title: miR-155 plays selective cell-intrinsic roles in brain infiltrating immune cell populations during neuroinflammation

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

summary: The pro-inflammatory microRNA-155 (miR-155) is highly expressed in the serum and CNS lesions of patients with multiple sclerosis (MS). The whole-body deletion of miR-155 in mice confers resistance to a mouse model of MS, EAE, by reducing the encephalogenic potential of CNS-infiltrating Th17 T cells. However, cell intrinsic roles for miR-155 during EAE have not been formally determined. Here we utilize single-cell RNA sequencing and cell-specific conditional miR-155 knockouts to determine the importance of miR-155 expression in distinct immune cell populations. Time course single-cell sequencing revealed reductions in T cells, macrophages, and dendritic cells in whole-body miR-155 knockout mice compared with wild-type controls at day 21. Deletion of miR-155 in T cells, driven by CD4 cre, reduced disease severity similar to whole-body miR-155 knockouts. CD11c cre-driven deletion of miR-155 in dendritic cells also significantly reduced EAE disease score, with both T cell and dendritic cell-specific knockouts showing a reduction in Th17 T cell infiltration into the CNS. Although miR-155 is highly expressed in infiltrating macrophages during EAE, deletion of miR-155 using LysM cre did not affect disease severity. Taken together, these data show that while miR-155 is highly expressed in most infiltrating immune cells, miR-155 has distinct roles and requirements depending on the cell type. This provides insights into which functionally relevant cell types should be targeted by the next generation of miRNA therapeutics.

overall_design: Experimental autoimmune encephalomyelitis (EAE) was induced in WT and miR-155KO mice. 0, 13, or 21 days post-EAE induction, DAPI(-) CD45(+) live cells from the brains of (n=5 per group) were sorted via flow cytometry. Sorted immune cells were processed for single-cell RNA-sequencing via 10x platform.

first: Jacob

middle: W

last: Thompson

middle: M


title: Mechanism of RNAm6A methylation modification regulating NLRP3 inflammasome activation for hand, foot and mouth disease progression

status: Public on Jun 13 2023

city: Zhengzhou

first: Shuaiyin

last: Chen

address: No. 100 Kexue Avenue, Zhengzhou

country: China

institute: Zhengzhou University

type: Expression profiling by high throughput sequencing

summary: During the life cycle of Enterovirus 71 (EV71), N6-methyladenosine (m6A) modification has an important impact on viral replication and the cellular response to viral infection, but the effect of m6A modification on cellular RNAs and pathways during infection is still unknown. The purpose of this research was to investigate the role of m6A in regulating host cell inflammatory response and disease progression during EV71 infection. Methylation RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) results show the m6A methylation modification map of control and EV71-infected groups of RD cells. And multilevel validation showed that decreased expression of demethylase FTO (fat mass and obesity-associated protein) was responsible for the elevated total m6A levels in EV71-infected RD cells and that TXNIP may be a target gene for demethylase FTO action. Further functional experiments showed that demethylase FTO silencing promoted TXNIP expression, activation of NLRP3 inflammasome and promoted the release of pro-inflammatory factors in vitro, and demethylase FTO overexpression showed the opposite result. Further tested in an animal model of severe EV71 infection, with results consistent with in vitro. In conclusion, our findings suggested that depletion of demethylase FTO in the presence of EV71 infection increased the m6A level of TXNIP mRNA 3ʹ UTR, increased mRNA stability, and promoted TXNIP expression, which activated the NLRP3 inflammasome and led to the release of pro-inflammatory factors, ultimately promoted HFMD progression. This could help with the development and prevention of m6A modification inhibitor-based drugs for viral-related inflammation and disease.

sample_organism:
Homo sapiens
Enterovirus A71

platform_organism:
Homo sapiens
Enterovirus A71

overall_design: The type of samples: RD cell. The experimental conditions and variables: Enterovirus 71 (EV71). Contains EV71-infected RD cell samples, three replicates; control RD cell samples, three replicates.

first: Shuayin

first: Quanman

last: Hu

first: Yaqi

last: Xie

first: Dong

last: Li


title: Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells

city: Gif-sur-yvette

first: Matthieu

last: Gerard

address: Route Nationale

country: France

institute: CEA

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report a comprehensive analysis of nucleosomal and subnucleosomal organization at cis-regulatory elements (CREs) in mouse embryonic stem (ES) cells. We used chromatin fragmented by a moderate dose of micrococcal nuclease (MNase) as input for ChIP-seq with antibodies against histones and transcription factors and high-coverage deep-sequencing. Centrifugation of chromatin through sucrose gradients, followed by ChIP-seq, allowed the characterization of different subclasses of subnucleosomal particles having distribution patterns specific to enhancers, gene promoters and CTCF binding sites. We also provide datasets showing that this particular chromatin organization of CREs is conserved in the human melanoma 501Mel cell line.

overall_design: We used MNase ChIP-seq to define the distribution of subnucleosomal particles, canonical nucleosomes, and transcription factors enrichment.

first: Marina

middle: C

last: Nocente

first: Anida

last: Mesihovic Karamitsos

first: Emilie

last: Drouineau

first: Sophie

last: Chantalat

last: Gérard


title: Anti-miR-93-5p therapy prolongs sepsis survival by restoring the peripheral immune response

city: Berlin

first: Mihnea

middle: P.

last: Dragomir

state: Berlin

address: 1 Charitéplatz

department: Pathology

country: Germany

institute: Charité - Universitätsmedizin

summary:
Sepsis remains a leading cause of death and currently has no pathogenesis-specific therapy. Hampered progress is partly due to the lack of insight into deep mechanistic processes. Deciphering the functions of microRNAs in sepsis pathogeny became a dynamic research topic in the last decade. To screen for new microRNA targets for sepsis therapeutics, we used human samples: microRNA array data from peripheral blood mononuclear cells (PBMCs) from sepsis patients and controls, whole blood samples from sepsis survivors; and multiple animal models: mouse cecum ligation-puncture (CLP)-induced sepsis, mouse viral microRNA challenge, and baboon Gram-positive and Gram-negative sepsis models. miR-93-5p met the criteria for a therapeutic target, being overexpressed in baboons which died early after induction of sepsis and downregulated in humans who survived after sepsis. Therapeutically, inhibiting miR-93-5p prolonged the overall survival of mice with CLP-induced sepsis, with a stronger effect in old mice. Mechanistically, anti-miR-93-5p therapy reduced inflammatory monocytes and increased circulating effector memory T cells, especially CD4+ subset. Ago2-immunoprecipitation in miR-93-knockout T cells identified important regulatory receptors, CD28 and CD160, as direct miR-93-5p target genes. In conclusion, miR-93-5p is a potential therapeutic target in sepsis in the elderly through its regulation of both innate and adaptive immunity.
We applied the Ago2-RIP Chip (Ribonucleoprotein ImmunoPrecipitation followed by microarray analysis) to identify miR-93-5p target mRNAs. This methodology uses beads coupled to either anti-Ago2 antibody (or an IgG control) to pull down the RISC complex together with any miRNA-interacting mRNAs. To define target genes of miR-93-5p, we assessed mRNA transcripts enriched in the Ago2-IP fraction of JURKAT parental cells or control cells (where miR-93-5p is present) but not in the two KO clones (where miR-93-5p is absent) by microarray

overall_design: Pulldown of RISC complex via Ago2 in Jurkat miR-93 wildtype and knockout cells in order to define miR-93 targetome

middle: P

first: George

middle: A

last: Calin

first: Melanie

last: Winkle


title: Open Chomatin Analysis of human pluripotent stem cell cell-derived FLK1+ vascular mesoderm cells in AATS versus AATSI basal medium

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

summary:
Purpose: Identify accessible chromatin profile between AATS and AATSI condition hPSC-derived FLK1+ mesoderm progenitor cells
Methods:ATAC-seq
Results: insulin addition (AATSI) led to partial open chromatin status of non-vascular mesderm lineage
Conclusions: insulin hindered FLK1+ cells' vascular mesoderm differentiation potential

overall_design: Perform ATAC-seq of hPSC-derived FLK1+ vascular mesoderm cells in AATS and AATSI basal medium

first: Yonglin

last: Zhu


title: The mechanism of promoting proliferation of rumen epithelial cells in Tan sheep by adding succinate to the diet based on the interaction between rumen microbiota and host.

status: Public on Jun 12 2023

city: Yinchuan

first: Wenyi

last: Ren

address: 489 Helanshan West Road, Xixia District, Yinchuan City, Ningxia

department: College of Animal Science and Technology

institute: Ningxia University

summary: A healthy rumen is crucial for normal growth and improved production performance of ruminant animals. Rumen microbes participate in and regulate rumen epithelial function, and the diverse metabolites produced by rumen microbes are important participants in rumen microbe-host interactions. SCFAs, as metabolites of rumen microbes, have been widely studied, and propionate and butyrate have been proven to promote rumen epithelial cell proliferation. Succinate, as an intermediate metabolite in the citric acid cycle, is a final product in the metabolism of certain rumen microbes, and is also an intermediate product in the microbial synthesis pathway of propionate. However, its effect on rumen microbes and rumen epithelial function has not been studied. It is unclear whether succinate can stimulate rumen epithelial development. Therefore, in this experiment, Chinese Tan sheep were used as experimental animals to conduct a comprehensive analysis of the rumen microbiota community structure and rumen epithelial transcriptome, to explore the role of adding succinate to the diet in the interaction between the rumen microbiota and host.

overall_design: Thirty-six 5-month-old Tan sheep with similar health statuses and weights were selected and randomly divided into four groups, with 9 sheep in each group, and reared in individual pens (4 m × 4 m). The four groups were as follows: control group (basal diet), experimental group I (basal diet + 0.5% succinate), experimental group II (basal diet + 1% succinate) and experimental group III (basal diet + 2% succinate).

first: Lili

last: Zhang

first: Xiaofeng

last: Xu

first: Yuchen

last: Cheng


title: BCG vaccination reprograms the function of myeloid cells and aggravates necrotizing enterocolitis in neonates

city: Tianjin

last: Zhou

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

institute: Tianjin Medical University

summary: Bacillus Calmette–Guérin (BCG) vaccination immediately after birth provides overall protection against immune disorders in healthy infants. However, for vulnerable infants such as preterm or low birth weights, delayed BCG vaccination is usually recommended.  The mechanism underlying this clinical application remains obscure. Here we reported that BCG vaccination abrogated the transitory appearance of immunosuppressive myeloid cells in neonatal mice, that is myeloid-derived suppressor cells (MDSCs) represented as the important immunoprotection against inflammatory diseases in early life. A combination of single-cell transcriptome, metabolite profiling, and functional analysis revealed that the upregulation of mTOR/HIF1a signaling and the enhanced glycolysis explained the underlying mechanism. Consequently, BCG vaccination significantly exacerbated the severity of necrotizing enterocolitis (NEC), a common clinical emergency primarily affecting preterm or low birth weight infants. Adoptive transfer of MDSCs or pharmalogical inhibition of glycolysis or mTOR signaling efficiently relieved the severity of NEC upon BCG vaccination. These observations suggest that BCG may diminish the protective mechanism of myeloid cells and enhances the susceptibility of NEC in vulnerable neonates.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq and scRNA-seq data for PMN-MDSCs or myeloid cells isolated from neonatal mice treated with BCG or PBS.

