title: RNAseqcharacterization ofB. burgdorferi-inducedinnate immune memoryandregulation ofLyme carditis through Acod1

city: Boston

first: Linden

state: MA

address: 136 Harrison Avenue

department: Microbiology

institute: Tufts University School of Medicine

summary: Borrelia burgdorferi (Bb), which causes Lyme disease, establishes long term infection and leads to disease manifestations that are mostly a result of host immune responses to the pathogen. Disease symptoms often resolve without treatment, suggesting innate immune memory may play a role in dampening inflammation over time. We used an in vitro model of repeated stimulations in macrophage and performed RNA sequencing on acute and memory states. We categorized differentially expressed genes based on their response to acute infection as well as their memory response compared to acute. We discuss four expression subsets representing important cellular changes to repeated stimulation and focus on genes that are negative regulators of inflammation induced during the acute phase and mediate long-term immunosuppression. We identified Aconitate decarboxylase 1 (Acod1), a negative regulator of inflammatory responses, and confirmed its role during in vivo long-term infection with Bb, with a specific role in Lyme carditis.

overall_design: Mouse Bone marrow derived macrophages were either left unstimulated, stimulated at 6 hours with Borrelia burgdorferi or stimulated at both 6 and 24 hours

first: Tanja

last: Petnicki-Ocwieja

first: Julie

last: McCarthy

first: Urmila

last: Powale


title: Single Cell Transcriptomics identifies a WNT7A-FZD5 Signaling Axis that maintains Fallopian Tube Stem Cells in Patient-derived Organoids [scRNA-seq]

status: Public on Nov 01 2023

city: Oxford

first: Ahmed

middle: Ashour

last: Ahmed

state: Oxfordshire

address: John Radcliffe Hospital, Headley way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

type: Expression profiling by high throughput sequencing

summary: Despite its significance to reproduction, fertility, sexually transmitted infections and various pathologies, the fallopian tube (FT) is relatively understudied. Strong evidence points to the FT as the tissue-of-origin of high grade serous ovarian cancer (HGSOC), the most fatal gynaecological malignancy. HGSOC precursor lesions arise specifically in the distal FT (fimbria) which is reported to be enriched in stem-like cells. Investigation of the role of FT stem cells in health and disease has been hampered by a lack of characterization of FT stem cells and lack of models that recapitulate stem cell renewal and differentiation in vitro. Using optimized organoid culture conditions to address these limitations, we found that FT stem cell renewal is highly dependent on WNT/β-catenin signaling and engineered endogenous WNT/β-catenin signaling reporter organoids to biomark, isolate and characterize putative FT stem cells. Using functional approaches as well as bulk and single cell transcriptomic analyses, we show that an endogenous hormonally-regulated WNT7A-FZD5 signaling axis is critical for self-renewal of human FT stem cells, and that WNT/β-catenin pathway-activated cells form a distinct transcriptomic cluster of FT cells enriched in ECM remodelling and integrin signaling pathways. In addition, we find that the WNT7A-FZD5 signaling axis is dispensable for mouse oviduct regeneration. Overall, we provide a deep characterization of FT stem cells and their molecular requirements for self-renewal, paving the way for mechanistic work investigating the role of stem cells in FT health and disease.

overall_design:
SMART-seq2 based scRNA-seq of patient-derived Fallopian tube Wnt/β-catenin signalling reporter organoids
Please note that in both the processed data files (counts_batch1.csv and counts_batch2.csv) every data column represents one cell (respectively 768 and 384 total). However, while for the Batch1, there are raw data file for each (barcoded) sample (768 pairs of FASTQ files), only one pair of FASTQ files are provided for the Batch2  (represented as one sample records). As two batches were sequenced at two different times, the first one was demultiplexed per index while the second one received whole lane demultiplexing.
The cell_info_batch*.csv files contain all the barcodes information, together with the indication of the WNT status and the patient provenience for each cell.

first: Abdulkhaliq

last: Alsaadi

first: Zhiyuan

last: Hu

first: Mara

last: Artibani

first: Francesca

last: Silvestri


title: HIRA-mediated loading of histone variant H3.3 controls androgen-induced transcription by regulation of AR/BRD4 complex assembly at enhancers [ChIP-Seq]

status: Public on Nov 02 2023

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

country: USA

institute: University of Florida

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To study the function of histone variant H3.3 pathway in androgen receptor-driven transcription in prostate cancer (PCa) we knocked out androgen receptor (AR) and H3.3 chaperones HIRA and DAXX in R1-AD1 (wild type AR) and R1-D567 (deltaLBD AR) cell lines. Integrative analysis with RNA-seq, ChIP-seq and ATAC-seq revealed that HIRA KO deregulates androgen-induced gene expression in PCa by reducing H3.3 incorporation, diminishing H3.3S31Ph and H3K27Ac, thus modifying recruitment of BRD4 and altering AR binding within enhancers of target genes.

overall_design: ChIPA-seq data for histone H3.3, H3K27Ac, H3.3S31Ph, AR and BRD4 in R1-AD1 FLAG-HA-H3F3A (WT androgen receptor) and R1-D567 FLAG-HA-H3F3A (deltaLBD androgen receptor) prostate cancer cells and its derivatives (AR KO, HIRA KO, DAXX KO, HIRA shRNA)

first: Viacheslav

last: Morozov

first: Alexander

last: Ishov


title: Hypermethylation suppresses microRNA-219a-2 to activate the ALDH1L2/GSH/PAI-1 pathway for fibronectin degradation in renal fibrosis

city: AUGUSTA

first: Qingqing

last: Wei

state: Georgia

address: 1460 Laney Walker Blvd.

department: Cellular Biology & Anatomy

institute: Augusta University

type: Methylation profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Hypermethylation suppresses microRNA-219a-2 to activate the ALDH1L2/GSH/PAI-1 pathway for fibronectin degradation in renal fibrosis [RIP-Seq]

summary: Epigenetic regulations, such as DNA methylation and microRNAs, play an important role in renal fibrosis. Here, we report the regulation of microRNA-219a-2 (mir-219a-2) by DNA methylation in fibrotic kidneys, unveiling the crosstalk between these epigenetic mechanisms. Through genome-wide DNA methylation analysis and pyro-sequencing, we detected the hypermethylation of mir-219a-2 in renal fibrosis induced by unilateral ureter obstruction (UUO) or renal ischemia/reperfusion, which was accompanied by a significant decrease in mir-219a-5p expression. Functionally, overexpression of mir-219a-2 enhanced fibronectin induction during hypoxia or TGF-b1 treatment of cultured renal cells. In mice, inhibition of mir-219a-5p suppressed fibronectin accumulation in UUO kidneys. ALDH1L2 was identified to be the direct target gene of mir-219a-5p in renal fibrosis. Mir-219a-5p suppressed ALDH1L2 expression in cultured renal cells, while inhibition of mir-219a-5p prevented the decrease of ALDH1L2 in UUO kidneys. Knockdown of ALDH1L2 enhanced PAI-1 induction during TGF-b1 treatment of renal cells, which was associated with fibronectin expression. In conclusion, the hypermethylation of mir-219a-2 in response to fibrotic stress attenuates mir-219a-5p expression and induces the up-regulation of its target gene ALDH1L2, which may reduce fibronectin deposition by suppressing PAI-1.

overall_design: The RNA induced silencing complex was pulled down from negative control and microRNA-219 overexpressed HEK293 cells. The RNA from the precipitates were extracted for RNA-seq analysis.

first: Zheng

last: Dong


title: MiRNA expression in a patient-derived CRC model after treatment with TGFB1

city: Dresden

middle: Arthur

last: Wurm

address: Fetscherstrasse 74

country: Germany

institute: NCT Dresden

type: Non-coding RNA profiling by high throughput sequencing

summary: We determined the miRNA expression changes upon activation and inactivation of the TGFB signaling cascade

overall_design: We treated a patient-derived CRC spheroid model with recombinant TGFB1 or a vehicle control for 7 days, and let them recover for additional 7 days in the absence of TGFB1.  Here, we analyzed the miRNA expression pattern by small RNA sequencing and determined miRNAs expression in all conditions.

middle: A

first: Hanno

last: Glimm


title: Hypermethylation suppresses microRNA-219a-2 to activate the ALDH1L2/GSH/PAI-1 pathway for fibronectin degradation in renal fibrosis [RRBS]

overall_design: To investigate the differentially methylated genes in kidney fibrosis, C57BL/6 mice were subjected to unilateral ureter obstruction for 7 days (UUO7D), bilateral kidney ischemia 25 minutes and 1 week reperfusion, bilateral kidney ischemia 25 minutes and 1 month reperfusion, or sham operation. The genomic DNA from the kidney cortex and outer medulla were extracted for bisulfite sequencing.

first: Xiao

last: Xiao

first: Huidong

last: Shi


title: Nascent elongating transcript sequencing (NET-seq) with SI3 domain-deleted Escherichia coli reveals different pause profiles from wildtype

city: Madison

first: Robert

last: Landick

state: Wisconsin

address: 1550 Linden drive

department: Department of Biochemistry

institute: University of Wisconsin–Madison

summary: Transcriptional pausing is a fundamental mechanism that aids gene regulation by cellular RNA polymerases (RNAPs). In many bacterial lineages, a large, surface-exposed domain inserted into the catalytic trigger loop (TL) of RNAP called sequence insertion 3 (SI3) modulates transcription pausing. However, the in vivo roles of SI3 remain largely unknown due in part to the lethality of SI3 deletion. Here we describe construction of a viable Escherichia coli strain with a complete SI3 deletion enabled by a suppressor missense mutation in the portion of rpoC encoding the TL (ß′A941T; ∆SI3*). The ∆SI3* RNAP exhibited increased transcript elongation rate relative to ∆SI3 RNAP lacking the TL substitution, which may explain viability of the ∆SI3* strain. Using NET-seq, we found that transcriptional pausing in the ∆SI3* strain was increased at some sites and decreased at others compared to wild-type E. coli, except in ribosomal RNA genes. The ∆SI3*-enhanced pauses had a sequence motif similar to the consensus elemental pause sequence whereas ∆SI3*-suppressed pauses had less similarity to the consensus motif and appeared associated with upstream RNA structures thought to stabilize pausing (pause hairpins; PHs). These putative PH-stabilized pause signals were enriched in 5′ untranslated regions and protein coding regions in the E. coli genome. These results suggest that the SI3 domain affects different classes of pause signals differently and imply potential roles of these pauses in protein-coding regions.

overall_design: Examination of nascent transcripts in WT and ∆SI3* E. coli of biological triplicates. A B. subtilis strain is used as spike-in control for quantitative analysis.

first: Yu

last: Bao


title: Single-cell RNA-Seq of fibroblasts derived from one patient with idiopathic pulmonary fibrosis.

city: Shanghai

first: Tao

last: Ren

address: No. 600, Yi Shan Road

country: China

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

summary: Fibroblast appears to play a central role in the pathogenesis of IPF. We performed scRNA-seq of fibroblast from IPF patient, and evaluate its cell-cell interaction combined with the engrafted bronchial BCs. Our study reveals that engrafted BCs isolated from small bronchi can mediate anti-fibrotic effect by interacting with adjacent fibroblasts.

overall_design: Fibroblast profiles of 1 patient with idiopathic pulmonary fibrosis were generated by deep sequencing, using BD Rhapsody Analysis pipeline (Version: 1.8).

