title: Epigenetic silencing by SMYD3 represses tumor intrinsic interferon response in HPV-negative squamous cell carcinoma of the head and neck [RNA-seq]

status: Public on May 26 2023

city: Bethesda

first: Vinutha

last: Balachandra

state: MD

address: 10 Center Drive

department: National Cancer Institute, Genetics Branch

country: USA

institute: National Institute for Health

summary: Cancers often display immune escape, but the mechanisms and potential for reversibility are incompletely understood. Epigenetic dysregulation has been implicated in the immune escape of various cancer types. We have identified the epigenetic modifier SET and MYND-domain containing protein 3 (SMYD3) as a mediator of immune escape in human papilloma virus (HPV)-negative head and neck squamous cell carcinoma (HNSCC), an aggressive disease with poor response to immunotherapy with pembrolizumab, a programmed-death-1 (PD-1) targeting antibody. SMYD3 depletion increased the sensitivity of HNSCC cancer cells to IFN-β, resulting in upregulation of type I IFN response and antigen presentation machinery genes. We found that SMYD3 binds to and regulates the transcription of Ubiquitin-Like PHD And RING Finger Domain-Containing Protein 1 (UHRF1), a key epigenetic reader of trimethylated lysine 9 on histone H3 (H3K9me3), which binds to H3K9me3-enriched promoters of key immune-related genes, recruits DNMT1 and silences their expression. SMYD3 further maintains the repression of immune-related genes through the deposition of H4K20me3 within the promoters and/or gene body regions of these genes. In an anti-PD-1 immune checkpoint resistant syngeneic mouse model of HPV-negative HNSCC, Smyd3 depletion induced influx of CD8+ T-cells, upregulated PD-L1 and MHC class I molecules, and increased sensitivity to anti-PD-1 therapy. SMYD3 overexpression was associated with decreased CD8 T-cell infiltration in tumor samples from patients with HPV-negative HNSCC and poor response to neoadjuvant pembrolizumab. Overall, these data highlight a previously unreported function of SMYD3 as a master epigenetic regulator of anti-tumor immune response in HPV-negative HNSCC and provide a rationale for translational approaches combining SMYD3 depletion strategies with checkpoint blockade to overcome anti-PD-1 resistance in this devastating disease.

overall_design: For samples VS265-VS279, HN-6 (parental control cells) and 5-3 cells (SMYD3 KO cell line) were grown and exposed to human IFN-β for 24h prior to cell collection. For samples VS7-VS14 and VS748-VS753, HN-6 cells were transfected with control siRNA or siSMYD3 or siUHRF1 for 72h and exposed to human IFN-β for 24h prior to cell collection. For samples VS212-VS217, HN-6 cells were exposed to PBS or SMYD3 targeting ASOs (ASO 081) for 72h and exposed to human IFN-β for 24h prior to cell collection. Two to three biological replicates were generated per condition. RNA was extracted using the Direct-zol RNA miniprep kit (Zymo Research).

first: Vassiliki

last: Saloura

first: Nupur

last: Nigam

first: Benjamin

last: Bernard

first: Samantha

last: Sevilla

first: Sohyoung

last: Kim

first: Mohd

middle: S

last: Dar


title: Rpb9 plays a critical role in global co-transcriptional splicing in mouse ESC (Fraction chrRNA-seq)

status: Public on May 27 2023

city: San Diego

first: Yajing

last: Hao

state: CA

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

type: Expression profiling by high throughput sequencing

summary: To define the function of Rpb9 on co-transcriptional splicing, we used auxin-inducible Rpb9 degron system in mouse embryonic stem cells (mESCs) with auxin treatment for 3 hours to sufficiently deplete Rpb9. To measure co-transcriptional splicing, we fractionated mESCs cells (spiked in with Drosophila S2 cells for data normalization) into cytosolic (Cyt), nucleoplasm (NP), and chromatin/particle (Chr) fractions. We purified total RNA from Chr compartment, depleted ribosomal RNAs, and constructed two independent libraries for RNA-seq, which showed excellent reproducibility.

overall_design: Characterization of co-transcriptional splicing after degradating Rpb9 in mESC cells

first: Changwei

last: Shao

first: Xiang-Dong

last: Fu


title: Identification of miR-151a as a universal endogenous control for exosome cargo normalization in human cancer

city: Madrid

first: Carlos

last: Rodriguez Antolin

address: Paseo de la Castellana

department: Genetics

country: Spain

institute: Hospital La Paz Institute for Health Research

type: Non-coding RNA profiling by high throughput sequencing

summary: The exosomal particles in the blood of cancer patients possess many times more tumor markers than free circulating. Among these elements, miRNAs have great biomedical relevance due to their stability and feasible detection. However, there is not available in the market any reliable endogenous control for the exosomal compartment, nor specific for the miRNA content, preventing the obtainment of standardization measures in cancer liquid-biopsy. In this study, we firstly identified three miRNAs out of a panel of nine potential normalizers that arised from an integrative analysis comparing the global miRNA exosomal profile by miRNA-seq of six lung and ovarian human cancer cell lines under different chemotherapy conditions. Their value as normalizers were also tested in 14 additional human cancer cell lines from different tumor types and after radiotherapy and an alternative chemotherapy treatment. Its translational validation comprised 124 prospective samples, 70 plasma from NSCLC patients, 12 from glioblastoma patients, 10 healthy donors and 16 paired samples from plasma and ascites fluid from ovarian cancer patients. The variability and normalizing properties were tested in comparison with the tissue-origin gold standard miR-16. Our results indicate that miR-151a is constantly represented in the exosomal content with minimal variability compared with miR16 independently of many conditions tested, providing for the first time a universal normalizer for the exosomal compartment that will impact the use of liquid biopsy.

overall_design: miRNA-seq from paired cisplatin-sensitive/resistant Cell line-derived exosomes was used to analyze small RNA expression profiling

first: Julia

last: Jiménez

first: Miranda

last: Burdiel

last: Rodríguez-Antolín

first: Olga

last: Pernía

first: Rocío

last: Rosas-Alonso

first: Ana

last: Sastre-Perona

first: Julian

last: Colmenarejo

first: Alvaro

last: Garcia-Guede

first: Carmen

last: Rodríguez-Jiménez

first: María

middle: D

last: Diestro

first: Virginia

last: Martínez-Marín

first: Oliver

last: Higueras

first: Patricia

last: Cruz

first: Itsaso

last: Losantos-García

first: Javier

last: de Castro

first: Inmaculada

last: Ibáñez de Cáceres


title: Epigenetic silencing by SMYD3 represses tumor intrinsic interferon response in HPV-negative squamous cell carcinoma of the head and neck [ChIP-seq]

first: Vinutha

last: Balachandra

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: For samples VS427, VS435-VS440, VS409-VS415 and VS669-VS674, HN-6 (parental control cells) and 5-3 cells (SMYD3 KO cell line) were exposed to human IFN-β for 24h prior to collection. For VS531 and VS539-VS544, HN-6 cells were transfected with control or SMYD3 targeting siRNAs for 72h and exposed to human IFN-β for 24h prior to collection. Three biological replicates were generated per condition. Cells were then processed using CUT&RUN assays targeting SMYD3 (Abcam 187149), H3K4me3 (EpiCypher, 13-0041) and H4K20me3 (ThermoFisher, MA5-36090).

first: Saloura

last: Vassiliki

first: Nigam

last: Nupur

first: Bernard

last: Benjamin

first: Sevilla

last: Samantha

first: Kim

last: Sohyoung

first: Dar

last: Mohd Saleem


title: IL-17 signalling is critical for controlling subcutaneous adipose tissue wasting and parasite burden during chronic Trypanosoma brucei infection [bulk RNA-seq]

city: Manchester

first: Matthew

middle: Christopher

last: Sinton

state: Greater Manchester

address: Core Technology Facility

department: Division of Immunology, Immunity to Infection and Respiratory Medicine

country: United Kingdom

institute: University of Manchester

summary: In the skin, Trypanosoma brucei colonises the subcutaneous white adipose tissue (WAT) and harbours a pool of parasites competent for forward transmission. The interaction between parasites, adipose tissue, and the local immune system is likely to drive adipose tissue wasting and weight loss observed in cattle and humans infected with T. brucei.  However, mechanistically, this process is not fully understood. Here, using several complementary approaches including mass cytometry by time of flight, bulk and single cell transcriptomics, we found that T. brucei infection drives a local expansion of several IL-17A-producing cells in the murine WAT, including TH17 and V6+ T cells. We also found that global IL-17 deficiency, or mice lacking IL-17 receptor expression specifically on adipocytes, were protected from infection-induced WAT wasting and weight loss. Unexpectedly, we found that abrogation of IL-17 signalling on adipocytes results in higher burden of extravascular parasites in the WAT. Taken together, our study highlights the central role of IL-17 signalling on adipocytes in controlling WAT responses to infection, suggesting that adipocytes are a critical coordinator of the tissue immune response to T. brucei infection.

overall_design: 3T3-L1 preadipocytes were differentiated to an adipocyte lineage before being treated with 100ng of recombinant IL-17A for 24 hours

middle: C

first: Praveena

last: Chandrasegaran

first: Paul

last: Capewell

first: Anneli

last: Cooper

first: Alex

last: Girard

first: John

last: Ogunsola

first: Georgia

last: Perona-Wright

first: Dieudonné

middle: M

last: Ngoyi

first: Nono

last: Kuispond

first: Bruno

last: Bucheton

first: Mamadou

last: Camara

first: Shingo

last: Kajimura

first: Cécile

last: Bénézech

first: Annette

last: MacLeod

first: Juan

middle: F

last: Quintana


title: Maternal rhythm restricts neonatal inflammation via metabolic reprograming of myeloid cells

city: Tianjin

first: Jie

last: Zhou

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

country: China

institute: Tianjin Medical University

summary: Disruption of circadian rhythm during pregnancy produced adverse health outcomes in offspring. However, the role of maternal circadian rhythms in infants’ immunity and their susceptibility to inflammation remains poorly understood. Here we reported that disruption of circadian rhythms in pregnant mice profoundly aggravated the severity of neonatal inflammatory disorders, including necrotizing enterocolitis (NEC) and sepsis. The diminished production of maternal-derived docosahexaenoic acid (DHA) and the impaired immunosuppressive function of myeloid-derived suppressor cells (MDSCs) in neonates played a dominant role in this process. Mechanistically, DHA enhanced the immunosuppressive function of neonatal MDSCs viaPPARγ mediated mitochondrial oxidative phosphorylation. Transfer of MDSCs or perinatal supplementation of DHA relieved neonatal inflammation induced by maternal rhythms disruption. These observations revealed an important role of maternal circadian rhythms in the control of neonatal inflammation via metabolic reprograming of myeloid cells.