first: Yingying

last: Chen

first: Xianfu

last: Yi

first: Xutong

last: Fan

first: Mulin

middle: J


title: In vivo CRISPR screens for Toxoplasma using metabolism sublibrary in WT and Ifngr1-deficient  mice

city: Suita

first: Yuta

last: Tachibana

state: Osaka

address: 3-1, Yamadaoka

department: Research Institute for Microbial Diseases (RIMD)

country: Japan

institute: Osaka University

summary: We performed in vivo CRISPR screen of Toxoplasma targeting metabolism-related genes to identify in vivo fitness genes in WT and Ifngr1-deficient mice.

overall_design: This sublibrary targeting 361 genes which consisted 3610 gRNAs targeting metabolism-related genes together with dispensable and essential control genes. We performed in vivo CRISPR screens to identify novel virulence factors of Toxoplasma.

first: Masahiro

last: Yamamoto


title: In vivo CRISPR screens for Toxoplasma using endomembrane-nucleus sublibrary in WT and Ifngr1-deficient  mice

summary: We performed in vivo CRISPR screen of Toxoplasma targeting endomembrane and nucleus-related genes to identify in vivo fitness genes in WT and Ifngr1-deficient mice.

overall_design: This sublibrary targeting 395 genes which consisted 3945 gRNAs targeting endomembrane and nucleus-related genes together with dispensable and essential control genes. We performed in vivo CRISPR screens to identify novel virulence factors of Toxoplasma.


title: ZXDC is highest expressed transcription factor on TBLR1-overexpressed HeLa cells

city: Guangzhou

first: Yifang

last: Mao

state: Other (Non U.S.)

address: 58 Zhongshan Second Road, Guangzhou

institute: Sun Yat-sen University

summary: In our previous study, we revealed that transducing (beta)-like 1X-linked (TBLR1) is a potential prognostic marker which has a negative effect on the overall survival in cervical cancer patients.This transcriptome sequencing results of TBLR1-overexpressing and TBLR1-knockdown cervical cells identified ZXDC (ZXD family zinc finger C) as the most significantly differently expressed transcription factor (TF) among all TFs (Figure S1), indicating its potential role in cervical cancer progression.

overall_design: We established TBLR1-overexpressed HeLa cells, and then randomly picked three sets of control and TBLR1-overexpressed HeLa cells to do gene expression profiling.

first: Mian

last: He

first: Yue

last: Li

first: Xingyu

last: Jiang

first: Peng

last: Guo

first: Ying

last: Ouyang

first: Xiangfu

first: Meng

last: Xia

first: Lixin

last: Wu

first: Zihao

last: Tang

first: Tianyi

last: Liang


title: Gene expression profile at single cell level of aortic cells from 3 adult R26-DreER;Ki67-CrexER;R26-GFP (ProTracer) mice after 8weeks of tamoxifen treatment.

city: Shanghai

first: zixin

last: liu

address: 320 Yueyang road, Life Science Research Building A2112

institute: Center for Excellence in Molecular Cell Science

summary: The heterogeneity of endothelial cell proliferation is not addressed. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of aortic endothelial cell proliferation.

overall_design: Aortic cells were isolated by digestion with Collagenase type 1 at 37℃ for 30 minutes. The cell suspension was filtered through a 70 µm cell strainer and then pelleted by centrifugation at 300g for 5 minutes.  After washing cells with 500ml HBSS, cells were loaded onto the 10x Chromium controller the generate Gel Bead-in-Emulsions (GEMs), which were further processed into single cell 5’ gene expression libraries using Chromium Single Cell 5’ Library Kit (v1.1). Sequencing was performed on Illumina Hiseq X Ten PE150 platform. Fastq files were processed by CellRanger (v.4.0.0) pipeline.

first: Yi

first: Zixin

last: Liu

first: Ximeng

last: Han

first: Feng

first: Ben

first: Bin


title: Gene-regulatory network study of rheumatoid arthritis in single-cell chromatin landscapes of peripheral blood mononuclear cells

city: Shenzhen

first: Cantong

last: Zhang

address: 1017 Dongmen North Road, Luohu District, Shenzhen, China

institute: Shenzhen's hospital

summary: Rheumatoid arthritis is a chronic autoinflammatory disease with an elusive etiology. Assays for transposase-accessible chromatin with single-cell sequencing (scATAC-seq) contribute to the progress in epigenetic studies. However, the impact of epigenetic technology on autoimmune diseases has not been objectively analyzed. Therefore, scATAC-seq was performed to generate a high-resolution map of accessible loci in peripheral blood mononuclear cells (PBMCs) of RA patients at the single-cell level. The purpose of our project was to discover the transcription factors (TFs) that were involved in the pathogenesis of RA at single-cell resolution. In our research, we obtained 22 accessible chromatin patterns. Then, 10 key TFs were involved in the RA pathogenesis by regulating the activity of MAP kinase. Consequently, two genes (PTPRC, SPAG9) regulated by 10 key TFs were found that may be associated with RA disease pathogenesis and these TFs were obviously enriched in RA patients (p<0.05, FC>1.2). With further qPCR validation on PTPRC and SPAG9 in monocytes, we found differential expression of these two genes, which were regulated by eight TFs (ZNF384, HNF1B, DMRTA2, MEF2A, NFE2L1, CREB3L4 (var. 2), FOSL2::JUNB (var. 2), MEF2B). What is more, the eight TFs showed highly accessible binding sites in RA patients. These findings demonstrate the value of using scATAC-seq to reveal transcriptional regulatory variation in RA-derived PBMCs, providing insights on therapy from an epigenetic perspective.

overall_design: Rheumatoid arthritis (RA) is a chronic auto-inflammatory disease with significant unknown etiology. Assay for transposase accessible chromatin in single cells sequencing (scATAC-seq) is related to great progress in epigenetic study, including cancer biology. However, the impact of this technology on autoimmune disease has not been objectively analyzed. Hence, scATAC-seq was performed to profile a high-resolution map of accessible loci in RA at a single-cell level. We identified five major clusters using cell type-specific marker genes and further obtained 22 patterns of transcription factor (TF) among them. Consequently, our findings revealed five genes associated with RA pathogenesis in the T cell activity pathway and 43 remarkable enriched TF motifs in RA patients. Also, Dendritic cells and Natural killer cells showed abnormal signals in the virus infection-related pathways. These findings could provide insights into epigenetic therapy in the future.

first: Haiyan

last: Yu

first: Yong

last: Dai


title: In vivo CRISPR screens for Toxoplasma using ROP/GRA sublibrary in WT and Ifngr1-deficient  mice

first: Yuta

last: Tachibana

summary: We performed in vivo CRISPR screen of Toxoplasma targeting ROP/GRA genes to identify in vivo fitness genes in WT and Ifngr1-deficient mice.

overall_design: This sublibrary targeting 376 genes which consisted 3757 gRNAs targeting 376 putative or known ROP/GRA and RON genes together with dispensable and essential control genes. We performed three independent in vivo CRISPR screens to identify novel virulence factors of Toxoplasma.

first: Masahiro

last: Yamamoto


title: TGF-beta treated airway epithelium

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

country: USA

institute: University of North Dakota Genomics Core

summary: Despite being exposed to respiratory syncytial virus (RSV) infection multiple times in our lives, infants, older-adults, and immunocompromised patients are vulnerable to RSV-associated severe diseases, such as bronchiolitis and pneumonia. Respiratory viral infections are known to promote pulmonary fibrosis formation, which are often associated with a cellular remodeling process epithelial-mesenchymal transition (EMT). However, there is no information on whether RSV causes EMT in bronchial epithelial cells. Our results suggest that RSV-infection does not induce EMT in three different in vitro lung models: epithelial A549 cell line, primary normal human bronchial epithelial cells, and pseudostratified airway epithelium. Interestingly, RSV infection increased cell surface area and perimeter in the infected airway epithelium, which is distinct from the TGF-β1 driven cell elongation. Genome-wide transcriptome analysis also revealed that RSV infection is not involved in cell motility and locomotion. Thus, our results suggest that RSV infection does not induce EMT in the airway epithelium

overall_design: Airway epithelium of a healthy adult primary normal human bronchial epithelial (MHNE) cells treated with 10ng/ml TGF-beta for six days

first: Masfique

last: Mehedi

first: Sattya

middle: N

last: Talukdar


title: Morphologic and molecular analysis of liver injury after SARS-CoV-2 vaccination reveals distinct characteristics

city: Basel

first: Sarp

last: Uzun

address: Schönbeinstrasse 40

country: Switzerland

institute: University Hospital Basel, Institute of Medical Genetics and Pathology

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

overall_design: Refer to individual Series


title: Morphologic and molecular analysis of liver injury after SARS-CoV-2 vaccination reveals distinct characteristics [TCR-seq, BCR-seq]

summary: Background and Aims: Liver injury after COVID-19 vaccination is very rare and shows clinical and histomorphological similarities with autoimmune hepatitis (AIH). Little is known about the pathophysiology of COVID-19 vaccine-induced liver injury (VILI) and its relationship to AIH. Therefore, we compared VILI with AIH.  Methods: Formalin-fixed and paraffin-embedded liver biopsy samples from patients with VILI (n=6) and from patients with an initial diagnosis of AIH (n=9) were included. Both cohorts were compared by histomorphological evaluation, whole-transcriptome and spatial transcriptome sequencing, multiplex immunofluorescence and immune repertoire sequencing.  Results: Histomorphology was similar in both cohorts but showed more pronounced centrilobular necrosis in VILI. Gene expression profiling showed that mitochondrial metabolism and oxidative stress-related pathways were more and interferon response pathways less enriched in VILI. Multiplex analysis revealed that inflammation in VILI was dominated by CD8+ effector T cells, similar to drug-induced autoimmune like hepatitis (DI-AILH). In contrast, AIH showed a dominance of CD4+ effector T cells and CD79a+ B and plasma cells. T-cell receptor (TCR) and B-cell receptor (BCR) sequencing showed that T- and B-cell clones were more dominant in VILI than in AIH. In addition, many T-cell clones detected in the liver were also found in the blood. Interestingly, analysis of TCR beta chain and Ig heavy chain variable-joining gene usage further showed that TRBV6-1, TRBV5-1, TRBV7-6 and IgHV1-24 genes are used differently in VILI than in AIH.   Conclusions: Our analyses support that SARS-CoV-2 vaccination-induced liver injury is related to AIH but also shows distinct differences from AIH in histomorphology, pathway activation, cellular immune infiltrates, and TCR usage. VILI may be a separate entity, which is distinct from AIH and more closely related to DI-AILH.

overall_design: Total RNA isolated from formalin-fixed parafin embedded (FFPE) liver biopsy samples of COVID-19 vaccine-induced liver injury (VILI) (n=6) and autoimmune hepatitis (AIH) (n=9). T-cell receptor and B-cell receptor libraries produced from each sample.