first: Yue

last: Hong

first: Shan

last: Shan

first: Zeyu

last: Liu


title: Comparison of T cell response to S. aureus and E. coli derived virulence determinants using RNA sequencing

city: Münster

first: Kari

middle: Lavinia

last: vom Werth

address: Robert-Koch-Str. 41

department: Institute of Hygiene

institute: University Hospital Münster

summary: We aimed to compare transcriptomic changes in T cells in response to sterile bacterial culture supernatants derived from different E.coli and S.aureus strains. Gene expression was analyzed at two different time points.

overall_design: Jurkat T cells were treated with sterile supernatants from bacterial overnight cultures or left untreated as control. Two S.aureus strains (USA300, ST398) and three E.coli strains (536, IHE3034, MG1655) were used. RNA was isolated 1h and 6h after exposure. Three biological replicates per treatment were included.

middle: L

first: Andreas

last: Huge

first: Stefanie

last: Kampmeier

last: Mellmann


title: The protective role of TLR4 in intestinal epithelial cells through the regulation of the gut microbiota in DSS-induced colitis in mice

first: Yunjie

address: No.800 Xiangyin Road

institute: Naval Medical University

summary: Abstract.  Background: The cause of ulcerative colitis (UC) is not yet fully understood. Previous research has pointed towards a potential role for mutations in NOD2 in promoting the onset and progression of inflammatory bowel disease (IBD) by altering the microbiota of the gut. However, the relationship between toll-like receptor 4 (TLR4) and gut microbiota in IBD is not well understood. To shed light on this, the interaction between TLR4 and gut microbiota was studied using a mouse model of IBD. Methods: To examine the function of TLR4 signaling in intestinal injury repair, researchers developed Dextran Sulfate Sodium Salt (DSS)-induced colitis and injury models in both wild-type (WT) mice and TLR4 knockout (TLR4-KO) mice. To assess changes in the gut microbiota, 16S rRNA sequencing was conducted on fecal samples from both the TLR4-KO and WT enteritis mouse models. Results: The data obtained depicted a protective function of TLR4 against DSS-induced colitis. The gut microbiota composition was found to vary considerably between the WT and TLR4-KO mice groups as indicated by β-diversity analysis and operational taxonomic units (OTUs) cluster. Statistical analysis of microbial multivariate variables depicted an elevated abundance of Escherichia coli/Shigella, Gammaproteobacteria, Tenerlcutes, Deferribacteres, Enterobacteria, Rikenellaceae, and Proteobacteria in the gut microbiota of TLR4-KO mice, whereas there was a considerable reduction in Bacteroidetes at five different levels of the phylogenetic hierarchy including phylum, class, order, family, and genus in comparison with the WT control. Conclusion: TLR4 may protect intestinal epithelial cells from damage in response to DSS-induced injury by controlling the microbiota in the gut.

first: Cheng

last: Huang

first: Zhiqian

last: Hu

first: Hao

last: Wang


title: Distant antimetastatic effect of enterotropic colon cancer-derived α4β7 CD8 T cells [scRNA-seq]

city: Toulouse

first: Christel

last: Devaud

address: 2 Avenue Hubert Curien

country: France

institute: INSERM

summary: Despite the high prognostic value of immune infiltrates in colorectal cancer (CRC), metastatic disease remains resistant to immunotherapy by immune checkpoint blockade (ICB). Here we show in a metastatic CRC multi-tumor preclinical model that orthotopically-implanted primary colon tumors can spontaneously exert a colon-specific and immune-dependent antimetastatic effect on distant hepatic lesions. An immune signature, integrating antitumor CD8 T cells, dendritic cells and protumor macrophages, that we called MicroEnvironment (ME)-score, was predictive of the antimetastatic effect. ScRNA-Seq and phenotypic analyses revealed that enterotropic α4β7 integrin expressing tumor neoantigen-specific CD8 T cells were key components of the systemic immune response responsible for the antimetastatic effect. Accordingly, the presence of concomitant colon tumors improved the efficacy of proof-of-concept ICB on liver lesions and generated a protective memory immune response whereas antibody-mediated partial depletion of α4β7+ cells abrogated the control of metastatic disease by the primary tumor. Finally, in a metastatic CRC patients’ cohort, we show increased expression of genes encoding the α4β7 integrin and of the ME-score in ICB responsive metastases concomitant with increased proportions of circulating α4β7+ CD8 T cells. Our findings identify a systemic cancer immunosurveillance role for gut primed tumor-specific α4β7+ CD8 T cells.

overall_design: Single-cell RNA sequencing was performed on sorted T cells from mice liver and colon tumors and blood samples, harvested at day 10 post tumor implantations (intra-hepatic (IH)+intra-colon (IC) concomitant injections (IH+IC group) or IH alone (al.) injections). Each sample corresponds to a pool of 18 (for IH+IC group) or 9 (for IH al. group) IH tumors; 18 (for IH+IC group) IC tumors; 18 (for IH+IC group) or 9 (for IH al. group) blood samples.

first: Virginie

last: Feliu

first: Carlos

last: Gomez-Roca

first: Marie

last: Michelas

first: Noémie

last: Thébault

first: Françoise

last: Lauzeral-Vizcaino

first: Anna

last: Salvioni

first: Lise

last: Scandella

first: Emeline

last: Sarot

first: Carine

last: Valle

first: Camille-Charlotte

last: Balança

first: Clara-Maria

last: Scarlata

first: Jean-Pierre

last: Delord

first: Maha

last: Ayyoub


title: Effect of depletion of Suv39h1 on gene expression of TGF-β stimulated mouse primary renal fibroblasts

city: nanjing

first: li

state: Jiangsu

address: Longmian Avenue

department: Basic Medicine College

institute: nanjing medical university

summary: To investigate the the role of suv39h1 in the regulation of kidney fibrosis in vitro, we established suv39h1fl/fl mice and isolated renal fibroblasts.Fibroblasts were treated with Cre recombinant adenovirus (Ad-Cre) or GFP recombinant adenovirus(Ad-GFP) , and then  TGF-β was added to the cells after starving overnight.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ad-Cre treated renal fibroblasts and Ad-GFP treated fibroblasts.   Fibroblast activation was induced by treatment with TGF-β.

first: Ming

last: Kong

first: Xiaoyan

last: Wu

last: Li

first: Yong

last: Xu


title: SRSF2 in Sertoli cells is essential for testicular development and spermatogenesis in mice

city: BEIJING

address: Malianwa street

institute: China Agriculture University

summary: To investigated the function of SRSF2 in Sertoli cells, we generated the specific deletion of Srsf2 in Sertoli cells.

overall_design: To compare the gene expression and alternative dsplicing between Ctrl and cKO

first: Xiaomei

last: Xie


title: Aberrant accumulation of Kras-dependent enhancer RNAs during tumor progression renders cancer cells susceptible to PAF1 depletion due to R-loop accumulation IV

city: Beijing

first: Xiangzheng

last: Liu

address: Tsinghua University, Haidian  District, Beijing

institute: Tsinghua University

summary: Kras is the most commonly mutated oncogene in human cancer and mutant Kras is responsible for over 90% of pancreatic ductal adnocarcinoma (PDAC), the most leath cancer. Here, we identified that RNA polymerase II associated factor 1 complex (PAF1C) is specifically required for the survival of PDAC but not normal adult panreatic cells.  We show that PAF1C maintains cancer cell genomic stability by restraining the over accumulation of enhancer RNAs (eRNAs) driven by mutant Kras. Loss of PAF1C leads to cancer-specific lengthening and accumulation of eRNAs on chromatin and therby abbarrent R-loop formation, TC-NER pathway activation and double stranded DNA breaks, which in turn trigger cell death.  We also demonstrate that the sepcific demand for PAF1C by cancer cells is due to the global activation of enhancers and thus eRNA transcription during tumorigenesis. The work provides a novel insight in how transcription addiction is caused during tumorigenesis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data  for pancreatic ductal adenocarcinoma cell line with Paf1 knockdown and Myc knockdown

first: Xinhong

first: Mo

last: Chen


title: Deletion of NuRD component Mta2 in nephron progenitor cells causes developmentally programmed FSGS [E17.RNAseq]

status: Public on Nov 05 2023

city: St. Louis

first: Jeannine

middle: M

last: Basta

state: MO

department: Internal Medicine/Nephrology

institute: Washington University in St. Louis

summary: Low nephron endowment at birth is a risk factor for chronic kidney disease. The prevalence of this condition is increasing due to higher survival rates of preterm infants and children with multi- organ birth defect syndromes that affect the kidney and urinary tract. We created a mouse model of congenital low nephron number due to deletion of Mta2 in nephron progenitor cells. Mta2 is a core component of the Nucleosome Remodeling and Deacetylase (NuRD) chromatin remodeling complex. These mice developed albuminuria at 4 weeks of age followed by focal segmental glomerulosclerosis (FSGS) at 8 weeks, with progressive kidney injury and fibrosis. Our studies reveal that altered mitochondrial metabolism in the post-natal period leads to accumulation of neutral lipids in glomeruli at 4 weeks of age followed by reduced mitochondrial oxygen consumption. We found that NuRD cooperated with Zbtb7a/7b to regulate a large number of metabolic genes required for fatty acid oxidation and oxidative phosphorylation. Analysis of human kidney tissue also supported a role for reduced mitochondrial lipid metabolism and ZBTB7A/7B in FSGS and CKD. We propose that an inability to meet the physiological and metabolic demands of post-natal somatic growth of the kidney promotes the transition to CKD in the setting of glomerular hypertrophy due to low nephron endowment.

overall_design: We measured RNA expression by RNA-seq in control Mta2flx/flx and mutant Six2Cre Mta2flx/flx E17 kidneys.

first: Michelle

last: Brennan

first: Michael

last: Rauchman


title: Effect of depletion of prune2 on gene expression of TGF-β stimulated mouse primary renal fibroblasts

first: LI

address: longmian avenue

summary: To investigate the the role of prune2 in the regulation of kidney fibrosis in vitro, we designed prune2 siRNA and isolated renal fibroblasts.Fibroblasts were treated with prune2 siRNA or scrambled siRNA, and then  TGF-β was added to the cells after starving overnight.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for prune2 siRNA treated renal fibroblasts and scrambled siRNA treated fibroblasts .

first: Zhao

last: Qianwen

first: Wu

last: Xiaoyan

first: Li

first: Xu

last: Yong


title: Aberrant accumulation of Kras-dependent enhancer RNAs during tumor progression renders cancer cells susceptible to PAF1 depletion due to R-loop accumulation III

overall_design: Comparative chromatin-associated RNA-seq data of pancreatic ductal adenocarcinoma cell line with Rosa26 knockout vs. Paf1 knockout.


title: Evolution of lmiRNAs and their targets from MITEs for rice adaptation

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

summary: Twenty-four nucleotide long miRNAs (lmiRNAs) direct DNA methylation at target genes and regulate their transcription. The evolutionary origin of lmiRNAs and the range of lmiRNA-mediated regulation remain obscure. Here, we reannotated lmiRNAs and their targets in rice by applying stringent criteria. We found that the majority of lmiRNAs are derived from MITEs and most sites targeted by MITE-derived lmiRNAs reside within MITEs, suggesting co-evolution of lmiRNAs and their targets through MITE amplification. lmiRNAs undergo dynamically changes under stressed conditions and the genes targeted by lmiRNAs show an enrichment for stress responsive genes, suggesting that lmiRNAs are widely involved in plant response to stresses. We constructed the evolutionary histories of lmiRNAs and their targets. lmiRNAs emerged before or when the AA genome was diverged, while the emergence of lmiRNA targets coincided with or followed the emergence of lmiRNAs. Furthermore, we found that the sequences of a lmiRNA target site underwent variations, coincident with the divergence of rice accessions and the distribution of rice accessions in different geographical locations and climatic conditions. Our findings highlight MITEs as an important origin of lmiRNAs and suggest that the evolution of lmiRNA-target regulatory modules may contribute to rice adaptation to environmental changes.

