title: RNA-seq of murine CD8+ tumor-infiltrating T cells following treatment with pembrolizumab and/or ABL503

status: Public on Apr 30 2024

city: Daejeon

first: Seung Hyuck

last: Jeon

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

type: Expression profiling by high throughput sequencing

summary: We aimed to analyze the transcriptomic changes in CD8+ tumor-infiltrating T cells induced by anti-PD-1 treatment and/or anti-PD-L1x4-1BB bispecific antibody treatment

overall_design: C57BL/6 hPD-1/hPD-L1/h4-1BB mice were inoculated with syngeneic MC38 tumor cells overexpressing human PD-L1. When the mean tumor volume reached 150–200 mm3, the mice were randomly grouped to receive the treatment. At day 4 after the treatment, CD8+ TILs were sorted.

first: Seung

middle: H

first: Gihoon

last: You

first: Junsik

last: Park

first: Youseung

last: Chung

first: Kyungjin

first: Hyunjoo

last: Kim

first: Jaehyoung

first: Youngkwang

first: Woo-Chan

last: Son

first: Da

middle: S

last: Jeong

first: Jung-Yun

last: Lee

first: Dai

last: Han

first: Jaeho

last: Jung

first: Su-Hyung


title: A first comprehensive analysis of Transcribed Ultra Conserved Regions uncovers important regulatory functions of novel non-coding transcripts in gliomas

city: Charlottesville

first: Roger

last: Abounader

email: ra6u@virginia.edu, mkg7x@virginia.edu

state: VA

address: 21 Hospital Drive

department: Microbiology

country: USA

institute: University of Virginia

summary: Transcribed Ultra-Conserved Regions (TUCRs) represent a severely understudied class of putative non-coding RNAs (ncRNAs) that are 100% conserved across multiple species. We performed the first-ever analysis of TUCRs in glioblastoma (GBM) and low-grade gliomas (LGG). We leveraged large human datasets to identify the genomic locations, chromatin accessibility, transcription, differential expression, correlation with survival, and predicted functions of all 481 TUCRs, and identified TUCRs that are relevant to glioma biology. Of these, we investigated the expression, function, and mechanism of action of the most highly upregulated intergenic TUCR, uc.110, identifying it as a new oncogene. Uc.110 was highly overexpressed in GBM and LGG, where it promoted malignancy and tumor growth. Uc.110 activated the WNT pathway by upregulating the expression of membrane frizzled-related protein (MFRP), by sponging the tumor suppressor microRNA miR-544. This pioneering study shows important roles for TUCRs in gliomas and provides an extensive database and novel methods for future TUCR research.

overall_design: To identify genes that are deregulated when the ultraconserved region uc.110 is knocked down, we performed RNA-Seq on GBM A172 cells treated with siRNAs targeting uc.110 or with scrambled control siRNA

first: Myron

last: Gibert Jr


title: Transcriptome profiling of castration resistant prostate cancer cells treated with novel AR N-terminal inhibitor

city: Montreal

first: Jian Hui

last: Wu

state: Quebec

address: 3755 Cote-Saint-Catherine

country: Canada

institute: Jewish General Hospital, McGill University

summary: This study aimed at exploring how would the novel AR N-terminal inhibitor affect the androgen receptor (AR) transcriptome, especially a subset of genes that are uniquely upregulated by AR-V7 in castration resistant prostate cancer cells. We performed next-generation sequencing-based gene expression profiling (RNA-sequencing) on the castration-resistant prostate cancer celll line LNCaP-95. LNCaP-95 expresses high level of endogeneous AR-V7, and also acquired an adaptive shift towards AR-V7-mediated AR signaling activity. Beside regulating the transcription of a subset of canonical wildtype AR genes, AR-V7 also mediates a distinct transcriptional program that is independent of wildtype AR in LNCaP-95. In this experiment, LNCaP-95 cells were treated with vehicle control or the AR-N terminal inhibitor SC912. The subsequent AR transcriptomic change following compound treatment, especially the AR-V7 unique genes were assessed by RNA-seq.

overall_design: A total of two treatment groups were analyzed in this study, and each treatment group contains four biological replicates. LNCaP-95 cells were treated with DMSO or 2 μM SC912 for 24 hours, total RNA was isolated and then submitted for RNA-sequencing analysis.

first: Qianhui

last: Yi

first: Jian

first: Henry

middle: G

last: Yu


title: Establishment and characterization of canine mammary gland tumor(MGT) cell lines

city: Buk-gu

first: Chan-Ho

address: Yongbongro 77

department: Animal Science

institute: Chonnam national university

summary:
To investigate the canine mammary gland tumor, we established 8 cell lines
We then performed gene expression profiling analysis using data obtained from RNA-seq of 10 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for canine mammary gland tumor cell lines and canine normal cells (MDCK, TP53 K/O fibroblast).

first: Seo-Young

first: Yeong-Bin

last: Baek

first: Hyun-Jin

first: Hwang-phill

first: Young-Jun

first: Jeong-En

last: Song

first: Su-Bin

first: Kyeong-Seo

last: Moon

first: Hyo-Jin

first: Sang-Ik

first: Chang-Min

first: Sung-Hak


title: Inactivation of mitochondrial MUL1 E3 ubiquitin ligase deregulates mitophagy and prevents diet-induced obesity in mice

city: Orlando

first: Antonis

last: Zervos

state: FL

address: 12722 Research Parkway

department: Burnett School of Biomedical Science

institute: University of Central Florida

summary: Obesity is a growing epidemic affecting billions of people worldwide and a major risk factor for a multitude of chronic diseases and premature mortality.  Accumulating evidence suggests that mitochondria have a profound role in diet-induced obesity and the associated metabolic changes, but the molecular mechanisms linking mitochondria to obesity remain poorly understood. Our studies have identified a new function for mitochondrial MUL1 E3 ubiquitin ligase, a protein known to regulate mitochondrial dynamics and mitophagy, in the control of energy metabolism and lipogenesis. Genetic deletion of Mul1 in mice impedes mitophagy and presents a metabolic phenotype that is resistant to high-fat diet (HFD)-induced obesity and metabolic syndrome. Several metabolic and lipidomic pathways are perturbed in the liver and white adipose tissue (WAT) of Mul1(-/-) animals on HFD, including the one driven by Stearoyl-CoA Desaturase 1 (SCD1), a pivotal regulator of lipid metabolism and obesity. In addition, key enzymes crucial for lipogenesis and fatty acid oxidation such as ACC1, FASN, AMPK, and CPT1 are also modulated in the absence of MUL1. The concerted action of these enzymes, in the absence of MUL1, results in diminished fat storage and heightened fatty acid oxidation.  Our findings underscore the significance of MUL1-mediated mitophagy in regulating lipogenesis and adiposity, particularly in the context of HFD. Consequently, our data advocate the potential of MUL1 as a therapeutic target for drug development in the treatment of obesity, insulin resistance, NAFLD, and cardiometabolic diseases.

overall_design: To characterize gene profiling and assess a metabolic phenotype caused by the deletion of Mul1 in mice, standard RNA-sequencing for gene profiling expression of protein-coding sequences (mRNA) was performed using liver tissues from Mul1(+/+) and Mul1(-/-) mice on HFD (n =3 per group).Liver tissue from WT and KOanimals

first: Lucia

last: Cilenti

first: Jacopo

last: Di Gregorio

first: Rohit

last: Mahar

first: Camilla

middle: T

last: Ambivero

first: Muthu

last: Periasamy

first: Matthew

middle: E

last: Merritt


title: Effects of hindlimb ischemia on bone marrow leukocytes and hematopoietic stem and progenitor cells

city: Pittsburgh

first: Partha

last: Dutta

state: PA

address: 200 Lothrop Street

department: Medicine

institute: University of Pittsburgh

summary: We identified the genes regulated by hindlimb ischemia in leukocytes and hematopoietic stem and progenitor cells isolated from the bone marrow in mice. We selected some of these genes based on their expression and further evaluated their functions using a wise array of techniques.

overall_design: Hindlimb ischemia (HI) was performed in mice, and leukocytes and hematopoietic stem and progenior cells (HSPC) were sorted from the bone marrow on days 2 and 7 after HI. mRNA was extracted from these samples and single cell RNA sequencing was performed.

first: Lee

last: Ohayon


city: Gaithersburg

first: Atsushi

last: Sakamoto

state: MD

address: 19 Firstfield Road

institute: CVPath Institute

summary:
Cell phenotype switching is increasingly being recognized in atherosclerosis. Intraplaque hemorrhage (IPH) is thought to be a major contributor to plaque progression in part by stimulating the influx of CD163+ macrophages.
We explored the hypothesis that CD163 macrophages cause plaque progression through the induction of pro-apoptotic endothelial to mesenchymal transition (EndMT) within the fibrous cap.

overall_design: Transcriptomic profiles of human aortic endothelial cell (HAOEC) which exposed to M(con) or M(Hb) macrophage supernatant for 6 hours were examined by ClariomTM S microarray.

first: Masayuki

last: Mori

first: Rika

last: Kawakami

first: Aloke

middle: V

last: Finn


title: Follistatin-like 1 guarantees the immunomodulatory properties of mesenchymal stem cells during liver fibrotic therapy

city: Xi’an

first: Xiaohong

last: Zheng

state: Shaanxi

address: 127 Changle West Road

department: Xijing Hospital of Digestive Diseases

country: China

institute: Fourth Military Medical University

summary: Mesenchymal stem cell (MSC) therapy has been shown to be a promising option for liver fibrosis treatment. However, critical factors affecting the efficacy of MSC therapy for liver fibrosis remain unknown. Follistatin-like 1 (FSTL1), a TGF--induced matricellular protein, is documented as an intrinsic regulator of proliferation and differentiation in MSCs. In the present study, we characterized the potential role of FSTL1 in MSC-based anti-fibrotic therapy and further elucidated the mechanisms underlying its action. Human umbilical cord-derived MSCs were characterized by flow cytometry. FSTL1low MSCs was achieved by FSTL1 siRNA. Migration capacity was evaluated by wound-healing and transwell assay. A murine liver fibrotic model was created by carbon tetrachloride (CCl4) injection, while control MSCs or FSTL1low MSC were transplanted via intravenous injection 12 weeks post CCl4 injection. Histopathology, liver function, fibrosis degree, and inflammation were analysed thereafter. Inflammatory cell infiltration was evaluated by flow cytometry after hepatic nonparenchymal cell isolation. An MSC-macrophage co-culture system was constructed to further confirm the role of FSTL1 in the immunosuppressive capacity of MSCs. RNA sequencing was used to screen target genes of FSTL1. FSTL1low MSCs had comparable gene expression for surface markers to wildtype but limited differentiation and migration capacity. FSTL1low MSCs failed to alleviate CCl4-induced hepatic fibrosis in a mouse model. Our data indicated that FSTL1 is essential for the immunosuppressive action of MSCs on inflammatory macrophages during liver fibrotic therapy. FSTL1 silencing attenuated this capacity by inhibiting the downstream JAK/STAT1/IDO pathway. Our data suggest that FSTL1 facilitates the immunosuppression of MSCs on macrophages and that guarantee the anti-fibrotic effect of MSCs in liver fibrosis.

overall_design: hUC-MSC transfected with FSTL1 siRNA for 24 h

first: Ying

last: Han


title: Gene expression in 15 weeks of neurons differentiated from MPS II-induced pluripotent stem cells

city: Taipei

first: Tzu-Yu

last: Chen

address: No.1 Jen Ai road section 1 Taipei 100 Taiwan R.O.C.

