of Clinical Pharmacy

country: Saudi Arabia

institute: Imam Abdulrahman Bin Faisal University

summary: Multiple variations in olfactory receptor genes are contributing to ASD in females of Arab origin

overall_design: case control study

first: Maram

last: Alismail

first: Hind

last: Alsuwat

first: Abdulla

last: AlSulaiman

first: Sayed

last: AbdulAzeez

first: J Francis

last: Borgio


title: COX-2/PGE2 upregulation contributes to the chromosome 17p-deleted lymphoma

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: Chromosome 17p deletions are one of the most frequent chromosomal alterations in human cancers and also lymphoma. Although it has been assumed to be equal to p53 loss for a long time, there are emerging evidence suggesting that there would be additional p53–independent mechanisms. Our previous work identified ALOX15B, an arachidonate lipoxygenase, as a 17p tumor suppressor in lymphoma. Interestingly, five of the six ALOX genes locate on this region and frequently co-deleted with TP53. Among them, ALOX15B, ALOX12B and ALOXE3 are adjacent to one another and proximal to the centromere relative to TP53, while ALOX12 and ALOX15 are distal to the centromere relative to TP53. Herein, we show that each of the five 17p ALOX genes repress Myc-driven lymphomagenesis in mice. Mechanistically, deficiency of the ALOX arachidonate metabolism pathway activates the paralleling COX-PGE2 pathway, resulting in increasing PTGS2 expression and PGE2 level. PGE2 prevents apoptosis of pre-B cells and Ptgs2 knockdown extends the latency of Myc;shAlox15b lymphoma in vivo. Further, shAlox15b lymphoma cells are more sensitive to COX-2 inhibitor celecoxib than control lymphoma cells. Importantly, the ALOX-COX metabolism unbalance is also observed in human cancers with del(17p). Taken together, our studies reveal the tumor suppression functions of all of the five ALOX genes on chromosome 17p in lymphoma and an unprecedented arachidonate metabolism unbalance between the ALOX and COX pathways underlying human cancers with 17p deletions.

first: Xiangyu

first: Xuelan

last: Chen

first: Zhengmin

last: Xu

first: Lu

last: Qi

first: Pengpeng

last: Liu

first: Mei

first: Qi

last: Zhang

first: Xiaohang

last: Hang

first: Minghai

last: Tang

first: Dan

last: Wen

first: Scott

last: Lowe

first: Ting

last: Niu

first: Chong

first: Yu


title: ARF suppression by MYC but not MYCN confers increased malignancy of Group 3 medulloblastoma

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

summary: Group 3 medulloblastoma (MB) carries the worst prognosis of the four molecular subgroups of MB. MYC amplifications represent the most common genetic alteration in Group 3 MB. By specifically driving MYC in hindbrain cells using a Tet-OFF system, we established a novel murine model of MB (GMYC) that accurately recapitulates human Group 3 MB. GMYC tumours develop with 60-70% penetrance, without p53 mutations, and are monoclonal as revealed by multicolour cell fate tracing. Compared to MYCN-driven Group 3 tumours driven from the same promoter, the ARF suppressor gene was significantly downregulated in GMYC tumours and specifically silenced by methylation in MYC-amplified human MB. While MYCN-driven tumour malignancy was more sensitive to ARF depletion, it dramatically increased the metastatic spread of MYC-driven tumours. Finally, the DNMT inhibitor decitabine could restore ARF levels and suppress MYC-driven tumour growth providing a promising targeting approach for these high-risk tumours.

overall_design: Total of 14 tumor biopsies were profiled for RNA expression; six from GMYC model and eight from GTML model. In addition, two GMYC Arf knock-out cell lines, four GTML Arf k-o cell lines, three GMYC cell lines treated with Onalespib, three GMYC cell lines treated with DMSO, three GTML2 cell lines treated with Onalespib  and three GTML2 cell lines with DMSO were also sequenced.

first: O

last: Mainwaring

first: H

last: Weishaupt

first: S

last: Hutter

first: G

last: Rosén

first: L

last: Breinschmid

first: A

last: Sundström

first: K

last: Annusver

first: M

last: Kasper

first: FJ


title: Prolidase deficiency causes spontaneous T cell activation and lupus-like autoimmunity

