title: Intergenerational Neuroprotection by an Intestinal Sphingolipid in Caenorhabditis elegans

city: Clayton

first: Stuart

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

summary: In animals, maternal diet and environment can influence the health of offspring. Whether and how maternal dietary choice impacts the nervous system across multiple generations is not well understood. Here, we show that feeding Caenorhabditis elegans with ursolic acid (UA), a natural plant product, reduces adult-onset neurodegeneration intergenerationally. UA provides neuroprotection by enhancing maternal provisioning of sphingosine-1-phosphate (S1P) - a bioactive sphingolipid. Intestine-to-oocyte S1P transfer is required for intergenerational neuroprotection and is dependent on the RME-2 lipoprotein yolk receptor. S1P acts intergenerationally by upregulating transcription of the acid ceramidase-1 (asah-1) gene in the intestine. Spatially regulating sphingolipid metabolism is critical as inappropriate asah-1 expression in neurons causes developmental axon outgrowth defects. Our results show that sphingolipid homeostasis impacts the development and intergenerational health of the nervous system. The ability of specific lipid metabolites to act as messengers between generations may have broad implications for dietary choice during reproduction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ursolate treated vs untreated C. elegans

first: Wenyue

last: Wang

first: Roger

last: Pocock


title: Hnf4 controls gut and liver gene programs in the thymus [CUT&Tag]

status: Public on Jun 26 2023

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We profiled medullary thymic epithelial cells and intestinal epithelial cells by CUT&Tag to investigate mechanisms of T-cell tolerance.

overall_design: CUT&Tag of mTECs and IECs

first: Daniel

middle: A

last: Michelson

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Genome-wide identification of target genes for the transcription factor Sox9 in early postnatal NG2 glia.

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

country: Germany

type: Expression profiling by high throughput sequencing

summary: To identify expression patterns dependent on the transcription factor Sox9 in oligodendroglia in a genome-wide and unbiased approach, we sorted oligodendroglia from wild type and Sox9-overexpressing mice and isolated total RNA which was followed by RNA-Seq studies. Among others we detected substantial changes in the expression of genes associated proliferation, differentiation and myelination of oligodendrocytes.

overall_design: We generated mRNA profiles of wild type (ctrl) and Sox9-overexpressing cells (tgSox9) using the Illumina NovaSeq 6000, PE 2x150 platform.

first: Lisa

last: Hassel


title: Mesenchymal-like tumor cells and myofibroblastic cancer-associated fibroblasts are associated with progression and immunotherapy response of clear-cell renal cell carcinoma [spatial transcriptomics]

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

country: France

institute: I.G.B.M.C. - Institut de génétique et de biologie moléculaire et cellulaire

summary: Immune checkpoint inhibitors (ICI) represent the cornerstone for treatment of patients with metastatic clear-cell renal cell carcinoma (ccRCC). Despite a favorable response for a subset of patients, others experience primary progressive disease highlighting the need to precisely understand plasticity of cancer cells and their crosstalk with the microenvironment to better predict therapeutic response and personalize treatment. Single-cell RNA sequencing of ccRCC at different disease stages and normal adjacent tissue (NAT) from patients identified 46 cell populations, including 5 tumor subpopulations, characterized by distinct transcriptional signatures representing an epithelial to mesenchymal transition gradient and a novel inflamed state. Deconvolution of the tumor and microenvironment signatures in public datasets and in data from the BIONIKK clinical trial (NCT02960906) revealed a strong correlation between mesenchymal-like ccRCC cells and myofibroblastic cancer-associated fibroblasts (myCAFs), which are both enriched in metastases and correlate with poor patient survival. Spatial transcriptomics and multiplex immune staining uncovered spatial proximity of mesenchymal-like ccRCC cells and myCAFs at the tumor-NAT interface. Moreover, enrichment in myCAFs was associated with primary resistance to ICI therapy in the BIONIKK clinical trial. This data highlights the epithelial-mesenchymal plasticity of ccRCC cancer cells and their relationship with myCAFs, a critical component of the microenvironment associated with poor outcome and ICI resistance.

overall_design: Two tumoral samples from patients presenting clear-cell Renal Cell Carcinoma were analyzed by Spatial transcriptomics.

first: Antonin

last: Fattori

first: Alexandra

last: Helleux

first: Céline

last: Keime

first: Gabriel

last: Malouf

first: Irwin


title: Hnf4 controls gut and liver gene programs in the thymus [CUT&RUN]

summary: We profiled medullary thymic epithelial cells by CUT&RUN to investigate mechanisms of T-cell tolerance.

overall_design: CUT&RUN of mTECs

first: Juliana

last: Lee


title: LncRNA profile of human liver tissues: hepatocellular carcinoma vs. matched noncancerous liver tissue

status: Public on Jun 25 2023

city: Guangzhou

first: Rui

last: Xu

state: Guangdong

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-Sen University Cancer Center

summary: LncRNA profiling of hepatocellular carcinoma vs. matched noncancerous liver tissue, aimed to analyze the lncRNA expression proﬁle of hepatocellular carcinoma (HCC) and identify prognosis-related lncRNAs.

overall_design: 400 samples

first: Huiyun


title: Regulatory variants in a novel distal enhancer regulate the expression of CYP3A4 and CYP3A5: ATAC-Seq and 4C data from human hepatocytes

city: Gainesville

first: Danxin

state: FL

address: 1345 Center Drive MSB PG-05B

department: Pharmacotherapy and Translational Research

institute: University of Florida

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

overall_design: Refer to individual Series


title: Mesenchymal-like tumor cells and myofibroblastic cancer-associated fibroblasts are associated with progression and immunotherapy response of clear-cell renal cell carcinoma


title: Circadian clock regulation by compartmentalized protein translation

status: Public on Jun 24 2023

city: Beijing

first: Xuerui

last: Yang

state: Beijing

address: Tsinghua University

department: School of Life Sciences

institute: Tsinghua University

summary: Cells exquisitely compartmentalize many biochemical reactions through phase-separated membrane-less organelles. Besides spatial organization, many biological processes are temporally regulated. While both transcription and translation oscillate in a rhythmic manner, the regulatory mechanism of the latter is understudied. Here we report that the translational regulation during circadian cycles is associated with oscillating phase separation controlled by Ataxin-2 and Ataxin-2L. Ataxin-2/2L forms rhythmic condensates through phase separation in the mammalian central clock suprachiasmatic nucleus to selectively concentrate the transcripts of the core clock genes and recruit the mRNA translation machinery. The rhythmic translational activation is abolished in cells and mouse circadian behavior is altered in the absence of Ataxin-2/2L. During aging or neurodegeneration, Ataxin-2/2L form large, irreversible puncta that no longer regulate translation. Overall, our results unveil Ataxin-2/2L’s role as the master regulators of rhythmic translation via a oscillating phase-separation, and explained the reason for their dysfunction in disease states.

overall_design: Ribosome profiling of U2OS WT, Ataxin-2 KO, Ataxin-2L KO and DKO cells at 4 hours and 12 hours after synchronization with DXMS.

first: Yanrong

last: Zhuang

first: Zhiyuan

last: Li

first: Shiyue

last: Xiong

first: Chujie

last: Sun


title: Peptide-mediated inhibition of the transcriptional regulator Elongin BC induces apoptosis in cancer cells

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

summary: Inhibition of protein-protein interactions (PPIs) via designed peptides is an effective strategy to perturb their biological functions. The Elongin BC heterodimer (ELOB/C) binds to a BC-box motif and is essential for cancer cell growth. Here, we report a peptide that mimics the high-affinity BC-box of the PRC2-associated protein EPOP. This peptide tightly binds to the ELOB/C dimer (kD = 0.46 ± 0.02 nM) and blocks the association of ELOB/C with its interaction partners, both in vitro and in the cellular environment. Cancer cells treated with our peptide inhibitor showed decreased cell viability, increased apoptosis, and perturbed gene expression. Therefore, our work proposes that blocking the BC-box-binding pocket of ELOB/C is a feasible strategy to impair its function and inhibit cancer cell growth. Our peptide inhibitor promises novel mechanistic insights into the biological function of the ELOB/C dimer and offers a starting point for therapeutics linked to ELOB/C dysfunction.

overall_design: RNA-Seq in PC3 prostate cancer cells after shRNA mediated knockdown Elongin B and Elongin C, compared to Control cells (3 replicates). RNA-Seq after BC-Box peptide (WT, Mutant and scrambled peptide) treatment of PC3 cells (3 replicates)

first: Sabrina

last: Fischer

first: Bastian

last: Stielow

first: Andrea

last: Nist


title: Testosterone deficiency altered mortality and the expression profile of protease inhibitors in an elastase-induced mouse model of emphysema

city: Fukuoka

first: Aono

last: Kentaro

state: Fukuoka

address: Jyonan-ku, Nanakuma, 8-19-1

department: Faculty of pharmacy

country: Japan

institute: Fukuoka university

summary: To evaluate the effect of testosterone on the pathophysiology of COPD, we created porcine pancreas elastase (PPE)-induced emphysema mouse model in sham or orchiectomized (ORX) mice [sham/PBS, sham/PPE, ORX/PBS, and ORX/PPE]. We performed microarray analysis to compare the gene expression levels in the lungs of each mice group. The results demonstrated that the levels of genes encoding protease inhibitor activity in ORX/PPE mice were lower than those in sham/PPE mice.

overall_design: Total RNAs were extracted from the frozen lung tissue using TRIzol reagent. The samples represent a pool of RNA from 5 individual mice in each group. They were used for hybridization to the SurePrint G3 Mouse Gene Expression Microarray 8x60K v2.

first: Kentaro

last: Aono

first: Junichi

last: Matsumoto

first: Mitsuhisa

last: Koga

first: Koji

last: Tominaga

first: Rina

last: Miyoshi

first: Yuna

last: Sakai

first: Yasufumi

last: Kataoka

first: Atsushi

last: Yamauchi


title: Regulatory variants in a novel distal enhancer regulate the expression of CYP3A4 and CYP3A5: ATAC-Seq and 4C data from human hepatocytes [ATAC-seq]

first: Danxin

last: Wang

summary: The cytochrome P450 3As (CYP3As) are abundantly expressed in the liver and metabolize many commonly prescribed medications. Their expression is highly variable between individuals with little known genetic cause. Despite extensive investigation, cis-acting genetic elements that control the expression of CYP3As remain uncharacterized. Using chromatin conformation capture (4C assays), we detected reciprocal interaction between a distal regulatory region (DDR) and the CYP3A4 promoter. The DRR colocalizes with a variety of enhancer marks and was found to promote transcription in reporter assays. CRISPR-mediated knockout of the DRR decreased expression of CYP3A4, CYP3A5, and CYP3A7, supporting its role as a shared enhancer regulating the expression of three CYP3A genes. Here we provided data generated from ATAC-Seq analysis of human primary hepatocytes originating from both black and white donors.

overall_design: ATAC-Seq for human primary hepatocytes generated from both black and white donors.

first: Joseph

middle: M

last: Collins


title: The lysine demethylase LSD1 controls the balance between inflammatory and antiviral responses against coronaviruses

city: Milan

first: Luca

last: Mazzarella

state: M

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: IEO European Institute of Oncology IRCCS

summary:
Innate responses to coronavirus are highly cell-specific and remain to date incompletely understood. Tissue-resident macrophages, which are infected by SARS-CoV2 in patients but inconsistently in vitro, exert critical but conflicting effects by secreting both anti-viral type I Interferons and tissue-damaging inflammatory cytokines. Steroids, the only class of host-targeting drugs approved for Covid19, indiscriminately suppress both responses, possibly impairing viral clearance. Here we set up in vitro culture systems with the prototypical murine coronavirus MHV that allow to separately investigate cell-intrinsic and -extrinsic proinflammatory and antiviral activities. We then studied the role of the lysine-demethylase LSD1, previously implicated in innate responses in cancer. We show that the NF-κB-dependent inflammatory response is selectively inhibited by ablating LSD1 with negligible impact on antiviral interferon response. LSD1 ablation additionally unleashed an interferon-independent antiviral response and blocked viral egress through the lysosomal pathway. A cell-intrinsic antiviral and anti-inflammatory activity of LSD1 inhibition was confirmed on in vitro and a recently developed aerosolized in vivo model of human SARS-COV2 infection.
These results show that LSD1 controls innate responses against coronaviruses at multiple levels and provide a mechanistic rationale for repurposing LSD1 inhibitors, a class of drugs extensively studied in oncology, for Covid-19 treatment.

overall_design:
Transcriptional evaluation of the impact of DDP in bone marrow-derived macrophages infected with Murine hepatitis virus strain A59 and on aerosolized mice infected with SARS-COV2 infection.

