title: Transcriptome-wide N6-methyladenosine modification profiling of mRNAs during infection of Newcastle disease virus in Chicken Macrophages

city: Changchun

first: li

middle: jin

last: dou

state: China

address: Changchun, 130062, China

department: College of Veterinary Medicine

institute: Jilin University

summary: N6-methyladenosine (m6A) modification is the most prevalent post-transcriptional modification of mRNA in eukaryotes and has been reported to play an important role in viral infection. However, the role of m6A modification during Newcastle disease virus infection (NDV) is not clear. In this study, we profiled the transcriptome-wide m6A modification of mRNA in NDV-infected chicken macrophages using MeRIP-seq. we identified a total of 9496 significantly changed peaks, of which 7015 peaks distributed across 3320 genes were significantly up-regulated and 2481 peaks distributed across 1264 genes were significantly down-regulated. Combined analysis of m6A peaks and mRNA expression revealed 1234 mRNAs with significantly altered methylation and expression levels after NDV infection, and m6A modification tended to have a negatively correlation with mRNA expression, suggesting that m6A modification may regulate the process of NDV infection by regulating gene expression, especially innate immunity-related genes. To our knowledge, This is the first comprehensive characterization of m6A patterns of the mRNA in chicken macrophages after NDV infection, and provides a valuable basis for further exploring the role of m6A modification in the process of NDV infection.

overall_design: Transcriptome-wide N6-methyladenosine modification profiling of mRNAs in NDV-infection HD11 cells and Control HD11 cells

first: Jindou

last: Li

first: Jiaxin

last: Ding

first: Zhuang


title: miRNA expression analysis of erythroblasts derived from SCD CD34+ HSPCs transduced with the βAS3m/miR7m compared to control- (βAS3m/miRnt or βAS3) or mock-transduced samples

status: Public on May 24 2023

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

country: Italy

institute: University of Padova

type: Non-coding RNA profiling by high throughput sequencing

summary: We have investigated changes in miRNA expression occurring in samples transduced with a lentiviral vector expressing the βAS3m transgene and the miR7m targeting the sickle β-globin

overall_design: we performed miRNA-seq analysis in erythroblasts (day 13 of the erythroid differentiation) derived from SCD CD34+ HSPCs (2 donors) that were transduced with the different LVs or not.

first: Mégane

last: Brusson

first: Cécile

last: Masson

first: Annarita

last: Miccio


title: Gene expression analysis of erythroblasts derived from SCD CD34+ HSPCs transduced with the βAS3m/miR7m compared to control- (βAS3m/miRnt or βAS3) or mock-transduced samples

type: Expression profiling by high throughput sequencing

summary: We have investigated gene expression changes occurring in samples transduced with a lentiviral vector expressing the βAS3m transgene and the miR7m targeting the sickle β-globin

overall_design: We performed RNA-seq analysis in erythroblasts (day 13 of the erythroid differentiation) derived from SCD CD34+ HSPCs (2 donors) that were transduced with the different LVs or not.


title: Gene and miRNA expression analysis of erythroblasts derived from SCD CD34+ HSPCs transduced with the βAS3m/miR7m compared to control- (βAS3m/miRnt or βAS3) or mock-transduced samples

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

overall_design: Refer to individual Series


title: RNAseq of cultured neonatal rat ventricular cardiomyocytes treated with siRNA for Btg1 and Btg2 knockdown.

city: Cincinnati

first: Katherine

middle: E

last: Yutzey

state: Ohio

address: 3333 Burnet Ave

department: Molecular Cardiovascular Biology

country: USA

institute: Cincinnati Children's Hospital Medical Center

summary: Total RNA was isolated from n=3 culture wells per siRNA treatment group, from 6 independent primary neonatal rat cardiomyocyte isolations. RNA was pooled to obtain n=3 independent samples per siRNA treatment group for sequencing. The siRNA treatment groups were= siScr (Scramble control), siBtg12 (Btg1/Btg2 double knockdown), siBtg1 (Btg1 single knockdown), siBtg2 (Btg2 single knockdown).

overall_design: Total RNA from siRNA-mediated Btg1 and Btg2-depleted cultured neonatal rat cardiomyocytes were used for RNAseq.

first: Nivedhitha

last: Velayutham


title: Single cell RNA sequencing of human muscle stem cells in aging

city: San Francisco

first: Emilie

last: Barruet

state: California

address: 513 Parnassus Av

institute: UCSF

summary: In this study we investigated transcriptional age-related changes in human muscle stem cells. We show that there is an overall loss of transcriptional heterogeneity with aging and identified new genes that are differentiatlly expressed through aging.

overall_design: We performed additional single cell RNA sequencing of highly purified human satellite cells from freshly harvested human muscles of 12 healthy donors

first: Jason

middle: H

last: Pomerantz


title: An antibody independent verification method quantifies m6A in the chicken β-actin zipcode

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

summary: N6-Methyladenosine (m6A) in mRNA regulates almost every stage in the mRNA life cycle, and the development of the high throughput detection of methylated sites in mRNA using MeRIPSeq or miCLIP revolutionized the m6A research field. Both methods are based on immunoprecipitation of fragmented mRNA. However, it is well documented that antibodies often have nonspecific activities, thus verification of identified m6A sites using an antibody-independent method would be highly desirable. Currently such approaches are limited. Here we present RedBaron, an improved biochemical method for the site-specific detection and quantification of m6A in RNA. We demonstrate that the RedBaron method is able to accurately quantify m6A levels at specific transcripts in vivo. We used this assay for the site-specific detection and quantification of m6A within the chicken β-actin (ACTB) zipcode sequence in chicken embryos and in fibroblast cells. We demonstrate that methylation of this site in the β-actin zipcode enhances ZBP1 binding in vitro, whilst methylation of a nearby adenosine abolishes

overall_design: Fragmented poly(A) RNA from 3 replicates of chicken embryos stage Hamburger-Hamilton 27 was immunoprecipitated using anti-m6A-antibody from NEB, and subjected to next generation sequencing. The sequencing results were compared to the RNAseq results from the same samples.

first: Francis

last: Baron

first: Nathan

last: Archer

first: Eleanor

last: Bellows

first: Simon

last: Welham

first: Catrin

last: Rutland

first: Christopher

middle: J

last: Hayes

first: Zsuzsa

last: Bodi

first: Rupert

middle: G

last: Fray


title: RNA sequencing to study the molecular relationships between temperature, aging, and NPR-8

city: Spokane

first: Yiyong

last: Liu

state: WA

address: 412 E Spokane Falls Blvd

institute: Washington State University

summary: To gain molecular insights into NPR-8-dependent longevity response to temperature, we employed RNA-seq to compare gene expression in young and old wild-type and npr-8(ok1439) animals propagated at different temperatures.

overall_design: Five replicates of eight groups of RNA samples (0-day-old and 9-day-old adult wild-type and npr-8(ok1439) animals propagated at 20°C and 25°C for at least two generations) were collected and subjected to RNA-seq analysis.

first: Durai

last: Sellegounder

first: Sankara

middle: N

last: Palani


title: MitoKO: A library of base editors for precise ablation of all protein-coding genes in the mouse mitochondrial genome

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

institute: University of Cambridge

summary: We design and apply a highly optimized library of double-stranded DNA deaminase (DddA)-derived cytosine base editors (DdCBEs) - MitoKO - to precisely ablate every mtDNA protein coding gene in the mouse mitochondrial genome

overall_design: Base editing of citosine to timine to introduce premature STOP codons in protein-encoding genes of the mouse mtDNA

first: Pedro

last: Silva-Pinheiro


title: Genome-wide AR binding under androgen deprivation condition upon TRAF4 overexpression

city: Houston

first: Ping

last: Yi

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report that TRAF4-mediated AR ubiquitination alters AR genomic binding profile under androgen deprivation condition.

overall_design: Examination of AR genome-wide binding in control and TRAF4 overexpressing cells


title: Comprehensive profiling of activity and specificity of CRISPR/Cas9 under cellular environment by deep learning

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake university

summary: This study aims to predict the activity and specificity of CRISPR/Cas9 by deep learning at genome-scale among different cell lines. Here, we have focused on embracing and modifying a system for evaluating SpCas9 activity of on-target and off-target using >1,000,000 guide RNAs (gRNAs) covering ~20,000 protein-coding genes and ~10,000 non-coding genes in synthetic constructs with a high-throughput manner. With the help of deep learning algorithms in the field of artificial intelligence, three prediction models with the best generalization performance now are constructed: Aidit_Cas9-ON, Aidit_Cas9-OFF, and Aidit_Cas9-DSB. Moreover, through systematically investigating the influence of diverse cellular environment on gRNA activity and specificity, we noticed that distinct features are favored from H1 cell line compared with the other 2 cell lines for on-target activity and the overall distribution of repair outcomes is markedly different across 3 cell lines, especially in Jurkat. Finally, we identify a key effect protein DNTT strongly influences editing outcomes induced by CRISPR/Cas9. We confirm that this study will greatly facilitate CRISPR-based genome editing.

overall_design: All 929,180 gRNAs (“ON-Target” and “OFF-Target” library) were cloned into a lentivirus backbone with 20-nt random nucleotide as barcode sequences (BC). The BC was incorporated to eliminate the confounding issues stemmed from plasmid propagation and PCR amplification. An average of 300x coverage was maintained over the course of library preparation. To establish a uniform system to record the gRNA activities, we expanded cells from mono clones with stable SpCas9 expression to eliminate the heterogeneity (K562-cas9; Jurkat-Cas9; H1-cas9). The gRNA-target paired assessment cassette and BC were packed into lentivirus, transduced into cells, and integrated into the genome of host cells. We applied high MOI transduction to achieve decent cell-to-library coverage with practical amount of cell population, under the rationale that the relative indel frequencies and the indel frequency ranks are preserved under different amount of transduced lentivirus. K562 and Jurkat cells were harvested at day-3.5 post-transduction and H1 cells were collected at day-5. We amplified the gRNA-target cassette together with the BC from both the plasmid libraries and the gDNA collected from the edited cells. Amplicons were undergone high throughput sequencing (HTS) and the editing outcome were determined.

first: Heng

last: Zhang

first: Jianfeng

last: Yan


title: High fat diets rich in fish oil promote hair loss via epidermal fatty acid binding-mediated immunoregulation

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: While fats are essential nutrients in healthy diets, how dietary fats affect immune cell function and overall health are not well understood. We fed mice various high-fat diets (HFD) which mimicked human diets rich in different fatty acid (FA) components. Surprisingly, we observed that mice consuming the fish oil diet exhibited the most severe hair loss compared to those consuming other diets, which supported the evidence that people in regions with a high intake of fish had a tendency of increased hair loss. Mechanistically, omega-3 FAs in fish oil promoted atypical expansion of skin CD8+γδ+ T cells which inhibited hair follicle stem cell activity. We further identified that the epidermal fatty acid binding protein (E-FABP) was pivotal in promoting omega-3 FA-induced CD8+γδ+ T cells by activating the reactive oxygen species (ROS)/IL-36 signaling pathway in dermis macrophages. Our findings have implications for the prevention, etiology and therapy of hair loss in humans, including these with alopecia areata.