overall_design: PMN-MDSCs from Circadian Rhythm Disruption model spleens and Control spleens of neonatal mice (PND7) were subjected to RNA-seq

first: Zhaohai

last: Cui

first: Haixu

last: Xu


title: U2AF1 plays a critical role in global co-transcriptional splicing (Fraction chrRNA-seq)

first: Yajing

last: Hao

summary: In order to measure the impact of U2AF1 on co-transcriptional splicing, we treated HeLa cells with control siRNA or U2AF1 siRNA. To measure co-transcriptional splicing, we fractionated HeLa cells into cytosolic (Cyt), nucleoplasm (NP), and chromatin/particle (Chr) fractions. We purified total RNA from Chr compartment, spiked in with in vitro transcribed EGFP and FireFly luciferase RNA for data normalization, depleted ribosomal RNAs, and constructed two independent libraries for RNA-seq.

overall_design: Characterization of co-transcriptional splcing  after U2AF1 knock-down in Hela cells

first: Changwei

last: Shao

first: Xiang-Dong

last: Fu


title: Impact of tissue source type on gene expression profiles of normal human kidney

status: Public on May 28 2023

city: Groton

first: Seda

last: Arat

state: CT

address: 445 Eastern Point Road

institute: Pfizer

summary: Normal human tissue is critical as a reference control in biomedical research. Yet access to high quality human tissue can be challenging due to clinical, logistical and ethical issues. Possible human normal tissue source types include non-transplantable tissues from organ donors (OD), post-mortem cadaveric tissues (CAD), and surgical resections of normal adjacent tissues (NAT) in cancer patients. But few studies have comprehensively explored the impact of these source types on the biological profile of the tissue. We assembled a panel of human normal kidney tissue from 91 donors representing OD, CAD, and NAT, as well as the matching kidney tumor. Histopathologic and molecular profiles by RNASeq analysis revealed clear differences between tumor and normal samples, regardless of the source type. Among the normal samples, there was a general similarity between source types, with little evidence of a field cancerization effect in the NAT. Differential gene expression and enrichment analyses indicated differences among source types in immune system and inflammatory processes, response to extracellular stimuli, ion transport and metabolic pathways. We conclude that all three normal source types are suitable for reference kidney control samples, but important differences are to be noted for particular research areas and tissue banking strategies.

overall_design: 111 samples (28 from cadaveric, 22 from organ donor, 30 from normal adjacent tissue and 31 matching kidney tumor)

first: Renee

last: Huynh

first: Steven

last: Kumpf

first: Jessie

last: Qian

first: Ahmed

last: Shoieb

first: Richard

last: Virgen-Slane

first: Frank

last: Voigt

first: Zhiyong

last: Xie

middle: L

last: Jakubczak


title: Transcriptome analysis reveals the mechanism of common carp brain injury after exposure to lead

city: Changchun

first: zhang

last: yue

address: xincheng street num 2888

institute: Jilin Agricultural University

summary: The purpose of this study was to clarify the possible mechanism of common carp brain injury after exposure to lead through transcriptome analysis. Transcriptome analysis showed that 2141 differentially expressed genes were identiﬁed. Among these, 502 genes were up-regulated and 1639 genes were down-regulated. Meanwhile, GO enrichment analysis showed Transport, biological_process, DNA-templated (regulation of transcription) and signal transduction contained the most differential genes in the biological process. Furthermore, KEGG pathway enrichment analysis showed Ion channels, GnRH signaling pathway, cell adhesion molecules, Wnt signaling pathway, and calcium signaling pathway were significantly enriched. In addition, 10 differentially expressed genes were selected for qRT-PCR detection, and the results demonstrated that the selected genes exhibited the same trends with the RNA-Seq results, which indicates the transcriptome sequencing data is reliable. In conclusion, the above results provide a theoretical basis for clarifying the relationship between lead exposure and brain injury in common carp and for further studying of the genes related to lead poisoning.

overall_design: we aimed to investigate the effects of lead on brain injury of common carp and clarify the possible mechanism by transcriptome analysis.

first: Yue

last: Zhang


title: ACSS2 Regulates HIF-2α Degradation through the E3-Ubiquitin Ligase MUL1 in Clear Cell Renal Cell Carcinoma

city: Nashville

first: Zachary

last: Bacigalupa

state: TN

address: 1161 21st Ave S

department: Medicine

institute: Vanderbilt University Medical Center

summary: ACSS2 is a key contributor to the acetyl-CoA pool and has a role in supporting biosynthetic processes, as well as acetylation. To investigate the role of ACSS2 in regulating chromatin accessibility in ccRCC, we performed ATAC-seq on 786-O cells treated with DMSO or ACSS2i for 24 hours.

overall_design: We treated 786-O cells with DMSO or 5 µM ACSS2i for 24 hours and performed ATAC-seq to assess changes to accessible regions.

first: Xiang

last: Ye


title: RNA-Seq analysis reveals critical transcriptome changes by sodium butyrate in DN mouse model

city: Chongqing

first: Hansen

last: Yang

state: Chongqing

address: No.1 Medical College Road

department: Department of Cell Biology and Genetics

institute: Chongqing Medical University

summary: Diabetic nephropathy (DN) as a common complication of diabetes is the primary cause of end-stage renal disease. Sodium butyrate (NaB) is a short chain fatty acid in the metabolic products of intestinal bacterium, and its kidney protective effect has been reported in DN. However, its underlying mechanism remains unclear. The aim of the present study was to investigate the effect of NaB on globe transcriptome changes in DN. In our study, eight-week-male db/db mice which were established DN mice were randomly divided into two groups: the DN+NaB group (DN mice treated with NaB, 5g/kg/day) and the DN group (DN mice treated with saline). Also, the normal db/m mice were used as NC group. Further, blood glucose, body weight, urinary microalbumin and urinary creatinine of mice were measured in three groups. Whole-transcriptome analysis was performed by RNA sequencing (RNA-Seq) to evaluate profiling of lncRNAs and messenger RNAs (mRNAs). Bioinformatic analysis was performed to predict the potential NaB-related lncRNAs and genes in DN. The expressions of lncRNAs and mRNAs were tested by quantitative real-time polymerase chain reaction (qRT-PCR) in renal tissues and mesangial cells treated with NaB. The results of the present study demonstrated that NaB ameliorated renal dysfunction in DN mice. Moreover, RNA-Seq results identified that 17 lncRNAs and 180 mRNAs reversely changed in DN+NaB group when compared with those in DN group. Additionally, the integrated co-expression networks of NaB-related lncRNAs revealed these lncRNAs interacted with 155 key mRNAs. The co-expression networks of mRNAs associated to immune response, antigen processing and presentation and acute inflammatory response to antigenic stimulus. The qRT-PCR data showed that eight mRNAs and seven lncRNAs were dysexpressed by NaB in DN mice and mesangial cell under high glucose condition. Furthermore, the co-expression network of inflammation related lncRNAs and mRNAs demonstrated that those 17 reversed lncRNAs and 37 mRNAs also play essential roles in inflammatory response. In summary, the present study suggests that NaB ameliorates diabetes induced renal dysfunction and regulates transcriptome changes in DN. NaB related lncRNA-mRNA may play roles in the protective effect of NaB in DN.

overall_design: RNA-Seq was used to detect the differentially expressed genes among DN mouse (N=4) , normal control (N=4) and DN mouse treated with NaB (N=4) .

first: Yan

last: Sun


title: AIM2 negatively regulate FOXP3 expression in mouse CD4+ T cells

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

summary: Absent in melanoma 2 (AIM2) is a cytosolic dsDNA sensor that has been broadly studied for its role in inflammasome assembly and innate immune defense against intracellular pathogens. However, very little is known about the function of AIM2 in adaptive immune cells. The purpose of this study was to investigate whether AIM2 has a cell-intrinsic role in CD4+ T cell differentiation or function. We found that AIM2 is expressed in both human and mouse CD4+ T cells and that its expression is affected by T cell receptor (TCR) activation. AIM2-deficient (Aim2-/-) mouse CD4+ T cells upregulate the expression of regulatory T cell (Treg)-associated genes, both in unstimulated conditions and after TCR activation. Naïve CD4+ T cells from Aim2-/- mice also show a higher tendency to differentiate into FOXP3+ cells in vitro, while their capacity to differentiate into Th1 or Th17 cells remains unaltered. In agreement with these data, in a T cell transfer model of colitis, Aim2-/- naïve T cells induce ameliorated disease and also display a higher ability to differentiate into FOXP3+ cells. Our results suggest that AIM2 negatively regulates FOXP3 expression and Treg cell differentiation. We show that AIM2 function is not confined to innate immune cells but is also important in adaptive CD4+ T cells. Our data identify AIM2 as a regulator of Treg cell differentiation and therefore as a potential intervention target for restoring T cell homeostasis.

overall_design: Sequencing of mRNA libraries from splenic CD4+ T cells isolated from wild type (C57BL6) and AIM2-deficient mice (Aim2-/-). Cells were either left unstimulated or stimulated with anti-CD3/CD28 antibodies.

first: Beatriz

last: Lozano-Ruiz

first: Claudia

last: Martínez-Cardona

first: David

last: Moreno

middle: R

last: Cortazar

first: Pedro

last: Zapater

first: Rubén

last: Francés

first: José

last: González-Navajas


title: RNA sequencing of  MV4;11 cells harbouring FLT3-ITD mutations

city: Tokyo

first: Kotoko

last: Yamatani

address: Building A 6F, Hongo Bunkyo-ku 2-1-1

country: Japan

institute: Juntendo University

summary: The purpose of the experiment is to investigate whether more co-mutations exists in MV4;11 cells harboring FLT3-ITD/D835 than cells with FLT3-ITD only.

overall_design: We performed RNA-Seq, analyzed mutations and compared cells with or without D835.

first: Yoko

last: Tabe


title: Single-minded 2 is required for left-right asymmetric stomach morphogenesis

city: Raleigh

first: Nirav

last: Amin

state: NC

address: 1060 William Moore Drive

department: Molecular Biomedical Sciences

institute: North Carolina State University

summary: Structural birth defects are the leading cause of infant mortality in the United States. Many of these defects are associated with abnormal anatomical left-right asymmetry. Despite the importance of orienting organs along the left-right (L-R) axis during development, very little is known about the molecular events that control this process. To elucidate the genetic mechanisms that shape the L-R asymmetry of individual organs, we sought to identify genes that are expressed in L-R asymmetric patterns during organ development. To accomplish this goal, we took advantage of the exceptionally large Budgett’s frog (Lepidobatrachus laevis) embryo to profile gene expression by RNA-seq in the left versus right halves of the developing stomach. Using this data, we have constructed a de novo Lepidobatrachus transcriptome and identified ~26,000 unique transcripts with human homology based on reciprocal BLAST analyses. Over 300 transcripts were L-R asymmetrically expressed within the stomach. Among these candidates are some of the few genes already known to play a role in L-R asymmetric development, validating our strategy for L-R gene discovery.

overall_design: A total of 7 biological replicates were used for the left and right halves of stomachs. NNY1-10 were individual stomachs that were dissected and sequenced. NNY11-14 had 5 stomach halves pooled per sample.

