title: Interconnected lineage trajectories link conventional and NK-like exhausted CD8+ T cells beneficial in T1D [P452_3]

summary: While distinct NK-like CD57+ and PD-1+ CD8+ exhausted T cell populations (Tex) were both linked to beneficial immunotherapy response in autoimmune Type 1 Diabetes (T1D) patients, relationships between these cell types are poorly understood. We show that PD-1+ and CD57+ Tex populations in this context were epigenetically similar, but CD57+ Tex cells displayed unique increased chromatin accessibility of inhibitory Killer Cell Immunoglobulin-like Receptor (iKIR) and other NK cell genes. PD-1+ and CD57+ Tex also showed reciprocal expression of Inhibitory Receptors (IRs) and iKIRs accompanied by chromatin accessibility of Tcf1 and Tbet transcription factor target sites, respectively. CD57+ Tex showed unappreciated gene expression heterogeneity and shared clonal relationships with PD-1+ Tex, with these cells differentiating along four interconnected lineage trajectories: Tex-PD-1+, Tex-CD57+, Tex-Branching, and Tex-Fluid. Our findings demonstrate new relationships between Tex populations in human autoimmune disease and suggest that modulating common precursor populations may enhance response to autoimmune disease treatment.

overall_design: We performed bulk Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq) on PBMC samples selected from 4 donors with new onset T1D that were responders to alefacept (T1DAL Trial, ITN). Donors were sampled at baseline (Week 0/Visit 0) and 104 wk (Visit 30) post-treatment with alefacept. PBMC samples were stained with a flow cytometry panel (Table S4) and sorted with the FACS Aria II (Becton Dickinson) cell sorter into 3 subsets of non-naïve CD8+ T cells (singlet, live, CD14- CD19- CD56- CD3+ CD8+ CD4-, not CD45RA+ CCR7+): (1) Double Negative non-Tex (DN, KLRG1- TIGIT-), (2) CD57+ Tex (KLRG1+TIGIT+, CD57+), and (3) CD57- Tex (KLRG1+TIGIT+, CD57-). These subsets were compared for downstream differential accesibility analysis.

first: S

last: Long

first: Peter

last: Linsley

first: Kirsten

last: Diggins

first: Alice

last: Wiedeman

first: Elisavet

last: Serti

first: Vivian

middle: H

last: Gersuk

first: Gerald

last: Nepom

first: Bryce

last: Fuchs


title: Effect of knockdown or overexpression of CYP1B1 on gene expression during proliferation process of colorectal cancer cells (RKO and SW480).

status: Public on Jan 17 2024

city: Shanghai

first: Lei

last: Jin

state: Shanghai

address: Shanghai Fenglin Road

country: China

institute: Fudan University

type: Expression profiling by high throughput sequencing

summary: To investigate the function of CYP1B1 in the regulation of proliferation process, we established SW480 cells in which target gene has been knocked down by shRNA and established RKO cells in which target gene has been upregulated by overexpressed plasmid.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells (RKO-Control vs RKO-CYP1B1, SW480-shNT vs SW480-shCYP1B1).

first: Ju

last: Huang

last: Guo

first: Ming

last: Lu


title: Early Involvement of Peripherally Derived Monocytes in Inflammation in an NMO-Like Mouse Model [microglia]

city: Seouol

first: Moonhang

last: Kim

state: Seoul

address: 71, Daehak-ro, Jongno-gu, Seoul, Korea

country: South Korea

institute: Biomedical Research Institute

summary: Neuromyelitis optica (NMO) is an autoimmune inflammatory disease that primarily affects the spinal cord and optic nerves in the central nervous system (CNS). It is characterized by the presence of immunoglobulin G (IgG) antibodies against aquaporin 4, a protein found in astrocytes (known as NMO-IgG). Monocytes/macrophages and microglia accumulate at the active injury sites and contribute to the disease process. However, it is unclear whether these active cells originate from circulating monocytes/macrophages or resident microglia. Recent studies have investigated the role of microglia/macrophages in multiple sclerosis (MS) using specific microglial markers, such as P2ry12 and Tmem119, and have shown that active cells are derived from microglia. In contrast, the function of monocyte/macrophages and microglia in NMO has not been extensively studied. Therefore, this study aims to analyze the functions of monocytes/macrophages and microglia using microglial markers (P2ry12 and Tmem119) in an NMO-like mouse model and evaluate their role in the pathophysiology of NMO.

overall_design: Cells were labeled with CD45, CD11b, P2ry12, Ly6C and Ly6G, and sorted CD45+CD11b+P2ry12+ cells for microglia

first: SungMin


title: Long non-coding RNAs and their potential function in postharvest senescence of Sparassis latifolia packaged with oriented polypropylene film

city: Fuzhou

first: mengting

last: weng

address: Xin dian town, jin'an district

institute: Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary:
To investigate the role of lncRNAs in postharvest senescence of Sparassis latifolia, We stored the fruiting bodies of S. latifolia at 4 ℃ for 0, 8, 16 and 24 days with OPP film packaging after harvest and profiled the lncRNA and mRNA transcriptome.
We then performed gene expression profiling analysis using data obtained from RNA-seq of fruiting body at 4 time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  fruiting body of Sparassis latifolia at 4 time points.

first: Mengting

last: Weng

first: Di

last: Zhang


title: Gene expression profile at single cell level of cells from OS tissue of OS lung metastatic patient

city: Kunming

first: Chenhong

last: Zheng

address: No. 174 Renmin West Road

institute: Yunnan Cancer Hospital

summary: The tumor microenvironment remains unclear in OS lung metastatic patient. We used single cell RNA-seq to analyze the non-immune and immune landscape of the tumor microenvironment in OS patients.

overall_design: Single cells were isolated from OS tissue of OS lung metastatic patient.

first: Zhihong

last: Yao


title: Interactions between insulin resistance, epigenetics, and donor sex in control of gene expression in human iPS cell-derived myoblasts

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

country: USA

institute: Joslin Diabetes Center

summary: About 25% of people within the general population are insulin resistant, increasing the risk for type 2 diabetes (T2D) and metabolic disease. Transcriptomic analysis of iPS cells differentiated into myoblasts (iMyos) from insulin resistant (I-Res) versus insulin sensitive (I-Sen) non-diabetic individuals reveals 306 genes increased and 271 genes decreased in expression in iMyos from insulin resistant donors with differences of 2-folds or more. Over 30 of the genes changed in I-Res iMyos are associated with T2D by SNP polymorphisms and functionally linked to insulin action and control of metabolism. Interestingly, we also identified >1500 differences in gene expression that were dependent on sex of the cell donor, some of which modified the insulin resistance effects. Many of these sex-differences were associated with increased DNA methylation in cells from females and reversed by 5-azacytidine. By contrast, the insulin sensitivity differences were not reversed and thus appear to reflect genetic or methylation-independent epigenetic effects.

overall_design: Comparing gene expression profile of insulin sensitive (I-Sen) and insulin resistant (I-Res) iPSCs-derived myoblasts (iMyos) from males and females (total N=16)

first: Nida

last: Haider

first: C

middle: R

last: Kahn


title: Effect of long-chained auxin conjugates on gene  expression in the seedlings of Brassica rapa

city: ZAGREB

first: Branka

last: Salopek Sondi

address: Bijenička cesta 54

department: Division of Molecular Biology

country: Croatia

institute: Ruđer Bošković Institute

summary: Auxin amino acid conjugates are considered storage forms of auxins available as a source of active auxins on the plant demand. We treated Brassica rapa seedlings with 0.01 mM indole-3-acetyl-L-alanine (IAA-Ala), indole-3-propionyl-L-alanine (IPA-Ala), and indole- 3-butyryl-L-alanine (IBA-Ala) and examined their effects on the transcriptome. All auxin conjugate treatments caused similar patterns in transcription profiles compared to the control, but with different intensities of over- and under-expression depending on the treatment. Most auxin-related DEGs were identified after IBA-Ala treatment, followed by IPA-Ala and IAA-Ala, respectively.

overall_design: Seeds of Chinese cabbage (Brassica rapa L. ssp. pekinensis (Lour.) Hanelt cv. Cantonner Witkrop) were sterilized and germinated, and the 1-day-old seedlings were placed on 1 % agar plates, supplemented with the hormones indole-3-acetyl-L-alanine (IAA-Ala), indole-3-propionyl-L-alanine (IPA-Ala) or indole-3-butyryl-L-alanine (IBA-Ala) in 0.01 mM concentration. Seedlings on hormone-free agar plates were used as a control. Following incubation of the seedlings under continuous light for a further 24 h at 22 °C, total RNA was isolated from 100 mg of whole seedlings. Two biological replicates per treatment were sequenced, and two biological replicates were sequenced as a control against which changes of gene expression were ascertained.

middle: S

last: Sondi

first: Ana

last: Smolko

first: Jelena

last: Repar


title: Gene expression profile at single cell level of Wilms tumors and normal kidney tissues from an infant with Denys-Drash syndrom

city: Nanjing

first: Mingshun

state: Jiangsu

address: 101 Longmian Road

institute: Nanjing Medical University

summary: Denys-Drash syndrom is a rare disease. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of kidney tissue cells in an infant with Denys-Drash syndrom.

overall_design: Samples from kidney tissues, including Wilms tumors and normal kidney tissues, were  analyzed using scRNAseq.

first: Tao

last: Li

first: Jiangfeng

last: Zhou


title: Gene expression data of colorectal cancer patient-derived cells treated with tankyrase inhibitors

city: Tokyo

first: Tetsuo

last: Mashima

address: Koto-ku, Ariake 3-8-31

department: Cancer Chemotherapy Center

country: Japan

institute: Japanese Foundation for Cancer Research

summary: Tankyrase, a poly(ADP-ribose) polymerase family member, regulates multiple cellular processes. Tankyrase inhibitors efficiently suppress colorectal cancer (CRC) cell proliferation. To examine the mechanism of anti-proliferative effect of tankyrase inhibitors (G007LK and RK582), we analyzed gene expression profiles of patient-derived CRC cells (JC11 and JC494) left untreated or treated with 0.3 µM G007LK or RK582 for 24 h by cDNA microarray analysis.

overall_design: The patient-derived CRC cells, JC11 and JC494, were left untreated (DMSO) or treated with 0.3 µM G007LK or RK582 for 24 h. After the treatment, cells were collected and then gene expression data were obtained.

first: Mingjue

last: Chen

first: Yukiko

last: Muramatsu

first: Fumiyuki

last: Shirai

first: Satoshi

last: Nagayama

first: Ryohei

last: Katayama

first: Hiroyuki

last: Seimiya


title: sRNA sequencing to compare small non-coding RNA profiles of hepatocellular carcinoma cell lines Huh7, HepG2, and Hep3B against the normal liver cell HL7702

city: Nanning

first: liao

last: zhouxiang

address: Shuangyong road #22

institute: Guangxi Medical University

summary: To evaluate small non-coding dysregulation in HCC cells, we sequenced hepatocellular carcinoma cell lines Huh7, HepG2, and Hep3B and normal liver cell HL7702 to compare their mall non-coding RNA profiles.

overall_design: We performed gene expression profiling analysis using data obtained from sRNA-sequencing of 4 different cell lines.