overall_design: Transcriptional profile of mice on low fat diet (LFD), fish oil diet, or cocoa butter diet for both wild type (WT) and epidermal fatty acid binding protein (E-FABP) knockout mice with n=3 in each group.

first: Jiaqing

last: Hao

first: Rong

last: Jin

first: Jun

last: Zeng

first: Quan

last: Luo

first: Anita

last: Mandal

first: Guanmin

last: Jiang

first: Junling

last: Li

first: Huaiyu

last: Zheng

first: Yanwen

last: Sun

first: Sobha

middle: R

last: Bodduluri

first: Yin

last: Huang

first: Yanmei

first: Di

last: Yin

first: Yuan

last: Hua

first: Qi

first: Xiaohong

first: Lianliang

first: Ailin

last: Tao

first: Chin

middle: K

last: Ng

first: Shujun

middle: C

first: Haribabu

first: Nejat

last: Egilmez

first: Edward

last: Sauter

first: Bing


title: Antiphospholipid antibodies induce Proinflammatory and Procoagulant Pathways in Endothelial cells.

city: Athens

first: Marios

last: Agelopoulos

state: Attica

address: 4 Soranou Ephessiou Str

department: Center of Basic Research

country: Greece

institute: Biomedical Research Foundation Academy of Athens

summary: Antiphospholipid syndrome (APS) is an autoimmune thrombophillia characterized by recurrent thrombotic events and/or pregnancy morbidity in the presence of antiphospholipid antibodies detected either as anti-cardiolipin, anti-β2 Glycoprotein I (anti-β2GPI) or Lupus anticoagulant (LA). Endothelial deregulation characterizes the syndrome. To address the gene expression changes occurring in the endothelial cells in the context of APS, we performed transcriptome analysis of Human Umbilical Vein Endothelial cells (HUVECs) stimulated with anti-β2GPI-β2GPI complexes.

overall_design: RNA-seq analysis in naive and induced Huvec cells

first: Panayiotis

last: Vlachoyiannopoulos


title: Neutrophil extracellular traps trigger inflammatory bone destruction in periodontitis

status: Public on May 23 2023

city: Bethesda

first: Niki

last: Moutsopoulos

address: 30 convent Dr

institute: NIDCR

summary: Neutrophil recruitment and activation are hallmarks of the prevalent inflammatory disease, periodontitis. However, the mechanisms by which neutrophils contribute to in inflammatory bone destruction remain unclear. Herein, we document that neutrophil extracellular traps (NETs) have a direct role in mediating inflammatory pathology. In an established animal model of periodontitis, we demonstrate that genetic or pharmacologic inhibition of NETs formation, or removal of NETs by DNase-Ⅰ, alleviates inflammatory bone loss in vivo. Investigating the mechanisms by which NETs drive periodontal inflammation, we find that extracellular histones have a direct role in disease progression. Consistent with findings in animal models, histones bearing classic NET-associated post-translational modifications are correlated with disease severity and are significantly elevated in local lesions and systemic circulation of patients with periodontitis. Our work reveals NETs-associated components as pathogenic mediators, potential biomarkers, and therapeutic targets for periodontitis.

overall_design:
Examine the changes in the transcriptom in oral mucosal tissues with or without ligature placement in mice with vehicle or DNase l.
contributor: NIDCD/NIDCR Genomics and Computational Biology Core

first: Tae

middle: S

last: Kim

first: Lakmali

middle: M

last: Silva

first: Drake

middle: W

last: Williams

first: Teresa

last: Greenwell-Wild

first: Liam

last: O’Neil

first: Thomas

last: Bugge

first: Mariana

last: Kaplan

first: Carmelo

last: Carmona-Rivera


title: A comprehensive analysis of the mechanism of FOS in the progression of endometrialcyst of ovary to endometriosis-associated ovarian cancer

first: Lijing

last: Zhao

state: jilin

address: Office Building, School of Nursing, Jilin University, No. 965 Xinjiang Street

department: gynaecology and obstetrics

institute: The second hospital of jilin university

summary:
Background: Endometrialcyst of ovary (EMC) may develop into endometriosis-associated ovarian cancer over time (EAOC). EAOC pathogenesis is unknown. This study investigated the likely mechanism of EAOC publishing related with orthotopic endometrial, searched for a feasible biomarker using RNA sequencing, and examined the molecular function of this biomarker in ectopic endometrial cells from EAOC and EMC patients.
Methods: RNA sequencing was performed on 5 EAOC and 4 EMC tissue samples. Differential expression analysis employed RNA-seq data. To identify biomarkers, differential genes were used in PPI network design, GO pathway enrichment, and GSEA pathway enrichment. Immunohistochemical staining revealed FOS expression in various endometrium. Lv-FOS was utilized to up-regulate FOS in hEnSCs, and cell counting kit-8 (CCK-8), colony formation assay, and scratch assay were performed to assess cell viability, proliferation, and migration. Western blot showed protein expression alterations.
Results: 249 genes were differently expressed, including FOS. Pathway enrichment study demonstrated that MAPK, AP-1, ERK, and other signaling pathways were involved in EMC-to-EAOC conversion. FOS upregulation in hEnSCs increased cell viability, proliferation, and migration. Western blot results showed that FOS, CDK4, cyclinD1, P21, and invasion-related proteins p-stat3, MMP2, and MMP9 were up- or down-regulated, respectively.
Conclusion: Mitosis and cell cycle affect EMC to EAOC progression. FOS expression, a novel biomarker, promotes EMC transition into EAOC and endometrial cell proliferation, invasion, and migration.
Keywords: FOS, endometrialcyst of ovary, endometriosis-associated ovarian cancer, biomarker

overall_design: The aim of this study was to elucidated the potential eutopic endometrium-related pathogenesis of EAOC, and to find a feasible biomarker of EAOC in eutopic endometrium using RNA sequencing. Subsequently, the protein expression of the biomarker was testified by Immunohistochemistry in eutopic endometrium tissue.Finally, the molecular function of the biomarker was explored by eutopic endometrial cells from EAOC and EM patients, respectively.

first: Junyu

last: Chen

first: Kang

last: He

first: Kai

last: Wang

first: Zeyu


title: Ovarian follicle extracellular vesicle-microRNAs mediated response of beef cows to environmental heat stress

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: Elevated ambient temperature during the summer season is a main cause of stress in dairy and beef cows, leading to impaired reproductive function and fertility. Follicular fluid extracellular vesicles (FF-EVs) play an important role in intrafollicular cellular communication by in part mediating the deleterious effects of heat stress (HS). Here we aimed to investigate the changes in FF-EV miRNA cargoes in beef cows in response to HS during the summer (SUM) compared to the winter (WIN) season using high throughput sequencing of FF-EV-coupled miRNAs.

overall_design: dry beef cows (n=11) were subjected to synchronization and stimulation for follicular dynamics. Ovum pick-up (OPU) was conducted on all animals in the summer (August 2021) and winter (February 2021) seasons by ultrasound-guided transvaginal follicle aspiration. Rectal temperatures were collected on each OPU and environmental data were collected daily for three weeks before each OPU. The FFs were collected from each target group (4 biological replicates/group; 8 mL FF/replicate) and subjected to differential centrifugation and high-speed ultracentrifugation (120,000xg for 70 min x2) to isolate EVs. Isolated EVs were characterized using a western blot, nanosight tracking analysis, and transmission electron microscopy. MiRNA-enriched total RNA was isolated from EVs and small-RNA library preparation and RNAseq (NovaSeq6000; Illumina) were performed.

first: Kamryn

last: Joyce

first: Nico

last: Menjivar

first: Daniella

last: Heredia

first: Camila

last: Rojas

first: Angela

last: Gonella-Diaza

first: Dawit

last: Tesfaye


title: On the role of DOM under varying climate change conditions in Crocosphaera

city: Marseille

last: Vannier

address: Campus de Luminy, 163 Av. de Luminy

country: France

institute: Aix-Marseille University

summary: Diazotrophs provide the main source of reactive nitrogen to the ocean, sustaining primary productivity and CO2 uptake. Climate change is raising temperatures, decreasing pH and reducing nutrient availability. How microbes respond to these changes is largely unexplained. Similarly, the role of DOM in the growth and survival of certain diazotrophic organisms is poorly understood. Moreover, growing evidence indicates some diazotrophs are capable of utilizing distinct DOM compounds via osmotrophy providing them with additional metabolic plasticity and ecological advantages compared to other non-diazotrophic microbes. We aimed to understand how osmotrophy could modify carbon uptake and alleviate energy stress in diazotrophs under ongoing climate change perturbations. We hypothesized that Crocosphaera preferentially uses DOM when labile as a carbon source in present pH conditions, as compared to future more acidic scenarios with higher access to inorganic carbon. Alternatively, the lower pH may cause Crocosphaera to be energy limited when trying to maintain intracellular homeostasis which would favour DOM uptake as an extra source of energy.

overall_design: We exposed cultures of the unicellular cyanobacterium Crocosphaera watsonii WH8501 to current and future climate change scenarios (RCP 4.5 and 6.0 from IPCC 2014) combining temperature and pH levels (26ºC and pH 8.1, 28ºC and pH 8.0 and 30ºC and pH 7.9). We followed their growth, nitrogen and dissolved inroganic carbon fixation rates, DOM specific uptake rates and gene expression responses along 8 days comparing DOM amended samples with not amended controls. We discuss how the different treatments alter Crocosphaera metabolism, allowing or not to cope with warmer and more acidic ocean conditions, while providing an improved mechanistic understanding of the role of osmotrophy in diazotrophs and allowing for a better comprehension of the global nitrogen cycle in the future ocean.

first: Alba

last: Filella

first: Jacqueline

last: Umbricht

first: Angelina

last: Klet

last: Vogts

first: Oliver

last: Grosso

first: Frédéric

last: Gazeau

first: Thibaut

last: Wagener

first: France

last: Van Wambeke

first: Maren

last: Voss

first: Lasse

last: Riemann

first: Mar

last: Benavides


title: Epitranscriptomic profiling of N4-acetylcytidine-related RNA acetylation in spinal dorsal horn of rat with cancer-induced bone pain

city: Jiaxing

first: Lei

last: Yang

address: 1882 Zhonghuan South Road

institute: Affiliated Hospital of Jiaxing University

summary: To evaluate ac4C acetylation in the spinal dorsal horn of rats with bone cancer pain.