first: Matthias

last: Matter

first: Byron

last: Calgua

first: Ilaria

last: Arborelli


title: Morphologic and molecular analysis of liver injury after SARS-CoV-2 vaccination reveals distinct characteristics [RNA-seq]

overall_design: Tissue microarrays with formalin-fixed parafin embedded (FFPE) liver biopsy samples from COVID-19 vaccine-induced liver injury (VILI) (n=6) and autoimmune hepatitis (AIH) (n=8) were constructed and spatial transciptomics experiment performed with GeoMx Digital Spatial Profiler by using whole Transcriptome Atlas probes and morphology markers

first: Jonathan

last: Thevenet

first: Stéphanie

last: Tissot


title: BMP7 expression in mammalian cortical radial glial cells increases the length of the neurogenic period

first: Guoping

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary:
Purpose:To asses changes in gene expression profiles of single cell from the E39 Ferret Cortex. Mouse E18 littermate controls cortex, and Smo CKO (SmoF/F hGFAP-Cre) mice.
Methords: E39 ferret cortex, E18 wild type and Smo CKO cortices were carefully dissected under a fluorescent stereoscope, and incubated in 4 ml of papain solution for 20 min at 37℃, The cortical tissues were gently triturated, filtered through a 40 mm strainer, and washed with HBSS to obtain the single cell suspension. The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-seq libraries, following the manufacturer’s instructions. The cDNA libraries were purified, quantified using Agilent 2100 Bioanalyzer, and sequenced on the Illumina Hiseq4000
Results: E18 SmoF/F (control) cortex, 10524 cells, 1954 genes/cell; hGFAP-Cre; SmoF/F cortex, 7596 cells, 2104 genes/cell; E39 ferret cortex, 23482 cells, 1759 genes/cell.

sample_organism:
Mustela putorius furo
Mus musculus

platform_organism:
Mustela putorius furo
Mus musculus

overall_design: scRNA-seq: Individual cells were sampled from mice cortices of E18 wild type mice and Smo CKO mice,and E39 ferret cortex.

first: Zhenmeiyu

last: Li

first: Lin

last: Yang

first: Mengge

last: Sun

first: Zhuangzhi

first: Zhejun

last: Xu

first: Yanjing

last: Gao

first: Xin

last: Jiang

first: Zihao

last: Su

first: Xiaosu

first: John

middle: L

last: Rubenstein

first: Zhengang


title: Bulk RNA-seq of Pglyrp1 KO Tumor Infiltrating CD8+ T cells

city: Boston

first: Linglin

last: Huang

state: MA

address: 60 Fenwood Road, HBTM 10016F

department: Neurology

institute: Brigham and Women’s Hospital

summary: To characterize the role of Pglyrp1 in tumor immunity, we performed bulk RNA-seq for MC38-OVA tumor infiltrating CD8+ T cells from wild type and Pglyrp1-deficient mice.

overall_design: We profiled MC38-OVA tumor infiltrating CD8+ T cells from WT mice (n = 4) and Pglyrp1 KO mice (n = 4).

first: Alexandra

last: Schnell

first: Brianna

last: Regan

first: Vasundhara

last: Singh

first: Vijay

middle: K

last: Kuchroo


title: Colon cancer cells DLD1 cells incubated with kynurenine, TCDD, or CH223191 for 1 hour

city: Dallas

first: Jiwoong

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: The ligand-activated transcription factor Aryl Hydrocarbon Receptor (AHR) regulates cellular detoxification, proliferation, and immune evasion in a range of cell types and tissues, including cancer cells. In this study, we used RNA-seq to identify the signature of AHR target genes regulated by the pollutant 2,3,7,8-tetrachlorodibenzodioxin (TCDD) and the endogenous ligand kynurenine (Kyn), a tryptophan-derived metabolite. This approach identified a signature of six genes (CYP1A1, ALDH1A3, ABCG2, ADGFR1, and SCIN) as commonly activated by endogenous or exogenous ligands of AHR in multiple colon cancer cell lines. Among these, the actin-severing protein Scinderin (SCIN) was necessary for cell proliferation; SCIN downregulation limited cell proliferation and its expression increased it. SCIN expression is elevated in a subset of colon cancer patient samples, which also contain elevated β-catenin levels. Remarkably, SCIN expression promotes nuclear translocation of β-catenin and activates the WNT pathway. Our study identified a new mechanism for adhesion-mediated signaling in which SCIN, likely via its ability to alter the actin cytoskeleton, facilitates the nuclear translocation of β-catenin.

overall_design: Cultured cells exposed to 10uM of each chemical

first: Maralice

last: Conacci Sorrell


title: Biological effect of azacitidine (CC-486) on peripheral T-cell lymphoma

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

type: Methylation profiling by high throughput sequencing

summary:
TCL with T-follicular helper phenotype (PTCL-TFH) has recurrent mutations affecting epigenetic regulators, which may contribute to aberrant DNA methylation and chemoresistance. This phase 2 study evaluated oral azacitidine (CC-486), a DNA methyltransferase inhibitor, plus CHOP as initial treatment for PTCL and prioritized enrollment for PTCL-TFH (ClinicalTrials.gov - NCT03542266). CC-486 at 300 mg daily was administered for 7 days prior to C1 of CHOP, and for 14 days before CHOP C2-6. The primary endpoint was end-of-treatment CR. Secondary endpoints included ORR, safety and survival. Correlative studies assessed mutations, gene expression and methylation in tumor samples.
Grade 3-4 hematologic toxicities were mostly neutropenia (71%), with febrile neutropenia uncommon (14%). Non-hematologic toxicities included fatigue (14%) and GI symptoms (5%). In 20 evaluable patients, CR was 75%, including 88.2% for PTCL-TFH (n=17). At a median follow-up of 21 months, 2-yr PFS was 65.8% for all and 69.2% for PTCL-TFH, while 2-yr OS was 68% for all and 75.6% for PTCL-TFH. The frequencies of the TET2, RHOA, DNMT3A, and IDH2 mutations were 76.5%, 41.1%, 23.5% and 23.5%, respectively, with TET2 mutations significantly associated with CR (p=0.007), favorable PFS (p=0.004) and OS (p=0.015), and DNMT3A mutations associated with adverse PFS (p=0.016). CC-486 priming upregulated genes related to apoptosis (p<0.01) and inflammation (p<0.01), with a decrease in TFH proliferation based on gene expression and cell-type deconvolution analysis. DNA methylation did not show significant shift. This safe and active initial therapy regimen is being further evaluated in the ALLIANCE randomized study A051902 in CD30-negative PTCL.

overall_design: RNA and DNA methylation profiles of PTCL tissue samples pre (C1D-6) and post (C1D1) CC-486 treatment were generated by Illumina sequencing

first: Jia

last: Ruan

first: Alison

last: Moskowitz

first: Neha

last: Mehta-Shah

first: Lubomir

last: Sokol

first: Zhengming

last: Chen

first: Riyaad

last: Rahim

first: Nikita

last: Kotlov

first: Grigorii

last: Nos

first: Vladislav

last: Maksimov

first: Andrea

last: Sboner

first: Michael

last: Sigouros

first: Koen

last: van Besien

first: Steve

last: Horwitz

first: Sarah

last: Rutherford

first: Erin

last: Mulvey

first: Jenny

last: Xiang

first: Alicia

last: Alonso

first: Morton

last: Coleman

first: Ari

last: Melnick

first: Olivier

last: Elemento

first: Giorgio

last: Inghirami

last: Leonard

first: Peter

last: Martin

first: Leandro

last: Cerchietti

middle: V


title: Tumor-educated platelet blood tests for Non-Small Cell Lung Cancer detection and management

city: Amsterdam

first: Mafalda

last: Antunnes

state: zuid holland

address: de boelelaan 1118

department: NRG

country: Netherlands

institute: Amsterdam UMC

summary: We report RNA-seq data of 766 blood platelet samples, including 399 Non-Small Cell Lung Cancer (NSCLC) patients from different stages (I-IV) and 367 asymptomatic individuals (Controls). Our data explains how tumor-educated platelet (TEP)-derived spliced RNA can serve as a biomarker for minimally-invasive clinical blood tests on assisting the detection and management of lung cancer patients.

overall_design: Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing EDTA anti-coagulant by standard centrifugation. Total RNA was extracted from the platelet pellet, subjected to cDNA synthesis and SMARTer amplification, fragmented by Covaris shearing, and prepared for sequencing using the Truseq Nano DNA Sample Preparation Kit. Subsequently, pooled sample libraries were sequenced on the Illumina Hiseq 2500 or 4000 platform. All steps were quality-controlled using Bioanalyzer 2100 with RNA 6000 Picochip, DNA 7500 and DNA High Sensitivity chips measurements. For further downstream analyses, reads were quality-controlled using Trimmomatic, mapped to the humane reference genome using STAR, and intron-spanning reads were summarized using HTseq.

last: Antunes-Ferreira

first: Silvia

last: D'Ambrosi

first: Mohammad

last: Arkani

first: Myron

last: Best

first: Thomas

last: Wurdinger


title: Transcriptional comparison of Testicular Adrenal Rest Tumors with fetal and adult tissues

city: Nijmegen

first: Mariska

middle: AM

last: Schröder

address: Geert Grooteplein

department: Department of Pediatric Endocrinology and Department of Laboratory Medicine

institute: Radboud university medical center

summary: By comparing the transcriptome of TART with fetal- and adult- testis and adrenal tissues, this study aimed to unravel the origin of TART. Sixteen TART samples were previously obtained from patients with CAH (n=7) or recurrent Cushing’s Disease (n=1). Adult adrenal (n=11), adult testis (n=10), fetal adrenal (n=13), and fetal testis (n=5) tissues were obtained.

overall_design: Transcriptomic comparisson of Testicular Adrenal Rest Tumors (TART) (n=16) obtained from patients with Congenital Adrenal Hyperplasia (n=7) or recurrent Cushing's Disease (n=1) with  adult adrenal (n=11), adult testis (n=10), fetal adrenal (n=13), and fetal testis (n=5) tissues, and Leydig Cell Tumors (n=7).

first: Fred

last: Sweep

first: Antonius

middle: E

last: van Herwaarden

first: Rod

middle: T

last: Mitchell

first: Alan

last: Rowan

first: Darren

last: Korbie

first: Hedi

last: Claahsen - van der Grinten

first: Paul

last: Span


title: Inflammatory blood neutrophils in COPD are derived from activated bone marrow progenitors

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Chronic obstructive pulmonary disease (COPD) is a major respiratory disease characterized by small airway inflammation, emphysema and severe breathing difficulties. Low-grade systemic inflammation is an established hallmark of severe disease, however, the molecular changes in peripheral immune cells remain far from understood. We combined multi-color flow cytometry with single-cell RNA sequencing and showed that blood neutrophil numbers are significantly increased in COPD and they are a heterogeneous population. A transcriptomic state that expressed interferon response genes correlated with alveolar damage and acute exacerbations. Furthermore, bronchoalveolar neutrophils expressed gene signatures corresponding to certain blood neutrophil states. Last, our data in a murine model of cigarette smoke exposure demonstrated that bone marrow neutrophil progenitors are expanded in smoke-treated animals and display signs of immune activation. Our study provides evidence that COPD systemic inflammation may derive from an activated haematopoietic precursor compartment.

overall_design: Seven- to eight-week-old female BALB/c mice were exposed to normal air or cigarette smoke for 3 months. Live bronchoalveolar, CD45+ whole blood and CD45+ bone marrow cells were collected and sorted. For each compartment, cells from all animals per group were pooled together and sequenced.