first: Nanette

last: Nascone-Yoder


title: SMS2 suppresses hepatocellular carcinogenesis by impairing p85/p110 interaction

city: Shanghai

first: Wenqing

last: Tang

address: 180 Fenglin Road, Xuhui District

institute: Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Disease, Zhongshan Hospital, Fudan University

summary: Phosphoinositide 3-kinase (PI3K) signaling, which requires spatial compartmentalization in plasma membrane micro domains, is aberrantly activated in hepatocellular carcinoma (HCC). As a synthetic enzyme of sphingomyelin, sphingomyelin synthase 2 (SMS2) regulates membrane fluidity and microdomain structure. SMS2 functions in various diseases such as atherosclerosis, and diabetes and lung injury. However, the role of SMS2 in HCC tumorigenesis is unclear. In the present study, we found that SMS2 was substantially reduced in tumor tissues and predicted poor prognosis in HCC patients. Function assays in vitro showed that SMS2 could remarkably prevent cell proliferation, cell cycle, cell migration and invasion. Experiments in vivo revealed that SMS2-deficient mice exhibited more severe carcinogenesis and metastasis induced by diethylnitrosamine/carbon tetrachloride. The result of transcriptome sequencing showed that SMS2 was involved in PI3K/Akt signaling pathway. Further study verified that SMS2 could inhibit the expression of PI3K subunit p110α by promoting the ubiquitination of p110α. SMS2 downregulation changed lipid metabolism and PTEN distribution in lipid raft, attenuated p85α-PTEN interaction, thus promoting p85α-p110α interaction. Finally, we found that loss of SMS2 could inhibiting PTEN localization in lipid rafts. The tumor suppression effect of SMS2 on HCC cells could be rescued by p110α expression. Taken together, our findings not only demonstrates that SMS2 is a prospective tumor suppressor and prognosis indicator in HCC, but also provide understanding of the molecular mechanisms by which PI3K/AKT signaling is activated.

overall_design: we compared the whole genome gene expressions of two different cell lines with and without overexpression of SMS2

first: Yi

last: Zhou

first: Meiyi

last: Li

first: Fansheng

last: Meng

first: She

last: Chen

first: Shuncai

last: Zhang

first: Biwei

first: Ruyi

last: Xue

first: Ling

last: Dong

first: Si


title: Epigenetic silencing by SMYD3 represses tumor intrinsic interferon response in HPV-negative squamous cell carcinoma of the head and neck.

status: Public on May 25 2023

first: Vinutha

last: Balachandra

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

overall_design: Refer to individual Series


title: Cell-Free Plasma MicroRNAs that Identify Patients with Glioblastoma

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

summary: This retrospective multicenter pilot study aims to determine potential cell-free microRNAs (cfmiRs) that identify patients with primary GBM (pGBM) tumors and to monitor Glioblastoma (GBM) recurrence.

overall_design: CfmiRs were detected in pre-operative plasma samples from patients with pGBM (n=32) and recurrent GBM (rGBM, n=13) using the HTG miRNA whole transcriptome assay (WTA) assessing for 2,083 miRs. As controls plasma samples from normal healthy donors (NHD, n=73) were assessed. 265 cfmiRs were found differentially expressed (DE) in plasma samples from pGBM patients compared to NHDs (FDR <0.05). Additionally, we found 179 cfmiRs DE in rGBM, of which 68 cfmiRs were commonly DE in pGBM. Using Random Forest algorithm, specific cfmiR classifiers were found in the plasma of pGBM, rGBM, and both pGBM and rGBM combined. Two common cfmiR classifiers, miR-3180-3p and miR-5739, were found in all of the comparisons. In receiving operating characteristic (ROC) curves analysis for rGBM miR-3180-3p showed a specificity of 87.7% and a sensitivity of 100% (AUC=98.5%); while miR-5739 had a specificity of 79.5% and sensitivity of 92.3% (AUC=90.2%). This study demonstrated that pGBM and rGBM plasma have specific miR-signatures. CfmiR-3180-3p and cfmiR-5739 have potential utility in diagnosing patients with pGBM tumors and monitoring GBM recurrence using a minimally invasive blood assay.

first: Matias

middle: A

last: Bustos

first: Negin

last: Rahimzadeh


title: Targeting sulfation-dependent mechanoreciprocity between matrix and osteoblasts to mitigate bone loss

city: Xi'an

first: Chao

last: Zheng

address: Changle west road

institute: Fourth Military Medical University

summary: Sulfation is a widespread modification for biomolecules so far poorly explored. Through cross phenotype meta-analysis for human bone mineral density up to 426824 participants and phenotypic characterization of multiple mutant mouse lines, we identified a causative role of the sulfate transporter SLC26A2 deficiency in osteoporosis. Ablation of SLC26A2 in osteoblasts caused severe bone loss and accumulation of immature bone cells and elicited a peculiar pericellular matrix (PCM) outcome, undersulfation coupled with decreased stiffness. Consequently, such altered chemophysical properties of PCM disrupted focal adhesion formation of osteoblasts. Based on bulk RNA sequencing and functional assays, we held a mechano-reciprocal tandem inhibition of FAK and YAP/TAZ responsible for impinged osteoblast maturation by SLC26A2 deficiency, where sulfation and stiffness of PCM were compromised by defective sulfate uptake and thus to exert an outside-in impediment to FAK-dependent YAP/TAZ activity required for osteoblast maturation. Moreover, pharmacological abrogation of the Hippo kinases and forced wheel-running concordantly ameliorated SLC26A2-deficient osteoporosis via enforcement of YAP/TAZ activity. Intriguingly, “guilt by association” analysis of single-cell sequencing data suggested coordination between sulfate metabolism, focal adhesion and YAP/TAZ activity during osteoblast-to-osteocyte transition. As seen in ovariectomized mice and patients with osteoporosis, tandem inhibition of FAK and YAP/TAZ apparently engaged in pathology of broader types of osteoporosis beyond SLC26A2 context. Collectively, these data unveil an unanticipated role of sulfation in developmental mechanoreciprocity between matrix and osteoblasts, which could be leveraged to prevent bone loss.

overall_design: To better understand molecular mechanisms underlying disrupted osteoblast maturation caused by SLC26A2 deficiency, we applied bulk RNA sequencing (bulk-seq) to Col2.3kb-Cre; Slc26a2 fl/fl (CKO) and Col2.3kb-Cre; Slc26a2 fl/+ (Control) femoral cortical bone shafts at post natal day 7 (P7).


title: A distinct neurogenomic response to a tradeoff between social challenge and opportunity in male sticklebacks (Gasterosteus aculeatus)

city: Urbana

first: Tina

last: Barbasch

address: 505 S Goodwin Ave

department: Evolution, Ecology, and Behavior

institute: University of Illinois Urbana Champaign

summary: We characterized the behavior and brain gene expression profiles of males confronted by a tradeoff between courtship and territorial defense

overall_design: Male sticklebacks were exposed to a courtship opportunity, a territorial challenge, a courtship opportunity and a territorial challenge together, and a control. The diencephalon and telencephalon of males exposed to each of these treatments was sequenced and used to profile patterns of gene expression

first: Colby

last: Behrens

first: Mira

last: McLain

first: Eric

last: Arredondo

first: Alison

last: Bell


title: Tunica-Specific Transcriptome of Abdominal Aortic Aneurysm

city: Stockholm

first: Joy

last: Roy

address: BioClinicum J8:20, Karolinska University Hospital

department: Department of Molecular Medicine and Surgery

country: Sweden

institute: Karolinska Institutet

summary: Our objective was to map the tunica-specific pathophysiology of AAA

overall_design: Genome-wide expression analysis performed on 246 samples of media and adventitia from thrombus-covered and thrombus-free aspects of the abdominal aortic vessel wall of 76 patients with AAA and 13 organ donor controls.

first: Moritz

last: Lindquist Liljeqvist

first: Rebecka

last: Hultgren

first: Otto

last: Bergman

first: Christina

last: Villard

first: Malin

last: Kronqvist

first: Per

last: Eriksson


title: Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry

city: West Haven

first: Matthew

last: Simon

state: Connecticut

address: 300 Heffernan Dr, 300 Hefferna Dr

institute: Yale University

summary: RNA metabolic labeling using 4-thiouridine (s4U) can be used to capture the dynamics of RNA synthesis and decay. The power of this approach is dependent on appropriate quantification of labeled and unlabeled sequencing reads, which can be compromised by the apparent loss of s4U-labeled reads in a process we refer to as dropout. Here we show that s4U-containing transcripts can be selectively lost when RNA samples are handled under sub-optimal conditions, but that this loss can be minimized using an optimized protocol. We demonstrate a second cause of dropout in nucleotiderecoding and RNA sequencing (NR-seq) experiments that is computational and downstream of library preparation. NR-seq experiments involve chemically converting s4U from a uridine analog to a cytidine analog and the apparent T-to-C mutations are then used to identify the populations of newly synthesized RNA. We show that high levels of T-to-C mutations can prevent read alignment with some computational pipelines, but that this bias can be overcome using improved alignment pipelines. Importantly, kinetic parameter estimates are affected by dropout independent of the NR chemistry employed, and all chemistries are practically indistinguishable in bulk, short-read RNA-seq experiments. Dropout is an avoidable problem that can be identified by including unlabeled controls, and mitigated through improved sample handing and read alignment that together improve the robustness and reproducibiltiy of NR-seq experiments.

overall_design: NR-seq performed in HEK 293T cells with three published nucleotide conversion chemistries. RNA collection and data processing were performed with common protocols and those designed to minimize loss of s4U-labelled RNA and T-to-C mutation containing sequencing reads. All experiments performed in duplicate.

first: Joshua

middle: T

last: Zimmer

first: Isaac

middle: W

last: Vock

first: Jeremy

last: Schofield

first: Lea

last: Kiefer

first: Michelle

middle: H

last: Moon


title: Bulk RNA-seq analyses of mandibular condylar cartilage in a post-traumatic temporomandibular joint osteoarthritis rabbit model

city: New York

first: Ikue

last: Tosa

state: New York

department: College of Dental Medicine

institute: Columbia University

summary: We performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells from post-traumatic temporomandibular joint osteoarthritis model to investigate the signaling pathways critical for cellular functions during  temporomandibular joint osteoarthritis pathology.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and osteoarthritis model in superficial zone cells and condylar cartilage cells from temporomandibular joints.

first: Angela

last: Ruscitto

first: Ziyi

last: Wang

first: Kira

middle: Z

last: Chen

first: Mitsuaki

last: Ono

first: Mildred

last: Embree


title: Mouse microglia express unique miRNA-mRNA networks to facilitate age-specific functions in the developing central nervous system

city: Brisbane

first: Alexander

last: Walsh

state: Queensland

address: QBI Building 79, University of Queensland, St Lucia

country: Australia

institute: University of Queensland


title: Mouse microglia express unique miRNA-mRNA networks to facilitate age-specific functions in the developing central nervous system [mRNA-seq]

summary: To investigate the expression of miRNA/mRNA regulatory networks in a developmental cohort of C57Bl/6 mice. This submission is the mRNA sequencing dataset.