country: Taiwan

institute: National Taiwan University College of Medicine

summary: To investigate the gene expression in the regulation of neuron differentiation between healthy human control and MPS II. We then performed gene expression profiling analysis using mRNAs of 3 healthy human control iPSC- and 9 MPS II-iPSC-dervied 15 weeks neurons.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for healthy human control iPSC- and MPS II-iPSC-dervied 15 weeks neuron.

first: Hsiang-Po

last: Huang


title: Biallelic loss-of-function variants of ZFTRAF1 cause neurodevelopmental disorder with microcephaly and hypotonia

city: Cologne

first: Muhammad Sajid

last: Hussain

address: Weyertal 115b

department: Cologne Center for Genomics

country: Germany

institute: University of Cologne

summary:
Main purpose of the project is to investigate the consequences of loss-of-function variants of ZFTRAF1 on transcriptome profiling of the patient compared to control. In this data, we seen differential expression of genes involved in the autophagy and mRNA processing.
To identify the globally dysregulated expression of genes, we performed tbul transcriptome profiling from RNA-seq of 2 different patient samples along with three controls.

overall_design: Whole-transcritome profiling analysis for human primary fibroblast cells derived from syndromic microcephaly patients and control.

first: Muhammada

first: Maria

last: Asif


title: In vivo self-assembly and targeted delivery of EGFR siRNA-encapsulating small extracellular vesicles to EGFR-positive cancer cells for NSCLC therapy

city: Nanjing

first: Zheng

last: Fu

address: Xianlin district 163

institute: NJU

summary:
We designed a synthetic biology circuit encoding both an EGFR-targeting peptide (GE11) and an EGFR siRNA under the control of the cytomegalovirus (CMV) promoter. After uptake by mouse liver cells via intravenous injection, this genetic circuit can reprogram the liver cells to produce and self-assemble EGFR siRNAs into secretory small extracellular vesicles (sEVs) tagged with the GE11 peptide, after which the siRNA-encapsulating sEVs are further transported via the blood circulation and guided by the GE11 peptide to EGFR-positive tumour cells for NSCLC therapy.
RNA sequencing-based transcriptomic profiling confirmed the safety and low off-target activity of in vivo self-assembled EGFR siRNAs.

overall_design: EGFR DEL19 transgenic mice were administered doxycycline for 25 days and analysed by micro-CT to ensure spontaneous tumour formation in the lungs. Mice were then intravenously injected with the CMV-scrR, CMV-siRE or CMV-GE11-siRE circuit (10 mg/kg) every 2 days for a total of 7 injections. After treatment, mice were sacrificed, and normal tissues and tumours were harvested to determine the global transcriptome alterations by RNA sequencing.

first: Zhen

last: Zhou


title: CD49a expression and induction of cytotoxicity on human tissue-resident CD8+ T cells is controlled by RUNX2 and RUNX3 transcription factor activity

city: Huddinge

first: Ram Vinay

last: Pandey

state: Stockholm

address: Hälsovägen 7, Neo

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Sepsis-secreted G6PD supports guanine generation and Histone H3K27 demethylation to drive inflammatory macrophages

city: wuhan

first: chaoqun

last: wang

address: bayi road

institute: wuhan University

summary: Sepsis is a complex syndrome associated with physiological, pathological, and biochemical abnormalities resulting from infection. Sepsis is the major cause of acute respiratory distress syndrome (ARDS). Extracellular vesicles (EVs) are serving as new messengers to mediate cell-cell communication in vivo. The function of EVs in sepsis patients are not well defined. We found sepsis EV encapsulating G6PD induced pro-inflammatory effects in the lung tissue by reprogramming purine metabolism. Most notably, guanine accumulation led to EZH2-mediated H3K27Me3 level. Finally  Our study provides a novel mechanism  of how EV reviried puring metabolism in lung tissue and leading to acute lung damage.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C57BL/6 lung established by Sham, CLP (cecal ligation and puncture), CLP+GW.

first: Chaoqun

last: Wang

first: Wei

last: Yan


title: Whole transcriptomic analysis of Korean osteoarthritis patients.

city: Busan

first: Jaewan

last: Jeon

address: 875, Haeun-daero, Haeundae-gu, Busan, Republic of Korea

institute: Jaewan Jeon

summary: A database of genes showing differences in expression in synovium tissues and normal synovium tissues of Korean patients with advanced osteoarthritis was established.

overall_design: Synovium tissue in osteoarthritis patients was secured when operating, and normal tissue was secured in patients requiring surgery due to sports damage. Confirmation of synovial tissue was performed by a pathologist and whole transcriptomic analysis was performed with the identified tissue.

first: Sang

middle: W

last: Moon

first: Hwan-Kwon

last: Do


title: Effect of Dexamethasone, IL-1B and Dex+IL-1B on gene expression in Th17 cells

city: Cleveland

first: William

last: Miller-Little

address: 10900 Euclid Ave

institute: Case Western Reserve University

summary: To investigate the response of Th17 cells to IL-1B and Dexamethasone, and the ability of IL-B to alter the steroid-responsiveness of Th17 cells

overall_design: We performed gene expression analysis using data obtained from RNA-Seq of Th17 cells treated with different stimuli

middle: A


title: EIF6 conditions drug-tolerant persister-like transdifferentiation in small cell lung carcinoma (eIF6_KD)

city: Chengdu

first: Haoning

last: Peng

state: Sichuan

address: No.37 Guoxue Alley, Wuhou District

department: Department of Thoracic Surgery

institute: West China Hospital, Sichuan University

summary: Drug-tolerant persister cells withstand treatments by adapting their identity through lineage-dependent plasticity during systemic anti-cancer therapies. This phenomenon is evident in small-cell lung carcinoma (SCLC), a lethal neuroendocrine cancer initially responsive (60-80%) to platinum-based chemotherapy but succumbing to resistance within 6 months in advanced stages. This resistance associates with the transdifferentiation of residual tumour cells into a non-neuroendocrine state, a process intricately tied to SCLC's chemotolerance, yet molecular mechanisms governing this lineage conversion remain completed understood. Here we use paired cytoplasmic RNA-seq and polysomal RNA-seq to compare gene expression between NE and non-NE SCLC cell lines on both transcriptional and translational level. We report that first-line chemotherapy induces translation initiation factor eIF6 in drug-tolerant persister-like cells in SCLC, correlating with the non-neuroendocrine state in SCLC. Intervening eIF6 inhibits non-neuroendocrine transdifferentiation, thus enhancing SCLC responsiveness to chemotherapy. This study sheds light on eIF6's potential therapeutic interventions to mitigate treatment resistance in SCLC.

overall_design:
To investigate function of eIF6 in H69 and H69M cells, we established stable eIF6-KD H69 and H69M cell lines by lenitivirus infection containing shRNA targeting eIF6.
Comparative gene expression profiling analysis of RNA-seq data for H69_sheIF6 cells vs. H69_shNTC cells and H69M_sheIF6 cells vs. H69M_shNTC cells

first: Zhile

first: Mengyao

first: Lunxu

last: Liu

first: Shensi

last: Shen


title: Next Generation Sequencing to identify the differential expression genes of murine lung tissues upon the stimulation of LPS with/without  recombinant TSLP  pretreatment

city: Wuhan

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

institute: Huazhong University of Science and Technology

summary: The murine lung tissues from Vehicle (V) group, LPS (L) group, and LPS+TSLP (T) group were collected to perform next-generation sequencing (NGS).  Illumina RNA Library Prep kit was used to perform  library preparation and then paired-end library sequencing was performed by Illumina  NovaSeq 6000 and sequence analysis was determined using the Illumina data analysis pipeline.

overall_design: Differential gene expression of  murine lung tissues from Vehicle (V) group, LPS (L) group, and LPS+TSLP (T) group.

first: Xiufang

last: Weng


title: Gene expression profile in HLA-A02:01-restricted cytotoxic T-cells specific to HTLV-1 in ATL patients

city: Saitama

first: Hideki

last: Nakasone

address: 1-847, Amanuma-cho, Omiya-ku

department: Hematology

country: Japan

institute: Jichi Medical University Saitama Medical Center

summary:
We compared gene expression of CTLs specific to HTLV-1 between the eaarly death group with aggressive disease status and long-term survivors with stable disease status.
We then performed gene expression profiling analysis using data obtained from RNA-seq of seven patients with acute ATL in 4, chronic ATL in 2, and an asymptomatic HTLV-1 carrier.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  HTLV-1 Tax-CTLs after sorting from actual patient samples.

first: Machiko

last: Kusuda


title: Functional Interaction between APOE4 and mutant APP promotes cerebrovascular changes in young animals

city: Singapore

first: Jessica

middle: R

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

country: Singapore

institute: Nanyang Technological University

summary: The Apolipoprotein E4 (ApoE4) allele is one of the strongest risk factors for late-onset Alzheimer’s disease (AD) and is associated with a breakdown of the blood-brain barrier and vascular dysfunction (Nation et al 2019; Liu and Bu 2022). Importantly, these vascular pathologies are exacerbated when APOE4 is coexpressed with familial mutations in APP or components of the γ-secretase complex (Montagne and Zlokovic 2021), suggesting that the interactions between APOE4 and AD mutations can drive progression of the disease. However, most studies have been done in aging animals and few look at the impact of APOE4 expression in young animals and how that potentially contributes toward late-stage disease susceptibility. Here, we examined the potential functional interaction between APP mutations and ApoE4 in the progression of AD pathophysiology by comparing the hippocampal transcriptomes of 3-month-old female mice of 4 different genotypes: AppNL-G-F/NL-G-F , which harbours three knock-in mutations in the humanised Aβ region of APP  (APP-TKI; Saito et al., 2014), mice with a single allele of human ApoE4 knocked-in, ApoE4+/wt (ApoE4), crosses of these two mouse lines, to create AppNL-G-F/NL-G-F;Apoe4+/wt (double-mutant or DM) mice, and wild-type (WT) mice that served as controls. RNAseq revealed nascent microglial activation signatures in both APP-TKI and double mutant datasets, as well as subtle but significant differences between APP-TKI and double mutant in expression of a subset of vascular remodeling genes.

overall_design: Hippocampal transcriptomes of 3-month-old female wild-type, APP knock-in, ApoE4 and double mutant mice

first: Toh

last: Ch'ng

first: George

middle: J

last: Augustine


title: Differential transcriptome analysis of naïve T cell activtion, TH1 cell differentiation and TH1 cell reactivation

first: Martha

last: Kiljan

address: Elsenbornerstraße, 26

institute: University Hospital Cologne

summary: In this study, we investigated the transcriptional changes of reactivated T helper 1 (TH1) cells that occur independently of changes during naïve T cell priming and T cell differentiation.

overall_design:
Bulk RNAseq analysis of in vitro cultured and sorted murine naïve, activated naïve, differentiated TH1 and reactivated TH1 cells
The mouse strain used is on a C57/BL6 background. Specifically C57BL/6-Tg(Nr4a1-EGFP/cre)820Khog/J mice crossed with B6.Cg-Tg(TcraTcrb)425Cbn/J mice were used for the experiment (Mouse strain also called OT-II/Nur77GFP)

first: Oscar

last: Camacho

first: Jan

last: Herter


title: The effects of knock-out PARP1 on HepG2.