first: Zhouxiang

last: Liao

first: Lichao

last: Yang

first: Min

last: He


title: RNA profiling of extracellular vesicles from human plasma

city: Hamburg

first: Andreas

last: Neueder

address: Falkenried 94

department: Center for Molecular Neurobiology (ZMNH)

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary: Total RNA from 59 human plasma samples was used to generate signatures of extracellular vesicles used as basis for evaluation of potential disease states

overall_design: RNA profiling of extracellular vesicles from plasma

first: Philipp

last: Nitzschner

first: Ronja

last: Wagner

first: Julia

last: Hummel

first: Franziska

last: Hoschek

first: Maximilian

first: Alshaimaa

last: Abdelmoez

first: Björn

last: von Einem

first: Bernhard

last: Landwehrmeyer

first: Sarah

last: Tabrizi

first: Michael

last: Orth


title: Single-nuclei sequencing of late gestation rhesus macaques exposed to chorioamnionitis

city: Miami

first: Augusto

middle: F

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

summary: We used single-nuclei sequencign to determine the effect of chorioamnionitis to the developing cerebellum using a rhesus macaque model of chorioamnionitis induced by intra-amniotic LPS.

overall_design: Cerebellar hemispheres were sampled from rhesus macaque fetuses at 130-133 days of gestation 5 days after exposure to 1mg of intra-amniotic LPS or controls without intervention

first: Alan

last: Jobe

first: Claire

last: Chougnet

first: Roberta

last: Brambilla

first: Suhas

last: Kallapur


title: Gene expression profilings of neural progenitor cell derived from hiPSC with ROR2 knockdown

city: Kawasaki City

first: Takuya

last: Kuroda

state: Kanagawa

address: 3-25-26 Tonomachi, Kawasaki Ward,

institute: National Institute of Health Sciences

summary: Human induced pluripotent stem cells (hiPSCs) have the ability to differentiate into a variety of cells and to self-renew in vitro. Because of these two characteristics, hiPSCs have been expected to provide new applications for regenerative medicine/cell therapy. Although various in vitro differentiation protocols have been developed for the efficient derivation of specific cell types, hiPSC lines vary in their ability to differentiate into specific lineages. Therefore, surrogate markers that accurately predict the differentiation propensity of hiPSC lines could be helpful for the development and manufacture of hiPSC-derived cells for therapies and in vitro assays. Here, we tried to identify the marker genes that potentially predicts the differentiation propensity of hiPSCs into neural progenitor cells (NPCs). Using ten hiPSC lines, we searched for genes significantly correlated between expression levels in the undifferentiated state and neuronal differentiation efficiency using two differentiation induction methods, and selected genes that were commonly and predominantly correlated with neuronal differentiation. Among the genes correlated with NPC differentiation, we identified ROR2 as a novel predictive marker of NPC differentiation. ROR2 expression in hiPSCs correlates negatively with NPC differentiation capacity, and ROR2 knockdown enhances NPC differentiation. These findings suggest that ROR2 serves as a useful surrogate marker for selecting hiPSC lines appropriate for NPC differentiation.

overall_design: To investigate how the ROR2 suppress differentiation of hiPSCs to NPC, we compared gene expression profiles during differentiation of hiPSC into late-stage NPC between ROR2 knockdown and control lines.

first: Satoshi

last: Yasuda

first: Yoji

last: Sato


title: Comparative analysis of Retinal Angiogenesis during Inflammatory stage

city: Wuxi

first: Yanshan

last: Liu

address: No1800, Lihu Road

institute: Jiangnan University

summary: Choroidal neovascularization (CNV) and the resulting retinal angiogenesis are pathological hallmarks of wet Age-related macular degeneration (AMD). The pathogenesis of CNV is not fully understood, but accumulated evidence has suggested the role of inflammation in the early stage of CNV. To better understand the molecular landscape during the early stage, we performed RNA-Seq and mass spectrometry-based proteomic analysis in the retina of the laser-induced CNV mouse model. Both transcriptomic and proteomic data showed dramatic activation of inflammatory response 3 days post photocoagulation. Integrative analysis suggested a moderate correlation between RNA-Seq and mass spec. Up-regulation of angiogenic factor, basic fibroblast growth factor-2 (Fgf-2), but not vascular endothelial growth factor (Vegf) was observed at both RNA and protein levels, highlighting Fgf-2 as a biomarker and potential therapeutic target during the early stage of CNV. In addition, enrichment analysis indicated a large overlap of inflammation-related genes and pathways at both levels. We also compared our findings with human retinal RNA-Seq data from AMD patients and controls. By using a multi-omics and comparative approach, our findings demonstrate the molecular landscape during the inflammatory stage of mouse CNV and provided new insight into the translation from the mouse model to understanding human AMD and its potential intervention and therapies.

overall_design: C57BL/6 mice (8-12 weeks) were pursued from Zhaoyan New Drug Research Center. The animals were maintained (5 mice/cage) in an air-conditioned room (24 ± 1°C) with a 12-h light/12-h dark cycle and free access to food and water and were allowed to acclimatize for 1 week before the experiment began. All animal experiments were performed by the requirements of the Animal Welfare Committee of Wuxi School of Medicine, Jiangnan University. All mice were anesthetized by intraperitoneal injection of hydrated chloral. Then pupils were dilated with topical administration of compound tomidlamide eye drops. Laser photocoagulation (75 um spot size, 0.1s duration) was conducted by 532nm laser (Quantel medical, VITRA, France) with slit lamp microscope (Haag-Streit, BQ900, Germany) at the 3, 6, 9, and 12 o’clock positions to burn the retina. For each mouse, only the right eye (oculus dextrus, OD) was undertaken laser induction. The left eye (oculus sinister, OS) was used as an autologous negative control. Three days and seven days post laser induction, mice were sacrificed and retinas were isolated for RNAseq.

first: Jian-Huan

last: Chen

first: Yan-Shan

first: Jia-Qi

last: Pan

first: Zhi-Yuan

last: Wei


title: Analysis of the overlapping tri-nucleosome association with genomic and synthetic DNA

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Nucleosome consists of a histone octamer wrapped by 145 bps of DNA and serves as a fundamental unit of chromatin. The overlapping di-nucleosome (OLDN) is found as another chromatin unit, in which 250 bps of DNA continuously wraps around the intimately associated histone octamer-hexamer complex. In the present study, our genome-wide analysis found a higher nucleosome stacking structure, overlapping tri-nucleosome (OLTN), in which about 350 bps of DNA wrap around the histone octamer-hexamer-hexamer complex. We quantified the length of DNA associated with the 20-mer histone core, and also we found that the OLTN localizes downstream of the transcription start sites as well as the OLDN does. The results suggest that nucleosome stacking structures may be formed for gene regulation.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: MNase-seq of presumable fragments of OLTN, OLDN, and nucleosome using HeLa cell genomic DNA and synthetic DNA

first: Masahiro

last: Nishimura

first: Takeru

last: Fujii

first: Hiroki

last: Tanaka

first: Kazumitsu

last: Maehara

first: Kayo

last: Nozawa

first: Yoshimasa

last: Takizawa

first: Hitoshi

last: Kurumizaka


title: Interconnected lineage trajectories link conventional and NK-like exhausted CD8+ T cells beneficial in T1D [P362-1]

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

overall_design: We performed single cell RNA-sequencing (scRNA-seq) and single cell TCR-sequqencing on the same cells using the 10X platform. We sequenced CD8+ non-naïve memory cells from 6 Responders and 6 Non-responders (NR) at 104 wk following their treatment with the T cell targeting therapy alefacept (LFA3-Ig) (T1DAL trial). 12 total samples were sequenced each from individual donors (one sample per donor).

first: S

middle: A

last: Long

first: Peter

last: Linsley

first: Kirsten

last: Diggins

first: Alice

last: Wiedeman

first: Elisavet

last: Serti

first: Vivian

last: Gersuk

first: Gerald

last: Nepom

first: Bryce

last: Fuchs


title: Single-cell genomics analysis reveals complex genetic interactions in an in vivo model of acquired BRAF inhibitor resistance.

city: Iowa City

first: Adam

middle: J

last: Dupuy

state: IA

address: 375 Newton Road

institute: University of Iowa

summary: Single cell transposon insertion site profiles were generated from A375 xenograft tumors that had aquired BRAF inhibitor resistance in vivo as a consequence of Sleeping Beauty transposon mutagenesis.

overall_design: These data were extracted from a modified 10X Genomics CNV worflow.


title: Gene expression data of APC-mutated colorectal cancer patient-derived cells treated with tankyrase inhibitors

first: Tetsuo

last: Mashima

summary: Tankyrase, a poly(ADP-ribose) polymerase family member, regulates multiple cellular processes. Tankyrase inhibitors efficiently suppress APC-mutated colorectal cancer (CRC) cell proliferation. To examine the mechanism of anti-proliferative effect of tankyrase inhibitors (G007LK and RK582), we analyzed gene expression profiles of patient-derived APC-mutated CRC cells (JC21 and JC475) left untreated or treated with 0.3 µM G007LK or RK582 for 24 h by cDNA microarray analysis.

overall_design: The patient-derived CRC cells, JC21 and JC475, were left untreated (DMSO) or treated with 0.3 µM G007LK or RK582 for 24 h. After the treatment, cells were collected and then gene expression data were obtained.

first: Mingjue

last: Chen

first: Yukiko

last: Muramatsu

first: Fumiyuki

last: Shirai

first: Satoshi

last: Nagayama

first: Ryohei

last: Katayama

first: Hiroyuki

last: Seimiya


title: Single cell RNAseq of human primary lung adenocarcinomas [scRNA-seq]

city: Tianjin

first: Hao

last: Wang

address: Tianjin Medical University, 22 Qixiangtai Road, Heping District, Tianjin 300070, China

institute: Tianjin Medical University

summary: To study heterogenous cellular function and behaviors, we isolated individual cells from freshly resected and dissociated two human primary lung adenocarcinomas, removed DAPI-positive dead cells, and performed single cell analysis using the 10x Genomics Chromium platform.

overall_design: 2 sample of human primary lung adenocarcinoma

first: Zhe

last: Liu


title: Enhancing High-Quality Fat Survival: A Novel Strategy Using Cell Free Fat Extract

status: Public on Jan 16 2024

city: Changsha

first: Mengqi

last: Nie

address: Xiangya Road

institute: Xiangya Hospital of Central South University

summary: High-quality fat (HQF) contains a higher proportion of stromal vascular fraction, adipose-derived stem cells, and extracellular matrix components, surpassing the effectiveness of the traditional Coleman fat grafting method and improving volumetric filling. However, this high-quality fat strategy inevitably leads to a significant amount of unused fat being wasted. CEFFE, a cell-free extract derived from autologous fat tissue, is enriched with bioactive molecules. In this study, we further process the remaining fat from preparing HQF into CEFFE to promote the survival of transplanted fat. Our study introduces CEFFE, from the remaining fat from preparing HQF, as a promising adjunct to HQF grafting, showcasing notable enhancements in graft survival, adipose tissue integrity, and angiogenesis. The observed positive effects on ADSCs, including augmented stemness and adipogenic differentiation potential, further contribute to the overall improvement in fat graft outcomes. While these findings present a novel strategy for addressing the limitations of traditional fat grafting, additional research and clinical studies are imperative to validate the long-term efficacy, safety, and broader applicability of CEFFE in enhancing fat graft survival and promoting tissue regeneration.