overall_design: Sequenced the miRNAome and mRNAome of primary mouse microglia during brain development and adult homeostasis (three age groups; P6, P15 and 8 weeks). Sequenced and compared small RNA expression in both CD45+ microglial cells and CD45- bulk CNS cells in each sample. mRNA expression was sequenced in CD45+ microglial cells.

first: Michele

last: Binder

first: Brendan

last: E Ansell

first: Sarrabeth

last: Stone

first: Saskia

last: Freytag

first: Trevor

middle: J

last: Kilpatrick


title: Mouse microglia express unique miRNA-mRNA networks to facilitate age-specific functions in the developing central nervous system [smRNA-seq]

summary: To investigate the expression of miRNA/mRNA regulatory networks in a developmental cohort of C57Bl/6 mice. This submission is the miRNA sequencing dataset.


title: Long noncoding RNA expression levels in BXPC-3 cells under different nutritional conditions.

city: WuHan

first: ZHUO

last: WENFENG

address: 湖北省武汉市硚口区航空路13号

institute: The Huazhong University of Science and Technology

summary: In order to explore the relationship between long non-coding RNA expression and EMT in pancreatic cancer under different nutritional conditions, we carried out Microarray-based gene expression analysis.BXPC-3 cells were cultured under three conditions: nutrient-sufficient, low glucose and low glutamine for 48 hours and then long non-coding RNA Microarray-based gene expression analysis was carried out to observe the changes in long non-coding RNA expression, so as to explore the specific mechanism of EMT in pancreatic cancer cells under nutritional stress conditions.

overall_design: Microarray analysis for lncRNAs was conducted with BxPC-3 cells cultured with saturating nutrient medium, Glc- medium and Gln- medium for 48 h.

first: Zhao

last: Gang


title: Relation between TP53 GOF mutation and Osimertinib treatment in EGFR mutant lung cancer

city: Fukuoka

first: RITSU

last: IBUSUKI

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Respiratory Medicine

institute: Kyushu University

summary:
Background: Although TP53 gain-of-function (GOF) mutations promote cancer survival, its effect on EGFR-TKI efficacy remains unclear. We established EGFR-mutant lung cancer cell lines expressing various TP53 genotypes using CRISPR-Cas9 technology and found that TP53-GOF mutant cells develop an early resistance to EGFR-TKI osimertinib.The goal of this study is to elucidate the mechanisms underlying resistance to osimertinib treatment in TP53 GOF mutations through comprehensive gene analysis using RNA-seq with next-generation sequencing (NGS).
Methods: Total RNA was isolated from PC-9 cells overexpressing TP53 R248Q mutation (PC9/p53R248Q: TP53 GOF mutation) and PC-9 cells overexpressing empty vector plasmid (PC9/p53EV: TP53 null) treated with DMSO or osimertinib for 24hours, using the RNeasy Micro Kit , in accordance with the manufacturer’s instructions. RNA samples were quantified by NanoDrop-2000 spectrophotometer, and the quality was confirmed with a 2200 TapeStation. rRNA was removed using MGI Easy rRNA Depletion Kit  according to manufacturer's instructions followed by library construction using MGIEasy RNA Directional Library Prep Set (MGI). MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples. All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) , and RNA sequencing reads were mapped to hg38 using HISAT2 software . Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Results: We explored the functions of specifically upregulated genes in TP53 GOF mutation after osimertinib treatment by KEGG pathway-enrichment analysis and found that the cytokine-cytokine receptor interaction was the most significantly altered pathway. Hallmark pathway analysis identified the TNF-α/NF-κB pathway was significantly enriched. Furthermore, TRRUST analysis showed enhanced activity of transcription factors especially RELA (p65) and NF-kB1.
Conclusions: TP53 GOF mutaion induces osimertinib resistance by activating TNF-α/NF-κB pathway.

overall_design: mRNA profiles of PC9/p53R248Q cells and PC9/p53EV cells treated by osimertinib or DMSO (control) for 24 hours.

first: Ritsu

last: Ibusuki

first: Eiji

last: Iwama


title: The expression profile  analysis of lncRNAs and mRNAs for cervical cancer

city: Guangzhou

first: Xu

last: Xin

address: Jingxi road

institute: southen medical university

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

summary: To further explore the  expression profile of lncRNAs and mRNAs in cervical cancer, six cases of HPV-positive cervical cancer tissues (including three HPV16 and three HPV18 positive patients) and three HPV-negative normal cervical tissues were collected randomly that were confirmed by histopathological. These patients did not accept any local or systemic treatment.

overall_design: We collected three  HPV18, HPV16 and HPV-negative normal cervical tissues from patients separately.

first: JueYu

last: Zhou


title: RNA sequencing of enterocytes differentiated from human iPS cells

city: Yokohama

first: Shoen

last: Kume

address: Kanagawa, Yokohama City Midori Ward Nagatsutacho4259-B1 Building 812

department: Life Science and Technology

institute: Tokyo Institute of Technology

summary: Our RNA-seq results showed that valproic acid (VPA) works synergistically with activated Vitamin D3 (VD3) to enhance the expression of enterocyte-function-related genes in iPS-derived enterocyte-like cells.

overall_design: To elucidate the effect of VPA and VD3 on the differentiation of human iPS cell-derived enterocytes, we performed RNA-seq and analyzed the global expression profile at the maturation stage.

first: Sylvia

last: Leo

first: Yusuke

last: Kato


title: Whole-Transcriptome RNA expression profiling for human normal arterial intimae and advanced atherosclerotic plaques

city: Nanjing

first: Shuwen

last: Cheng

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

summary: To analyze the cause of arterial plaque formation and development, our arteries in patients with normal donors and severe arterial plaques sampling, the transcriptome sequencing, to explore its molecular mechanism.

overall_design: We conducted total RNA sequencing of human normal arterial intimae and advanced atherosclerotic plaques. Totally 6 samples were generated.

first: Ben

last: Li


title: RNA sequencing of enterocytes differentiated from human iPS cells [RNAseq1]

summary: Our RNA-seq results show the changes in gene expression during differentiation and maturation of iPS-derived enterocytes, as well as that treatment during the last stage with Vitamin D3 (VD3) enhanced enterocyte-related gene expression. Caco-2 and RNA from human adult small intestine were also sequenced as comparison.

overall_design: To elucidate the effect of VD3 on the differentiation of human iPS cell-derived enterocytes, we performed RNA-seq and analyzed the global expression profile at each differentiation stage.


title: TXNRD1 drives innate immune response in senescent cells and promotes age-associated inflammation

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Generation of stable integration-free pig induced pluripotent stem cells under WNT-inhibited condition

city: Beijing

first: Jianyong

last: Han

address: 2rd, Yuanmingyuan West Road

department: State Key Laboratory of Agrobiotechnology

institute: China Agricultural University

summary: Genome integration-free pig induced pluripotent stem cells (iPSCs) bring tremendous value in preclinical testing of regenerative medicine, as well as conservation and exploitation of endangered or rare local pig idioplasmatic resources. However, due to a lack of appropriate culture medium, efficient induction and stable maintenance of pig iPSCs with practical value remains challenging. Here, we established an efficient induction system for exogenous gene-independent iPSCs under WNT-inhibited condition previously used for generation of stable pig pre-gastrulation epiblast stem cell lines (pgEpiSCs). WNT suppression was found to play an essential role in establishment of exogenous gene-independent iPSCs. Strikingly, stable integration-free pig iPSCs could be reprogrammed from pig somatic cells using episomal vectors in this cultured condition. The iPSCs had pluripotency features and transcriptome characteristics approximating pgEpiSCs. More importantly, this induction system may be used to generate integration-free iPSCs from elderly disabled rare local pig somatic cells, and the iPSCs could be gene-edited and used as donor cells for nuclear transfer. Our results provide novel insights into potential applications for genetic breeding of livestock species and pre-clinical evaluation of regenerative medicine.

overall_design: Pig iPSCs were obtained in 3i/LAF system. Characterization assays were carried out to prove the pluripotency of pig iPSCs.

first: Qianqian

last: Zhu

first: Dengfeng

last: Gao


title: The enteric nervous system relays psychological stress to intestinal inflammation [SnRNASeq_ENS]

city: Aachen

first: Kai Markus

last: Schneider

address: Pauwelsstraße 30

country: Germany

institute: University Hospital RWTH Aachen

summary: Mental health profoundly impacts inflammatory responses in the body. This is particularly apparent in inflammatory bowel disease (IBD), where psychological stress is associated with disease flares. Here, we discover a critical role for the enteric nervous system (ENS) in mediating the aggravating effect of chronic stress on intestinal inflammation. We find that chronically elevated levels of glucocorticoids drive the generation of an inflammatory subset of enteric glia that promotes monocyte- and TNF-mediated colitis via CSF1. Additionally, glucocorticoids cause transcriptional immaturity in enteric neurons, acetylcholine deficiency, and dysmotility via TGFβ2. We verify the connection between the psychological state, intestinal inflammation, and dysmotility in two cohorts of human IBD patients. Together, these findings offer a mechanistic explanation for the impact of the brain on peripheral inflammation, define the ENS as a relay between psychological stress and gut inflammation, and suggest that stress management could serve as a valuable component of IBD care.

overall_design: WT mice were exposed to 7days of daily restraint stress, dexamethasone injections or control treatment as detailed in the methods section. After 7 days ENS nuclei were isolated  from total colon tissue of stress and control mice.

first: Christoph

last: Thaiss


title: The enteric nervous system relays psychological stress to intestinal inflammation [ScRNASeqCD45seq]

overall_design: WT mice were exposed to 7days of daily restraint stress  or control treatment as detailed in the methods section. After 7 days CD45+ leukocytes were isolated  from total colon tissue of stress and control mice.


title: The enteric nervous system relays psychological stress to intestinal inflammation [ColonBulkseq]

overall_design: WT mice were exposed to 7days of daily restraint stress or control treatment as detailed in the methods section. After 7 days mRNA was isolated from total colon tissue of stress and control mice.