city: Qingyuan

first: Qingtian

last: Huang

address: 35 Yinquan North Road, Qingcheng District

institute: Guangzhou Medical University

summary: Given the critical role of PARP1 in liver cancer cells, our aim was to find evidence of PARP1-mediated gene regulation in the HepG2 hepatoma cell line.

overall_design: We divided the samples into two groups, HepG2-WT group and HepG2-sgPARP1 group. The PARP1 gene was knocked out in HepG2 cells using CRISPR-Cas9 technology.

first: Jie

last: Yang

first: Yanfen

last: Wang

first: Ling

last: Qi


title: BMP effector Mad knockdown in Drosophila musculature of wandering third instar larvae

city: New York

first: Mary

last: Baylies

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: To investigate the effect of reducing BMP signaling via Mad knockdown in Drosophila body wall muscles.

overall_design: Performed gene expression profiling analysis using data obtained from RNA-seq of 2 experimental groups (MadRNAi vs mCherryRNAi), with 3 samples each. Each sample contains the transcriptome of 6-10 Drosophila larval muscle enriched lysates.

first: Victoria

last: von Saucken

middle: K


title: Isoform-specific translational control is evolutionarily conserved in primates

city: Santa Cruz

first: Jeremy

last: Sanford

state: CA

address: 1156 High St

institute: University of California, Santa Cruz

summary: Alternative splicing (AS) influences the expression of human genes in diverse ways. We previously used subcellular fraction-sequencing (Frac-Seq) to reveal an unexpected connection between alternative splicing and isoform-specific mRNA translation. Here we apply comparative transcriptomics to explore alternative splicing coupled translational control (AS-TC) across 13 million years of primate evolution. We used Frac-seq to identify polyribosome associated mRNA isoforms from human, chimpanzee and orangutan induced pluripotent stem cell lines. We discovered orthologous AS-TC events with either conserved or species-specific translation patterns. Exons sequences associated with similar sedimentation profiles between species show strong sequence conservation compared to orthologous exons with divergent sedimentation profiles, suggesting exonic cis-regulatory elements influence to translational control. To test this hypothesis we created luciferase reporters from orthologous exons with divergent sedimentation profiles differing by a single nucleotide. Remarkably, single nucleotide substitutions were sufficient to drive species-specific expression of luciferase reporters. Together these data establish that cis-acting elements regulate AS-TC across primate species.

sample_organism:
Pan troglodytes
Pongo abelii
Homo sapiens

overall_design: Subcellular Fractionation and RNA sequencing

first: Jolene

last: Draper

first: Julia

last: Philipp

first: Zach

last: Neeb

first: Richard

last: Thomas

first: Solomon

last: Katzman

first: Sofie

last: Salama

first: David

last: Haussler


title: RNA-seq of murine 4-1BB- and 4-1BB+ CD8+ tumor-infiltrating T cells in HCC patients

city: Daejeon

first: Seung Hyuck

last: Jeon

address: 291 Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

summary: We aimed to analyze the transcriptomic differences in CD8+ tumor-infiltrating T cells according to 4-1BB expression in HCC

overall_design: 4-1BB- and 4-1BB+ CD8+ tumor-infiltrating T cells were sorted from ex vivo HCC samples

first: Seung

first: Gihoon

last: You

first: Junsik

last: Park

first: Youseung

last: Chung

first: Kyungjin

first: Hyunjoo

last: Kim

first: Jaehyoung

first: Youngkwang

first: Woo-Chan

last: Son

first: Da

last: Jeong

first: Jung-Yun

last: Lee

first: Dai

last: Han

first: Jaeho

last: Jung

first: Su-Hyung


title: Acute social isolation alters synaptic plasticity in lateral habenula and social decision

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

institute: Kangwon National University

summary: The lateral habenula (LHb) is an essential hub brain region modulating the monoamine system such as dopamine, serotonin. Hyperactivity of LHb has implications for psychiatric disorders such as depression, anxiety, and schizophrenia, which are commonly associated with social dysfunction. However, the role of LHb in social behavior has remained elusive. Here, we find that experiencing acute social isolation affects synaptic function in LHb and social behavior. After acute social isolation, long-term depression (LTD) in LHb is impaired and rescued by activating the 5-HT4 receptor (5-HT4R). Indeed, Htr4 expression in LHb is up-regulated following acute social isolation. Finally, acute social isolation enhances the social preference for familiars such as housing-mates to stranger conspecifics. Consistent with electrophysiological results, pharmacological activation of 5-HT4R in LHb restored innate social preference. These results suggest that acute social isolation influences social decisions with 5-HT4R-dependent synaptic modification in LHb.

overall_design: The transcriptomic profiles of lateral habenula tissues obtained from group-housed and socially isolated mice

first: Jeongyeon

first: Miseon

last: Kang


title: Single-nucleus transcriptomic sequencing and cross integration comparison of multiple species revealed new cell composition and specific gene marker in hippocampal aging

city: kunming

first: Rui-ze

last: Niu

address: Chunrong West Road

institute: kunming medical university

summary: Brain aging is a major risk factor for many brain diseases, which seriously affects the quality of life and even life span, and poses an increasingly serious threat to human health. Research shows that anti-aging and an extra year of life expectancy could bring $38 trillion in economic gains. Therefore, it is urgent to study the mechanism of brain aging, find effective ways to improve aging and improve the quality of life of the aging population. In the early stage, we established the culture system of activated urine stem cells (aUSCs), which can significantly improve the nerve cell senescence in vitro and brain aging of natural aging mice and macaques, suggesting that aUSCs have strong anti-brain aging ability; The results of single-nucleus sequencing of mouse hippocampus suggested that anti-aging was achieved by changing the glial cell subset to constitutively inhibit inflammatory signaling to reduce inflammatory response. Based on this, this topic continues to conduct aUSCs intervention on naturally aging rhesus monkeys to study the anti-brain aging effect and potential mechanism of aUSCs in non-human primates; Meanwhile, the human cerebral organoid model was applied to further study the anti-brain aging effect and potential mechanism of aUSCs in the human brain. Therefore, this topic not only screens seed cells for state-supported stem cell transformation applications, but also provides solutions for the problems caused by world aging, which has great scientific significance and economic value. In order to explore the mechanism of aUSCs anti-brain aging, we used single-cell sequencing to analyze the effect of aUSCs on the hippocampus of aging mice.

overall_design: Single-nucleus RNA-sequencing of hippocampus from mouse.

first: Shi

last: Lan-Lan

first: Rui-Ze

first: Jia

last: Liu


title: The synergistic effect of pulsed-focused ultrasound and umbilical cord mesenchymal stem cells in facilitating recovery from acute kidney injury through mitochondrial regulation and heat shock proteins

city: Palo Alto

first: Avnesh

last: Thakor

state: California

address: 3155 Porter Drive,

institute: Stanford University

summary: Acute Kidney Injury (AKI) remains a significant challenge with limited therapeutic interventions. This study explored the use of pulsed-focused ultrasound (pFUS) to prime the kidney, followed by mesenchymal stem cell (MSC) therapy to treat AKI. Our data showed that MSCs can mitigate some of the adverse effects of AKI, with these effects being greater with the use of umbilical cord (UC)-MSCs compared to bone marrow (BM)-MSCs. Next, we examined the effect of pFUS on the acutely injured kidney and found that compared to a single sonication, repeated sonication using pFUS at low acoustic doses (LpFUS) resulted in a substantial reduction in pro-inflammatory and immuno-modulatory cytokines. We then investigated the synergetic effect of repeated LpFUS followed by UC-MSC therapy; here, we found the therapeutic effects of UC-MSCs were enhanced resulting in a significant reduction in the blood urea nitrogen (BUN), improved body weight, and modulation of the kidney microenvironment with the expression of cytokines that created a more anti-inflammatory and regenerative milieu. Detailed transcriptomic analysis of acutely injured kidney tissue samples treated with LpFUS+UC-MSCs showed up-regulation of mitochondrial genes, specially PGC1α and DRP1, mitochondrial-associated proteins involved in the respiratory chain, nuclear genes encoding mitochondrial proteins, mitochondrial function, and specific heat shock proteins (i.e., HSP70 and HSP90). In conclusion, our results show that the therapeutic effect of UC-MSCs for treating AKI can be augmented by priming the kidney with repeated LpFUS before UC-MSC therapy. This innovative approach holds promise for advancing the treatment of AKI.

overall_design: In the current study, we studied the effect of different acoustic intensities on the acutely injured kidney in a mouse model. Specifically, we examined their temporal effects on the kidney and the effect of repetitive sonications. Once an optimal set of parameters was determined, we evaluated whether priming the kidney with pFUS would synergistically benefit MSCs obtained from umbilical cord (UC) and bone marrow (BM). To understand the mechanism of action of these effects, we then undertook transcriptomic profiling of kidney tissue samples to identify the pathways in AKI modulated using this approach.

first: Shashank

last: Chetty

first: Abantika

last: Ganguly

first: Rosita

last: Primevera

first: Shaini

last: Patel

first: Shobha

last: Regmi

first: Jing

last: Wang

first: Jeremy

last: Dahl


title: CD49a expression and induction of cytotoxicity on human tissue-resident CD8+ T cells is controlled by RUNX2 and RUNX3 transcription factor activity [RNA-seq]

first: Ram Vinay

last: Pandey

summary: CD49a marks highly cytotoxic epidermal tissue-resident memory (TRM)-cells, but their molecular circuitry and relationships to circulating populations are poorly defined. We demonstrate enrichment of RUNX family transcription factor binding motifs in human epidermal CD8+CD103+CD49a+ TRM-cells, paralleled by high RUNX2 and RUNX3 protein expression. Clonal overlap between epidermal CD8+CD103+CD49a+ TRM-cells and circulating memory CD8+CD45RA–CD62L+ T-cells identified a reservoir of circulating cells with potential to seed cytotoxic TRM-cells in new sites. Upon IL-15 and TGF-β stimulation, subsets of circulating CD8+CD45RA–CD62L+ T-cells acquired CD49a expression and cytotoxic transcriptional profiles in a RUNX2 and RUNX3 dependent manner. In contrast, knock-out of RUNX3, but not RUNX2, prevented CD103 expression. In melanoma, high RUNX2, but not RUNX3, transcription correlated with a cytotoxic CD8+CD103+CD49a+ TRM cell signature and overall patient survival. Together, our results indicate that combined RUNX2 and RUNX3 activity promotes the differentiation of cytotoxic CD8+CD103+CD49a+ TRM-cells, providing immunosurveillance of infected and malignant cells.

overall_design:
Bulk RNA-seq upon in vitro differentiation. Memory CD45RA- CD62L+ CD27+ CD8 T cells have been FACS sorted from 3 healthy donors and used for bulk RNA-seq (day 1) or differentiated in vitro for 14 days in Trm-like polarizing conditions including IL-15, TGF-b and CD3/28 stimulation in ECM-coated wells. Upon differentiation, CD8 T cells have been FACS sorted on the basis of CD69, CD103 and CD49a expression for bulk RNA-seq.
Bulk RNA-seq upon RUNT transcription factors gene deletion. CRISPR/Cas9 gene deletion was performed for RUNX2, RUNX3 and a control gene on FACS sorted memory CD45RA- CD62L+ CD27+ CD8 T cells from 5 healthy donors. Subsequently, edited cells have been cultured in in vitro for 14 days in Trm-like polarizing conditions including IL-15, TGF-b and CD3/28 stimulation in ECM-coated wells. Upon differentiation, bulk CD8 T cells have been FACS sorted for bulk RNA-seq. Two different targeting guides were used for both RUNX2 (AB and AC) and RUNX3 (AD and AE).
Bulk RNA-seq on skin Trm cells. CD103+ CD49a- and CD103+ CD49a+ CD8 Trm cells from the skin epidermis of 6 healthy donors were FACS sorted in RNA lyses buffer and used for bulk RNAseq.
This dataset includes a re-analysis of 12 Samples in GSE83637 (GSM2211621-GSM2211624, GSM2211627-GSM2211634). The processed data for this re-analysis is included in the supplementary file GSE232236_GSE83637_RNAseq_raw_gene_count_matrix.txt. This file include raw read counts for each re-analysis Sample.