overall_design: sRNA-seq and WGBS-seq of 4-week-old seedling of NIP, dcl3a-17, osnrpd1-1. sRNA-seq line has three replication.

first: Tianxiao

last: Huang

first: Yan

first: Wei

last: Wang

first: Le

first: Jingrui


title: Single Cell Transcriptomics identifies a WNT7A-FZD5 Signaling Axis that maintains Fallopian Tube Stem Cells in Patient-derived Organoids.

first: Ahmed

last: Ahmed


title: Aberrant accumulation of Kras-dependent enhancer RNAs during tumor progression renders cancer cells susceptible to PAF1 depletion due to R-loop accumulation II

first: Xiangzheng

overall_design: Comparative gene expression profiling analysis of RNA-seq data  for mouse pancreas with Rosa26 knockout vs. Paf1 knockout.

first: Xinhong


title: Transcriptional control of motor pool formation and motor circuit connectivity by the LIM-HD protein Isl2

city: Gwangju

first: Mi-Ryoung

last: Song

address: 123, Cheomdangwagi-ro

country: South Korea

institute: Gwangju Institute of Science and Technology

summary: The fidelity of motor control requires the precise positional arrangement of motor pools and the establishment of synaptic connections between these pools. In the developing spinal cord, motor nerves project to specific target muscles and receive proprioceptive input from the muscles via the sensorimotor circuit. LIM-homeodomain transcription factors are known to successively restrict specific motor neuronal fates during neural development; however, it remains unclear to what extent they contribute to limb-based motor pools and locomotor circuits. Here, we showed in mice that deletion of Isl2 resulted in scattered motor pools, primarily in the median motor column and lateral LMC (LMCl) populations, and lacked Pea3 expression in the hindlimb motor pools, accompanied by reduced terminal axon branching and disorganized neuromuscular junctions. Transcriptomic analysis of Isl2-deficient spinal cords revealed that a variety of genes involved in motor neuron differentiation, axon development, and synapse organization were downregulated in hindlimb motor pools. Moreover, the loss of Isl2 impaired sensorimotor connectivity and hindlimb locomotion. Together, our studies indicate that Isl2 plays a critical role in organizing motor pool position and sensorimotor circuits in hindlimb motor pools.

overall_design: RNA-seq of the ventral brachial and lumbar spinal cords, E12.5 embryonic spinal cords (from 3 animals of Isl2+/- and 3 animals of Isl2 KO). Ventral spinal cords were harvested and trimmed around the Hb9::GFP reporter.

first: Yunjeong

last: Lee


title: Aberrant accumulation of Kras-dependent enhancer RNAs during tumor progression renders cancer cells susceptible to PAF1 depletion due to R-loop accumulation I

overall_design: Examination of H3K27ac distribution in normal mouse pancreas with Paf1 knockout vs. Rosa knockout

first: Mo


title: Identification of Candidate Genes Responsible for Rhizome Induction in Acorus calamus through Transcriptome Analysis

city: Ulaanbaatar

first: Bolortuya

last: Ulziibat

state: Tuv

address: 54b peace avenue

department: Institute of Biology

country: Mongolia

institute: Mongolian academy of sciences

summary: To identify the genes responsible for rhizome extension, we transcriptome analysis performed in leaves and rhizome of cut and uncut explants (leaves cut and leaves uncut explants)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for leaves and rhizome of cut and uncut explants after 4 days and a month of cutting


title: Limiting metabolic stress by redirecting glucose flux during in vitro expansion improves efficacy of T cell therapies for cancer

city: Pittsburgh

first: Greg

last: Delgoffe

state: PA

address: 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

summary: Adoptive cell therapies for cancer treatment often fail due to a lack of T cell survival and persistence within the patient. Redirecting glycolytic processing with dichloroacetate (DCA) during in vitro expansion improves immediate and long-term T cell engraftment by up to 8x - ultimately resulting in a drastic improvement in tumor clearance. Here we use bulk RNA sequencing to interrogate the changes in transcriptional programs resultant of DCA treatment that may confer the observed improvement in engraftment and tumor clearance of DCA-treated T cells.

overall_design: Gene expression analysis of bulk RNA-seq of CD8+ T cells from 6 different mice (OT-1 or pmel-1) and 2 different experiments (3 mice per experiment) expanded with or without DCA for 7 days.

first: Andrew

middle: T

last: Frisch

first: Yiyang

first: Yupeng

first: Konstantinos

last: Lontos

first: Supriya

last: Joshi

first: Jessica

last: Jana

first: Leandro

middle: C

last: Hermida

first: Dayana

middle: B

last: Rivadeneira


title: Transcriptome Profiling of PRRSV Infected Porcine Alveolar Macrophages By Single Cell Sequencing

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: Porcine reproductive and respiratory syndrome (PRRSV) is a devastating pathogen for the pig industry worldwide. PRRSV mainly infects porcine alveolar macrophage (PAM). In the present study, single-cell RNA sequencing (scRNA-seq) was employed to characterize the host transcriptome responses of PAMs infected with a virulent PRRSV strain in vivo and ex vivo. Increase ofpro-inflammatory and anti-apoptotic genes was correlated with the increase of infection (expression of the virus ORF7 transcript).

overall_design: For the in vivo study, weaned pigs were infected with 10^6 TCID50 ofthe PRRSV strain expressing green fluorescent protein (FL12-GPF) and PAMs were collected at 4- and 7- days post infection for scRNA-seq. For the ex vivo study, PAMs collected from healthy pigs were infected with 1 MOI of the PRRSV FL12-GFP and samples were collected at 0-, 6- and 12- hours post-infection for scRNA-seq.

first: Kassandra

last: Durazo-Martinez

first: Hiep

last: Vu

first: Jayeshbhai

last: Chaudhari

first: Thao

first: Marc

last: Libault

first: Sandra

last: Thibivilliers


title: Comparison of miRNA expression between primary tissue, patient-derived cancer model, and FFPE tissue

first: Alexander

last: Wurm

summary: We investigated whether we could use RNA from tumor purified formalin-fixed paraffin-embedded (FFPE) tissue for small RNA sequencing to obatin comparable results to RNA from the primary tumor.

overall_design: Therefore, we utilized four patient tumors and compared RNA from three different sources each: The primary tumor (or the metastasis), a patient-derived cancer model (PDCM), which was either a spheroid, organoid, or frozen viable, and the FFPE tissue from the routine pathology procedure.

first: Hanno

last: Glimm


title: Neuronal Acetylcholine Couples Gonadal Gap Junction/Notch Signaling Axis to Gut Defense

city: Changsha

first: Zhang

middle: xiu

last: mei

address: tian ma road

institute: Haijun Tu

summary: Gap junctions mediate intercellular communications across cellular networks in the nervous and the immune systems, while the role in the intestinal innate immunity is poorly understood. Here, we identified that an innexin gene inx-14 encoding one of heterotypic and heteromeric gap junction subunits acts in the gonad to attenuate the intestinal defense through PMK-1/p38 pathway. The RNA-seq analyses revealed that GLP-1/Notch signaling was downregulated, while lysosome, and PMK-1/p38 MAPK signalings were upregulated by the germline-specific inx-14 RNAi in C. elegans. Loss function of either inx-14, or glp-1 exhibited enhanced resistance to PA14 infection and upregulated lysosome and PMK-1/p38 signalings. Additionally, inx-14 knockdown by germline specific RNAi upregulated muscarinic acetylcholine receptor (mAChR) genes gar-1/gar-2/gar-3. We further revealed that acetylcholine mAChR GAR-2/GAR-3 signaling functions in the intestine and downstream of lysosome signaling but upstream of PMK-1/p38 pathway to facilitate the intestinal defense. Our findings reveal a novel role for gonadal gap junction/INX-14 in host intestinal defense against pathogens and expand our understanding the functions of reproductive system in the host intestinal defense.

overall_design: Using vector and inx-14 RNAi  in DCL569 ( germline-specific RNAi ) background in the condition of PA14 infection or OP50 fed, then design some different assays to identify the important tips obtained from RNA-seq data analysis.

first: Haijun

last: Tu

first: Xiumei

first: Yirong

last: Wang


title: Gene expression profiling of renal tissues isolated from C57BL/6J mice treated with DMXAA

city: Nanjing

first: Lingling

last: Lu

state: State...

address: Guangzhou Road 72

institute: Children's hospital of Nanjing Medical University

summary: Flavonoid derivative DMXAA, also known as vadimezan or ASA404, is considered one of the most promising vascular disrupting agents that displays remarkable antitumor properties. To investigate the effect of DMXAA on gene expression in renal tissues, C57BL/6J mice were intraperitoneal injected with DMXAA or vehicle (10 mg/kg daily) for three days, then renal tissues were harvested and performed RNA-seq.

overall_design: C57BL/6J mice were treated with DMXAA (2 replicates) or vehicle (3 replicates) as described in the previous section. Mice received vehicle injection served as controls. Renal tissues were harvested to perform RNA-seq, and the data obtained from RNA-seq was used to perform comparative gene expression analysis.

first: Weihua

last: Liu

first: Shumin

last: Li

first: Songming

last: Huang

first: Aihua

first: Wei

last: Gong


title: Expression of miRNAs in patient-derived cancer models and models of drug resistance

address: Fetscherstrasse 74

summary: We examined whether tumor samples can be stratified according to miRNA expression profiles.

overall_design: We performed miRNA sequencing in 12 patient derived cancer models (PDCMs, organoids/spheroids) and models of drug resistance. These included the melanoma WM1366 cell line and both related BRAF/MEK inhibitor resistant daughter cell lines WM1366VCi and WM1366DTi. In addition, we included 8 patient-derived 3D cancer models, represented by two spheroid models (CRC02-SP, CRC03-SP) and three organoid models (CRC01-OG, CRC03-OG, CRC04-OG) from patients with CRC. In addition, we studied one organoid model from a patient with cancer of unknown primary (CUP01-OG), and one spheroid culture from a patient with teratoma (TER01-SP). To also test whether and how miRNA expression differs between related samples, we included a normal colon mucosa organoid culture (CRC01NM-OG) for the CRC patient 1 (CRC01-OG). In addition, we created an irinotecan resistant subclone of the CRC patient 2 spheroid culture (CRC02-SP) by constantly adding increasing concentrations of SN38 for at least 4 passages.