title: TXNRD1 drives innate immune response in senescent cells and promotes age-associated inflammation II

summary: Sterile inflammation, also known as “inflammaging”, is a hallmark of tissue ageing.  Cellular senescence contributes to tissue aging in part through secretion of proinflammatory factors known as senescence-associated secretory phenotype (SASP).  Thioredoxin reductase 1 (TXNRD1) genetic variability is associated with aging and age-associated phenotypes such as late-life survival, activity of daily living, and physical performance at old age. TXNRD1’s role in regulating tissue ageing has been attributed to its enzymatic role in reducing reactive oxygen species.  Here we show that TXNRD1 drives SASP and inflammaging through the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) innate immune response pathway independent of its enzymatic activity

overall_design: RNA-seq of Young and Aged mice, with Aged mice under control and TRi-1 or Auranofin treatment

first: Rugang

last: Zhang

first: Xue

last: Hao


title: Mice with humanized livers reveal the involvement of hepatocyte circadian clocks in the phase entrainment of rhythmic behavior and physiology

city: Lausanne

first: Cédric

last: Gobet

address: EPFL

country: Switzerland

institute: EPFL

summary: The circadian clock represents an evolutionarily acquired gene network that synchronizes physiology to anticipate environmental changes caused by the succession of day and night. While most mammalian cells have a circadian clock, their synchronization depends on a central pacemaker located in the suprachiasmatic nuclei (SCN) of the hypothalamus that integrates light signals. While peripheral organs can be also synchronized by feeding cues and can be uncoupled from the central pacemaker, no impact of peripheral organs on the central clock has been yet observed. Here, we used a mouse chimeric model in which mouse hepatocytes have been replaced by human hepatocytes that have different circadian and signaling properties to characterize such potential feedback. Remarkably, we observed that liver humanization rewired the liver diurnal gene expression and advance the circadian clock by approximately 4 hours. Strikingly, this phase advance was also observed in the muscle and for the entire rhythmic physiology of the animals, with an impact of human hepatocytes on the circadian function of the central clock. Like mice with a deficient central clock, the humanized animals shifted their physiology more rapidly to the light phase under day feeding. This data prompt to reconsider the role of peripheral clocks on the central pacemaker and offers new perspective to understand the impact of diseased organs on the global circadian physiology.

overall_design: RNA-seq from chimeric mice implemented with mouse/human hepatocytes, sampled around the clock in liver, muscle, arcuate nucleus, and suprachiasmatic nucleus.

first: Anne-Sophie

last: Delbès

first: Mar

last: Quinones

first: Julien

last: Castel

first: Raphaël

middle: G

last: Denis

first: Jeremy

last: Berthelet

first: Benjamin

last: Weger

first: Etienne

last: Challet

first: Aline

last: Charpagne

first: Sylviane

last: Metairon

first: Julie

last: Piccand

first: Marine

last: Kraus

first: Bettina

last: Rohdes

first: John

last: Bial

first: Elisabeth

last: Wilson

first: Lise-Lotte

last: Vedin

first: Mirko

middle: E

last: Minniti

first: Matteo

last: Pedrelli

first: Paolo

last: Parini

first: Frédéric

last: Gachon

first: Serge

last: Luquet


title: Stereopure phosphoryl guanidine backbone chemistry increases the potency and durability of gene silencing by RNA interference

city: Cambridge

first: Jigar

last: Desai

state: MA

address: 733 Concord Avenue

institute: Wave Life Science

summary:
To investigate the potential of "off target" of RNAi knockdown, primary mouse hepatocytes were treated with molecules targeting Ttr.
We then performed gene expression profiling analysis using data obtained from RNA-seq of cell at two different doses along with an untreated control.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary mouse hepatocytes cells of RNAi targeting Ttr.

first: Wei

last: Liu

first: Naoki

last: Iwamoto

first: Subramanian

last: Marappan

first: Khoa

last: Luu

first: Snehlata

last: Tripathi

first: Erin

last: Purcell-Estabrook

first: Juili

last: Shelke

first: Himali

last: Shah

first: Anthony

last: Lamattina

first: Qianli

last: Pan

first: Brett

last: Schrand

first: Frank

last: Favaloro

first: Mugdha

last: Bedekar

first: Arindom

last: Chatterjee

first: Paloma

last: Giangrande

first: Tomomi

last: Kawamoto

first: Genliang

last: Lu

first: Jake

last: Metterville

first: Milinda

last: Samaraweera

first: Priyanka

middle: S

last: Prakasha

first: Hailin

last: Yang

first: Yuan

last: Yin

first: Michael

last: Byrne

first: Pachamuthu

last: Kandasamy

first: Chandra

last: Vargeese


title: The CRISPR Screen sequencing raw data

first: Zhe

last: Ma

state: JS

address: Tonwei Road No.1

institute: nanjing agricultural university

summary: The hBMEC CRISPR/Cas9 library was seeded in eight T225 flasks with 2 × 107 cells each and incubated for 3 days. The hBMECs doubled every 3 days, generating a total of 3.2 × 108 cells, which were divided into four parts, yielding 8 × 107 cells per experimental condition (~1,000× coverage per perturbation in each library). A quarter of the cells were used as the input library and the remaining three quarters for SzM cytotoxicity screens. The cell libraries were treated with purified SzM protein diluted in DMEM (10% FBS) at a final concentration of 50 μg/ml for 48 hr; when ~50% cells were dead, the surviving cells were out grown in fresh DMEM (10% FBS) without SzM protein. These cells were divided into two parts, one part for genomic DNA extraction, and the other for the next round of screening. The same treatment with 50 μg/ml purified SzM protein for 48 hr was used in the 2nd round and the 3rd rounds, using the same protocol outlined above. After the 3rd round, all cells were harvested for genomic DNA extraction.

overall_design: Genomic DNA was obtained from the input  hBMEC CRISPR/Cas9 library and after each of the three rounds of screening with SzM protein,  the Blood and Cell Culture DNA Maxi Kit. PCR was used to amplify sgRNA sequences and the products were sequenced for amplicon sequencing analysis by the Novegene Co., Ltd.

first: Fei

first: Mingli

last: Zhu


title: miRNA expression profiling for human normal arterial intimae and advanced atherosclerotic plaques

first: Shuwen

last: Cheng

summary: To analyze the cause of arterial plaque formation and development, our arteries in patients with normal donors and severe arterial plaques sampling, the transcriptome sequencing, to explore its molecular mechanism. This part including the quantification of miRNA.

overall_design: We conducted miRNA sequencing of human normal arterial intimae and advanced atherosclerotic plaques. Totally 6 samples were generated.

first: Ben

last: Li


title: The enteric nervous system relays psychological stress to intestinal inflammation

first: Kai Markus

last: Schneider

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

overall_design: Refer to individual Series

first: Christoph

last: Thaiss


title: TXNRD1 drives innate immune response in senescent cells and promotes age-associated inflammation I

first: Priyankara

last: Wickramasinghe

overall_design: RNA-seq of growing and senescent cells in control and TXNRD1 inhibited conditions

first: Rugang

last: Zhang

first: Xue

last: Hao


title: Analysis of LPS-induced gene expression of OTULIN-deficient murine macrophages by RNA sequencing

status: Public on May 24 2023

city: Ghent

first: Yannick

last: Gansemans

address: Ottergemsesteenweg 460

department: Pharmaceutical Sciences

country: Belgium

institute: Ghent University

summary: In order to unravel the role of the linear deubiquitinase OTULIN in LPS-induced gene expression in macrophages, we performed RNA-sequencing on primary bone marrow-derived macrophages of mice lacking OTULIN selectively in myeloid cells. Myeloid cell-specific OTULIN knock-out mice develop an auto-inflammatory phenotype and macrophages derived from these mice display increased LPS-induced inflammasome activation and cell death. Through analysing LPS-induced gene expression analyses on OTULIN-deficient macrophages we aimed to identify signalling pathways and genes that regulate inflammasome activation and cell death in these cells, in order to get new insights on the molecular events that regulate the development of autoinflammation in myeloid cell specific OTULIN-deficient mice.

overall_design: RNA was sequenced from BMDMs from Otulin floxed mice (WT) and from Otulin floxed mice carrying a Cre recombinase under the LysM-promotor (KO) at 0, 3, 6, 12 and 24 hrs post LPS treatment. Four biological replicates were included per genotype.

first: Maria

last: Doglio

first: Filip

last: Van Nieuwerburgh

first: Andy

last: Wullaert


title: Spatially informed gene signatures for response to immunotherapy in Melanoma

city: New Haven

first: Thazin

middle: N

last: Aung

address: 310 Cedar St

department: Pathology

summary: Gene signatures have been shown to predict the response/resistance to immunotherapies but with only modest accuracy. Reduction in this precision might be due to the lack of spatial information which prevents the ability from distinguish tumor from tumor-microenvironment (TME) genes. Here we collected gene expression data spatially from three compartments (CD68+macrophages, CD45+leukocytes and S100+tumor cells) of 59-immunotherapy-treated melanoma specimens using Digital Spatial Profiling-Whole Transcriptome Atlas. We developed a computational pipeline to discover compartment-specific gene signatures and determine if adding spatial information can improve patient stratification. We achieved AUC≥0.90 for CD45, AUC≥0.94 for CD68, and AUC≥0.86 for S100B signatures, whereas AUC≥0.70 for pseudo-bulk () signature. Cross-testing in different compartments (e.g., CD45 signature in CD68 and S100B compartments) showed poor performance indicating compartment-specificity. Our novel spatial S100B signature showed the best performance with AUC≥0.80 in the validation cohort (N=46). Testing our signatures in computationally deconvolved pseudo-compartments revealed lower AUCs. We conclude that the spatially defined compartment signatures utilize tumor and TME-specific information, leading to more accurate prediction of treatment outcome, and thus merit prospective clinical

sample_organism:
Homo sapiens
unidentified

platform_organism:
Homo sapiens
unidentified

overall_design: Using DSP-WTA, we generated the first spatial transcriptomic map from pretreatment samples of 59 melanoma patients (discovery cohort) treated with ICIs (pembrolizumab; PEMBRO, nivolumab; NIVO, or ipilimumab plus nivolumab; IPI+NIVO), who had unresectable stage III or IV melanoma at the time of treatment. Our aim was to understand the spatial gene expression enrichment within the tumor and TME and to develop spatially defined compartment-specific gene signatures that would enable us to predict immunotherapy outcomes. We built a computational pipeline to develop robust compartmentalized signature models for analyzing compartment/cell type-specific WTA data that uniquely provided differentially expressed (DEX) genes in spatially defined molecular compartments compared to bulk RNA-seq observations.

first: Jonathan

last: Warrell

first: Mark

last: Gerstein

first: David

last: Rimm


title: Effect of low serum culture condition on gene expression of Lewis tumor cells

city: Wuhan, China

first: Xiao

last: Yang

state: 湖北省

address: 武汉市江汉区马场路109号协和医院肿瘤中心

institute: Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

summary: To understand the changes after low serum culturing at the transcriptional level, we performed RNA sequencing (RNA-seq) transcriptomic profiling under normal (10% FBS) and low-serum (2% FBS) conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Lewis cells under normal or low serum culture conditions.

first: Yajie

last: Sun

first: Yan

last: Hu


title: MicroRNA Control of the Myogenic Cell Transcriptome and Proteome: The Role of miR-16

city: Fayetteville

first: Francielly

last: Morena da Silva

state: AR

address: 155 Stadium Dr

institute: University of Arkansas

summary:
To investigate the role of miR-16 in myogenic cells and whether it has consequences for muscle developmental growth, exercise-induced hypertrophy, and regenerative repair after injury, all of which rely on myogenic progenitors.
We performed gene expression profiling analysis using data obtained from miRNA-seq of 2 different conditions.