**Submitter declares that raw data were not submitted due to patient privacy concerns**

first: Beatrice

last: Zitti

first: Ram

first: Yenan

last: Bryceson


title: Orchestrating endothelial cell fate regulation and function during multiple organs’ development, stress and aging at single cell resolution

city: Beijing

first: Yaxi

address: 5 Yiheyuan Road

institute: Peking University

summary: CoBATCH-supported single cell protein-bound elements profiling five tissues from Cdh5+ lineage endothelial cells (EC) collected from four stages of the mouse lifespan, discovering that intrinsic epigenetic plasticity grammarred by the TF regulome which educated by tissue microenvironment.

overall_design: We applied CoBTACH to comprehensively trace Cdh5+ cells lineage for various histone modifications and TFs, obtaining total ~20,000 cells derived from 5 organs (heart, liver, lung, brain, kidney) across the lifespan of mouse. Each sample represents a single cell.

first: Xianhong

last: Yu

first: Haiqing

last: Xiong

first: Xiaoge

first: Aibin

last: He


title: Single cell RNA sequencing reveals limited effects of Lrrk2 genotype in a mouse model of acute CNS inflammation

status: Public on Apr 29 2024

city: Bethesda

first: Mark

last: Cookson

address: NIHBC 35 - PNRC I BG RM 1A-116

institute: National Institutue on Aging, NIH

summary: BACKGROUND: Previous data implicates neuroinflammation in the pathogenesis of Parkinson’s disease (PD). Of the genes associated with PD, Leucine rich repeat kinase 2 (LRRK2) is expressed in microglia, resident brain inflammatory cells. However, the extent to which LRRK2 affects neuroinflammatory responses is unclear. OBJECTIVE: To examine whether mutations in Lrrk2 affect responses to neuroinflammation in vivo.  METHODS: We injected cohorts of mice carrying mutations in Lrrk2, homologous to those causing human PD, with a single intrastriatal injection of lipopolysaccharide (LPS) or control. We used single cell RNA-Sequencing to examine cell type specific responses to treatment and genotype and validated key results with orthogonal approaches. RESULTS: We found that our chosen paradigm of acute LPS exposure evokes robust transcriptional changes consistent with a multicellular neuroinflammatory response. We also found evidence of peripheral immune cell recruitment into the brain and interaction with brain-resident microglia. However, the transcriptional effects of Lrrk2 mutations were limited to small numbers of genes, including down regulation of gene ontogeny terms related to lysosomes, predominantly in microglia. CONCLUSIONS: Our data clearly demonstrate that many cells in the brain respond to a single inflammatory insult with strong transcriptional responses and that, even in a model focussed on CNS injection, there is interaction between peripheral and central immune cells. In contrast, the quantitative effects of Lrrk2 mutations are modest at least at the level of transcription, demonstrating that additional studies are needed to clarify whether Lrrk2 affects neuroinflammation in an endogenous context.

overall_design: We injected WT, Lrrk2 G2019S, and Lrrk2 R1441C knockin mice intrastriatally with PBS or LPS, and extracted the striatum and midbrain for scRNA-seq processing.

first: Alice

last: Kaganovich

first: Liam

last: Horan-Portelance

first: Jinhui

last: Ding

first: Rebekah

last: Langston

first: Natalie

last: Landeck


title: mRNA-seq analysis of rex-1 deletion in C. elegans

city: New York City

first: Sevinc

last: Ercan

state: NY

address: 31 Washington Place

department: Biology

institute: New York University

summary: In embryos, DCC binding across the length of the ~17.7 Mb X chromosome initiates at a set of recruitment elements on the X (rex). Individual rex sites collectively contribute to recruitment and repression, thus deletion of one or few rex sites causes subtle changes, as measured by mRNA-seq in mixed-stage embryos. We previously constructed a strain deleting rex-1, located ~6 kb downstream of dpy-23 (https://doi.org/10.7554/eLife.23645). Here we performed mRNA-seq in rex-1 deletion embryos.

overall_design: mRNA-seq  in  controls and rex-1 deletion embryos.

first: Haoyu


title: lncRNA profile of CAFs derived EVs

city: 广州

first: li

last: xiaobai

address: 381 Wushan Road, Tianhe District, Guangzhou

institute: south china university of technology

type: Non-coding RNA profiling by high throughput sequencing

summary: Perineural invasion (PNI) is a unique biological feature of pancreatic cancer and is a key cause of pancreatic cancer metastasis, recurrence and poor postoperative survival, but its mechanism is largely unclarified. Clinical sample analysis and endoscopic ultrasonographic elasticity scoring indicated that cancer-associated fibroblasts (CAFs) are closely related to the occurrence of PNI. Furthermore, CAF-derived extracellular vesicles played an extremely important role in PNI in a dorsal root ganglion (DRG) coculture model and sciatic nerve model. To explore the lncRNA packaged in CAFs EVs, we conducted the lncRNA profile of CAFs derived EVs.

overall_design: NFs and CAFs were isolated from pancreatic cancer and conditional medium were collected for EVs isolation. Then the RNA packaged by EVs were  extracted for lncRNA-seq.

first: Shangyou

last: Zheng

first: Chonghui

last: Hu

first: Ting

last: Ting

first: Rufu

last: Chen


title: LncRNA and mRNA expression profiles of Schizosaccharomyces pombe under normal conditions and DNA damage inducing conditions.

city: Hefei

first: Bingbing

last: Ren

state: Anhui

address: University  of  Science  and  Technology  of  China,  443  Huangshan  Road, Hefei, Anhui

summary: We explored transcriptional responses of the fission yeast to DNA damage. RNA-seq was used to characterize changes in expression profiles of all known lncRNAs and mRNAs in wild type cells and cells treated by four DNA damage agents: Camptothecin, Hydroxyurea, Methyl methanesulfonate and Phleomycin.

overall_design: Examination expression profiles of lncRNAs and mRNAs of the fission yeast wild type cells and four DNA damage agents treated cells. Two replicates for each.

first: Tianyi

first: Ruikun

last: Wu

first: Ge

last: Shan


title: effect of Schisandrol B treatment in human aortic valve interstitial cells

first: Xing

last: Liu

state: Hubei

address: JieFang Avenue 1277

department: Cardiovascular Surgery

institute: Wuhan Union Hospital

summary: Calcific aortic valve disease (CAVD) primarily involves osteogenic differentiation in human aortic valve interstitial cells (hVICs). Schisandrol B (SolB), a natural bioactive constituent, has known therapeutic effects on inflammatory and fibrotic disorders. However, its impact on valve calcification has not been reported. Transcriptome sequencing was used to analyze potential molecular pathways affected by SolB treatment. To explore the therapeutic mechanism of SolB, human valve interstitial cells were induced to undergo osteogenic differentiation by OM, with or without SolB treatment meanwhile. Among the signaling pathways enriched, the P53 signaling pathway was identified as the upstream regulator of other enriched pathways such as Cell cycle, Oocyte meiosis, Cytokine-cytokine receptor interactions. These pathways were regulated by the P53 signaling pathway and were reported to be stimulated by DNA damage, an early stage of pathological change in CAVD. The cytokine-cytokine receptor interaction signaling pathway was reported to correlate with calcified aortic valve disease. taken together, our data revealed potential therapitic mechanism p53 signaling of Schisandrol B treatment in hVICs calcification.

first: Qiang


title: Comparision of bone marrow cells between trisomy 8+ myelofibrosis vs. normal cells.

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: The goal of this study is to characterize gene expression profiles in individual hematopoietic cell types comparing trisomy 8+ myelofibrosis patients vs. normal donors.

overall_design: Primary bone marrow cells were collected from trisomy 8+ myelofibrosis patient or healthy normal donors. Following mononuclear cell isolation and RBC lysis, cells were applied to scRNA-seq analysis.

first: Seongseok

last: Yun

first: Nicole

last: Vincelette

first: Xiaoqing

last: Yu


title: Transcriptional  changes following HIV infection of choroid plexus brain organoids

city: San Francisco

first: Warner

last: Greene

address: 1650 Owens St

institute: Gladstone institutes

summary: We employed iPSC-derived choroid plexus brain organoids to explore the impact of HIV infection on microglia, elucidating alterations in the host gene profile within the central nervous system.  We conducted single-cell RNA sequencing to elucidate the changes in microglia upon HIV infection, leading to neural cell damage

overall_design: Choroid plexus brain organoids were infected with mock medium or HIV virus. We pooled 8 or more brain organoids and performed 10x single-cell RNA sequencing. To investigate changes in gene expression in microglia upon HIV infection, we enriched these cells using CD11B+ microbeads

first: Weili

last: Kong


title: MYC-Alarmin Axis as a Novel Therapeutic Vulnerability in Triple Negative Myeloproliferative Neoplasms

summary: Despite advances in our understanding of the underlying genetic abnormalities in myelofibrosis (MF) and the development of JAK2 inhibitors, there is an urgent need to devise new treatment strategies, particularly in triple negative MF patients who lack mutations in the JAK2 kinase pathway. Here we report that MYC copy number gain (e.g., trisomy 8) is frequently identified in triple negative MF where MF development and progression rely on MYC-directed activation of S100A9, a Danger Associated Molecular Pattern (DAMP) protein that plays pivotal roles in inflammation. Notably, MYC-S100A9 axis underlies complex network of inflammatory signaling that involves various hematopoietic cell types in the bone marrow microenvironment. Accordingly, small molecules targeting the MYC-S100A9 pathway effectively ameliorated the MF phenotypes, highlighting MYC-alarmin axis as a novel therapeutic vulnerability in a subgroup of MF patients.

overall_design: The goal of this study is to compare gene expression profiles in hematopoietic cellsl in bone marrow following overexpression of MYC in hematopoietic stem cells.

middle: D

first: John

middle: L

last: Cleveland


title: Effect of inhibition of oxidative stress on transcriptome profiles in rats with spinal cord injury.

city: Bengbu City

first: Lin

last: Zhang

address: 2600 Donghai Avenue

institute: Bengbu Medical College

summary: The occurrence and development of secondary injury after spinal cord injury (SCI) is a key role affecting SCI recovery, and oxidative stress plays an important role in secondary injury. α-lipoic acid (ALA) is recognized as a powerful antioxidant that mitigates secondary damage and exerts neuroprotective effects. However, the mechanism by which ALA provides antioxidant role remains unknown. The application of ALA to rats after SCI was used to explore the effect of ALA on local gene transcription and expression after SCI and its role in SCI recovery.

overall_design: In this experiment, a rat T9 segment impact contusion model was constructed using the American PSI spinal cord percussion device HI-0400. Experimental groups: sham, model control group (SCI_Veh), ALA treatment group (SCI_ALA). Spinal cord samples were taken from rats in the sham group, SCI_Veh, and SCI_ALA group 3 days after injury, and then total RNA was extracted from it, and the expression of three sets of differential genes was analyzed by transcriptome sequencing technology.