Comparative gene expression profiling analysis of RNA-seq data for lung cells derived from Sars-CoV2 delta variant infected mice.

first: Emanuele

last: Bonetti

first: Valeria

last: Fumagalli

first: Fabio

last: Santoro

first: Roberto

last: Ravasio


title: RNA sequencing to identify UNC-25-regulated genes in C. elegans defense against pathogen P. aeruginosa infection

city: Changsha

first: Xibin

last: Tian

address: Tianma Road

institute: Hunan University

summary:
Purpose: To gain molecular insights on how UNC-25 regulates C. elegans innate immunity, we used RNA sequencing to profile gene expression in unc-25(e156) animals relative to wild-type animals with or without P. aeruginosa (PA14) infection.
Methods: Synchronized L1 worms were placed onto NGM plates seeded with E. coli OP50 and grown at 20 °C until the L4 stage. Worms were washed off the plates, collected with M9 solution and subsequently transferred to modified NGM plates containing E. coli OP50 or P. aeruginosa PA14 for 24 h at 25 °C. Then, the animals were washed off the plates with M9 solution and frozen in TRIzol (Transgen, ER501-01, China) with liquid nitrogen. Total RNA was isolated using a TransZol Up Plus RNA kit (Transgen, ER501-01, China).
Results: RNA seq analyses shows enriched and signficant changed immune genes, neuropeptides, transcription factors and pathways that are dependent of GABA signaling.
Conclusion: Our studies uncover that GABA signaling enhance the resistence to pathogen induced killing.

overall_design: Three replicates of four groups of RNA samples (unc-25(e156) and wild-type L4-stage animals with or without exposure to P. aeruginosa for 24 hrs) were sequenced. Gene expression was compared between groups to identify UNC-25-regulated genes under uninfection or infection conditions.

first: Junqiang

last: Liu

first: Haijun

last: Tu


title: Targeting IRAK1-S100A9 Axis Overcomes the Resistance to Paclitaxel in Nasopharyngeal Carcinoma

first: lizhen

last: liu

address: Panyu

institute: Sun Yat-sen University cancer center

summary: Resistance to chemotherapy is one of the main causes of mortality in late-stage nasopharyngeal carcinoma (NPC) with dismal prognosis and limited therapeutic options. Therefore, there is an urgent need to exploit new therapeutic targets to improve current clinical outcome. In this study, we identified pacritinib, a late stage clinical drug targeting IRAK1, as a sensitizer to resistance of paclitaxel in NPC. Through analysis of both chemoresistant cellular models and clinical samples of relapse and metastasis, we have shown that aberrant IRAK1-S100A9 deregulation is correlated with chemoresistance and prognosticates poor clinical outcome. Further functional studies demonstrated that genetic and pharmacological inhibition of IRAK1-S100A9 axis overcomes the resistance to paclitaxel and combination of pacritinib with paclitaxel exhibited superior anti-tumor effect in both in vivo and in vitro models.

overall_design: 1.RNA-seq for S26 patental (S26 P) cells, S26 resistant cells (S26 R) and S26 R cells treated with pacritinib (Pac) (duplicate). 2.RNA-seq for 22 human tissue samples including 8 NPC samples with complete response (CR) and 14 samples with partially response (PR) to paclitaxel-based chemotherapy.

first: Lizhen

first: Sailan

first: Peng

last: Deng

first: Qiang

last: Yu

first: Haiqiang

last: Mai

first: Jing

last: Tan


title: Inflammatory Cytokines Induce Sustained CTLA-4 Cell Surface Expression on Human MAIT Cells

status: Public on Jun 23 2023

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Mucosal-associated invariant T (MAIT) cells acquire effector function in response to proinflammatory signals, which synergize with TCR-mediated signals. We asked if cell-intrinsic regulatory mechanisms exist to curtail MAIT cell effector function akin to the activation-induced expression of inhibitory receptors by conventional T cells. We examined human MAIT cells from blood and oral mucosal tissues by RNA sequencing and found differential expression of immunoregulatory genes, including CTLA-4, by MAIT cells isolated from tissue. Using an ex vivo experimental setup, we demonstrate that inflammatory cytokines were sufficient to induce CTLA-4 expression on the MAIT cell surface in the absence of TCR signals. Even brief exposure to the cytokines IL-12, IL-15, and IL-18 was sufficient for sustained CTLA-4 expression by MAIT cells. These data suggest that control of CTLA-4 expression is fundamentally different between MAIT cells and conventional T cells. We propose that this mechanism serves to limit MAIT cell-mediated tissue damage.

overall_design: CD8+MAIT cells were sorted from tissue or blood and analyzed via RNA sequencing from patients. Tissue samples were scored for inflammation

first: Julia

middle: D

last: Berkson

first: Chloe

middle: K

last: Slichter

first: Hannah

last: DeBerg

first: Martha

last: Delaney

first: Amanda

middle: S

last: Woodward-Davis

first: Nicholas

middle: J

last: Maurice

first: Yi

last: Lwo

first: Alex

last: Ko

first: Jessica

last: Hsu

first: Yu-Wen

last: Chiu

first: Peter

last: Linsley

first: Douglas

last: Dixon

first: Martin

last: Prlic


title: Glucocorticoids regulate murine megakaryocyte transcriptome

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Total RNA from in vitro-differentiated murine megakaryocytes incubated for 6hr with 100nM dexamethasone or its vehicle was analyzed using a genome-wide expression microarray using Affymetrix Mouse Transcriptome Array 1.0 arrays.

overall_design: 6 dexamethasone-treated samples + 6 vehicle-treated samples = 12 samples.

first: Matias

last: Godzielski

first: John

last: Cidlowski


title: Loss of endothelial cell heterogeneity in arteries after obesogenic diet

city: Charlottesville

first: Brant

middle: E

last: Isakson

state: Virginia

department: Cardiovascular Research Center

institute: University of Virginia


title: αKG-driven RNA polymerase II transcription of cyclin D1 licenses malic enzyme 2 to promote cell cycle progression

city: beijing

first: zhenxi

last: zhang

address: Dongdan Santiao No. 5

institute: PUMC

summary: Increased metabolic activity usually provides energy and nutrients for biomass synthesis and is indispensable for the progression of the cell cycle. Here, we found an unexpected role for α-ketoglutarate (αKG) generation in regulating cell cycle gene transcription. A reduction in cellular αKG levels triggered by malic enzyme 2 (ME2) or isocitrate dehydrogenase 1 (IDH1) depletion leads to a pronounced arrest in G1 phase, while αKG supplementation promotes cell cycle progression. Mechanistically, αKG directly binds to RNA polymerase II (RNAPII), increasing the level of RNAPII binding to the cyclin D1 gene promoter, consequently enhancing cyclin D1 transcription. Notably, αKG addition is sufficient to restore cyclin D1 expression in ME2- or IDH1- depleted cells, facilitating cell cycle progression and proliferation in these cells. Therefore, our findings reveal a previously unappreciated function of αKG in gene transcriptional regulation and cell cycle control.

overall_design: The sample contains siCtrl, siME2 and siME2+ α KG cells

first: yang

last: yanting

first: zhang

last: zhenxi

first: li

last: wei


title: Complement C3aR depletion reverses HIF-1α induced metabolic impairment and improves microglial phagocytic and barrier function in response to Aβ pathology.

city: HOUSTON

first: chuangye

last: Qi

state: Texas

address: One plaza

department: Huffington Center

institute: Baylor College of Medicine

summary: Complement C3aR is primarily expressed in microglial cells in the brain. Our study found elevated expression of C3aR in microglia in Alzheimer's disease. To understand the underlying molecular mechanism, we sorted microglia based on their C3aR expression from 9-month-old wild-type and APP-KI mice. Through RNA-seq analysis, we identified metabolic perturbations in C3aR-positive microglia from 9-month-old APP-KI mice. Furthermore, we performed RNA-seq on sorted microglial cells from wild-type, C3aR knockout, APP-KI, and APP-KI;C3aR knockout mice. This analysis revealed a dampening of metabolic dysfunction in the absence of C3aR.

overall_design: Bulk RNA-seq of sorted microglia from the brains of 9-month-old WT and APP-KI based on C3aR expression; and bulk RNA-seq of sorted microglial cells from 9-month-old WT, C3aRKO, APP-KI  and APP-KI;C3aRKO mice.

first: Hui

last: Zheng


title: Copy number alteration burden differentially impacts immune profiles and molecular features of hepatocellular carcinoma

city: Barcelona

first: Roser

last: Pinyol

address: C/Rosselló

country: Spain

institute: IDIBAPS

summary: Here, we show that in hepatocellular carcinoma (HCC, the most prevalent form of primary liver cancer), tumours with a high burden of broad genomic alterations presented immune exclusion. On the other hand, HCC tumours with a reduced rate of broad genomic alterations were enriched in the HCC immune class, exhibited inflammatory traits and were cleared from CTNNB1 mutations. Overall, we propose that, in HCC, the acquisition of high-levels of broad copy number alterations might be implicated in the development of immune evasion, and that tumours presenting a reduced rate of these broad alterations display an immune profile which may indicate a favourable response to immunotherapies.

overall_design:
Genomic DNA extracted from human hepatocellular carcinomas/adjacent tissues was genotyped using HumanOmniExpressExome-8v1_A (Illumina)
To investigate the impact of the burdens of broad and focal copy-number alterations (CNAs) on the molecular and immune features of HCC, we conducted SNP array analysis (HumanOmniExpressExome-8v1_A from Illumina) on 150 HCC tumor samples and their corresponding non-tumour adjacent liver tissues.  We used these data to compute CNA segments per sample and to generate scores capturing the burden of broad and focal CNAs (those spanning >=50% and <50% of a chromosome arm, respectively). We then evaluated differences in tumor molecular features associated with these scores (using already published mutation profiles, clinical and transcriptomic data).