overall_design: Comparative gene expression profiling analysis of miRNA-seq data for C2C12 myoblasts treated with miR-16 knockdown vs empty vector control.

first: Seongkyun

last: Lim

last: Lee

first: Pieter

last: Koopmans

first: Ivan

last: Vechetti

first: Ferdinand

last: von Walden

first: Nicholas

middle: P

last: Greene

first: Kevin

last: Murach


title: Effect of Tet2 deletion on gene expression in mice

city: Su zhou

first: Xingyun

last: Xu

address: Ren ai Street

institute: Soochow University

summary:
To investigate the effect of Tet2 on gene expression, we established Nestin Cre+ Tet2lox/lox (Tet2 cKO) mice and Nestin Cre- Tet2lox/lox (WT) mice , collected their habenular tissue, and compared the differential gene expressions at mRNA levels.
We then performed gene expression profiling analysis using data obtained from RNA-seq in the habenular of 2-month mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in the habenular of Tet2 cKO mice and WT mice, n=3.

first: Hang

last: Zhou

first: Hainan

last: Wu

first: Zhigang

last: Miao

first: Bo

last: Wan

first: Haigang

last: Ren

first: Wei

last: Ge

first: Guang-Hui

last: Wang

first: Xingshun


title: RNA-Seq in HepG2-shNC and HepG2-shLINC01977 cells

first: Anliang

last: Xia

address: 321 Zhongshan Road

summary: Total RNA was extracted from HepG2 cells with sh-NC (n = 3) or sh-LINC01977 (n = 3). RNA samples were analyzed by RNA sequencing based on the manufacturer’s protocols. Briefly, Illumina HiSeq 4000 platform was used to sequence the RNA samples for the subsequent generation of raw data. R package was utilized to select genes with significantly differential expression based on fold change ≥2.0 and P≤0.05 between sh-NC and sh-LINC01977 cells. KEGG pathway and GSEA enrichment analysis were used for functional pathway analysis.

overall_design: mRNA profiles of HepG2-shNC and HepG2-shLINC01977cells


title: Transcriptome analysis of three barley varieties in response to barley yellow mosaic disease

city: Yangzhou

first: Rugen

address: 88 South Daxue Road, Yangzhou, Jiangsu Province

department: Agricultural College

institute: Yangzhou university

summary: We used a transcriptome sequencing approach to analyze different expression levels of three barley varieties under both infected and uninfected conditions

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BaYMV and/or BaMMV-infected and disease-resistant barley leaves

first: Mengna

last: Zhang

first: Yi

last: Hong

first: Juan

last: Zhu

first: Yuhan

last: Pan

first: Hui

first: Chao

last: Lv

first: Baojian

last: Guo

first: Feifei


title: Semaphorin 4B is an ADAM17-cleaved adipokine that inhibits adipocyte differentiation and thermogenesis

city: Belfast

first: Colin

last: Adrain

address: 97 Lisburn Road

institute: Queen's University Belfast

summary:
Objective: The metalloprotease ADAM17 (also called TACE) plays fundamental roles in homeostasis by shedding key signaling molecules from the cell surface. Although its importance for the immune system and epithelial tissues is well-documented, little is known about the role of ADAM17 in metabolic homeostasis. The purpose of this study was to determine the impact of ADAM17 expression, specifically in adipose tissues, on metabolic homeostasis.
Methods:
We used histopathology, molecular, proteomic, transcriptomic, in vivo integrative physiological and ex vivo biochemical approaches to determine the impact of adipose tissue-specific deletion of ADAM17 upon adipocyte and whole organism metabolic physiology.
Results: ADAM17adipoq-cre mice exhibited a hypermetabolic phenotype characterized by elevated energy consumption and increased levels of adipocyte thermogenic gene expression. On a high fat diet, these mice were more thermogenic, while exhibiting elevated expression levels of genes associated with lipid oxidation and lipolysis. This hypermetabolic phenotype protected mutant mice from obesogenic challenge, limiting weight gain, hepatosteatosis and insulin resistance. Activation of beta-adrenoceptors by the neurotransmitter norepinephrine, a key regulator of adipocyte physiology, triggered the shedding of ADAM17 substrates, and regulated ADAM17 expression at the mRNA and protein levels, hence identifying a functional connection between thermogenic licensing and the regulation of ADAM17. Proteomic studies identified Semaphorin 4B (SEMA4B), as a novel ADAM17-shed adipokine, whose expression is regulated by physiological thermogenic cues, that acts to inhibit adipocyte differentiation and dampen thermogenic responses in adipocytes. Transcriptomic data showed that cleaved SEMA4B acts in an autocrine manner in brown adipocytes to dampen the expression of genes involved in thermogenesis, adipogenesis, and lipid uptake, storage and catabolism.
Conclusion: Our findings identify a novel ADAM17-dependent axis, regulated by beta-adrenoceptors and mediated by the ADAM17-cleaved form of SEMA4B, that modulates energy balance in adipocytes by inhibiting adipocyte differentiation, thermogenesis and lipid catabolism.

overall_design: The samples for the RNA seq are primary adipocytes differentiated from immortalised preadipocytes obtained from the interscapular brown adipose tissue of wildtype C57BL/6J mice. The preadipocytes were transduced with empty vector (Plex) or truncated (soluble) semaphorin 4B. Matured adipocytes differentiated from these preadipocytes (Empty vector and truncated sema4B) were thereafter treated with or without the adrenergic receptor agaonist, norepinephrine. Each condition had 3 technical replicates

first: A

last: Amin

first: C

first: S

last: Maguire


title: Dedifferentiation-derived neural stem cells exhibit perturbed temporal progression

city: Hobart

first: Owen

last: Marshall

state: Tas

address: 17 Liverpool St

institute: Menzies Institute for Medical Research

summary: One of the key regulatory mechanisms of brain size and neuronal diversity is through control of NB identity via cell fate maintenance. Dedifferentiation is the reversion of differentiated cells to a stem cell like fate, whereby, the gene expression program of mature cells is altered and genes associated with multipotency are expressed. Beyond the fact that misexpression of these factors and pathways caused the formation of ectopic NBs, whether these dedifferentiated NBs faithfully produce the correct number and types of neurons or glial cells, or undergo timely terminal differentiation, has not been assessed. These characteristics are key determinants of overall CNS size and function, thus are important parameters when considering whether dedifferentiation leads to tumourigenesis or can be appropriately utilized for regenerative purposes. Appropriate terminal differentiation as well as neuronal diversity are key characteristics of NSCs, and are specified through temporal patterning of the NSCs driven by the successive expression of temporal transcription factors (tTFs). In this study, we found that ectopic NSCs induced via bHLH transcription factor Deadpan (Dpn) expression in the optic lobes of the developing Drosophila CNS fail to undergo appropriate temporal progression, where they express mid-tTF, Sloppy-paired 1 (Slp-1) at the expense of late-tTF Tailless (Tll); consequently generating an excess of Twin of eyeless (Toy) positive neurons and fewer Reversed polarity (Repo) positive glial cells. Dpn overexpression also resulted in stalled progression through the cell cycle, and a failure to undergo timely terminal differentiation. Mechanistically, DamID studies demonstrated that Dpn directly binds to both Dichaete (D), a Sox-box transcription factor known to repress Slp-1, as well as a number of cell cycle genes. Promoting cell cycle progression or overexpression of D were able to re-trigger the progression of the temporal series in dedifferentiated NBs, restoring both neuronal diversity and timely NB terminal differentiation.

overall_design: Targeted DamID-seq (TaDa) for Dpn 3rd instar larval neuroblasts (neural stem cells, NSCs) with Dam-only control; and NanoDam for Dpn in medulla neuroblasts, with corresponding w1118 genetic background control; two replicates per sample.

first: John

last: McMullen

first: Louise

middle: Y

last: Cheng


title: Circadian transcriptomic analysis of mouse liver

city: Lille

first: Alexandre

last: Berthier

address: U1011, Bâtiment J&K, Bd du Pr Leclerc

country: France

institute: Inserm

summary:
Determination, using microarrays, of the mouse hepatic global programme of gene expression variations around the clock when animals had ad libitum food access
The unique functional versatility of the liver is paramount for the organism homeostasis.  Both liver development and adult life are controlled by tightly regulated transcription factor networks, among which nuclear receptors (NRs) regulate essential functions of parenchymal and nonparenchymal cells. Acting as transcription factors sensitive to extracellular cues such as steroidal hormones, lipid metabolites, xenobiotics… and modulated by intracellular signaling pathways, NRs orchestrate many aspects of hepatic physiology.  While liver functional zonation and adaptability to fluctuating conditions are known to rely on a sophisticated cellular architecture, the exact functions of NRs in liver cell types remain poorly characterized. As a first step toward the accurate mapping of NR functions in mouse liver, we characterized their levels of expression in whole liver as a function of time and diet, and explored NRs isoform expression in hepatocytes, cholangiocytes, Kupffer cells, hepatic stellate cells and liver sinusoidal cells.  In addition, we leveraged liver single cell RNAseq studies to provide here an up-to-date compendium of NR expression in mouse liver in space and time.

overall_design: All time points were analyzed in triplicats

first: Céline

last: Gheeraert

first: Philippe

last: Lefebvre


title: Extracellular succinate induces spatially organized biofilm formation in Clostridioides difficile

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

summary: we report that succinate, a metabolite abundantly produced by the dysbiotic gut microbiota, induces in vitro biofilm formation of C. difficile  strains. We characterized the morphology and spatial composition of succinate- induced biofilms, and compared to non-induced or deoxycholate-induced biofilms, biofilms induced by succinate are significantly thicker, structurally more complex, and poorer in proteins and exopolysaccharides (EPS).

overall_design: Total RNA was extracted from 4 independent biological replicates of 630 C. difficile strains at 4 conditions with 240µM Deoxycholate for the 1687 mutant and the wild type strains and with plasmid empty or that contains the 1687 gene.