overall_design: By interfering with the expression of NAT0, the relationship between some up-regulated genes and their ac4C acetylation in CIBP was verified.

first: Longsheng

last: Xu

first: Shang

last: Zheng

first: Beibei

last: Liu

first: Chengfei

first: Qinghe

last: Zhou

first: Xiangyao

last: Li


title: Effect of PM2.5-treatment and TMPRSS2-overexpression on gene expression in lung cancer cells

city: Taoyuan

first: Jang-Hau

last: Lian

address: No. 5, Fuxing Street

country: Taiwan

institute: Chang Gung Memorial Hospital

summary: Lung cancer cells exposed to PM2.5 for 90 days or overexpressed TMPRSS2 were employed as a cellular model to evaluate the effects of long-term exposure to PM2.5 on lung cancer progression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PM2.5-treated or TMPRSS2-overexpressing lung cancer cells

first: Chi-Yuan

last: Chen


title: Effect of high glucose on gene expression alteration in ARPE-19 cells

city: guiyang

first: liu

middle: zhang

last: nian

address: Qing Road, University Town, Huaxi District, Guiyang City, Guizhou Province

institute: Guizhou Medical University

summary: To investigate the overall gene expression pattern and explore potential drug targets of diabetic retinopathy, we used high glucose media to treat the main endothelial cells in retina, ARPE-19 cells, and then performed the gene expression profiling analysis containing mRNA and LncRNA information.

overall_design: Comparative gene expression profiling analysis of mRNA-seq and LncRNA seq data for ARPE-19 cells at normal and high glucose media for 72 h.

first: Shiquan

last: Gan

first: Xiao

last: Feng

first: Xiangchun

last: Shen

first: Zhangnian

first: Zike


title: Effect of PM2.5-treated and TMPRSS2-overexpressed on gene expression in lung cancer cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PM2.5-treated or TMPRSS2-overexpressed lung cancer cells


title: Unraveling the underlying regulatory mechanism of the efficacy of uterine-derived decellularized extracellular matrix for endometrial regeneration and fertility enhancement

city: Sungnam

first: Danbi

last: Lee

address: sampyeongro 335, Seongnam-Si, Kyounggido, Republic of Korea

department: Department of biological sciences

country: South Korea

institute: CHA university

summary: endometrial regenerative effects of Intrauterine administration of UdECMs

overall_design: To investigate the undelying regulatory mechanism of endometrial regeneration via UdECM, 3 of uteri from thin endometrium mouse model, UdECM treated mouse was compared

first: Youn-Jung

last: Kang

first: Jungho

last: Ahn

first: Tugce

last: Sen

first: Hyeonji

last: Kim

first: Jae

middle: Y

first: Jinah

last: Jang

first: Dong-Woo

last: Cho


title: Transcriptomics of Ts65Dn mice with viral-mediated overexpression of miR-200b

city: Illkirch

first: Damien

last: PLASSARD

address: 1 rue Laurent Fries

institute: IGBMC

summary: This project aims to identify transcriptomic changes in the Down Syndrome mouse model (Ts65Dn) in two brain regions, hippocampus and preoptic area. Also, we aim to identify possible transcriptomics rescue effect in Ts55Dn with viral-mediated overexpression of miR200. In total, we have 3 groups of hippocampal and 3 groups of preotic area tissue (WT control virus, 65Dn control virus and 65Dn miR200 - N=4 per group).

overall_design: mRNA profiles of Ts65Dn mice, control mice, in the hippocampus and preoptic area and as a function of a viral-mediated overexpression of miR-200b

first: Paolo

last: Giacobini

first: Vincent

last: Prevot


title: Chronic Exposure to Low Levels of Parabens Increases Mammary Cancer Growth and Metastasis in Mice

city: Davis

first: Michele

last: La Merrill

state: CA

address: 4138 Meyer Hall

department: Department of Environmental Toxicology

institute: University of California, Davis

summary: Methylparaben (MP) and propylparaben (PP) are commonly used as food, cosmetic, and drug preservatives. These parabens are detected in the majority of US women and children, bind and activate estrogen receptors (ER), and stimulate mammary tumor cell growth and invasion in vitro. Hemizygous B6.FVB-Tg (MMTV-PyVT)634Mul/LellJ female mice (n =20/treatment) were exposed to MP or PP at levels within the US Food and Drug Administration’s “human acceptable daily intake.” These paraben-exposed mice had increased mammary tumor volume compared with control mice (P< 0.001) and a 28% and 91% increase in the number of pulmonary metastases per week compared with the control mice, respectively (P< 0.01). Indeed, mammary tumors from PP-exposed mice had an increased retention of introns (P< 0.05). Our data suggest that parabens cause substantial mammary cancer metastasis in mice as a function of their increasing alkyl chain length and highlight the emerging role of aberrant spliceosome activity in breast cancer metastasis.

overall_design: RNA-seq was conducted for 59 primary mammary tumors (19 from vehicle group, 20 from methylparaben group, and 20 from propylparaben group)

first: Jason

last: Tong

first: Sarah

last: Elmore

first: Shenq-Shyang

last: Huang

first: Phum

last: Tachachartvanich

first: Katherine

last: Manz

first: Kurt

last: Pennell

first: Machelle

middle: D

last: Wilson

first: Alexander

last: Borowsky

middle: A


title: Transcriptomes change differently in different cancer cells upon SYK stable knockdown

city: Shanghai

first: mengdi

last: dai

address: 555 Zuchongzhi Rd, Bldg. 2, RM.409  shanghai, P.R. China

institute: SIMM

summary:
Purpose: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) to find out the difference between SYK stable knockdown and negative control group in each cancer cell line, and find the transcriptomes change upon SYK knockdown.
Methods: mRNA profiles of cell lines were generated using Illumina PE150, then GSEA was used for analyzing the association between SYK knockdown and the mesenchymal or epithelial signature.
Results: The result showed epithelial signatures were up-regulated, while mesenchymal signatures were down-regulated upon SYK knockdown in RNA-seq data.
Conclusions: Our study systematically examined the cellular transcriptomes affected by SYK knockdown, with biologic replicates, generated by RNA-seq technology. SYK knockdown results in the transcriptional change of multiple epithelial and mesenchymal markers, leading to mesenchymal state switching.

overall_design: mRNA profiles of SYK stable knockdown and corresponding negative control generated from 3 cancer cell lines, individually.

first: M

last: Geng

first: J

last: Ding


title: Human Dermal Fibroblast Subpopulations and Epithelial Mesenchymal Transition Signals in Hidradenitis Suppurativa Tunnels are Normalized by Spleen Tyrosine Kinase Antagonism in Vivo

city: Liverpool

first: John

last: Frew

address: Elizabeth St

department: Dermatology

country: Australia

institute: Liverpool Hospital

summary:
Nanostring nCounter Human Fibrosis V2.0 Panel
Hidradenitis Suppurativa is a chronic inflammatory disease of which the pathogenesis is incompletely understood.  Dermal fibroblasts have been previously identified as a major source of inflammatory cytokines, however information pertaining to the characteristics of subpopulations of fibroblasts in HS remains unexplored. Using in silico-deconvolution of whole-tissue RNAseq, Nanostring gene expression panels and confirmatory immunohistochemistry we identified fibroblast subpopulations in HS tissue and their relationship to disease severity and lesion morphology. Gene signatures of SFRP2+ fibroblast subsets were increased in lesional tissue, with gene signatures of SFRP1+ fibroblast subsets decreased. SFRP2+ and CXCL12+ fibroblast numbers, measured by IHC, were increased in HS tissue, with greater numbers associated with epithelialized tunnels and Hurley Stage 3 disease. Pro-inflammatory CXCL12+ fibroblasts were also increased, with reductions in SFRP1+ fibroblasts compared to healthy controls.  Evidence of Epithelial Mesenchymal Transition was seen via altered gene expression of SNAI2 and altered protein expression of ZEB1, TWIST1, Snail/Slug, E-Cadherin and N-Cadherin in HS lesional tissue. The greatest dysregulation of EMT associated proteins was seen in biopsies containing epithelialized tunnels. The use of the oral Spleen tyrosine Kinase inhibitor Fostamatinib significantly reduced expression of genes associated with chronic inflammation, fibroblast proliferation and migration suggesting a potential role for targeting fibroblast activity in HS.

overall_design: Baseline and Week 4 Data

first: A

last: Flora


title: Regulatory logic of endogenous RNAi in silencing de novo genomic conflicts

city: New Yor

first: Jeffrey

last: Vedanayagam

state: NY

address: 1275 York Avenue

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

summary: Although the biological utilities of endogenous RNAi (endo-RNAi) have been largely elusive, recent studies reveal its critical role in the non-model fruitfly Drosophila simulans to suppress selfish genes, whose unchecked activities can severely impair spermatogenesis. In particular, hairpin RNA (hpRNA) loci generate endo-siRNAs that suppress evolutionary novel, X-linked, meiotic drive loci. The consequences of deleting even a single hpRNA (Nmy) in males are profound, as such individuals are nearly incapable of siring male progeny. Here, comparative genomic analyses of D. simulans and D. melanogaster mutants of the core RNAi factor dcr-2 reveal a substantially expanded network of recently-emerged hpRNA-target interactions in the former species. The de novo hpRNA regulatory network in D. simulans bears compelling signatures of sex chromosome conflict and provides insight into molecular strategies that underlie hpRNA emergence. In particular, our data support the existence of ongoing rapid evolution of Nmy/Dox-related networks, recurrent targeting of testis HMG Box loci by hpRNAs, and connections to transposons. Importantly, the impact of the endo-RNAi network on gene expression flips the convention for regulatory networks, since we observe strong derepression of targets of the youngest hpRNAs, but only mild effects on the targets of the oldest hpRNAs. These data suggest that endo-RNAi are especially critical during incipient stages of intrinsic sex chromosome conflicts, and that continual cycles of distortion and resolution may contribute to speciation.

sample_organism:
Drosophila melanogaster
Drosophila simulans

overall_design: Comparative analysis of testis transcriptomic data (RNA-seq and small RNA) between wildtype and core RNAi factor mutant dcr2 in two closely related Drosophila species namely, D. melanogaster and D. simulans.

first: Ching-Jung

last: Lin

first: Ranjith

last: Papareddy

first: Michael

last: Nodine

first: Alex

last: Flynt

first: Jiayu

last: Wen

first: Eric

last: Lai


title: Determining the effect of RPA49 on RNA polymerase I occupancy in vivo

status: Public on May 22 2023

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

institute: University of Alabama at Birmingham

summary: The central goal of this project was to determine the role of the RNA polymerase I (Pol I) subunits RPA34 and RPA49 in rRNA synthesis. Previous studies by various groups have demonstrated that these two subunits may play a role in transcription initiation and elongation by  on Pol I occupancy in vivo, but this is still not clearly defined. Here, we deployed a high-resolution technique, native elongating transcript sequencing (NET-seq), to test the effects of RPA34 and RPA49 on Pol I occupancy in vivo. We found that when RPA34 was deleted, there was a significant reduction in Pol I occupancy across the rDNA template. Additionally, when RPA49 was deleted, Pol I occupancy was even further reduced across the template. Collectively, our findings suggest that perhaps RPA34 acts to stabilize RPA49 and these subunits may act primarily as transcription initiation factors for Pol I.

overall_design: NET-seq was conducted in triplicate for three strains of yeast: wild-type (WT), rpa34△, and rpa49△. The WT strain was used as the control.

first: David

last: Schneider


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [13F, 14A, 14B]

city: La Jolla

first: Joseph

last: Ecker

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 (13F_210318, 14A_210325, 14A_210401, 14B_201217, 14B_210107, 14B_210610, 14B_210617).