first: Bassaganyas

last: Laia

first: Pinyol

last: Roser

first: Esteban-Fabró

last: Roger


title: Molecular Adaptation to Ambient Salinity Oscillations in Greater Amberjack (Seriola dumerili): Implications to Aquaculture

city: Shenzhen

first: Yuqi

last: Liu

address: 66 Gongchang Road, Guangming District

institute: Sun yat-sen university

summary: Ambient salinity is one of the crucial abiotic factors that poses substantial impacts on fish growth, development and reproduction. Greater amberjack (Seriola dumerili) is of high economic value because, and its reproduction and survival are sensitive to water salinity. To better understand the molecular adaptive mechanism to salinity fluctuations in greater amberjack, we performed comparative transcriptome analysis for gill and kidney between the optimum salinity (30 ppt, CK) and undesired regimes (10 and 40 ppt). For the gill, the skeletal development was provoked upon either hypo- or hyper-salinity stimuli, and the development of pronephros, as well as vascular endothelial cells and cortisol-mediated mitochondria-rich cell, was activated in response to the salinity alterations in kidney. These enhancements may encourage the maintenance of the gill and kidney structures and alleviate the salinity-induced damage. Ion channels NKCC1 and CFTR and the transporters for ammonium and other substances were highly upregulated in the gills and kidney, respectively, which act important roles in the osmoregulation of greater amberjack. More important, undesirable alterations of ambient salinity were found to pose adverse impacts on the immune function of greater amberjack, which may increase the risk of pathogen infection and reduce the security and yield of aquaculture of greater amberjack. In addition, deviation from the optimum salinity condition may result in undesirable uptake and accumulation of environmental toxins in greater amberjack, which attracts further attention to the food safety. Collectively, these novel findings advance our knowledge on adaptative mechanisms to ambient salinity oscillations in greater amberjack and provide a theoretical guidance for the optimal breeding mode for the aquaculture of greater amberjack.

overall_design: To investigate the molecular adaptive mechanism to salinity fluctuation in greater amberjack, we performed comparative transcriptome analysis for gill and kidney between the optimum salinity (30 ppt, CK) and undesired regimes (10 and 40 ppt) for 72 hours and conducted transcriptome-wide bulk RNA-seq of the treated juvenile amberjack.

first: Yuchen

last: Yang


title: Gene expression profiling of total RNA isolated from hiPSC-derived DPPCs, hiPSC-derived NCSCs, cultured hDPC spheres, cultured hDPC

city: Seoul

first: Jin Yong

last: Kim

address: 101 Daehak-ro, Jongno-gu

department: Department of Dermatology

country: South Korea

institute: Seoul National University College of Medicine

summary: During development, dermal papilla precursor cells (DPPCs) initiate embryonic hair follicle (HF) formation with epidermal placode cells. Obtaining DPPCs with trichogenic ability is critical for human HF regeneration because dermal papilla cells (DPCs) rapidly loseDuring development, dermal papilla precursor cells (DPPCs) initiate embryonic hair follicle (HF) formation with epidermal placode cells. Obtaining DPPCs with trichogenic ability is critical for human HF regeneration because dermal papilla cells (DPCs) rapidly lose their trichogenic ability in culture. Here, we generated trichogenic DPPCs from human induced pluripotent stem cells (iPSCs) via neural crest stem cells (NCSCs), based on the developmental evidence at the hair placode stage. SDC1+CD133− cells showed signature DP gene expression, spontaneous sphere formation and represented intermediate population in the differentiation way from NCSCs to DPCs. hiPSC-derived DPPCs generated HF equivalents in vitro and reconstituted de novo human HFs in vivo combined with hiPSC-derived epithelial stem cells. Remarkably, trichogenic ability of DPPC was only proven in the specific time window, providing insights into the loss of trichogenicity in cultured DPC. Thus, this study provides an in vitro model for studying DPC development and biology.

overall_design: Generation of trichogenic dermal papilla precursor cells from human induced pluripotent stem cells for human hair follicle regeneration

first: Bo Mi

last: Kang

first: Ohsang

last: Kwon


title: Effects of TMEM216 on the transcriptomes of E12 mice embryos

city: Qingdao

first: ying

middle: ying

last: wang

address: 72 Binhai RD

institute: Shandong university

summary: RNA-seq analysis of tissues from E12 Tmem216+/+ and Tmem216-/- embryos were performed to identify the mechanism underlying TMEM216 affecting ciliogenesis. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten. Our results demonstrate that TMEM216 deficiency impairs Hh signaling pathway of mice.

overall_design: mRNA profiles of E12 Tmem216+/+ and Tmem216-/-  embryos

first: Yingying

last: Wang


title: Pyroptosis initiates inflammatory macrophage-mediated cytokine storms in COVID-19 patients

city: Hefei

first: Jinghe

last: Zhang

state: Anhui

address: Huangshan Road 443

institute: University of Science and Technology of China

summary: In this dataset contains 3 cases of transcriptome information from 3 normal lung tissue, they respectively from lung squamous carcinoma tissue adjacent to carcinoma (C5), pneumonia lesions (C55) and lung bronchiectasis disease (C56), 6 cases from lung tissue samples of COVID - 19 patients (S528, S527, S59, S519, S52, S523).

overall_design: Pulmonary mRNA profiles of 6 COVID patients and 3 healthy donors.

first: Haibo

last: Wu


title: Gene expression profile at single cell level of mouse submandibular glands (SMG) after transient activation of Hedgehog signaling

city: College Station

first: Fei

address: 206 Olsen Blvd

institute: Texas A&M University Health Science Center

summary: Transient activation of Hedgehog signaling rescues radiation damage of SMG. We used single cell RNA sequencing (scRNA-seq) to analyze effects of transient activation of Hedgehog signaling on the diversity of SMG cells and their paracrine/juxtacrine interactions.

overall_design: Hedgehog signaling in SMGs of adult male C57BL/6 mice was transiently activated by intra-gland injection of Smoothened agonist (SAG), and SMGs were collected 4 days later and analyzed using scRNAseq.

first: Qingguo

last: Zhao

first: Linying

first: Simin

last: Pan


title: Tdrd3-null mice show post-transcriptional and behavioral impairments associated with neurogenesis and synaptic plasticity [RNA-Seq]

city: Baltimore

first: Xingliang

last: Zhu

state: Maryland

address: 251 Bayview Blvd

institute: National Institute on Aging, National Institutes of Health

summary: To study the function of Tdrd3 in the brain.

overall_design: We then performed gene expression profiling analysis using 2 replicates for Tdrd3 and WT, 3 repeats for Top3b and WT.

first: Yutong

last: Xue

first: Seung

last: Lee


title: Tdrd3-null mice show post-transcriptional and behavioral impairments associated with neurogenesis and synaptic plasticity [PRO-Seq]

summary: To study the post-transcriptional regulation of Tdrd3 in the brain.

overall_design: We then performed nascent RNA PROseq analysis using 2 replicates for Tdrd3 and WT


title: An advanced ADSC therapy for keloid prevention using identification of functional subgroups by single cell transcriptomic analysis

city: tianjin

first: xiaoxi

last: song

address: pudongjiedao

institute: tasly

summary: The clinical treatments for keloids  are poor efficacy,There is evidence forADSCs acting as a physiological response to local injury or as rejuvenating mechanisms.But the use of exogenous ADSCs fulfill the general accepted criteria for cell-based therapies, but still need further investigations into their efficiency.  In this study, we firstly employed microarray techniques and bioinformatics analysis to screen for whole transcriptome differences involved in keloids, enabling the identification of DEGs and functional molecular associated with keloids mechanism. Secondly, we developed functional clustering of stem cells and marker genes of each cluster through single cell sequencing of ADSCs from healthy adults and pigs by bioinformatics analysis. Finally, we identified ADSC subpopulations with KK and KF therapeutic potential, respectively. anti-fibrotic transcriptomic identification and quantitative clustering was performed, and the function of specific ADSCs cluster was investigated in the hypertrophic scar prophylaxis using the miniature pig model. This study might open the way to a new era of mesenchymal stem cells in the treatment of keloids for promising therapeutic advancements.

overall_design: pADSCs were isolated from Bama miniature pigs adipose tissue,and analyzed using scRNAseq.

first: Shuang

last: Ma

first: Pengfei

last: Han

first: Xiaoxi

last: Song


title: Transcriptome analysis reveals GmZF351-affected gene expression in leaf and root.

city: Beijing

first: Wei

last: Wei

address: Chaoyang District, Beichen West Road, Campus #1, No 2

institute: Chinese Academy of Science

summary: GmZF351 has previously been characterized as a seed preferred gene participating mainly in oil accumulation. Here we report that over-expression of GmZF351 confers drought and salt tolerance in transgenic soybean seedlings. When soybean seedlings grew to V1 stage, leaves and roots were cut for RNA sequencing. Transcriptome analysis shows that GmZF351 regulates expression of downstream genes related to abiotic stress process.

overall_design: GmZF351 overexpressing soybean line OE-34 and the control plants Jack were grown in pots. When the first tri-foliate leaves were fully expanded (V1 stage), leaves and roots of transgenic and control plants were cut for RNA extraction. For each sample, three biological repeats were set.


title: Endothelial TIE1 restricts angiogenic sprouting to coordinate vein assembly in synergy with its homologue TIE2

city: Suzhou

first: Yulong

last: He

address: 199 Ren-Ai Road

institute: Soochow University

summary: To investigate the receptor tyrosine kinase TIE1 in the regulation of vein development, we generated Tie1 knockout mouse line in which Tie1 expression is completely ablated.

overall_design: Comparative gene expression profiling  by RNA-seq analysis of the skin samples from Tie1 knockout and control mice.

first: Xudong

last: Cao

first: Taotao

last: Li

first: Beibei

last: Xu


title: The MADS-box transcription factor AoRLMA is involved in the regulation of mycelium morphogenesis, conidial production, cell wall integrity and pathogenic processes in Arthrobotrys oligospora

city: Kunming

first: Jiangliu

last: Yang

address: No. 2, Cuihu North Road, Wuhua District, Kunming

institute: Yunnan University

summary: As a dynamic structure with a barrier between the cell and the outside world, maintenance of cell wall integrity (CWI) is important for fungal growth, development and pathogenicity processes. Here we characterized a MADS-box transcription factor RlmA (AoRlmA) downstream of the CWI regulatory pathway in the nematode-trapping fungus Arthrobotrys oligospora. Deletion of  AorlmA caused a reduction in mycelial growth and the number of nuclei, and significant downregulation of transcript levels of genes related to nucleus synthesis and DNA damage repair, such as rad3, spo11, and rad25. Meanwhile, the ΔAorlmA mutant strains showed a significant reduction in spore production compared with the wild-type (WT) strain, and the transcript levels of sporulation-related genes was downregulated in the ΔAorlmA mutant during the early and middle stages of condiation, such as flbA, medA, and vosA. Meanwhile, the mycelial cell wall of the ΔAorlmA mutant strain showed breakage. Also, the transcript levels of genes related to cell wall synthesis were significantly down-regulated in the mutant strain compared to the WT strain, and the mutant strain was more sensitive to stresses of cell wall synthesis disruptors, oxidative stress and osmotic stress than the WT strain. Compared with the WT strain, the ΔAorlmA mutant strain not only had a reduced number of traps and nematicidal ability, but also, the shape of the traps of the mutants has also changed. In addition, In addition, AoRlmA also regulates autophagy and endocytosis. Transcriptome analysis of ΔAorlmA mutant strains showed that AorlmA regulates redox, cell wall synthesis, DNA replication and damage repair, and pathogenic processes. Metabolomic analysis showed that AorlmA is involved in the biosynthesis of secondary metabolites of A. oligospora. To summarise, our data suggest that AorlmA is involved in growth, sporulation, spore germination, maintenance of cell wall integrity, DNA replication and damage repair, pathogenesis, autophagy and secondary metabolite biosynthesis processes.