first: Emile

last: Auria

first: Juliana

last: Da Fonseca

first: Marc

last: Monot


title: Pre- and post-sexual maturity liver-specific ERα knockout does not impact hepatic mitochondrial function or steatosis but does alter gene expression

city: College Station

first: Kartik

last: Shankar

email: kartik.shankar@cuanschutz.edu, kartikster@gmail.com, kartik.shankar@usda.gov, kartik.shankar@ag.tamu.edu

state: TX

address: 498 Olsen Blvd TAMU 2250 TAMU 2250

department: RAFSRU

institute: USDA ARS

summary: Compared to males, premenopausal women and female rodents are protected against hepatic steatosis and present with higher functioning mitochondria (greater hepatic mitochondrial respiration and reduced H2O2 emission). Despite evidence that estrogen action mediates female protection against steatosis, mechanisms remain unknown. Here we validated a mouse model with inducible reduction of liver ERα (LERKO) via AAV Cre. We phenotyped the liver health and mitochondrial function of LERKO mice (n=10-12 per group) on a short-term high-fat diet (HFD), and then tested if timing of LERKO induction at 2 timepoints (sexually immature: 4 wks old (n=11 per group) vs. sexually mature: 8-10 wks old (n=8 per group)) would impact HFD-induced outcomes. We opted for an inducible LERKO model due to known estrogen-mediated developmental programming, and report both receptor and tissue specificity with our model. Control mice were ERαfl/fl receiving AAV with GFP only. Results show that there were no differences in body weight/composition or hepatic steatosis in LERKO mice with either short-term (4 wk) or chronic (8 wk) high-fat feeding. Similarly, LERKO genotype nor timing of LERKO induction (pre vs post sexual maturity) did not alter hepatic mitochondrial O2 and H2O2 flux, coupling, or OXPHOS protein. Transcriptomic analysis showed that hepatic gene expression in LERKO was significantly influenced by developmental stage. Together, these studies suggest that hepatic ERα is not required in female protection against HFD-induced hepatic steatosis nor does it mediate sexual dimorphism in liver mitochondria function.

overall_design: RNA was extracted from liver tissue from individual mice in four groups (sexullay immature and mature, LERKO and flox mice, n = 4 per group)

last: Thyfault

first: Kelly

last: Fuller


title: Transcriptomic responses in the blood and sputum of cigarette smokers compared to e-cigarette vapers

city: Chicago

first: Adam

last: Williams

state: Ilinois

address: 240 East Huron

department: Department of Medicine, Allergy and Immunology

institute: Northwestern University

summary: Objectives: To identify transcriptomic differences in the blood and sputum of e-cigarette users compared to conventional cigarettes smokers and healthy controls and describe biological pathways affected by these tobacco products. Methods: Cross-sectional analysis of whole blood and sputum RNA-sequencing data from 8 smokers, 9 e-cigarette users (e-cigs) and 4 controls. Weighted gene co-network analysis (WGCNA) identified gene module associations. Ingenuity Pathway Analysis (IPA) identified canonical pathways associated with tobacco products. Main Results: In blood, a three-group comparison showed 16 differentially expressed genes (DEGs); pair-wise comparison showed 7 DEGs between e-cigs and controls, 35 DEGs between smokers and controls, and 13 DEGs between smokers and e-cigs. In sputum, 438 DEGs were in the three-group comparison. In pair-wise comparisons, there were 2 DEGs between e-cigs and controls, 270 DEGs between smokers and controls, and 468 DEGs between smokers and e-cigs. Only 2 genes in the smokers vs. control comparison overlapped between blood and sputum. Most gene modules identified through WGCNA associated with tobacco product exposures also were associated with cotinine and exhaled CO levels. IPA showed multiple canonical pathways altered by conventional smoking but none by e-cigarette use. Conclusion: Cigarette smoking and e-cigarette use led to transcriptomic changes in both blood and sputum. However, conventional cigarettes induced much stronger transcriptomic responses in both compartments.

overall_design: Cross-sectional with 23 samples from blood and 23 samples from induced sputum

first: Mario

last: Perez

first: Marina

last: Yurieva

first: Spandana

last: Poddutoori

first: Eric

middle: M

last: Mortensen

first: Laura

last: Crotty Alexander


title: RANK+TLR2+ Myeloid Subpopulation Converts Autoimmune to Joint Destruction in Rheumatoid Arthritis

city: Baltimore

first: Kathleen

last: Noller

state: MD

address: 3400 N. Charles Street

institute: Johns Hopkins University

summary: Joint destruction is the major clinic burden in patients with rheumatoid arthritis (RA). It is unclear, though, how this autoimmune disease progresses to the point of deterioration of the joint. Here, we report that in a mouse model of RA the upregulation of TLR2 expression and its a(2,3) sialylation in RANK+ myeloid monocytes mediate the transition from autoimmunity to osteoclast fusion and bone resorption, resulting in joint destruction. The expression of a(2,3) sialyltransferases were significantly increased in RANK+TLR2+ myeloid monocytes, and their inhibition or treatment with a TLR2 inhibitor blocked osteoclast fusion. Notably, analysis of our single-cell RNA-sequencing (scRNA-seq) libraries generated from RA mice revealed a novel RANK+TLR2- subset that negatively regulated osteoclast fusion. Importantly, the RANK+TLR2+ subset was significantly diminished with the treatments. Moreover, the RANK+TLR2- subset could differentiate into a TRAP+ osteoclast lineage, but the resulting cells did not fuse to form osteoclasts. Our scRNA-seq data showed that Maf is highly expressed in the RANK+TLR2- subset, and the a(2,3) sialyltransferase inhibitor induced Maf expression in the RANK+TLR2+ subset. The identification of a RANK+TLR2- subset provides a potential explanation for TRAP+ mononuclear cells in bone and their anabolic activity. Further, TLR2 expression and its a(2,3) sialylation in the RANK+ myeloid monocytes could be effective targets to prevent autoimmune-mediated joint destruction.

overall_design: Intestinal GCs of the RedMUC298trTg mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of mCherry signal and analyzed using scRNAseq.

first: Zhang

last: Weixin

first: Noller

last: Kathleen

first: Zhen

last: Gehua

first: Crane

last: Janet

first: Wan

last: Mei

first: Cahan

last: Patrick

first: Cao

last: Xu


title: Cell type and age-dependent effects of Brap loss of function on cerebral cortical gene expression

first: Jayasri

last: Nanduri

state: IL

address: 5841 S. Maryland Avenue

institute: University of Chicago

summary: To determine the impact of Brap loss of function on cellular senescence in cerebral cortex, we performed gene expression profiling analysis of mice with Brap conditional deletions in neural progenitors, postnatal neurons, and vascular endothelium cells, respectively. To understand the premature death caused by Brap conditional deletions in neural progenitors or neurons, we also analyzed mice at two different ages.

overall_design: Comparative gene expression profiling analysis of cerebral cortical RNA-seq data of mice with Brap conditional deletions in neural progenitors, postnatal neurons, or vascular endothelium cells and their wild type-like control littermates at 3 months of age.  Comparative gene expression profiling analysis of cerebral cortical RNA-seq data of mice with Brap conditional deletions in neural progenitors and their wild type-like control littermates at 10 months of age.

first: Yuanyi

last: Feng


title: Circadian transcriptomic analysis of mouse liver during a time restricted feeding

first: Alexandre

last: Berthier

summary:
Determination, using microarrays, of the mouse hepatic global programme of gene expression variations around the clock when animals had food access restricted to the active periode (ZT12 to ZT24)  after a 11 days training periode
The unique functional versatility of the liver is paramount for the organism homeostasis.  Both liver development and adult life are controlled by tightly regulated transcription factor networks, among which nuclear receptors (NRs) regulate essential functions of parenchymal and nonparenchymal cells. Acting as transcription factors sensitive to extracellular cues such as steroidal hormones, lipid metabolites, xenobiotics… and modulated by intracellular signaling pathways, NRs orchestrate many aspects of hepatic physiology.  While liver functional zonation and adaptability to fluctuating conditions are known to rely on a sophisticated cellular architecture, the exact functions of NRs in liver cell types remain poorly characterized. As a first step toward the accurate mapping of NR functions in mouse liver, we characterized their levels of expression in whole liver as a function of time and diet, and explored NRs isoform expression in hepatocytes, cholangiocytes, Kupffer cells, hepatic stellate cells and liver sinusoidal cells.  In addition, we leveraged liver single cell RNAseq studies to provide here an up-to-date compendium of NR expression in mouse liver in space and time.

first: Céline

last: Gheeraert

first: Manjula

last: Vinod

first: Philippe

last: Lefebvre


title: Single Cell RNA-Sequencing Identifies ferroptotic differences of alveolar macrophages in COPD

city: Chengdu

first: Yi

last: Li

state: Sichuan

address: 88# Keyuan South Road, Hi-Tech District

institute: West China Hospital

summary: Chronic obstructive pulmonary disease (COPD) is currently the fourth leading cause of morbidity and mortality in the world and is predicted to be the third leading cause of death. It is characterized by chronic airway inflammation, lung destruction and remodeling, resulting in irreversible airflow obstruction. We utilized single cell RNA-sequencing (scRNA-Seq) to identify ferroptotic differences and associated biological processes involved in the pathogenesis of COPD. We performed scRNA-Seq on lung tissue obtained from donors with non-COPD and mild-to-moderate COPD to identify disease-related genes within different cell types. We identified two populations of alveolar macrophages (AMs) in the human lung that were dysregulated in COPD patients. We discovered that M2-like AMs modulate susceptibility to ferroptosis by disrupting lipid and iron homeostasis both in vivo and in vitro. The discrepancy in sensitivity to ferroptosis can be determined and regulated by HO-1. In contrast, M1-like AMs showed the ability to attenuate oxidative stress and exert resistance to ferroptosis. In addition, the expression of genes within M2-like AMs is also involved in defects in phagocytosis and lysosome distortion. Present scRNA-seq transcriptomic analysis provides a rich data source to further explore lung health and disease, and the development of therapeutic strategies specifically targeting ferroptosis-sensitive alveolar macrophages might be used to develop therapeutic targets..

overall_design: Examination of expression profiling at single-cell level between non-COPD, mild and moderate COPD.

first: Zhoufeng

last: Wang

first: Li

last: Zhang

first: Weimin


title: DEREGULATED INTRACELLULAR PATHWAYS DEFINE NOVEL MOLECULAR TARGETS FOR HBV-SPECIFIC CD8 T CELL RECONSTITUTION IN CHRONIC HEPATITIS B

city: Parma

first: Marco

last: Morselli

state: Parma

address: Parco Area delle Scienze, 23/A

country: Italy

institute: University of Parma

summary:
Background and aims: In chronic HBV infection elevated ROS levels by dysfunctional mitochondria can cause increased protein oxidation, proteostasis engulfment and DNA damage in exhausted virus-specific CD8 T cells. Aim of this study was to understand how these defects are mechanistically interconnected, to further elucidate T cell exhaustion pathogenesis and to design novel T cell-based therapies.   Methods: DNA damage and DNA repair mechanisms, including parylation, CD38 expression, histone acetylation and telomere length were studied by flow cytometry in dextramer-stained HBV-specific CD8 T cells from chronic HBV patients. FLU-specific CD8 cells from the same patients and healthy subjects served as controls. Correction of intracellular signaling alterations and improvement of anti-viral T cell functions by the NAD precursor NMN and by CD38 inhibition, was assessed by fluorescent probes and antibodies in flow cytometry  Results: Elevated DNA damage was associated with defective DNA repair processes, including NAD-dependent parylation, in HBV-specific CD8 cells of chronic HBV patients. NAD depletion in these patients was indicated by the overexpression of CD38, the major NAD consumer, and by the significant improvement of DNA repair mechanisms, mitochondrial and proteostasis functions and epigenetic regulation by NAD supplementation, which could also improve the overall HBV-specific antiviral CD8 T cell function.  Conclusions: Our study delineates a model of CD8 T cell exhaustion whereby multiple functionally interconnected intracellular defects, including telomere shortening, are causally related to NAD depletion suggesting similarities between T cell exhaustion and cell senescence. Correction of these deregulated intracellular functions by NAD supplementation can also restore anti-viral CD8 T cell activity and thus represents a promising potential therapeutic strategy for chronic HBV infection.
Gene expression profiling analysis using data derived from low input RNA-seq of  patients' virus-specific CD8 T cells either upon in vitro culture or ex-vivo isolated from total PBMCs

overall_design: Comparative gene expression profiling analysis of RNA-seq in chronic hepatitis B patients. Differences in expression of DNA repair-related genes between patients CD8 T cells specific for different viral epitopes were analyzed, compared with the same cells isolated from resolved subjects.