overall_design: Collect ADSCs samples after 3 days of cultivation with either 0% CEFFE (control group) or 10% CEFFE in 10% FBS DMEM low-glucose medium. Analyze differential gene expression between the FE treatment and control groups using RNA-Seq data.

first: Yi

last: Tian

first: Shaorong

last: Lei

first: Dingyu

last: Wu


title: A single fiber view of the nucleosome organization of eukaryotic chromatin

city: Dresden

first: Mark

last: Boltengagen

state: Saxony

address: Fiedlerstraße 42

department: Physiological Chemistry

institute: Dresden Technical University

summary: Nucleosomes arrange into extended arrays, much like beads on a string. They are often phased at genomic landmarks and are thought to be evenly spaced. Here we tested to what extent this stereotypic organization describes the nucleosome landscape in Saccharomyces cerevisiae using a long-read nucleosome-sequencing technique called Fiber-Seq. Fiber-Seq maps the nucleosome pattern on individual chromatin fibers. As such, it is ideally suited to measure the density of nucleosomes per read and quantitate the nucleosome occupancy throughout the genome. We document substantial deviations from the stereotypical nucleosome organization, with unexpectedly long linker DNAs between individual nucleosomes, genomic regions lacking entire nucleosomes, heterogeneous phasing of arrays, truly irregular spacing of arrays and read-to-read variation in nucleosome densities. We exploited the technology to test mechanistic models for the biogenesis of nucleosome arrays. We can rule out transcription elongation playing a decisive role in array formation and detect signatures for a clamping activity of remodelers of the ISWI and CHD1 families after acute nucleosome depletion in vivo. Given that nucleosomes are cis-regulatory elements, the cell-to-cell heterogeneity that Fiber-Seq uncovers provides much needed information to understand chromatin structure and function.

overall_design: Methylation profiling of S. cerevisiae strains using the Oxford Nanopore MinION and R9.4.1 version chemistry. Genomic DNA was treated by M.SssI, extracted and Nanopore sequencing was applied to detect DNA cytosine modification.

first: Daan

last: Verhagen

first: Michael

last: Wolff

first: Elisa

last: Oberbeckmann

first: Ulrich

last: Gerland

first: Philipp

last: Korber

first: Felix

last: Mueller-Planitz


title: Gene expression profile at the single cell level of human breast tissues of BRCA1/BRCA2 mutation carriers

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

summary: Goal of this study is to develop the single cell map of breast tissues of women who carry germline mutations in BRCA1 or BRCA2 genes. Towards this goal, we performed single cell RNA sequencing (sc-RNAseq) of cells isolated from cryopreserved tissues.


title: Lactacidosis impairs energy homeostasis of primary vascular smooth muscle cells - possible pathomechanisms during septic vasoplegia

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

institute: Martin Luther University - Halle-Wittenberg

summary: RNAsequencing was performed for human primary aortic smooth muscle cells (HAoSMCs) from male donors, after incubation at pH 7.4 (control condition or with Na+-Lactate) or at pH 6.8 (ajusted with HCl or lactic acid).

overall_design: HAoSMCs were incubated at pH 7.4 (control condition or with Na+-Lactate) or at pH 6.8 (ajusted with HCl or lactic acid) for 48 h (N = 5)

first: Stefanie

last: Ruhs

last: Terpe

last: Gekle

last: Bucher


title: Notch3 Deficiency Impairs Vascular Smooth Muscle Cell Contractility and Glymphatic Function in the Brain

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: While most cases of vascular dementia represent complex interactions between host genetics and environmental factors, mendelian forms of vascular dementia also exist. Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), is a mendelian disease characterized by progressive vascular deterioration, cognitive deficits, and strokes. Mutations in the NOTCH3 receptor underlies the pathologies in CADASIL. NOTCH3 is primarily expressed in vascular smooth muscle cell (vSMC) and its’ expression is critical for differentiation and functional integrity of arterial vSMCs, albeit through unclear mechanism(s). To elucidate the contribution of NOTCH3 in the maintenance of cerebral vascular architecture and function, we performed micro-computed tomography (micro-CT) on the brains of aged Notch3-deficient animals. Micro-CT assessment of the cerebral vasculature architecture showed significant abnormalities including severe vessel dilation and tortuosity (dolicoectasia) of the middle cerebral artery and its branches in the Notch3-/- compared to aged-match controls. To identify the molecular pathway from NOTCH3 dysregulation to the observed cerebral vascular dysfunction, we performed single-cell RNASeq on cerebral arteries isolated from young (4w) and old (104w) Notch3-/- animals. Evaluation of the vSMC-specific transcriptomes indicated significant loss of proteins associated with muscle contraction and increased extracellular matrix production in animals that lack NOTCH3. Using a combination of immunofluorescence microscopy and in vitro functional assays, we confirmed that continued expression of Notch3 is a critical requirement for maintenance of vSMC contractile function. Impaired contractility also affected flow of cerebrospinal fluid in the parenchyma of Notch3-/- . MRI and behavioral assessments were performed in the Notch3-/- animals to elucidate the relationship between impaired vascular contractility to cognitive function. Taken together these findings link the molecular dysfunction of NOTCH3 through its regulation of vascular contractility and cerebral vessel architecture to altered neurological function and clarify the molecular pathways to cellular pathology of Notch3 driven dementias.

overall_design: Single cell RNA sequencing on wildtype and Notch3 knock out mice in young and old ages

first: Milagros

last: Romay

first: M

middle: L

last: Iruela-Arispe


title: PAX5 promotes heterocharomatin formation

first: Yan

middle: Xue

last: miao

state: Tianjin

address: 22 Qixiangtai Road,Heping District,Tianjin,China

department: Department of Immunologyc

summary: Heterochromatin has a high density of DNA and low rates of gene transcription.H3k9me3 is a conserved histone modification, and is best known for its role in constitutive heterochromatin formation.H1155, which is a neuroendocrine large cell lung cancer cell line, has a dense nucleus and a high level of occupancy of H3K9me3. PAX5 is a neurogenesis and B lymphocyte development transcription factor, and endogenous expressed in neuroendocrine carcinoma, including H1155 cell line. To assess whether PAX5 promotes heterochromatin formation in H1155, we knock out PAX5 in H1155 cell (KO-PAX5) by CRISPR/Cas9 and use H3K9me3 to performed ChIP-seq.

overall_design: ChIP-seq analysis of H1155-WT (control) and KO-PAX5 (experimental group) with H3K9me3 antibody, two replicates. In order to calibrate the data, we mix 1% of Drosophila Schneider 2 (S2) cells with the tested cells and perform sonication, sipike in antibosy were added at the same time with H3K9me3.

first: Xuemiao

last: Yan

first: Zhe

last: Liu


title: Toll-Like Receptor-Induced Nucleosome Remodeling Achieved by Broadly Acting NF-kB in Collaboration with Transcription Factors Conferring Selectivity [BMDM_ATAC_2]

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

summary: Macrophages play a critical role in bridging the innate and adaptive immune systems, which requires timely and precise transcription control when responding to danger signals. Gene expression networks in macrophages have been profiled extensively in recent decades with the advancement of high-throughput sequencing technologies. However, unveiling critical mechanistic insights into control of diverse transcriptional networks has proven to be challenging. Recent evidence has suggested that the accessibility of chromatin structure can provide an integral means of transcription regulation. We have used the relatively recent Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq) method to assess chromatin accessibility with optimal resolution in mouse bone marrow derived macrophages during the course of lipid- A stimulation. This advanced method enabled us to characterize the chromatin state of genome-wide regulatory regions. By applying a quantitative systematic approach, we obtained mechanistic insights into the highly selective role of the major transcription factors, NF-κB and IRF3, in nucleosome remodeling and transcription regulation.

overall_design: Bone-marrow derived macrophages (background: C57Bl/6)  were stimulated with Lipid A (100 ng/mL), Pam3CSK4 (100 ng/mL) or Poly (I:C) (100 µg/ml) for 0 or 2 hours. Chromatin was collected and treated with Tn5 transposase to profile DNA accessibility.

first: A

middle: C

last: Feng

first: F

middle: M

last: Melo

first: S

middle: T


title: Death Receptor 5 Antisense Long Noncoding RNA and Cisplatin Modulate Macromolecular and Metabolic Changes in HeLa Cells

city: Izmir

first: Bünyamin

last: Akgül

state: Urla

address: Gulbahce Campus

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

summary: We have performed a transcriptomics study in which we first apply cisplatin to HeLa cells. Total RNA was isolated from control as well as treated cells and apoptosis was confirmed by Annexin V and 7AAD staining in flow cytometry. Total RNAs were subjected to deep-sequencing to identify differentially expressed mRNAs. We then took advantage of bioinformatic tools to identify which pathways are affected by Cisplatin treatment

overall_design: Total RNA was isolated from negative control and Cisplatin (80 uM) treated HeLa cells in triplicate to perform deep-sequencing. Negative controls from GSE160227 data was used as negative control in this study

first: Dilek

last: Gurer

first: Ipek

last: Erdogan

first: Ulvi

last: Ahmadov

first: Osama

last: Sweef

first: Bunyamin

last: Akgul


title: Differentially expressed genes induced by UVB stimulation between the P2ry6+/+ and P2ry6-/- mice

city: shanghai

first: xu

last: peng

state: Please select region, state or province

address: shanghai  dongchuan road 500号

institute: east china  normal  university

summary: Considering that human skin cancer is predominantly attributed to UV radiation from sunlight, additional investigations are needed to elucidate the role of P2RY6 in UVB-induced skin carcinogenesis. Surprisingly, we find that P2ry6 deletion exhibits marked promotion to UVB-induced skin papilloma formation compared with wild-type mice, suggesting its tumor-suppressive role in UVB-induced skin cancer. Additionally, P2ry6 knockout promotes mouse skin hyperplasia induced by short-term UVB irradiation, while UDP, the ligand of P2RY6, can inhibit UVB-induced skin damage. Furthermore, UVB irradiation can significantly upregulate P2RY6 expression in mouse and human skin cells. These results indicate that P2RY6 plays a crucial protective role in resisting UVB-induced skin damage and carcinogenesis. At the molecular level, P2RY6 deletion inhibits ubiquitination and expression of XPC after UVB irradiation in keratinocytes, resulting in the accumulation of CPDs (cyclobutane pyrimidine dimers). P2RY6 deletion also activates PI3K/AKT signaling pathway in vitro and in vivo. The CPD accumulation and inflammatory responses enhanced by P2RY6 deletion are reversed by an AKT inhibitor. These findings suggest that P2RY6 acts as a tumor suppressor in UVB-induced skin cancer by regulating PI3K/AKT signaling pathway.

overall_design: Twenty pairs of two-month-old P2ry6+/+ and P2ry6-/- mice were housed in SPF conditions with free access to food and tap water. In order to induce epidermal hyperplasia, the dorsal skins of mice were shaved, followed by UVB irradiation at a dose of 180mJ/cm2, administered three times per week for two consecutive weeks.   In order to induce skin tumor formation, mice were irradiated with 180mJ/cm2 UVB for initial ten weeks, increasing 10mJ/cm2 every week to the dose of 300mJ/cm2 at week 22 and keeping it until to week 40. The tumors on the backs of the mice were counted weekly after becoming visible. The incidence of mouse tumors and multiplicity of tumors were also calculated.