status: Public on Dec 20 2022

city: Oxford

first: Katherine

last: Bull

address: Wellcome Centre for Human Genetics

institute: University of Oxford

summary: Prolidase Deficiency (PD) is a multi-system disorder caused by mutations in the PEPD gene, which encodes a ubiquitously-expressed metallopeptidase essential for the hydrolysis of dipeptides containing C-terminal proline or hydroxyproline. PD typically presents in childhood with developmental delay, skin ulcers, recurrent infections and in some patients, autoimmune features which can mimic systemic lupus erythematosus (SLE). The basis for the autoimmune association is uncertain, but might be due to self-antigen exposure with tissue damage, or indirectly driven by chronic infection and microbial burden. Here we address the question of causation and show that Pepd null mice have increased anti-nuclear autoantibodies and raised serum IgA, accompanied by kidney immune complex deposition, consistent with an SLE-like disease. These features are associated with an accumulation of CD4 and CD8 effector T cells in the spleen and liver. Pepd deficiency leads to spontaneous T cell activation and proliferation into the effector subset, which is cell intrinsic and independent of antigen receptor specificity or antigenic stimulation. However, an increase in KLRG1+ effector CD8 cells is not observed in mixed chimeras, in which the autoimmune phenotype is also absent. Our findings link autoimmune susceptibility in PD to spontaneous T cell dysfunction, likely to be acting in combination with immune activators that lie outside the haemopoietic system but result from the abnormal metabolism or loss of non-enzymatic prolidase function. This knowledge provides insight into the role of prolidase in the maintenance of self-tolerance and highlights the importance of treatment to control T cell activation.

overall_design: Splenic T cells of 4 replicates of CD45.2+ WT or 4 replicates CD45.2+ Pepd-/- T cells isolated from WT:WT or WT:Pepd-/- mixed chimeric mice were subjected to 3' scRNAseq in combination with ADT T cell markers. Samples were multiplexed by hashtagging, WT are B0301-B0304, Pepd-/- are B0305-B0308.

first: Rose

last: Hodgson


title: Sirtuin 6 is a negative regulator of FcεRI signaling and anaphylactic responses

city: Jeollabuk-do

first: Hoang chan

last: Yu

state: Jeollabuk-do

address: 전북 덕진구 건지로 2, 전북대학교 의과대학 생화학교실 생명과학관 305호, jbnu

department: biochemistry

country: South Korea

institute: jbnu

summary: Sirt6 acts as a negative regulator of FcεRI signaling cascade in mast cells by suppressing PTPRC transcription. Activation of Sirt6 may therefore represent a promising and novel therapeutic strategy for anaphylaxis.

overall_design: RNA-Seq in WT and KO BMMCs to identify any transcriptional changes caused by Sirt6 deficiency

first: Hyun-Young

last: Jang

first: Sang-Myeong

last: Lee

first: Byung-Hyun

last: Park


title: Labelling transcriptional response to dissociation in zebrafish larvae using scSLAMseq

city: Berlin

first: Anika

last: Neuschulz

address: Hannoversche Strasse 28

institute: Max-Delbrück-Center for Molecular Medicine

summary: Transcriptional response to dissociation is known to cause artefacts in single cell data sets. We used 4sU to label newly made transcripts during dissociation in order to to later remove them from the data set

overall_design: 4sU was added to the dissociation buffer while the larvae were enzymatically dissociated for 30 min. Two of the three samples were FACS sorted afterwards and one of the two was additionally incubated on ice for 30 minutes to simulate waiting times after sorting.


title: Toxicogenomic signatures associated with methylmercury induced developmental toxicity in the zebrafish embryos.

city: Beijing

first: Ruihong

last: Wang

address: No. 8 Dayangfang, Anwai Beiyuan, Chaoyang District, Beijing

department: State Key Laboratory of Environmental Criteria and Risk Assessment

institute: Chinese Research Academy of Environmental Sciences

summary: Methylmercury (MeHg) is a teratogen with adverse effects on embryogenesis from fish to man. The adverse developmental outcomes of MeHg are well understood, but molecular understanding of teratogenic effects is rather limited. We performed here a genome - wide transcriptional analyses of 6, 30 and 50 μg/L MeHg treated zebrafish embryos from 4 to 72 h post-fertilization (hpf) using RNA-sequencing and self-printed microarray, and conducted a systematical comparison of MeHg - induced transcriptomic responses observed in this and our previous studies. We found that genes linked to gene ontology in terms of oxidative stress, visual, photoreception and cilium, and GABAergic synapse were enriched in embryo exposed from 4 to 72 hpf. The significantly altered genes involved in MAP kinase, TGF beta signaling pathway, oxidative phosphorylation, and glutathione metabolism were enriched across different exposure scenarios. We obtain 22 genes significantly regulated by MeHg, particularly the significant changes were determined in embryos exposed to 6 μg/L MeHg, which did not cause obviously teratogenic effects. Our findings show that the genes whose expression is altered by MeHg in embryonic stages may play important roles in adverse developmental endpoints and might be served as signatures for teratogenic effects.

overall_design: Identifying the marker genes which are able to assess the toxic effect of zebrafish embryos exposed to MeHg by differential genes expression analysis of RNA-seq data.Embryos were respectively exposed to 0, 6, 30, 50 μg/L MeHg at 4 to 72 hpf.

first: Lixin

last: Yang

first: Shaojuan

last: Guo


title: A CpG island-encoded mechanism protects genes from premature transcription termination

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

platform_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus


title: Measuring stress response upon tissue dissociation using SLAMseq in bulk and single cells