first: Theodore

middle: S

last: Kapellos

last: Ulas

first: Matthias

last: Becker

first: Philip

last: Hansbro

last: Schulze


title: Anti-miR-93-5p therapy prolongs sepsis survival by restoring the peripheral immune response

city: OKC

first: Jonathan

middle: Daniel

last: Wren

state: OK

address: 825 NE 13th St

department: Arthritis & Clinical Immunology

institute: Oklahoma Medical Research Foundation

summary: Escherichia coli and Staphylococcus are among the most common causes of bacterial sepsis, a deadly syndrome characterized by uncontrolled activation of coagulation and complement enzymatic cascades an exaggerated immune response. We performed in vivo experimental sepsis in baboons to characterize the host response to bacterial infection in blood cells. We demonstrate that bacterial infection leads to early induction of proinflammatory genes followed by a delayed activation of anti-inflammatory pathways. In addition, we observe changes in genes and pathways associated coagulation and complement as well as with leukocyte adhesion, migration and cell death.  Our study provides important insights into the temporal kinetics of gene expression in leukocytes during bacterial sepsis.

overall_design:
Characterization of gene expression changes in blood leuckocytes during the time course of sepsis progression in baboons
mRNA profiling of blood leukocytes from baboons challenged with lethal doses (1-3x10E10 colony forming units) Gram negative (E. coli) and Gram positive (S. aureus) bacteria, as a function of time before sepsis (0 hours) versus post-infection (2, 4, 8, 24 hours )

first: Florea

last: Lupu

first: Ravi

last: Keshari

first: Constantin

last: Georgescu

middle: D


title: CAPG silencing promotes CRC cell apoptosis and ferroptosis via P53 pathway

status: Public on Jun 11 2023

first: yingying

last: zhao

state: State...

address: Tianhe District, Guangzhou, Guangdong Province

institute: Sun Yat-Sen University

summary: Colorectal cancer (CRC) is the third most common cancer in the world and the second leading cause of cancer-related deaths. However, there are few effective therapeutic targets for colorectal cancer. Here, we report that Capping Actin Protein, Gelsolin Like (CAPG), a protein involved in actin related movement, is significantly overexpressed in human CRC tissues, and that expression levels are inversely correlated with overall survival. CAPG knockdown CRC cell lines inhibited cell proliferation, blocked cell cycle in G1 phase, increased apoptosis rate and promoted the occurrence of ferroptosis. RNA-seq data suggested that CAPG silencing promotes cell cycle arrest, apoptosis, and ferroptosis by activating the P53 pathway. Therefore, CAPG has potential to serve as a prognostic marker as well as a cancer therapy target in the future.

overall_design: Comparative gene expression profiling of RNA-seq data for doxycycline-induced knockdown HCT116 cells (shCAPG), with or without doxycycline-treated.

first: Ping

last: Yuan

first: Yingying

last: Zhao

first: Chuyue

last: Wang

first: Weili

last: Wu


title: Whole blood RNA sequencing analysis in methemoglobinemia

first: Daisuke

last: Okuzaki

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Methemoglobinemia is a condition in which methemoglobin (MetHb) is increased and the oxygen carrying capacity of tissues is decreased, causing a lack of oxygen to the whole body. The patient, 31 years old, was brought to our hospital with symptoms of dyspnea due to inhalation of gas from an acetic acid phosphonitrate storage tank at a factory. An arterial blood gas test was performed and the methemoglobin level was 23.1%. After administration of methylene blue, the methemoglobin level normalized and the symptoms improved. RNA sequencing was performed on blood samples. In this study, we first evaluated RNAs from the whole blood in the patients with methemoglobinemia. The RNA-seq analysis showed that activated “Hydrogene peroxide catabolic process” was associated with the pathogenesis of methemoglobinemia. These results are reported here because they explain the pathogenesis of methemoglobinemia.

overall_design: We analyzed gene expression pattern of RNAs from the whole blood in the patients with methemoglobinemia.

first: Yuki

last: Togami

first: Hisatake

last: Matsumoto


title: m6A-seq and RNA-seq in Arabidopsis dcl1 mutant

city: Xuzhou

first: Tao

last: Xu

state: Jiangsu

address: Shanghai Road 101

institute: Jiangsu Normal University

summary: N6-methyladenosine (m6A) modification is essential for plant growth and development. Recently, a possible involvement of miRNAs in m6A modification is reported in animal. To understand a potential involvement of miRNAs in sequence-specific deposition of m6A marks in plants, in this study, we performed m6A-seq and RNA-seq for a mutant of dicer-like 1 (dcl1), a key component in miRNA biogenesis in Arabidopsis. And the difference of m6A modification was compared between Col-0 mutant and dcl1 mutant.

overall_design: The Arabidopsis seedling of Col-0 and dcl1 mutant seedlings were collected at 3-week-old growth stage. And the RNA was extracted and subjected to m6A and RNA sequencing with three biological replicates.

first: Hunseung

last: Kang


title: Bulk RNA-seq of intestinal organoids upon treatment with LXR agonist GW3965

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

country: Sweden

institute: KTH

summary: Liver X Receptor (LXR) activation in intestinal epithelial organoids promotes their growth in vitro. To investigate the downstream effect of LXR activation in intestinal epithelial cells and identify potential pathways driving regeneration, we carried out an unbiased transcriptomic analysis of intestinal epithelial organoids stimulated with the LXR agonist GW3965. In detail, wild type small intestinal crypts were seeded in vitro and stimulated with vehicle (DMSO) or GW3965. After six hours, closing crypts (organoids) were collected for RNA extraction and were analyzed by RNA sequencing.

overall_design: Small intestinal crypts were isolated from two C57BL/6J male mice and seeded in vitro in Matrigel and organoids growth media. DMSO (vehicle) or GW3965 (2uM) was added in the overlaying media. Crypts from each mouse were stimulated with both vehicle and GW3965 (n=2 in each experimental group). After 6 hours, organoids were collected and RNA extracted and submitted for RNAseq analysis.

first: Eduardo

last: Villablanca


title: The Parasite Intraerythrocytic Cycle and Human Circadian Cycle are Coupled During Malaria Infection

city: Durham

first: Robert

last: Moseley

address: 124 Science Drive

institute: Duke University

summary: During infections with malaria parasites P. vivax, patients exhibit rhythmic fevers every 48 hours.  These fever cycles correspond with the time parasites take to traverse the Intraerythrocytic Cycle (IEC) and may be guided by a parasite-intrinsic clock.  Different species of Plasmodia have cycle times that are multiples of 24 hours, suggesting they may be coordinated with the host circadian clock. We utilized an ex vivo culture of whole blood from patients infected with P. vivax to examine the dynamics of the host circadian transcriptome and the parasite IEC transcriptome.  Transcriptome dynamics revealed that the phases of the host circadian cycle and the parasite IEC were correlated across multiple patients, suggesting that the cycles are coupled.  In mouse model systems, host-parasite cycle coupling appears to provide a selective advantage for the parasite.  Thus, understanding how host and parasite cycles are coupled in humans could enable anti-malarial therapies that disrupt this coupling.

sample_organism:
Plasmodium vivax
Homo sapiens

platform_organism:
Plasmodium vivax
Homo sapiens

overall_design: This was a minimal risk study enrolling ten Thai adults diagnosed with Plasmodium vivax infection by rapid diagnostic test or microscopy at various medical facilities in Na Chaluai and Buntharik Districts in Ubon Ratchathani Province, Thailand, between September and November, 2016. Those meeting initial inclusion criteria (age >18 years) and exclusion criteria (no signs/symptoms of severe malaria, no antimalarial use in the past 4 weeks and not pregnant), underwent venipuncture for peripheral blood smear and complete blood count. Whole blood samples were drawn from each subject with hematocrit levels that exceeded 25%, a parasitemia level at least 0.1% and the parasite population that was well-aligned in their IEC stage at early trophozoite only or with the majority (>80%) in the same stage, either early trophozoites or late trophozoites. Whole blood samples were cultured ex vivo over the subsequent 48 hours and subsamples were flash frozen approximately every 3 hours.  RNA was then isolated from the whole blood samples, which included a mixture of human mRNA from PBMCs and parasite RNA from infected RBCs. RNA reads were mapped to both human and parasite transcriptomes and transcript abundance was quantified for both organisms at each time point and for each study participant.

first: Francis

last: Motta

first: Kevin

last: McGoff

first: Chun-Yi

last: Cho

first: Christina

middle: M

last: Kelliher

first: Lauren

last: Smith

first: Michael

last: Ortiz

first: Adam

middle: R

last: Leman

first: Sophia

last: Campione

first: Nicolas

last: Devos

first: Suwanna

last: Chaorattanakawee

first: Nichaphat

last: Uthaimongkol

first: Worachet

last: Kuntawunginn

first: Chadin

last: Thongpiam

first: Chatchadaporn

last: Thamnurak

first: Montri

last: Arsanok

first: Mariusz

last: Wojnarski

first: Pattaraporn

last: Vanchayangkul

first: Nonlawat

last: Boonyalai

first: Philip

first: Michele

last: Spring

first: Krisada

last: Jongsakul

first: Ilin

last: Chuang

first: John

last: Harer

first: Steven

middle: B

last: Haase


title: RNA-sequencing for Bnt07G011994-overexpressed Arabidopsis

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

summary: Bnt07G011994 is a ramie KNOX gene, and its overexpression caused a significant decrease in fiber number in transgenic Arabidopsis, indicating a negative role of this gene in modulating fiber growth. To obtain insights into the potential functional mechanism of Bnt07G011994, we performed RNA sequencing for wild and Bnt07G011994-overexpressed Arabidopsis. After comparing their transcriptomes, a total of 251 differentially expressed genes were identified.

overall_design: Wild and Bnt07G011994-overexpressed Arabidopsis were grown in a greenhouse at 22°C under a 15 h light/ 9 h dark cycle. When the stems reached to about 10 cm-length, stems of each individual were collected as a sample for RNA sequencing.


title: Gene expression profiles  of different cells and brain regions in mice

first: Lining

last: Liang

address: 190,Kaiyuan Ave.