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

last: Nunn

first: Jesse

last: Dixon

last: Behrens


title: Combined Proteomics and Transcriptomics Identifies Serpin Family C Member 1 Associated Protein as a Biomarker of Endometriosis

city: Beijing

first: Song

address: No. 5, Dong Dan San Tiao

institute: Peking Union Medical College Hospital

summary: Objective: To explore potential biomarkers indicating endometriosis.   Results: A sum of 979 mRNAs and 39 proteins were tested to be significantly differentially expression in the standard cluster compared with the endometriosis cluster. Venn analysis showed a filtered signature of only two down-regulated molecules in the EM group, i.e., fetuin B and serpin family C member 1; the latter showed a big variance between the control category and the EM set in the authentication test.  Conclusion: Serpin family C member 1 may be a useful possible biomarker for the analysis of EM.

overall_design: Materials and methods: A proteomics method and combined quantitative transcriptomics was adopted to highlight markers in the Endometriosis (EM). Venn analysis was used to integrate the ribonucleic acid sequencing (RNA-seq) and protein profiles. Promising candidate markers were tested by enzyme-related immunosorbent assay.

first: Xiaoyan

last: Li

first: Xi

last: Wang

first: Qi

last: Yu


title: Distinct immune modulatory roles of regulatory T cells in gut versus joint inflammation in TNF driven spondyloarthritis [I]

city: Ghent

first: Carolien

last: Vlieghe

address: Corneel Heymanslaan 10

department: Department of Internal Medicine and Pediatrics (Rheumatology Unit)

country: Belgium

institute: VIB Inflammation Research Center-University of Ghent

summary:
Objectives: Gut and joint inflammation commonly co-occur in spondyloarthritis (SpA) which strongly restricts therapeutic modalities. The immunobiology underlying differences between gut and joint immune regulation, however, is poorly understood. We therefore assessed the immunoregulatory role of CD4+FOXP3+ regulatory T (Treg) cells in a model of Crohn’s-like ileitis and concomitant arthritis.
Methods: RNA-sequencing (RNA-seq) and flow cytometry were performed on inflamed gut and joint samples and tissue-derived Tregs from TNF∆ARE mice. In situ hybridization of TNF and its receptors (TNFR) was applied to human SpA gut biopsies. Soluble(s) TNFR levels were measured in serum of mice and SpA patients and controls. Treg function was explored by in vitro co-cultures and in vivo by conditional Treg depletion.
Results: Chronic TNF exposure induced several TNF superfamily (TNFSF) members (4-1BBL, TWEAK and TRAIL) in synovium and ileum in a site-specific manner. Elevated TNFR2 mRNA levels were noted in TNF∆ARE/+ mice leading to increased sTNFR2 release. Likewise, sTNFR2 levels were higher in SpA patients with gut inflammation and distinct from inflammatory and healthy controls. Tregs accumulated at both gut and joints of TNF∆ARE mice, yet their TNFR2 expression and suppressive function was significantly lower in synovium versus ileum. In line herewith, synovial and intestinal Tregs displayed a distinct transcriptional profile with tissue restricted TNFSF receptor and p38MAPK gene expression.
Conclusions: These data point to profound differences in immune-regulation between Crohn’s ileitis and peripheral arthritis. Whereas Tregs control ileitis they fail to dampen joint inflammation. Synovial resident Tregs are particularly maladapted to chronic TNF exposure.

overall_design: Tregs and conventional CD4+ T cells (Tconv) were selectively purified via FACS-sorting based on the fluorescent Foxp3-GFP reporter (DEREG crossed mice) from ileum and ankle joints and associated draining LNs (resp. mesenteric LN and inguinal + popliteal LN) of TNF∆ARE (DEREG) mice and littermate control (WT DEREG) mice in 3 independent experiments. RNA was isolated from cells and processed for bulk RNA-seq. A comparative gene expression profiling analysis of RNA-seq data of Treg and Tconv samples was performed, comparing TNFdARE and WT conditions.

first: Koen

last: Venken

first: Matthias

last: Jarlborg

first: Decruy

last: Tine

first: Celine

last: Mortier

first: Elisabeth

last: Gilis

first: Ann

last: De Craemer

first: Julie

last: Coudenys

first: Isabelle

last: Cambré

first: Fleury

last: Devan

first: Alexander

last: Klimowicz

first: Filip

last: Van den Bosch

first: Anne

last: Hoorens

first: Triana

last: Lobaton

first: Sytze

last: de Roock

first: Tim

last: Sparwasser

first: Gerald

last: Nabozny

first: Peggy

last: Jacques

first: Dirk

last: Elewaut


title: Distinct immune modulatory roles of regulatory T cells in gut versus joint inflammation in TNF driven spondyloarthritis [II]

first: Carolien

last: Vlieghe

overall_design: Ileum and synovium samples from TNFdARE and littermate control WT mice (n=3 per strain) were collected, RNA was isolated and processed for bulk RNA-seq. A comparative gene expression profiling analysis of RNA-seq data of ileum and synovium samples was performed, comparing TNFdARE and WT conditions.

first: Koen

last: Venken

first: Matthias

last: Jarlborg


title: Distinct immune modulatory roles of regulatory T cells in gut versus joint inflammation in TNF driven spondyloarthritis

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

overall_design: Refer to individual Series


title: Mbnl2 loss alters novel context processing and impairs object recognition memory

city: Los Angeles

first: Sita

last: Reddy

address: HMR 702A, 2011 Zonal Avenue

institute: University of Southern California

summary: Myotonic dystrophy type I (DM1) patients demonstrate visuospatial dysfunction and impaired performance in tasks requiring recognition or memory of figures and objects. In DM1, CUG expansion RNAs inactivate the Muscleblind-like (MBNL) proteins. We show that constitutive Mbnl2 inactivation in Mbnl2ΔE2/ΔE2 mice, selectively impairs object recognition memory in the novel object recognition test. When exploring the context of a novel arena in which the objects are later encountered, the Mbnl2ΔE2/ΔE2 dorsal hippocampus responds with a lack of enrichment for learning and memory related pathways, mounting instead transcriptome alterations predicted to impair growth and neuron viability. In Mbnl2ΔE2/ΔE2 mice, saturation effects may prevent deployment of a functionally relevant transcriptome response during novel context exploration. Post-novel context exploration alterations in genes implicated in tauopathy and dementia are observed in the Mbnl2ΔE2/ΔE2 dorsal hippocampus. Thus MBNL2 inactivation in DM1 patients may alter novel context processing in the dorsal hippocampus and impair object recognition memory.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the dorsal hippocampus in 129sv/C57BL/6j Mbnl2 WT and KO mice

first: Abinash

last: Khandelwal

first: Jesse

last: Cushman

first: Jongkyu

last: Choi

first: Irina

last: Zhuravka

first: Abha

last: Rajbhandari

first: Parvin

last: Valiulahi

first: Xiandu

last: Li

first: Chenyu

last: Zhou

first: Lucio

last: Comai


title: Zc3h10 controls mitochondrial function coupling iron and cardiolipin homeostasis [RIP-seq]

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Institute

summary: Mitochondria are the energy-generating hubs of the cell. In spite of considerable advances, our understanding of the factors that regulate the molecular circuits that govern mitochondrial function remains incomplete. Using a genome-wide functional screen, we have identified the poorly characterized protein Zinc finger CCCH-type containing 10 (Zc3h10) as regulator of mitochondrial physiology. We show that Zc3h10 is a nuclear RNA binding protein that controls the fate of Slc25a37 and Prelid3a mRNA transcripts, two nuclear-encoded mitochondrial proteins central for iron and cardiolipin homeostasis. Depletion of Zc3h10 results in mitochondrial dysfunction and reduced TCA cycle flux. Notably, we have identified a loss-of-function mutation of Zc3h10 in humans (Tyr105 to Cys105) that is associated with decreased mitochondrial function, increased body mass index, fat mass, fasting glucose and triglycerides. Cells from Cys105 homozygotes display alterations in Slc25a37 and Prelid3a levels and defects in mitochondrial iron and cardiolipin homeostasis that derive in mitochondrial dysfunction.

overall_design: RIP-seq of Zc3h10 in C2C12 myoblasts.

first: Matteo

last: Audano

first: Mattia

last: Pelizzola

first: Nico

last: Mitro


title: Identification of a glycosphingolipid+ immune regulatory innate-like CD8 T-cell network in old mice

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

country: Germany

institute: University of Ulm

summary: The reciprocal decline in naive (TN) and increase in virtual (TVM) and true memory (TTM) CD8 T-cell frequencies upon aging is incompletely understood. We established the glycosphingolipid asialo-GM1 (AsGM1) marker present on >70% of TVM/TTM and 5-15% TN to target their immune-regulatory and homeostatic potential. We identified a novel AsGM1+ old CD8 TN-subset that was related to antigen-experienced AsGM1+ CD8 TTM and showed an initial immune-regulatory (Pdcd1, Il10) gene expression signature. The program for AsGM1+ CD8 T-subsets was imprinted genetically in young and old hematopoietic stem cells that reconstitute young and old donor-type immune systems in lymphophenic RAG1-/- mice within 16 weeks, respectively. However, antibody-mediated depletion of AsGM1+ T cells in old mice revealed a disturbed recovery of CD8 TVM resulting in a rejuvenated T-subset composition and T-cell priming capacity upon DNA-vaccination. Old CD8 TVM and IL10+ PD-1+ TTM exerted immune-regulatory functions and suppressed CD3/CD28-mediated activation of TN in vitro. Glycosphingolipids thus are attractive to identify and target novel T-subsets.

overall_design: RNA-seq was performed using CD8 T cell subpopulations from young and old C57BL/6J mice


title: Zc3h10 controls mitochondrial function coupling iron and cardiolipin homeostasis.