overall_design: RNA-seq analysis between six wild-type samples and six ΔAorlmA mutant samples, with three biological replicates per sample, and prediction of multiple cytological processes that may affect trap formation in Arthrobotrys oligospora.

first: Wenjie

last: Wang

first: Jinkui


title: PIF3 regulates different genes in the endosperm and embryo

city: Geneva

first: Urszula

last: Piskurewicz

address: 30, Quai Ernest-Ansermet

department: 30, Quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

summary:
To identify the genes regulated by PIF3 under higher temperatures in the endosperm and embryo, we performed an RNA-seq analysis. We compared the transcriptome of WT and pif3 endosperm from seeds imbibed for 24h and 48h at 30˚C, which is a time when WT and pif3 seeds have not yet germinated
We also compared the transcriptome of WT and pif3 embryos, after removing their endosperm 4h upon seed imbibition, cultured for 24h and 48h at 30˚C, which are times when WT and pif3 hypocotyl length was comparable

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and pif3 endosperm and embryo tissues.

first: Mayumi

last: Iwasaki

first: Luis

last: Lopez-Molina


title: Gene expression profile at single cell level of mouse submandibular glands (SMG)

first: Fei

last: Liu

summary: SMG contains multiple types of cells with complex paracrine/juxtacrine interactions. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of SMG cells and their paracrine/juxtacrine interactions.

overall_design: SMGs were collected from nontreated adult male C57BL/6 mice and analyzed using scRNAseq.

first: Qingguo

last: Zhao

first: Linying

last: Zhang

first: Simin

last: Pan


title: Effect of depleting GNB1L on PIKK mRNA levels to explore the regulatory mechanism of GNB1L on PIKK proteins

first: Fuwen

last: Yao

address: Sungang Road 3001

institute: Shenzhen Second People's Hospital

summary: Our screens identified GNB1L, a high-confidence hit, as a novel positive regulator of DDR signaling. We therefore generated HEK293A-GNB1L-dTAG cells which the GNB1L-dTAG-HA protein decreased to markedly lower levels in the presence of dTAGv-1 than that in cells treated with dTAG-NEG , we next examined whether depletion of GNB1L affects DDR signaling. Notably, depletion of GNB1L diminished all IR-induced DDR signaling. Moreover, depletion of GNB1L also significantly reduced basal DDR signaling as well as PIKKs. To determine whether GNB1L depletion specifically affects PIKKs instead of other DDR factors, we carried out label-free quantitative proteomics analysis by comparing the proteomes in NEG-treated versus in dTAGv-1-treated GNB1L-dTAG cells. The data showed that GNB1L depletion specifically reduced PIKK kinases and ATRIP rather than other DDR factors. Obviously, PIKK kinases, ATRIP and mTOR are major downregulated substrates affected by GNB1L depletion. Therefore, we performed RNA-seq to rule out the possibility that GNB1L regulates PIKK protein levels via transcriptional regulation. The differentially expressed genes (DEGs) as well as the GO analysis confirmed that depleting GNB1L had no effect on PIKK mRNA levels . These data suggested that GNB1L specifically regulates PIKK protein levels instead of other DDR factors.

overall_design: To investigate whether depletion of GNB1L affects PIKK mRNA levels therefore influencing PIKK proteins, we generated HEK293A-GNB1L-dTAG cells which the GNB1L-dTAG-HA protein decreased to markedly lower levels in the presence of dTAGv-1 than that in cells treated with dTAG-NEG. HEK293A-GNB1L-dTAG cells were treated with 1 μM NEG or dTAGv-1 for 3 days followed by RNA extraction with kit (Qiagen; 217004). We prepared 3 replicates for each group. All the following mRNA sequencing processes until the generation of FASTQ files were completed by Cancer Genomics Center at the University of Texas Health Science Center at Houston. Total RNA was extracted from each condtion and RNAseq was performed and analysed for the differentially expressed genes (DEGs) as well as the GO analysis.

first: Min

last: Huang


title: Mitochondrial Activity in Dnmt3aR878H Hematopoietic Stem and Progenitor Cells Drives Their Selective Advantage and Alters Response to Extrinsic Signaling

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: Maine

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

summary: Hematopoietic stem cells (HSCs) with certain somatic mutations, most commonly in the DNA methyltransferase DNMT3A, gain a clonal growth advantage leading to the development of clonal hematopoiesis (CH). The distinct functional differences that allow DNMT3A-mutant HSCs to gain a fitness advantage and outcompete wild-type HSC in the context of aging are not fully elucidated. We recently discovered that HSC aging is initiated by decline in local production of insulin-like growth factor 1 (IGF1). Here, we used a mouse model of DNMT3A-mutant CH (Dnmt3aR878H/+) to investigate the extent to which decline in IGF1 alters the selective advantage of Dnmt3aR878H/+ HSCs. Upon transplant into IGF1-deficient recipient mice, Dnmt3aR878H/+ HSCs gained enhanced selective advantage over wild-type HSCs and maintained lineage balanced blood production. As IGF1/mTOR signaling is well understood to regulate energy metabolism, we investigated underlying metabolic differences between Dnmt3aR878H/+ and wild-type HSCs. Dnmt3aR878H/+ HSPCs had similar glycolytic capacity as wild-type HSCs but enhanced mitochondrial reserve capacity and mitochondrial activation potential. To evaluate whether mitochondrial function is a targetable dependency of Dnmt3aR878H/+ HSCs, we administered the mitochondrial-targeted molecule MitoQ resulting in the depletion of their mitochondrial reserve capacity. We find that MitoQ reduces the competitive advantage of Dnmt3aR878H/+ hematopoiesis. To identify the mechanism(s) by which MitoQ alters Dnmt3aR878H/+ phenotypic expansion we evaluated transcriptional changes after MitoQ treatment and find altered response to Igf1/mTOR signaling compared to wild-type HSC. The altered response to Igf1/mTOR signaling in part mediates the Dnmt3aR878H/+ hematopoietic selective advantage. Taken together, our work supports that mitochondrial metabolic regulation is a key mechanism by which DNMT3A-mutant HSCs gain a selective advantage. Targeting this mechanism may maintain polyclonal hematopoiesis during aging and reduce the risk of CH-associated disease.

overall_design: Hematopoietic stem and progenitor cells from 4 Dnmt3aMutant mice and 4 MxCre control mice were treated with MitoQ  and enriched for LSK followed by single cell RNA-seq.

first: Kira

last: Young


title: Progesterone receptor mediates ovulatory transcription through RUNX transcription factor interactions and chromatin remodelling

city: Adelaide

first: Thao

last: Dinh

state: South Australia

address: North Terrace

institute: University of Adelaide

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

overall_design: Refer to individual Series


title: GR and BRG1 cistromes of murine primary bone marrow derived macrophages treated with LPS and Dex+LPS [ChIP-seq]

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

summary: We mapped the genome wide binding profile of the chromatin remodeller BRG1 in wild type bone marrow derived macrophages (BMDMs) after 3h LPS and LPS plus Dex treatment by ChIPseq. Additionally, we profiled the GR cistrome in Dex + LPS-treated BMDMs after 3h treatment by ChIPseq.

overall_design: We performed ChIP sequencing against GR in BMDMs treated for 3 hours with 100 ng/ml LPS and 1 mM Dex.  Furthermore, we profiled the genomic occupancy of BRG1 in BMDMs treated with 100 ng/ml LPS or 100 ng/ml LPS plus 1 mM Dex for 3 hours. Two biological replicates were submitted for sequencing for each epitope and treatment conditions.

first: Aikaterini

last: Mechtidou

first: Celine

last: Jouffe

first: Nina

middle: H

last: Uhlenhaut


title: RNA-seq analysis of axillary buds of tomato WT, 156OE and rSBP15OE plants

city: Piracicaba

first: Diego

last: Brito

state: São Paulo

address: Av. Padua Dias, 11

department: ESALQ

country: Brazil

institute: University of São Paulo

summary: Shoot branching (SB) is an undesired trait in many crops, including tomato, as it may redirect assimilates away from developing flowers and fruits. Better understanding of the molecular mechanisms underlying bud arrest could help to generate plants with improved architecture and reduced lateral SB. We have previously shown that overexpression of the microRNA156 (miR156) in tomato increases the number of side branches; here, we have characterized in detail how the miR156/SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL/SBP) hub modulates axillary bud (AB) development by connecting multiple phytohormones with known SB-associated genes. We have demonstrated that miR156-targeted SlSBPs modulate SB by regulating the action of distinct hormones, such as gibberellin, auxin and abscisic acid (ABA). Our results showed that plants overexpressing a miR156-resistant version of SlSBP15 (rSBP15) displayed arrest ABs throughout development.

overall_design: To unravel the underlying molecular mechanisms within buds, we conducted NGS-based transcriptomics analyses (RNA-Seq) to compare the transcriptome in the ABs from 25-dpg WT (MT), 156-OE, and rSBP15 plants.

middle: P

first: Fabio

last: Nogueira


title: Chromatin accessibility profiles of murine primary bone marrow derived maccrophages treated with LPS or LPS and Dex [ATAC-seq]

summary: We mapped the open chromatin regions in wild type LPS and LPS plus Dex treated murine bone marrow derived macrophages (BMDMs).

overall_design: BMDMs were treated for 3 hours with 100 ng/ml LPS plus 1 mM Dex or 3h with 100ng/ml LPS in combination with 0.1% EtOH as vehicle control. Four biological replicates were submitted for sequencing for each treatment condition.

first: Fillipo

last: Cernilogar

first: Gunnar

last: Schotta


title: Tdrd3-null mice show post-transcriptional and behavioral impairments associated with neurogenesis and synaptic plasticity

first: Xingliang

last: Zhu


title: Non-cell-autonomous regulation of interneuron specification mediated by extracellular vesicles

city: Planegg-Martinsried

first: Filippo M.