first: Xu

last: Peng

first: Dang

last: Yongyan


title: Differentially expressed genes induced with or without UVB stimulation in mice

summary: Skin cancer is the most prevalent cancer in humans, especially in the United States, Australia, and New Zealand. Australia and New Zealand are the two countries with the highest rates of skin cancer in the world, about four times higher than the United States, the United Kingdom and Canada. According to statistics, one American dies of skin cancer every hour. Studies have shown that ultraviolet radiation is the main cause of skin cancer, and ultraviolet rays are mainly divided into UVA, UVB and UVC according to wavelength, UVA and UVB can cause DNA damage, and UVB is the main factor that induces skin cancer. UVB is primarily a direct damage to cellular DNA and generally includes the formation of pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs). UVB can also cause mutations in tumor suppressor genes such as p53, ptch, and ras. These bases the mutation will promote the activation of related signaling pathways, thereby inducing the production of tumors.In this study, we will use gene chip technology to screen out UVB-sensitive genes, and then select the genes of the UVB-sensitive GPCR family from these genes, and further use PCR for verification, so as to identify UVB-sensitive GPCRs, which will provide a basis for further experimental research.

overall_design: The 6-8 week old mice were divided into two groups, a dark-treated (con) and UVB-treated group, with 3 mice in each group. The hair on the back of each mouse was shaved, and after two days, the mice in the UVB-treated group were anesthetized and placed in a UVB irradiation meter to irradiate the back of the mouse with UVB at a dose of 180mj/cm2. Three times a week, irradiation for 2 weeks,The darkened group did not receive UVB exposure.


title: Toll-Like Receptor-Induced Nucleosome Remodeling Achieved by Broadly Acting NF-kB in Collaboration with Transcription Factors Conferring Selectivity [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for Brg1, RelA and IRF-3 were performed in bone marrow-derived macrophages stimulated with lipid-A for 0, 30, 60 or 120 minutes.

first: An-Chieh

first: Brandon

last: Thomas


title: Distinct Transcriptomes of Two Populations of Aortic Valve Endothelial Cells

city: Palo Alto

first: Yu

address: 1215 Welch Road

department: CVI

institute: Stanford University

summary: Bulk RNA-sequencing of CD34+/c-kit+ aortic valve endothelial cells and CD34-/c-kit- aortic valve endothelial cells

overall_design:
Endothelial cells stripped from 2 diseased (calcific aortic valve disease) and 2 control (healthy) aortic valve leaflets were sorted for CD34+/c-kit+ (DP) and CD34-/c-kit- (DN) cell populations, which were subsequently assessed for their transcriptomes using bulk RNA-sequencing

***************************************************************
Submitter states that missing raw files are due to patient privacy concerns.
***************************************************************

first: Ian

last: Chen


title: EVIDENCE OF STEADY-STATE FIBROBLAST SUBTYPES IN THE NORMAL HUMAN BREAST AS CELLS-OF-ORIGIN FOR PERTURBED-STATE FIBROBLASTS IN BREAST CANCER

city: Copenhagen

first: Mikkel

last: Morsing

state: Nørrebro

address: Blegdamsvej 3b

department: Department of Cellular and Molecular Medicine and Danish Stem Cell Center

country: Denmark

institute: University of Copenhagen

summary: ABSTRACT Background:  Human breast cancer most frequently originates within a well-defined anatomical structure referred to as the terminal duct lobular unit (TDLU). This structure is endowed with its very own lobular fibroblasts representing one out of two steady-state fibroblast subtypes – the other being interlobular fibroblasts. While cancer associated fibroblasts (CAFs) are increasingly appreciated as covering a spectrum of perturbed states, we lack a coherent understanding of their relationship – if any - with the steady-state fibroblast subtypes. To address this, we here established two autologous CAF lines representing inflammatory CAFs (iCAFs) and myofibroblast CAFs (myCAFs), and compared them with already established interlobular- and lobular fibroblasts with respect to their origin and impact on tumor formation.  Methods:  Primary breast tumor derived CAFs were transduced to express human telomerase reverse transcriptase (hTERT) and sorted into CD105low and CD105high populations using fluorescence activated cell sorting (FACS). The two populations were tested for differentiation similarities to iCAF and myCAF states through transcriptome-wide RNA-Sequencing (RNA-Seq) including comparison to an available iCAF-myCAF cell state atlas. Inference of origin in interlobular and lobular fibroblasts relied on RNA-seq profiles, immunocytochemistry and growth characteristics. Osteogenic differentiation and bone formation assays in culture and in vivo were employed to gauge for origin in bone marrow mesenchymal stem cells (bMSCs). Functional characteristics were assessed with respect to contractility in culture and interaction with tumor cells in mouse xenografts. The cells’ gene expression signatures were tested for association with clinical outcome of breast cancer patients using survival data in The Cancer Genome Atlas database (TCGA).   Results:  We demonstrate that iCAFs have properties in common with interlobular fibroblasts while myCAFs and lobular fibroblasts are related. None of the CAFs qualify as bMSCs as revealed by lack of critical performance in bone formation assays. Functionally, myCAFs and lobular fibroblasts are almost equally tumor promoting as opposed to iCAFs and interlobular fibroblasts. A myCAF gene signature is found to associate with poor breast cancer specific survival. Conclusions:  We propose that iCAFs and myCAFs originate in interlobular and lobular fibroblasts, respectively, and more importantly, that the tumor promoting properties of lobular fibroblasts renders the TDLU an epicenter for breast cancer evolution.

overall_design: Human breast primary carcinoma derived hTERT immortalized iCAFs and myCAFs each in technical duplicate. For purpose of comparison to normal breast derived fibroblasts, the data for iCAFs and myCAFs was integrated with previously published normal human breast hTERT immortalized interlobular- and lobular fibroblasts , each in technical duplicate (Morsing et. al. 2020, GSE153646)

last: Bagger

first: Jonas

last: Sjölund

first: Jiyoung

last: Kim

first: Katharina

last: Kohler

first: René

last: Villadsen

first: Abbas

last: Jafari

first: Moustapha

last: Kassem

first: Kristian

last: Pietras

first: Lone

last: Rønnov-Jessen

first: Ole

middle: W

last: Petersen


title: Epitranscriptomics m6A analyses reveal distinct m6A marks in tumor necrosis a (TNF-a)-treated HeLa cells

first: Bünyamin

last: Akgül

summary: We have performed a epitranscriptomics study in which we first tretaed TNF-alpha in HeLa cells and DMSO was used as a negative control. Total RNA was isolated from TNF-alpha treated cells as well as control cells and apoptotic rate was determined by flow cytometry. Total RNAs were subjected to miCLIP to identify differentially m6A methylated RNAs. We then transcriptionally analyzed apoptotic genes which have differential m6A methylation in TNF-alpha tretament by qPCR. Afterthat, candidate genes were examined at the level of translation by polysome fractioantion assay.

overall_design: Total RNA was isolated from negative control (DMSO) and TNF-alpha treated HeLa cells in triplicate to perform miCLIP assay.

first: Azime

last: Alasar

first: Ozge

last: Tuncel

first: Buket

last: Saglam

first: Ayse

middle: B

last: Gelmez

first: Ipek

middle: E

last: Vatansever

first: Bunyamin

last: Akgul


title: Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

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

overall_design: Refer to individual Series


title: Nucleolar detention of NONO shields DNA double-strand breaks form aberrant transcripts

city: würzburg

first: Kaspar

last: Burger

institute: University of Würzburg

summary: RNA-binding proteins emerge as effectors of the DNA damage response (DDR). The multifunctional non-POU domain-containing octamer-binding protein NONO/p54nrb marks nuclear paraspeckles in unperturbed cells, but also undergoes re-localization to the nucleolus upon induction of DNA double-strand breaks (DSBs). However, NONO nucleolar re-localization is poorly understood. Here we show that the topoisomerase II inhibitor etoposide stimulates the production of RNA polymerase II-dependent, DNA damage-inducible antisense intergenic non-coding RNA (asincRNA) in human cancer cells. Such transcripts originate from distinct nucleolar intergenic spacer regions and form DNA–RNA hybrids to tether NONO to the nucleolus in an RNA recognition motif 1 domain-dependent manner. NONO occupancy at protein-coding gene promoters is reduced by etoposide, which attenuates pre-mRNA synthesis, enhances NONO binding to pre-mRNA transcripts and is accompanied by nucleolar detention of a subset of such transcripts. The depletion or mutation of NONO interferes with detention and prolongs DSB signalling. Together, we describe a nucleolar DDR pathway that shields NONO and aberrant transcripts from DSBs to promote DNA repair.

overall_design: enhanced Cross-linking immunoprecipitation (eCLIP) sequencing for NONO in control cells and Etoposide treated cells

first: Barbara

last: Trifault

first: Victoria

last: Mamontova

first: Giacomo

last: Cossa

first: Sabina

last: Ganskih

first: Yuanjie

last: Wei

first: Julia

last: Hofstetter

first: Pranjali

last: Bhandare

first: Apoorva

last: Baluapuri

first: Daniel

last: Solvie

first: Carsten

middle: P

last: Ade

first: Peter

last: Gallant

first: Elmar

last: Wolf

first: Dorthe

last: Larsen

first: Blanca

last: Nieto

first: Mathias

last: Munschauer


title: Association of Vitamin D with severity and outcome of COVID-19: Clinical and Experimental Evidence

city: Athens

first: Spyros

last: Foutadakis

address: Soranou

country: Greece

institute: Biomedical Research Foundation Academy of Athens

summary: We investigated the association between endogenous vitamin D and the severity of COVID-19 as well as the mechanisms of action of vitamin D supplementation. Vitamin D deficiency and insufficiency were associated with increased severity and unfavourable outcome after 28 days. Vitamin D levels were negatively associated with biomarkers of COVID-19 severity. Vitamin D supplementation after challenge of mice with COVID-19 plasma led to reduced levels of TNFα, IL-6, IFNγ and MPO in the lung, as well as down-regulation of pro-inflammatory pathways as derived from RNA-seq experiments. Thus, vitamin D demonstrates a protective effect against severity and unfavorable outcome in COVID-19, possibly through attenuation of tissue-specific hyperinflammation.

overall_design: Differential gene expression analysis using RNA-seq in lungs from mice treated with intravenous injection of plasma from patients with COVID-19 ARDS  versus mice treated with intravenous injection of plasma from patients with COVID-19 ARDS  plus 1,25(OH)D3 supplementation

first: Evangelos

last: Giamarellos-Bourboulis


title: THE BITTER TASTE RECEPTOR AGONIST DENATONIUM INHIBITS STEMNESS CHARACTERISTICS IN HEMATOPOIETIC STEM CELLS

city: Bologna

first: Maria Antonella

last: Laginestra

address: Via di Barbiano 1/10

department: Experimental Oncology Laboratory

country: Italy

institute: IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy

summary: Bone marrow microenvironmental stimuli profoundly impact hematopoietic stem cell fate and biology. As G protein-coupled receptors, the bitter taste receptors (T2Rs) are key in transmitting extracellular stimuli into an intracellular response, within the oral cavity but also in extraoral tissues. Their expression in the bone marrow (BM)-derived cells suggests their involvement in sensing the BM microenvironmental fluctuation. In the present study, we demonstrated that umbilical cord blood (UCB)-derived CD34+ cells express fully functional T2Rs along with the signal transduction cascade components and their activation by the prototypical agonist, denatonium benzoate, significantly modulated genes involved in stemness maintenance and regulation of cell trafficking. The activation of these specific pathways was confirmed in functional in vitro experiments. Denatonium exposure exerted an antiproliferative effect on UCB-derived CD34+ cells, mainly affecting the most undifferentiated progenitor frequency. It also reduced their clonogenicity and repopulating potential in vitro. In addition, the T2R signaling activation impaired the UCB-derived CD34+ cell trafficking, mainly reducing the migration toward the chemoattractant agent CXCL12 and modulating the expression of the adhesion molecules CD62L, CD49d, and CD29.  In conclusion, our results in UCB-derived CD34+ cells expand the observation of T2R expression in the setting of BM resident cells and shed light on the role of T2Rs in the extrinsic regulation of hematopoietic stem cell functions.

overall_design: To identify  changes in gene expression in response to DEN exposition in UCB-derived CD34+ cells, we performed GEP analysis after in vitro activation of the T2R pathway by DEN on two pools of UCB-derived CD34+ cells using GeneChip Human Transcriptome Array 2.0

first: Valentina

last: Pensato

first: Maria

first: Paolo

last: Falvo

first: Stefania

last: Orecchioni

first: Giovanna

last: Talarico

first: Elena

last: De Marchi

first: Samantha

last: Bruno

first: Sara

last: Mongiorgi

first: Giulia

last: Mitola

first: Francesco

last: Bertolini

last: Adinolfi

first: Michele

last: Cavo

first: Antonio

last: Curti

last: Salvestrini


title: Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin with biotinylated transposons [ATAC-seq]

city: Shanghai

first: Haizhu

last: Zhang

address: No. 131 Dong'an Road, Xuhui District

department: Institutes of Biomedical Sciences

institute: Fudan University

summary: This study introduced a method for directly identifying the transcriptional machinery on accessible chromatin (ATAC-MS) in a proteome scale. The goals of this study are to integrate ATAC-seq with ATAC-MS to investigate the real-time in vivo transcriptional regulatory processes in organisms.

overall_design: ATAC-seq was applied to identify changes in chromatin accessibility and transcription factors binding motifs in different cells.

first: Chen

last: Ding


title: The initiating IL-10 production dominates the therapy of mesenchymal stem cell scaffold in spinal cord injury

city: Hangzhou

first: Jiajia

last: Wang

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: spinal cord injury (SCI) is an acute damage to central nevous system, resulting in severe morbidity and permanent disability. Locally implanting scaffold system immobilized mesenchymal stem cellshas been widely proven to promote the locomotor function recovery of SCI rat, but the underlying mechanism remains elusive. Here we constructed a hyaluronic acid scaffold system (HA-MSC) to accelerates human MSC adhesive growth and prolongs the survival time of MSC in the lesion of SCI rats. And the residual MSCs regulate the local immune responses by upregulating anti-inflammatory cytokines. Interestingly, the dramatically increased but transient expression of IL-10 is found secreted by MSCs in the first week. Blocking the function of the initiating produced IL-10 by antibody totally abolishes the neurological and behavioral recovery of SCI rats, indicating a core role of IL-10 in SCI therapy of HA-MSC implantation. Transcriptome analyses indicate that IL-10 selectively promotes the migration and cytokine secretion programs of MSC, which in turn help MSC to exert its anti-inflammatory therapeutic effects. Our findings thus highlight a novel role of IL-10 in regulating MSC migration and cytokine secretion and determine the vital role of IL-10 in the domination of MSC treatment for spinal cord repair.

overall_design: 3 ctrl and 3 rhIL-10 treated hMSCs

first: Lijun

last: Yang

first: Jian

last: Cao

first: Jianqing

last: Gao


title: Toll-Like Receptor-Induced Nucleosome Remodeling Achieved by Broadly Acting NF-kB in Collaboration with Transcription Factors Conferring Selectivity [ATAC_MQ]

first: Stephen

last: Smale

overall_design: J2 virus immortalized Bone-marrow derived macrophages stimulated with lipid-A for 0, 30, 60 or 120 minutes. Chromatin was collected and treated with Tn5 transposase to profile DNA accessibility.

first: An-Chieh

last: Feng

first: Brandon

last: Thomas


title: Spreading of inflammation: the skin-joint axis

city: Erlangen

first: Simon

last: Rauber

address: Ulmenweg 18

department: Medicine 3

summary: The spread of inflammation from the skin to the joints is a key issue in the pathogenesis of psoriatic arthritis (PsA). Psoriasis (PsO), one of the most common skin diseases, usually precedes joint manifestations, suggesting skin-joint disease spread, which occurs in about 30% of psoriasis patients. Until now, it has been unclear why the inflammatory process remains restricted to the skin in some patients with PsO, whereas it spreads to tendons and joints in others. Using a preclinical model of PsA, we aimed to elucidate the skin-joint axis, i.e. the spread of psoriatic inflammation from the skin to the joints. KAEDE transgenic mice expressing a photo-convertible fluorescent reporter were used to assess cell trafficking from inflamed skin to other organs in the mouse model of IL-23 overexpression (IL-23OE) induced PsA. Psoriatic skin lesions were irradiated with UV light to induce the photoswitch from KAEDE-GREEN to KAEDE-RED. Migrating cells were characterised by scRNAseq.

overall_design:
Stromal and immune cells from synovial joints and skin were isolated by fluorescence-activated cell sorting from minicircle-induced IL-23 overexpression on day 7. Two libraries were generated corresponding to either Balb/c or C67BL/6 background. Viable CD45+ Ly6G- and viable CD45- were isolated and labelled with hashtag antibodies against CD45 and B2m.
Please note that processed data genated from both GEX and HTO are linked to the corresponding *GEX sample records.

first: Maria

middle: G

last: Raimondo

first: Hashem

last: Mohammadian

first: Hannah

last: Labinsky

first: Aleix

last: Rius Rigau

first: Andreas

last: Ramming


title: Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin with biotinylated transposons [ChIP-Seq]

overall_design: ChIP-seq targeting RFX1 was applied to C2C12 cells in proliferation stage and differentiation day2 stage.


title: Toll-Like Receptor-Induced Nucleosome Remodeling Achieved by Broadly Acting NF-kB in Collaboration with Transcription Factors Conferring Selectivity [RNA-Seq]

overall_design: Bone morrow-derived macrophages (BMDMs) and J2 virus immortalized bone marrow-derived macrophages (MQs) stimulated with lipid-A for 0, 30, 60 or 120 minutes. RNA was collected for RNA-seq to obtain gene expression profile.


title: NF-kB Broadly Orchestrates Nucleosome  Remodeling during the Primary Response to  Toll-Like Receptor 4 Signaling  [scATAC-seq]

summary: Inducible nucleosome remodeling at hundreds of latent enhancers and several promoters helps shape the transcriptional response to Toll-like receptor 4 (TLR4) signaling in macrophages. However, the identities of the transcription factors that promote TLR-induced remodeling have remained elusive. An analysis strategy that enriched ATAC-seq profiles for genomic regions most likely to undergo remodeling uncovered a unique relationship between NF-kB and TLR4-induced remodeling events. A critical functional role for NF-kB in remodeling was then revealed by CRISPR-Cas9 mutagenesis of NF-kB genes and binding motifs. This critical role is broad and possibly universal during the TLR4 primary response. Remodeling selectivity at defined regions is often conferred by collaboration between NF-kB and other inducible factors, including IRF3 and MAP kinase-induced factors. Thus, NF-kB is unique among TLR4-induced transcription factors in its broad contribution to inducible nucleosome remodeling, alongside its well-established ability to activate poised enhancers and promoters assembled into open chromatin.

overall_design: Unstimulated or 2 hour Lipid A (100ng/ml, Sigma Aldrich, Cat# L6895-1MG) stimulated bone marrow derived macrophages (BMDM) from Wildtype male mice were harvested from the tissue culture dish (35 mm) to generate single cell suspension. Quality of cells were monitored by microscopic examination and cells viability were more than 95% based of trypan blue exclusion staining and counting in hemocytometer.  About 1 million cells were processed for nuclei isolation followed by transposition as per 10X scATAC seq instruction manual, followed by NGS library prep and sequencing in Illumina NovaSees 6000 S1 platform at 100 cycle.

first: Prabhat

middle: K

last: Purbey


title: Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon (various cell lines II)

summary: This study introduced a method for directly identifying the transcriptional machinery on accessible chromatin (ATAC-MS) in a proteome scale. The goals of this study are to integrate ATAC-seq with   ATAC-MS to investigate the real-time in vivo transcriptional regulatory processes in organisms.

overall_design: ATAC-seq was applied to identify changes in chromatin accessibility in different cells.


title: The Role of IL-1beta in acrylamide induced neurotoxicity in mice

city: Noda City

first: Gaku

last: Ichihara

address: 2641 Yamazaki

institute: Tokyo University of Science

summary: To invistigate the role of IL-1B in acrylamide toxicity in mice, we establish the IL-1B knockdown mice to invistagate if it have a protective effect against acrylamide neurotoxicity

overall_design: We obtained data from 6 groups (6 mice/each) (3 groups wild type , and 3 groups IL-1B KO mice) of acrylamide exposed mice (0, 12.5, 25 mg/kg) body weight  using oral gavage for 28 days

first: Alzahraa

last: Fergany

first: Cai

last: Zong

first: Frederick

last: Ekuban

first: Aina

last: Suzuki


title: Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon [fractionation]

first: Haizhu

last: Zhang

overall_design: ATAC-seq was applied to identify changes in chromatin accessibility and transcription factors binding motifs in different fractions separated by SAX fractionation.

first: Chen

last: Ding


title: Utilising Psych Arrays for the identification of CNVs and SNPs from Schizophrenia cases and controls from South-India.

city: Hyderabad

first: Kommu

middle: Naga

last: Mohan

state: Hyderabad

address: Jawahar nagar

department: Biological Sciences

country: India

institute: Birla Institute of Technology and Science

summary:
Genotyping data on 192 schizophrenia cases and 181 healthy controls was generated using Psych Array V 1.3
Aim: To identify  CNVs and SNPs associated with increased risk of schizophrenia

overall_design: Blood samples were collected under the supervision of experienced psychiatrists,the isolated DNA was used for the generation of genotyping data.