title: Stem cell-like reprogramming is required for leukemia initiating activity in B-ALL

city: TOULOUSE

first: Vincent

last: Fregona

state: Terres australes françaises

address: 2 avenue hubert curien

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

overall_design: Refer to individual Series


title: Cell quiescence and reprogramming are distinctive features of pre-leukemic stem cells [H2Bgfp]

summary:
The leukemic stem cell concept is well established in B-acute lymphoblastic leukemia (B-ALL). However, the question of how a primary oncogene reprograms stem cell-like properties in committed B-cells and leads to a pre-neoplastic population remains unclear. Here, we used the PAX5-ELN oncogenic model to demonstrate a causal link between the differentiation blockade, the self-renewal and the emergence of pre-leukemic stem cells (pre-LSCs). Through multi-parametric immunophenotyping, we show that PAX5-ELN oncoprotein disrupts the differentiation of pre-leukemic cells by enforcing the IL7r/JAK-STAT signaling pathway. This disruption is associated with the induction of rare and quiescent pre-LSCs that sustain the leukemia-initiating activity, as assessed using the H2B-GFP model. Integration of transcriptomic and chromatin accessibility data reveals that those quiescent pre-LSCs lose B-cell identity and reactivate an immature molecular program, reminiscent of human B-ALL chemo-resistant cells. Collectively, our study sheds new lights on the biological mechanisms underlying the cell-of-origin of leukemia.
We  performed gene expression profiling analysis using data obtained from RNA-seq of quiescent or proliferative B-cells PEtg mice.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for B-cell progenitors PEtg quiescent and proliferative
H2B-GFP high = quiescent
H2B-GFP low = proliferating

first: Bastien

last: Gerby


title: Chronic TCDD treatment increases liver myofibroblast activation through aryl hydrocarbon receptor signaling in hepatocytes

city: Saltlake city

first: Michael

last: Jurynec

state: UT

institute: University of Utah

summary: The goal of this project was to determine how AhR activity in hepatocytes and HSCs impact liver fibrosis by studying mice with AhR-deficient hepatocytes (AhRΔHep) or AhR-deficient HSCs (AhRΔHSC) during TCDD-induced liver fibrosis as measured by evidence of steatosis, inflammation, HSC activation, and collagen deposition. Overall, our studies indicate that chronic TCDD exposure increases AhR signaling in hepatocytes that result in indirect HSC activation and the development of liver steatosis, whereas hepatic inflammation do not appear to play a major role.

overall_design: Female AhRΔHep mice, AhRΔHSC mice, and AhRfl/fl mice were treated with 100 µg/kg TCDD or peanut oil every four days for 92 days and then euthanized. Treatment groups consisted of 3 mice. Overall 6 treatments can be found.

first: Shivakumar

middle: R

last: Veerabhadraiah

first: Giovan

middle: N

last: Cholico

first: Sarah

middle: E

last: Kobernat

first: Wendy

last: Harvey

first: Kenneth

last: Cornell

first: Kristen

last: Mitchell


title: Cell quiescence and reprogramming are distinctive features of pre-leukemic stem cells [RNA-seq CTV]

summary:
The leukemic stem cell concept is well established in B-acute lymphoblastic leukemia (B-ALL). However, the question of how a primary oncogene reprograms stem cell-like properties in committed B-cells and leads to a pre-neoplastic population remains unclear. Here, we used the PAX5-ELN oncogenic model to demonstrate a causal link between the differentiation blockade, the self-renewal and the emergence of pre-leukemic stem cells (pre-LSCs). Through multi-parametric immunophenotyping, we show that PAX5-ELN oncoprotein disrupts the differentiation of pre-leukemic cells by enforcing the IL7r/JAK-STAT signaling pathway. This disruption is associated with the induction of rare and quiescent pre-LSCs that sustain the leukemia-initiating activity, as assessed using the H2B-GFP model. Integration of transcriptomic and chromatin accessibility data reveals that those quiescent pre-LSCs lose B-cell identity and reactivate an immature molecular program, reminiscent of human B-ALL chemo-resistant cells. Collectively, our study sheds new lights on the biological mechanisms underlying the cell-of-origin of leukemia.
We  performed gene expression profiling analysis using data obtained from RNA-seq of quiescent, slowly prolfierative or highly proliferative B-cells coming from WT or PEtg mice.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for B-cell progenitors PEtg quiescent and proliferative and Wt proliferative.
CTVhigh = quiescent
CTVlow = proliferating


title: Cell quiescence and reprogramming are distinctive features of pre-leukemic stem cells [ATAC-seq]

summary: The leukemic stem cell concept is well established in B-acute lymphoblastic leukemia (B-ALL). However, the question of how a primary oncogene reprograms stem cell-like properties in committed B-cells and leads to a pre-neoplastic population remains unclear. Here, we used the PAX5-ELN oncogenic model to demonstrate a causal link between the differentiation blockade, the self-renewal and the emergence of pre-leukemic stem cells (pre-LSCs). Through multi-parametric immunophenotyping, we show that PAX5-ELN oncoprotein disrupts the differentiation of pre-leukemic cells by enforcing the IL7r/JAK-STAT signaling pathway. This disruption is associated with the induction of rare and quiescent pre-LSCs that sustain the leukemia-initiating activity, as assessed using the H2B-GFP model. Integration of transcriptomic and chromatin accessibility data reveals that those quiescent pre-LSCs lose B-cell identity and reactivate an immature molecular program, reminiscent of human B-ALL chemo-resistant cells. Collectively, our study sheds new lights on the biological mechanisms underlying the cell-of-origin of leukemia.

overall_design:
We perform genome accessibility analysis using data obtained from ATAC-seq of quiescent and proliferative B-cells coming from PEtg mice.
H2B-GFP high = quiescent
H2B-GFP low = proliferating


title: Distant antimetastatic effect of enterotropic colon cancer-derived α4β7 CD8 T cells [3' single-cell RNA-seq]

first: Christel

last: Devaud

summary: Despite the high prognostic value of immune infiltrates in colorectal cancer (CRC), metastatic disease remains resistant to immunotherapy by immune checkpoint blockade (ICB). Here we show in a metastatic CRC multi-tumor preclinical model that orthotopically-implanted primary colon tumors can spontaneously exert a colon-specific and immune-dependent antimetastatic effect on distant hepatic lesions. An immune signature, integrating antitumor CD8 T cells, dendritic cells and protumor macrophages, that we called MicroEnvironment (ME)-score, was predictive of the antimetastatic effect. ScRNA-Seq and phenotypic analyses revealed that enterotropic α4β7 integrin expressing tumor neoantigen-specific CD8 T cells were key components of the systemic immune response responsible for the antimetastatic effect. Accordingly, the presence of concomitant colon tumors improved the efficacy of proof-of-concept ICB on liver lesions and generated a protective memory immune response whereas antibody-mediated partial depletion of α4β7+ cells abrogated the control of metastatic disease by the primary tumor. Finally, in a metastatic CRC patients’ cohort, we show increased expression of genes encoding the α4β7 integrin and of the ME-score in ICB responsive metastases concomitant with increased proportions of circulating α4β7+ CD8 T cells. Our findings identify a systemic cancer immunosurveillance role for gut primed tumor-specific α4β7+ CD8 T cells.

overall_design: Single-cell RNA sequencing was performed on 4 mouse intra-hepatic (IH) tumor samples, harvested at day 10 post tumor-implantation. Each sample correspond to a pool of 7 IH tumors with 1 control sample (IH alone) and 3 different (low, intermediate and high) ME-score samples, with a total of 6949 cells.

first: Virginie

last: Feliu

first: Carlos

last: Gomez-Roca

first: Marie

last: Michelas

first: Noémie

last: Thébault

first: Françoise

last: Lauzeral-Vizcaino

first: Anna

last: Salvioni

first: Lise

last: Scandella

first: Carine

last: Valle

first: Camille-Charlotte

last: Balança

first: Clara-Maria

last: Scarlata

first: Jean-Pierre

last: Delord

first: Maha

last: Ayyoub


title: Distant antimetastatic effect of enterotropic colon cancer-derived α4β7 CD8 T cells [bulk RNA-seq]

overall_design: Bulk RNA sequencing was performed on 17 human metastatic samples (from a MSS (MicroSatellite Stable profile) metastatic CRC cohort).


title: FOXC2 and WT1 regulate transcriptional reprogramming during the podocyte response to injury

city: Boston

first: Jordan

last: Kreidberg

address: 99 Brookline Ave

institute: BIDMC Research North

summary: In the context of human disease, the mechanisms whereby transcription factors reprogram gene expression in reparative responses to injury are not well understood. We have studied the mechanisms of transcriptional reprogramming in disease using murine kidney podocytes as a model for tissue injury. Podocytes are a crucial component of glomeruli, the filtration units of each nephron. Podocyte injury is the initial event in many processes that lead to End Stage Kidney Disease. FOXC2 is a transcription factor known to regulate gene expression in podocytes. FOXC2 and WT1 are both required for podocyte differentiation. Using murine models and human kidney organoids, we investigated FOXC2-mediated transcriptional reprogramming during the course of podocyte injury. Correlating FOXC2 and WT1 ChIP-seq analyses demonstrated that they co-bind many genes expressed in podocytes. Reprogramming the transcriptome involved highly dynamic changes in the binding of FOXC2 and WT1 to target genes during a reparative injury response.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for FOXC2

first: Sandrine

last: Ettou

first: Anya

last: Greenberg

first: Liang

last: Sun

first: Dongwon

last: Lee


title: RNA-seq expression analysis of Pcf11 mutations Pcf11-13 and Pcf11-DNL

city: Bar Harbor

first: Joel

middle: H

last: Graber

state: ME

address: 159 Old Bar Harbor Rd

department: Bioinformatics Core

institute: MDI Biological Laboratory

summary: High Throughput bulk-sample RNA-sequencing expression data, was collected for triplicate samples of two distinct mutations of Pcf11 and a matched wildtype w303 samples under standard growth conditions.  The overall goal was quantification of expression abundance and pre-mRNA processing changes in response to these mutations.

overall_design: RNA was prepared from three biological replicates of each mutant strain (Pcf11-13 and the novel mutant Pcf11-DNL, as described in the associated manuscript) and submitted to Genewiz for poly(A) selection and standard RNA sequencing using the Illumina HiSeq 3000 platform, with 2x150 bp paired end runs, and a return of 15-20 million read pairs per sample.

first: Jason

last: Kuehner

first: Katarzyna

last: Kaczmarek-Michaels

first: Nathaniel

middle: J

last: Maki

first: Christian

last: Wilson

first: Erika

last: Pearson

first: Franco

last: Puleo

first: Caleb

last: McGrath

first: Derick

last: Hoskinson

first: Claire

last: Moore


title: Differential expression of murine syngeneic orthotopic glioblastoma tumour models

first: Catherine

middle: J.

last: Wu

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Bulk RNA sequencing analysis of murine syngeneic orthotopic GL261-luc2 and CT2A-luc glioblastoma tumour models

overall_design: GL261-luc2, CT2A-luc, GL261-hCD19-luc2, or CT2A-hCD19-luc cells were implanted into murine brains. GL261-luc2 and CT2A-luc tumors were extracted from mouse brains and total RNA was extracted using RNeasy Plus Mini kit and sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina. mRNAs were enriched with Oligod(T) beads and fragmented for 15 minutes at 94 °C. First-strand and second-strand cDNA were synthesized, end repaired, adenylated at 3’ends, and ligated to universal adapters; followed by index addition and library enrichment by PCR with limited cycles and sequencing using a 2x150bp Paired End configuration on the Illumina HiSeq. GL261-hCD19-luc2 and CT2A-hCD19-luc tumors were extracted from mouse brains and tumor cells were first isolated from dissociated ex vivo tumours by bead-based positive magnetic selection for hCD19. RNA was isolated using the RNeasy Mini kit. First-strand Illumina-barcoded libraries were generated using the NEB RNA Ultra Directional kit, including 12 cycles of PCR enrichment. Libraries were subsequently sequenced on an Illumina NextSeq 500 instrument using paired-end 37bp reads.