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

summary: We performed RNA-seq analysis on neural progenitor cells (NPCs) acutely treated (12 hours) with Extracellular vesicles (EVs) purified by the conditioned medium of dorsally patterned and ventrally patterned  human cerebral organoids originated from control-  or E370K mutant- iPSCs cells. The aim of this experiments was to dissect if EV content leads to transcriptional changes on receiving cells.

first: Rossella

last: Di Giamo

first: Silvia

last: Cappello

first: Fabrizia

last: Pipicelli


title: Evaluating the role of cardiac fibroblast p53 in governing the pathologic remodeling response to pressure overload in the heart

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary:
Cardiomyopathy is characterized by the deposition of extracellular matrix by activated resident cardiac fibroblasts, called myofibroblasts. A current lack of therapeutic approaches to blunt the development of pathological fibrosis and ventricle chamber stiffening that ultimately leads to heart failure necessitates the investigation of the mechanisms that underlie myofibroblast activation. We previously observed that increased degradation of p53 occurs during the cardiac fibroblast expansion phase that acutely follows pressure overload. We created tissue-specific mouse models to delete p53 in quiescent resident cardiac fibroblasts and in activated myofibroblasts, then evaluated consequences to cardiac physiology, cellular biology, and fibrotic remodeling.  We then performed RNA sequencing to further elucidate the effects of p53 deletion in cardiac fibroblasts on gene expression at the single cell level.  We confirmed these results with a series of in vitro experiments in primary mouse cardiac fibroblasts.
Results - Here, we demonstrate that p53 knockout in resident cardiac fibroblasts significantly accelerates proliferation and temporarily insulates the heart from fibrotic remodeling and functional decline in response to pressure overload, but ultimately results in a more deleterious phenotype than in wildtype animals.  Conversely, p53 knockout in activated myofibroblasts does not result in a delay in functional loss, and is uniformly deleterious to the heart.  Single-cell RNA sequencing revealed that p53 knockout is associated with the development of constitutively mitotic fibroblasts, and increased recruitment of fibroblasts into a main activation trajectory that involves four states: quiescent, early transitional, late transitional, and fully activated.  A quiescent, functionally specialized vascular support fibroblast population that is ubiquitous in the wildtype animal is additionally recruited into activation in the p53 knockout condition, resulting in the eventual extreme functional decline seen in these animals.  In vitro experimentation using viral deletion of p53 supports these findings - quiescent fibroblasts lacking p53 are resistant to activation, but activated myofibroblasts lacking p53 do not reverse their activation.  This was found to be due to parallel hyperactivation of Cdkn2a/Rb1-mediated G1 cell cycle arrest in the p53 knockout condition, which was supported by in vivo studies.
Conclusions - These data establish p53 as a major regulator of the myofibroblast activation response to pressure overload.  Moreover, the single-cell studies establish an activation trajectory for resident cardiac fibroblasts, and elucidate the fundamental importance of clinical intervention prior to irreversible myofibroblast activation seen in chronic stages of pressure overload.

overall_design: 2 CF-p53WT, 2 CF-p53KO (Tcf21:Cre driver)

first: Ryan

last: Burke

first: Janet

last: Lighthouse

first: Eric

last: Small


title: Benzene toxicity

city: Louisville

first: Sanjay

last: Srivastava

state: Kentucky

address: 302 E. Muhammad Ali

department: Medicine

institute: University of Louisville

summary: Benzene is abundant air pollutant that has been associated with several diseases in particularly cardiovascular disease.  Despite of known health risks, effects of benzene on cardiovascular health is not well studied. In this study, in a well-controlled animal model, we are characterizing how benzene influences cardiovascular system.

overall_design: Forteen weeks old male C57Bl/6J mice on Normal Chow were exposed to 50ppm benzene (6hr/day, 5 days a week) for 6 weeks. Control group was exposed to carbon and HEPA filters purified air.  Sequencing of mRNAs was performed on lungs and liver tissues of benzene exposed and air contol mice.

first: Marina

middle: V

last: Malovichko

first: Shizuka

last: Uchida


title: A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation

first: Yue

last: Huo

address: Dongcheng District, Dongdan 3 Tiao 5 Hao

department: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

summary:
Background:
Cellular RNA binding proteins (RBPs) have multiple roles in post-transcriptional control, and some have been shown to bind DNA. However, the global localization and the general chromatin-binding ability of RBPs have not been well-characterized and remain undefined in hematopoietic cells.
Results:
We first provided a full view of RBPs’ distribution pattern in nucleus and screened for chromatin-enriched RBPs (Che-RBPs) in different human cells. Subsequently, by generating ChIP-seq, CLIP-seq and RNA-seq datasets and conducting combined analysis, the transcriptional regulatory potential of certain hematopoietic Che-RBPs were predicted and from which quaking (QKI5) emerged as a potential transcriptional activator during monocytic differentiation. QKI5 was over-represented in gene promoter regions, independent of RNA or transcription factors. Furthermore, promoter-occupied QKI5 activated the transcription of several critical monocytic differentiation-associated genes, including CXCL2, IL16 and PTPN6. Finally, we showed that the differentiation-promoting activity of QKI5 is largely dependent on CXCL2, irrespective of its RNA-binding capacity.
Conclusions:
Our study indicates that Che-RBPs are versatile factors that orchestrate gene expression in different cellular contexts, and identifies QKI5, a classic RBP regulating RNA processing, as a novel transcriptional activator during monocytic differentiation.

overall_design:
H3K4me3 and Pol II ChIP-seq with input in untreated THP-1 cells and QKI5 knockdown THP-1 cells.  QKI5 CLIP-seq with input in untreated THP-1 cells and QKI5 knockdown THP-1 cells.
Please note that each processed data was generated from both replicates and is linked to the corresponding *rep1 records.

last: Ren

first: Weiqian

last: Li

first: Jia

last: Yu

first: Fang

last: Wang

first: Xiaoshuang


title: Commercial ChIP-Seq library preparation kits performed differently for different classes of protein targets

city: Houston

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: ChIP-Seq is a powerful method commonly used to study global protein-DNA interactions including both transcription factors and histone modifications. We have found that the choice of ChIP-Seq library preparation protocol plays an important role in overall ChIP-Seq data quality. However, very few studies have compared ChIP-Seq libraries prepared by different protocols using multiple targets and a broad range of  input DNA levels. In this study, we evaluated the performance of four ChIP-Seq library preparation protocols [NEB NEBNext Ultra II, Roche KAPA HyperPrep, Diagenode MicroPlex, and Bioo (now PerkinElmer) NEXTflex] on three target proteins, chosen to represent the three typical signal enrichment patterns in ChIP-Seq experiments: sharp peaks (H3K4me3), broad domains (H3K27me3) and punctate peaks with a protein binding motif (CTCF). We also tested a broad range of different input DNA levels from 0.10 to 10 ng for H3K4me3 and H3K27me3 experiments. Our results suggest that the NEB protocol may be better for preparing H3K4me3 (and potentially other histone modifications with sharp peak enrichment) libraries; the Bioo protocol may be better for preparing H3K27me3 (and potentially other histone modifications with broad domain enrichment) libraries, and the Diagenode protocol may be better for preparing CTCF (and potentially other transcription factors with well-defined binding motifs) libraries.  For ChIP-Seq experiments using novel targets without a known signal enrichment pattern, the NEB protocol might be the best choice as it performed well for each of the three targets we tested across a wide array of input DNA levels.

overall_design: In this study, we evaluated the performance of four ChIP-Seq library preparation protocols (Bioo, Diagenode, KAPA, and NEB) on three separate targets, to represent the three typical signal enrichment patterns in ChIP-Seq experiments: sharp peaks (H3K4me3), broad domains (H3K27me3), and punctate peaks over sequences bearing a protein binding motif (CTCF). We also tested a broad range of different input DNA levels ranging from 0.10 to 10 ng for creating our H3K4me3 and H3K27me3 ChIP-Seq libraries. To ensure the reproducibility of our results, two independent sets of ChIP-Seq experiments were carried out for H3K4me3 and H3K27me3, and three independent sets of ChIP-Seq experiments were carried out for CTCF.

first: Melissa

last: Simpler

first: Luis

last: Coletta

first: Sally

last: Gaddis

first: Kevin

last: Lin

first: Jianjun

last: Shen


title: Transcriptome profiling of mouse CD4+ T cells in the presence or absence of acetate

status: Public on Jun 22 2023

city: St. Petersburg

first: Jianhua

last: Xiong

state: FL

address: 600 Fifth Street S

institute: Johns Hopkins University

summary: Transcription profiling was performed on mouse CD4+ T cells treated with or without 10 mM acetate for 24 h. We then performed gene expression profiling analysis using data obtained from RNA-seq of mouse CD4+ T cells.

overall_design: RNA sequencing for transcription profiling was performed on mouse CD4+ T cells treated with or without 10 mM acetate for 24 h.

first: Junfang

last: Lyu


title: NUP98 and RAE1 sustain progenitor self-renewal programs downstream to HDAC activity to antagonize nucleolar targeting

city: Evanston

first: Xiaomin

last: Bao

state: IL

address: 633 Clark St

institute: Northwestern University

summary: Here we determine the target gene sets controlled by NUP98 and RAE1 in maintaining the undifferentiated state of primary human keratinocytes via HDAC activity.

overall_design:
We use primary human keratinocytes pooled from 6 donors. RNA-seq data comparing keratinocytes with NUP98 knockdown or RAE1 knockdown (3 independent shRNAs for each gene) vs their controls (2 independent control shRNAs for each gene) were generated. To determine NUP98's binding sites on the genome, we performed NUP98 ChIP-seq im undifferentiated and differentiated keratinocytes (day 4, with 1.2mM CaCl2). HDAC inhibition RNA-seq data were generated comparing DMSO treated cells to SAHA (10 uM) or romidepsin (100nM) treated cells for 24 hrs. HDAC1 ChIP-seq was done in untreated keratinocytes as well as in NUP98-knockdown versus control (2 independent shRNA and 2 independent control shRNA). To determine if HDAC inhibition affects NUP98 chromatin binding, NUP98 ChIP date on DMSO, SAHA, and romidepsin treated cells were also generated.

We use primary human keratinocytes pooled from 6 donors. To determine NUP98 and HDAC1 binding sites on the genome, we performed NUP98 and HDAC1 ChIP-seq in differentiated keratinocytes (day 4, with 1.2mM CaCl2) . To determine RAE1 binding sites on the genome, we performed expressed and HA tagged RAE1 and used an HA antibody for ChIP.

first: Amy

last: Neely

first: Junghun

last: Kweon

first: Sarah

last: Llyod

first: Patric

last: Ho

first: Laura

last: Blumensaadt

first: Ziyou


title: Gene expression profile at single cell level of BPH cells

city: Shanghai

first: Tianyu

last: Cao

address: No. 100 Haining Road, Hongkou District

department: Urology

institute: Shanghai General Hospital

summary: Single-cell sequencing data from three large prostates (>80mL volume) and three small prostates (less than 80mL volume).No cell sorting was conducted so all cells within the BPH environment could be represented.

overall_design: Human prostate transition zone tissue resected during ThuLEP were mechanically and enzymatically digested, scRNA-seq was performed for all 6 samples.

first: Feng

last: Xie

first: Youwei

last: Shi

first: Dapeng

last: Zhou

first: Yifeng

last: Jing


title: Neuronal chromatin remodeling factors in the mammalian nervous system

city: Mississauga

first: Ho Sung

last: Rhee

state: ON

address: 3359 Mississauga Rd

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

summary: Chromatin remodeling factors play important roles in accessibility formation of regulatory DNA. The mechanism by which chromatin remodeling factors regulate regulatory DNA regions that activate expression of cell type-specific genes during the nervous system development remains unknown. Chromatin remodeling complexes have neuron-specific factors, which are often mutated in patients with neurological disease. Here we demonstrate that neuronal chromatin remodeling factors activate neuronal gene expression during the nervous system development.