first: K

middle: N

first: Minali

last: Singh


title: Induction and suppression of Haemaphysalis longicornis ticks antiviral RNA interference responses by arthropod-borne RNA viruses (RNA-Seq)

first: Yang

last: Li

address: 2005 Songhu Road

summary: Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne bunyavirus that causes severe clinical symptoms and mortality in humans. Haemaphysalis longicornis tick has been identified as the competent vector for SFTSV transmission. Although antiviral RNA interference (RNAi) in insects has been well documented, the degree to which RNAi contributes to antiviral defense in ticks is still largely elusive. In this study, utilizing arthropod-borne RNA viruses, including SFTSV, we find abundant virus-derived small interfering RNAs (vsiRNAs) are induced in H. longicornis after infection through either microinjection or natural blood-feeding. Furthermore, we identify a Dicer2-like homolog, the core protein of antiviral RNAi pathway, in H. longicornis and knocking down this gene exacerbated virus amplification. To counteract this antiviral RNAi of ticks, viruses have evolved suppressors of RNAi (VSRs). Here, we show that reduced viral replication inversely correlated with the accumulation of vsiRNAs in ticks after infection with recombinant sindbis virus (SINV) expressing heterologous VSR proteins. Elucidating the antiviral RNAi pathway of ticks by model arthropod-borne RNA viruses in vivo is critical to understanding the virus-host interaction, providing a feasible intervention strategy to control tick-borne arbovirus transmission.

overall_design: RNA from Haemaphysalis longicornis ticks infected with SFTSV  by blood feeding and control samples were detected by RNA-seq.

first: Yanxin

last: Ren

first: Zhengwei

last: Zhong

first: Yan

last: Xu

first: Zhi

last: Ye

first: Liting

last: Ma

first: Jingwen

last: Wang


title: Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon (293T)

overall_design: ATAC-seq was applied to identify changes in chromatin accessibility and transcription factors binding motifs in 293T.


title: Candidate biomarkers of EV-microRNA in detecting REM sleep behavior disorder and Parkinson’s disease

first: Wei

last: Liu

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

summary: Our study provides a valuable resource for small RNA profiles in normal, iRBD and PD plasma EVs, and showed that the EV-miRNAs have the potential to serve as biomarker for diagnosing the PD patients and iRBD patients.

overall_design: Extracellular vesicle small RNA profiles of human blood plasma by next generation sequencing

first: Ying

last: Cao

first: Yuanyuan

first: Ligang

last: Wu


title: Gene expression profiling of human fibroblast MRC5 cells exposed to cigarette smoke condensate (CSC)

status: Public on Jan 15 2024

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

country: France

institute: Inserm 1052

summary: Smoking is the main risk factor for many lung diseases including chronic obstructive pulmonary disease. Cigarette smoke (CS) contains carcinogenic and reactive oxygen species that favor DNA mutations and perturb the homeostasis and environment of cells. CS induces lung cell senescence resulting in a stable proliferation arrest and a senescence-associated secretory phenotype. It was recently reported that senescent cell accumulation promotes several lung diseases.

overall_design: Normal human fibroblast cells (MRC5) were cultured with or without Cigarette Smoke Condensate

first: Jean-Michel

last: Flaman

first: Alberta

last: Palazzo

first: David

last: Bernard


title: Comparative Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provide Insights into Type 2 Diabetes Genetics

city: Farmington

first: Eishani

middle: Kumar

last: Sokolowski

state: CT

address: 263 Farmington Avenue

institute: University of Connecticut Health Center

overall_design: Refer to individual Series


title: Microglial Trem2 shapes neuronal bioenergetics during development

city: Rozzano

first: Simona

last: Lodato

address: via Manzoni 56

institute: IRCCS Humanitas Research Hospital

summary: Triggering receptor expressed on myeloid cells 2 (Trem2) is a myeloid cell-specific gene expressed in microglia, whose variants are associated with multiple neurodegenerative diseases. TREM2 receptor modulates phagocytosis, cytokine production and metabolism, enabling appropriate surveillance of the brain by microglia and ensuring their proper response to damage signals. Here, we demonstrate that TREM2 plays a key role in controlling the bioenergetic profile of pyramidal neurons during development. In the absence of Trem2, developing neurons in hippocampal CA1 -but not in CA3- subfield display compromised energetic metabolism and defective basal, maximal and ATP-dependent respiration, accompanied by reduced mitochondrial mass and abnormal organelle ultrastructure. This is paralleled by a significant transcriptional rearrangement of hippocampal pyramidal neurons at birth, with a pervasive alteration of metabolic, oxidative phosphorylation and mitochondrial signatures. The developmental trajectories of the excitatory lineages indicate that lack of Trem2 causes a delay in the maturation of CA1 neurons, paired with specific alterations in the mitochondrial TOM complex which persist in the mature hippocampus. In addition, the mitochondrial defects and faulty neuronal differentiation are maintained also after neuron isolation from the brain context, suggesting that the lack of TREM2-mediated communication between microglia and neurons at early developmental windows is sufficient to derange the forthcoming maturation of neuronal metabolism. Our results unveil a novel role of TREM2 in controlling neuronal development by regulating the metabolic fitness of neurons in a region-specific manner.

overall_design: Hippocampi of the Trem2 +/+ and -/- mice were dissected at P1, dissociated to single cell suspension and analyzed using scRNAseq.

first: Matteo

last: Miotto

first: Sara

last: Mancinelli

first: Michela

last: Matteoli

first: Erica

last: Tagliatti

first: Genni

last: Desiato

first: Morini

last: Raffaella


title: Glyphosate infiltrates the brain and increases pro-inflammatory cytokine TNFα: implications for neurodegenerative disorders

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

summary:
Background: Herbicides are environmental contaminants that have gained much attention due to the potential hazards they pose to human health. Glyphosate, the active ingredient in many commercial herbicides, is the most heavily applied herbicide worldwide. The recent rise in glyphosate application to corn and soy crops correlates positively with increased death rates due to Alzheimer's disease and other neurodegenerative disorders. Glyphosate has been shown to cross the blood-brain barrier in in vitro models, but has yet to be verified in vivo. Additionally, reports have shown that glyphosate exposure increases pro-inflammatory cytokines in blood plasma, particularly TNFα.
Methods: Here, we examined whether glyphosate infiltrates the brain and elevates TNFα levels in 4-month-old C57BL/6J mice. Mice received either 125, 250, or 500 mg/kg/day of glyphosate, or a vehicle via oral gavage for 14 days. Urine, plasma, and brain samples were collected on the final day of dosing for analysis via UPLC-MS and ELISAs. Primary cortical neurons were derived from amyloidogenic APP/PS1 pups to evaluate in vitro changes in Aβ40-42 burden and cytotoxicity. RNA sequencing was performed on C57BL/6J brain samples to determine changes in the transcriptome.
Results: Our analysis revealed that glyphosate infiltrated the brain in a dose-dependent manner and upregulated TNFα in both plasma and brain tissue post-exposure. Notably, glyphosate measures correlated positively with TNFα levels. Glyphosate exposure in APP/PS1 primary cortical neurons increases levels of soluble Aβ40-42 and cytotoxicity. RNAseq revealed over 200 differentially expressed genes in a dose-dependent manner and cell-type-specific deconvolution analysis showed enrichment of key biological processes in oligodendrocytes including myelination, axon ensheathment, glial cell development, and oligodendrocyte development.
Conclusions: Collectively, these results show for the first time that glyphosate infiltrates the brain, elevates both the expression of TNFα and soluble Aβ, and disrupts the transcriptome in a dose-dependent manner, suggesting that exposure to this herbicide may have detrimental outcomes regarding the health of the general population.

overall_design: We sequenced RNA extracted from C57BL/J6 mice, after receiving either 125, 250, or 500 mg/kg/day of glyphosate, or a vehicle via oral gavage for 14 days.

first: Joanna

last: Winstone

first: Khyatiben

middle: V

last: Pathak

first: Winslow

last: Wendy

middle: S

first: Jennifer

last: White

first: Ritin

last: Sharma

first: Matttew

last: Huentelman

first: Patrick

last: Pirrotte

first: Ramon

last: Velazquez


title: Using human stem cell derived in vitro modeling to characterize the effect of MYCN overexpression on early hSAP development and tumor formation

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

summary: In this study we use human stem cell derived in vitro modelling to characterize the effect of MYCN overexpression on early hSAP development and tumor formation. We developed and characterized a human in vitro pluripotent stem cell-based model via sequential single-cell RNA sequencing throughout sympathoadrenal development.

overall_design: We differentiated an induced pluripotent stem cell (iPSC) line with a doxycycline inducible MYCN construct along the hSAP developmental trajectory in vitro. We induced MYCN overexpression at multiple timepoints during the critical time frame for the hSAP developmental window during differentiation, as defined by expression changes of key genes including PLP1, ASCL1 and STMN2, covering both early and late hSAP development. During this window we induced MYCN overexpression for 48hrs at four time-points (day 24, 26, 28 and 30). We then collected cells for single cell RNA-seq.

first: Stéphane

last: Van Haver

first: Frank

last: Speleman

first: Stephen

last: Roberts


title: The function of TEAD1 in cardiac fibroblast activation [ChIP-Seq]

first: shuai

last: song

address: No. 1609 Xietu Road, Xuhui District, Shanghai

department: Department of Cardiology

institute: Zhongshan  Hospital, Fudan University

summary: Cardiac fibroblasts (CFs) are the primary cells tasked with extracellar matrix reorganization and significantly associated with heart failure (HF). Previous studies have shown that TEAD1 deficiency deteriorated heart development and homeostasis. However, the role of TEAD1 in fibroblasts during cardiac remodeling was still undiscovered. Our study demonstrated that TEAD1 was upregulated predominently in cardiac fibroblasts in mice 4 weeks after transverse aortic constriction (TAC) and Ang-II infusion. Echocardiographic and histological analyses demonstrated that CFs- and myofibroblasts-specific TEAD1 deficiency ameliorated TAC-induced cardiac remodeling and treatment with TEAD1 inhibitor, VT103, mimiced this phenotypic effect. Mechanistically, RNA-seq analysis , ChIP-Seq analysis identified TEAD1 promotes the fibroblast-to-myofibroblast transition through the Wnt signalling pathway. In conclusion, TEAD1 is an essential regulator of the pro-fibrotic CFs phenotype associated with pathological cardiac remodeling via the BRD4/Wnt4 signalling pathway.

overall_design: To fully understand the molecular mechanisms underlying TEAD1-mediated cardiac remodeling, we whole-genome chromatin immunoprecipitation-sequencing (ChIP-seq) to identify the transcriptomic changes the gene regulatory elements bound by TEAD1 in NMCFs. Cell extracts were collected from NMCFs in different experimental groups, including OE-NC (overexpression negative control), and OE-TEAD1 (TEAD1 overexpression).


title: RNA sequencing analysis of IP (with GFP antibody)  and Input samples of the mPFC of stressed DBA mice expressing GFP-L10a

city: Kyoto

first: Shusaku

last: Uchida

state: Kyoto

address: 53 Kawaharamachi, Sakyo-ku

institute: Kyoto University

summary: We performed high-throughput profiling of gene expression in aPVT-projectors in the mPFC of DBA2/J mice subjected to subchronic and mild social defeat stress. DBA mice were subjected to 5-day of social defeat stress and then tested their social interaction and anhedonic state. After behavioral tests, mice were divided into five subtypes: SA, social interaction deficit, ANH: anhedonia, SA:ANH, both social dificit and anhedonia, RES, resilience and non-stressed (NS) control. Mice were euthanized for tissue collection. We then conducted the Immunoprecipitation and RNA-seq. Our study provided insights into the understanding of the molecular mechanisms underlying behavioral heterogeneity.

overall_design: DBA mice were subjected to 5-day of social defeat stress (smSDS). Total five groups were set up as described above.