overall_design: Gene expression profiling in C2C12 myotubes depleted for Zc3h10 and controls; 4sU-labeled and total RNA profiling in wild-type and Zc3h10 depleted C2C12 myoblasts; RIP-seq of Zc3h10 in C2C12 myoblasts.


title: MAGL deficiency in liver macrophages

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Comparative expression profile of liver macrophages  from mice invalidated (MAGL Mye-/-) or not (MAGL fl/fl) for MAGL

overall_design: RNA was extracted from liver F4/80+Cd11b+ macrophages  sorted from MAGL Mye-/- mice and MAGL fl/fl control mice, 24 hours after one intraperitoneal  injection of CCl4 at 0.6 mg/kg of body weigth

first: Manon

last: Allaire

first: Hélène

last: Gilgenkrantz


title: Inhibition of Osteoblast Proliferation by Formaldehyde

first: Yan

last: Wang

address: No. 10, Xitoutiao, You An Men, Fengtai District

department: Department of Biochemistry and Molecular Biology

institute: Capital Medical University

summary: RNA-seq analysis was performed to identify key signaling responding to formaldehyde in MC3T3-E1.

overall_design: Two independent sample groups were exposed to formaldehyde for 100 μM and 300 μM  (FA_100 and FA_300) in MC3T3-E1 and were analyzed through RNA-seq.

first: Wei

last: Huang


title: Global transcriptomic profile in the halotolerant cyanobacterium Halothece sp. PCC 7418 cells acclimated to different salinity conditions

status: Public on May 21 2023

city: Nagoya

first: Hakuto

last: Kageyama

state: Aichi

address: 1-501, Shiogamaguchi, Tempaku-ku

country: Japan

institute: Meijo University

summary: Halotolerant species are of interest since they occur naturally in environments with excess toxic ions. The cyanobacterium Halothece sp. PCC 7418 (hereafter referred to as Halothece) exhibits remarkable halotolerance and was used to examine stress-responsive regulatory mechanisms. The effects of salinity environment on Halothece transcriptomes were examined using RNA sequencing.

overall_design: Halothece sp. PCC7418 cells were acclimated to low salinity (0.5 M NaCl) or high salinity (2.5 M NaCl). Then, total RNA was extracted and analyzed by RNA-seq analysis.

first: Rungaroon

last: Waditee-Sirisattha


title: Impaired angiogenesis in diabetic critical limb ischemia is mediated by a miR-130b-INHBA signaling axis

city: Valencia

first: Daniel

last: Perez-Cremades

state: Valencia

address: 15 Blasco Ibañez Avenue

department: Physiology Department

country: Spain

institute: University of Valencia


title: TRANSITIONAL DENDRITIC CELLS ARE DISTINCT FROM CONVENTIONAL DC2 PRECURSORS AND MEDIATE PRO-INFLAMMATORY ANTIVIRAL RESPONSES

city: Stanford

first: Juliana

last: Idoyaga

address: 299 Campus Drive

institute: Stanford University

summary: High-dimensional approaches revealed emerging heterogeneity within dendritic cells (DC), including a population of transitional DC (tDC) present in mouse and human. However, tDC origin and relationship to other DC subsets are not fully understood. Here, we show that tDC are distinct from other well-characterized DC and conventional DC precursors (pre-cDC). We demonstrate that tDC originate from bone marrow progenitors shared with plasmacytoid DC (pDC). In the periphery, tDC contribute to the pool of ESAM+ type 2 DC (DC2), and these DC2 harbor pDC-related developmental features. Different from pre-cDC, tDC have lower turnover, capture antigen, respond to stimuli, and activate antigen-specific naïve T cells, all characteristics of differentiated DC. Different from pDC, viral sensing by tDC results in IL-1b secretion and fatal immune pathology in a murine coronavirus model. Our findings suggest that tDC are a distinct pDC-related subset with a DC2 differentiation potential and unique pro-inflammatory function during viral infections.

overall_design: Examination of immune cells in murine bone marrow and spleen. Cells were CD135 enriched and sorted for live cells. Cells were barcoded, pooled and run on 2 lanes. Sorted splenocytes were mixed 1:1 from 2 gates:  CD3-/CD19-/NK1.1-/Ly6G- and CD3-/CD19-/NK1.1-/Ly6G-/Xcr1-/CD11blo to enrich for tDC. BM cells were gated as CD3-/CD19-/NK1.1-/Ly6G-. After sort, cells were counted and resuspended at a concentration of 600 cells per uL. Cells suspensions were processed for 10X Genomics.

first: Marcela

last: Alcántara-Hernández

first: David

last: Seong

first: Rebecca

last: Leylek

first: Fernando

last: Sulczewski

first: Raul

last: Maqueda-Alfaro


title: Cytomegalovirus-induced inactivation of TSC2 disrupts the coupling of fatty acid biosynthesis to glucose availability resulting in a vulnerability to glucose limitation

city: Rochester

first: Joshua

last: Munger

state: New York

address: 601 Elmwood Ave, Room 3-7544, Box 712

department: Biochemistry and Biophysics

institute: University of Rochester

summary: Human cytomegalovirus (HCMV) modulates cellular metabolism to support productive infection, and the HCMV UL38 protein drives many aspects of this HCMV-induced metabolic program. However, it remains to be determined whether virally-induced metabolic alterations might induce novel therapeutic vulnerabilities in virally infected cells. Here, we explore how HCMV infection and the UL38 protein modulate cellular metabolism and how these changes alter the response to nutrient limitation. We find that expression of UL38, either in the context of HCMV infection or in isolation, sensitizes cells to glucose limitation resulting in cell death. This sensitivity is mediated through UL38’s inactivation of the TSC complex subunit 2 (TSC2) protein, a central metabolic regulator that possesses tumor-suppressive properties. Further, expression of UL38 or the inactivation of TSC2 results in anabolic rigidity in that the resulting increased levels of fatty acid biosynthesis are insensitive to glucose limitation. This failure to regulate fatty acid biosynthesis in response to glucose availability sensitizes cells to glucose limitation, resulting in cell death unless fatty acid biosynthesis is inhibited. These experiments identify a regulatory circuit between glycolysis and fatty acid biosynthesis that is critical for cell survival upon glucose limitation and highlight a metabolic vulnerability associated with viral infection and the inactivation of normal metabolic regulatory controls.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MRC5 fibroblast lentiviraly transduced to express HCMV UL38 gene or an empty vector (control) using the pLenti CMV/TO Puro plasmid

first: Irene

last: Rodríguez-Sánchez

first: Xenia

middle: L

last: Schaffer

first: Matthew

middle: H

last: Raymonda


title: Effect of SRCAP on gene expression during PRRSV infection of Marc-145 cells.

city: Taian

first: Guofei

last: Ding

address: Daizong Street, Taishan District, Tai'an City, Shandong Province

institute: shandong agricultural university

summary:
To investigate the SRCAP regulation of gene transcription during PRRSV infection, we established Marc-145 cell lines in which SRCAP gene has been knocked down by siRNA.
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 Marc-145 cells and its KD derivatives (siSRCAP).

first: Yihong

last: Xiao


title: Zc3h10 controls mitochondrial function coupling iron and cardiolipin homeostasis [RNA-seq]

first: Stefano

last: de Pretis

overall_design: Profiling of 4sU-labeled and total RNA in wild-type and Zc3h10 depleted C2C12 myoblasts

first: Matteo

last: Audano

first: Mattia

last: Pelizzola

first: Nico

last: Mitro


title: CCD18co colonic fibroblast cell line treated with various pro-inflammatory stimuli, and analized by single cell RNA sequencing (scRNA-seq) to analyze pro-fibrotic signatures

city: San Diego

first: Marco

last: Maruggi

address: 10777 Science Center Dr

institute: Pfizer

summary: CCD18co cells are representative of colonic human fibroblasts. We wanted to understand if there was a stimulus that could induce the cells to acquire the same pro-fibrotic signatures that are found in patients with Ulcerative Colitis or Crohn's Disease. We stimulated the cells with various pro-fibrotic stimuli, and analyzed the signatures by single cell RNA sequencing (scRNA-seq)

overall_design: CCD18co cells were dissociated from in-vitro culture by Trypsinization, counted, and processed as illustrated in the 10X Genomics 3' RNA sequencing pipeline

first: Maria

last: Paraskevopoulou

first: Shane

last: Horman

first: Shan

last: Yu


title: Chromosomal abnormalities of 564 miscarriages

city: FuZhou

first: Haiwei

last: Wang

state: FuJian

address: Daoshan road 180

institute: Fujian Maternity and Child Health Hospital

summary: Chromosomal abnormalities are important causes of miscarriages. To delinate the chromosomal abnormalities in miscarriages, 564 miscarriages were collected and analyzed using single nucleotide polymorphism (SNP) array. 336 (59.6%) miscarriages were with abnormal copy number variations (CNVs), including 325 (57.6%) miscarriages with pathogenic CNVs and 11 (2%) miscarriages with variations of unknown significance (VOUS). The remaining 228 (40.4%) miscarriages had no clinically relevant chromosomal variants.

overall_design:
542 chorionic villus samples, five amniotic fluid samples and 17 skin tissues from aborted embryos were obtained. Chromosomal abnormalities, including homozygosity, triploidy, trisomy and chromosomal deletions/duplications in 564 miscarriages were detected by SNP array. Chromosome Analysis Suite (ChAS) was used to analyze the SNP arrays.
CEL files for 191 samples were lost.


title: Transcriptome of Anthurium andraeanum under cold stress

city: Ji'nan

first: Chunxia

last: Wu

state: Shandong

address: No.1,University Road,Science Park,Changqing District

department: Life Sciences

institute: Shandong Provincial Key Laboratory of Plant Stress

summary: The transcriptome of leaves from two Anthurium cultivars, Oregon (Elegang, E, cold tolerant) and Fantasy love (Menghuan, MH, cold sensitive) under cold stress were sequenced by Illumina Novaseq™ 6000. Sequencing generated a total of 129.44 Gb of raw reads and an average of 7.19 Gb of reads for each sample. The analysis showed differences of transcriptomes between the control and the cold treatment samples. We identified numerous differentially expressed genes that exhibited distinct expression patterns. These genes have known or potential roles inAnthurium cold tolerance.Therefore, we are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to the cold stress response of A. andraeanum.

overall_design: The full-flowering plants were grown in the growth chambers for three days with a 12/12 h day/night cycle at 25℃. For cold treatments, the plants were grown at 15℃ for three days, then the temperature was decreased to 6℃ for three days and then 4℃ for three days. The control plants were grown at 25℃ throughout the experiment. Leaves were collected at 25℃(control/CK), three days after the treatments at 6℃ and 4℃ for RNAseq. Three independent experimental replicates were performed, each consisting of three independent biological replicates.