first: Bryan

last: Iorgulescu

first: Neil

last: Ruthen

first: David

last: Reardon


title: Distant antimetastatic effect of enterotropic colon cancer-derived α4β7 CD8 T cells

first: Christel

last: Devaud

address: 2 Avenue Hubert Curien

overall_design: Refer to individual Series.


title: Gene expression profiling and RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast


title: DRS expression and polyA site measurement of Pcf11 mutations in yeast

summary: Direct-RNA Sequencing expression data, quantifying both abundance and 3'-processing (cleavage and polyadenylation) site was obtained for two distinct mutations of Pcf11 and matched wildtype w303 samples under both standard growth conditions, as well as under growth in a caffeine-supplemented medium, since these mutations have been shown to increase susceptiblity to caffeine-related phenotypes.  The overall goal was quantification of expression and pre-mRNA processing changes in response to these mutations.

overall_design: Direct RNA Sequencing data was obtained for 8 yeast samples, including two distinct mutations of Pcf11 (YDR228C), Pcf11-13 and Pcf11-deltaNL, under growth in either YAPD media, or YAPD with inclusion of 20mM caffeine.  Resulting sequenced data was processed to get both gene expression and polyA site selection


title: Anabaena PCC7120 infection with Cyanophage A1

city: Freiburg

first: Marcus

last: Ziemann

state: Baden württemberg

address: Schänzlestraße 1

institute: Albert-Ludwigs-Universität Freiburg

summary: In order to examine the response of Anabaena sp. PCC 7120 to an infection of the Cyanophage A1, we have used customized microarrays to identify genes potentially up- or downregulated by the infection. For this we compared cell culture before and after infection.

overall_design: The Anabaena sp. PCC 7120 cultures incubated under optimal conditions before split into two cultures of the same size. One culture was infected with a MOI of 2 and both cultures incubated further by 30 centigrade for one hour. Afterwards, the cells were harvested. This experiment was repeated in order to receive replicates.

first: Viktoria

last: Reimann

first: Wolfgang

last: Hess

first: Jens

last: Georg


title: Single cell analysis of meningeal ectopic lymphoid tissue and lumbar lymph nodes in a spontaneous EAE model

city: Munich

first: Gildas

last: Lepennetier

address: Ismaninger Straße 22

department: Neurology

institute: Klinikum Rechts der Isar

summary: Objective: To investigate how similar meningeal ectopic lymhpoid tissue (mELT) is to secondary lymphoid tissues and find unique features of mELT that could  allow therapeutic targetting of mELT specifically.   Methods: We utilized a spontaneous chronic experimental autoimmune encephalomyelitis (EAE) model of mice with mutant T and B cell receptors specific for myelin oligodendrocyte glycoprotein (MOG), which develop meningeal inflammatory infiltrates resembling those described in Multiple Sclerosis (MS). We identified differences in cell composition and gene expression between mELT and lumbar lymph nodes using single cell sequencing.

overall_design: single cell gene expression and B cell receptor sequences of meningeal ectopic lymphoid tissue and lumbar lymph nodes in 3 Thx2D2 mice

first: Klaus

last: Lehmann-Horn

first: Jolien

last: Diddens

first: Monika

last: Pfaller

first: Rosa

last: Brand


title: RNA-Seq analysis of colonic mesenchyme lacking tumor necrosis factor receptor 1

city: Los angeles

first: Xiangming

last: Ding

state: California

address: 4650 Sunset Blvd

institute: CHLA

summary: Our study reports a role for mesenchymal TNFR1 in maintaining colonic mesenchymal cell diversity and facilitation of a function epithelial stem cell niche. Through RNA-seq profiling, we show that a TNFR1-deficient mesenchyme has altered anchoring and cell substrate junctions, focal adhesions, extracellular matrix, and actin binding processes. We find specific reduction in the key stem cell niche factor,  RSPO3, crucial for Lgr5+ stem cell maintenance, downregulated 5.1-fold in the TNFR1 deficient mesenchyme. Pathways classically associated with proliferation and differentiation, including Phosphoinositide 3-kinase (P13k) and Mitogen-activated protein kinase (MAPK), and those involved in migration, namely Ras-proximate-1 or Ras-related protein 1 (RAP1), TGF-β and RAS, were significantly enriched in TNFR1-/- mesenchyme compared to controls. In particular, Itga6, representing the integrin alpha 6 subunit, was one of the most highly upregulated transcripts. Therefore, the transcriptome profiling of the TNFR1 deficient mesenchyme deletion suggests an important role for TNFR1 in the regulation of mesenchymal cell-matrix interactions and niche transcript expression.

overall_design: To determine a functional role for TNFR1 signaling in the colonic mesenchyme and its interaction with the epithelial stem cell niche, we investigated sub-epithelial mesenchymal cell populations in control (TNFR1+/-) and TNFR1-/- mice through immunostaining, whole lysate cell preps, epithelial-mesenchyme co-cultures and through RNA-Seq of amplified primary control (TNFR1+/-) and TNFR1-/- colonic myofibroblasts (CMFs).

first: Safina

last: Gadeock

first: Long

last: Hung

first: D

last: Polk


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of Yolk Sacs of E16.5 Wild Type and Rsu1-/- mouse embryos

city: Shenzhen

first: Yi

last: Deng

state: Guangdong Province

address: 1088 Xueyuan Blvd., Nanshan District

department: Department of Biology

institute: Southern University of Science and Technology

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived yolk sac transcriptome profiling (RNA-seq) of E16.5 Rsu1-/-  mouse embryos to that of the wild-type controls
Methods: Yolk sac mRNA profiles of yolk sac isolated from E16.5 wild-type (WT) and ras suppressor 1 (Rsu1−/−) emdbryos were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 platform. The sequence reads that passed quality filters were were mapped to human reference genome GRCh38 by HISAT2 v2.2.1 with default parameters.
Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the mouse genome and identified ___ transcripts in the yolk sacs of E16.5 WT and Rsu1−/− embryos with HISAT2 v2.2.1 workflow . Approximately __ % of the transcripts showed differential expression between the WT and Rsu1−/− yolk sac, with a fold change ≥2.0 and p value <0.05. Altered expression of 12 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method.
Conclusions: Our study represents the first detailed analysis of E16.5 Rsu1-/- yolk sac transcriptomes, which would expedite genetic network analyses and permit the dissection of complex biologic functions of Rsu1 during late embryogenesis.

overall_design: Yolk sac mRNA profiles of E16.5 wild type (WT) and Rsu1-/- mouse embyros

first: Hui

last: Zhao


title: Otsuka Long-Evans Tokushima fatty rats with Roux-en-Y gastric bypass surgery

city: Seoul

first: Chan Woo

last: Kang

state: Seoul

address: 50 Yonsei-ro Seodaemun-gu

institute: Yonsei University

summary: Objective: The mechanisms underlying type 2 diabetes resolution after Roux-en-Y gastric bypass (RYGB) are unclear. We previously observed temporal migrations in small intestinal glycolysis, suggesting that glucose excretion may contribute to glucose homeostasis. This study aimed to evaluate the mechanisms underlying serum glucose excretion and its contribution to glucose homeostasis by using 2-deoxy-2-[18F]-fluoro-D-glucose (FDG) positron emission tomography. Design: FDG distribution in reconstructed intestinal limbs of sham- or RYGB-operated obese rats was identified. RNA sequencing was performed in areas of high or low FDG uptake.

overall_design: RNA-seq was performed to investigate the relative effects of RYGB gastric bypass intervention on the small intestine. N=3 replicates were profiled.

first: CheolRyong

last: Ku

first: Aurther

last: Cho

first: ChanWoo

first: InKu

last: Kwon


title: Caenorhabditis elegans sequencing

city: Santa Cruz

first: Joshua

last: Arribere

state: CA

address: 1156 High St

department: Department of Molecular, Cell, and Developmental Biology

institute: University of California at Santa Cruz

summary: RNA-seq, monosome Ribo-seq, and disome Ribo-seq were performed to study the effect of deletion of ZNF-598 on No-Go mRNA Decay.

overall_design: Analysis of wildtype and znf-598(-) C. elegans samples expressing a No-Go mRNA Decay reporter by RNA-seq, Ribo-seq using cycloheximide, and Ribo-seq using anisomycin.

first: Parissa

last: Monem


title: RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

first: Joel

last: Graber

summary: High Throughput bulk-sample ChIP-seq data targeted to RNA-polymerase II was collected for duplicate samples of two distinct mutations of Pcf11 and a matched wildtype w303 samples under standard growth conditions.  The overall goal was quantification of changes in transcriptional activity in response to these mutations.

overall_design: High throughput DNA-sequencing data was obtained for 6 yeast samples (w303 background), with duplicate samples of two mutations of Pcf11 (YDR228C), Pcf11-13 and Pcf11-dQN, and matched wildtype.  Sequence was obtained for RNApolymerase II associated samples (using the anti-pan CTD mouse monoclonal antibody) and for matched input control

first: Jason

last: Kuehner

first: Katarzyna

last: Kaczmarek-Michaels

first: Nathaniel

last: Maki

first: Christian

last: Wilson

first: Erika

last: Pearson

first: Franco

last: Puleo

first: Caleb

last: McGrath

first: Derick

last: Hoskinson

first: Claire

last: Moore


title: Single cell analysis of meningeal ectopic lymphoid tissue and secondary lymphoid tissues in a spontaneous EAE model

first: Gildas

last: Lepennetier

summary: Objective: To investigate how similar meningeal ectopic lymhpoid tissue (mELT) is to secondary lymphoid tissues and find unique features of mELT that could allow therapeutic targetting of mELT specifically.   Methods: We utilized a spontaneous chronic experimental autoimmune encephalomyelitis (EAE) model of mice with mutant T and B cell receptors specific for myelin oligodendrocyte glycoprotein (MOG), which develop meningeal inflammatory infiltrates resembling those described in Multiple Sclerosis (MS). We identified differences in cell composition and gene expression between mELT and secondary lymphoid tissues (lumbar and inguinal lymph nodes and the spleen) using single cell sequencing.