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

summary: To investigate the differences in gene expression  among various cells and tissues, hippocampus, cerebellum, cortex, primary glial cells and primary neurons were isolated from mice, mouse embryonic fibroblasts (MEFs) were isolated from day 13.5 embryos, R1 mbryonic stem cells (ESCs) were clutured in galetin-coated plates in N2B27+2i medium. Total RNA were extracted and subjected to RNA-Seq analysis.

overall_design: RNA sequencing of various mouse cell types and tissues.

first: Jinlong

last: Chen

first: Hao

last: Sun

first: Hui

last: Zheng


title: Comparative RNA sequencing-based transcriptome profiling of ten grapevine rootstocks: shared and specific sets of genes respond to mycorrhizal symbiosis

status: Public on Jun 10 2023

city: Dijon

first: Pierre-Emmanuel

last: COURTY

address: 17 rue Sully

institute: INRAE Dijon

summary: Arbuscular mycorrhizal symbiosis improves water and nutrient uptake by plants and provides them other ecosystem services. Grapevine is one of the major crops in the world. V. vinifera scions are generally grafted onto a variety of rootstocks that confer different levels of resistance against different pests, tolerance to environmental stress, and influence the physiology of the scions. Arbuscular mycorrhizal fungi are involved in the root architecture and in the immune response to soil-borne pathogens. However, the fine-tuned regulation and the transcriptomic plasticity of rootstocks in response to mycorrhization are still unknown. We compared the responses of 10 different grapevine rootstocks to arbuscular mycorrhizal symbiosis (AMS) formed with Rhizophagus irregularis DAOM197198 using RNA sequencing-based transcriptome profiling. We have highlighted a few shared regulation mechanisms, but also specific rootstock responses to R. irregularis colonization. A set of 353 genes was regulated by AMS in all ten rootstocks. We also compared the expression level of this set of genes to more than 2,000 transcriptome profiles from various grapevine varieties and tissues to identify a class of transcripts related to mycorrhizal associations in these 10 rootstocks. Then, we compared the response of the 351 genes upregulated by mycorrhiza in grapevine to their Medicago truncatula homologs in response to mycorrhizal colonization based on available transcriptomic studies. More than 97% of these homologs were expressed in at least one transcriptome profile, and 64% in all profiles. At the intra-specific level, we described for the first time shared and specific grapevine rootstock genes in response to R. irregularis symbiosis. At the inter-specific level, we defined a shared subset of mycorrhiza-responsive genes

overall_design: To investigate the effect of mycorrhization on grapevine rootsotck, Rootstocks of seven hybrids (110 Richter, 140 Ruggeri, 1103 Paulsen, Selection Oppenheim4, 420A Millardet et de Grasset, 41B Millardet et de Grasset and 101.14 Millardet et de Grasset) and some of their parentals (V. riparia, V. rupestris and V. berlandieri) were chosen. We perfomed RNA extraction from root and we sequenced mRNA from mycorrhizal and non mycorrhizal plants

first: Antoine

last: Sportes

first: Mathilde

last: Hériché

first: Arnoud

last: Mounier

first: Celien

last: Durney

first: Diederik

last: van Tuinen

first: Sophie

last: Trouvelot

first: Daniel

last: Wipf

last: Courty


title: Single-cell RNA-sequencing analysis for the molecular taxonomy of primate hippocampus after sevoflurane exposure

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: We thus isolated hippocampus from rhesus macaques and performed single-cell RNA-sequencing analysis. The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V2 Reagent Kits (10X Genomics, Pleasanton, USA).

overall_design: Two groups (Ctrl; Sevoflurane); two male macaques were included in group Ctrl, one male macaque was included in group sevoflurane. Tissues of each group were mixed and then divided into 4 samples.

first: Lei

last: Zhang


title: Impact of Hb contamination in obtaining reference profiles of exRNAs in healthy individuals (3)

first: Ionita

middle: Calin

last: Ghiran

address: 3 Blackfan Circle

institute: Beth Israel Deaconess Medical Center

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

summary: Impact of hemolysis on profiles of exRNAs in healthy individuals

overall_design: The goal of the project was to investigate the effect of hemoglobin released during blood collection on the levels of circulating miRNAs. Blood from 5 subjects, 3 females and 2 males were collected in EDTA, heparin and serum vacutener tubes. Cell free plasma was then mixed with increasing concentrations of hemoglobin, 0.05, 0.5 and 5%, and miRNAs analyses using RT-PCR.


title: Comprehensive gene expression analysis using RNA sequencing between male and female patients with idiopathic carpal tunnel syndrome

city: Kurume-city

first: Fumiko

last: Arakawa

address: Asahi-machi  67

department: Department of Pathology

institute: Kurume University, School of Medicine

summary:
We aimed to identify genes with considerable expression changes between male and female patients with idiopathic carpal tunnel syndrome (ICTS). For this purpose, we collected subsynovial connective tissues from 6 male and 6 female patients diagnosed with idiopathic carpal tunnel syndrome during surgery. We extracted the total RNA from the collected specimens and performed a comprehensive gene expression analysis using RNA sequencing by comparing between male and female patients.
We analyzed the changes in gene expression in male patients relative to that in female patients, and as a result, 26 genes were extracted. In the RNAseq analysis, the expression of these genes (IGF1, COL1A1, and COL3A1) was upregulated in the male patient group.

overall_design: Analysis of gene expression variation in males based on females by RNAseq using SSCT (subsynovial connective tissue) from carpal tunnel syndrome

first: Yusuke

last: Ogura

first: Hiroaki

last: Miyoshi


title: Next Generation Sequencing (NGS) analysis of mice pancreatic islets from control and IMP2 islet specific knockout (Rip2;IMP2).

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

summary: The goal of this study is to understand how IMP2 contributes to T2D traits by regulating pancreatic beta cell growth and function. Islets from control and Rip2;IMP2 mice were generated by deep sequencing. In additon, we also perfomred IMP2 RIP-Seq to identify IMP2 targets.

overall_design: We looked at 4 Samples.

first: Ning

last: Dai

first: Fi


title: Whole transcriptome analysis of cancer-associated fibroblast

city: Okayama

first: Shuta

last: Tomida

address: 2-5-1 Shikata-cho, Kita-ku

department: Center for Comprehensive Genomic Medicine

institute: Okayama University Hospital

overall_design: Cancer-associated fibroblasts (CAFs) are important components in tumor microenvironment (TME) and have been reported to interact with cancer cells, leading to tumor progression and drug resistance. We investigated how CAFs promotes tumor progression of non-small cell lung cancer (NSCLC).

first: Fumiaki

last: Takatsu

first: Ken

last: Suzawa


title: Gene expression profiling of HUVEC-s expressing PIK3CA with H1047R point mutation

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

summary: Sporadic venous malformations (VM) and angiomatosis of soft tissue (AST) are benign, congenital slow-flow vascular anomalies that have no available targeted therapies. Depending on the size and location of the lesion, symptoms vary from motility disturbances to pain and disfigurement. By analyzing tissue samples from 36 patients with VM or AST, we uncover that the majority of the samples carry a somatic mutation in either TEK or PIK3CA gene. In the current data set, we study the role of PIK3CA point mutation p.H1047R on the transcriptional profile of human umbilical vein endothelial cells (HUVEC-s).

overall_design: RNA-Seq of human umbilical vein endothelial cells (HUVEC-s) transduced with lentivirus encoding either wild type PIK3CA or PIK3CA with the pathological point mutation p.H1047R.

first: J

middle: P

last: Laakkonen

first: M

middle: U

last: Kaikkonen

first: T


title: High-throughput sequencing of SCC9 in normal  cells and Cucurbitacin B treated cells

city: ChangChun

first: Boqiang

last: Tao

address: Xi'an Road

institute: Jilin University

type: Non-coding RNA profiling by high throughput sequencing

summary: Through high-throughput sequencing of SCC9 normal cells and cells treated with cucurbitin B, we found that lncRNAs were differentially expressed before and after treatment with cucurbitin B.  LncRNA can regulate the occurrence and development of tongue squamous cell carcinoma cells by targeting miRNA.

overall_design: Detection of lncRNA in tongue squamous cell carcinoma cells before and after treatment with cucurbitin B.

first: Wang

last: Dongxu

first: Tao

last: Boqiang

first: Liu

last: Weiwei

first: Yang

last: Shuo


title: Glioblastoma stem cells after treatment with anti-E2F, anti-STAT3 or their combination.

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

summary: Malignant gliomas, including glioblastoma (GBM), are uniformly lethal with inferior prognosis and lack of effective treatment. Although the H2AZ2 variant histone is overexpressed in diverse cancer types where it promotes cancer cell proliferation, there are no H2AZ2 inhibitors to-date for clinical intervention. Here, we explored approaches to pharmacologically target the H2AZ2-dependent pathways in GBM.

overall_design: RNA-seq from glioblastoma stem cell specimens (TS-543) following treatment with  DMSO, HLM006474, S3I-201 or combination of HLM006474 and  S3I-201.

first: Jeehyun

last: Yoon

first: Derrick

last: Sek Tong Ong


title: Chem-CRISPR/dCas9FCPF - a platform for chemically induced epigenome editing

status: Public on Jun 09 2023

city: Frankfurt

first: Xinlai

last: Cheng

address: Max-von-Laue-Strasse 15. R. 3.652

department: Pharmaceutical Chemistry

institute: Goethe university Frankfurt

summary: Epigenetic aberration is one of the major driving factors in the initiation, promotion, and progression of human cancer and it is also often associated with acquired therapeutic resistance. Several chemical epigenetic modulators have been reported. However, results from animal models and clinical trials have indicated that severe on- and off-target toxicity is one of the leading factors behind failures in epidrug development. CRISPR/dCas9 technology provides a powerful tool for precise epigenetic regulation at the single-gene level. This approach requires ectopic expression of exogenous epigenetic modulatory proteins, which cause side effects and technical challenges for preparation and delivery. Recently, we have shown that Cas9 tagging with the peptide motif (FCPF) was recognized by perfluoro biphenyl derivatives. Here, we introduced the FCPF-tag into dCas9 and report a chemically induced platform for epigenome editing (Chem-CRISPR/dCas9FCPF). By conjugating JQ1, a BRD4 inhibitor, to perfluoro biphenyl (JQ1-FCPF), we demonstrate that JQ1-FCPF covalently binds to CRISPR/dCas9 and specifically inhibits BRD4 in proximity to the promoters/enhancers of c-MYC with the guidance of c-MYC sgRNAs. Thus, we achieved epigenetic modulation of c-MYC with high efficiency and specificity.

overall_design: BRD4 ChIP-Seq experiment on K562 cells to study specificity of dCas9-based, chemical-mediated epigenome editing

first: Maximilian

last: Sprang

first: Miguel

middle: A

last: Andrade-Navarro


title: Cell type specializations of the vocal-motor cortex in songbirds

city: Portland

first: Claudio

last: Mello

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health & Science University

summary: The identification of molecular specializations in cortical circuitry supporting complex behaviors, such as learned vocalizations, requires understanding the neuroanatomical context from which these circuits arise. In songbirds, the robust nucleus of the arcopallium (RA) provides the sole descending projection for fine motor control of vocalizations. Using single nuclei transcriptomics and spatial gene expression mapping in zebra finches, we were able to define cell types and molecular specializations that distinguish RA from adjacent regions involved in non-vocal motor and sensory processing. We describe an RA-specific vocal projection neuron, differential composition of inhibitory neuron subtypes, and unique glial specializations. We show how several cell-specific molecular features arise in a sex-dependent manner during development. Based on the molecular data, we were also able to electrophysiologically probe, for the first time, predicted GABAergic subtypes within RA. To facilitate future utilization of the data, we have developed interactive apps that allow integration of cell level molecular data with developmental and spatial distribution data from our gene expression brain atlas (ZEBrA). With this resource, users can explore molecular specializations of vocal-motor neurons and support cells that likely reflect adaptations key to the physiology and evolution of vocal control circuits.

overall_design: 2 samples

first: Alexander

last: Nevue

first: Benjamin

last: Zemel

first: Samantha

last: Friedrich

first: Henrique

last: von Gersdorff


title: Transcriptional patterns of peripheral blood mononuclear cells (PBMCs) in SARS-CoV-2 infected patients with different severity and outcome

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

summary: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological pathogen of coronavirus disease 2019 (COVID-19), a highly contagious disease, spreading quickly and threatening global public health. The symptoms of the disease vary from mild reactions to severe respiratory distress or even fatal outcomes probably due to the different status of innate immunity which is the first line to combat the virus. Here in the study, we unveiled the underlying transcriptional patterns of peripheral blood mononuclear cells (PBMCs) using SARS-CoV-2 infected patients with different severity and outcome. Through systemic analysis, an anti-microbe peptide, α-defensin-1 (DEFA1) was identified to be elevated in both plasma and PBMCs in COVID19 patients, and the function and mechanism is studied.

overall_design: PBMC samples from the patients and normal controls were lyzed with TRIzol reagent (Invitrogen, Carlsbad, USA) to extract the total RNA respectively for the subsequent transcriptome sequencing. A total RNA of 10 mg for each sample was obtained to generate the RNA cDNA sequencing library to following a previous study with some adjustments. The mRNA libraries were purified and quantified for the sequencing analysis with Illumina HiSeq™ 2500 analyzer (Illumina, San Diego, United States) according the of the manufacturer’s instructions per RNA sample. The entire operating processes of the experiment were performed with the help of the Shanghai NovelBio Bio-Pharm Technology Co.,Ltd.

first: Xijing

last: Qian


title: The Validation set of the genomic nodal index (GNI) in 2014

city: Suita

first: Yoshiaki

last: Sota

address: Yamadaoka 2-15

department: Breast and Endocrine Surgery

institute: Osaka University

summary: The aim of this study was to construct a prediction model for axillary lymph node metastasis (ALNM) using a DNA microarray assay for gene expression in breast tumor tissues. Luminal A breast cancers, diagnosed by PAM50 testing, were analyzed, and a prediction model (genomic nodal index (GNI)) consisting of 292 probe sets for ALNM was constructed in a training set of patients (n=388), and was validated in the first (n=59) and the second (n=103) validation sets. AUCs of ROC were 0.820, 0.717, and 0.749 in the training, first, and second validation sets, respectively. GNI was most significantly associated with ALNM, independently of the other conventional clinicopathological parameters in all cohorts. It is suggested that GNI can be used to identify the patients with a low risk for ALNM so that sentinel lymph node biopsy can be spared safely.  This DATA set: J03 contains 120 (n+ 60, n- 60) samples of the above first and second validation sets from Japan (OUH_1,2). A long time passed, and now it is unclear how these 120 cases were distributed among the first and second validation sets.   *Note: This old data has been updated multiple times by others.  Then, there are some differences from the original 2014 paper and unclear points still remain.  Therefore, do not use it for formal analysis aimed at public insurance coverage etc. This is for research purposes only. Please cite this paper when writing a new paper. PMID: 25016059  DOI: 10.1016/j.canlet.2014.07.003

overall_design: RNA was extracted from 120 fresh frozen tumor samples obtained from radical breast cancer surgery and hybridized on Affymetrix microarrays.

first: Ryo

last: Tsunashima

first: Yasuto

last: Naoi


title: Dual inhibition of KRASG12D and pan-ERBB is synergistic in pancreatic ductal adenocarcinoma

city: La Jolla

first: Herve

last: Tiriac

state: CA

address: 3855 Health Sciences Drive

department: Surgery

institute: UCSD Health

summary: Pancreatic ductal adenocarcinoma (PDAC) is a lethal cancer with a low survival rate. Recently, new drugs that target KRASG12D, a common mutation in PDAC, have been developed. We studied one of these compounds, MRTX1133, and found it was specific and effective at low nanomolar concentrations in patient-derived organoid models and cell lines harboring KRASG12D mutations. Treatment with MRTX1133 upregulated the expression and phosphorylation of EGFR and HER2, indicating that inhibition of ERBB signaling may potentiate MRTX1133 anti-tumor activity. Indeed, the irreversible pan-ERBB inhibitor, afatinib, potently synergized with MRTX1133 in vitro, and cancer cells with acquired resistance to MRTX1133 in vitro remained sensitive to this combination therapy. Finally, the combination of MRTX1133 and afatinib led to tumor regression and longer survival in orthotopic PDAC mouse models. These results suggest that dual inhibition of ERBB and KRAS signaling may be synergistic and circumvent the rapid development of acquired resistance in patients with KRAS mutant pancreatic cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We analyzed the effect of a KRAS inhibitor (MRTX1133) on pancreatic cancer cells (SUIT2 human pancreatic cancer cell and FC1242 mouse pancreatic cancer cell). Cells were treated with MRTX1133 acutely or chronically and whole RNA was extracted and sequenced.


title: Chem-CRISPR/dCas9 -a chemically induced platform for epigenome editing

overall_design:
Analysis of gene expression upon various treatments
Total RNA obtained from isolated K562 cells after 1 h treatment, including DMSO as control, JQ1 -sgRNA, JQ1 +sgRNA, JQ1-FCPF -sgRNA, JQ1-FCPF +sgRNA


title: IgM from common variable immunodeficiency patients narrowly recognizes erythrocyte and platelet glycans

city: Philadelphia

first: Tian

last: Tian

state: PA

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

summary: Autoantibody-mediated cytopenias (AICs) regularly occur in profoundly IgG-deficient common variable immunodeficiency (CVID) patients. The isotypes, antigenic targets, and origin(s) of disease-causing autoantibodies in this patient population are unclear. Herein, we report that erythrocytes and platelets from CVID patients with AICs (CVID+AIC) are coated with autoreactive IgM. Glycan array-based analyses of CVID+AIC plasma IgM revealed narrow reactivities to erythrocytic I/i antigens and platelet expressed I/i antigen-related glycans but starkly lower binding to hundreds of other pathogen and tumor-associated carbohydrates. Polyclonal B-cell receptors with corresponding I/i antigen reactivities were highly enriched among CVID+AIC circulating marginal zone (MZ) B cells. Within secondary lymphoid tissues, MZ B cells secreted copious IgM when activated by IL-10 secreting FOXP3-CD25hiTfh cells. In lymph nodes from immunocompetent controls, MZ B cells localized outside of GCs near rare FOXP3-CD25+ cells and plentiful FOXP3+ regulatory T cells. In CVID+AIC lymph nodes, counterpart cells localized to similar anatomic positions but CD25hiTfh cells greatly outnumbered regulatory T cells. In total, our findings indicate glycan-reactive IgM autoantibodies produced outside of GC borders may contribute to the autoimmune pathogenesis of CVID.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FACS-isolated tonsillar GC B cells and marginal zone B cells

first: Carole

last: Le Coz

first: Samuel

first: Hakon

last: Hakonarson

first: Neil

last: Romberg


title: ASH2L, a COMPASS core subunit, is involved in the cell invasion and migration of triple-negative breast cancer cells through the epigenetic control of histone H3 lysine 4 methylation.

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

summary: ASH2L (Absent-Small-Homeotic-2-Like protein) is a core subunit of the COMPASS (COMplex of Proteins ASsociated with Set1) complexes, the most notable writer of the methylation of histone H3 lysine 4 (H3K4). The COMPASS complex regulates active promoters or enhancers, and its dysfunction is associated with aberrant development and disease. Here, we demonstrated that ASH2L mediated the cell invasion and migration activity of triple-negative breast cancer cells through the interaction with the COMPASS components and the target genomic regions. Transcriptome analysis indicated a potential correlation between ASH2L and the genes involved in inflammatory/immune responses. Among them, we found that the intrinsic expression of IL1B (interleukin 1 beta), an essential proinflammatory gene, was directly regulated by ASH2L. These results revealed a novel role of ASH2L on the maintenance of breast cancer malignancy possibly through H3K4 methylation of the target inflammatory/immune responsive genes.

overall_design: Comparison between negative control cells and the ASH2L sh3 knockdown cells. There are two biological replicates for each conditions.

first: Gerelsuren

last: Batbayar

first: Akihiko

last: Ishimura

first: Hanbing

last: Lyu

first: Sasithorn

last: Wanna-udom

first: Makiko

last: Meguro-Horike

first: Minoru

last: Terashima

first: Takahisa

last: Takino

first: Takeshi

last: Suzuki


title: Screening autism-associated environmental factors in differentiating human neural progenitors with fractional factorial design-based transcriptomics

city: Solna

first: Abishek

last: Arora

state: Stockholm

address: NKS BioClinicum J9:30, Akademiska stråket 1

department: Department of Women's and Children's Health

institute: Karolinska Institutet

summary: Research continues to identify genetic variation, environmental exposures, and their mixtures underlying different diseases and conditions. There is a need for screening methods to understand the molecular outcomes of such factors. Here, we investigate a highly efficient and multiplexable, fractional factorial experimental design (FFED) to study six environmental factors and four human induced pluripotent stem cell line derived differentiating human neural progenitors. We showcase the FFED coupled with RNA-sequencing to identify the effects of low-grade exposures to these environmental factors and analyse the results in the context of autism spectrum disorder (ASD). We performed this after five-day exposures on differentiating human neural progenitors accompanied by a layered analytical approach and detected several convergent and divergent, gene and pathway level responses. We revealed significant upregulation of pathways related to synaptic function and lipid metabolism following lead and fluoxetine exposure, respectively. The lipid changes were validated using mass spectrometry- based metabolomics after fluoxetine exposure. Our study demonstrates that the FFED can be used for multiplexed transcriptomic analyses to detect relevant pathway-level changes in human neural development caused by low-grade environmental risk factors. Future studies will require multiple cell lines with different genetic backgrounds for characterising the effects of environmental exposures in ASD.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for four iPSC derived neuroepithelial stem (NES) cell lines exposed to six autism associated environmental factors during neuronal differentiation.
*** Submitters declare that it is not legally permitted to submit the raw data to GEO or a restricted-access database such as dbGaP or EGA****

first: Martin

last: Becker

first: Cátia

last: Marques

first: Marika

last: Oksanen

first: Danyang

last: Li

first: Francesca

last: Mastropasqua

first: Michelle

last: Watts

first: Manish

first: Anna

last: Falk

first: Carsten

middle: O

last: Daub

first: Ingela

last: Lanekoff

first: Kristiina

last: Tammimies


title: A single-cell transcriptome atlas of pig skin characterizes anatomic positional heterogeneity

city: Chengdu

first: Qin

last: Zou

address: No.211, Huimin Road

institute: Sichuan Agricultural University

summary: Heterogeneity in the main three cell types from different anatomic skin sites will contribute to a better understanding of hereditary information

overall_design: We performed single-cell RNA sequencing of six different anatomical skin regions from the Chenghua pig (head, ear, shoulder, back, abdomen, leg) and one region from LW pig (back).

first: Rong

last: Yuan


title: ERK5 S496 phosphorylation, but not ERK5 kinase activation, promotes senescence-associated cell growth (SACG) and inflammation of myeloid cells and atherosclerosis via upregulating SUMOylation at a novel site (K518) on NRF2 and aryl hydrocarbon receptor

city: Houston

first: Shengyu

state: TX

address: 6670 Bertner Ave, R10-109, floor 10

institute: Houston Methodist Research Insitute

summary: ERK5 is a dual kinase-transcription factor, which contains an N-terminal kinase domain and transactivation domains in the C-terminal half. Many ERK5 kinase inhibitors have been developed and tested to treat cancer and inflammatory diseases. However, recent data have raised questions regarding the functional role of ERK5 kinase inhibitors. We aimed to investigate how ERK5 reprograms myeloid cells (MC) to the senescence-associated secretory phenotype (SASP), consequently leading to atherosclerosis. We showed that atherosclerosis was inhibited in ERK5 S496A (dephosphorylation mimic) knock-in (KI) mice. Furthermore, ERK5 S496 phosphorylation was required for not only SASP but also senescence-associated cell growth (SACG) observed in the plaque via upregulation of aryl hydrocarbon receptor (AHR). We also discovered a key effect of ERK5 S496 phosphorylation on SUMOylation at a novel site of NRF2 (i.e., K518), which inhibited NRF2 transcriptional activity without affecting ERK5 kinase activity and antagonized oxidized LDL (oxLDL)-induced SASP. Specific ERK5 kinase inhibitors (AX15836 and XMD8-92) both inhibited oxLDL-induced ERK5 S496 phosphorylation, suggesting that ERK5 S496 phosphorylation was involved at least in part of the effects of these inhibitors. We have discovered a novel mechanism, in which ERK5 S496 phosphorylation directly inhibits NRF2 activity by upregulating NRF2 K518 SUMOylation, and induces SACG and atherosclerosis.

overall_design: We prepared the tissue section from the plaques in wild-type, and ERK5 S496A KI mice fed a high-fat diet (HFD) or normal chow diet (NCD) for 12 weeks after AAV8-PCSK9 injection.

first: Jun-ichi

last: Abe

first: Masaki

last: Imanishi

first: Aijun

last: Zhang

first: Kyung

last: Ko

first: Venkatasubrahman

middle: K

last: Samanthapudi

first: Ling-Ling

last: Lee

first: Anita

last: Deswal

first: Joerg

last: Herrmann

first: Steven

middle: H

last: Lin

first: Eduardo

middle: N

last: Chini

first: Ying

last: Shen

first: Keri

middle: L

last: Schadler

first: Thi-Hong-Minh

last: Nguyen

first: Anisha

last: Gupte

first: Cielito

last: Reyes-Gibby

first: Sai-Ching

middle: J

last: Yeung

first: Nicolas

last: Palaska

first: John

last: Cooke

first: Henry

last: Pownall

first: Momoko

last: Yoshimoto

first: Keigi

last: Fujiwara

first: Dale

last: Hamilton

first: Jared

last: Burks

first: Guangyu

last: Wang

first: Nhat-Tu

last: Le

first: Sivareddy

last: Kotla


title: Effect of LL37 plus LDL on gene expression in THP-1 macrophages

first: Yoahiyuki

last: Nakamura

address: 9500 Gilman Drive

institute: UCSD

summary: To investigate gene expression after treatment of LL37 and LDL, we treated THP-1 macropahges with LL37 and/ or LDL.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THP-1 cells without treatment and with LDL monotherapy, LL37 monotherapy and LDL plus LL37 combined treatment

first: Yoshiyuki


title: N6-methyladenosine-enhanced FZR1 translation contributes to gemcitabine insensitivity in pancreatic cancer via quiescence maintenance [m6A-seq]

city: Guangzhou

first: Rui

last: Li

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary:
Herein, by detecting the global m6A profile in a panel of gemcitabine-sensitive and gemcitabine-insensitive PDAC cells, we identified the key role of hyper-m6A modification of the master G0/G1 regulator Fizzy and Cell Division Cycle 20 Related 1 (FZR1) in regulating gemcitabine sensitivity. Targeting m6A modification of FZR1 improves the gemcitabine treatment response of gemcitabine-insensitive PDAC cells in vitro and in vivo.
Mechanistically, Gem Nuclear Organelle Associated Protein 5 (GEMIN5) was identified as a novel m6A mediator that specifically binds to m6A-modified FZR1 and recruits the eIF3 translation initiation complex to accelerate FZR1 translation. Upregulation of FZR1 maintains the G0/G1 quiescent state and impairs gemcitabine sensitivity of PDAC cells. Further clinical analysis showed that both high levels of FZR1 m6A modification and FZR1 protein indicated a poor response to gemcitabine.

overall_design: m6A-seq data for six PDAC cell lines and GEMIN5 PAR-CLIP-seq of PANC-1

first: Jiachun

last: Su


title: N6-methyladenosine-enhanced FZR1 translation contributes to gemcitabine insensitivity in pancreatic cancer via quiescence maintenance [PAR-CLIP-Seq]

first: Ziming

last: Chen

first: Hongzhe

last: Zhao


title: Divergent Functions of Histone Acetyltransferase Paralogs KAT2A and KAT2B in Keratinocyte Stemness and Differentiation

first: Chin Yan

last: Lim

state: Singapore

address: 8A Biomedical Grove

institute: A*STAR Skin Research Labs

summary: The mammalian epidermis undergoes constant renewal replenished by a pool of stem cells and terminal differentiation of their progeny. This is accompanied by changes in gene expression and morphology orchestrated, in part, by epigenetic modifiers. Here, we defined the role of histone acetyltransferase KAT2A in epidermal homeostasis and provided a comparative analysis that revealed key functional divergence with its paralogue, KAT2B. In contrast to KAT2B's reported function in epidermal differentiation, KAT2A supports the undifferentiated state in keratinocytes. RNA-seq analysis of KAT2A- and KAT2B- depleted keratinocytes revealed dysregulated epidermal differentiation. Depletion of KAT2A led to premature expression of epidermal differentiation genes in the absence of inductive signals, whilst loss of KAT2B delayed differentiation. KAT2A acetyltransferase activity was indispensable in regulating epidermal differentiation gene expression. The metazoan-specific N-terminus of KAT2A was also required to support its function in keratinocytes. We further showed that the interplay between KAT2A- and KAT2B- mediated regulation was important for normal cutaneous wound healing in vivo. Overall, these findings reveal a distinct mechanism in which keratinocytes utilize a pair of highly homologous histone acetyltransferases to support divergent functions in self-renewal and differentiation processes.

overall_design: RNA-seq

first: Benjamin

middle: W

last: Walters

first: Chin

middle: Y

first: Chew Teng

last: Tan

first: Christabel

middle: T

last: Dube

first: Kang Ting

last: Lee

first: Jace

last: Koh

first: Yasmin Hui Binn

last: Ong

first: Rifkhana

last: Fathima Shah Jahan

first: Vanessa Xue Hui

first: Tiak Ju


title: Effect of Schisandrin on Rheumatoid Synovial Fibroblast-like Synoviocytes

first: lin

last: wei

state: Guangdong

address: No. 58, Zhongshan Second Road

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: To explore how Schisandrin (SCH) regulates biological functions of fibroblast-like synovioctyes (FLSs) from rheumatoid arthritis (RA) patients, we evaluated the transcriptome of SCH-treated RA FLSs compared with untreated control using RNA sequencing analysis.

overall_design: Comparative gene expression profiling using RNA-seq data from human RA FLSs treated with SCH or DMSO

first: Wei

last: Lin


title: Glucocorticoid-stimulated senescence phenotype in differentiated bone marrow adipocytes treated with PPARgamma inhibitor

city: baltimore

first: Mei

last: Wan

state: Maryland

address: 720 Rutland Ave,Ross research buil

department: Department of Orthopedics

institute: Johns Hopkins Hospital

summary: Glucocorticoids, powerful anti-inflammatory and immunosuppressive agents, can decrease bone mass and quality and increase bone marrow adiposity. Here, we show that a small number of bone marrow adipocytes (BMAds) in mice undergo rapid cellular senescence in response to glucocorticoid treatment. The senescent BMAds acquire a senescence-associated secretory phenotype (SASP), which reinforces and spreads senescence in the bone/bone marrow microenvironment in a paracrine manner. Mechanistically, glucocorticoid treatment increases the synthesis of oxylipins such as 15d-PGJ2 in BMAds to positively regulate the activity of PPARγ, which stimulates the expression of key cellular senescence effector genes. PPARγ activation, in turn, promotes oxylipin synthesis in BMAds, forming a positive feedback loop. Inhibition of the initial BMAd senescence by deleting p16INK4a from adipocytes or pharmacological suppression of the SASP efficiently interrupts the secondary spread of senescent cells and alleviates glucocorticoid-induced bone deficits. We identify senescent BMAds as initial mediators for glucocorticoid-induced bone deterioration and reveal a lipid metabolism circuit that robustly triggers the senescence of BMAds.

overall_design: In vitro stimulation of differentiated bone marrow adipocytes with or without glucocorticoid and /or PPARgamma inhibitor GW9662.

first: Xu

last: Cao

first: Xiaonan

last: Liu


title: RNA-seq of Niemann-Pick Type C mouse microglia throughout disease course

city: Palo Alto

first: Liana

middle: Nicole

last: Bonanno

state: California

address: 3801 Miranda Ave, Bldg 100 Rm D3-111

department: Neurology

institute: Stanford University

summary: Here we perform RNAsequencing on isolated microglia from wild-type and NP-C mice throughout disease course. We sequence microglia from WT and NPC mice at 1, 3, 6, and 9 weeks old. We also treat mice with the CSF1R inhibitor PLX5622 and sequence remaining microglia from treated and control mice.

overall_design: Mice were sacrificed (n=3-4/group) at stated age for both WT and NPC mice. Microglia were isolated via FACS. For PLX5622 treatment, microglia were isolated from 5 mice peer group.

first: Tony

last: Wyss-Coray


title: Effects of fucosylation inhibitors on ATRA differentiation in myeloid leukemia cells

status: Public on Jun 08 2023

city: Sendai-shi

first: Susumu

last: Suzuki

institute: Tohoku Medical and Pharmaceutical University

summary: Differentiation therapy with all-trans retinoic acid (ATRA) is well established for acute promyelocytic leukemia (APL). However, the narrow application and tolerance development of ATRA remain to be improved. In this study, we challenged glycosylation inhibitor to obtain better efficiency than ATRA alone. As a result, we found that the combination of fucosylation inhibitor 6-alkynylfucose (6AF) with ATRA have profound effect for differentiation, shown by expression changes of differentiation markers CD11b, CD11c, with significant morphological change in NB4 and HL-60 cells. From lectin blot assay, we found that ATRA or 6AF alone could decrease core fucosylation, the combination of these two agents efficiently decreases the expression of core fucosylation. To reveal molecular mechanisms to reveal 6AF effect for ATRA induced differentiation, we next performed microarray analysis using NB4 cells. From pathway analysis using DAVID software, we found that C-type lectin receptor (CLR) signaling pathway was enriched as high significance. From real time PCR analysis, using NB4 and HL-60 cells, FcRI, CLEC6A, CASP1, IL-1, EGR2/3, the components of CLR, and Akt, were indeed upregulated by 6AF in ATRA induced differentiation. These suggest that the involvement of CLR signaling pathway in 6AF effect of ATRA induced differentiation.

overall_design: We use 4 samples. As a control, we used DMSO sample. The other samples are ATRA, 6AF and ATRA+6AF. All samples were exposed to reagents for 72 hours.

first: Shinichiro

last: Takahashi


title: Single cell RNA-Seq analysis of human skeletal muscle organoids

city: Muenster

first: Hyun-Woo

last: Jeong

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

summary: We performed single cell RNA sequencing analysis of human iPSC-derived skeletal muscle organoids at 12 week post differentiation stage.