title: Comparative Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provide Insights into Type 2 Diabetes Genetics [RNA-seq]

first: Eishani

last: Sokolowski

summary: Endoplasmic reticulum (ER) and inflammatory stress responses are two pathophysiologic factors contributing to islet dysfunction and failure in Type 2 Diabetes (T2D). However, how human islet cells respond to these stressors and whether T2D-associated genetic variants modulate these responses is unknown. To fill this knowledge gap, we profiled transcriptional (RNA-seq) and epigenetic (ATAC-seq) remodeling in human islets exposed to ex vivo ER (thapsigargin) or inflammatory (IL-1β+IFN-γ) stress. 5,427 genes (~32%) were associated with stress responses; most were stressor-specific, including upregulation of genes mediating unfolded protein response (e.g. DDIT3, ATF4) and NFKB signaling (e.g. NFKB1, NFKBIA) in ER stress and inflammation respectively. Islet single-cell RNA-seq profiling revealed strong but heterogeneous beta cell ER stress responses, including a distinct beta cell subset that highly expressed apoptotic genes. Epigenetic profiling uncovered 14,968 stress-responsive cis-regulatory elements (CREs; ~14%), the majority of which were stressor-specific, and revealed increased accessibility at binding sites of transcription factors that were induced upon stress (e.g. ATF4 for ER stress, IRF8 for inflammation). Seventy-six stress-responsive CREs overlapped known T2D-associated variants, including 20 residing within CREs that were more accessible upon ER stress. Among these, we linked the rs6917676 T2D risk allele (T) to increased in vivo accessibility of an islet ER stress-responsive CRE and allele-specific beta-cell nuclear factor binding in vitro. We showed that MAP3K5, the only ER stress-responsive gene in this locus, promotes beta cell apoptosis. Consistent with its pro-apoptotic and putative diabetogenic roles, MAP3K5 expression inversely correlated with beta cell abundance in human islets and was upregulated in beta cells from T2D donors. Together, this study provides new genome-wide insights into human islet stress responses and putative mechanisms of T2D genetic variants.

overall_design: Primary human pancreatic islets from cadaveric organ donors were exposed for 24 hours to thapsigargin (250 nM; ERS) or 0.025% DMSO solvent control or to 25 U/mL of IL1β + 1000 U/mL of IFNγ (R&D Systems; CYT) vs. untreated control. Islet gene expression in these samples was assessed using RNA-seq.

first: Romy

last: Kursawe

first: Vijay

last: Selvam

first: Redwan

last: Bhuiyan

first: Asa

last: Thibodeau

first: Chi

last: Zhao

first: Cassandra

last: Spracklen

first: Duygu

last: Ucar

first: Michael

middle: L

last: Stitzel


title: Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon (various cell lines I)

first: Haizhu

last: Zhang

summary: This study introduced a method for directly identifying the transcriptional machinery on accessible chromatin (ATAC-MS) in a proteome scale. The goals of this study are to integrate ATAC-seq with  ATAC-MS to investigate the real-time in vivo transcriptional regulatory processes in organisms.

overall_design: ATAC-seq was applied to identify changes in chromatin accessibility and transcription factors binding motifs in HeLa cells treated with TNFα, MCF7 treated with E2/4HT and  C2C12 during differentiation.

first: Chen

last: Ding


title: Comparative Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provide Insights into Type 2 Diabetes Genetics [ATAC-seq]

overall_design: Primary human pancreatic islets from cadaveric organ donors were exposed for 24 hours to thapsigargin (250 nM; ERS) or 0.025% DMSO solvent control or to 25 U/mL of IL1β + 1000 U/mL of IFNγ (R&D Systems; CYT) vs. untreated control.  Whole islet chromatin accessibility from treated vs. respective control cells was determined using ATAC-seq.


title: Genome-wide analysis of deregulated gene expression by tumor cells (CD45-) or myeloid cells (CD45+) in cocultures infected with measles virus (MV)

city: Nantes

first: Jean-Francois

last: Fonteneau

address: 8 quai Moncousu BP70721

institute: INSERM

summary: Analysis of gene induced upon infection by MV in cocultures of tumor cells (CD45-) and myeloid cells (CD45+). The hypothesis tested in the present study was that MV induce innate immune response in tumor cells and myeloid cells cocultured together.

overall_design: Monocytes or macrophages were cocultured with malignant pleural mesothelioma cells. After 24h, cells were infected with Schwarz attenuated measles virus. After 72h, CD45 positive cells were sorted from cocultures using human CD45 MicroBeads. PolyA RNA were extracted immediately from CD45 positive (myeloid cells) and negative cells (tumor cells).

first: Camille

last: Chatelain

first: Jean-François


title: Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5′TOP mRNAs [S4U label]

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

summary: To investigate the changes in mRNA stablity upon loss of LARP1, we performed SLAM-seq and half-life measurements on WT and derived LARP1 KO cells. The canonical and 5′TOP mRNA cell lines used for single-molecule imaging were treated as  biological replicates for the SLAM-seq analysis.

overall_design: WT cells (canonical and 5′TOP mRNA cell lines) and derived LARP1 KO clones were analyzed by RNA-seq, using independent replicates (cells harvested on different days).

first: Hochstoeger

last: Tobias

first: Ewa

last: Piskadlo

first: Chao

middle: A

last: Jeff


title: Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5′TOP mRNAs

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


title: Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5′TOP mRNAs [LARP1]

summary: To investigate the changes in gene expression upon loss of LARP1, we performed RNA-seq and differential gene expression analysis on WT and derived LARP1 KO cell lines. The canonical and 5′TOP mRNA cell lines used for single-molecule imaging were treated as biological replicates for the differential gene expression analysis.

overall_design: WT cells (canonical and 5′TOP mRNA cell lines) and derived LARP1 KO clones (4 for each cell line, 8 clones total) were analyzed by RNA-seq, using independent replicates (cells harvested on different days).

first: Tobias

last: Hochstoeger

first: Jeff

last: Chao


title: Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5′TOP mRNAs [4EBP1/2]

summary: To investigate the changes in gene expression upon loss of 4EBP1/2, we performed RNA-seq and differential gene expression analysis on WT and derived 4EBP1/2 KD cell lines. The canonical and 5′TOP mRNA cell lines used for single-molecule imaging were treated as biological replicates for the differential gene expression analysis.

overall_design: WT cells (canonical and 5′TOP mRNA cell lines) and derived 4EBP1/2 KD cell lines were analyzed by RNA-seq, using indepedent replicates (cells harvested on different days) run as paired-end reads.


title: Construction of earthworm chromatin accessibility landscape at a single-cell level using CH-ATAC-seq

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

summary: The assay for transposase-accessible chromatin using sequencing (ATAC-seq) at single-cell level can provide different perspectives of regulatory patterns based on  cell type-specific accessible regions.  While human genomic elements have been well studied, understanding how nuclear acid sequence regulates the expression of target genes in a genome-wide level in other organisms remains a major challenge. Batch effects, expensive machines are still constraints nowadays to build a cross-species landscape for further analysis, a platform with high throughput and low cost will be extremely required.Here, we constructed a cross-species accessible chromatin landscape by combinatorial-hybridization-based single-cell ATAC-seq, a single-cell ATAC-seq platform with high throughput and signal-noise ratio using fresh nuclei as input.

overall_design: Whole bodies of wild-type  Eisenia andrei at 4 months were  dissociated into single-nucleus suspensions, followed by single-cell DNA library construction, high-throughput sequencing, and bioinformatics analysis.

first: Guodong

first: Yuting

last: Fu

first: Lei

last: Yang

first: Fang

last: Ye

first: Peijing

first: Shuang

first: Xiaoping

last: Han

first: Jingjing

last: Wang


title: Smart-seq2 of spinal cord motor neurons reveals transcriptomic changes in mice with spinal cord injury after synergistic bidirectional electrical stimulation of specific frequencies

city: Suzhou

first: Yaobo

last: Liu

state: Jiangsu

address: 199 Ren-Ai Road, Suzhou Industrial Park

department: Institute of neuroscience

institute: Soochow University

summary: The characteristics of electrical signals-mediated neural circuits reconstruction remain poorly understood. We initially developed a spinal-muscle synergistic bidirectional electrical stimulation (SBES) protocol to mimic feedforward and feedback electrical signals in spinal sensorimotor circuits. The results indicate that sensorimotor circuits could be precisely reassembled in structure and function levels by 10-20 Hz SBES. To gain mechanistic insights into the reassembly of the spinal sensorimotor circuits with 10-20 Hz SBES, we performed gene expression profiling analysis in motoneurons. Gene ontology (GO) analysis showed that one group of GO terms accounted for a large fraction of the upregulated transcripts. This group includes axon growth-related cellular functions, such as cell adhesion, regulation of cell growth, and cell projection assembly. Statistical analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed sixteen signaling pathways were involved, two of which were related to the regulation of axonal regeneration (PI3K-Akt signaling pathway and cAMP signaling pathway). This study provides insights into neural signal decoding during spinal sensorimotor circuit reconstruction.

overall_design: Spinal cord motoneurons of mice in the sham group (n = 3 mice), untrained group (n = 3 mice), 10-20 Hz SBES group (n = 3 mice), were labeled with TRDA and sacrificed 4 weeks after SCI. The freshly isolated spinal cord was sliced on a Vibratome (Leica, Germany) into 200- to 300-μm-thick coronal sections. Fluorescence-labeled motoneurons were visualized under a fluorescence microscope (Zeiss) using a miniature operating system (Eppendorf, Germany), and the motoneurons were aspirated by glass electrodes and placed in preservation solution (Invitrogen, USA). TRDA-labeled neurons were individually homogenized in 1 ml TRIzol (Invitrogen), and RNA was extracted with a RNeasy Mini Kit (Qiagen) or equivalent. Total RNA (1 μg) was used to synthesize double-stranded cDNA.

first: Kai

last: Zhou

first: Dan

first: Wei

last: Wei

first: Hui


title: Molecular changes in the lung during otseosarcoma pre-metastatic niche formation

city: Guangzhou

first: Chuangzhong

last: Deng

state: Guangdong China

address: 651 Dongfeng East Rd

department: Department of Musculoskeletal Oncology

institute: Sun Yat-sen University Cancer Center

summary: To profile the molecular changes in the lung during osteosarcoma pre-metastatic niche formation, we performed RNA-seq of lungs harvested from D0 and D14 after orthotopic implantation of K7M2 cells in balb/c mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for lungs harvested from D0 and D14 after orthotopic implantation of K7M2 cells in balb/c mice. We performed gene expression profiling analysis using data obtained from RNA-seq of three independent experiments.

first: Jin


title: Gene expression pattern during nitrate treatment (WT, hb52-KO)

city: Bunkyo-ku

first: Yasuhito

last: Sakuraba

state: Tokyo

address: Yayoi 1-1-1

department: Agro-Biotechnology Research Center

institute: The University of Tokyo

summary: To examine the effect of the mutation of Arabidopsis HB52 on nitrate-induciblle gene exoression, we performed microarray analysis using wild-type and hb52-KO mutant.

overall_design: 5 day-old Arabidopsis Col-0 wild-type and hb52-KO were treated with 10 mM KNO3 or 10 mM KCl (control) for 1 day.