title: Effect of temperature on global transcriptomic profile in the halotolerant cyanobacterium Halothece sp. PCC 7418

first: Hakuto

last: Kageyama

summary: Halotolerant species are of interest since they occur naturally in environments with excess toxic ions. The cyanobacterium Halothece sp. PCC 7418 (hereafter referred to as Halothece) exhibits remarkable halotolerance and was used to examine stress-responsive regulatory mechanisms. The effects of temperature on Halothece transcriptomes were examined using RNA sequencing.

overall_design: Halothece sp. PCC7418 cells were exposed to 24 h heat or cold shock. Then, total RNA was extracted and analyzed by RNA-seq analysis.

first: Rungaroon

last: Waditee-Sirisattha


title: ER reprogramming promotes a select pro-metastatic secretome in high FOXA1-expressing ER-positive endocrine-resistant and metastatic breast cancer [ChIP-seq]

city: Houston

first: Xiaoyong

last: Fu

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Aberrant activation of the forkhead protein FOXA1 is observed in advanced hormone-related cancers. However, to date, key mediators of high FOXA1 signaling remain elusive. We demonstrate that ectopic high FOXA1 (H-FOXA1) expression promotes estrogen receptor-positive (ER+) breast cancer (BC) metastasis in a xenograft mouse model. Mechanistically, H-FOXA1 reprograms ER-chromatin binding to elicit a core gene signature (CGS) and an ER-dependent secretome highly enriched in ER+ endocrine-resistant (EndoR) cells. ER+ BC MCF7-parental (P) cells treated with estrogen deprivation or estrogen, and with doxycycline (Dox)-inducible FOXA1 overexpression were used in this study. We found that a majority of the lost or retained ER binding induced by H-FOXA1 overlapped with the ER binding sites in P cells induced by estrogen vs. tamoxifen treatment. The lost ER binding sites were also significantly enriched for the ER binding under E2 vs. ED, which corresponds to 11% of the total E2-stimulated ER binding, suggesting that H-FOXA1 induces a loss of selective E2-stimulated ER binding sites. In addition, we found that the proportion of H-FOXA1-induced ER-loss regions were significantly enriched for the unique ER binding sites in P vs. tamoxifen-resistant (TamR) cells, yet no enrichment of the ER-gain regions was observed in the unique ER binding in TamR vs. P cells. Our findings uncover H-FOXA1-induced ER reprogramming driving EndoR and metastasis, possibly via a H-FOXA1/ER-dependent secretome that warrants further studies to clarify its involvement in disease progression of ER+ metastatic breast cancer.

overall_design: Examination of ER-chromatin binding in MCF7-P cells upon ectopic FOXA1 overexpression and in MCF7-P cells upon estrogen-deprivation vs. estrogen treatment.

first: Rinath

last: Jeselsohn

first: Carmine

last: De Angelis

first: Agostina

last: Nardone

first: Myles

last: Brown

first: Rachel

last: Schiff


title: Impaired angiogenesis in diabetic critical limb ischemia is mediated by a miR-130b-INHBA signaling axis [ischemic gastrocnemius]

first: Daniel

last: Perez-Cremades

summary: We report transcriptomic changes in the EC fraction of the gastrocnemius muscle after intramuscular injection of negative control mimic and miR-130b mimic.

overall_design: we performed intramuscular deliver of negativ control mimic or mir-130b mimic into the ischemic gastrocnemius following femoral artery ligation in db/db mice (4 injections in total). Two weeks post injury, gastrocnemius muscle was harvested and EC fraction was isolated by using CD31 antibody-bound magnetic beads. RNA-Seq analysis was performed using Illumina HiSeq2500 V4 2x150 bp  (Genewiz, South Plainfield, NJ).

first: Henry

last: Cheng

last: Pérez-Cremades

first: Rulin

last: Zhuang

first: Anurag

last: Jamaiyar

first: Jingshu

last: Chen

first: Aspasia

last: Tzani

first: Jorge

last: Plutzky

first: Philip

middle: P

last: Goodney

first: Mark

last: Creager

first: Marc

last: Sabatine

last: Bonaca

last: Feinberg


title: ER reprogramming promotes a select pro-metastatic secretome in high FOXA1-expressing ER-positive endocrine-resistant and metastatic breast cancer [RNA-seq]

last: Fu

summary: Aberrant activation of the forkhead protein FOXA1 is observed in advanced hormone-related cancers. However, to date, key mediators of high FOXA1 signaling remain elusive. We demonstrate that ectopic high FOXA1 (H-FOXA1) expression promotes estrogen receptor-positive (ER+) breast cancer (BC) metastasis in a xenograft mouse model. Mechanistically, H-FOXA1 reprograms ER-chromatin binding to elicit a core gene signature (CGS) highly enriched in ER+ endocrine-resistant (EndoR) cells. We identified Secretome14, a CGS subset encoding ER-dependent cancer secretory proteins, strongly predicts poor outcomes of ER+ BC and is elevated in ER+ metastases vs. primary tumors, irrespective to the ESR1 mutations. Parental (P) ER+ BC cells and their endocrine-resistant (EndoR) derivatives, and ER+ BC cells expressing doxycycline (Dox)-inducible ectopic FOXA1 were used in this study. Differential gene expression analysis was performed in EndoR vs. P cells and P cells +Dox vs. -Dox. We found that the FOXA1-CGS was highly enriched in the altered transcriptomes of two ER+ BC cell models (ZR75-1 and T47D) expressing ectopic H-FOXA1. The enriched hallmark gene sets, shared by the H-FOXA1 cell models, include “inflammatory response”, “complement”, and “interferon gamma response” for the H-FOXA1-induced, and “estrogen response early” and “estrogen response late” for the H-FOXA1-repressed genes. These findings point to the common transcriptional profile exhibiting an immune- over estrogen-responsive signature induced by H-FOXA1. In addition, we found that both the tamoxifen-resistant (TamR) and estrogen deprivation-resistant (EDR) derivatives of the 600MPE P cells were enriched for the H-FOXA1-induced CGS and FOXA1/ER-activated Secretome14. Our findings uncover H-FOXA1-induced ER reprogramming driving EndoR and metastasis, possibly via a H-FOXA1/ER-dependent secretome that warrants further studies to clarify its involvement in disease progression of ER+ metastatic BC.

overall_design: RNA-seq of ER+ breast cancer cell models and derivatives with resistance to endocrine therapy, and ER+ breast cancer cells with Dox-inducible ectopic FOXA1 overexpression using Illumina NextSeq500 (single-end) and Illumina NovaSeq6000 (paired-end) system, respectively.

last: Jeselsohn

last: De Angelis


title: ER reprogramming promotes a select pro-metastatic secretome in high FOXA1-expressing ER-positive endocrine-resistant and metastatic breast cancer

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

overall_design: Refer to individual Series


title: Myelodysplastic Syndrome haematopoietic Stem and Progenitor Cells manuplate bone marrow mesenchymal stromal cells for their advantage

city: London

first: Dominique

last: Bonnet

state: London

address: 1 Midland Rd

institute: Francis Crick Institute

summary: We cultured bone marrow haematopoietic stem and progenitor cells with bone marrow mesenchymal stromal cells to understand the interaction between the two cell types.

overall_design: Cell were co-cultured either in direct contact or in transwell for 5 days and then each cell type was isolated using FACS. RNA-Seq was performed on the respective cell types.

first: Syed

last: Mian


title: RNA-Sequencing results of EPB41-depletion PC9 cells and control cells

status: Public on May 20 2023

city: Jinan

first: Jupeng

last: Yuan

address: Jiyan road 440#

department: Cancer Research Center

institute: Shandong Cancer Hospital Affiliated to Shandong University

summary: We aimed to detect the mRNA expression levels in stable-transfected PC9 cells after transfection with EPB41 knock-dwon or control virus.

overall_design: EPB41 depletion and control cells were established through lentiviral viral infection. RNAs were extracted at log phase of cell growth. RNA-Sequencing of  EPB41 depletion cells (referring to shEPB41-1 and shEPB41-2) and its control (shNC) was performed according to standard protocols without replications.

first: Ming

last: Yang


title: LncRNA SOX9-AS1 triggers a transcriptional program involved in metabolic reprogramming, cell migration and invasion in triple-negative breast cancer

city: Ciudad de México

first: Mireya

last: Cisneros-Villanueva

state: Ciudad de Mexico

address: Periférico Sur No. 4809, Arenal Tepepan, 4809

country: Mexico

institute: Instituto Nacional de Medicina Genómica

summary: The regulatory role of the lncRNA SOX9-AS1 in TNBC and basal-like subtypes is poorly understood. We performed SOX9-AS1 gene silencing using two short-harping constructs, which were transfected in MDA-MB-468 and HCC1187 TNBC cell lines that had high SOX9-AS1 expression, and the genome-wide RNA-seq analysis of both transfects was performed. Data showed that 351 lncRNAs and 740 mRNAs were differentially expressed in MDA-MB-468. Meanwhile 56 lncRNAs and 100 mRNAs were also severally modulated in HCC1187 cells (LogFC ≥ 1.5 or ≤ −1.5, p.adj value <0.05). Pathway analysis revealed that the protein-encoding genes potentially regulates metabolic reprogramming, and epithelial-mesenchymal transition. SOX9-AS1 is a master regulator of a plethora of genes that can reflect our understanding of the important role of this lncRNA in the molecular cell biology of TNBC and basal-like subtypes.

overall_design: Differential gene expression analysis of RNA-seq data for MDA-MB-468 and HCC1187 cells treated with sh-CONTROL vs sh-SOX9-AS1

first: M

last: Fonseca-Montaño

first: D

last: Sotelo-Hernandez

first: A

last: Hidalgo-Miranda


title: lncRNA expression profiles of 10 paired thyroid cancer tissues including normal tissues, tumor tissues and metastatic lymph nodes

summary: The incidence of thyroid cancer (THC) is growing rapidly worldwide. Exploring the mechanisms underlying pathogenesis and dedifferentiation of thyroid cancer is compellingly needed. Considering the important role of lncRNAs playing in tumorigenesis, we systemically screened differentially expressed lncRNAs by RNA sequence of pairing THC specimens.

overall_design: In order to identify landscape of lncRNAs during THC progression and metastasis, RNA sequencing of paired THC tissues was performed, and the different expressed lncRNAs were reanalyzed referring to the results of TANRIC visualization. Filtered lncRNAs were supposed to be functional during carcinogenesis and metastasis of THC.