first: Ming-Ming

last: Bian

first: Yao-Mei

last: Xu

first: Hua-Zheng

last: Yan

first: Jian-Xiong

last: Gao

first: Gui-Qiang

last: Fu

first: Yang-Yang

last: Wang

first: Yu-Qing

first: Jian-Guo

first: He-Zuo

last: Lü


title: Influence of DNA-methylation at multiple stages of limb chondrogenesis

city: Mexico City

first: Mario

middle: Alberto

last: Perez-Maldonado

state: Mexico City

address: Circuito Mario de la Cueva s/n

department: Institute of Biomedical Research

country: Mexico

institute: UNAM

type: Methylation profiling by high throughput sequencing

summary: Limb development is a well-established model for understanding cell fate decisions, and the formation of skeletal elements is coordinated through a sequence of events that control chondrogenesis spatiotemporally. It has been established that epigenetic control participates in cartilage maturation. Our research has shown for the first time that the inhibition of DNA methylation in interdigital tissue with 5-azacytidine results in the formation of an ectopic digit. This discovery suggested that DNA methylation dynamics could regulate the fate of cells between chondrogenesis and cell death during autopod development. We sequenced WGBS libraries from in-vivo interdigital tissue treated with 5-azacytidine or DMSO to identify genome-wide methylation changes during the early stages of 5-azacytidine-induced chondrogenesis.

overall_design: Whole Genome Bisulfite Sequencing libraries (WGBS) from interdigital tissue implanted beads, soaked in 250µM 5-azacytidine or DMSO for 4 hours.

last: Pérez-Maldonado

first: Ximena

last: González-González

first: Jesús

last: Chimal-Monroy

first: Jessica

middle: C

last: Marín-Llera


title: The choroidal nervous system: A link between corticoids and chorioretinopathy

city: Paris

first: Bastien

last: Leclercq

state: Ile-de-France

address: 15 Rue de l'École de Médecine

country: France

institute: INSERM

summary: Transgenic mice overexpressing human mineralocorticoid receptor (hMR) under the control of the ecologic promotor 1 (P1 hMR mice) were used as well as their WT littermates. We observed anatomical signs of choroid neuropathy in these mice. Bulk-transcriptomic analysis of retinal pigment epithelium/choroid complex was peformed to identify potential mechanisms.

overall_design: Animals were sacrified and eyes were freshly dissected to extract RNA from RPE/choroid complex for transcriptomic analysis.

first: Min

last: Zhao

first: Justin

last: Guegan


title: Capture of TAD reorganization endows variant patterns of gene transcription (RNA-Seq)

city: Shanghai

first: He

state: Shanghai

address: Tongji University, 1239 Siping Road, Yangpu District, Shanghai

institute: School of Life Science and Technology, Tongji University

summary: TAD (Topologically Associating Domain) reorganization occurs commonly in cell nucleus and contributes to gene activation and inhibition through separation or fusion of adjacent TADs. However, identification of functional genes impacted by TAD alteration and revealing of TAD-reorganization mechanism underlying gene transcription remain to be fully elucidated. Here, we firstly developed a novel approach termed Inter3D to specifically dig out genes regulated by TAD reorganization. By constructing the comprehensive TAD reorganization medicating epigenomic landscapes in tumor cells, we showed that TAD separation interrupted the intrachromosomal loop at MYL12B locus and abrogated its transcription, while TAD fusion generated the chromosomal interaction and triggered CYP27B1 activation. Our study provides a comprehensive insight into capture of TAD rearrangement-mediated gene loci and moves towards recognizing the functional role of TAD reorganization in gene transcription.

overall_design: To address the questions about TAD reorganization, we developed a novel easy-to-use pipeline for Interactome identification with 3D multi-genomics (Inter3D) by performing integrative analysis of multi-omics datasets, including 3D genomics, epigenomics and transcriptomics. TAD boundaries are rich in various architectural proteins, among which we paid more attention to CTCF regulated ones. In details, Inter3D first identifies the CTCF-medicated TAD boundary alterations using Hi-C and CTCF ChIP-seq datasets of normal ARPE19 cells and cancer WERI-RB1 cells. Next, incorporating with the RNA-seq datasets of ARPE19 and WERI-RB1 cell lines, Inter3D identifies the candidate DEGs between variant samples regulated by CTCF binding alteration and TAD alteration. Finally, Inter3D identifies the candidate enhancers in promoter-distal peaks robust in ATAC-seq datasets of ARPE19 and WERI-RB1 cell lines, ruling out false positive target genes regulated by enhancer only rather than 3D structure.

first: Tianyi

last: Ding

first: Shaliu

first: Qi

last: Liu


title: Capture of TAD reorganization endows variant patterns of gene transcription (ATAC-Seq)

last: Zhang


title: Capture of TAD reorganization endows variant patterns of gene transcription (Hi-C)


title: Novel human cellular model of CDA IV enables comprehensive analysis revealing molecular basis of disease phenotype.

city: Bristol

first: Jan

last: Frayne

address: Biomedical Sciences Building, University Walk

department: School of Biochemistry

country: United Kingdom

institute: University of Bristol

summary: Red blood cell disorders can result in severe anemia. One such disease, congenital dyserythropoietic anemia IV (CDA IV) is caused by heterozygous mutation E325K in the transcription factor KLF1. However, studying the molecular basis of CDA IV is severely impeded by paucity of suitable and adequate quantities of material from anaemic patients and rarity of the disease. We therefore took a novel approach, creating a human cellular disease model system for CDA IV, which accurately recapitulates the disease phenotype. Next, using comparative proteomics we reveal extensive distortion of the proteome and a wide range of disordered biological processes in CDA IV erythroid cells. These include down-regulated pathways governing cell cycle, chromatin separation, DNA repair, cytokinesis, membrane trafficking and global transcription, and upregulated networks governing mitochondria biogenesis. The diversity of such pathways elucidates the spectrum of phenotypic abnormalities that occur with CDA IV and impairment to erythroid cell development and survival, collectively explaining the CDA IV disease phenotype. The data also reveal far more extensive involvement of KLF1 in previously assigned biological processes, along with novel roles in the regulation of intracellular processes not previously attributed to this transcription factor. Overall, the data demonstrate the power of such a model cellular system to unravel the molecular basis of disease and how studying effects of a rare mutation can reveal fundamental biology.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wildtype and KLF1+/E325K cells.

first: Ivan

last: Ferrer-Vicens

first: Daniel

last: Ferguson

first: Marieangela

last: Wilson

first: Kate

last: Heesom

first: James

last: Bieker


title: Investigation of ST8SIA1 expression in icaritin-treated and untreated melanoma cell lines

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

summary:
We identified that upregulation of ST8SIA1 promotes melanoma brain metastasis.
The goal of this RNA-seq is to analyze the ST8SIA1 expression in icaritin-treated and untreated melanoma cell lines (DP-0574 and WP-0614 cell lines)
In vitro functional studies demonstrate that ST8SIA1 overexpression promotes cell proliferation and colony formation and that this can be halted by icaritin treatment.

overall_design: mRNA profiles of icaritin-treated or control untreated cells were generated by deep sequencing using Illumina NextSeq 550, in triplicate.

first: Romela

middle: I

last: Ramos


title: Analysis of MLK3-dependent gene expression in carcinogen-induced murine hepatocellular carcinoma

city: Chicago

first: Basabi

last: Rana

state: Illinois

address: 840 S. Wood Street

department: Surgery

institute: University of Illinois at Chicago

summary: Hepatocellular carcinoma (HCC) is one of the most common gastrointestinal (GI) malignancies and a major cause of death worldwide, with limited therapeutic options. Although Mixed Lineage Kinase 3 (MLK3), a MAPKKK, has emerged as a key regulator of acute liver injury, inflammation, and non-alcoholic steatohepatitis (NASH), its role in HCC remains unclear. TCGA databases suggest an elevated expression of MAP3K11 (gene of MLK3) and TMA studies show higher MLK3 activation in human HCCs compared to the normal livers. We demonstrate here that MLK3 kinase activity is upregulated in Diethylnitrosamine/phenobarbital (DEN/PB)-induced HCC, and MLK3 deficiency (MLK3-/-) alleviates HCC progression. Histological and biochemical analyses reveal that MLK3-/- reduces DEN/PB induced cell proliferation in vivo and MLK3 inhibition by si/shRNA or pharmacological inhibitors reduces cell proliferation and colony formation in vitro.  Interestingly, MLK3-/- does not impair DEN-induced liver injury phenotypes at the early stage.  RNA-sequencing analysis shows that MLK3-/- modulates the gene signature of various biological pathways, including epithelial-mesenchymal transition (EMT), and reduces TGFβ1&2 expressions. HCC cells overexpressing MLK3 promote EMT, and induction of TGFβ, suggesting MLK3 to be an upstream regulator of TGFβ signaling. In addition, MLK3-/- significantly reduces the activated hepatic stellate cell (HSC) signature, which is increased in DEN/PB-Wild-Type livers. Further analysis suggested that MLK3 might promote a paracrine increase in TGFβ expression leading to pSmad2 induction and HSC activation. Our work thus shows that MLK3 promotes HCC proliferation, TGFβ expression, and HSC activation, implying that pharmacological inhibition of MLK3 may have a significant clinical impact on HCC progression.

overall_design: A total of 10 samples were analyzed. There were 4 experimental groups: water treated Wild-type (WT) and MLK3-Knockout (MLK3-KO) and DEN/PB-treated WT and MLK3-KO. 2 biological replicates were included for each water treated sample, and 3 biological replicates were included for each DEN/PB-treated sample.

first: Rong

last: Ke

first: Navin

last: Viswakarma


title: Single-Cell ATAC+RNAseq from CD34+ cells of a Primary Myelofibrosis patient evolved to secondary Acute Myeloid Leukemia

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Department of Biomedical, Metabolic and Neural Sciences

country: Italy

institute: University of Modena and Reggio Emilia

summary: To characterize the impact of chromatin remodelers’ mutations in MPN onset and development and identify regulatory elements driving gene expression modulations during disease progression, we  performed a single-nucleus RNAseq coupled with single-cell ATACseq experiment on CD34+ cells from the chronic and blast phase of a Primary Myelofibrosis patient.

overall_design: Comparative gene expression and chromatin accessibility profiling analysis of single cell ATAC+RNA-seq data for bone marrow CD34+ cells from during Primary Myelofibrosis (sample1) and after secondary Acute Myeloid Leukemia transformation (sample2).