overall_design: single cell gene expression and Bcell receptor sequences of meningeal ectopic lymphoid tissue, blood, spleen, inguinal and lumbar lymph nodes in 3 Thx2D2 mice

first: Klaus

last: Lehmann-Horn

first: Jolien

last: Diddens

first: Tanya

last: Georgieva

first: Verena

last: Friederich


title: Fracture Hematoma Micro-Architecture Plays a Crucial Role in Determining Bone Healing Outcomes

city: Brisbane

first: Zewen Kelvin

last: Tuong

state: QLD

address: 62 Graham Street, Centre for Children's Health Research (CCHR), South Brisbane, QLD, 4101

country: Australia

institute: The University of Queensland

summary: The fracture hematoma that forms between the broken fragments of bone serves as a natural fibrin scaffold. However, there is no data regarding the differences between the micro-architectural and biological properties of hematomas formed in normally healing, delayed healing, and non-healing bone defects. Mimicking these three conditions in the rat femur, we demonstrate clear differences in fibrin clot morphology, which directly affect the gene expression pattern. Specifically, RNA-sequencing reveals that the expression of essential osteogenic genes in normally healing defects are significantly up-regulated, whereas in delayed and non-healing defects they are down-regulated. Surprisingly, there were no substantial differences between delayed and non-healing defects. Most importantly, this study demonstrates that the healing outcome has already been determined at the earliest stage of bone healing. These findings could be used to develop biomaterial scaffolds mimicking the micro-architectural properties of normally healing fracture hematoma as a treatment strategy for bone defects.  The hypothesis of this study was that the micro-architectural properties of the initially formed hematoma has a significant effect on the regulation of the biological process at the fracture site, which ultimately determines the outcome of bone healing. Three different healing models were investigated - normally healing, delayed healing, and non-healing defects. The results demonstrated that the intrinsic micro-architectural properties of hematomas between those groups varied distinctly in terms of fiber diameter, porosity, and density of the formed fibrin network. Those differences influenced biological responses, as evidenced by a higher expression of osteogenic genes in normally healing compared to delayed and non-healing defects, and the failed activation of BMP-2 in non-healing defects. More importantly, our results demonstrate healing outcomes are already determined at the initial (hematoma) stage of bone healing.

overall_design:
Three different healing models were investigated - normally healing, delayed healing, and non-healing defects.  PreOP group also  examined.
3 Samples/Group:                                                                                Experimental Group 1: Normal Healing (0.5 mm defect)                                                                                Experimental Group 2: Delayed Healing (1.5 mm defect)                                                                                Experimental Group 3: Nonunion (5.0 mm defect)                                                                                Reference Sample: preOP (healthy bone piece removed at surgery from 5.0 mm defects)

first: Anna

last: Woloszyk

first: Zewen

middle: K

first: Louis

last: Perez

first: Leonardo

last: Aguilar

first: I

last: Bankole

first: Chris

last: Evans

first: Vaida

last: Glatt


title: Study the differential gene expression in SK-MEL-147 cells treated with different epigenetic modulator

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: The study evaluated the modulation of gene expression in SK-MEL-147 cell lines using different epegenetic modulator.

overall_design: Total RNA was extracted from SK-MEL-147 cell after treatment with different epigenetic modulators, followed by poly-A selection and RNA-sequencing using Illumina Hi-Seq 2500 platform, with three biological replicates for each treated sample.

first: Raj

last: Kumar


title: Antisense RNA technology induces the loss of function of steroidogenic factor 1 leading to abortion of tilapia

city: Wuxi

first: Jun

last: Qiang

address: 9 Shanshi East road

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

summary: As a precise and efficient genetic engineering method, gene editing technology for animals and plants will gradually move towards large-scale applications, and will have a disruptive impact on the breeding of related traits. By using antisense RNA interference technology to interfere with the mRNA expression and protein translation of the SF-1 gene, we have successfully cultivated tilapia with defective gonadal development. The results of the study showed that the weights of male and female fish in the experimental group were significantly higher than those of the control group. The gonadal weight and gonadal index of the experimental group were significantly lower than those of the control group and the negative control group. HE staining showed that the number of spermatogonia in the testis tissue of the experimental group was significantly reduced, the cavity in the seminiferous tubules was significantly enlarged and increased, the number of sperm cells was significantly decreased, and the number of sperm was relatively rare. However, a large number of stage V oocytes accumulated in the ovarian tissue of female fish in the experimental group, and many of them were gray-white. The mRNA and protein expression levels of SF-1 gene in the gonadal tissues were extremely significantly lower than those of the control and negative controls. The combined analysis of transcriptome and proteome showed that Steroid hormone biosynthesis, Arachidonic acid metabolism and Cell adhesion molecules are involved in the regulation of the gonads of male fish after SF-1 gene silencing. However, ECM-receptor interaction, Retinol metabolism, Nicotinate and nicotinamide metabolism and cytochrome P450 may be involved in the regulation of female fish SF-1 gene silencing. SF-1 silencing may cause developmental defects in the external reproductive organs of male and female fishes and inhibit the development of gonadal tissues through different regulatory pathways. This provides data support for the further functional analysis of SF-1 on fish and the treatment of abnormal human SF-1 expression.

overall_design: The use of the present disclosure preferably comprises the following steps: 1) cloning the Anti-SF1-1-I, Anti-SF1-1-II, Anti-SF1-2-I and Anti-SF1-2-II into expression vectors to obtain recombinant vectors; 2) using the recombination vectors as templates, and performing PCR amplification with specific primers to obtain four amplified products; 3) after mixing the four amplified products with a cationic liposome and a spermatozoa preservative fluid respectively, equilibrating at 15-30oC for 20-40 min to obtain transfection reagents; 4) mixing the transfection reagents with the eggs for transfection to obtain transfected eggs; 5) mixing the transfected eggs with sperms for fertilization and hatching to obtain abortive tilapia fries.

first: Zhe-Ming

last: Cao

first: Jun-Hao

last: Zhu

first: Jie

last: He

first: Hong-Xia

last: Li

first: Yi-Fan

last: Tao

first: Jin-Wen

last: Bao

first: Pao

last: Xu


title: Potential toxicity of inorganic ions in the particulate matter: ion permeation in lung and disruption of cell metabolism

city: Daejeon

first: Yoosik

last: Kim

state: Daejeon

address: Daejeon

institute: KAIST

summary: Exposure to ambient particulate matter (PM) is associated with adverse health effects. Yet, due to the complexity of its chemical composition, the molecular effects of PM exposure and the mechanism of PM-mediated toxicity remain largely unknown. Here, we show that water-soluble inorganics such as nitrate and sulfate ions, rather than PM themselves, are responsible for perturbing gene expression in the lungs by rapidly penetrating the lung surfactant barrier to the alveolar region. Furthermore, from high-throughput sequencing of lung adenocarcinoma cells, we find that exposure to nitrate and sulfate ions activates the cholesterol biosynthetic metabolism and induces the expression of genes related to tumorigenesis and inflammatory response, particularly interferon-gamma. Transcriptome analysis of mouse lungs exposed to nitrate/sulfate aerosols further supports our findings. Notably, we find that exposure to nitrate/sulfate mixture leads to a unique gene expression pattern that is not observed when nitrate or sulfate is treated alone. Our work suggests the water-soluble ions as a potential source of PM-mediated toxicity and provides a roadmap to unveil the working mechanism of health hazards of PM exposure.

overall_design: mRNA-sequencing was performed in A549 cells or mouse lung tissue under ammonium nitrate or sulfate treatment. Two replicates were used for each sample

first: Jayoung

last: Ku


title: LIM homeobox-2 suppresses hallmarks of adult and pediatric liver cancers by controlling MAPK/ERK and Wnt/beta-catenin pathways

city: Bordeaux

first: Christophe François

last: Grosset

address: 146 rue Léo Saignat

institute: INSERM

summary: Hepatocellular carcinoma (HCC) and Hepatoblastoma (HB) are two liver cancers characterized by high gene deregulation, chromosomal rearrangements and typical mutations in genes related to the Wnt/β-catenin (Wnt) pathway. LHX2, a transcriptional factor member of the LIM homeobox gene family, has important functions in embryogenesis, liver development but also tumorigenesis. LHX2 is an oncogene in may solid tumors and leukemia but its role in liver cancer is unknown. To address this question we analyzed the expression of LHX2 in HCC and HB using various transcriptomic datasets and found a strong connection between LHX2 down-regulation and Wnt activation in these two liver cancers. In HB LHX2 downregulation correlated with multiple poor outcome parameters including higher patient age, intermediate- and high-risk tumors and patients’ survival. A forced expression of LHX2 reduced the proliferation, the migration and the survival of hepatoma cells in vitro through the inactivation of MAPK/ERK and Wnt signalings. In vivo, LHX2 impeded the development of tumors in the chick embryo and repressed the Wnt pathway in Xenopus embryo. RNA-sequencing data and bioinformatic analyses confirmed the deregulation of many biological functions and molecular processes associated with cell migration, cell survival and liver carcinogenesis in LHX2-expressing hepatoma cells. At a mechanistic level, LHX2 induced the disassembling of beta-catenin and T-cell factor 4 and the expression of multiple inhibitors of Wnt (e.g. TLE/Groucho) and MAPK/ERK (e.g. DUSPs) pathways. Collectively, our findings demonstrate the tumor suppressive function of LHX2 in adult and pediatric liver cancers.

overall_design: Transcriptome profile in Huh7 cell overexpressing LHX2 vs CTRL cells

first: Christophe

middle: F

first: Nicola

last: Mosca

first: Fatma-Zohra

last: Khoubai

first: Philippe

last: Veschambre

first: Sandrine

last: Fedou

first: Emeric

last: Dubois

last: Avignon

first: Juan

last: Carrillo-Reixach

first: Stefano

last: Caruso

first: Carolina

last: Armengol

first: Jessica

last: Zucman-Rossi

first: Catherine

last: Guettier

first: Charlotte

last: Mussini

first: Pierre

last: Thiébaud


title: Isolated and characterized colorectal cancer stem cells and normal stem cells isolated from colorectal cancer tissues and normal colon tissues by whole genome expression microarray

city: New Delhi

first: Aditi

last: Bhattacharya

state: Delhi

address: Lab No. 3027A, Department of Biochemistry, Teaching Block, AIIMS

department: Biochemistry

country: India

institute: All India Institute of Medical Science, New Delhi

summary:
Cancer stem cells (CSCs) are pluripotent cells that have been implicated in tumor proliferation, metastatic dissemination, and recurrence of various cancers. The prognosis of colorectal cancer, which often presents late due to absence of early symptoms, depends on the stage at presentation. In the present study we have isolated and characterized cancer stem cells from colorectal cancer tissues and normal stem cells from normal colon tissues. Only sporadic colorectal cancer cases were considered where the patient had not received any neo-adjuvant therapy to avoid any bias introduced in the cellular transcriptome by external agents. Normal colon tissues were taken from adjacent region of resected specimen as well as non-cancerous operative colon cases.
For our study, we have used cancer and normal stem cell markers defined in established literature. For isolating cancer stem cells by FACS, CD44 and CD166 tagged to phycoerythrin (PE) and Alexa Fluor 647 respectively, were used. For isolating normal colon stem cells, CD29, tagged to PE, and Lgr5, tagged to Alexa Fluor 647 were used. Only dual marker-positive cells were isolated to get an enriched population. Tumor sphere assay was done on representative samples to validate the stemness of isolated cells. RNA was isolated from the isolated cell populations and microarray was done to study the whole genome transcriptomic changes.

overall_design: 4 x 44k Whole genome expression arrays of Isolated and Characterised colorectal Cancer stem cells (n=3), Cancer non stem cells (n=3), normal stem cells (n=3) and normal non-stem cells (n=3) total RNA obtained from colorectal cancers tissues and normal colon tissues.

first: Muzaffer

last: Bhat

first: Sudip

last: Sen


title: Identification of transcriptional difference between platinum-sensitive and resistant patients with ovarian cancer (OV)

city: Shanghai

first: Shengli

last: Li

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

summary:
Purpose: The goals of this study are to characterize the transcriptional dysregulation of OV. More importantly, the transcriptome differences betweeen platinum-sensitive and resistant patients are compared to identify RNAs that may impact platinum resistance.
Methods: High-throughput RNA sequencing (RNA-seq) was employed to capture the transcriptional changes in OV compared to normal samples. StringTie was used to quantify gene expression and DESeq2 was utilized to compared expression changes between different sample groups.