overall_design: Examination of RNA-seq profiles of mouse ES cell-derived neurons by deep sequencing

first: Kaitlin

last: Montanera

first: Ssu-Yu

last: Yeh

first: Alyssa

last: Ialongo


title: Increased bindings of C/EBP-beta at the −165 kb Zeb2 enhancer  upon systemic IL-6 exposure suppress cDC1 development

city: Saint Louis

first: Sunkyung

last: KIM

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in Saint Louis

summary: Type 1 conventional dendritic cells (cDC1) are required for effective CD8 T cell responses to many viruses and tumors and for effective checkpoint blockade immunotherapy. Recently, cytokines produced in association with certain tumors were reported to impair anti-tumor immune responses by reducing the abundance of cDC1. However, the reported mechanism of this reduction remains unclear, attributed either to reduced cDC1 development or decreased peripheral cDC1 survival. Here we show that tumor-derived IL-6 blocks cDC1 development from both in murine and human systems. We show that mechanism of this blockade is the IL-6-dependent increase in C/EBPβ expression in the common dendritic cell progenitor (CDP). C/EBPβ and NFIL3 compete for binding to sites in the -165 kb Zeb2 enhancer, and support or repress Zeb2 expression respectively. At homeostastis, pre-cDC1 specification occurs upon Nfil3 induction and consequent Zeb2 suppression.  However, IL-6 strongly induces C/EBPβ expression in CDPs and increase C/EBPβ bindings at the -165 kb Zeb2 enhancer, thereby preventing normal NFIL3-dependent pre-cDC1 specification.  Importantly, the ability of IL-6 to block cDC1 development is dependent on the presence of C/EBPβ binding sites in the -165 kb Zeb2 enhancer, as this effect is lost in Δ1+2+3 mutnat mice in which these binding sites are mutated. These results explain how tumor-associated IL-6 suppresses cDC1 development and suggest therapeutic approaches preventing abnormal C/EBPβ induction in CDPs may help reestablish cDC1 development to enhance anti-tumor immunity.

overall_design: Analysis of C/EBPβ bindings by CUT&RUN in Hoxb8-transformed BM progenitor cell line upon IL-6 stimulation

last: Kim

first: Jing

last: Chen

first: Tian-Tian

last: Liu

first: Kenneth

last: Murphy


title: Loss of PBAF Promotes Effector Differentiation and Limits CD8+ T Cell Exhaustion in Chronic Viral Infection and Cancer [multiomics]

city: Chicago

first: Weiguo

last: Cui

address: 303 E Chicago Ave

department: Pathology

summary: To gain insights into how PBAF complex regulates dynamic chromatin structure changes in LCMV-specific CD8+ T cells during chronic viral infection and examine the how PBAF-deficiency alters the transcriptional and epigenetic heterogeneity of CD8+ T cells, we performed single cell RNA + ATAC multiomic sequencing on Arid2- and Pbrm1-deficient CD8+ T cells and their wild-type counterpart.

overall_design: Naive P14 CD8 T cells isolated from mouse spleens were transfected with CRISPR ribonucleoprotein (RNP) to knock out Pbrm1 (sgPbrm1) or Arid2 (sgArid2). 2500 transfected CD45.1+ P14 T cells were transferred to CD45.1- C57BL/6 mice followed by LCMV Clone 13 infection. P14 T cells were FACS-sorted from spleens on day 21 p.i. and extracted nuclei were used for 10x single cell RNA+ATAC-seq library construction following the 10x protocol.

first: Jian

last: Shen

first: Ryan

last: Brown

first: Arjun

last: Kharel


title: Single Cell lineage Tracing Identifies Cancer Testis Antigens as Mediators of Chemoresistance in Small Cell Lung Cancer

city: Sioux Falls

first: Michael

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

summary: Small Cell Lung Cancer (SCLC) is often a heterogeneous tumor, where dynamic regulation of key transcription factors can drive multiple populations of phenotypically different cells which contribute differentially to tumor dynamics. This tumor is characterized by a very low 2-year survival rate, high rates of metastasis, and rapid acquisition of chemoresistance. The heterogeneous nature of this tumor makes it difficult to study and to treat, as it is not clear how or when this heterogeneity arises. Here we describe temporal, single-cell analysis of SCLC to investigate tumor initiation and chemoresistance in both SCLC xenografts and in situ SCLC mouse models. We identify an early population of tumor cells with high expression of AP-1 network genes that are critical for tumor growth. Furthermore, we have identified and validated the cancer testis antigens (CTAs) PAGE5 and GAGE2A as mediators of chemoresistance in human SCLC. CTAs have successfully been targeted in other tumor types and may be a promising avenue for targeted therapy in SCLC.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For cell lines, cisplatin = 2.876 uM and etoposide = 0.110 uM. For mice, cisplatin = 5 mg/kg and etoposide = 10 mg/kg on day one. On days two and three they were treated with etoposide = 10 mg/kg.

first: Hannah

last: Wollenzien

first: Yohannes

last: Afeworki


title: Exosomal microRNAs in tubal fluid may be involved in tubal epithelial structure damage and reproductive dysfunction associated with tubal endometriosis.

city: shanghai

first: yiqin

last: zhang

address: No. 910, Hengshan Rd

institute: International Peace Maternity and Child Health Hospital

summary: Endometriosis (EM) is a well-recognized disease that causes infertility in women of reproductive age. Tubal EM adversely affects fallopian tube function and female reproductive outcomes. Our study aimed to evaluate the effect of tubal EM on tubal epithelial ultrastructure and to explore the possible mechanisms of tubal infertility by analyzing the differential expression of exosomal microRNAs (miRNAs) in tubal fluid. We obtained human fallopian tube epithelium and tubal fluid samples from patients with and without tubal EM. We used scanning electron microscopy (SEM) and transmission electron microscopy (TEM) to assess ultrastructural changes. Exosomal miRNAs in tubal fluid were extracted for microarray. We visualized epithelial damage in the tubal EM group using electron microscopy. The number of organelles decreased, and organelle structure was destroyed. A total of 14 differentially expressed exosomal miRNAs were detected in tubal fluid (fold change >2 and P value <0.05). Four miRNAs (miR-1273f, miR-5699-5p, miR-6087, miR-6747-5p) were validated by quantitative real-time polymerase chain reaction (qRT-PCR). Bioinformatic analysis showed that most of the target genes participated in embryo transport, regulation of cell communication, anatomical structure morphogenesis, and immune system processes. We verified that tubal EM damaged the tubal epithelial ultrastructure in human specimens and identified differentially expressed exosomal miRNAs in tubal liquid. These findings may elucidate the pathogenesis of tubal EM-associated infertility.

overall_design: Tubal EM is a common gynecological disease associated with infertility. This study shows the differentially expressed exosomal miRNAs in tubal fluid which may be related to EM-associated infertility.

first: Yiqin

last: Zhang

first: Huiyu

last: Sun


title: Gene expression of C28/I2 cells with FABP4

city: Shenzhen

first: Yan

last: WANG

address: 1068 Xueyuan Ave

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

summary: FABP4 has been reported to trigger ADAMTS4 overexpression in chondrocytes. Here we described the transcriptional changes of FABP4-treatment.

overall_design: Transcriptional profiling was employed to test the expression profiles of C28/I2 cells in FABP4 treatment.

last: Wang

first: Qian

last: Xie

first: Jianhui

last: Liang


title: nCounter analysis of patients progressed to TKIs

city: Barcelona

first: Miguel

last: Molina-Vila

state: Barcelona

address: Sabino de Arana 16, -1.7

institute: Hospital Universitario Dexeus

summary: A prevalence study was conducted for MET amplification and overexpression in liquid biopsy samples from patients with NSCLC who relapsed on ALK, ROS1 or RET tyrosine kinase inhibitors. MET-mediated resistance was detected in 37.5% of tissue biopsies, which allow the detection of MET overexpression, compared to 7.4% of liquid biopsies. This study highlights the importance of considering MET overexpression as a resistance driver to fusion targeted therapies

overall_design: 28 liquid biopsy samples from non-small cell lung cancer patients (NSCLC) with ALK, ROS1 and RET fusions in progression to ALK TKIs (crizotinib, alectinib, lorlatinib, ceritinib) were analyzed by nCounter

first: Nadine

last: Reischmann

first: Carolin

last: Schmelas

first: Núria

last: Ariza

first: Daniel

last: Kuntze

first: Silvia

last: García-Roman

first: Manon

last: Simard

first: Doreen

last: Musch

first: Christina

last: Esdar

first: Joachim

last: Albers

first: Niki

last: Karachaliou


title: Effects of MED1 knock out on dental epithelia

city: rochester

first: Roman

last: Thaler

state: MINNESOTA

address: 200 First street SW

institute: Mayo Clinic

summary: Lineage commitnent and differentiation of dental stem cells was analyzed upon MED1 knock out in mice by RNA-Seq

overall_design: Mandibles from control or Krt14-Cre driven MED1 fl/fl mice were dissected and RNA was extracted from the cervial loop head region (CLH) as well as the cervial loop tail region. For all samples RNA was extracted usingcommercially available extraction kits and standard protocols.

first: Oda

last: Yuko


title: Identification of B-cell specific checkpoint molecules regulating anti-tumor immunity

city: Boston

first: Linglin

last: Huang

state: MA

address: 60 Fenwood Road, HBTM 10016F

department: Neurology

institute: Brigham and Women’s Hospital

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

overall_design: Refer to individual Series


title: Bulk RNA-seq for B-cell specific checkpoint molecules regulating anti-tumor immunity

summary: The role of B cells in anti-tumor immunity is still debated and accordingly, most therapies have focused on targeting T and NK cells to inhibit tumor growth1,2. Here, using high-throughput flow cytometry, bulk and single-cell RNA- and BCR-sequencing of B cells temporally during B16F10 melanoma growth, we identified a subset of B cells that expands specifically in the draining lymph node over time in tumor bearing-mice. The expanding B cell subset expresses the cell surface molecule T cell immunoglobulin and mucin domain 1 (TIM-1) and a unique transcriptional signature, including multiple co-inhibitory molecules such as PD-1, TIM-3, TIGIT and LAG-3. While conditional deletion of these co-inhibitory molecules on B cells had little or no effect on tumor burden, selective deletion of Havcr1 (the gene encoding TIM-1) in B cells both dramatically inhibited tumor growth and enhanced effector T cell responses. Loss of TIM-1 enhanced the type 1 interferon response in B cells, which augmented B cell activation and increased antigen presentation and co-stimulation, resulting in increased expansion of tumor-specific effector T cells. Our results demonstrate that manipulation of TIM-1-expressing B cells enables engagement of the second arm of adaptive immunity to promote anti-tumor immunity and inhibit tumor growth.