first: Chiara

last: Carretta

first: Paola

last: Guglielmelli

first: Alessandro

middle: M

last: Vannucchi


title: Attenuation of Fibroblast Activation and Fibrosis by Adropin in Systemic Sclerosis (SSc)

city: Würzburg 97074

first: Chunguang

last: Liang

state: Bayern

address: Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland

department: Bioinformatics

institute: Biozentrum

summary: Fibrotic diseases impose a major socioeconomic challenge on modern societies with limited treatment options. Adropin, a peptide hormone encoded by the energy-homeostasis-associated (ENHO) gene, is implicated in metabolism and vascular homeostasis, but its role in the pathogenesis of fibrosis remains enigmatic. Here, we used machine learning approaches in combination with functional in vitro and in vivo experiments to characterize Adropin/ENHO as a potential regulator involved in fibroblast activation and tissue fibrosis in systemic sclerosis (SSc). We demonstrated consistent downregulation of Adropin/ENHO in SSc skin across different SSc cohorts. The prototypical profibrotic cytokine TGFβ reduced Adropin/ENHO expression in a JNK-dependent manner. Restoration of Adropin signaling by therapeutic application of bioactive Adropin34-76 peptides in turn inhibited TGFβ-induced fibroblast activation and fibrotic tissue remodeling in primary human dermal fibroblasts, three-dimensional full-thickness skin equivalents, the mouse models of bleomycin-induced pulmonary fibrosis and sclerodermatous chronic graft-versus-host-disease (sclGvHD), and precision-cut human skin slices (PCSS). Knockdown of GPR19, receptor of Adropin, abrogated the antifibrotic effects of Adropin in fibroblasts. RNA-seq demonstrated that the antifibrotic effects of Adropin34-76 were functionally linked to deactivation of GLI1 dependent profibrotic transcriptional networks, which was experimentally confirmed in vitro, in vivo and ex vivo. ChIP-seq confirmed Adropin34-76-induced changes in TGFβ/GLI1 signaling. Our study thus characterizes the TGFβ-induced downregulation of Adropin/ENHO expression as a potential pathomechanism of SSc as a prototypical systemic fibrotic disease that unleashes uncontrolled activation of profibrotic GLI1 signaling. We also provide evidence in multiple preclinical models that Adropin34-76 might offer potential for the treatment of fibrosis.

overall_design: In this study, we aimed to characterize the role of Adropin/ENHO in fibroblast activation and fibrotic tissue remodeling in SSc as a prototypic multisystem fibrotic disorder. Machine learning based evaluation of bulk RNA-seq datasets identified ENHO as a signature gene in SSc. Furthermore, these machine learning-derived results have been corroborated by various approaches, including DEG analysis. Screening of two large external cohorts, the PRESS and the GENISOS (15, 16), as well as our internal cohort with 133 SSc patients and 92 controls in total, demonstrated downregulation of Adropin/ENHO in dermal fibroblasts of SSc patients. Screening of different profibrotic mediators revealed that the reduction of Adropin/ENHO was mediated by profibrotic cytokine TGFβ, which was confirmed by overexpression of TβRICA or pharmacological inhibition of TGFβ signaling by the TβRI selective inhibitor SD-208 in mice. Screening using inhibitors targeting TGFβ mediated signaling pathways identified the suppression of ENHO expression was dependent on JNK signaling, which was also confirmed by siRNA mediated knockdown. Studies on cultured human dermal fibroblasts, 3D full-thickness human skin equivalents, complementary murine models with pre-established fibrosis and PCSS were used to demonstrate that administration of bioactive peptides Adropin34-76 ameliorated fibroblast-to-myofibroblast differentiation, collagen release and tissue fibrosis. Study designs and timeline diagrams were shown in Fig. 4A, 5A, 5D and 7A respectively. Transcriptional profiling was used to reveal that the antifibrotic effects of Adropin34-76 were functionally linked to Hedgehog signaling and GLI1 deactivation, which was experimentally confirmed in vitro, in vivo and ex vivo. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed to further investigate the intricate interactions between TGFβ and GLI1 signaling in response to Adropin treatment. Knockdown of GPR19, a putative receptor of Adropin, abrogated the antifibrotic effects of Adropin in fibroblasts.

first: Minrui

first: Nicholas

last: Dickel

first: Andrea-Hermina

last: Györfi

first: Bilgesu

last: SafakTümerdem

first: Yi-Nan

last: Li

first: Aleix

last: Rigau

first: Xuezhi

last: Hong

first: Lichong

last: Shen

first: Alexandru-Emil

last: Matei

first: Thuong

last: Trinh-Minh

first: Cuong

last: Tran-Manh

first: Xiang

last: Zhou

first: Ariella

last: Zehender

first: Alexander

last: Kreuter

first: Hejian

last: Zou

first: Georg

last: Schett

first: Meik

last: Kunz

first: Jörg

middle: H

last: Distler


title: The effect of acidosis on adipose-derived stem cell

first: Yihong

last: Chen

state: China

address: Department of Cardiology, Shanghai Changzheng Hospital, Second Military Medical University, No. 415, Fengyang Road, Huangpu District

department: Department of Cardiology

summary: The acidic microenvironment plays a key role to result in the poor survival and limited function of transplanted stem cells in ischemic diseases.In this study, different pH levels of medium were performed to treat adipose-derived stem cells (ADSCs) with 24/48h time- exposure, to explore the effect of extracellular acidosis on ADSCs.

overall_design: Adipose-derived stem cells (ADSCs) were treated with different pH levels of medium( pH=7.4/7.2/7.0/6.5)  for 24h/48h, to explore the transcriptic  alteration following with extracellular acidosis.

first: Chun

last: Liang


first: Minrui

address: 12 Wulumuqi Zhong Road

institute: Fudan University

first: Nicholas

last: Dickel

first: Andrea-Hermina

last: Györfi

first: Bilgesu

last: SafakTümerdem

first: Chunguang


title: Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [ATAC-seq]

first: Wulan

last: Deng

address: Beijing Haidian District Yiheyuan Road #5

department: BIOPIC

institute: Peking University

summary: To dissect the molecular mechanisms of the transcription factor FOXA2 accessing nucleosomal targets and controlling cell fates, we combined live-cell single-molecule imaging, genome editing, chromatin binding, chromatin accessibility, and RNA sequence analysis. Using the hESC differentiation cellular system to anterior primitive streak (APS) and definitive endoderm (DE), we demonstrated by RNA-seq that FOXA2 is a lineage-determining transcription factor for DE formation and that its intrinsically disordered C-terminal domain (CTD) is essential for its normal function. Through ChIP-seq and ATAC-seq at multiple time points of exogenous expression, we also showed that the CTD is required for FOXA2 effectively accessing targets in closed chromatin and altering chromatin accessibility. Together with the single-molecule kinetics captured by fluorescence microscopy, this study uncovers new mechanistic insights on the activity of lineage-determining transcription factors in engaging chromatin and accessing nucleosomal targets.

overall_design:
We generated homozygous genome-edited human embryonic stem cell lines (H7 hESC) with deletion of the entire protein-coding region, or the CTD, or both the CTD and NTD at the FOXA2 locus. Wild-type and edited hESCs were differentiated to APS and DE for poly-A RNA-seq. We generated U2OS cell lines with inducible expression of FOXA1/2/3 and SOX2 full length and mutants with the Tet-on system. Cells were induced with Dox for 4 days for ChIP-seq and ATAC-seq.
Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) was performed on wild-type U2OS cells and U2OS cells with inducible expression of Flag-tagged FOXA2 full length and the CTD deletion mutant as well as SOX2  full length and SOX2-FOXA2 CTD fusion protein for 4 days.

first: Di

last: Niu

first: Bo

last: Wang


title: Genetic and Environmental interactions contribute to immune variation in rewilded mice

city: Frederick

first: Yongmei

last: Zhao

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

summary: The relative and synergistic contributions of genetics and environment to inter-individual immune response variation remain unclear, despite its implications for understanding both evolutionary biology and medicine. We used single cell RNA sequencing (scRNA-seq) to quantify the interactive effects of genotype and environment on immune traits by investigating three inbred mouse sttrain rewilded in an outdoor enclosure and infected with the parasite, Trichuris muris

overall_design: Single cell suspensions from the mesenteric lymph node  were prepared by mashing the tissues individually through a 70μm cell strainer and washed with RPMI from murine mesenteric lymph nodes. 2000 cells from each individual mouse (Block 1 (n = 51); Block 2 (n = 71)) were labelled with the Ab-Hash Tag Oligonucleoutides (HTO) and analyzed using scRNAseq.

first: Oyebola

last: Oyesola

first: Nina

last: Howard

first: Kimberly

last: Zaldana

first: Kasalina

last: Kiwanuka

last: Downie

first: Andrea

last: Graham

first: P'ng

last: Loke


title: Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [ChIP-seq]

city: Beijing

overall_design:
We generated homozygous genome-edited human embryonic stem cell lines (H7 hESC) with deletion of the entire protein-coding region, or the CTD, or both the CTD and NTD at the FOXA2 locus. Wild-type and edited hESCs were differentiated to APS and DE for poly-A RNA-seq. We generated U2OS cell lines with inducible expression of FOXA1/2/3 and SOX2 full length and mutants with the Tet-on system. Cells were induced with Dox for 4 days for ChIP-seq and ATAC-seq.
Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) was performed on wild-type U2OS cells and U2OS cells with inducible expression of Flag-tagged FOXA1/2/3 full length and the CTD deletion mutant as well as SOX2  full length and SOX2-FOXA2 CTD fusion protein for 4 days.


title: Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [RNA-seq]

overall_design:
We generated homozygous genome-edited human embryonic stem cell lines (H7 hESC) with deletion of the entire protein-coding region, or the CTD, or both the CTD and NTD at the FOXA2 locus. Wild-type and edited hESCs were differentiated to APS and DE for poly-A RNA-seq. We generated U2OS cell lines with inducible expression of FOXA1/2/3 and SOX2 full length and mutants with the Tet-on system. Cells were induced with Dox for 4 days for ChIP-seq and ATAC-seq.
RNA-Seq of poly-A enriched RNA in human H7 embryonic stem cells (undifferentiated, APS and DE stages), homozygous Halo-FOXA2 knock-in clone KI14, FOXA2 knock-out clones KO1, KO21, KO30, homozygous delta C-teminus FOXA2 clone dC11, and homozygous delta C- and N-termini clone dCdN10.

first: Claudia

last: Cattoglio


title: Transcriptomic heterogeneity of endothelial cells during devleopmental angiogenesis

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

institute: Medical College of Wisconsin

summary: Efficient angiogenesis, the formation of new blood vessels from pre-existing vessels, underlie tissue growth during development. Blood vessels in the mouse ear has been shown to dramatically expand at the neonatal stage to meet the needs of postnatal tissue growth. Yet, it is not clear at the transcriptome level how endothelial cells lining the innermost layer of blood vessels drive angiogenesis at this developmental stage. The highly heterogeneous endothelial cell types during angiogenesis render traditional bulk RNA-sequencing unsuitable. Therefore, we utilized single-cell RNA- and CITE-seq to profile transcriptomic heterogeneity of both blood and lymphatic endothelial cells during developmental angiogenesis in mouse ear.

overall_design: CD31+, Cdh5CreERT2-Rtom+ cells were isolated from neonatal (P8) mouse ears. 10x genomics single-cell RNAseq together with CITE-seq was performed in duplicate to obtain single-cell transcriptome data and measurement of expression levels of 5 specific proteins.

first: Ziqing

last: Liu

first: Data

last: Ruter

first: Victoria

last: Bautch


title: Next Generation Sequencing Facilitates Quantitative Analysis of 786-O and sunitinib resistant 786-O (7R) cell lines

first: Jie

address: No.168, Changhai Rd., Yangpu District

department: Department of Urology

institute: Changhai Hospital, Naval Medical University(Second Military Medical University)

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the different gene between 786-O and 7R cell lines

overall_design: Total RNA profiles of 786-O and 7R were generated by deep sequencing, in triplicate, using Illumina HiSeq X Ten.