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus


title: Role of the HCMV immediate early proteins in controlling the HCMV transcriptome

city: Chicago

first: Mary

last: Hummel

address: 303 E. Chicago Ave

institute: Northwestern University

summary: Purpose: to investigate the role of the HCMV immediate early genes in controlling the HCMV and cellular transcriptomes

sample_organism:
Homo sapiens
Human betaherpesvirus 5

platform_organism:
Homo sapiens
Human betaherpesvirus 5

overall_design: MRC5 cells were infected with the TB40r mGFP-IE-FKBP strain of HCMV.  Infected cells were cultured for 5 days in the presence or absence of shield-1, and then processed for RNAseq analysis.

first: Eleonora

last: Forte

first: Matthew

last: Schipma


title: Labelling transcriptional response to dissociation in mouse hippocampus using scSLAMseq

overall_design: 4sU was added to the dissociation buffer while the hippocampi were enzymatically dissociated for 30 min.

first: Neuschulz

last: Anika

first: Bakina

last: Olga


title: Transcriptome sequencing Analysis of Plutella xylostella (P. xylostella) after DMNT treatment.

city: Hefei

first: Chen

last: Hongyi

address: 130 Changjiang West Road

institute: Anhui Agricultural University

summary: Purpose: To investigate the molecular mechanism underlying the function of DMNT function on P. xylostella larvar, we performed a whole genome transcriptome sequencing (RNA-seq) analysis

overall_design: Transcriptome sequencing analysis of 2st instar larva after DMNT treatment at 12h.

first: Peijin

last: Li

last: Chen

first: Hongyi

first: Shijie

last: Huang


title: Sequencing analysis of six eukaryotic transcriptome in Arabidopsis thaliana

summary: To dissect the molecular mechanism of NCBP function in the context of P. xylostella resistance, we performed a transcriptome deep sequencing (RNA-seq) analysis.

overall_design: 2-week-old Arabidopsis thaliana

first: Taoshan

last: Jiang


title: Mechanistic study comparing cartilage formation from human mesenchymal stromal cells and iPSC-derived multipotent cells [bulk RNA-seq]

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Multipotent progenitor cells (iMPCs) created from induced pluripotent stem cells (iPSCs) is a promising cell source for cartilage regeneration. In most studies, bone morphogenetic proteins (BMPs) were shown to significantly enhance transforming growth factor-b (TGFb)-induced iMPC chondrogenesis. In contrast, TGFb alone is sufficient to induce robust chondrogenesis of human primary mesenchymal stromal cells (MSCs). Currently, the mechanism underlying this difference between iMPCs and MSCs has not been fully understood. In this study, we first generated iMPCs from human iPSCs and examined their differentiation capacity at different passages. We then optimized the conditions for chondrogenesis and determined that medium supplemented with TGFb and BMP6 led to robust cartilage formation from iMPCs with minimal hypertrophy. Moreover, the cartilage generated from this new method was resistant to osteogenic transition upon subcutaneous implantation and led to a hyaline cartilage-like regeneration in osteochondral defects in rats. Interestingly, TGFb alone induced phosphorylation of Smad2/3 in iMPCs but not Smad1/5, which led to poor chondrogenesis. In contrast, TGFb resulted in the phosphorylation of both Smad2/3 and Smad1/5 and robust chondrogenesis in human MSCs. We further discovered that the remarkably low level of Activin receptor-like kinase 1 (ACVRL1/ALK1) in iMPCs, when compared to MSCs, partially accounts for this difference. For instance, overexpression of ALK1 in iMPCs activated both Smad1/5 and Smad2/3 upon TGFb only treatment and resulted in a high level of chondrogenesis, which was not observed in control iMPCs. In summary, this study describes a robust method to generate chondrocytes with low hypertrophy for hyaline cartilage repair and elucidates the difference between MSCs and iMPCs in response to TGFb.

overall_design: mRNA profiles of two conditions. MSC_B3: MSC under TGFβ3 stimulation; iMPC_ B3: iMPC under TGFβ3 stimulation. Three repeats per condition

first: Shiqi

last: Xiang

first: Zixuan

last: Lin

first: Meagan

last: Makarcyzk

first: Xiurui

last: Zhang

first: Karen

last: Clark

first: Eileen

first: Silvia

first: Tingjun

last: Hao

first: Madalyn

last: Fritch

first: Peter

middle: G

last: Alexander

first: Hang


title: Role of the HCMV immediate early proteins in controlling the HCMV and cellular epigenomes

first: Mary

last: Hummel

summary: Purpose: to investigate the role of the HCMV immediate early proteins in controlling the HCMV and cellular epigneomes during lytic infectioin

overall_design: MRC5 cells were infected with TB40r mGFP-IE-FKBP strain of HCMV.  Infected cells were cultured for 5 days in the presence or absence of shield-1.  Infected cells were harvested and processed for Pol 2 and H3K27Ac ChIP-seq analysis.

first: Eleonora

last: Forte

first: Matthew

last: Schipma


title: Mechanistic study comparing cartilage formation from human mesenchymal stromal cells and iPSC-derived multipotent cells [scRNA-seq]

overall_design: Single cell profile for iMPCs.


title: A CpG island-encoded mechanism protects genes from premature transcription termination [SET1_RNAseq]

first: Emilia

last: Dimitrova

summary: Transcription must be highly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, we reveal that actively transcribed CpG island-associated gene promoters recruit SET1 chromatin modifying complexes to enable gene expression. Counterintuitively, this effect is independent of SET1 complex histone modifying activity, and instead relies on the capacity of these complexes to interact with the RNA Polymerase II-binding protein, WDR82. Unexpectedly, we discover that SET1 complexes sustain gene transcription by counteracting the activity of the ZC3H4/WDR82 protein complex, which we show can pervasively terminate both genic and extragenic transcription. Therefore, we discover a new gene regulatory mechanism whereby CpG island elements nucleate a protein complex that protects genic transcription from premature termination, effectively distinguishing genic from non-genic transcription to enable gene expression.

overall_design: Gene expression profiling using spike-in calibrated RNA-seq of embryonic stem cells in which dTAG-SET1A, dTAG-SET1B, or dTAG-SET1A/B can be conditionally depleted upon addition of dTAG13. Also included is a control of WT ESCs treated with dTAG13.

first: Amy

last: Hughes

first: Robert

last: Klose


title: Augmenting hematoma-scavenging capacity of innate immune cells by CDNF reduces brain injury and promotes functional recovery after intracerebral hemorrhage

status: Public on Dec 19 2022

city: Helsinki

first: Vassilis

last: Stratoulias

state: <None>

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: We show that intracerebroventricular administration of recombinant human cerebral dopamine neurotrophic factor (rhCDNF) accelerates hemorrhagic lesion resolution, reduces peri-focal edema, and improves neurological outcomes in an animal model of collagenase-induced ICH. We demonstrate that CDNF acts on microglia/macrophages in the hemorrhagic striatum by promoting scavenger receptor expression, enhancing erythrophagocytosis and increasing anti-inflammatory mediators while suppressing the production of pro-inflammatory cytokines. Administration of rhCDNF results in upregulation of the Nrf2-HO-1 pathway, but alleviation of oxidative stress and unfolded protein responses in the perihematomal area. Finally, we demonstrate that intravenous delivery of rhCDNF has beneficial effects in an animal model of ICH and that systemic application promotes scavenging by the brain’s myeloid cells for the treatment of ICH.

overall_design: Comparison of CD11+positive cells extracted from hemorrhagic striatum of rhCDNF or saline treated animals

first: Tseng

last: Kuan-Yin

first: Mikko

last: Airavaara

first: Juho

last: Väänänen

first: Liew

last: Hock-Kean


title: Zinc Finger MYND-Type Containing 8 (ZMYND8) is epigenetically regulated in mutant Isocitrate Dehydrogenase 1 (IDH1) glioma to promote radioresistance.

city: Ann Arbor

first: Maria

last: Castro

state: MI

address: 1150 East Medical Center Drive

department: Neurosurgery

institute: University of Michigan Medical School

overall_design: Refer to individual Series


title: Engineering an inhibitor resistant human CSF1R variant for microglia replacement [InVivo_RNA]

city: Irvine

first: Mathew

last: Blurton-Jones

address: 845 Health Sciences Road

institute: University of California, Irvine

summary:
iPSC-derived hematopoietic progenitor cells expressing either the wildtype or G795A CSF1R variant were xenotransplanted into neonatal mice and subsequently aged for
two months to compare in vivo gene expression differences between the two CSF1R genotypes.

overall_design: Gene expression comparisons between iPSC-derived microglia expressing either the wildtpe of G795A CSF1R variant following neonatial xenotransplantation into the murine brain

first: Blurton-Jones

last: Mathew

first: Hasselmann

last: Jonathan

first: Chadarevian

last: Jean Paul


title: An in vivo avian paradigm to model human melanoma disease and perform fast and relevant preclinical studies

city: LYON

first: Julie

last: CARAMEL

address: 28 Rue Laennec

institute: Cancer Research Center of Lyon

summary: Metastatic melanoma patients carrying a BRAFV600 mutation can be treated with BRAF inhibitors (BRAFi), in combination with MEK inhibitors (MEKi), but innate and acquired resistance invariably occurs. Innate resistance can involve transcriptional and epigenetic-based phenotypic adaptations, remaining yet unpredictable. We describe here the development of a highly efficient patient-derived xenograft model adapted to patient melanoma biopsies, using the avian embryo as a host (AVI-PDXTM). In this particular paradigm, we depict a fast and reproducible tumor intake of patient samples within the embryonic skin, preserving key molecular and phenotypical features. We provide the proof of concept that the AVI-PDXTM allows modeling melanoma patient diversity of responses to BRAFi/MEKi, in very short delays, hence positioning it as a valuable tool for the design of personalized medicine assays.

overall_design: GLO and GLO-R cells are a pair of BRAFV600-mutated melanoma cells derived from a metastatic patient, before (GLO) and after (GLO-R) emergence of resistance to vemurafenib + cobimetinib treatment

first: Loraine

last: Jarrosson

first: Stéphane

last: Dalle

first: Clélia

last: Costechareyre

first: Yaqi

last: Tang

first: Maxime

last: Grimont

first: Maud

last: Plaschka

first: Marjorie

last: Lacourrège

first: Romain

last: Teinturier

first: Myrtille

last: Le Bouar

first: Delphine

last: Maucourt-Boulch

first: Anaïs

last: Eberhardt

first: Valérie

last: Castellani

last: Caramel

first: Céline

last: Delloye-Bourgeois


title: sgRNA cassette sequencing from CHP212 cells treated with Nutlin

city: Aurora

first: Matthew

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary: Genome-wide CRISPR/Cas9-based screen to identify positive regulators of p53 function

overall_design: CHP212 cells transduced with the GeCKOv2 A and B libraries were treated with 2 rounds of Nutlin to discover positive modulators of p53 function

first: Maria

middle: M

last: Szwarc

first: Joaquín

last: Espinosa


title: Zinc Finger MYND-Type Containing 8 (ZMYND8) is epigenetically regulated in mutant Isocitrate Dehydrogenase 1 (IDH1) glioma to promote radioresistance [ChIP-seq]

last: Castro

summary: Mutant isocitrate dehydrogenase 1 (mIDH1) alters the epigenetic regulation of chromatin, leading to a hypermethylation phenotype in adult glioma. This work focuses on identifying gene targets epigenetically dysregulated by mIDH1 to confer therapeutic resistance to ionizing radiation (IR). We evaluated changes in the transcriptome and epigenome in a radioresistant mIDH1 patient-derived glioma cell culture (GCC) following treatment with an mIDH1 specific inhibitor AGI-5198. We identified Zinc Finger MYND-Type Containing 8  (ZMYND8) as potential target of mIDH1 reprogramming. We suppressed ZMYND8 expression by shRNA knockdown and genetic knockout (KO) in mIDH1 glioma cells then assessed cellular viability to IR. We assessed the sensitivity of mIDH1 GCCS to pharmacological inhibition of ZMYND8-interacting partners: HDAC, BRD4, and PARP. Inhibition of mIDH1 lead to an upregulation of gene networks involved in replication stress. We found that the expression of ZMYND8, a regulator of DNA damage response was decreased in three patient-derived mIDH1 GCCs after treatment with AGI-5198. Knockdown of ZMYND8 expression sensitized mIDH1 GCCs to radiotherapy marked by decreased cellular viability. Following IR, mIDH1 glioma cells with ZMYND8 knockout (KO) exhibit significant phosphorylation of ATM and sustained γH2AX activation. ZMYND8 KO mIDH1 GCCs were further responsive to IR when treated with either BRD4 or HDAC inhibitors. PARP inhibition further enhanced the efficacy of radiotherapy in ZMYND8 KO mIDH1 glioma cells. These findings indicate the impact of ZMYND8 in the maintenance of genomic integrity and repair of IR-induced DNA damage in mIDH1 glioma.

overall_design: In this study, we sought to determine radioresistance mechanisms in IDH-mutant gliomas that contribute to glioma cell survival in response to radiotherapy. We utilized a radioresistant patient-derived glioma cell culture SF10602, which retained the endogenous mutations in IDH1-R132H, ATRX and TP53 after adaptation to in vitro culture. In order to identify pathwaysaltered by mIDH1 inhibition in SF10602, we performed ChIP-seq by administering 5µM AGI-5198 every 2 days for 10 days.

first: Stephen

last: Carney

first: Tingting

last: Qin

first: Maureen

last: Sartor

first: Pedro

last: Lowenstein


title: PolyA RNA-seq from CHP212 WT and FAM193AKO cells treated with Nutlin-3

summary: Analysis of steady-state mRNA levels in CHP212 WT and FAM193AKO cells following DMSO or Nutlin-3a treatment.

overall_design: Two independent biological replicates each of CHP212 WT and FAM193AKO cells treated with DMSO or 10 uM Nutlin-3a for 12 hours.

first: Joaquin


title: Zinc Finger MYND-Type Containing 8 (ZMYND8) is epigenetically regulated in mutant Isocitrate Dehydrogenase 1 (IDH1) glioma to promote radioresistance [RNA-seq]

overall_design: In this study, we sought to determine radioresistance mechanisms in IDH-mutant gliomas that contribute to glioma cell survival in response to radiotherapy. We utilized a radioresistant patient-derived glioma cell culture SF10602, which retained the endogenous mutations in IDH1-R132H, ATRX and TP53 after adaptation to in vitro culture. In order to identify pathwaysaltered by mIDH1 inhibition in SF10602, we performed RNA-seq by administering 5µM AGI-5198 every 2 days for 1 week.

first: Rebecca

last: Tagett


title: Single cell transcriptional profiles of islet1-derived ECs and the other ECs in the tail of 48 hpf zebrafish embryos

city: Suita

first: Hiroyuki

last: Nakajima

state: Osaka

address: 6-1 Kishibeshinmachi

department: Department of Cell Biology

country: Japan

institute: National Cerebral and Cardiovascular Center Research Institute

summary: We report transcriptional heterogeneity of venous endothelial cells (ECs) in the tail of zebrafish embryos, which consist of HSPC-niche-constituting ECs and caudal vessel (CV)-constituting ECs. To characterize isl1-derived ECs which derive from the endoderm and mainly constitute the HSPC niche in the caudal hematopoietic tissue (CHT), we performed single cell RNA sequencing (scRNA-seq) of isl1-derived ECs and the other ECs separately isolated from the tails of zebrafish embryos. Our analyses revealed that tail venous ECs were split into 5 distinct sub-clusters where isl1-derived ECs and the other ECs were similarly distributed to all venous EC clusters, and further revealed that genes whose expression levels are different between isl1-derived ECs and the other ECs tend to show similar changes across all of the clusters even after their diversification.

overall_design: We isolated live TagRFP+/EGFP+ cells (for isl1-derived ECs) and TagRFP-/EGFP+ cells (for the other ECs) separately by FACS sorting from the tails of TgBAC(isl1:TagRFP);Tg(dab2:EGFP) embryos at 48 hpf. Then, barcoded single-cell cDNA libraries were prepared using the Chromium Single Cell 3’ Reagents Kits v3.1 and were then sequenced using Illumina NovaSeq6000.

first: Takuya

last: Yamamoto

first: Ayano

last: Chiba

first: Naoki

last: Mochizuki


title: Combination CTLA4Ig and anti-CD40L treatment modifies T and B cell metabolic profiles and promotes BCR and membrane protein remodeling in a mouse model of SLE

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

summary: Systemic lupus erythematosus (SLE) is a complex autoimmune disease with significant morbidity - demanding further examination of tolerance inducing treatments. Short-term treatment of lupus-prone NZB/WF1 mice with combination CTLA4Ig and anti-CD40L but not single treatment alone, suppresses disease for > 6 months via modulation of B and T cell function while maintaining immune responses to exogenous antigens. Three months after a 2-week course of combination costimulatory blockade, we found a modest decrease in the number of activated T and B cells in both combination and single treatment cohorts compared to untreated controls. However, only combination treatment group showed a 50% decrease in spare respiratory capacity of splenic B and T cells. RNA-sequencing and gene set enrichment analysis of germinal center (GC) B cells confirmed a reduction in the oxidative phosphorylation signature in the combination treatment cohort. This cohort also manifested an increase in expression of B Cell Receptor (BCR) associated signaling molecules and an increase in phosphorylation of PLCγ in GC B cells after stimulation with anti-IgG and anti-CD40. GC B cells from combination treatment mice also displayed a signature involving remodeling of GPI-linked surface proteins. Accordingly, we found a decrease in cell surface expression of the inhibitory molecule CD24 on class-switched memory B cells from aged NZB/W mice that corrected in the combination treatment cohort. Since both a profound decrease in BCR signaling and increased immune cell metabolism enhance loss of tolerance in lupus-prone mice, our findings help to explain the restoration of tolerance observed after short-term combination costimulatory blockade.

overall_design: Examination of phenotypic changes in B and T cell subsets in NZBWF1/J mice treated with short term CTLA4IG and Anti-CD40L

first: Chirag

last: Raparia

first: Zhengzi

last: Yi

first: Anne

last: Davidson


title: Transcription profile analysis of wild type bone marrow derived-macrophages in response to Anisomycin, type I and type II interferons and the combination of them

status: Public on Dec 18 2022

city: Vienna

first: Laura

last: Boccuni

address: Dr-Bohr-Gasse, 9

department: Department of Microbiology, Immunobiology and Genetics

country: Austria

institute: University of Vienna

summary: The innate immune system acts as the first line of defense against invasion of microbial pathogens. Here, macrophages play a substantial role in recognition, phagocytosis and killing of pathogens and the regulation of the innate immune response. Here, interferons play a crucial role in augmenting the antimicrobial functions of macrophages and their ability to produce mediators of immunoregulation. Pathogen recognition activates many different signaling pathways that interact to produce an innate response commensurate with the microbial challenge. The co-occurrence of signaling by sensors of stress and IFN receptors is a hallmark of innate responses to many viral and bacterial pathogens. Our results show how Anisomycin, a drug that induces stress-activation of MAPK pathways, regulates mRNA expression of interferon stimulated genes (ISG) upon IFNg and IFNb stimulation

overall_design: Methods: Bone marrow-derived macrophages (BMDM) mRNA of wild-type (WT) untreated, as well as 2h20 Anisomycin, 2h IFNb and IFNg treated or pre-treated with Anisomycin (20min) and then stimulated with IFNg and IFNb for for 2h and then were generated by deep sequencing, in triplicate, using Illumina sequencing.