overall_design: Transcriptome-wide comparison of platinum-sensitive and resistant OV patients


title: Analysis of gene expression in USP16 knockdown PC3 prostate cancer cells

city: shanghai

first: Jianchao

last: Ge

state: shanghai

address: N0.801,Heqing Road,Minhang District

department: Shanghai Fifth People's Hospital

institute: Fudan University

summary: Total RNA was obtained from PC3 cells with or without USP16 knockdown to perform a High-throughput sequencing. In our study, USP16 is necessary for prostate cancer cell proliferation in vitro and in vivo. Therefore, we perform the RNA-seq to explore potential mechanisms of USP16 regulating cell growth.

overall_design: The prostate cancer cell line PC3 expressing shRNA targeting USP16 or a vector control. The gene transcript expression profiles were generated by deep sequencing.

first: Guowei

last: Shi


title: Screening and characterizing the effects of mmu_circ_0000296 on spinal cord injury

status: Public on Oct 31 2023

city: Harbin

first: Zaixing

last: Jiang

state: Heilongjiang

address: 157 Health-care Road, Harbin City, Heilongjiang Province, China

institute: Harbin Medical university

summary: Spinal cord injury (SCI) is a common pathologic disorder that often presents with sensory and motor deficits, severely affecting patients' daily lives. Circular RNAs (circRNAs), a class of non-coding RNAs, have been reported to be involved in regulating the development of SCI. We used RNA sequencing technology and bioinformatics analysis to find the expression and regulation patterns of circRNAs and mRNAs in a mouse model of SCI, from which we screened the potential RNA-mmu_circ_0000296 that affects the progression of SCI in the acute phase. Based on STRING, ENCORI, miRTarBase database and Cytoscape software to construct the relational network of endogenous competing RNAs (ceRNAs) and protein-protein interaction (PPI) network. Finally, in order to validate the above bioinformatics results, the differential expression of circ_0000296 was verified in mouse SCI model and LPS-induced cell model, respectively. Not only that, in in vitro experiments, we found that circ_0000296 overexpression could inhibit microglia polarization toward M1 type, reduce inflammation level, and then inhibit neuronal apoptosis. These findings will help to elucidate and refine the effects of circRNAs on the pathophysiological progression of spinal cord injury and suggest that mmu_circ_0000296 may be one of the targets for spinal cord injury therapy.

overall_design: To screen circRNAs affecting spinal cord injury, we established SCI mouse models. 3 control mice underwent laminectomy at the T10 level without spinal cord injury, and the other 3 experimental mice were placed on the spinal cord impingement platform after laminectomy at the T10 level, and the spinal cord was moderately contused at the T10 level using a modified Allen weight descender (10 g weight with a vertical height of 20 mm). Following surgery, daily bladder massages were given until full spontaneous or voluntary urination and daily antibiotics were given for three days. For the SCI model consistency, the following criteria were required for inclusion: (I) mice weighing between 20 and 25 g; (II) 10 g weight and 20 mm vertical height requirements for weight reduction devices; (III)tail wagging, hind limb twitching right after SCI, and flaccid paralysis of the hind limbs when awake. Exclusion criteria included: (I) The animals    weight and age were below average. (II) During a laminectomy, the spinal cord unintentionally suffered damage. (III) The mice   s hindlimbs could still move after they emerged from anesthesia.   6 mice were executed on the 2nd day after surgery, and spinal cord tissues about 1 cm long around the T10 level were taken for high-throughput RNA sequencing.


title: Trappc1 is essential for naive T cell survival

city: Beijing

first: Zhaoqi

last: Zhang

state: Beijing

address: Beijing China Institute of Zoology，Chinese Academy of Sciences

institute: University of Chinese Academy of Sciences

summary: T lymphocytes are pivotal in adaptive immunity. The role of trafficking protein particle complex (TRAPPC) in regulating T cell development and homeostasis are unknown. Using CD4cre-Trappc1flox/flox (Trappc1 cKO) mice, we found that Trappc1 deficiency in T cells significantly decreased cell number of naïve T cells in the periphery, whereas thymic T cell development in Trappc1 cKO mice was identical as in WT mice. In the culture assays and mouse models with adoptive transfer of the sorted WT (CD45.1+CD45.2+) and Trappc1 cKO naive T cells (CD45.2+) to CD45.1+ syngeneic mice, Trappc1-deficienct naive T cells showed significantly reduced survival ability compared with WT cells. RNA-seq and molecular studies showed that Trappc1 deficiency in naive T cells reduced protein transport from the endoplasmic reticulum to Golgi apparatus, enhanced unfolded protein responses, increased P53 transcription, intracellular Ca2+, Atf4-CHOP, oxidative phosphorylation and lipid peroxide accumulation, and subsequently led to ferroptosis.

overall_design: Naive CD4+ T cells and naive CD8+ T cells were sorted by CD4+/CD8+CD62L+CD44low from the mLNs and spleens of 4 weeks old WT and CD4-cre Trappc1 cKO mice. The total RNA of the sorted naive CD4+ T cells and naive CD8+ T cells were extracted using TRIzol reagent (Thermo Fisher, 15596018), and sequencing were done by the Annoroad Gene Technology Co., Ltd (Beijing). Differential expressed genes were carried out by DEseq2 software38. KEGG pathway enrichment was performed by KOBAS 3.0.28 (http://kobas.cbi.pku.edu.cn/)37,59. Protein and protein interaction network were analyzed by String (https://string-db.org/) and visualized by Cytoscape60.

first: Chenxu

last: Zhao

first: Yong


title: Whole genome methylation analysis in blood and in specific cell blood subtypes in Parkinson’s disease.

city: Barcelona

first: Mario

last: Ezquerra

state: Catalonia

address: Villarroel 170

country: Spain

institute: Fundacio Clinic/IDIBAPS

summary: we analysed the whole epigenomic profile of different blood subtypes, neutrophiles, monocytes, lymphocytes B and T, from 5 de novo and drug-naïve PD patients and 5 age and gender matched healthy control.

overall_design: 1st experiment: DNA from Lymphocytes B and T, monocytes and neutrophils of  5 controls and 5 incidental parkinson's disease patients (PD) were isolated using Milteinyi purification columns. Infinium Human Methylation 850K BeadChip Kit (Illumina) was used to analyse the methylation pattern. 2nd experiment:Whole DNA from blood of 15 PD and 15 controls were obtained by standart methods and analysed by using Infinium Human Methylation 850K BeadChip Kit (Illumina).The EZ DNA Methylation Kit (Zymo Research) was used for bisulfite conversion of 1,000 ng genomic DNA following manufacturer instructions. Bisulfite‐converted DNA was hybridized onto the Infinium Human Methylation 850K BeadChip Kit (Illumina).

first: Ruben

last: Fernandez-Santiago


title: Gene expression profiling of benign and matched tumour prostate tissue from patients diagnosed with prostate cacner (PCa)

city: Exeter

first: Zhuofan

last: Mou

address: Heavitree Road

department: Department of Clinical and Biomedical Sciences

institute: University of Exeter

summary: An integrated transcriptome-wide gene expression analysis, including differential gene expression analysis and weighted gene co-expression network analysis (WGCNA), was carried out based on transcriptomics data from a series of nine matched, histologically confirmed PCa and benign samples using the Affymetrix Clariom D Human array. The analysis identified a set of potential gene markers highly associated with tumor status (malignant vs. benign). We then used these genes to establish a minimal progression-free survival (PFS)-associated gene signature (GS) (PCBP1, PABPN1, PTPRF, DANCR, and MYC) using the least absolute shrinkage and selection operator (LASSO) and stepwise multivariate Cox regression analyses from The Cancer Genome Atlas prostate adenocarcinoma (TCGA-PRAD) dataset. Our signature was able to predict PFS over 1, 3, and 5 years in the TCGA-PRAD dataset, with an area under the curve (AUC) of 0.64–0.78, and our signature remained as a prognostic factor independent of age, Gleason score, and pathological T and N stages. A nomogram combining the signature and Gleason score demonstrated improved predictive capability for PFS (AUC: 0.71–0.85) and was superior to the Cambridge Prognostic Group (CPG) model alone and some conventionally used clinicopathological factors in predicting PFS. In conclusion, we have identified and validated a novel five-gene signature and established a nomogram that effectively predicted PFS in patients with PCa. These findings may improve current prognostic tools for PFS and contribute to clinical decision-making in PCa treatment.

overall_design: A total of 18 samples were analysed (nine matched pairs of malignant PCa and benign samples)

first: Jack

last: Spencer

first: Bridget

last: Knight

first: Joseph

last: John

first: Paul

last: McCullagh

first: John

middle: S

last: McGrath

first: Lorna

middle: W

last: Harries


title: Effect of TCDD exposure in adult female and male mice on the expression of miRNA in the ovaries and testes and associated reproductive functions

city: Columbia

first: Narendra

middle: P

last: Singh

state: South Carolina

address: 6439 Garners Ferry Road,

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina

summary: The current study demonstrates for the first time that exposure of adult male and female mice to TCDD results in significant alterations in a large number of miRNAs in the ovaries and the testes.  These findings suggest that environmental contaminants such as TCDD may alter reproductive functions through alterations in the expression of miRNAs.  Future studies will focus on whether such miRNA changes also occur in the germ cells which would explain how TCDD exerts transgenerational effects on the reproductive system by regulating epigenetic pathways involving miRNA

overall_design: Mice were dosed at 10µg/kg body weight. Male and female mice were either treated with TCDD or vehicle, the latter consisting of an equal amount of DMSO in corn oil, On day 3, ovaries and testes were harvested and single cell suspensions were prepared. miRNA arrays were performed using total RNAs including microRNA and using Affymetrix microarray platform

first: Alina

last: Hall

first: Donald

last: Mattison

first: Ioulia

last: Chatzistamou

first: Mitzi

last: Nagarkatti

first: Prakash


title: Genome-wide identification of notochord enhancers comprising the regulatory landscape of the Brachyury (T) locus in mouse

city: Berlin

first: Frederic

last: Koch

address: Ihnestraße 63-73

department: Developmental Genetics

institute: Max Planck Institute for Molecular Genetics

summary: The node and notochord are important signaling centers organizing dorso-ventral patterning of cells arising from neuro-mesodermal progenitors forming the embryonic body anlage. Due to the scarcity of notochordal progenitors and notochord cells, a comprehensive identification of regulatory elements driving notochord-specific gene expression has been lacking. Here we have used ATAC-seq analysis of FACS-purified notochordal cells from TS12-13 mouse embryos to identify 8921 putative enhancers of notochordal cells. In addition, we established a new model for generating notochordal cells in culture, and identified 3728 enhancers occupied by the essential notochordal regulators Brachyury (T) and/or Foxa2. We describe the regulatory landscape of the T locus comprising 8 putative enhancers occupied by these factors and confirmed the regulatory activity of 3 of these elements. Moreover, we characterized one new notochord enhancer, termed TNE2, in embryos. TNE2 complements the loss of TNE in the trunk notochord, and is essential for notochordal cell proliferation and differentiation in the tail. Our data demonstrate the essential role of Foxa2 in the choice of T expressing cells between the notochordal fate and the NMP/mesodermal trajectory

overall_design: Transcriptomes (RNA-Seq), chromatin accessibility (ATAC-Seq) and chromatin IPs (ChIP-Seq) of histone modifications and the T and Foxa2 transcription factors in various FACS sorted (based on Noto, T and Foxa2 expression) or bulk samples from either E8.5/E9.5 embryos or mESCs differentiated in vitro into neuromesodermal, notochord or mesoderm (progenitor)-like cells.