first: Changming

last: An


title: scRNA-sequencing of mesenchymal cells and immune cells sorted from the lung of PBS or HDM challenged mice

city: New Brunswick

first: Qi

state: NJ

address: 89 French St

institute: Rutgers RWJMS

summary: We compared the transcriptomes of mesenchymal cells and immune cells in mice sensitized and challenged with house dust mite (HDM) extracts and those in control PBS-treated mice, using single cell RNA-seq (scRNA-seq). Data with mesenchymal cells and data with immune cells were obtained from separate experiments. For scRNA-seq of mesenchymal cells, each sample was pooled from cells from 3 mice and 2 different samples per group (for a total of 6 mice) were used. For scRNA-seq of immune cells, each sample was from cells of one individual mouse.

overall_design: We used the 10X Genomics platform to prepare scRNA-seq libraries to detail the global programme of different gene expression in mesenchymal cells and immune cells in the lungs between PBS and HDM challanged mice .

first: En

last: Xu


title: KDM6B Overexpression Cooperates with TET2 Deficiency in Chronic Myelomonocytic Leukemia

first: Yue

last: Wei

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

summary: We report the RNA-Seq results including uniquely altered RNA expression and associated biological signals in BM LSK cells from mice and BM CD34+ cells from human CMML that carry both KDM6B overexpression and Tet2 deficiency

overall_design: examining overall RNA expression alterations in BM LSK cells from mice carrying both KDM6B overexpression and Tet2 deficiency

first: Guillermo

last: Garcia-Manero

last: Lu

first: Kevin

last: Lin


title: Identification of KLF4 regulated transcriptional features in breast cancer

first: Haiwei

last: Wang

summary: Kruppel-like factor 4 (KLF4), as a eukaryotic transcription factor, participates in the regulation of cell proliferation, differentiation, embryonic development and other important life processes. KLF4 is also closely related to the occurrence and development in variety types of tumor. To determine the functions of KLF4 in breast cancer, we over-expressed KLF4 in breast cancer LM2-4175 cells and used gene expression profiling to identify KLF4 regulated genes.

overall_design: The stable KLF4 over-expressed LM2-4175 cell lines were generated by transduction a lentiviral-mediated expression plasmid. Total RNA from LM2-4175 control cells and KLF4 over-expressed LM2-4175 cells was collected and profiled to Affymetrix microarray.


title: RNA-Sequencing results of SLC26A4-AS1 overexpressing C643 cells and control cells

summary: We aimed to detect the mRNA expression levels in stable-transfected C643 cells after transfection with SLC26A4-AS1 overexpressing or control virus.

overall_design: SLC26A4-AS1 overexpressing C643 cells were established through lentiviral viral infection. RNAs were extracted at log phase of cell growth. RNA-Sequencing of SLC26A4-AS1 overexpressing cells (referring to AS1 ) and its control (PLVX) was performed according to standard protocols without replications.


title: Targeting KRASG12V mutations with HLA class II restricted TCR for the immunotherapy in solid tumors

status: Public on May 19 2023

city: Shanghai

last: Ai

address: 197 Ruijin Second Road, Shanghai

department: General Surgery

institute: Shanghai Jiaotong University

summary: To investigate the sequences of TILs, the sorted T cells were used for the following TCR sequencing analysis by 10X genomics Single Cell Sequencing. For the quality inspection and counting of single cell suspension, the cell survival rate is generally required to be more than 80%.

overall_design: Gene expression profiling analysis of single cell sequencing data for B13 TILs clontypes.

first: Fanlu

last: Li


title: c-kit+ progenitor cell (CPC) and extracellular vesicle total and small RNA sequencing

city: Atlanta

first: Michael

last: Davis

state: GA

address: 2015 Uppergate Dr

institute: Emory University

summary: To investigate transcriptomic differences between parent cell and extracellular vesicles from c-kit+ cardiac-derived progenitor cells collected from congenital heart disease patients

overall_design: Total and small RNA sequencing from CPCs and CPC extracellular vesicles

first: Jessica

last: Hoffman

first: Hyun-Ji

last: Park

first: Sruti

last: Bheri

first: Micahel

middle: E


title: Gene expression analysis in islets from miR-203 TG mice [RNA-seq]

city: Nanjing

first: Yuqian

last: Yang

state: Jiangsu

address: 101 Longmian Avenue

department: Biochemistry and Molecular Biology

institute: Nanjing Medical University

summary: To investigate the effect of miR-203 in type 2 diabetes, target genes of miR-203 need to be investigated. The β cell specific miR-203 transgene (miR-203 TG) mice was constructed, and RNA-seq was then performed on mouse islets.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of islets from 10-week-old WT and TG mice.

first: Lu

last: He

first: Yunxia

last: Zhu

first: Xiao

last: Han


title: Non-pathogenic and pathogenic leaf-colonising bacteria elicit qualitatively similar responses

city: Christchurch, Canterbury

first: Moritz

last: Miebach

state: Canterbury

address: 20 Kirkwood Avenue, University of Canterbury Private Bag 4800

department: School of Biological Sciences

country: New Zealand

institute: University of Canterbury

summary: Leaves are colonised by a complex mix of microbes, termed the leaf microbiota. Even though the leaf microbiota is increasingly recognised as an integral part of plant life and health, our understanding of its interactions with the plant host is still limited. Here, mature, axenically grown Arabidopsis thaliana plants were spray-inoculated with diverse leaf-colonising bacteria. Whole transcriptome sequencing revealed that four days after inoculation, leaf transcriptional changes to colonisation by non-pathogenic and pathogenic bacteria differed in strength but not in the type of response.

overall_design: Examination of aboveground Arabidopsis thaliana tissue treated either with different bacterial leaf colonisers (pathogenic and non-pathogenic) in comparison to mock-treated plants. Plants were grown in the ‘Litterbox’ system. Plants were 4-weeks-old at time of inoculation and sampled 96 h post inoculation.

first: Lea

last: Faivre

first: Daniel

last: Schubert

first: Paula

last: Jameson

first: Mitja

middle: N

last: Remus-Emsermann


title: Non-pathogenic leaf-colonising bacteria elicit plant immune responses in a colonisation density-dependent manner

summary: Leaves are colonised by a complex mix of microbes, termed the leaf microbiota. Even though the leaf microbiota is increasingly recognised as an integral part of plant life and health, our understanding of its interactions with the plant host is still limited. Here, mature, axenically grown Arabidopsis thaliana plants were spray-inoculated with different densities of the non-pathogenic bacterium Williamsia sp. Leaf354. High bacterial titers caused disease phenotypes and led to severe transcriptional reprogramming with a strong focus on plant defence.

overall_design: Examination of aboveground Arabidopsis thaliana tissue treated with different bacterial densities of the non-pathogenic bacterium Williamsia sp. Leaf354 in comparison to mock treated plants. Plants were grown in the ‘Litterbox’ system. Plants were 6-weeks-old at time of inoculation and were sampled 96 h post inoculation.


title: Effect of depletion of pre-existing senescent cells in aged hamstrers  on gene expression in lungs

city: BESANCON

first: Fabrice

last: Bouilloux

address: 18 rue Alain Savary

institute: BIOMNIGENE

summary: To investigate the potential role of senescent cells in COVID19-like pathology, aged hamsters were treated with the senolytics ABT-263 one day prior to a SARS-CoV-2 infection

overall_design:
We performed gene expression profiling analysis using data obtained from RNA-seq of vehicle-treated aged hamsters and ABT-263-treated aged hamsters at day 7 post-infection
Comparative gene expression profiling analysis of RNA-seq data

first: François

last: Trottein


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [13E-F]

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

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 (13E_210311, 13E_210318, 13F_210311).

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

middle: G

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: A Treg specific long non-coding RNA maintains immune-metabolic homeostasis in ageing liver [Young Treg]

first: Chenbo

last: Ding

state: None Selected

address: 280 Chongqing South Rd

institute: Shanghai Jiao Tong University School of Medicine

summary: We then performed gene expression profiling analysis using data obtained from RNA-seq of young Altre-WT and Altre-KO Tregs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for young Altre-WT and Altre-KO Tregs.


title: Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration

city: Utrecht

first: Phong

middle: Dang

last: Nguyen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied, little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad, a structure that regulates calcium handling and excitation-contraction coupling, played a key role in the redifferentiation process. A component of the cardiac dyad called leucine-rich repeat–containing 10 (Lrrc10) acted as a negative regulator of proliferation, prevented cardiomegaly, and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: Samples 1-6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 after cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10-mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.

first: Iris

last: Gooijers

first: Giulia

last: Campostrini

first: Arie

middle: O

last: Verkerk

first: Hessel

last: Honkoop

first: Mara

last: Bouwman

first: Dennis

last: de Bakker

first: Tim

last: Koopmans

first: Aryan

last: Vink

first: Gerda

last: Lamers

first: Avraham

last: Shakked

first: Jonas

last: Mars

first: Sonja

last: Chocron

first: Kerstin

last: Bartscherer

first: Eldad

last: Tzahor

first: Christine

last: Mummery

first: Teun

last: de Boer

first: Milena

last: Bellin

first: Jeroen

last: Bakkers


title: A Treg specific long non-coding RNA maintains immune-metabolic homeostasis in ageing liver [Altre-WT and Altre-KO]

first: Chenbo

last: Ding

summary: To investigate the cooperative function Altre in the regulation of Tregs with aging, we established Altre CD4-CRE and Foxp3-CRE mice in which Altre has been knockout in CD4+ T cells or Tregs.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of Tregs at 14 month old.
Comparative gene expression profiling analysis of RNA-seq data for Tregs in Altre-WT and Altre-KO mice during young and aged.


title: Stressing Out Epigenetics: A Profile of the Global Effects of Stress on DNA Modifications in the Brain (RNA-Seq)

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

summary: Differential 5mC and 5hmC regions across different social defeat conditions were correlated to paired RNAseq data in order to elucidate the epigenetic contribution to differences in stress response.

overall_design: 5mC and 5hmC were enrihced from mouse cortex

first: Janise

last: Kuehner


title: Stressing Out Epigenetics: A Profile of the Global Effects of Stress on DNA Modifications in the Brain (ChIP-Seq)


title: A Treg specific long non-coding RNA maintains immune-metabolic homeostasis in ageing liver [Naive T cells, Th17 and Tregs]

summary: We then performed gene expression profiling analysis using data obtained from RNA-seq of Naive T cells, Th17 and Tregs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Naive T cells, Th17 and Tregs.


title: Stressing Out Epigenetics: A Profile of the Global Effects of Stress on DNA Modifications in the Brain