first: Thomas

last: Decker


title: Chromatin accessibility analysis of wild type bone marrow-derived macrophages in response to Anisomycin, type I interferons and the combination of them or with p38 MAPK inhibitor PH-797804 (ATAC-Seq IFNb)

summary: The innate immune system acts as the first line of defense against invasion of microbial pathogens. Here, macrophages play a substantial role in recognition, phagocytosis and killing of pathogens and the regulation of the innate immune response. Here, interferons play a crucial role in augmenting the antimicrobial functions of macrophages and their ability to produce mediators of immunoregulation. Pathogen recognition activates many different signaling pathways that interact to produce an innate response commensurate with the microbial challenge. The co-occurrence of signaling by sensors of stress and IFN receptors is a hallmark of innate responses to many viral and bacterial pathogens. Our results show changes in chromatin accessibility upon Anisomycin, a drug that induces stress-activation of MAPK pathways, IFNb stimulation and the combination of both or with p38 inhibitor PH-797804, Anisomycin and IFNb.

overall_design: Methods: Bone marrow-derived macrophages (BMDM) chromatin of wild-type (WT) untreated, as well as 2h20 Anisomycin, 2h IFNb treated or pre-treated with Anisomycin (20min) and then stimulated with IFNb for for 2h or pre-treated with PH-797804 followed by pre-treatment with Anisomycin and stimulated with IFNb and then were generated by deep sequencing, in triplicate, using Illumina sequencing.


title: Chromatin accessibility analysis of wild type bone marrow-derived macrophages in response to Anisomycin, type II interferon and the combination of them or with p38 MAPK inhibitor PH-797804 (ATAC-Seq IFNg)

summary: The innate immune system acts as the first line of defense against invasion of microbial pathogens. Here, macrophages play a substantial role in recognition, phagocytosis and killing of pathogens and the regulation of the innate immune response. Here, interferons play a crucial role in augmenting the antimicrobial functions of macrophages and their ability to produce mediators of immunoregulation. Pathogen recognition activates many different signaling pathways that interact to produce an innate response commensurate with the microbial challenge. The co-occurrence of signaling by sensors of stress and IFN receptors is a hallmark of innate responses to many viral and bacterial pathogens. Our results show changes in chromatin accessibility upon Anisomycin, a drug that induces stress-activation of MAPK pathways, IFNg stimulation and the combination of both or with p38 inhibitor PH-797804, Anisomycin and IFNg.

overall_design: Methods: Bone marrow-derived macrophages (BMDM) chromatin of wild-type (WT) untreated, as well as 2h20 Anisomycin, 2h IFNg treated or pre-treated with Anisomycin (20min) and then stimulated with IFNg for for 2h or pre-treated with PH-797804 followed by pre-treatment with Anisomycin and stimulated with IFNg and then were generated by deep sequencing, in triplicate, using Illumina sequencing.


title: Stress signaling boosts interferon-induced gene transcription in macrophages

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


title: RNA-seq of T in PBMC and TILs

city: Shanghai

first: Yuetong

last: Wang

address: 320 Yue Yang Road, Room 713

department: Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences

institute: Chinese Academy of Sciences

summary:
Purpose: Transcriptome profiling (RNA-seq) was used to compare the expression differences between T in PBMC and TILs
Methods:Paired TILs and T in PBMC cells were sorted from fresh patient blood and tumor samples. Then the mRNA were sequeced using xTen platform. The sequence reads that passed quality filters were analyzed.
Results: by extract mRNA from tumor infiltrated T cells from ovarian cancer patient sample and T cells from patient bllod samples, we compared the different expressed genes from TIL and T in blood. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to T cell exhausetion.
Conclusions:  We conclude that T in PBMC and TILs share different transcriptome characterization.

overall_design: Paired TILs and T in PBMC cells were sorted from fresh ovarian patient blood and tumor samples.

first: Wang

last: Yuetong

first: Fan

last: Gaofeng


title: Transcriptome analysis of toosendanin (TSN)-treated macrophages

city: Philadelphia

first: Yi

last: Fan

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

summary: The effects of TSN on global RNA expression was tested on tumor endothelial cell (EC)-educated macrophages using RNAseq.

overall_design: Human PBMC-derived monocytes were treated with 10 ng/ml CSF1 for 3 days, and followed by treatment of conditioned-medium collected from human GBM tumor-derived endothelial cells in the presence of 50nM TSN for another 1 day. RNA was isolated and analyzed by RNAseq.

first: Yang

first: Zhang

last: Duo


title: Diurnal transcriptome landscape of a multi-tissue response to time restricted feeding in mammals