title: Genome-wide mapping of H3K27me3 in Daxx-depleted cells

city: Taipei

first: Hsiu-Ming

last: Shih

address: 128 Sec. 2, Academia Rd. Nankang,

department: Institute of Biomedical Sciences

institute: Academia Sinica

summary: We discovered Daxx can negatively regulated H3K27me3 level via facilitating long non-coding RNA HOTAIR degradation. To further explore the biological consequence and search for affected genes, we used high throughput sequencing technology to demonstrate the enrichment of H3K27me3 on the human genome and target genes repression after depletion of Daxx. This study revealed a novel role of Daxx in regulating histone modifications via modulates long non-coding RNA stability.

overall_design: Examination of H3K27me3 distribution in Daxx-depleted and untreated HEK293T cells

first: Tien-Chi

last: Huang

first: Yen-Sung


title: CD49a expression and induction of cytotoxicity on human tissue-resident CD8+ T cells is controlled by RUNX2 and RUNX3 transcription factor activity [ATAC-seq]

city: Huddinge

first: Ram Vinay

last: Pandey

address: Hälsovägen 7, Neo

department: Department of Medicine

institute: Karolinska Institutet

summary: CD49a marks highly cytotoxic epidermal tissue-resident memory (TRM)-cells, but their molecular circuitry and relationships to circulating populations are poorly defined. We demonstrate enrichment of RUNX family transcription factor binding motifs in human epidermal CD8+CD103+CD49a+ TRM-cells, paralleled by high RUNX2 and RUNX3 protein expression. Clonal overlap between epidermal CD8+CD103+CD49a+ TRM-cells and circulating memory CD8+CD45RA–CD62L+ T-cells identified a reservoir of circulating cells with potential to seed cytotoxic TRM-cells in new sites. Upon IL-15 and TGF-β stimulation, subsets of circulating CD8+CD45RA–CD62L+ T-cells acquired CD49a expression and cytotoxic transcriptional profiles in a RUNX2 and RUNX3 dependent manner. In contrast, knock-out of RUNX3, but not RUNX2, prevented CD103 expression. In melanoma, high RUNX2, but not RUNX3, transcription correlated with a cytotoxic CD8+CD103+CD49a+ TRM cell signature and overall patient survival. Together, our results indicate that combined RUNX2 and RUNX3 activity promotes the differentiation of cytotoxic CD8+CD103+CD49a+ TRM-cells, providing immunosurveillance of infected and malignant cells.

overall_design:
CD69+ CD8 T cells from the dermis (CD103-CD49a- and CD103+CD49a-) and epidermis (CD103+CD49a- and CD103+CD49a+) of 4 healthy donors were FACS sorted and directly used for Omni ATAC-seq.

**Submitter declares that raw data were not submitted due to patient privacy concerns**

first: Beatrice

last: Zitti

first: Ram

first: Yenan

last: Bryceson


title: Gene expression profiles of depletion of Daxx and HOTAIR

summary: In this study, we found that Daxx may modulate HOTAIR stability, and therefore, regulate H3K27me3 levels. To further examine the possible mechanism and biological consequence, we separately knocked down Daxx and HOTAIR with a lentivirus plasmid constructed with short hairpin RNA and siRNA oligonucleotides, respectively. We then used microarray analysis to identify several candidate genes regulated under the Daxx-HOTAIR axis.

overall_design: In order to knock down Daxx, HEK293T cells were transfected with a lentivirus plasmid constructed with a short hairpin RNA targeted to Daxx or to luciferase as a control. In the HOTAIR experiment, siRNA oligonucleotides were targeted to HOTAIR or to GFP as a control. Both were synthesized by Dharmacon. All transfections were performed by using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. Three independent knockdown experiments were performed with Daxx and HOTAIR. Total RNA was extracted after 3 days to perform microarray analysis.


title: Activation response of murine CD8 T cells to supernatant from IL-3-treated basophil cultures

status: Public on Apr 28 2024

city: Bar Harbor

first: Chih-Hao

last: Chang

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: CD8 T cells are critical in combating cancer, but their effectiveness is hindered by exhaustion due to the immunosuppressive tumor microenvironment. Here, we examine the role of IL-3 in coordinating anti-tumor immunity resulting in increased CD8 T-cell functionality. IL-3 treatment of tumor-bearing mice increases CD8 T-cell effector function and protections against tumor progression. However, there is no evidence that IL-3 had direct effect on CD8 T cells. Instead, IL-3 exerts influences basophils to excrete IL-4, which is responsible for inducing increased IFN-γ production and viability of CD8 T cells. Taken together, these findings unveil an IL-3-mediated CD8 T cell-basophil crosstalk that regulates anti-tumor immunity, and offers a encouraging approach for augmenting cancer immunotherapy.

overall_design: This experiments was designed to reveal the transcriptomic changes in CD8 T cells when activated in the presence of suppernatant derived from basophils stimulated with IL-3 or PBS.

first: Jian

last: Wei


title: Differential Gene Expression and Pathway Analysis in Growth Hormone-Secreting Pituitary Tumors According to Granulation Pattern

city: Gwang-ju

first: Yeongmin

last: Kim

address: Chundamguagiro

department: BMSE

institute: GIST

summary: This study investigated differential gene expression between granulation patterns in growth hormone (GH)-secreting pituitary tumors, aiming to elucidate novel transcriptomes that explain clinical variances in patients with acromegaly. Transcriptome analysis was conducted on 6 normal pituitary tissues and 15 GH-secreting pituitary tumors, including 9 densely granulated somatotroph tumors (DGSTs) and 6 sparsely granulated somatotroph tumors (SGSTs). We identified 3111 differentially expressed genes (DEGs) in tumors compared to normal pituitaries, with 1117 DEGs unique to a specific granulation within tumors. SGST showed enrichment of neuronal development and acute inflammatory response pathways, along with a significant enhancement of JAK–STAT, phosphatidylinositol 3-kinase, and MAPK signaling. The results suggest that granulation-specific gene expression may underpin diverse clinical presentations in acromegaly, highlighting the potential for further investigation into these transcriptomic variations and their roles in disease pathology, particularly the involvement of genes linked to neuronal development, inflammatory response, and JAK–STAT signaling in SGST.

overall_design: Prospective design

first: Kyungwon


title: MicroRNA sequencing of growing teratoma tissues

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

summary:
MicroRNA sequencing of slow and rapid growing teratoma. Teratoma without a growth trend were included as controls. In total, 9 samples were analyzed for their expressed microRNAs by sequencing.
YST and EC tissues were identified from the biobank of the Department of Urology (University Hospital Düsseldorf). Total RNA has been isolated and subsequently microRNA sequencing has been performed.

overall_design: MicroRNA sequencing of 3 slow and 3 rapid growing teratoma samples as well as 3 teratoma without a growth trend.


title: The Ubiquitin Ligase RBX2/SAG Regulates Mitochondrial Ubiquitination and Mitophagy

city: Augusta

first: Jianqiu

last: Zou

state: GA

address: 1460 Laney Walker Blvd

department: VBC

institute: Augusta University

summary: Clearance of damaged mitochondria via mitophagy is crucial for cellular homeostasis. While the role of ubiquitin (Ub) ligase PARKIN in mitophagy has been extensively studied, increasing evidence suggests the existence of PARKIN-independent mitophagy in highly metabolically active organs such as the heart. Here, we identify a crucial role for Cullin-RING Ub ligase 5 (CRL5) in basal mitochondrial turnover in cardiomyocytes. CRL5 is a multi-subunit Ub ligase comprised by the catalytic RING box protein RBX2 (also known as SAG), scaffold protein Cullin 5 (CUL5), and a substrate-recognizing receptor. Analysis of the mitochondrial outer membrane-interacting proteome uncovered a robust association of CRLs with mitochondria. Subcellular fractionation, immunostaining, and immunogold electron microscopy established that RBX2 and Cul5, two core components of CRL5, localizes to mitochondria. Depletion of RBX2 inhibited mitochondrial ubiquitination and turnover, impaired mitochondrial membrane potential and respiration, and increased cell death in cardiomyocytes. In vivo, deletion of the Rbx2 gene in adult mouse hearts suppressed mitophagic activity, provoked accumulation of damaged mitochondria in the myocardium, and disrupted myocardial metabolism, leading to rapid development of dilated cardiomyopathy and heart failure. Similarly, ablation of RBX2 in the developing heart resulted in dilated cardiomyopathy and heart failure. Notably, the action of RBX2 in mitochondria is not dependent on PARKIN, and PARKIN gene deletion had no impact on the onset and progression of cardiomyopathy in RBX2-deficient hearts. Furthermore, RBX2 controls the stability of PINK1 in mitochondria. Proteomics and biochemical analyses further revealed a global impact of RBX2 deficiency on the mitochondrial proteome and identified several mitochondrial proteins as its putative substrates. These findings identify RBX2-CRL5 as a mitochondrial Ub ligase that controls mitophagy under physiological conditions in a PARKIN-independent, PINK1-dependent manner, thereby regulating cardiac homeostasis.

overall_design: We analyzed the transcriptomes of αMHC-driven Mer-Cre-Mer Tamoxifen-inducible adult Rbx2 knockout hearts (iRbx2KO) with RNA-seq of 4 knockout ventricles versus 4 wildtypes.

first: Wenjuan

last: Wang

first: Ermin

last: Li

first: Chen

last: Qu

first: Juan

last: Ayala

first: Yuan

last: Wen

first: Md

middle: S

last: Islam

first: Neal

last: Weintraub

first: David

last: Fulton

first: Qiangrong

last: Liang

first: Jiliang

last: Zhou

first: Jinbao

first: Yi

last: Sun

first: Huabo

last: Su


title: aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs [RNA-Seq]

city: Wuhan

first: Wenying

last: Zhong

address: Lion Rock Street

institute: Huazhong Agricultural University

summary: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for profiling histone modifications and transcription factors binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits, tubers and flowers is challenging due to their sturdy cell walls and complex constituents. Here, we present advanced ChIP (aChIP), an optimized ChIP-seq strategy that efficiently isolates chromatin from plant tissues while simultaneously removing plant cell walls and cellular constituents. aChIP enables precise profiling of histone modifications in all tested EIPOs as well as transcription factors and chromatin-modifying enzymes. Notably, it significantly enhances ChIP efficiency and uncovers numerous novel modified sites compared to previous methods in vegetativetissues. Remarkably, aChIP unveils the first histone modification landscape of dry rapeseed seeds, illuminating the intricate roles of histone marks in EIPOs. Together, aChIP is a potent, efficient, and sensitive approach for comprehensive chromatin protein profiling across virtually all plant tissues, advancing plant epigenomics and functional genomics research, particularly within EIPOs.

overall_design: To compare the differential expression across different organizations

first: Qing

last: Zhang

first: Lun

last: Zhao


title: Effect of intracellular acidification on senescence-related transcriptomic changes

city: Minato City

first: Satoshi

last: Kawakami

address: 4-6-1 Shirokanedai

department: The Institute of Medical Science

institute: The University of Tokyo

summary: Several remodeling of intracellular environments has been identified in senescent cells, including enlargement of cell / nuclear size and intracellular acidification. Although these alterations of intracellular environments were reported to be involved in unique characteristics of senescent cells, the contribution of intracellular acidification to senescence-associated cellular phenotypes is poorly understood. Here, we identified that upregulation of TXNIP and its paralog ARRDC4 as a hallmark of intracellular acidification in addition to KGA-type GLS1. These genes were also upregulated in response to senescence-associated intracellular acidification. Neutralization of the intracellular acidic environment ameliorated not only senescence-related upregulation of TXNIP, ARRDC4, and KGA, but also inflammation-related genes, possibly through suppression of glycolysis. Taken toghether, our data implied that the contribution of intracellular pH to senescence-associated cellular features, such as SASP.