overall_design: We dissociated organoids into single cell suspension and performed droplet-based single cell RNA-Seq analysis using 10X Genomics Chromium system

first: Mavrommatis

last: Lampros

first: Zaehres

last: Holm


title: RNA-Seq analysis of human skeletal muscle organoids

summary: We performed RNA sequencing analyses of human iPSC and iPSC-derived skeletal muscle organoids in different differentiation stages of 4wk, 8wk, and 16wk.

overall_design: Total RNA was extracted from single organoids or cultured cells and then analyzed by stranded RNA sequencing.


title: Transcriptome profiling of human skeletal muscle organoids

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

overall_design: Refer to individual Series


title: RNA sequencing of mouse after single sevoflurane exposure

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: we combined RNA sequencing analysis of mouse prefrontal cortex after single sevoflurane exposure

overall_design: 3 samples of mouse prefrontal cortex were used in this study.( Sevoflurane, 3 replicated sample were included in this group.)

first: Lei

last: Zhang


title: Histone 3 lysine 9 acetylation-specific reprogramming regulates esophageal squamous cell carcinoma progression and metastasis

city: Wenzhou

first: Chenghao

last: Li

state: Zhejiang

address: Wenzhou Medical University, Xueyuan Xi Road

institute: Wenzhou Medical University

summary: Dysregulation of histone acetylation is widely implicated in tumorigenesis, yet its specific roles in the progression and metastasis of esophageal squamous cell carcinoma (ESCC) remains unclear. We here profiled the genome-wide landscape of H3K9ac for paired adjacent normal (Nor), primary ESCC (EC) and metastatic lymph node (LNC) esophageal tissues from three ESCC patients. By integrating these data with the corresponding H3K27ac profiles, we identified a distinct epigenetic reprogramming specific to H3K9ac in EC and LNC samples compared to Nor samples, which predominantly targeted genes functionally associated with tumorigenesis and metastasis, and contributed to their transcriptomic aberrations. The findings were further verified by a publicy available single cell RNA-seq data and in vitro experiment, highlighting the potential therapeutic avenues for intervening ESCC through epigenetic modulation via H3K9ac.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of H3K9ac for paired adjacent normal (Nor), primary ESCC (EC) and metastatic lymph node (LNC) esophageal tissues from three ESCC patients.

first: Zhenhui

last: Chen

first: Yue

last: Zhou

first: PengCheng

first: Guoquan

first: Yunbo

last: Qiao

first: Yinghao

last: Yao

first: Jianzhong

last: Su


title: NR2F2 is a key downstream effector of NF1 loss in estorgen receptor positive breast cancer (RNA-seq)

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

summary:
NF1 loss-of-function mutations are enriched in hormone receptor positive (HR+) metastatic breast cancer (MBC) and mediate endocrine therapy resistance. To identify therapeutic vulnerabilities in this context, we performed CRISPR/Cas9 screens in wildtype and NF1 knockout isogenic HR+ models and identified NR2F2, an orphan nuclear receptor, to be essential specifically in NF1 loss cells. The NR2F2 dependence was induced as a consequence of NR2F2 upregulation via the activation of the MAPK pathway in these cells. Enforced overexpression of NR2F2 was sufficient to confer endocrine therapy resistance in the absence of NF1 loss, while of NR2F2 knockout or knockdown could enhance the efficacy of endocrine therapies in NF1 WT and NF1 loss models. Mechanistically, our comprehensive multi-omics approaches revealed that NR2F2 modulates chromatin accessibility and regulates ER-dependent transcription through its interaction with ER, transcriptional coregulators and chromatin remodelers at chromatin. Specifically, increased NR2F2 in NF1 loss cells dramatically enhanced the association with transcriptional corepressors, which resulted in attenuation of chromatin accessibility and ER occupancy, and impaired ER transcriptional program. Our findings identify the nuclear receptor NR2F2 as a downstream effector of NF1 loss, and it is essential and potentially druggable mediator of endocrine therapy resistance.
We performed gene expression profiling analysis using data obtained from RNA-seq of MCF7 sgNT, sgNF1, sgNR2F2 and double knockout (DKO) cells under different conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF7 sgNT, sgNF1, sgNR2F2 and double knockout (DKO) cells under different conditions.

first: Yanyan

last: Cai

first: Sarat

last: Chandarlapaty


title: Net39 protects muscle nuclei from mechanical stress during the pathogenesis of Emery-Dreifuss muscular dystrophy [snRNA-seq]

city: Dallas

first: kenian

last: chen

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

summary: Mutations in genes encoding nuclear envelope proteins lead to diseases known as nuclear envelopathies, characterized by skeletal muscle and heart abnormalities, such as Emery-Dreifuss Muscular Dystrophy (EDMD). The tissue-specific role of the nuclear envelope in the etiology of these diseases has not been extensively explored. We previously showed that global deletion of the muscle-specific nuclear envelope protein NET39 in mice leads to neonatal lethality due to skeletal muscle dysfunction. To study the potential role of the Net39 gene in adulthood, we generated a muscle-specific conditional knockout (cKO) of Net39 in mice. cKO mice recapitulated key skeletal muscle features of EDMD, including muscle wasting, impaired muscle contractility, abnormal myonuclear morphology, and DNA damage. The loss of Net39 rendered myoblasts hypersensitive to mechanical stretch, resulting in stretch-induced DNA damage. Net39 was downregulated in a mouse model of congenital myopathy, and restoration of Net39 expression through AAV gene delivery extended lifespan and ameliorated the muscle abnormalities. These findings establish NET39 as a direct contributor to the pathogenesis of EDMD by protecting against mechanical stress and DNA damage.

overall_design: Comparative gene expression profiling analysis of single nucleus RNA-seq data for three biological replicates of Gastrocnemius-plantaris (GP) muscles from control and Net39 adult-inducible conditional knockout mice (cKO) at 5 months of age.

first: Zhang

last: Yichi

first: Ramirez-Martinez

last: Andres

first: Chen

last: Kenian

first: Xu

last: Lin


title: Net39 protects muscle nuclei from mechanical stress during the pathogenesis of Emery-Dreifuss muscular dystrophy [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Ty1-tagged Net39 in C2C12 myotubes.


title: epigenetic control of neurogenesis-to-gliogenesis switch during mouse cortical development

city: Shanghai

first: XIAOSU

last: LI

state: Shanghai

address: 131 Dongan Road

institute: Fudan University

summary: Gene expression and chromatin accessiblity changes as cortical RG switch from neurogenesis to gliogenesis; the bivalent chromatin present in the temporally upregulated genes maintain them poised.

overall_design: ATAC-seq of P1 hGFAP-GFP FASC isolated cells, cut&tag of H3K4me3 and H3K27me3 to identfy the bivalent chromatin during cortical development

first: Xiaosu

first: Lin

last: Yang


title: DNA methylation profiles of human embryonic stem cells (HUES8) differentiated to pancreatic duct-like organoids.

city: Ulm

first: Alexander

last: Kleger

address: Albert Einstein Allee 23

institute: Ulm University

type: Methylation profiling by genome tiling array

summary: To investigate Keratin 19 (KRT19) expression dynamics in pancreatic development, we established a human pluripotent stem cell (PSC)-based KRT19-mCherry reporter system in various genetic backgrounds to monitor KRT19 expression from ist endogenous gene locus. A genuine differentiation protocol to generate mature pancreatic duct-like organoids (PDLO) was applied. While KRT19/mCherry expression became evident at early endoderm stage, mCherry signal  was present in nearly all cells at pancreatic endoderm (PE) and pancreatic progenitor (PP) stage. Interestingly, despite homogenous KRT19 expression, the mCherry positivity dropped to 50% after ductal maturation, indicating a permanent switch from biallelic to monoallelic expression. DNA methylation profiling separated the distinct differentiation intermediates with site specific DNA methylation patterns occuring at the KRT19 locus during ductal maturation. Accordingly, the monoallelic switch was partially reverted upon treatment with a DNA-methyltransferase inhibitor.

overall_design: DNA methylation profiles of the human embryonic stem cell line HUES8.  HUES8 cells were differentiated into pancreatic progenitors (PP) and pancreatic duct like organoids (PDLOs). A stage-resolved genome-wide DNA methylation analysis was performed using the Infinium MethylationEPIC BeadChip array (n = 20). One sample was treated with 5-Aza-2’-deoxycytidine (5-Aza).

first: Jana

last: Krüger

first: Anja

last: Fischer

first: Reiner

last: Siebert


title: TONSOKU is required for the maintenance of repressive epigenetic modifications in Arabidopsis [RNA-Seq]

city: Beijing

first: Danhua

last: Jiang

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: Epigenetic inheritance requires the faithful maintenance of epigenetic marks such as certain chromatin modifications through DNA replication. Plant TONSOKU (TSK) and its animal orthologue TONSOKU-like (TONSL) act as readers for newly synthesized histones and assist in DNA replication via facilitating DNA damage repair at post-replicative chromatin. However, whether TSK/TONSL regulates chromatin replication and the maintenance of chromatin modifications remain elusive. In this study, we demonstrate that TSK is dispensable for global histone and nucleosome accumulation but necessary for maintaining repressive chromatin modifications including H3K9me2, H2A.W, H3K27me3 and DNA methylation. TSK physically interacts with H3K9 methyltransferases SUVH5 and SUVH6, and the Polycomb protein RING1a/b. Moreover, TSK mutation strongly enhances defects in Polycomb pathway mutants. TSK is intended to only associate with nascent chromatin until it starts to mature. We propose that TSK ensures proper epigenetic inheritance by supporting the recruitment of epigenetic modifiers to post-replicative chromatin in a critical short window of time following DNA replication.

overall_design: Transcriptome, MNase, H3k27me3, H2A.W and H3K9me2 enrichment, and DNA methylation were examined in Col or tsk-4 mutant

last: Wang

first: Mande

last: Xue

first: Huairen

last: Zhang


title: TONSOKU is required for the maintenance of repressive epigenetic modifications in Arabidopsis [ChIPSeq-H3K27me3]


title: Net39 protects muscle nuclei from mechanical stress during the pathogenesis of Emery-Dreifuss muscular dystrophy [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for three biological replicates of Gastrocnemius-plantaris (GP) muscles from control and Net39 adult-inducible conditional knockout mice (cKO) at 5 months of age.


title: Effect of JAKinibs and BCL6 on endothelial activation by IFNγ

city: Los Angeles

first: Nicole

last: Valenzuela

address: 1000 Veteran Avenue, Room 1-520

institute: UCLA

summary: The durability of interferon signaling in human aortic endothelial activation was tested. Pro-adhesive and costimulatory gene expression, phenotype, secretome and JAK/STAT phosphorylation in human primary endothelial cells were measured under chronic and transient IFNγ stimulation, with various JAK inhibitors.

overall_design:
Primary human aortic endothelial cells, n=3 paired biological replicates per condition
Ecs were untreated or treated with 30min pre-treatment with ruxolitinib (2uM), FX1, BI-3812 or BI-3802 (each at 100uM) prior to 24hr treatment with IFNg

middle: M


title: TONSOKU is required for the maintenance of repressive epigenetic modifications in Arabidopsis [ChIP-Seq]