first: Shuichi

last: Yanagisawa


title: MOV10 facilitates messenger RNA decay in an N6-methyladenosine (m6A)-dependent manner to maintain the mouse embryonic stem cells state

city: Clayton

first: Partha

last: Das

state: VIC

address: 15 innovation walk

country: Australia

institute: Monash Biomedicine Discovery Institute, Monash University

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is the most predominant internal mRNA modification in eukaryotes, recognised by its reader proteins (so-called m6A-readers) for regulating subsequent mRNA fates – splicing, export, localization, decay, stability and translation – to control several biological processes. Although a few m6A-readers have been identified, yet the list is incomplete. Here, we identify a new m6A-reader protein, MOV10, in mouse embryonic stem cells (mESCs). MOV10 recognises m6A-containing mRNAs with a conserved GGm6ACU motif. Mechanistic studies uncover that MOV10 bound m6A-containing mRNAs facilitate mRNA decay within the cytoplasmic processing bodies (P-bodies) in an m6A-dependent manner.  Moreover, MOV10 decays the Gsk-3ß mRNA through m6A that stabilises the ß-CATENIN expression of a Wnt/ß-catenin signalling pathway to regulate downstream target expression of NANOG for maintaining the mESC state. Thus, our findings reveal how a newly identified m6A-reader, MOV10 mediates mRNA decay via m6A that impact ESC biology.

overall_design: RNAseq, m6A-seq, RIPseq,  Riboseq between Wild-type and KO mouse ESCs

first: Pushkar

last: Dakle


title: Paraxonase-2 agonist, Vutiglabridin alleviates non-alcoholic steatohepatitis via autophagy activation

city: Suwon-si

first: Hyeong min

last: Lee

address: 304, Sinwon-ro

department: Reasearch

institute: Glaceum

summary: Limited therapeutic agents have been developed for non-alcoholic steatohepatitis (NASH), a common immunometabolic disease. Glabridin, a novel anti-obesity candidate, is not druggable due to low in vivo chemical stability and bioavailability. We developed vutiglabridin (VUTI) and investigated therapeutic effects, molecular targets, and mechanisms of action in NASH. VUTI was therapeutically administrated in amylin-NASH, high fat-diet induced obesity, and thioacetamide-induced hepatic fibrosis mouse models. The mechanism of action of VUTI was studied using RNA sequencing, lipidome, and proteome analyses using mouse tissues. VUTI alleviated hepatic steatosis, fibrosis, and inflammation. Lipidome analysis revealed that VUTI affects the various individual lipid profiles. VUTI exerted therapeutic effects by increasing lipid catabolism, activating autophagy, and reducing mitochondrial oxidative stress, thus mitigating NASH pathogenesis. The cellular target of VUTI was paraoxonase-2 identified using chemical proteome analysis, which promotes its enzyme activity to enhance autophagy activation. VUTI, as a paraoxonase-2 agonist, mitigates all aspects of NASH and may be a promising therapeutic alternative for NASH.

overall_design: Comparison of gene expression profiling by drug treatment of NASH liver

first: Kyun-Hwan

last: Kim

first: Kwang-Pyo

first: Gu-Choul

last: Shin

first: Hyeong

middle: Y

first: Jihyeon

last: Hur

first: Sang-Ku

last: Yoo

first: Yun

last: Park

first: Hyung

first: Dongryeol

last: Ryu

first: Min-Ho

first: Jung

middle: H

first: Sang-Uk

last: Seo

first: Leo

last: Choi

first: Martin

middle: R

last: Madsen

first: Michael

last: Feigh


title: EGR1 increases the innervation density of epidermal sensory neurons via upregulation of ARTN in keratinocytes in atopic dermatitis

city: Seoul

first: Soon Young

address: 120 Neungdong-ro, Gwangjin-gu,

institute: Konkuk university

summary: Atopic dermatitis (AD) is the chronic inflammatory skin disease accompanied with severe pruritus. To explore the roles of EGR1 in atopic dermatitis and the relationship between EGR1 and pruritus-scratching behavior, we used a atopic dermatitis-like mouse model driven by house dust mite (HDM) treatment in wild type and EGR1 KO mice, followed with RNA-sequencing analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for skin tissue of Naïve-Egr1+/+ mice, HDM-challenged Egr1+/+, Naïve-Egr1-/-, and HDM-challenged Egr1-/-.

first: Hyunjin

last: Yeo

first: Young

first: Soon


title: Dynamics of chromatin and transcriptome in the HSPCs at different hematopoietic developmental stages [ATAC-seq]

city: shanghai

first: deng

middle: li

last: Hong

address: 280 chongqing south road

institute: shanghai jiao tong univerisity

summary: ATAC-seq and RNA-seq were used to compare the chromatin states and corresponding transcriptomes of developing HSPC. We found that the chromatin states and transcriptomes change markedly when HSPCs migrate from PL to FL and from FL to BM. Then we compared chromatin among E12.5 PL, E12.5 FL, and E16.5 FL, the proportion of fragments in the nucleosome-free region significantly increases in E12.5 and E16.5 FL-HSPCs compared with E12.5 PL-HSPCs; the motifs of ETS and Runt are enriched at the opeing or closing peaks from E12.5 PL to E12.5 FL and E12.5 FL to E16.5 FL, and the expression of these factors is either up-regulated or down-regulated; the motifs of bZIP and Zf are enriched at the closing and opening peaks from E12.5 PL to E12.5 FL and E12.5 FL to E16.5 FL respectively, In line, the expression of these factors is down-regulated or up-regulated.

overall_design: ATAC-seq

first: Xiao

last: Guo


title: Transcriptome sequencing of A549 cells

city: Vancouver

first: Bettina

middle: Maria

last: Fuglerud

state: BC

address: 675 W 10th Ave

country: Canada

institute: BC Cancer

summary: We analyzed the global effect of SOX9 knockdown and TGFB1 treatment by sequencing the transcriptomes of A549 cells transfected with siSOX9 or control siRNA and treated with TGFB1.

first: Pamela

last: Hoodless


title: PAX5 ChIP-seq in A549 cell line

city: Tianjin

first: Yan

middle: Xue

last: miao

address: 22 Qixiangtai Road,Heping District,Tianjin,China

department: Department of Immunologyc

institute: Tianjin Medical University

summary: A549 cell line expressing PAX5-flag  and performed ChIP-seq

overall_design: ChIP-seq analysis in A549 cell expressing PAX5-flag with flag antibody, two replicates

first: Xuemiao

last: Yan

first: Zhe

last: Liu


title: Dynamics of chromatin and transcriptome in the HSPCs at different hematopoietic developmental stages [RNA-seq]

overall_design: RNA-seq


title: Gene expression profiles of adipose tissue adjacent to and distant from breast cancer

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: It is widely recognized that cancer development and progression depend not only on tumor-cell intrinsic factors but also on its microenvironment and on the host characteristics. Adipocytes are the main stromal cells in the breast and an heterotypic interaction between breast epithelial cells and adipocytes has been demonstrated.  To date, the alterations associated with adipocyte dedifferentiation has to be further studied, especially in patients.  The aim of our work is to compare gene expression profile of adipose tissue adjacent to and distant from breast cancer in patients.

overall_design: Adipose tissues (AT) were collected during standard surgical approaches from 2015 to 2017 from 41 patients subjected to mastectomy. AT adjacent (within 2 cm from the reference tumor) to the tumor tissue and far from the tumor (preferentially more than 10 cm from the tumor and in general at the opposite site, peripherically) were obtained for each patient.


title: Aal-circRNA-407 regulates ovarian development of Aedes albopictus, a major arbovirus vector, via the miR-9a-5p/Foxl axis

first: Jinbao

last: Gu

state: Guangdong

address: No. 1023, Shatai South Road

department: Department of Pathogen Biology, School of Public Health

institute: Southern Medical University

summary: Aedes albopictus shows a rapid global expansion and dramatic vectorial capacity for various arboviruses, thus posing a severe threat to global health. Although many noncoding RNAs have been confirmed to play functional roles in various biological processes in Ae. albopictus, the roles of circRNA remain a mystery. In the present study, we first performed high-throughput circRNA sequencing in Ae. albopictus. Then, we identified a cysteine desulfurase (CsdA) superfamily gene-originated circRNA, namely, aal-circRNA-407, which was the third most abundant circRNA in adult females and displayed a fat body highly expressed manifestation and blood feeding-dependent onset. siRNA-mediated knockdown of circRNA-407 resulted in a decrease in the number of developing follicles and a reduction in follicle size post blood meal. Furthermore, we demonstrated that circRNA-407 can act as a sponge of aal-miR-9a-5p to promote the expression of its target gene Foxl and eventually regulate ovarian development. Our study is the first to report a functional circRNA in mosquitoes, expanding our current understanding of important biological roles in mosquitoes and providing an alternative genetic strategy for mosquito control.

overall_design: To examine the circRNA expression profiles of Aedes albopictus, we collected two-day-old virgin female and male Ae. albopictus (Foshan strain) (three biological replicates, n = 30 per replicate) and performed high throughput circRNA-seq.

first: Yonghui

last: Gao


title: Regulation of downstream pathway of NSUN2 knockdown in hypopharyngeal carcinoma FaDu cell line

city: Shanghai

first: Lixiao

last: Chen

address: No.85 Wujin road, Hongkou district, Shnaghai,200080, China

department: Otorhinolaryngology head and neck surgery

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

summary: It has been confirmed that nsun2 promotes cell proliferation and migration in hypopharyngeal cancer cell lines, but the pathway of nsun2 in hypopharyngeal cancer cell lines is poorly understood. We constructed stable cell lines by knocking down nsun2 to find the key genes of downstream pathway, and compared them with normal FaDu cell lines.It has been confirmed that nsun2 promotes cell proliferation and migration in FaDu cell line, but the pathway of nsun2 in FaDu cell line is poorly understood. We constructed stable cell lines by knocking down nsun2 to find the key genes of downstream pathway, compared them with normal FaDu cell lines.

overall_design: Three pairs of repeated experiments

first: Chen

last: LiXiao

first: Ding

last: Jian

first: Wang

last: Baoxin

last: Xinwei

first: Ying

last: Xinjiang

first: Yu

last: Ziwei

first: Dong

last: pin


title: Expression data from NCI-H1299 and NCI-H1299/CDDP cells

status: Public on Jan 14 2024

city: Shenyang

first: Qiuyue

last: Zhang

address: No. 103, Wenhua Road, Shenhe District

institute: Shenyang Pharmaceutical University

summary:
Non-small cell lung cancer (NSCLC) patients are prone to drug resistance during chemotherapy. Therefore, in order to compare the changes in the gene expression profiles of NSCLC cells before and after drug resistance, we constructed cisplatin-resistant cells (NCI-H1299/CDDP), and compared the gene expression profiles with those of the parental NCI-H1299 cells.
We used microarrays to study in detail the global gene expression changes before and after drug resistance in NSCLC cells and identified genes that were up- or down-regulated during this process.

overall_design: NCI-H1299 and NCI-H1299 cells were cultured with RPMI 1640 medium containing 10% fetal bovine serum and 1% penicillin-streptomycin , then were incubated in 37 °C cell incubator containing 5% CO2.When the cell density reached 90-100%, the cells were collected and total RNA was extracted