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

overall_design: Refer to individual Series


title: The CDK12-INTAC Axis Modulates LEO1 Phosphorylation for Processive Transcription Elongation

city: Wuhan

first: Yin

last: Zhinang

state: Hubei

address: Donghu road 185

institute: Wuhan University

summary: Cyclin-dependent kinase 12 (CDK12) interacts with Cyclin K to form a a functional nuclear kinase complex, which has been reported to phosphorylate the carboxyl-terminal domain (CTD) of RNA polymerase II (Pol II) for transcriptional regulation and co-transcriptional RNA processing. However, the precise mechanisms and targets of CDK12 action remain largely unknown. Here, we combined a chemical genetic screen and phosphoproteomic strategies and identified a landscape of nuclear CDK12 substrates, which included proteins that regulate transcription, chromatin organization, and RNA splicing. Next, we confirmed that the LEO1 subunit of the transcription elongation factor PAF1 complex (PAF1C) is a bona fide substrate of CDK12. Acute depletion of LEO1 reduces Pol II occupancy on the chromatin, while mutations of LEO1 phosphorylation sites to non-phosphorylatable alanine residues attenuated the association of PAF1C with elongating Pol II and chromatin, resulting in impaired processive transcription elongation. Furthermore, LEO1 C-terminus could interact with and be dephosphorylated by the Integrator-PP2A complex (INTAC), while acute depletion of INTAC in cells promotes the association between PAF1C and elongating Pol II on the chromatin. Together, this study provides a novel transcriptional regulatory mechanism that the CDK12-INTAC axis fine-tunes LEO1 phosphorylation for processive transcription elongation.

overall_design:
Determination of PAF1C and Pol II occupancy by ChIP-Rx
Determination of nascent RNA synthesis by TT-seq
Determination of elongating Pol II by PRO-seq

first: Kaiwei

last: Liang


title: Comparing transcriptional effects of radioprotection with dmPGE2 to that of other EP receptor agonists in both hematopoietic stem cells and bone marrow stromal cells

city: Indianapolis

first: Andrea

middle: Marie

last: Patterson

state: IN

address: 980 W. Walnut St.

department: Medicine

institute: Indiana University School of Medicine

summary: We report transcriptional analyses of individual and combined EP receptor stimulation in radioprotective administration of dmPGE2 and other EP receptor agonists with varying radioprotective capacities. We find that in both hematopoietic stem cells, and in BM stromal (non-hematopoietic) cells, dmPGE2 radioprotection is primarily mediated through EP4 stimulation, but full activity likely requires interactive stimulation of both EP4 and EP3.

overall_design: Mice (2 male and 2 female per treatment group for each cell type analyzed) were injected with either vehicle (Veh), EP3 agonist sulprostone (EP3), EP4 agonist rivenprost (EP4), both sulprostone and rivenprost (EP3+4), or misoprostol (Miso) 30 min prior to TBI at 853 cGy. Non-irradiated (NI) mice were concurrently injected with vehicle and sham-irradiated. Bone marrow was harvested 1 h post-TBI. For HSC samples, phenotypic HSCs (SLAM-LKS) were sorted by FACS prior to RNA extraction. For BM stroma, non-hematopoietic cells (CD45- Ter119-) were magnetically enriched prior to RNA extraction.

first: Christie

last: Orschell


title: Rootstock induced scion resistance against tobacco mosaic virus is associated with the induction of defense related transcripts and graft transmissible mRNAs

city: College Park

first: Madhu

last: Kappagantu

state: MD

address: 4291 Fieldhouse drive

institute: University of Maryland

summary:
To investigate graft conferred resistance against viral diseases a novel hetero-grafting system was developed using Nicotiana benthamiana scions grafted onto different tomato rootstocks.
RNAseq analysis was used to identify mobile tomato mRNAs within N. benthamiana scions

overall_design: Mapping the scion derived transcripts to rootstock genome to identify mobile RNA

first: Matthew

last: Brandon

first: Yvette

middle: B

last: Tamukong

first: James

last: Culver


title: A Treg specific long non-coding RNA maintains immune-metabolic homeostasis in ageing liver


title: Site-specific R-loop formation induces CGG repeat contraction and Fragile X gene reactivation

city: Boston

first: Hun-Goo

last: Lee

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Mass General Hospital

summary: Fragile X syndrome (FXS) is a neurodevelopmental disorder and a leading cause of intellectual disability. In FXS, the neuronal regulator, FMR1, is epigenetically silenced by a CGG repeat expansion. Here, we investigate conditions under which repeat expansion and gene silencing could be reversed. Surprisingly, inducing formation of R-loops (3-stranded RNA-DNA structures) within FMR1 is sufficient to initiate CGG contraction, promoter demethylation, and FMR1 reactivation. Recruiting RNaseH degrades the R-loop and abolishes the response. Targeting the nascent mRNA for degradation also eliminates the response. Thus, we have identified an exogenous nuclease-free method of contracting CGG repeats and reversing FMR1 silencing. We propose that DNA demethylation, new transcription, and R-loop formation engage in a feed-forward cycle to contract CGG repeats and reactivate FMR1.

overall_design: Four RNA-seq samples consisting of two replicates from the FXS full-mutation iPS cells expressing dCas9 and gNHG3(guide RNA targeting to FMR1 gene) and two replicates with scrambled guide RNA (gScr) as control.

first: Jeannie

middle: T


title: RNA-seq Analysis of with/without overexpression of ASC  in SAS cell line

city: Taoyuan

first: Chi-Sheng

last: Wu

address: No.259, Wenhua 1st Rd., Guishan Dist.

institute: Chang Gung University

summary: To investigate the genes regulated by ASC, we generated the RNA-seq data of oral cancer cell line SAS with/without overexpression of ASC gene .

overall_design: SAS cell line was stably expressed pLKO.AS2.neo.ASC and pLKO.AS2.neo plasmids, respectively.

first: Ian

last: Chang


title: RNA-Seq transcriptome analysis of ileum in Taiping chicken supplemented with fructooligosaccharide

city: Tianshui

first: Fang

last: Ma

state: Qinzhou District

address: South Xihe Road

department: College of Bioengineering and Technology

institute: Tianshui normal university

summary:
Purpose: Our data significantly advance understanding of Fructooligosaccharide regulatory mechanism  in  ileum of Taiping chicken
Methods: Using RNA-seq analysis to study the gene expression in ileum tissue after Taiping chicken was given Fructooligosaccharide
Results: A total of 164,629,826 and 152,047,552 raw reads were generated from the CT and FOS, respectively . After removing the interference data, about 164,028,872 and 151,452,588 clean reads were obtained
Conclusions: through high-throughput sequencing of the six libraries from ileum of Taiping chicken, the expression level of mRNA has significant changes after given probiotics

overall_design: Control group (CT), birds were fed a corn-soybean basal diet , Fructooligosaccharide group (FOS), birds were given a basal diet supplemented with 1 mL of  Fructooligosaccharide per litre of water


title: EGR3 regulates opioid-related nociception and motivation in male rats

status: Public on May 18 2023

city: Buffalo

first: Fraser

middle: James

last: Sim

state: NY

address: 3435 Main Street

department: Pharmacology

institute: University at Buffalo

summary: Chronic pain can be a debilitating condition, leading to profound changes in nearly every aspect of life. However, the reliance on opioids such as oxycodone for pain management is thought to initiate dependence and addiction liability. The neurobiological intersection at which opioids relieve pain and possibly transition to addiction is poorly understood. Using RNA sequencing pathway analysis in rats with complete Freund's adjuvant (CFA)-induced chronic inflammation, we found that the transcriptional signatures in the medial prefrontal cortex (mPFC; a brain region where pain and reward signals integrate) elicited by CFA in combination with oxycodone differed from those elicited by CFA or oxycodone alone. However, the expression of Egr3 was augmented in all animals receiving oxycodone. Furthermore, virus-mediated overexpression of EGR3 in the mPFC increased mechanical pain relief but not the affective aspect of pain in animals receiving oxycodone, whereas pharmacological inhibition of EGR3 via NFAT attenuated mechanical pain relief. Egr3 overexpression also increased the motivation to obtain oxycodone infusions in a progressive ratio test without altering the acquisition or maintenance of oxycodone self-administration. Taken together, these data suggest that EGR3 in the mPFC is at the intersection of nociceptive and addictive-like behaviors.

overall_design:
The experiment is a 2x2 factorial design, with pain (CFA or saline) and drug (oxycodone or saline) as independent variables.
Rats received injections of either CFA to induce chronic pain or saline as a control. Thereafter, they receive injections of oxycodone or saline (IP, daily, 7 days). Animals were euthanized at the end of the experiment and brains extracted. The mPFC was removed and RNA extracted for RNA-seq analysis.

first: Swarup

last: Mitra

first: Shruthi

last: Thomas

first: Jennifer

last: Martin

first: Jamal

last: Williams

first: Kristen

last: Woodhouse

first: Ramesh

last: Chandra

first: Jun

middle: X

last: Li

first: Mary

middle: K

last: Lobo

middle: J

first: David

middle: M

last: Dietz


title: Immunogenetic metabolomics revealed key enzymes that modulate CAR-T metabolism and function [DNA-edit]

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

summary: Immune evasion is a critical step of cancer progression that remains a major obstacle for current T cell-based immunotherapies. Hence, we seek to genetically reprogram T cells to exploit a common tumor-intrinsic evasion mechanism, whereby cancer cells suppress T cell function by generating a metabolically unfavorable tumor microenvironment (TME). Specifically, we use an in silico screen to identify ADA and PDK1 as metabolic regulators, in which gene overexpression (OE) enhances the cytolysis of CD19-specific CD8 CAR-T cells against cognate leukemia cells, and conversely, ADA or PDK1 deficiency dampens such effect. Additionally, ADA-OE in CAR-T cells improves cancer cytolysis under high concentrations of adenosine, the ADA substrate and an immunosuppressive metabolite in the TME. High-throughput transcriptomics and metabolomics in these CAR-Ts reveal alterations of global gene expression and metabolic signatures in both ADA- and PDK1- engineered CAR-T cells. Functional and immunological analyses demonstrate that ADA-OE increases proliferation and decreases exhaustion in α-CD19 and α-HER2 CAR-T cells. We then show ADA-OE improves tumor infiltration and clearance by α-HER2 CD4 and CD8 CAR-T with an in vivo colorectal cancer model.  Collectively, these data unveil systematic knowledge of metabolic reprogramming directly in CAR-T cells, and reveal potential targets for improving CAR-T based cell therapy.

overall_design: Genetic perturbations from CRISPR-RNP were quantified from a genomic locus of interest. For each comparison, indels were quantified from samples treated with target or control gRNA (n=3 per condition for eah comparison)

first: Paul

middle: A

last: Renauer


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [13CD]

first: Joseph

middle: R

last: Ecker

state: CA

department: Genomic Analysis Laboratory

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 (13C_210225, 13C_210304, 13D_200917, 13D_200924).

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

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: Immunogenetic metabolomics revealed key enzymes that modulate CAR-T metabolism and function [RNA-seq]

overall_design: RNA-seq