overall_design: To investigate the effect of intracellular acidification, we prepared nutlin3a-induced senescent cells and cultured them under normal or alkali environment. RNA-seq was performed to detect alkali-induced transcriptomic changes in senescent cells.

first: Makoto

last: Nakanishi


title: Hypoxia activates AMPK and drives NLRP3-mediated pyroptosis in periodontitis

city: qingdao

first: Qiuxia

last: Ji

address: jiangsu road

institute: qingdao university

summary: Hypoxia has a significant impact on periodontal homeostasis and is a contributing factor to periodontal pathogenicity. This study aimed to investigate the role and mechanism of hypoxia in  periodontitis.

overall_design: We performed RNA-seq on human acute monocytic leukemia（THP-1）cells.

first: Shuhan

first: Caixiu

last: Yang

first: Xiaoming

last: Xing

first: Lianjing

last: Cao

first: Xiangru

last: Gao

first: Zhaoyu

last: Lu


title: Expression data from human immortalized urothelial cell SV-HUC-1 and four Bladder cancer cells (5637, UMUC3, T24, and J82)

city: Tianjin

first: Guangming

last: Li

state: Tianjin

address: No. 22 Qixiangtai Road

department: Pathogen

institute: Tianjin Medical University

summary: To uncover the dysregulated genes in BCa, we performed the RNA-seq to detect the gene expression levels in four BCa cells (5637, UMUC3, T24, and J82) and human immortalized urothelial cell SV-HUC-1. To search for the differentially expressed genes of for cell lines (5637, J82, UMUC3, and T24) compared to the normal cell line SV-HUC-1.

overall_design: Human immortalized urothelial cell SV-HUC-1 was used as the normal cell line, 5637, UMUC3, T24, and J82 were four BCa cells. We sought to obtain the expression profiles of the normal cell line and four BCa cells, and found the dysregulated expression ones from the large amount genes in four BCa cells, compared with the normal cell line.

first: Liang

last: Dai

first: Yimin

last: Wang

first: Wangteng

last: Ma


title: Effects of PFOA, PFBA, PFHxA, PFOS, PFBS, PFHxS on gene expression in monolayer and non-neuroectoderm cells differentiated from H1

city: 北京市

first: Renjun

state: 北京

address: 双清路18号林业大学北门

institute: RCEES

summary: Per- and polyfluoroalkyl substances (PFAS) are a group of organic chemicals that contain multiple carbon-fluorine bonds, which make them highly stable and widespread in our environment, even in the human body. They have been detected in cord blood and showed correlation with neonatal health abnormalities such as weight loss. Here, we utilized human embryonic stem cell-based model to assess the early developmental toxicity of six PFAS (PFOA, PFHxA, PFBA, PFOS, PFHxS, and PFBS) and their skin developmental toxicity. We employed global monolayer differentiated model to mimic the early embryonic development and performed non-neural ectoderm (NNE) differentiation which can give rise to keratinocytes to imitate early skin development. Transcriptomic analysis revealed that PFOS caused the most differentially expressed genes (DEGs) both in day 16 global monolayer samples and NNE samples to making it the most toxic of the six PFAS. Further validation of gene expression levels showed that the TGF-β signaling pathways were involved in the early global developmental toxicity and in the early skin developmental toxicity of PFOS. Interestingly, our results showed that PFOS inhibited the ciliogenesis of NNE cells, which may interfere with the transduction of TGF-β, Notch, Hedgehog, and Hippo signaling pathways, ultimately inhibiting early embryonic skin development and posing a potential threat to the occurrence of congenital skin diseases. Overall, our study suggests a potential toxicity mechanism by which PFAS inhibit ciliogenesis to interfere with the transduction of important signaling pathways, leading to early global developmental toxicity as well as early embryonic skin developmental toxicity and potential congenital skin diseases.

overall_design:
To assess the early global developmental toxicity and the early skin developmental toxicity of the six PFAS (PFOA, PFHxA, PFBA, PFOS, PFHxS, and PFBS), we employed human embryonic stem cells (hESCs)-based global monolayer differentiation model and non-neural ectoderm (NNE) differentiation model to mimic early embryonic development and early skin development respectively.
We then performed transcriptome analysis based on RNA-seq to evaluate the toxic effect of the six PFAS on gene expression level. Samples were treated with 10 μM PFAS respectively for 8 days and 16 days during global monolayer differentiation while 8 days for NNE differentiation.

first: Miaomiao

first: Nuoya

last: Yin

first: Francesco

last: Faiola

first: Shichang

first: Shuxian


title: Illumina Infinium MethylationEPIC BeadChip (850k) analysis of growing teratoma tissues

first: Daniel

last: Nettersheim

type: Methylation profiling by genome tiling array

summary: Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of 12 different growing teratoma tissues. Samples were subgrouped based on growth speed into GTSslow to GTSrapid (see corresponding publication).

overall_design: Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of 4 slow, 4 mediun and 4 rapid growing teratoma samples.


title: PolyA RNA-seq from Medulloblastoma cells ± EYA2 knockdown

city: Aurora

first: Matthew

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary: Analysis of steady-state mRNA levels in two medulloblastoma-derived cell lines.

overall_design: Comparison of D425 and D458 medulloblastoma cell lines with Control vs two different EYA2-targeting shRNAs; n = 3 independent biological replicates each.

first: Melanie

last: Vincent

first: Arthur

last: Wolin

first: Heide

last: Ford


title: Therapeutic vaccine induced plasma cell differentiation is defective upon persistent HBsAg stimulation [scRNA]

city: Xiamen

first: Jinhang

last: He

state: Fujian

address: No.4221, South Xiang'an Road

institute: Xiamen University

summary: Background & Aims: The precise mechanism underlying the attenuation of the antigen-specific B cell response induced by therapeutic vaccination during chronic HBV infection remains unclear. The development of vaccines or strategies targeting this impediment through rational design could potentially result in significant advancements in the treatment of chronic hepatitis B. Methods: A mouse model with a knock-in of a B cell receptor specific to the hepatitis B virus surface antigen was generated under the name E6F6-B. This model was utilized to investigate the temporal and spatial patterns of humoral responses induced by therapeutic vaccination in the presence of persistent antigen stimulation. Through the use of multiple transcriptome sequencing techniques, the differentiation trajectory of HBsAg-specific B cells post therapeutic vaccination during chronic hepatitis B infection was elucidated. Results: In light of the E6F6-B transfer model, a significant reduction in antibody secreting cells were observed two weeks after vaccination. Additionally, an atypical pre-plasma cell population (BLIMP-1+ IRF4+ CD40- CD138-) was identified as a consequence of persistent BCR signaling in the absence of CD40 co-stimulation. A therapeutic antibody-induced suppression of BCR signaling revitalized the HBsAg-specific B cell response.

overall_design: Comparative gene expression analysis and enrichment analysis analysis of CD45.2+ E6F6-B cell RNA-seq data under normal condition and persistent HBsAg stimulation condition.

first: Ruoyao

last: Qi

first: Rao

last: Fu

first: Xing

last: Lei


title: VCAM-1 in atherosclerotic macrophages

city: Pittsburgh

first: Partha

last: Dutta

state: PA

address: 200 Lothrop Street

department: Medicine

institute: University of Pittsburgh

summary: We identified the genes regulated by VCAM-1 in atherosclerotic macrophages. We selected some of these genes based on their expression and further evaluated their functions using a wide array of techniques.

overall_design: Bone marrow chimeric Ldlr KO mice were generated by transplanting LysM+/+ Vcam1fl/fl or LysMcre/+ Vcam1fl/fl bone marrow. We sorted macrophages from atherosclerotic plaques of these mice. mRNA was extracted from these samples and bulk RNA sequencing was performed.

first: Jonathan

last: Florentin

first: Niranjana

last: Natarajan

first: Scott

last: O'Neil Patrick


title: Therapeutic vaccine induced plasma cell differentiation is defective upon persistent HBsAg stimulation [bulkRNA]

overall_design: Comparative gene expression analysis and enrichment analysis analysis of CD45.2+ E6F6-B cell RNA-seq data under normal condition and persistent HBsAg stimulation condition at different time points(7,14,21,28 days post CRT3-SEQ13 vaccinated)


title: Hepatocytes cyclooxygenase-2 deficiency improves liver injury via inhibition of endoplasmic reticulum stress and epithelial-mesenchymal transition

city: Chengdu

first: Yang

last: Tai

state: Sichuan

address: NO. 37, Xiang Xue Guo

institute: West China Hospital, Sichuan University

summary: The mechanism underlying the loss of normal liver tissues in liver cirrhosis, mainly hepatocytes, is not well-characterized. Endoplasmic reticulum (ER) stress-induced cell death has emerged as a potential mechanism for chronic liver diseases. We have previously demonstrated that cyclooxygenase-2 (COX-2) is closely related to the progress of liver cirrhosis. In this study, we aimed to verify whether hepatocytes COX-2 deficiency could protect liver injury via inducing ER stress in liver cirrhosis.

overall_design: Hepatocytes-specific COX-2 deletion mice (C57BL/6 background) were derived by breeder COX-2fl/fl mice with Alb-Cre mice. Male COX-2fl/fl/Alb-Cre+mice (COX-2 CKO) and their age-matched littermate control COX-2fl/fl/Alb-Cre- mice (WT) were used. Primary hepatocytes from COX-2 CKO or WT mice were isolated using a two-step perfusion method. For ER stress induction, cells were starved with 1% FBS for 2 hours and incubated with vehicle (DMSO) or tunicamycin (Tu, 6 μmol/L) for additional 24 hours.

first: Wei

last: Su

last: Gao

first: Hao

last: Wu

first: Chengwei

last: Tang


title: RNA-seq analysis of the gene expression profile of Huh7 cells upon incubation with different TGF-β-treated hepatic stellate cells (HSCs)-derived ectosomes

first: Qi-tao

last: Chen

state: Fujian Province

address: Xiang annan road

department: School of Life Sciences

summary:
Purpose: The goals of this study are to compare the gene expression profile of Huh7 cells treated with different ectosomes or not and to evaluate the function of ectosomal Hexokianse 1 (HK1) derived from HSCs.
Methods: Firstly, we treated different LX-2 HSCs with TGF-β (2 ng/mL) for 36 hours to activate HSCs, then ectosomes from LX-2 or HK1-KD LX-2 culture medium were isolated respectively by differential centrifugation processes. Secendly, Huh7 cells were preincubated with different ectosomes or not for 12 hours and then  fresh medium for another 12 hours. Lastly, different groups of Huh7 cells were prepared for RNA-seq.
Results: By Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the differentially expressed genes, a total of 124 pathways were found to be enriched in the ectosome-incubated Huh7 cells compared with the control Huh7 cells, while a total of 36 pathways were enriched in the ectosome-incubated Huh7 cells compared with the HK1-KD ectosome-incubated Huh7 cells.Gene set enrichment analysis (GSEA) also revealed enrichment of the N-glycosylation pathway in the ectosome-incubated Huh7 cells compared with the control Huh7 cells. Conversely, this pathway was negatively regulated in Huh7 cells incubated with HK1-KD HSC-derived ectosomes
Conclusion: the transferal of HSC-derived ectosomal HK1 into HCC cells regulates the N-glycosylation level of Huh7.

overall_design: Three groups of Huh7 were sequenced and every group had three independent samples.

first: Qiao-ling

last: Huang

first: Zhi-yuan

last: Zhang