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Time-restricted feeding (TRF) is an emerging behavioral nutrition intervention that sustains a daily cycle of feeding and fasting. TRF in animals and humans has shown pleiotropic health benefits arising from multiple organ systems, yet the molecular basis of TRF is not well understood. We subjected mice to isocaloric ad libitum feeding (ALF) or TRF of Western diet, and examined gene expression changes in 22 different brain regions and peripheral organs collected every 2 hour over 24 hour. We discovered TRF profoundly impacts gene expression. Nearly 80% of genes show significant differential expression or rhythmicity under TRF in at least one tissue. Functional annotation of these changes highlight tissue and pathway specific impacts of TRF. These findings and resources will offer a framework for future mechanistic studies, and guide human TRE interventions for various disease conditions with or without pharmacotherapies.

overall_design:
Diurnal mRNA expression profiles from 22 tissues from mice subjected to ad-libitum feeding (ALF) or 9 hr time-restricted feeding (TRF) of Western diet.
1035 libraries were sequenced. Each library was sequenced 1 to 4 times (1677 total samples). The 'description' column includes the library names of the samples.

first: Shaunak

last: Deota

first: Terry

last: Lin

first: Amandine

last: Chaix

first: Hiep

last: Le

first: Hugo

last: Calligaro

first: Ramesh

last: Ramasamy

first: Ling

last: Huang

first: Satchidananda

last: Panda


title: Labelling transcriptional response to dissociation using SLAMseq

first: Anika

last: Neuschulz

summary: Transcriptional response to dissociation is known to cause artefacts in single cell data sets. We used 4sU to label newly made transcripts during dissociation in order to to later remove them from the data set

overall_design: 10mM 4sU was added to the dissociation buffer while the samples were enzymatically dissociated for 30 min. A 4sU injected control was added to the zebrafish samples to identify high turnover genes

first: Victor

last: Badillo-Lisakowski

first: Irene

last: Gomez-Argente


title: Self-renewal of Differentiated Microglia Involves Two Distinct Mechanisms

city: San Francisco

first: Wulin

last: Tan

address: Room 345, Rock Hall, 1550 4th St

department: Anesthesia

institute: UCSF

summary: single cell gene expression profiling of microglia after peripheral nerve injury.

overall_design: microglia were sorted from lumbar part in the naïve animals or animals after peripheral nerve injury and single cell sequencing was performed.

first: Jacqueline

last: Leff

first: Paul

last: Su

first: Xiang

last: Gao

first: Jiao

last: Chen

first: Gokul

last: Kalyanasundaram

first: Zhonghui

last: Guan


title: Colonic mucosa of ulcerative colitis patients treated with biological agents

status: Public on Dec 17 2022

first: Shaocong

last: Mo

address: 12th Urumqi middle road

institute: Huashan Hospital, Fudan University

summary: Colonoscopy biopsies from patients with ulcerative colitis were collected prior to biological therapy. The sampled mucosa was the area of active lesion. Heterogenety of the samples were studied.

overall_design: All of mucosa underwent RNA-sequencing

first: Jie

last: Liu

first: Feifei

last: Luo


title: Transcriptome-wide analysis of N6-methyladenosine modification in the embryos of Spodoptera frugiperda

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: N6-methyladenosine RNA (m6A) is the most abundant modification of messenger RNA (mRNA), which has been demonstrated in regulating various post-transcriptional processes and playing key roles in sex determination, neuronal functions, and embryonic development in Drosophila and mice. However, the methylation profile and relevant functions in other insects remain largely unknown. Here, we analyzed transcriptome-wide profile of m6A modification in the embryonic development of a destructive agricultural pest Spodoptera frugiperda. Our study showed that differentially expressed m6A peak-modified genes were enriched in cell and organ development between the 2 h and 24 embryos. Our study reveals that RNA m6A epigenetic regulation in the embryonic development of S. frugiperda, and provides new insight for the embryonic development of insects.

overall_design: m6A mRNA modifications were profiled in 2 h and 24 h embryos of S. frugiperda after oviposition to reveal the epigenetic mechanism on embryonic development of insect.

first: Yaqing


title: Follistatin regulates sonic hedgehog-dependent tonotopic organization of the apical cochlea responsible for low-frequency hearing

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

institute: University of Louisville

summary: To show that FST cooperates with SHH to establish tonotopy by promoting apical cochlear characteristics responsible for low-frequency hearing in mammals, we analyzed cochlear gene expression, morphology, and auditory function of mouse mutants with loss or gain of SHH function in combination with loss or gain of follistatin (FST) function.

overall_design: Gene expression profiling analysis of RNA-seq data for 4-week-old control and Fst conditional Knock-out mutant mice cochlea cells divided into three regions along the tonotopic axis, base, middle, and apex.

first: Hei

middle: Y

last: Koo

first: Jae

first: Juw

last: Park

first: Jinwoong

last: Bok