overall_design: Analysis of B cells derived from tumor, dLN, ndLN and spleen of B16F10-bearing wild-type mice (n=3)

first: Lloyd

last: Bod

first: Yoon-Chul

last: Kye

first: Jingwen

last: Shi

first: Elena

last: Torlai Triglia


title: Ablation of cDC1 development by IL-6-induced C/EBPb support in the -165 kb Zeb2 enhancer

first: Sunkyung

last: KIM

summary: Type 1 conventional dendritic cells (cDC1) are required for effective CD8 T cell responses to many viruses and tumors and for effective checkpoint blockade immunotherapy. Recently, cytokines produced in association with certain tumors were reported to impair anti-tumor immune responses by reducing the abundance of cDC1. However, the reported mechanism of this reduction remains unclear, attributed either to reduced cDC1 development or decreased peripheral cDC1 survival. Here we show that tumor-derived IL-6 blocks cDC1 development from both in murine and human systems. We show that mechanism of this blockade is the IL-6-dependent increase in C/EBPβ expression in the common dendritic cell progenitor (CDP). C/EBPβ and NFIL3 compete for binding to sites in the -165 kb Zeb2 enhancer, and support or repress Zeb2 expression respectively. At homeostastis, pre-cDC1 specification occurs upon Nfil3 induction and consequent Zeb2 suppression.  However, IL-6 strongly induces C/EBPβ expression in CDPs, thereby preventing normal NFIL3-dependent pre-cDC1 specification.  Importantly, the ability of IL-6 to block cDC1 development is dependent on the presence of C/EBPβ binding sites in the -165 kb Zeb2 enhancer, as this effect is lost in Δ1+2+3 mutnat mice in which these binding sites are mutated. These results explain how tumor-associated IL-6 suppresses cDC1 development and suggest therapeutic approaches preventing abnormal C/EBPβ induction in CDPs may help reestablish cDC1 development to enhance anti-tumor immunity.

overall_design: mRNA profiles of mouse bone marrow CDP treated with Flt3L alone or Flt3L plus IL-6 to examine transcriptional control mechanism of IL-6 for CDP specification toward cDC1 and cDC2

last: Kim

first: Jing

last: Chen

first: Kenneth

last: Murphy


title: High-throughput functional characterization of combinations of transcriptional activators and repressors

city: Stanford

first: Adi

middle: Xiyal

last: Mukund

state: CA

address: 443 via Ortega, Shriram 036

institute: Stanford University

summary: Despite growing knowledge of the functions of individual human transcriptional effector domains, much less is understood about how multiple effector domains within the same protein combine to regulate gene expression. Here, we measure transcriptional activity for 8,400 effector domain combinations by recruiting them to reporter genes in human cells. In our assay, weak and moderate activation domains synergize to drive strong gene expression, while combining strong activators often results in weaker activation. In contrast, repressors combine linearly and produce full gene silencing, and repressor domains often overpower activation domains. We use this information to build a synthetic transcription factor whose function can be tuned between repression and activation independent of recruitment to target genes by using a small molecule drug. Altogether, we outline the basic principles of how effector domains combine to regulate gene expression and demonstrate their value in building precise and flexible synthetic biology tools.

overall_design: Demultiplexed sequencing reads were provided by Admera. Domain 1 and domain 2 reads were aligned separately using bowtie2, trimming 30 base pairs from both 5’ and 3’ ends, and were then each paired read was identified as a particular library member using a python script iterating over each read pair. The total number of reads for each library member was then summed up using another python script. Library members were required to have at least 5 ON reads or 5 OFF reads as well as 50 total reads across both ON and OFF subpopulations to be considered for downstream analysis. For every qualifying library member, the ON or OFF read count was then set to 5 if it was less than 5. Then, ON read counts were normalized by dividing each library member’s read count by the total number of ON reads, and the same was done for OFF counts. Overall enrichment scores were then computed by taking the log2 of the ratio of normalized ON read counts to normalized OFF read counts.

middle: X

first: Josh

last: Tycko

first: Sage

last: Allen

first: Stephanie

last: Robinson

first: Cecelia

last: Andrews

first: Joydeb

last: Sinha

first: Connor

last: Ludwig

first: Kaitlyn

last: Spees

first: Michael

middle: C

last: Bassik

first: Lacramioara

last: Bintu


title: Epigenetic remodeling for regeneration progam activation in human cells [scRNA]

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

summary: Regeneration occurs naturally in certain lower vertebrates, but is highly restricted in humans with a stable epigenome. Recently, we demostrated that the small moleucles could reprogram the human somtic cells to pluripotent stem cells, relying on the activation of regeneration-like gene program. Here，by performing systematically epigenome analysis, we revealed that the establishment of this regeneration-like state relies on a hierarchical epigenetic regulation process. In additon, we also found the major barriers that inhibite the activation of regeneration program.

overall_design: the single-cell RNA-sequencing were performed at the indicatied timepoints during the reprogramming process to detected the whole trancriptome of cells

first: Wang

last: Guan

first: Yanglu

last: Wang

first: Jingyang

first: Hongkui

last: Deng


title: Transcriptome profiling of mouse CD8+ T cells in the presence or absence of acetate

first: Jianhua

last: Xiong

state: Florida

address: 600 5th Street S

summary: To investigate the role of acetate in T cell survival and the underlying mechanism, transcription profiling was performed on mouse CD8+ T cells treated with or without 10mM acetate for 24h. We then performed gene expression profiling analysis using data obtained from RNA-seq of mouse CD8+ T cells.

overall_design: RNA sequencing for transcription profiling was performed on mouse CD8+ T cells treated with or without 10 mM acetate for 24 h.

first: Junfang


title: miR-181c is up-regulated in monoMAC cells related to increased cell death

city: Bethesda

first: Weixin

state: MD

address: 9000 Rockville Pike

department: DLM/CC

institute: NIH

summary: Somatic and germline mutations in GATA2 were recently identified in patients diagnosed with monoMAC, the hallmarks of which include monocytopenia, B-cell and NK-cell lymphopenia, susceptibility to opportunistic infections (e.g. MAC), and a strong propensity to develop hypocellular MDS/AML or CMML. GATA2 mutations are thought to result in loss of function or haploinsufficiency, but the precise mechanism for the development of cytopenias, immunodeficiency, and susceptibility to MDS remains to be elucidated.  MicroRNA (miR) represents a unique mechanism of post-transcriptional gene regulation.  In this study we generated microRNA profiles of patient derived monoMAC cell lines followed by functional studies to identify aberrant miRs and their targets, which could potentially cooperate with GATA2 deficiency in generating cytopenias and hematologic disease.  In our study, eight miRs were significantly differentially expressed (≥ 2-fold; p ≤ 0.05) as determined by microRNA microarray profiles; miR-9, miR-181a-2-3p, miR-181c, miR-181c-3p, miR-486-3p, and miR-582-5p showed increased expression in monoMAC  cell lines compared to controls, while miR-223 and miR-424-3p showed significantly decreased expression.  Among the differentially expressed miRs that were validated by quantitative RT-PCR  was miR-181c, which demonstrated a 2.2 fold increase in expression in monoMAC cell lines (p = 0.013).  Among the target transcripts potentially regulated by miR-181c, MCL1 expression was significantly decreased (2 fold; p = 0.018) in monoMAC cell lines in comparison to control cell lines.  Transient transfection of miR-181c in Ly8 cells resulted in 40% decrease of MCL1 mRNA level, suggesting that miR-181c negatively regulates MCL1 in MonoMAC.   These findings indicate that monoMAC/GATA2 deficiency is associated with significantly decreased expression of MCL1 possibly through negative regulation involving miR-181c.   Deletion of Mcl1 is known to cause apoptosis, loss of HSCs, and cytopenias in murine studies.  Thus, down-regulation of MCL1 seen in monoMAC/GATA2 deficiency may similarly favor unregulated apoptosis and the depletion of hematopoietic progenitors resulting in cytopenias, immunodeficiency, and risk of MDS/AML.

overall_design: miRNA profiling was performed using Agilent miRNA array platform with RNAs isolated from EBV-immortalized human B cells of healthy controls and monoMAC patients

first: Meghan

last: Corrigan-Cummins

first: Nga

last: Voon

first: Amy

last: Hsu

first: Donald

last: Vinh

first: Steven

last: Holland

first: Katherine

middle: R

last: Calvo


title: Single-cell RNA-seq for identification of B-cell specific checkpoint molecules regulating anti-tumor immunity

first: Linglin

last: Huang

overall_design: For the B cell atlas analysis or the examination of CD19cre/+ and TIM-1BKO mice, viable leukocytes were sorted by FACS-sorted from tumors (70% CD3e+ and CD19+ cells, 30% total CD45+ cells), dLN and ndLN (100% CD45+ cells) at three different time points as depicted in Extended Date Figure 2a. For the analysis of TIM-1-expressing B cells, viable B220+ CD19+ CD138+ and - cells derived from dLN, ndLN and spleen from C57Bl6/J mice were sorted by FACS. Cells were resuspended in PBS containing 2% FCS and stained with oligo tagged TotalSeq antibodies (BioLegend) for 30 minutes on ice. Cells were washed and pooled accordingly, centrifuged at 1,200 rcf for 5 minutes at 4°C and resuspended in PBS + 2% FCS. For the B cell temporal profiling, 9 samples were combined into each channel of the Chromium system (10x Genomics): Tumor, dLN, ndLN from three different timepoints: days 7, 10 and 16 of one replicate. For the examination of CD19cre/+ and TIM-1BKO, 6 samples were combined into each channel: tumor, dLN, ndLN derived from one biological replicate of each genotype. For the TIM-1 positive cells analysis, cells derived from LN were loaded in separate channels and the splenic cells TIM-1 positive and TIM-1 negative were combined. For samples that did not include scBCR-seq and/or scTCR-seq and 5' feature barcoding, sorted cells were separated into droplet emulsions using the Chromium Single Cell 3′ Solution (v2) according to manufacturer’s instructions (10x Genomics).

first: Lloyd

last: Bod

first: Jingwen

last: Shi

first: Elena

last: Torlai Triglia


title: Epigenetic remodeling for regeneration progam activation in human cells [scRNA+ATAC]

first: Yulin

overall_design: the Single Cell Multiome ATAC + Gene Expression were performed at the indicatied timepoints during the reprogramming process to detected the whole trancriptome of cells

first: Wang


title: Gene expression profile at single cell level of prostate from the different prostate cancer genetic mouse model [scRNA-Seq]

first: Hanling

address: Shanghai

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Science

summary:
To understand the cell types changes in prostate cancer progression, we carried out scRNA-seq of prostates from different kinds of genetic mouse model. After that, we found fibroblasts were changed obviously during prostate cancer progression. To confirm the function of the fibroblasts, LNCap was used to cocultured with all kinds of fibroblasts in control or ADT condition. To find out the key enviroment factors induced firoblast changing, RNA-seq, ATAC-seq and ChIP-seq of fibroblast in different treatment were taken. And finally, ADT, TGF-β1, and sox4 were confirmed as contributors of the stroma cell changes, which provided new strategies for prostate cancer treatment.
scRNA-seq were used to find out the cell lines diverisity of prostate cancer progressiom. RNA-seq of LNCap cocultured with different fibroblasts were taken to identify the pathway fibroblasts induced. RNA-seq, ATAC-seq and ChIP-seq of fibroblasts were carried out to find out the reason of fibroblast changes.

overall_design:
We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of cell types of prostate cancer.

Please note that the records have been updated with the group information file (4groups_barcodes_suffix.txt) on June 29, 2023.

first: Jun

last: Qin


title: Epigenetic remodeling for regeneration progam activation in human cells


title: Epigenetic remodeling for regeneration progam activation in human cells [bulkRNA]

summary: Regeneration occurs naturally in certain lower vertebrates, but is highly restricted in humans with a stable epigenome. Recently, we demostrated that the small moleucles could reprogram the human somtic cells to pluripotent stem cells, relying on the activation of regeneration-like gene program. Here, by performing systematically epigenome analysis, we revealed that the establishment of this regeneration-like state relies on a hierarchical epigenetic regulation process. In additon, we also found the major barriers that inhibite the activation of regeneration program.

overall_design: The ap-1 family proteins induclding FOS, FOSL1, FOSL2, JUN and JUNB were overexpressed in at early stage, then the total RNA was isolated and then sequenced were performed.

first: Yanglu

first: Jingyang

first: Hongkui


title: Cancer associated fibroblasts play an important role in prostate cancer progression


title: Cancer associated fibroblasts play an important role in prostate cancer progression [RNA-Seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LNCap cells cocultred with different kind of fibroblasts. Comparative gene expression profiling analysis of RNA-seq data for different kinds of fibroblasts.


title: Cancer associated fibroblasts play an important role in prostate cancer progression [ATAC-Seq]

overall_design: Examination of chromatin accessibility in  different kinds of CAFs.


title: Epigenetic remodeling for regeneration progam activation in human cells [CUT&TAG]

overall_design: the cut-tag were performed at the indicated timepoints during the reprogramming process to detect the histone modifications


title: Cancer associated fibroblasts play an important role in prostate cancer progression [ChIP-Seq]

overall_design: Examination of AR, sox4 binding and histone modifications in different kinds of CAFs.


title: Profiling of tumor-infiltrating natural killer (NK) cells and macrophages in untreated C57BL/6 mice and mice treated with combination immunotherapies

city: Cambridge

first: Dikshant

last: Pradhan

address: 70 Dudley Street

institute: Massachusetts Institute of Technology

summary: Treatments aiming to augment immune checkpoint blockade (ICB) in cancer often focus on T cell immunity, but innate immune cells may have important roles to play. Here we demonstrate a single-dose combination treatment (termed AIP) employing a pan-tumor-targeting antibody surrogate, half-life-extended interleukin-2 (IL-2), and anti-PD-1, which primes tumors to respond to subsequent ICB and promotes rejection of large established tumors in mice. NK cells and macrophages activated by AIP treatment underwent transcriptional reprogramming, rapidly killed cancer cells, governed the recruitment of cross-presenting dendritic cells (DCs) and other leukocytes, and induced normalization of the tumor vasculature, facilitating further immune infiltration. In order to parse out the contribution of each components in the 1X AIP treatment, we examined NK cells and macrophages from B16F10-bearing mice treated with AIP, AI, IP and AP or left untreated.

overall_design: Examination of tumor-infiltrating natural killer cells or macrophages from untreated C57BL/6 mice or mice treated with AP, IP, AI, or AIP drug combinations.

first: Chensu

first: Darrel

last: Irvine


title: Transcriptomic diversity and overlapping clonality across subsets of antibody-secreting and memory B cells from spontaneous germinal centers

first: Carlos

last: Castrillon

address: 200 Longwood Ave, Warren Alpert Building

institute: Harvard Medical School / Boston Childrens Hospital

summary: Affinity matured self-reactive antibodies are found in autoimmune diseases like systemic lupus erythematous. Here we used fate-mapping reporter mice and single cell transcriptomics coupled to antibody repertoire analysis to characterize the post-germinal center (GC) B cell compartment in a new mouse model of autoimmunity. Antibody secreting cells (ASCs) and memory B cells (MemBs) from spontaneous GCs grouped into multiple subclusters. ASCs matured into two terminal clusters, with distinct secretion, antibody repertoire and metabolic profiles. MemBs contained FCRL5+ and CD23+ subsets, with different in vivo localization in the spleen. GC-derived FCRL5+ MemBs share transcriptomic and repertoire properties with atypical B cells found in aging and infection and localize to the marginal zone, suggesting a similar contribution to rapid recall responses. While transcriptomically diverse, ASC and MemB subsets maintained an underlying clonal redundancy. Therefore, self-reactive clones could escape subset-targeting therapy by perpetuation of self-reactivity in distinct subsets.

overall_design: Chimeras were produced by transferring bone marrow from 564Igi and AicdaCreERT2-EYFP reporters (autoimmune) and AicdaCreERT2-EYFP and WT (immunized) into irradiate WT hosts. The latter were immunized with NP-OVA in alum, and boosted with NP-OVA. Fate-mapped AID-EYFP cells were isolated from spleens  by Fluorescence-activated cell sorting (FACS)  and analyzed using scRNAseq.

first: Michael

last: Carroll


title: Comparative transcriptome data of ARPE-19 cells with and without HTRA1 overexpression

city: Guangzhou

first: wenchang

last: Xu

address: Jinsui Road No.7

department: Zhongshan Ophthalmic Center

institute: Sun Yat-Sen University

summary: To explore the key signaling pathways that might be affected by up-regulated HTRA1, we performed RNA-seq analysis on ARPE-19 cells infected with HTRA1 adenovirus and negative control adenovirus for 24 h. Compare with control groups, there were 2810 differentially expressed genes (log2 |fold change|> 1, log10 adjusted p-values < 0.05) were identified to be associated with distinct biological processes. 1053 genes were significantly upregulated and 1757 genes were significantly downregulated in ARPE-19 cells overexpressing HTRA1. The KEGG pathways analysis of up-regulated and down-regulated genes and ranking the enrichment pathways according to the corrected p-value. In the KEGG pathways analysis of up-regulated genes, the metabolic pathways ranked first with 84 genes involved. And in the KEGG pathways analysis of down-regulated genes, the metabolic pathways ranked third with 104 genes involved. These results revealed that up-regulated HTRA1 prominently disturbed the metabolic pathways in ARPE-19 cells.

overall_design: The mRNA profiles of ARPE-19 cell with HTRA1 overexression (three replicates) and the control group without HTRA1 overexpression (three replicates)

first: Ling

last: Zhao

first: Wenchang


title: Neuronal mimicry mechanisms promote the growth small-cell lung cancer in the brain

first: Siqi

last: Cao

address: 300 Pasteur Drive

institute: Stanford Medical School

summary: Small cell lung cancer (SCLC) is a fatal form of cancer that frequently metastasizes to the brain. Here we investigated the mechanisms allowing SCLC cells to grow in the unique brain microenvironment. We found that neuronal programs upregulated in SCLC cells during tumor progression and upon growth in the brain are critical for SCLC growth in the brain. Mechanistically, the presence of SCLC cells in the brain re-activates astrocytes, which in turn promote the survival of SCLC cells by secreting neuronal pro-survival factors such as SERPINE1. We also identified Reelin, a molecule produced by developing neurons to recruit astrocytes, as a molecule secreted by SCLC cells to recruit astrocytes to the tumor site and promote SCLC growth in the brain. Thus, SCLC cells co-opt mechanisms normally at play between astrocytes and neurons to promote SCLC growth in the brain. Targeting such developmental neuronal programs may help treat brain metastases.

overall_design: 8 samples were analyzed: allografts transplanted into mouse brain (2 replicates), liver (3 replicates) and subcutaneous (3 replicates) and allowed to grow for 3 weeks before cell extraction

first: Fangfei

last: Qu

first: Julien

last: Sage


title: RNA-sequencing analysis of human hepatic organoids derived from human induced pluripotent stem cells

city: Daejeon

first: Ilkyun

last: Im

address: 141 Gajeong-ro, Yuseong-gu

department: Department of Predictive Toxicology

institute: Korea Institute of Toxicology

summary: Liver is a central organ for drug and xenobiotics metabolism in human body. Due to the differences in interspecies metabolism, human model system for liver metabolism is necessary. However, the hepatic model systems derived from human pluripotent stem cells for metabolic screening and assays did not recapitulate the most of metabolic capabilities of human liver or primary human hepatocytes to date. In this study, we developed human hepatic endoderm organoids which are expandable and subsequently differentiated human hepatic organoids having metabolic capabilities. To investigate the transcriptome of human hepatic organoids, we performed RNA-sequencing.

overall_design: human hepatic organoids derived from hiPSCs and treated by Fe or not

first: Han-Jin

last: Park

first: Hyemin

last: Kim


title: Target the MDSC of tumor in situ by MAPK signaling pathway inhibitor to promote tumor regression

city: ChengDu

first: Bin

last: Shao

state: sichuan

address: No.14,3Rd Section Of Ren Min Nan Rd

institute: sichuan university

summary: The study analyzed the PMN-MDSCs  and M-MDSCs genetic expression difference  in spleen and tumor in order to find out the key target molecules

overall_design: Comparison of gene expression between  PMN-MDSCs  and M-MDSCs  in spleen and tumor of mice

first: Jiayun

last: Yu


title: Integrative analysis of grapevine (Vitis vinifera L) transcriptome reveals regulatory network for Chardonnay quality formation

status: Public on Jun 21 2023

city: Nanjing

first: Jun

last: Kang

address: Xiaoling Wei Street

institute: Nanjing Agricultural Unversity

summary: Anthocyanins, total phenols, soluble sugar and fruit shape play a significant role in determining the distinct fruit quality and customer preference. However, for the majority of fruit species, little is known about the transcriptomics and underlying regulatory networks that control the generation of overall quality during fruit growth and ripening. This study incorporated the quality-related transcriptome data from 6 ecological zones across 3 fruit development and maturity phases of Chardonnay cultivars. With the help of this dataset, we were able to build a complex regulatory network that may be used to identify important structural genes and transcription factors that control the anthocyanins, total phenols, soluble sugars and fruit shape in grapes. Overall, our findings set the groundwork to improve grape quality in addition to offering novel views on quality control during grape development and ripening.

overall_design: Six ecoregions in Ningxia Province, China, were used for collecting grapevine (Vitis vinifera L. Chardonnay) at various developmental phases. The six ecological zones are HJZ, ZHYS, CC, XG, XLS and HSB. Fruits were taken out between 40 days following the early flowering period (DAP) and 120 days, which included 80 days, at various developmental phases. And named them as the enlargement period (40 DAP), the color transition period (80 DAP) and the maturity period (120 DAP). Small chunks of the fruit's flesh (without the skin or seeds) were sliced up and quickly frozen in liquid nitrogen before being kept at −80 °C for additional transcriptome study. Every experiment was broken down into three biological replicates, with 15 uniformly sized fruits in each repeat，Frozen fruit was used to extract total RNA and the Illumina HiSeq-2000 platform was used to create mRNA libraries for each sample and sequence the results.

first: Guangqing

last: Fu

first: Yanhua

last: Ren

first: Weimin

last: Wu


title: Overexpression of α-SMA led to differential gene expression in INS-1 cells (RNA-seq)

city: Ningbo

first: YANG

last: XI

address: Fenghua Road

department: School of medicine

institute: Ningbo University

summary: The goal of this study was to define the cohort of genes whose expression is regulated by α-SMA function in type 2 diabetic mellitus . Towards this goal, INS-1 cells stably expressing α-SMA (INS-SMA) were established. In addition, a control cells (INS-MOCK) was generated by transfection with empty vector. Subsequently, total RNA was isolated and then performed transcriptome RNA sequence.

overall_design: We had two groups: (1) INS-MOCK and (2) INS-SMA. Each group had 3 biological replicates.

first: Bu

last: Shizhong

first: Xi

last: Yang

first: Ye

last: Shazhou