first: Dennis

last: Schifferl

first: Manuela

last: Scholze-Wittler

first: Alba

middle: V

last: Luque

first: Milena

last: Pustet

first: Lars

last: Wittler

first: Jesse

last: Veenvliet

first: Bernhard

middle: G

last: Herrmann


title: RNA-sequencing (RNA-seq) analysis of gene expression of ASCs primed by LPS or dsDNA

first: jieming

last: Qu

address: Ruijin 2 road

institute: ruijin hospital

summary: In the inflammatory microenvironment, cytokines and products of pathogens could modulate the phenotype and activity of adipose tissue-derived mesenchymal stem cells (ASCs). So far, the gene expression profiles in lipopolysaccharide (LPS)- or double stranded DNA (dsDNA) -primed ASCs have less been extrapolated. We approached RNA-sequencing (RNA-seq) analysis and found that both LPS and dsDNA treatment markedly influence transcriptome regarding cytokine, chemotaxis/inflammatory genes and pattern recognition receptor (PRR) .

overall_design: Different gene expression of ASCs primed by LPS or dsDNA

first: Caixia

last: Di

first: Yanshan

last: Jiang


title: Aldafermin-producing E.coli Nissle 1917 effects on liver and adipose tissue gene expression profile of NAFLD mouse model

city: kuopio

first: Valeria

last: Iannone

address: Yliopistonranta 1

department: Clinical Nutrition

country: Finland

institute: University of Eastern Finland

summary: To investigate aldafermin-producting E.Coli Nissle 1917 effects in combination with dietary changes in NAFLD mouse model.

overall_design: NAFLD was induced in C57BL/6J male mice by American lifestyle-induced obesity syndrome diet and then switched to a standard chow diet for seven weeks. In addition to the dietary change, the intervention group received genetically engineered E.coli Nissle expressing aldafermin and the liver and epididymal adipose tissue gene expression profile was evaluated after the intervention. Two control groups were included during seven weeks of interventions: control1: NAFLD mouse model fed by chow diet; control 2: NAFLD mouse model receiving E.Coli Nissle 1917 without expression of peptides.

first: Ambrin

last: F Babu

first: Johnson

last: Lok

first: Carlos

last: Gomez-Gallego

first: Giuseppe

last: D'Auria

first: Ruben

last: Vazquez-Uribe

first: Troels

last: H Vaaben

first: Mareike

last: Bongers

first: Santtu

last: Mikkonen

first: Ida

last: Tikkanen

first: Mikko

last: Kettunen

first: Anton

last: Klåvus

first: Ratika

last: Sehgal

first: Dorota

last: Kaminska

first: Jussi

last: Pihlajamaki

first: Kati

last: Hanhineva

first: Hani

last: El-Nezami

first: Morten

last: O Alexander Sommer

first: Marjukka

last: Kolehmainen


title: Nat10 is involved in myocardial remodeling through ac4C-mediated transcriptomic regulation

city: Nanjing

first: Chuanxi

last: Yang

state: China

address: 300 Guangzhou Road, 210029, Nanjing, PR China

department: Department of Cardiology

institute: School of Medicine, Southeast University

summary:
Background: Heart failure (HF), characterized by cardiac remodeling, is associated with abnormal epigenetic processes and aberrant gene expression. Here, we aimed to elucidate the effects and mechanisms of N-acetyltransferase 10 (NAT10)-mediated N4?acetylcytidine (ac4C) acetylation during cardiac remodeling.
Methods: NAT10 and ac4C expression were detected in both human and mouse subjects with cardiac remodeling through multiple assays. Subsequently, acetylated RNA immunoprecipitation and sequencing (acRIP-seq), thiol (SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq), and ribosome sequencing (Ribo-seq) were employed to elucidate the role of ac4C-modified post-transcriptional regulation in cardiac remodeling. Additionally, functional experiments involving the overexpression or knockdown of NAT10 were conducted in mice models challenged with Ang II and transverse aortic constriction (TAC).
Results: NAT10 expression and RNA ac4C levels were increased in in vitro and in vivo cardiac remodeling models, as well as in patients with cardiac hypertrophy. Silencing and inhibiting NAT10 attenuated Ang II-induced cardiomyocyte hypertrophy and cardio-fibroblast activation. Next-generation sequencing revealed ac4C changes in both mice and humans with cardiac hypertrophy were associated with changes in global mRNA abundance, stability and translation efficiency. Mechanistically, NAT10 could enhance the stability and translation efficiency of CD47 and ROCK2 transcripts by upregulating their mRNA ac4C modification, thereby resulting in an increase in their protein expression during cardiac remodeling. Furthermore, the administration of Remodelin, a NAT10 inhibitor, has been shown to prevent cardiac functional impairments in mice subjected to TAC by suppressing cardiac fibrosis, hypertrophy, and inflammatory responses, while also regulating the expression levels of CD47 and ROCK2.
Conclusions: Therefore, our data suggest that modulating epitranscriptomic processes, such as ac4C acetylation through NAT10, may be a promising therapeutic target against cardiac remodeling.

overall_design: We performed ac4C-seq from human heart samples (six participants per group) and four mice groups (AAV9:CONi, AAV9:NAT10i, Ang II, and Ang II +AAV9:NAT10i, with three biological repeats per group) in Model 2 by Epibiotek (Guangzhou, China). SLAM-seq was performed to measure the effect of NAT10 on mRNA half-life transcriptome-wide in NMCMs and NMCFs (two biological repeats per group) with Epi? SLAM-seq Library Prep Kit (R202208-2, Epibiotek, China) by Epibiotek (Guangzhou, China) according to the manufacturer?s instructions. Ribo-seq was performed from three mice groups (AAV9:CONi, Ang II, and Ang II +AAV9:NAT10i, with three biological repeats per group) by Epibiotek (Guangzhou, China). RNA-seq was performed from human heart samples (six biological repeats per group) and four mice groups (AAV9:Coni, AAV9:NAT10i, Ang II, And Ang II +AAV9:NAT10i, With Three Biological Repeats Per Group) in Model 2 by Epibiotek (Guangzhou, China).

first: Jing

last: Zhang

first: Kun

last: Zhao

last: Shi


title: IL-17RA promotes pathologic epithelial inflammation in a mouse model of upper respiratory influenza infection

city: Grand Forks

first: Kai

last: Guo

state: ND

address: 1301 N Columbia Rd Stop 9037

institute: University of North Dakota

summary: The upper respiratory tract (nasopharynx or NP) is the first site of influenza replication, allowing the virus to disseminate to the lower respiratory tract or promoting community transmission. The host response in the NP regulates an intricate balance between viral control and tissue pathology. The hyper-inflammatory responses promote epithelial injury, allowing for increased viral dissemination and susceptibility to secondary bacterial infections. However, the pathologic contributors to influenza upper respiratory tissue pathology are incompletely understood. In this study, we investigated the role of IL-17RA as a modulator of influenza host response and inflammation in the upper respiratory tract. We used a combined experimental approach involving IL-17RA-/- mice and an air-liquid interface (ALI) epithelial culture model to investigate the role of IL-17 response in epithelial inflammation, barrier function, and tissue pathology. Our data show that IL-17RA-/- mice exhibited significantly reduced neutrophilia, epithelial injury, and viral load. The reduced NP inflammation and epithelial injury in IL-17RA-/- mice correlated with increased resistance against co-infection by Streptococcus pneumoniae (Spn). IL-17A treatment, while potentiating the apoptosis of IAV-infected epithelial cells, caused bystander cell death and disrupted the barrier function in ALI epithelial model, supporting the in vivo findings.

overall_design: 13 samples

first: Nadeem

last: Khan


title: A novel GATA2 enhancer single nucleotide mutation results in the MonoMAC syndrome phenotype in two second cousins

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

summary: Inherited or sporadic mutations in the transcription factor GATA2 have been shown to be responsible for MonoMAC syndrome, a GATA2 deficiency disease characterized by a constellation of findings including disseminated non-tuberculous mycobacterial infections, severe deficiencies of monocytes, natural killer cells, and B-lymphocytes, and myelodysplastic syndrome. Mutations in the GATA2 gene are found in ~90% of patients with a GATA2 deficiency phenotype and are largely missense mutations in the conserved second zinc-finger domain or truncation mutations elsewhere in the coding sequence. Mutations in an intron 5 regulatory enhancer element are also well described in GATA2 deficiency. Here we present a large multigeneration kindred with the clinical features of GATA2 deficiency but lacking an apparent GATA2 mutation. Whole Genome Sequencing revealed a unique Adenine-to-Thymine variant in the GATA2 -110 enhancer 116,855bp upstream of the GATA2 gene. The mutation creates a new E-box consensus in position with an existing GATA-box to generate a new hematopoietic regulatory composite element. The mutation segregates with the disease pattern in five generations of the family pedigree. Cell-type specific allelic imbalance of GATA2 expression is observed in a patient’s bone marrow with higher expression from the mutant-linked allele. Allele-specific overexpression of GATA2 is observed in CRISPR/Cas9-modified HL60 cultured cells and in luciferase assays with the enhancer mutation. This study demonstrates overexpression of GATA2 resulting from a single nucleotide change in an upstream regulatory enhancer element in patients with MonoMAC syndrome.

overall_design: RNA-sequencing of a HL-60 promyelocytic leukemia cell line engineered to harbor an  A-to-T inversion in the GATA2 -110 enhancer 116,855bp upstream of the GATA2 gene via CRISPR/Cas-9-mediated genome editing compared to WT control measured over four days.

first: Robert

last: West

first: Thomas

last: Bauer Jr


title: mRNA Sequencing of pups heart Knock-in Mfn2R400Q

city: St. Louis

first: Antonietta

last: Franco

state: MO

address: 1 Brookings Dr, St. Louis

department: Pharmacogenomics

institute: Washington Univeristy school of medicine in St. Louis

summary: We sequencing E18.5 pups heart carryng human Mfn2mutantion vs Ctrl mouse and we found different RNA profile

overall_design: Comparison transcritional signature amonge18.5 pups  Mfn2R400Q and Ctrl

first: Gerald

last: Dorn II

last: FRANCO


title: The pivotal ripening gene SlDML2 participates in regulating disease resistance in tomato

first: Leilei

last: Zhou

address: Xianshan street

institute: Institute of Botany, Chinese Academy of Sciences

summary: To decipher the molecular basis underlying SlDML2-mediated defense response to B. cinerea, a comparative transcriptomic analysis was performed using B. cinerea-infected tomato fruits of the sldml2-3 mutant and wild-type at 39-day post-anthesis. A total of 2310 differentially expressed genes (DEGs; fold change ≥ 2 and adjusted P value < 0.05) were identified, of which 1431 were up-regulated and 879 were down-regulated in fruits of the sldml2-3 mutant compared to the wild-type. This indicates an obvious transcriptome reprogramming caused by SlDML2 mutation in the process of B. cinerea infection.

overall_design: Transcriptome profiles in tomato fruits of wild-type and sldml2 mutant under B. cinerea infection were generated by RNA-seq, in triplicate, using Novaseq™ 6000 sequencer.

first: Guozheng

last: Qin