first: Ilaria

last: Montali

first: Camilla

last: Ceccatelli Berti

first: Greta

last: Acerbi

first: Giuseppe

last: Pedrazzi

first: Valeria

last: Barili

first: Teresa

last: Pollicino

first: Arianna

last: Alfieri

first: Carolina

last: Boni

first: Barbara

last: Montanini

first: Cristina

last: Musolino

last: Pesci

first: Alessandro

last: Loglio

first: Marta

last: Borghi

first: Riccardo

last: Perbellini

first: Amalia

last: Penna

first: Diletta

last: Laccabue

first: Marzia

last: Rossi

first: Andrea

last: Vecchi

last: Tiezzi

first: Valentina

last: Reverberi

first: Chiara

last: Boarini

first: Gianluca

last: Abbati

last: Massari

first: Pietro

last: Lampertico

first: Gabriele

last: Missale

first: Carlo

last: Ferrari

first: Paola

last: Fisicaro


title: Characterization of de novo promoter variants in autism spectrum disorder with massively parallel reporter assays

city: Piscataway

first: Justin

last: Koesterich

state: New Jersey

address: 679 Hoes Lane West

institute: Rutgers University

summary: To functionaly test thousands of promoter based Autism associated de novo variants, we established neural progenitor cells from human embryonic stem cells and performed massively parallel reporter assays to collect transcription rates associated with reference and alternate allele sequences

overall_design: functional analysis of ~7,000 sequence regions harboring Autism de novo variants was conducted utilizing massively parallel reporter assays in 3 replicates of Neural Progenitor Cells (NPCs) dervied from human embryonic stem cells.

first: Joon-Yong

last: An

first: Fumitaka

last: Inoue

first: Ajuni

last: Sohota

first: Nadav

last: Ahituv

first: Stephan

last: Sanders

first: Anat

last: Kreimer


title: Liver cells study

first: Lefebvre

last: Philippe

state: Nord

address: Blvd Pr. J.Leclerc

summary: To characterise liver cells from wt, untreated adult male mice. In particular we are interested on hepatocytes (HCs), hepatic stellate cells (HSCs), liver sinuisoidal endothelial cells (LSECs), Kupffer cells (KCs) and cholangiocytes (CHs).

overall_design: Livers from C57Bl6/J male mice (14-18 weeks) were sequentially digested (ZT2-3) by collagenease and/or pronase to isolate by FACS the 5 cell types mentioned above

first: Jerome

last: Eeckhoute

first: Philippe

last: Lefebvre


title: Effect of depletion of MIRE on gene expression of RCC4 cells.

city: Hefei

first: Bingyan

last: Li

state: Anhui

address: Huangshan Road Shushan District

institute: University of Science and Technology of China

summary:
To investigate the effect of depletion of MIRE on gene expression of RCC4 cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sh-ctrl and sh-MIRE.

first: BingYan

first: XiaoRui

last: Guo


title: FDXR Drives Primary and Endocrine Resistant Tumor Cell Growth in ER+ Breast Cancer via CPT1A-Mediated Fatty Acid Oxidation

city: wuhan

first: Gao

last: Ronghui

state: HuBei province

address: 115 DongHu Road

institute: 武汉大学医学研究院

summary:
The majority of breast cancers (BCs) harboring estrogen receptor (ER) have shown endocrine resistance. Our previous study has demonstrated that ferredoxin reductase (FDXR) promotes  mitochondrial function and ER+ breast tumorigenesis. Here, integrative analyses of targeted metabolomics assay and gene expression profiling show that FDXR potentiates fatty acid oxidation (FAO) through positive regulation of carnitine palmitoyltransferase 1A (CPT1A) expression. Treatment with ER antagonist (tamoxifen) or degrader (fulvestrant) leads to increased expression of FDXR and CPT1A. In line with this finding, we find that FDXR-CPT1A-FAO axis is required for primary and endocrine resistant breast cancer cell growth. Therapeutically,combining endocrine therapy with FAO inhibitor synergistically reduces primary and endocrine resistant breast cancer cell growth, thus providing a potential combinatory treatment for ER+ breast cancer.
We used microarrays to be able to elucidate to some extent the gene regulatory mechanisms of FDXR regulating breast cancer metabolism.

overall_design: T47D cells were infected with a retrovirus encoding the shRNA of FDXR(FDXR sh434) or  control vector (Vec).

first: Jing

last: Zhang

first: Chaojun

last: Yan


title: PRMT6 promotes breast tumorigenesis

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

summary: RNA-seq analysis was performed to identify key signaling responding to PRMT6 knockdown in MDA-MB-231

overall_design: Control (shSCR) MDA-MB-231 cells and PRMT6 knockdown (KD) (shPRMT6) MDA-MB-231 cells were analyzed through RNA-seq.

first: Yan

last: Wang


title: Paternal DCHP exposure on F1 male liver transcriptome

city: Riverside

first: Changcheng

last: Zhou

state: California

address: 900 University Avenue

department: Biomedical Sciences

institute: The University of California Riverside

summary:
Purpose: To investigate the effects of DCHP expoure on F1 male hepatic metabolic disorders
Methods: 8 week male WT mice were exposed to DCHP by oral gavage for 4 weeks, 3 week old F1 male mice were fed with HFD for 9 weeks,  glucose and insulin tolerant tests were performed at 10-11 week old, liver RNA was isolated for further transcriptome analysis
Results: Mice from DCHP exposure sires displayed glucose/insulin resistant phenotype, together with upregulation in inflammatoy related genes in the liver

overall_design: Male F0 mice were exposed to DCHP for 4 weeks, liver mRNA were sequenced from F1 male mice after 9 weeks of HFD feeding

first: Jingwei

last: Liu

first: Junchao

last: Shi

first: Tong


title: Effects of DCHP exposure on sperm small RNA expression profile utilizing two different RNA-seq methods

summary:
Purpose: To reveal the small RNA profiles in the sperm using traitional and PANDORA-seq methods
Methods: 8 week male WT mice were exposed to DCHP by oral gavage for 4 weeks. Sperm RNA was extracted for further processing
Results: PANDORA-seq revealed an abundant amount of tsRNA and rsRNA that were undetected by traditional-seq. Importantly, PANDORA-seq revealed that many differentially regulated sncRNAs also undetected with traditional-seq

overall_design: Sperm small RNA were sequenced from WT male mice after 4-week exposure to DCHP


title: A Carboxy-terminal Smarcb1 Point Mutation Induces Hydrocephalus Formation and Affects AP‑1 and Neuronal Signalling Pathways in Mice

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

summary: The BAF (BRG1/BRM-associated factor) chromatin remodelling complex is essential for the regulation of DNA accessibility and gene expression during neuronal differentiation. Mutations of its core subunit SMARCB1 result in a broad spectrum of pathologies, including aggressive rhabdoid tumours or neurodevelopmental disorders. Other mouse models have addressed the influence of a homo- or heterozygous loss of Smarcb1, yet the impact of specific non-truncating mutations remains poorly understood. Here, we have established a new mouse model for the carboxy-terminal Smarcb1 c.1148del point mutation, which leads to the synthesis of elongated SMARCB1 proteins. We have investigated its impact on brain development in mice using magnetic resonance imaging, histology, and single-cell RNA sequencing. During adolescence, Smarcb11148del/1148del mice demonstrated rather slow weight gain and frequently developed hydrocephalus including enlarged lateral ventricles. In embryonic and neonatal stages, mutant brains did not differ anatomically and histologically from wild-type controls. Single-cell RNA sequencing of brains from newborn mutant mice revealed that a complete brain including all cell types of a physiologic mouse brain is formed despite the SMARCB1 mutation. However, neuronal signalling appeared disturbed in newborn mice, since genes of the AP-1 transcription factor family and neurite outgrowth-related transcripts were downregulated. These findings support the important role of SMARCB1 in neurodevelopment and extend the knowledge of different Smarcb1 mutations and their associated phenotypes.

overall_design: We investigated the transcriptome of two newborn mutant mice that were homozygous for the Smarcb1 c.1148del point mutation and two newborn wildtype mice by single-cell RNA sequencing (scRNAseq). Each mouse brain was divided into one supratentorial and one infratentorial part. Single-cell suspensions were generated from all eight samples and further processed for scRNAseq.

first: Aliska

middle: K

last: Brugmans

first: Natalia

last: Moreno

last: Göbel

first: Dörthe

last: Holdhof

first: Flavia

last: de Faria

first: Marc

last: Hotfilder

first: Daniela

last: Jeising

first: Michael

middle: C

last: Frühwald

first: Boris

middle: V

last: Skryabin

first: Timofey

last: Rozhdestvensky

first: Lydia

last: Wachsmuth

first: Cornelius

last: Faber

first: Martin

last: Dugas

first: Julian

last: Varghese

first: Ulrich

last: Schüller

first: Thomas

last: Albert

first: Kornelius

last: Kerl


title: DCHP exposure

first: Changcheng

last: Zhou

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

overall_design: Refer to individual Series


title: PRMT6 and PARP1 sequencing in non-treated  MDA-MB-231 cells

first: yan

last: wang

summary: Here, we examined the interactions between PRMT6, poly(ADP-ribose) polymerase 1 (PARP1), and the cullin 4 B (CUL4B)-Ring E3 ligase (CRL4B) complex, to form a transcription-repressive complex that co-occupies the core clock gene PER3 promoter.

overall_design: Examination of PRMT6 and PARP1 target genes in MDA-MB-231 cell line.

first: Tianshu

last: Yang

first: Yan

last: Wang


title: Integrative analysis of gene expression and DNA methylation profiles in warts

city: Abha

first: Mansour

middle: Abdullah

last: Alghamdi

state: Aseer

address: Guraiger Campus

department: Medicine

country: Saudi Arabia

institute: King Khalid University

summary: Genome wide DNA methylation profiling of normal skin and common warts samples infected with the human papilloma virus (HPV). The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs. DNA was extracted from 24 paired wart and normal skin samples.

overall_design: Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip

first: Laith

last: AL-Eitan

first: Amneh

last: Tarkhan


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [14C, 14D]

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (14C_200917, 14C_200924, 14D_210325).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens