title: Characterization of a Distinct Rectal Mucosal Transcriptome among Transgender Women utilizing Cross-Sex Hormone Therapy

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: A comparison of rectal mucosal RNA transcriptome findings between transgender women using feminizing hormone therapy, men who have sex with men engaging in receptive anal intercourse, and males who had never engaged in anal intercourse demonstrates differential gene expression involving pathways critical for mucosal inflammation, suggesting the urgent need for further exploration into the immunologic effects of cross-sex hormone therapy in the rectal mucosa and the potential impact on HIV transmission risk at this site.

overall_design: Rectal mucosal biopsies were obtained from 9 transgender women using cross-sex hormone therapy and from these, total RNA was extracted for RNA-Seq analysis.  The RM transcriptome of TGW was compared to stored specimens from a prior study that included 10 MSM engaging in CRAI and 10 men who reported no history of AI; the previously stored specimens were re-sequenced from extracted RNA to control for batch effect.

first: Cassie

last: Ackerley

first: James

middle: M

last: Billingsley

first: Praveen

last: Amancha

first: S

middle: A

last: Smith

first: Rama

middle: R

last: Amara

first: Steven

last: Bosinger

first: Colleen

last: Kelley


title: Analysis and Verification of Exosomal miRNA Expression Profile of Serum in Patients with Acute Ischemic Stroke

status: Public on Mar 21 2023

city: luoyang

first: liyan

last: chen

address: kaiyuan road 263

country: China

institute: Henan University of Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: To understand the role of exosome miRNAs in AIS disease and to explore the miRNAs and the potential mechanisms related to the occurrence and development of the disease. This research collected serum samples from AIS patients and healthy volunteers and extracted exosome miRNA. The exosome miRNA associated with AIS was screened by illumina high-throughput sequencing . The differentially expressed target genes related to miRNAs were analyzed using bioinformatics analysis including GO functional enrichment analysis, KEGG pathway enrichment analysis, and the screening of key genes via PPI diagram. These differentially expressed mRNAs were indicated an important role in a variety of biological processes and multiple pathways of AIS disease.

overall_design: Serum exosomal miRNA expression profiles were measured in patients with acute ischemic stroke and healthy volunteers

first: gaofeng

last: Liang

last: Chen


title: Maternal factor Trim75 contributes to Zygotic Genome Activation program in mouse early embryos

status: Public on Mar 20 2023

city: Wenzhou

first: LIjun

state: Other

address: Wenzhou Medical University, Wenzhou City, Zhejiang Rrovince,China

institute: Wen Zhou Medical University

type: Expression profiling by high throughput sequencing

summary:
Zygotic genome activation (ZGA) marks the first transcription event in life, and human embryo developmental arrest has been highly correlated with ZGA failure in clinical studies.
We utilized published single-cell RNA sequencing data and RNA-seq data to identify Trim75 is a potential driver of minor ZGA and may recruit EP300 and establish H3K27ac in the gene body of minor ZGA genes.

overall_design: Single-cell RNA sequencing data of induced 2-cell-like transition state and RNA-Seq data of Trim75 overexpression data analysis.

first: Weibo

last: Hou

first: Lijun

first: Jingzhang

last: Ji


title: Mll1 in T follicular helper cell differentiation

city: La Jolla

first: Shane

last: Crotty

state: CA

address: 9420 Athena Circle

country: USA

institute: La Jolla Institute for Immunology

summary: T follicular helper (TFH) cells are essential for developing protective antibody responses following vaccination. Greater understanding of the genetic program leading to TFH differentiation is needed. Chromatin modifications are central in the control of gene expression. However, detailed knowledge of how chromatin regulators (CRs) regulate differentiation of TFH cells is limited. We screened a large shRNA library targeting all known CRs in mouse and identified the histone methyltransferase Mll1 as a positive regulator of TFH differentiation. Loss of Mll1 expression reduced formation of TFH cells following acute viral infection or protein immunization. In addition, expression of the TFH lineage-defining transcription factor Bcl6 was reduced in the absence of Mll1. Transcriptomics analysis identified Lef1 and Tcf7 as genes dependent on Mll1 for their expression, which provides one mechanism for the regulation of TFH differentiation by Mll1. Taken together, CRs such as Mll1 substantially influence TFH differentiation.

overall_design: RNA-Seq

first: Simon

last: Belanger

first: Sonya

last: Haupt

first: Caterina

middle: E

last: Faliti

first: Adam

last: Getzler

first: Jinyong

last: Choi

first: Huitian

last: Diao

first: Pabalu

middle: P

last: Karunadharma

first: Nicholas

last: Bild

first: Matthew

last: Pipkin


title: Transcriptional profiling for CRISPR activation of a myeloma-preferential dependency

city: Boston

first: Constantine

last: Mitsiades

state: MA

address: 450 Brookline Avenue Dept. of Medical Oncology

institute: Dana-Farber Cancer Institute, Harvard Medical School

summary: Clinical progress in multiple myeloma (MM), an incurable plasma cell (PC) neoplasia, has been driven by therapies which have limited applications beyond MM/PC neoplasias and do not target specific oncogenic mutations in MM. Instead, these agents target pathways critical for PC biology yet largely dispensable for malignant or normal cells of most other lineages. We systematically characterized the lineage-preferential molecular dependencies of MM through genome-scale CRISPR gene editing studies in MM vs. hundreds of non-MM lines. This identified a collection of genes whose disruption has more pronounced or recurrent impact on the MM cell fitness compared to other malignancies. These genes, some known, others not previously linked to MM, encode transcription factors, chromatin modifiers, endoplasmic reticulum components, metabolic regulators or signaling molecules. The current dataset describes the transcriptional profiling of a MM cell line with CRISPR activation for the myeloma-preferential dependency, POU2AF1. The transcriptional profile of CRISPR activation of an additional gene (PANK1), which does not serve as a MM-preferential dependency in CRISPR gene editing studies, is also described.

overall_design: LP1 cells were stably transduced with a construct for dCas9-Vp64 after lentiviral sgRNA transduction packaged with the pXPR-502 construct (RRID:Addgene_96923). LP1 cells transduced with POU2AF1 sgRNA for CRISPR-based activation of POU2AF1or control OR genes. The following sgRNA were used: PANK1_1 CACCGACGAGTTTCAACATG, PANK1_2 AGTTCTCTGGGCTTGCAGAG, POU2AF1_1 GCGCACAGTGGGGTGACAGG, POU2AF1_2 TGGCTGCAGAAACGTTGCAC, OR12D2 GAATGTCTGTCACTCCCAAG, OR6S1 GACCTGCAATTGGATAAACT

first: Ryosuke

last: Shirasaki

first: Ricardo

last: de Matos Simoes


title: Nrf2 drives hepatocellular carcinoma progression through acetyl-CoA-mediated metabolic, epigenetic and oncogenic regulatory networks

city: Augusta

first: Xingguo

last: Zhu

state: Georgia

department: Cancer Center

institute: Augusta University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Liver tumors had high levels of histone acetylation. Nrf2 knockout mice developed fewer tumors than Nrf2 wild-type mice.  The mechanistic study found that Nrf2 knockout reduced the generation of acetyl CoA from impaired glycolysis, TCA cycle, and fatty acid metabolism. Acetyl CoA is the substrate for protein acetylation including histone acetylation. Here we determined the genome-wide distribution of AcH3K27. We found that Nrf2 through regulating acetyl CoA production affects histone acetylation (AcH3K27) to modulate the expression of genes, whose products were involved in the glycolysis, TCA cycle, fatty acid metabolism, and oncogenic Myc/mTor signaling. Our findings supported an Nrf2-integrated metabolic, epigenetic and oncogenic signaling in driving liver tumor development.

overall_design: Comparison the genome-wide distribution of histone lysine 27 acetylation in liver tumors of Nrf2 WT (2 samples) and Nrf2 KO mice (2 samples) at 36 weeks of age.

first: Caixia

last: Xi

first: Junfeng

last: Pang


title: SARS-CoV-2 airway infection results in time-dependent sensory abnormalities in a hamster model

city: New York

first: Justin

middle: J

last: Frere

state: NY

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

summary: Despite being largely confined to the airways, SARS-CoV-2 infection has been associated with sensory abnormalities that manifest in both acute and long-lasting phenotypes. To gain insight on the molecular basis of these sensory abnormalities, we used the golden hamster infection model to characterize the effects of SARS-CoV-2 versus Influenza A virus (IAV) infection on the sensory nervous system. SARS-CoV-2-infected hamsters demonstrated mechanical hypersensitivity during acute infection; intriguingly, this hypersensitivity was milder, but prolonged when compared to IAV-infected hamsters. RNA sequencing (RNA-seq) of thoracic DRGs from acute infection revealed predominantly neuron-biased signaling perturbations in SARS-CoV-2-infected animals as opposed to type I interferon signaling in tissue derived from IAV-infected animals. RNA-seq of 31dpi thoracic DRGs from SARS-CoV-2-infected animals highlighted a uniquely neuropathic transcriptomic landscape, which was consistent with substantial SARS-CoV-2-specific mechanical hypersensitivity at 28dpi. Overall, this work elucidates novel transcriptomic signatures triggered by SARS-CoV-2 that may underlie both short- and long-term sensory abnormalities while also highlighting several therapeutic targets for alleviation of infection-induced hypersensitivity.

overall_design: RNA-sequencing of SARS-CoV-2-, IAV-, and mock-treated hamster dorsal root ganglion tissues at 1 and 4 days-post-infection to allow differential expression analysis among infection groups and time points. RNA-sequencing of SARS-CoV-2 and mock-treated hamster dorsal root ganglion tissues at 31 days-post-infection to allow differential expression analysis.

first: Randal

last: Serafini

first: Venetia

last: Zachariou

first: Benjamin

last: tenOever


title: Comparing the transcription level between fourth day and eighth day in Streptomyces avermitilis S0

city: Beijing

first: Keqian

last: Yang

address: NO.1 Beichen West  Road, Chaoyang District

institute: IMCAS

summary: Streptomyces avermitilis is a avermectin producer.Since the avermectin biosynthesis rate has a increased significantly in P3 fermentation stage( P1,24–96 h; P2:96–192 h, P3:192–240 h), but the sugar absorption rate decreased significantly in P3 fermentation stage, in order to improve the titer of avermectins, we conducted transcriptomic analysis of Streptomyces avermitilis S0 in fourth and eighth day, and  selected  native  promoters with appropriate temple using to express sugar transporters.

overall_design: We chose two time points in fourth and eighth day. The samples were collected at each time point named S0-4d, S0-8d.

first: Zhuoxu

last: Dong

first: Lei

last: Li

first: Guozhong

last: Du

first: Yanyan

last: Zhang

first: Weishan

last: Wang

first: Xiangjing

first: Shanshan

first: Wensheng

last: Xiang


title: Effect of PTX3 on gene expression of THP-1 macrophages

city: Tainan

first: Feng-Wei

last: Chen

address: No. 1 University Rd., Department of Biotechnology and Bioindustry Sciences

department: Institute of Basic Medical Sciences

country: Taiwan

institute: National Cheng Kung University

summary: We aimed to investigate the effect of PTX3 on macrophages functions. After PTX3 stimulation for 18 h in THP-1 macrophages, total RNA were harvested for RNA-seq analysis of ctrl (n = 1) and PTX3 group (n = 1).

overall_design: THP-1 macrophage differentiation was induced by treatment of 320 nM PMA for 6 h. THP-1 macrophages were then treated with or without 50 ng/ml PTX3 for 18 h (Ctrl, n =1 and PTX3, n = 1) and the RNA lysates were harvested for comparative gene expression profiling analysis of RNA-seq data.

first: Ju-Ming

first: Yung-Ling

last: Wu


title: Doublecortin-like kinase 1 activates NF-κB to induce inflammatory responses by binding directly to IKKβ

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

summary: Doublecortin-like kinase 1 (DCLK1), a microtubule-associated protein kinase, is involved in neurogenesis, and its levels are elevated in various human cancers. Recent studies suggest that DCLK1 may relate to inflammatory responses in the mouse model of colitis. However, cellular pathways engaged by DCLK1, and potential substrates of the kinase remain undefined. To understand how DCLK1 regulates inflammatory responses, we utilized the well-established lipopolysaccharide (LPS)-stimulated macrophages and mouse model. Through a range of macrophage-based and cell-free platforms, we discovered that DCLK1 binds directly with the inhibitor of κB kinase β (IKKβ) and induces IKKβ phosphorylation on Ser177/181 to initiate nuclear factor-κB (NF-κB) pathway. Deficiency in DCLK1, achieved by silencing or through pharmacological inhibition, prevented LPS-induced NF-κB activation and cytokine production in macrophages. We further show that mice with myeloid-specific DCLK1 knockout or DCLK1 inhibitor treatment are protected against LPS-induced acute lung injury and septic death. Our studies report a novel functional role of macrophage DCLK1 as a direct IKKβ regulator in inflammatory signaling and suggest targeted therapy against DCLK1 for inflammatory diseases.

overall_design: Monoclonal cell line RAW 264.7 cell lines which steadily expressed DCLK1 shRNA or negative control shRNA were plated at 200,000 cells/well in six-well plates. Cells were challenged with 500 ng/mL LPS for 6 h. Cells were then homogenized using RNAiso Plus (Takara, Japan) and total RNA was extracted using RNeasy Plus Mini Kit. A reference transcriptome analysis was performed by Lianchuan Bio (LC-Bio) Technologies (Hangzhou, Zhejiang). Paired-end sequencing was performed using the Illumina Novaseq 6000 (California, United States).

first: Wu

last: Luo

first: Guang

last: Liang


title: The miRNA expression profiles of round spermatids during GRTH/DDX25 mediated spermiogenesis: mRNA-miRNA Network analysis

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

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

overall_design: Refer to individual Series


title: The miRNA expression profiles of round spermatids during GRTH/DDX25 mediated spermiogenesis: mRNA-miRNA Network analysis [miRNAseq]

summary: GRTH/DDX 25 is a member of the DEAD-box family of RNA helicases that play an essential role in spermatogenesis. Regulation of spermatogenesis occurs at the levels of transcription, post-transcriptional and translational levels which needs to be explored in detail. miRNAs regulate the expression of important genes involved in spermatid elongation process. Differential miRNA expression in round spermatids (RS) of GRTH KO and GRTH-KI mice in comparison with mRNAs remains unexplored. Our miRNAseq analysis of small RNAs obtained from RS reveal differential expression of important miRNAs that regulate spermatid differentiation, apoptosis, chromatin compaction and ubiquitination. mRNAseq analysis of RS isolated from GRTH-KI and GRTH-KO mice models were also carried-out to study the putative miRNA targets and mRNA-miRNA interaction. mRNAseq analysis revealed specific set of mRNAs that are critical for sperm chromatin compaction, ubiquitination and spermatid elongation etc. miRNA-mRNA interaction prediction highlighted differentially expressed/enriched miRNA transcripts whose predicted mRNA targets were differentially expressed. Based on the interaction information of the miRNAs-mRNAs differential analysis, the miRNA-mRNA network was constructed.  These results demonstrate the importance of miRNA in the translational arrest and stability of germ cell specific mRNAs which are critical for later stages of spermiogenesis and fertility.

overall_design: Differential expression analysis of mRNA and miRNA transcriptomic profile in round spermatids. This study compares the miRNA/mRNA profiles of GRTH knock-out and GRTH knock-in round spermatids to wild-type to assess the role of GRTH in spermiogenesis.

first: Rajakumar

last: Anbazhagan

first: Raghuveer

last: Kavarthapu

first: Kiersten

last: Campbell

first: Fabio

last: Faucz

first: Maria

middle: L

last: Dufau


title: Hypoxia-induced pulmonary hypertension in calf right ventricle

city: Aurora

first: R.

middle: Dale

last: Brown

state: Colorado

address: 12700 East 19th Ave

institute: University of Colorado Anschutz Medical Campus

summary: Right ventricular (RV) failure is the major determinant of outcome in pulmonary hypertension (PH).  Calves exposed to 2-wks environmental hypoxia develop severe PH and unlike rodents, chronic hypoxia-induced PH in this species can lead to right heart failure.   We therefore sought to examine the molecular and structural changes in the RV in calves with hypoxia-induced PH, hypothesizing that we could identify mechanisms underlying compensated physiological function in the face of developing severe PH.  Calves were exposed to 14d of hypobaric hypoxia (PB=430 mm Hg, equivalent to 4570m elevation, n=29) or ambient normoxia (1525m, n=25).  Cardiopulmonary function was evaluated by right heart catheterization and pressure volume loops. Molecular and cellular determinants of RV remodeling were analyzed by cDNA microarrays, RealTime PCR, proteomics and immunochemistry.  Hypoxic exposure induced robust PH, with increased RV contractile performance and preserved cardiac output, yet evidence of dysregulated RV-pulmonary artery mechanical coupling consistent with advanced PH.  Analysis of gene expression revealed cellular processes associated with structural remodeling, cell signaling, and survival.  We further identified specific clusters of gene expression associated with (i) hypertrophic gene expression and pro-survival mechanotransduction through YAP-TAZ signaling, (ii) ECM remodeling, (iii) inflammatory cell activation and (iv) angiogenesis. A potential transcriptomic signature of cardiac fibroblasts in RV remodeling was detected. Proteomic and immunohistochemical analysis confirmed RV myocyte hypertrophy, together with localization of ECM remodeling, inflammatory cell activation, and endothelial cell proliferation within the RV interstitium.  In conclusion, hypoxia and hemodynamic load initiate coordinated processes of protective and compensatory RV remodeling to withstand the progression of PH.

overall_design: Age-matched male Holstein dairy calves were exposed to 14d hypobaric hypoxia (PH, 4570m equivalent, n=5) compared to ambient normoxic controls (CO, 1525m, n=5).  RV tissue was collected and analyzed by Affymetrix Bovine GeneChip cDNA oligonucleotide microarrays

first: R

middle: D

first: Sushil

last: Kumar


title: The miRNA expression profiles of round spermatids during GRTH/DDX25 mediated spermiogenesis: mRNA-miRNA Network analysis [mRNAseq]


title: Enzymatic Methylation Sequencing of Wt and mutant Arabidopsis plants grown at elevated carbon dioxide levels

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

type: Methylation profiling by high throughput sequencing

summary:
Plant growth response to elevated levels of CO2 in the environment needs to be deeply investigated to understand the impact of rising global carbon dioxide levels. While the response of plants directly exposed to elevated CO2 is relatively well-studied, the trans-generational impact of elevated CO2 exposure in plants returned to ambient conditions is unexplored. In this study, we show that plants develop a trans-generational memory of elevated CO2 exposure in the next generation even after returning the plants to ambient CO2 levels. By analysing whole genome methylation, we identified that cytosine DNA methylation mechanisms are key to both initiate and maintain this epigenetic memory across generations.

Grant ID: EF-1921724
Grant Title: Revealing how epigenetic inheritance governs the environmental challenge response with transformative 3D genomics and machine learning
Funding Source: National Science Foundation (NSF)

overall_design: Examination of genome-wide methylated cytosines in Wt and mutant Arabidopsis plants grown at ambient or elevated carbon dioxide environment using Enzymatic Methylation sequencing.

first: Kaushik

last: Panda


title: The development of mucositis by everolimus treatment of an oral 3D tissue model

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

country: United Kingdom

institute: University of Cambridge

summary: An oral mucosa tissue model was treated with 32 ng or 64 ng everolimus, an mTOR inhibitor, for 40 or 60 hours to study the transcriptome changes

overall_design: Everolimust treatment of oral mucosa

last: Lambros


title: RNA-seq analysis of total RNA from inflorescence stems of Arabidopsis Col-0, ccr-1, fer-4 and ccr-1/fer-4

city: Denton

first: Chang

last: Liu

address: 1155 Union Circle #311428

institute: University of North Texas

summary: A. thaliana lines with reduced lignin content through down-regulation of the lignin biosynthesis enzymes cinnamoyl CoA reductase (CCR) exhibit extensive cell wall remodeling which results in the release of a mixture of pectic oligosaccharide elicitors of pathogenesis-related (PR) protein gene expression through the salicylic acid signaling pathway. Loss of function of FERONIA, a CrRLK1-like subfamily receptor-like kinase resulted in loss of PR-1, -2 and- 5 gene activation in stems of the ccr1/fer-4 double mutant.

overall_design: We utilized RNA-seq analysis of total RNA from inflorescence stems of WT, ccr-1, fer-4 and ccr-1/fer-4 to determine the extent to which loss of function of FERONIA affected the expression of other genes that are up-regulated in ccr1-3.

first: Richard

last: Dixon

first: Xiaolan

last: Rao


title: VIP152 is a Selective CDK9 Inhibitor with Pre-Clinical In Vitro and In Vivo Efficacy in Chronic Lymphocytic Leukemia

city: Columbus

first: Steven

last: Sher

state: OH

department: Division of Hematology, Department of Internal Medicine

institute: The Ohio State University

summary: Chronic lymphocytic leukemia (CLL) is effectively treated with targeted therapies including Bruton tyrosine kinase inhibitors (ibrutinib or acalabrutinib) and BCL2 antagonists (venetoclax). When these become ineffective, treatment options are limited. Positive transcription elongation factor complex (P-TEFb), a heterodimeric protein complex composed of cyclin dependent kinase 9 (CDK9) and cyclin T1, functions to regulate short half-life transcripts by releasing RNA Polymerase II (POLII) from proximal-promoter pause by way of phosphorylation. The transcripts regulated by P-TEFb are frequently dysregulated in solid tumors and hematologic malignancies; however, therapies targeting inhibition of P-TEFb have not yet achieved approval for cancer treatment. This is due to lack of selective inhibitors and undesirable side-effect profiles of less selective inhibitors. VIP152 kinome profiling revealed CDK9 as the main enzyme inhibited at 100nM, with over a 10-fold increase in potency compared with other inhibitors currently in development for this target. VIP152 induced cell death as measured by apoptosis in CLL cell lines and primary patient samples. Transcriptome analysis revealed compensatory upregulation in translation machinery and inhibition of RNA degradation. Mechanistically, VIP152 inhibits the assembly of P-TEFb onto the transcription machinery and disturbs CDK9 binding partners such as HEXIM1, MEPCE, and LARP7. Finally, C57BL/6J immune competent mice were engrafted with CLL-like cells of Eµ-MTCP1 over-expressing mice and treated with either VIP152 or vehicle. VIP152-treated mice had a reduction of blood disease over time and an improved overall survival. These data suggest that VIP152 is a highly selective inhibitor of CDK9 that represents an attractive new therapy for CLL.

overall_design: We analyzed total cellular RNA from 4 different treatment naïve CLL patients following treatment with either DMSO or 1µM VIP152

first: Rosa

last: Lapalombella

first: John

middle: C

last: Byrd

first: Pearlly

last: Yan


title: Translational characterization of the temporal dynamics of metabolic dysfunctions in liver, adipose tissue and the gut during diet-induced NASH development in Ldlr−/−.Leiden mice

city: Rijswijk

first: Eveline

last: Gart

state: Zuid-Holland

address: Van vredenburchweg 659

country: Netherlands

institute: TNO

summary:
Title:  White adipose tissue inflammation and gut permeability develop prior to NASH development, associated with increased oxidative stress, intrahepatic diacylglycerol and proinflammatory chemokines in the liver of diet-induced obese and hyperinsulinemic Ldlr-/-.Leiden mice
Abstract:  NAFLD progression from simple steatosis to NASH and fibrosis is driven by an intricate interplay between molecular and cellular mechanisms. These drivers are not limited to the liver itself but also white adipose tissue and gut may contribute. Current knowledge on these drivers is mostly based on studies that investigate these at a single time point (typically end-stage disease). However, such studies provide no insight into the temporal dynamics and chronology, which therefore remain poorly understood. Ldlr-/-.Leiden mice were fed a high-fat diet (HFD) to induce obesity-associated NAFLD and compared to lean controls fed chow. Groups of mice were sacrificed after 8, 16, 28 and 38 weeks to study liver, white adipose tissue, gut and circulating factors to investigate the sequence of pathogenic events in these critical metabolically active organs as well as organ-crosstalk during NAFLD development. Ldlr-/-.Leiden mice on a HFD develop obesity, dyslipidemia and insulin resistance, essentially as observed in obese NASH patients, in this translational context WAT and gut dysfunction precede the development of NASH and liver fibrosis.

first: Wim

last: van Duyvenvoorde

first: Jessica

last: Snabel

first: Christa

last: de Ruiter

first: Joline

last: Attema

first: Martien

last: Caspers

last: Giera

first: Serene

last: Lek

first: Aswin

last: Menke

first: Jaap

last: Keijer

first: Kanita

last: Salic

first: Robert

last: Kleemann

first: Martine

last: Morrison


title: Nuclear m6A Reader YTHDC1 Promotes Muscle Stem Cell Activation/Proliferation by Regulating mRNA Splicing and Nuclear Export [LACE-seq]

city: Hong Kong

first: QIANG

last: SUN

address: Ngan Shing Street

department: Department of Orthopaedics and Traumatology

country: Hong Kong

institute: The Chinese University of Hong Kong

overall_design: YTHDC1 LACE-seq in ASC and C2C12 cells are performed

first: Huating

last: Wang

first: Yulong

last: Qiao

first: Qiang

last: Sun


title: Deciphering the involvement of the Hippo pathway co-regulators, YAP/TAZ in invadopodia formation and matrix degradation

city: Rehovot

first: Benjamin

last: Geiger

address: POB 26

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

summary: The paralogous transcriptional cofactors Yes-associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ, also called WWTR1), the main effectors of the Hippo signal transduction pathway, are emerging as pivotal determinants of malignancy in cancer. We aim to compare the transcriptome altered by knockdown of YAP, TAZ or both using siRNA in MDA-MB-231 (derived from human metastatic breast adenocarcinoma).

overall_design: Knockdown of YAP, TAZ or both using siRNA in MDA-MB-231 cell line and assess the transcriptomic profile.

first: Jubina

last: Balan

first: Bareket

last: Dassa

first: David

last: Morgenstern

first: Michal

last: Shreberk-Shaked

first: Moshe

last: Oren


title: Nuclear m6A Reader YTHDC1 Promotes Muscle Stem Cell Activation/Proliferation by Regulating mRNA Splicing and Nuclear Export [RNA-seq]

overall_design: Total RNA-seq and subcellular RNA-seq in YTHDC1 inducible degradation C2C12 cells, total RNA-seq and subcellular RNA-seq in WT and YTHDC1 iKO ASC cells


title: Transcriptomic changes in Sin3A deficient  CD4 T cells

city: Pamplona

first: Juan

middle: Jose

last: Lasarte

state: Navarra

address: Avda Pio XII, 55

department: Inmunología e Inmunoterapia

country: Spain

institute: Centro de Investigación Médica Aplicada

summary: Highly purified CD4+ T cells from Rosa26-CreERT2 +/- Sin3AF/F micewere then cultured in interleukin 7 (IL-7) in the absence or the presence of 4-hydroxytamoxifen (TAM) for 6 days  to allow Cre expression in the absence of cell division or differentiation . Next, we compared the behavior of Sin3A sufficient and deficient T cells in Th17 skewing conditions. RNA was then isolated and sequenced for the analysis of differential expression of mRNA transcripts

overall_design: Sin3A deficient and Sin3A suficient CD4 T cells were cultured  for 3  days in Th17 polarizing conditions. mRNA was then purified and analyzed by RNA-sec

first: Ana

last: Mondino


title: Profiling of microRNAs associated with Nucleolin (NCL) in human pulmonary artery smooth muscle cells

city: Incheon

first: Hara

last: Kang

address: 119 Academy-ro

country: South Korea

institute: Incheon National University

summary: Analysis of miRNAs associated with NCL via RNA immunoprecipitation in pulmonary artery smooth muscle cells using NCL antibodies to identify a distinct set of miRNAs regulated by NCL. Results provide insight into the regulatory mechanism of RNA binding proteins in vascular smooth muscle cells.

overall_design: microRNA expression profiles of the human pulmonary artery smooth muscle cells after RNA immunoprecipitation using NCL antibodies by Illumina NextSeq500.


title: Microarray gene expression analysis of  breast cancer cells overexpressing circular RNA circAAGAB

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

institute: National Taiwan University

summary: In our previous study, we found a circular RNA, circAAGAB, was downregulated under hypoxia. However, the role of circAAGAB in breast cancer cell is still unknown. Therefore, we overexpressed circAAGAB in MDA-MB-231 to research for its effects on breast cancer cells.

overall_design: Total RNA was extracted 24 h after the transfection of circAAGAB plasmid and control plasmid

first: Liang-Chan


title: Nuclear m6A Reader YTHDC1 Promotes Muscle Stem Cell Activation/Proliferation by Regulating mRNA Splicing and Nuclear Export


title: Multiomics profiling of young and old quiescent skeletal muscle stem cells

city: Palo Alto

first: Jamie

middle: O.

last: Brett

address: 3801 Miranda Avenue, Building 100, Room E4-216

department: Neurology and Neurological Sciences

institute: Stanford University


title: Multiomics profiling of young and old quiescent skeletal muscle stem cells [aging RNA-seq]

summary: To uncover new pathways that are important for skeletal muscle stem cell aging, we performed multiomics profiling, including transcriptomics, DNA methylomics, proteomics, and metabolomics on quiescent muscle stem cells from young and old mice. Our goals were to discover pathways that have been overlooked by isolated profiling approaches and to gain insight into which changes are causal, compensatory, correlational, and consequential. In our work, we found that glutathione metabolism is a key pathway of muscle stem cell aging that involves a compensatory feedback loop. Follow-up experiments showed that old muscle stem cells actually form a dichotomy between glutathione-high muscle stem cells and glutathione-low muscle stem cells. RNA-Seq showed that glutathione-high old muscle stem cells are able to synthesize adequate glutathione and thus compensate adequately for oxidative stress with increased glutathione turnover, while glutathione-low old muscle stem cells have failed to compensate for oxidative stress metabolically and instead show increased inflammatory signaling.

overall_design: C57BL/6 male mice were used at two ages: young (4 months) and old (22 months). Quiescent muscle stem cells were isolated from limb muscles by FACS (CD45- CD31- Sca1- VCAM+) and immediately used for analysis. Each replicate represents the muscle stem cells from a single animal. There are 4 replicates in each group.

middle: O

first: Thomas

last: Rando

first: Daniel

middle: I

last: Benjamin


title: Multiomics profiling of young and old quiescent skeletal muscle stem cells [aging WGBS]


title: Genome-wide circRNA profiling reveals that circGAS2-2 are abundantly expressed and regulates myoblast proliferation in indigenous Chinese duck breed

city: Nanchang

first: Biao

last: Chen

address: Zhimin street, Jingkai district

institute: Jiangxi Agricultural University

summary: The objective of this study was to identify candidate circular RNAs associated with duck muscle development. circRNA sequencing analysis was employed using female breast muscle samples embryo stage 13th day (E13) and embryo stage 19th day (E19). RNA-seq data and validation experiment in duck myoblast cells showed that circGAS2-2 significantly differential expressed between E13 and E19 group.

overall_design: Examination of circRNA profiles  in female muscle samples from embryo stage 13th day (E13) and embryo stage 19th day (E19).

first: Sanfeng

last: Liu


title: PWD/Ph-encoded genetic variants suppress ApcMin-triggered intestinal tumor formation by modulating the cellular Wnt/beta-Catenin response

city: Berlin

first: Markus

last: Morkel

address: Ihnestraße 63-73

country: Germany

institute: Max Planck Institute for molecular Genetics


title: Intestinal cancer modifier RNA-Seq

summary: Cancers predominantly arise from adult stem cells accumulating somatic driver mutations, but how genetic predisposition affects the penetrance of mutations in tumor initiation is not well understood. Here, we have analyzed gene expression in tumor-prone ApcMin/+ mice on highly variant C57BL/6J and PWD/Ph genetic backgrounds. We show that activation of beta-Catenin-driven and stem cell-specific gene expression in the presence of ApcMin or following APC loss is high in B6 mouse intestines, but remains moderate in intestines carrying PWD/Ph chromosome 5, suggesting that PWD/Ph variants restrict adenoma initiation by controlling stem cell homeostasis. Gene expression of modifier candidates and DNA methylation on chromosome 5 are predominantly cis-controlled and largely reflect the parental patterns, providing a genetic basis for inheritance of tumor susceptibility.

overall_design:
RNA-Seq of C57BL/6 and chromosome 5 exchange (consomic) PWD/C57BL/6 Apc(Min/+) mice.
Intestinal tissues of mice were analysed by RNA sequencing. Mice analysed differ in their status of the APC tumor suppressor locus, and are either APC(+/+) (=wildtype) or APC(min/+), that is, they carry an adenoma-inducing APCmin allele. Of the latter, normal intestinal tissue and intestinal adenoma tissue is analysed. The mice also have differences in their background genome, which is either C57BL/6 or PWD/Ph or a combination of both. Mice designated C5 carry a PWD/Ph chromosome 5, while the remaining genome is C57BL/6. Tissues are usually analysed in triplicates, as indicated. Furthermore, organoids were established from some tissues and analysed by RNA-seq, as indicated. Some organoid samples were treated with 5-aza-cytidine (AZA).

first: Bernhard

middle: G

last: Herrmann


title: Opioid receptor signaling suppresses leukemia by inducing TET-dependent DNA demethylation [RNA-seq]

city: Hangzhou

first: Jun

last: Lu

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Acute myeloid leukemia (AML) is a group of heterogeneous diseases with high malignancy. The ten-eleven translocation (TET) mediated DNA demethylation was known to be critically associated with AML pathogenesis. Through chemical compound screening, we found an opioid receptor agonist, namely loperamide hydrochloride (OPA1), most significantly suppressed AML cell viability. The potential therapeutic effects of opioid receptor agonists, especially OPA1, were then verified in AML cells in vitro, and AML mouse models carrying t(11q23) and t(8;21) in vivo. OPA1-induced activation of OPRM1 enhanced the transcription of TET2, increased DNA 5-hydroxymethylcytosine (5hmC) modification, and in turn, activated NFκB signaling. Notably, AML with TET2 mutations or chemotherapy resistance were sensitive to OPA1. Our results unveiled the previously unappreciated OPRM1-TET2-5hmC-TRAF2 regulatory axis in AML, and highlighted the therapeutic potential of opioid agonists, particularly OPA1, a FDA-approved antidiarrheal drug, in treating AML, especially TET2 mutated AML and chemotherapy-resistant AML, which were known to have poor prognosis.

overall_design: RNA profiles of THP-1 cells treated with DMSO or OPA1 were generated by deep sequencing.

first: Huanhuan

last: Zhao


title: Opioid receptor signaling suppresses leukemia by inducing TET-dependent DNA demethylation [5hmC-seq]

overall_design: Examination of 5hmC modifications in THP-1 cells treated with OPA1 or DMSO.


title: Opioid agonists as potential AML therapy

overall_design: Refer to individual Series


title: Pregnane X Receptor (PXR) protects against cisplatin-induced acute kidney injury

city: Dalian

first: Zhilin

last: Luan

state: China

address: 9 W., S. Lvshun Blvd.

institute: Advanced Institute for Medical Sciences, Dalian Medical University

summary:
Background: Cisplatin-induced acute kidney injury (CAKI) has been recognized as one of the most serious side effects of cisplatin. Pregnane X receptor (PXR) is a ligand-dependent nuclear receptor and serves as a master regulator of xenobiotic detoxification. Increasing evidence also suggests PXR has many nonxenobiotic functions including the regulation of cell proliferation, inflammatory response and glucose and lipid metabolism.
Methods: In this study, we aimed to investigate the role of PXR in cisplatin-induced nephrotoxicity. CAKI model was performed in wild-type or PXR knockout mice. Pregnenolone 16α-carbonitrile (PCN), a mouse PXR specific agonist, was used for PXR activation. The renal function, biochemical, histopathological and molecular alterations were examined in mouse blood, urine or renal tissues. Whole transcriptome analysis was performed by RNA sequencing. Dual-luciferase reporter and chromatin immunoprecipitation (ChIP) assays were applied to determine the regulation of PXR on its target genes.
Results: We found that PXR activation significantly attenuated CAKI as reflected by improved renal function, reduced renal tubular apoptosis, ameliorated oxidative and endoplasmic reticulum stress, and suppressed inflammatory factor expression. RNA sequencing analysis revealed that the renoprotective effect of PXR was associated with multiple crucial signaling pathways. In particular, PXR protected against cisplatin-induced AKI by the activation of PI3K/AKT pathway and the induction of multidrug and toxin extrusion 1 (MATE1), an important transporter mediating cellular excretion of cisplatin, in the kidney.
Conclusions: Our results demonstrate that PXR activation can preserve renal function in cisplatin-induced AKI and suggest a possibility of PXR as a novel therapeutic target for cisplatin-induced nephrotoxicity.

overall_design: Renal mRNA profiles of 8-week old wild type (WT) treated with or without cisplatin and/or PCN were generated by deep sequencing, in triplicate, using Illumina platform.

first: Youfei

last: Guan


title: Multiomics profiling of young and old quiescent skeletal muscle stem cells [GSH RNA-seq]

summary: To uncover new pathways that are important for skeletal muscle stem cell (MuSC) aging, we performed multiomics profiling, including transcriptomics, DNA methylomics, proteomics, and metabolomics on quiescent MuSCs from young and old mice. Our goals were to discover pathways that have been overlooked by isolated profiling approaches and to gain insight into which changes are causal, compensatory, correlational, and consequential. In our work, we found that glutathione metabolism is a key pathway of MuSC that involves a compensatory feedback loop. Follow-up experiments showed that old MuSCs actually form a dichotomy between glutathione-high MuSCs and glutathione-low MuSCs. RNA-Seq showed that glutathione-high old MuSCs are able to synthesize adequate glutathione and thus compensate adequately for oxidative stress with increased glutathione turnover, while glutathione-low old MuSCs have failed to compensate for oxidative stress metabolically and instead show increased inflammatory signaling.

overall_design: C57BL/6 male mice were used at two ages: young (4 months) and old (23 months). Quiescent MuSCs were isolated from limb muscles by FACS (CD45- CD31- Sca1- VCAM+). Sorted cells were immediately stained with ThiolTracker Violet (5 uM) to indicate glutathione (GSH) status and resorted by FACS. For young, all cells were recollected (almost all are GSH-high). For old, the population was split into GSH-high and GSH-low collection groups. Each replicate represents the cells from a single animal (young) or pooled two animals (old).

first: Pieter

last: Both


title: Transcriptome-based analysis of CCNY-mediated learning and memory in the hippocampus

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: CCNY-mediated regulation of learning and memory in the hippocampus by performing and analyzing transcriptome profiling.

overall_design: We isolated the hippocampi of wild-type and Ccny knockout mice after Morris water maze original and reversal learning tasks.

first: Eunsil

last: Cho

first: Jong-Hwan

first: Mirang

first: Seon-Young

first: Mikyoung

last: Park


title: RNA-seq from mice CD4+CD25+ splenocytes

status: Public on Mar 19 2023

city: Shanghai

first: Yile

last: Zhou

address: 180 Fenglin Road

institute: Fudan University

summary:
To better understand the function of CD4+CD25+ splenocytes from different ages, target cells from young(8-week old)  aged(18-month old) were sorted with magnetic beads.
We then performed gene expression profiling analysis using data obtained from RNA-seq of different cells from different age.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD4+CD25+ splenocytes of aged and young mice sorted with magnetic beads.

first: Huihui

last: Ju

first: Yan

last: Hu

first: Tingting

last: Li

first: Zhouyi

first: Yuan

last: Si

first: Xia

last: Sun

first: Yi

last: Shi

first: Hao

last: Fang


title: Comprehensive characterization of hepatic inflammatory changes in a mouse model of alpha-1 antitrypsin deficiency

city: Gainesville

first: Tongjun

last: Gu

state: FL

address: 2033 Mowry Road

department: ICBR

institute: The University of Florida

summary: In this study, we sought to thoroughly characterize the liver pathophysiology of a human transgenic mouse model for alpha-1 antitrypsin deficiency (AATD) with a strong manifestation of AATD-mediated liver disease. Male and female transgenic mice for normal variant human alpha-1 antitrypsin (Pi*M) and mutant human alpha-1 antitrypsin (Pi*Z) at 3 and 6 months of age with a C57BL/6J background were subjected to study. The progression of hepatic accumulation of mutant alpha-1 antitrypsin (ZAAT), hepatocyte injury, steatosis, liver inflammation and fibrotic features of this mouse model were monitored by performing an in vivo study.

overall_design: This study was performed with approval from the University of Florida Institutional Animal Care and Use Committee with strict adherence to the Guide for Care and Use of Laboratory Animals (NIH, 86-23). Transgenic Pi*Z and Pi*M were maintained on a C57BL/6J background. Mice were provided food, water and 12:12 hour dark:light cycles in a barrier facility. Intraperitoneal injection of lipopolysaccharide (LPS, InvivoGen, San Diego, CA) at a dose of 0.5ug LPS/g of body mass was performed 16 hours prior to euthanasia.

first: Nazli

last: Khodayari


title: RNA-Seq analylsis of human NASH and Normal liver tissues

city: Nanjing

first: Kangpeng

last: Jin

state: Jiangsu Province

address: 321 Zhongshan Road

department: Department of Hepatobiliary Surgery

institute: The Affiliated Drum Tower Hospital of Nanjing 9 University Medical School

summary: To understand the mechanisms of NASH, we detected mRNA level in human NASH (n=5) and normal tissue (n=5) by RNA-Seq.  The normal tissues were collected from the patients who received hepatic haemangioma surgery, and the steatotic liver samples were collected from the eligible patients who received bariatric surgery underwent liver biopsy or surgical resection at Nanjing Drum Hospital (Nanjing,China). This RNA-Seq might help us to find the important target genes and signaling pathway during NASH.

overall_design: mRNA level of human NASH and Normal liver tissues

first: Beicheng


title: Inhibition of BRD4 Rescues Cardiac phenotype in Myocyte-Specific Lamin A/C Null Mice

city: Houaton

first: Ali

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

institute: UTHSC, Houston

summary: Deletion of Lmna, encoding nuclear membrane protein LMNA, specifically in mouse cardiac myocytes activates BRD4 and leads to heart failure, arrhythmias, myocardial fibrosis, apoptosis, and premature death, which were partially rescued upon inhibition of BRD4.

overall_design: RNA-seq from Cardiac myocytes from 4 control  (WT) and 4 Myh6-cre:LmnaF/F vehicle treated and 4 Myh6-cre:LmnaF/F JQ1 treated

first: Gaelle

last: Auguste

first: Leila

last: Rouhi

first: Scot

last: Matkovich

first: Cristian

last: Coarfa

first: Matthew

last: Robertson

first: Grazyna

last: Czernuszewicz

first: Priyatansh

last: Gurha


title: Pre-weaning heat stress alters liver DNA methylation in dairy calves [Bisulfite-Seq]

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: The impact of postnatal heat stress exposure in neonatal calves is not well-understood, and adequate heat abatement methods during the pre-weaning phase are lacking. This study aimed to investigate the impact of pre-weaning heat stress on liver DNA methylation profiles.

overall_design: Holstein dairy calves were group housed and exposed to postnatal heat stress (HS; n = 6) or postnatal cooling (CL; n = 6) from birth to weaning. Liver tissue samples were harvested via biopsy at 42 days of age for Reduced-Representation Bisulfite Sequencing (RRBS-seq).

first: Jimena

last: Laporta


title: Small RNA sequencing facilitates  analysis of exosomal RNA transcriptomes

city: wuhan

first: xin

last: wang

address: Donghu road

institute: wuhan university

summary: Smal RNA is a type of single-stranded small-molecule RNA with a size of about 18-40 bases, mainly including microRNA, piRNA, snoRNA, snRNA, tRNA and so on. Small RNAs have important regulatory functions in cells and have the potential to be used as disease diagnostic markers or drug targets. We report the results of all small RNAs in exosomes from HTNV infected/uninfected HUVECs by high-throughput sequencing technology. We find that  the transcriptomes of Exo-NC group (exosomes from HTNV uninfected cells) and Exo-HV group (exosomes from HTNV infected cells) expressed distinctly different expression patterns of miRNA.

overall_design: Examination of  exosomes from HTNV infected/uninfected HUVECs

first: Qing-zhou

last: Chen

first: Xin

last: Wang

first: Yu-xing

last: Zan

first: Mei-rong

first: Jie

last: Yan

first: Wei-wei

last: Guo

first: Kai-Ji

last: Li

first: Yuan-yuan

last: Liu

first: Fan

last: Luo

first: Yong

last: Feng


title: Pre-weaning heat stress alters liver transcriptome in dairy calves [RNA-Seq]

summary: The impact of postnatal heat stress exposure in neonatal calves is not well-understood, and adequate heat abatement methods during the pre-weaning phase are lacking. This study aimed to investigate the impact of pre-weaning heat stress on liver gene expression profiles.

overall_design: Holstein dairy calves were group housed and exposed to postnatal heat stress (HS; n = 6) or postnatal cooling (CL; n = 6) from birth to weaning. Liver tissue samples were harvested via biopsy at 42 days of age for RNA Sequencing (RNA-seq).


title: Pre-weaning heat stress alters liver DNA methylation in dairy calves

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


title: Intestinal cancer modifier MeDIP-Seq

first: Markus

last: Morkel

overall_design:
Methyl-DNA immunoprecipitation (MeDIP)-Seq of C57BL/6 and chromosome 5 exchange (consomic) PWD/C57BL/6 Apc(Min/+) mice.
Intestinal tissues of mice were analysed by sequencing of immunoprecipitated methylated DNA. Mice analysed differ in their status of the APC tumor suppressor locus, and are either APC(+/+) (=wildtype) or APC(min/+), that is, they carry an adenoma-inducing APCmin allele. Of the latter, normal intestinal tissue and intestinal adenoma tissue is analysed. The mice also have differences in their background genome, which is either C57BL/6 or PWD/Ph or a combination of both. Mice designated C5 carry a PWD/Ph chromosome 5, while the remaining genome is C57BL/6. Tissues are usually analysed in triplicates, as indicated.

first: Bernhard

last: Herrmann


title: Gene expression profiling shows that CYCLIN-DEPENDENT KINASE 8 (CDK8) promotes the expression of defense-related genes in a higher-order jaz (jazD) mutant

city: East Lansing

first: Qiang

state: MI

address: 612 Wilson Rd

department: Plant Research Laboratories

institute: Michigan State University

summary: The decuple jaz mutation (jazD) promotes defense responses while inhibiting growth. We used RNA-sequencing to query the the transcriptomes of wild-type Col-0, cdk8-1, jazD and jazD cdk8-1 plants. The data highlight how CDK8 contributes to the expression of growth- and defense-related genes in jazD.

overall_design: Analysis of Col-0 (wildtype), cdk8-1, jazD, and jazD cdk8-1 (four genotypes), with three biological replicates per genotype - 12 total samples.

first: Gregg

last: Howe


title: H3K4me2/3 modulate the stability of RNA polymerase II pausing (RNA-Seq)

status: Public on Mar 18 2023

first: Aixia

last: Song

address: Dong'an Road

summary: Modifications of histones are intricately linked with the regulation of gene expression, with demonstrated roles in various physiological processes and disease pathogenesis. Methylation of histone H3 lysine 4 (H3K4), implemented by the COMPASS family, is enriched at promoters and associated cis-regulatory elements, with H3K4 trimethylation (H3K4me3) considered a hallmark of active gene promoters. However, the relative roles of deposition and removal of H3K4 methylation, as well as the extent to which these events contribute to transcriptional regulation have so far remained unclear. Here, through rapid depletion of either of two shared subunits of COMPASS family members, we reveal a dynamic turnover of H3K4me2 and H3K4me3 mediated by the KDM5 family of histone demethylases. Loss of H3K4me2 and H3K4me3 following COMPASS disruption does not impair the recruitment of TFIID and initiating RNA polymerase II (Pol II). Instead, their loss leads to reductions in the paused form of Pol II on chromatin while inducing the relative enrichment of the Integrator-PP2A (INTAC) termination complex, leading to reduced levels of elongating polymerases, thus revealing how H3K4me2 and H3K4me3 dynamics can regulate Pol II pausing to sustain or attenuate transcription.

overall_design: We performed ChIP-seq, PRO-seq, or RNA-seq to investigate the role of methylation of histone H3 lysine 4 (H3K4) in regulating transcription. In this study, samples for each condition were collected in biological duplicates. Cells were treated with dTAG13 for 6, 12,or 24 hours, the corresponding control cells were treated for the same duration with vehicle only (DMSO) at the same vol/vol dilution.

first: Shibin

last: Hu

first: Linna

last: Peng

first: Fei

middle: X


title: Small noncoding RNA Dysregulation is Implicated in Manganism in a Rat Model of Methylcyclopentadienyl Manganese Tricarbonyl-Induced Unrepaired Striatum Damage

city: Nanning

first: Qifeng

last: Zhu

address: No. 10, Hua-dong Rd

institute: Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine

summary: Excessive accumulation of manganese in brain can cause Parkinsonian-like symptoms, known as Manganism. Methylcyclopentadienyl Manganese Tricarbonyl (MMT), a gasoline antiknock additive, is one of environmental exposures of manganese, which can lead to manganism in Rats. Though some researches showed that small non-coding RNAs (sncRNAs) were differently expressed in Parkinson’s disease (PD) patients, it was still unclear whether and how sncRNAs dysfunction appeared in Manganism. Unfartunately, transfer RNA-derived small RNAs (tsRNAs) and ribosomal RNA-derived small RNAs (rsRNAs) are highly modified, including 3’ terminal modification such as 3’-phosphate and 2’,3’-cyclic phosphate that block the adapter ligation process, and RNA methylations such as m1A, m3C, m1G and m22G that interfere with reverse transcription. Thus, sncRNAs could escape from traditional small RNA-seq. Here, we present the differential expression of sncRNAs in MMT-induced unrepaired striatum in rats compared with control group, using PANDORA-seq, which could discover the highly modified sncRNAs. By removing sncRNAs modification, we found that 599 sncRNAs were differently expressed in Striatum of MMT-treated rats compared with control group, and 1155 sncRNAs in Mn-treated vs control. Further function analysis for predicted targets of these DE-sncRNAs shown that dysregulation of sncRNAs was implicated Manganism in rats.

overall_design: The rats were treated as previously described(Zhu et al., 2022). Briefly, After the animals had acclimated for one week, eighteen rats containing 9 males and 9 females (220 ± 20 g, 8-weeks-old) were divided randomly into three groups: Control, MMT and positive control (MnCl2) of rats (with 3 rats in each groups/sex). The MMT group were treated with 4 mg/kg MMT (about 1 mg Mn/kg) with corn oil via the intragastrical (i.g.) route once a day, six days per week, for 8 weeks. The control group were treated with corn oil (1 ml/kg administration volume) in the meantime. The rats in the MnCl2 group were given 200 mg/kg MnCl2·4H2O (i.g.) with physiological saline (10 ml/kg administration volume). Animals were weighed daily.

last: Jiang

first: Yuanbo

first: Lili

last: Lu

first: Fajian

last: He

first: Shuqi

last: Huang

first: Zhaoying

first: Jing

last: Yao

first: Ningning

last: Lei

first: Jianmin

first: Shijin


title: H3K4me2/3 modulate the stability of RNA polymerase II pausing (PRO-Seq)

last: Chen


title: Maternal administration of acetaminophen affects meiosis through its metabolite NAPQI targeting SIRT7 in fetal oocytes

city: Chongqing

first: Xinyi

last: Mu

address: 1 Yixueyuan Road, Yuzhong District, Chongqing, PR China

institute: Chongqing Medical University

summary: Acetaminophen (APAP) is clinically recommended as analgesic and antipyretic among pregnant women. However, accumulating laboratory evidence shows that the use of APAP during pregnancy may alter fetal development. Since fetal stage is a susceptible window for early oogenesis, we aim to assess the potential effects of maternal administration of APAP on fetal oocytes.  Maternal administration and the fetal ovary cultures showed that APAP (50 and 150 mg/kg.bw/day) caused meiotic aberrations in fetal oocytes through its metabolite NAPQI, including meiotic prophase I (MPI) progression delay and homologous recombination defects. Co-treatment with NAM or NRC, NAD+ supplements, efficiently restored the MPI arrest, while the addition of the inhibitor of SIRT7 invalidated the effect of the NAD+ supplement. Additionally, RNA sequencing revealed distorted transcriptomes of fetal ovaries treated with NAPQI. Further, the fecundity of female offspring was affected, exhibiting as delayed primordial folliculogenesis and puberty onset, reduced levels of ovarian hormones, and impaired developmental competence of MII oocytes. Short-term administration of APAP to pregnant mouse caused meiotic aberrations in fetal oocytes by its metabolite NAPQI, while co-treatment with NAD+ supplement efficiently relieves the adverse effects by interacting with SIRT7.

overall_design: Ovaries at 14.5 dpc were treated with 15 μM NAPQI or ethyl acetate, and were collected after 3-days culture. Then total RNA was isolated. The library products were sequenced by Next-Generation Sequencing. In the case of all the samples 3 replicates were included. In order to identify up-, or down-regulated genes the treated samples were compared to the control samples.

first: Fangfei

last: Liu


title: Immune gene signatures in human colorectal tumors with different GSNOR/ADH5 expression

status: Public on Mar 17 2023

city: Paris

first: Rafael

middle: Mena

last: Osuna

state: ile de France

address: 26 Rue D'ulm

department: Unit 932

country: France

institute: Institut Curie

summary: The study was designed to explore the relationships between GSNOR/ADH5 expression and the tumor immune microenvironment

overall_design: Twenty CRC tumors were analyzed using the Nanostring PanCancer immune profiling panel in a NanoString-nCounter DX platform

last: Mena-Osuna


title: CRISPR/Cas9-mediated gene knockout screen uncovers novel open reading frames encoded in lncRNA regulating ER+ breast cancer progression

city: Houston

first: Yiwen

state: TX

address: 1400 Pressler Street,  Unit 1410

department: Bioinformatics & Comp Biology

institute: UT MD Anderson Cancer Center

summary: A large number of lncRNAs has been found aberrant expression in breast cancer and paly functional role in tumor progression. However, the role of small peptide hidden in lncRNA are largely unexplored.  In this study, we applied the CRISPR/Cas9 screen and ribosome profiling to systematically discover nocanonical open reading frame encoded in long noncoding RNAs (lncRNAs) and explored their critical roles in ER+ breast cancer.

overall_design: CRISPR/Cas9 knockout screen and ribosome profiling to systematically discover nocanonical open reading frame encoded in long noncoding RNAs (lncRNAs) and explored their critical roles in ER-positive cancer progression.

first: Chen

last: Yiwen

first: Zheng

last: Caishang

first: Wei

last: Yanjun


title: Diclofenac inhibits esophageal squamous cell carcinoma through suppression of metabolic pathways and activation of p53 signaling

city: Philadelphia

first: Kelly

last: Whelan

state: PA

address: 3307 N Broad St. PAHB Rm 203

department: Fels Institute

institute: Temple University

summary: To investigate the molecular mechanisms of Diclofenac in ESCC cell line TE11

overall_design: We have treated ESCC cell line TE11 with 200 µM of Diclofenac for 48 hours. Then we performed RNA sequencing and Ingenuity Pathway Analysis.

first: Mohammad

middle: F

last: Kabir

first: Adam

last: Karami


title: Transcriptome analysis of murine Megakaryocytic-Erythroid Progenitors (MEPs) in a condition of iron deficiency (Tmprss KO)

city: New Haven, US & Trento, Italy

first: Toma

last: Tebaldi

state: CT

address: 300 George Street

department: CIBIO & Department of Internal Medicine, Yale Cancer Center

institute: Yale University & University of Trento

summary:
The mechanism underlying thrombocytosis in patients with iron deficiency anemia remains unknown. We present findings that support the hypothesis that low iron biases the commitment of Megakaryocytic-Erythroid Progenitors (MEP) toward the megakaryocytic (Mk) lineage in mice. In MEP of Transmembrane serine protease 6 knockout (Tmprss6-/-) mice, which exhibit iron deficiency microcytic anemia concomitant with thrombocytosis, we observed a megakaryocytic (Mk) bias, decreased labile iron, and decreased proliferation relative to wild-type (WT) MEP. Bone marrow transplantation assays suggest that the systemic iron deficiency of the Tmprss6-/- recipients contributes to the MEP lineage commitment bias. Genes involved in metabolic, VEGF, and ERK pathways were enriched among those differentially expressed between WT and Tmprss6-/- MEP. Corroborating our findings from the murine model of chronic iron deficiency anemia, primary human MEP also exhibited decreased proliferation and Mk-biased commitment when their iron sensing pathways were disrupted by knockdown of Transferrin Receptor 2. These data are consistent with a model in which low iron in the marrow environment affects MEP metabolism, attenuates ERK signaling, slows proliferation, and biases MEP toward Mk lineage commitment.
Keywords: megakaryocytic-erythroid progenitor (MEP), iron deficiency, Tmprss6

overall_design: In this study, we performed high-throughput sequencing of RNA isolated from MEP derived from WT and Tmprss6-/-  (KO) mice. Primary murine MEPs  (Lin-cKit+Sca-FcgRI/II-CD150+CD105-CD41-)  from 3 mice were pooled and sorted as one biological replicate. RNA-seq was performed in biological triplicates.

first: Juliana

last: Xavier-Ferrucio

first: Vanessa

last: Scanlon

first: Xiuqi

last: Li

first: Ping-Xia

last: Zhang

first: Nadia

last: Ayala-Lopez

first: Stephanie

last: Halene

first: Karin

last: Finberg

first: Diane

middle: S

last: Krause


title: miRNA levels in caput and cauda sperm in adult male guinea pigs following synthetic glucocorticoid exposure

city: Toronto

first: Christopher

last: Casciaro

state: ON

address: 1 King's College Circle

department: Department of Physiology

country: Canada

institute: University of Toronto

summary:
It has been demonstrated that males exposed to adversity prior to conception sire offspring exhibiting abnormal behaviour and neuroendocrine function. Epigenetic factors such as microRNA (miRNA) within sperm may be responsible for driving these effects. Synthetic glucocorticoids (sGC) are a class of drug that are commonly prescribed and may have implications for intergenerational transmission. Therefore, we hypothesized that caput and cauda sperm miRNA profiles will be altered following sGC exposure in guinea pigs.
We used miRNA microarray to evaluate the miRNA levels of caput and cauda sperm isolated from guinea pigs exposed to control and water treated with sGC. We  identified a subset of miRNAs with low levels in  cauda sperm of guinea pigs exposed to sGC.

overall_design: Caput and cauda sperm were isolated from adult male guinea pigs that either received control water (n=6) or water treated with the sGC dexamethasone (Dex) (n=6). Total RNA was extracted from caput sperm (n=6/group) and cauda sperm (n=6/group) microarray analysis was performed using miRNA 4.0 microarray (Affymetrix).

first: Hirotaka

last: Hamada

first: Alisa

last: Kostaki

first: Stephen

last: Matthews


title: Effect of paternal chronic stress on zebrafish progeny gene expression.

city: León

first: Vanesa

last: Robles

state: León

address: Facultad de Ciencias Biológicas y Ambientales. Campus de Vegazana. Área de Biología Celular

department: Molecular Biology

institute: Universidad de León

summary: To investigate the potential deleterious impact of chronic stress at molecular level in the progeny, we exposed zebrafish males to an unpredictable chronic stress protocol during 21 days

overall_design: We then performed gene expression profiling in the stress-exposed group and the control one.

first: David

last: Valcarce

first: Marta

last: Riesco

first: Leyre

last: Cuesta-Martín

first: Anna

last: Esteve-Codina

first: Juan

middle: M

last: Martínez-Vázquez


title: Mistranslation and developmental defects in an allelic series of tRNA isodecoder deletions [Ribo-seq]

city: Nedlands

first: Danielle

middle: Louise

last: Rudler

state: WA

address: 6 Verdun Street

department: Mitochondrial Medicine and Biology

country: Australia

institute: The Kids Research Institute

summary: We investigated the role of multi-copy tRNA genes and their requirement in mammals.

overall_design: RNA from mice brains were isolated from three control mice (WT) and three tRNA-Phe knockout mice, and was sequenced and analysed for ribosome profiling.

first: Aleksandra

last: Filipovska

first: Stefan

last: Siira


title: Cleavage Under Targets and Release Using Nuclease (CUT&RUN) assay of glucocorticoid receptor (NR3C1) in aggressive B-cell lymphomas [JC3]

city: Bethesda

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

summary: We determined that glucocorticoid treatment (prednisolone) affects oncogenic signaling in aggressive B-cell lymphomas. We sought to identify genes directly controlled and bound by NR3C1.

overall_design: CUT and RUN assay to NR3C1-bound regions in HBL1, SUDHL5, FL318, RAMOS cells treated with DMSO or prednisolone (10mM for HBL1, FL318, RAMOS or 25nm for SUDHL5) for 2h and 18h.

first: Jaewoo

last: Choi

first: Louis

last: Staudt


title: RNA sequencing/Gene expression studies of CSK inhibitor (CSKi) in diffuse large B-cell lymphoma (DLBCL) [JC2]

summary: We determined that CSKi treatment affects oncogenic signaling in DLBCL. We sought to measure gene expression change in DLBCL cells by RNA-sequencing following CSKi treatment.

overall_design: TMD8 and DOHH2 cells were treated in duplicates with DMSO or CSKi (500nm) for 1h, 3h, 6h and 24h.


title: Targeting oncogenic BCR signaling therapeutically by glucocorticoids and CSK inhibition

overall_design: Refer to individual Series


title: Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation


title: Rubella virus infection in endothelial cells reduces angiogenesis via interferon betainduced CXCL10

city: Leipzig

first: Jes-Niels

last: Boeckel

address: Johannisalle 30

department: Klinik und Poliklinik für Kardiologie

institute: Universitätsklinikum Leipzig

summary: Rubella virus infection during pregnancy can result in abortion, stillbirth and severe defects in embryogenesis resulting in congenital rubella syndrome (CRS). Low vaccination coverage in developing regions results in estimated 100,000 CRS cases in infants per year with a mortality rate over 30%. The molecular pathomechanisms and potential treatments remain largely unexplored. Endothelial cells (EC) of the placenta are infected by rubella virus (RuV). RuV reduced angiogenic and migratory capacity of primary human EC whereas cell cycle and apoptosis rate were not affected. Next generation sequencing analysis revealed an induction of antiviral type I and III interferons (IFN) that induced angiogenesis-inhibiting cytokines such as CXCL10. The transcriptional profile induced by RuV resembled the effects of IFN-β treatment. The cell culture data were confirmed using human serum from RuV IgM-positive patients that showed similar increase in CXCL10 and inhibited angiogenesis. RuV-mediated inhibition of angiogenesis was reversed by treatment with blocking and neutralizing antibodies targeting CXCL10 and IFN-β receptor. The data identify an important role for anti-viral IFN-mediated induction of CXCL10 in controlling EC function during RuV infection

overall_design: Comparative gene expression analysis of RNA-seq data of endothelial cells after treatment with Rubella and/or IFN-β and/or IFN-λ1

first: Vivien

last: Henschke

first: Hild

last: Konstanze

first: Erik

last: Schilling

first: Jan

last: Haas

first: Vanina

last: Filipova

first: Stephan

last: Erbe

first: Roman

last: König

first: Judith

last: Huebschen

first: Ulrich

last: Laufs

first: Claudia

last: Claus


title: Effect of chronic stress on zebrafish testicular gene expression

first: Vanesa

last: Robles

summary: To investigate the potential deleterious impact of chronic stress at molecular level in testicular tissue, we exposed zebrafish males to chronic stress during 21 days, covering around three complete cycles of spermatogenesis in the species

first: David

last: Valcarce

first: Marta

last: Riesco

first: Leyre

last: Cuesta-Martín

first: Anna

last: Esteve-Codina

first: Juan

last: Martínez-Vázquez


title: Tyrosinase-induced neuromelanin accumulation triggers rapid dysregulation and degeneration of the mouse locus coeruleus

city: Atlanta

last: Weinshenker

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

summary:
To investigate changes in noradrenergic neurons of the LC following infusion of human Tyrosinase (hTyr)
We performed gene expression profiling analysis using data obtained from RNA-seq of Pre-IP and IP samples following hTyr or EYFP infusion into the LC.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for LC-mRNA (IP) for hTyr-infused or EYFP-infused controls.
The background strain is C57Bl/6 and the exact cross is:
Th-cre (B6.Cg-7630403G23RikTg(Th-cre)1Tmd/J, The Jackson Laboratory, #008601) crossed with Slc6a2-eGFP/Rpl10a (B6;FVB-Tg(Slc6a2-eGFP/Rpl10a)JD1538Htz/J, The Jackson Laboratory, #031151).

first: Alexa

last: Iannitelli


title: HMGA1 induces FGF19 to drive pancreatic carcinogenesis and stroma formation

city: Baltimore

first: LI

last: LUO

state: MD

address: 720 Rutland Ave, Ross Build

department: Hematology

institute: Johns Hopskins University

summary: To investigate the effect of HMGA1 in pancreatic cancer. Here we established E3LZ10.7 cell lines in which HMGA1 has been knocked down by shRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq

overall_design: Comparative gene expression profiling analysis of RNA-seq data for E3LZ10.7 cells with or without HMGA1 silencing

first: Lionel

last: Chia

first: Bowen

last: Wang

first: Leslie

last: Cope

first: Linda

last: Resar

first: Reddy

last: Karen


title: Murine Pulmonary Interstitial Macrophage Subsets after Lipopolysaccharide

city: Denver

first: William

last: Janssen

state: CO

address: 1400 Jackson St

institute: National Jewish Health

summary: We sought to characterize pulmonary interstitial macrophage (IM) origin, subsets, and transcriptomic profiles during homeostasis and lipopolysaccharide (LPS) induced acute lung inflammation. During homeostasis, we used three complementary methods:  spectral flow cytometry, single-cell RNA-sequencing, and gene regulatory network enrichment to demonstrate that IMs can be divided into two core subsets distinguished by surface and transcriptional expression of folate receptor β (Folr2/FRβ). Within FRβ+ IMs we identified a subpopulation marked by co-expression of LYVE1. During acute LPS-induced inflammation, lung IM numbers expand. Lineage tracing revealed IM expansion was due to recruitment of monocyte-derived IMs. At the peak of inflammation, recruited IMs were comprised of two unique subsets defined by expression of genes associated with interferon signaling and glycolytic pathways. As recruited IMs matured, they adopted the overall transcriptional state of FRβ- resident IMs but retained expression in several origin-specific genes. FRβ+ IMs were of near-pure resident origin.

overall_design: Male resident IM lineage tracing mice had lungs harvested and digested at homeostasis (n=3), three days after LPS (n=4), or six days after intratracheal lipopolysaccharide. Cells underwent FACS sorting to separate 1)all CD45+ cells, 2) resident IMs, or 3)recruited (monocyte-derived) IMs. Sorted cells were analyzed by scRNAseq

first: Peter

last: Kitrick Moore

first: Kelsey

last: Anderson

first: Shannon

middle: A

last: McManus

first: Emily

last: King

first: Kara

last: Mould

first: Elizabeth

last: Redente

last: Henson

first: Alexandra

last: McCubbrey


title: Pre-clinical models of genetically heterogeneous multiple myeloma reveal immune evasion mechanisms and predict clinical immunotherapy outcomes

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

summary: The historical lack of pre-clinical models reflecting the genetic heterogeneity of multiple myeloma (MM) hampers advancing therapeutic discoveries. To circumvent this limitation, we have generated fifteen genetically diverse models that developed bone marrow tumors fulfilling MM pathogenesis. Transcriptomic analysis of tumor plasma cells revealed that MYC activation regulates time to progression. Bone marrow cell composition analysis classified myeloma tumors into immune-cold and inflamed categories, which condition immune checkpoint blockade responses in mouse multiple myeloma models.

overall_design: Bulk RNA sequencing from bone marrow samples isolated from multiple myeloma mouse models and RNA sequencing from sorted tumor plasma cells

first: Jose

last: Martinez-Climent

first: Marta

last: Larrayoz

first: Leandro

last: Cerchietti

middle: V


title: H3K4me2/3 modulate the stability of RNA polymerase II pausing (ChIP-Seq)

city: Shanghai

first: Aixia

last: Song

institute: Fudan University

summary: Modifications of histones are intricately linked with the regulation of gene expression, with demonstrated roles in various physiological processes and disease pathogenesis. Methylation of histone H3 lysine 4 (H3K4), implemented by the COMPASS family, is enriched at promoters and associated cis-regulatory elements, with H3K4 trimethylation (H3K4me3) considered a hallmark of active gene promoters. However, the relative roles of deposition and removal of H3K4 methylation, as well as the extent to which these events contribute to transcriptional regulation have so far remained unclear. Here, through rapid depletion of either of two shared subunits of COMPASS family members, we reveal a dynamic turnover of H3K4me2 and H3K4me3 mediated by the KDM5 family of histone demethylases. Loss of H3K4me2 and H3K4me3 following COMPASS disruption does not impair the recruitment of TFIID and initiating RNA polymerase II (Pol II). Instead, their loss leads to reductions in the paused form of Pol II on chromatin while inducing the relative enrichment of the Integrator-PP2A (INTAC) termination complex, leading to reduced levels of elongating polymerases, thus revealing how H3K4me2 and H3K4me3 dynamics can regulate Pol II pausing to sustain or attenuate transcription.

overall_design: We performed ChIP-seq, PRO-seq, or RNA-seq to investigate the role of methylation of histone H3 lysine 4 (H3K4) in regulating transcription. In this study, samples for each condition were collected in biological duplicates. Cells were treated with dTAG13 for 6, 12,or 24 hours, the corresponding control cells were treated for the same duration with vehicle only (DMSO) at the same vol/vol dilution.

first: Shibin

last: Hu

first: Linna

last: Peng

first: Fei

last: Chen


title: Mouse models of genetically heterogeneous multiple myeloma reveal mechanisms of immune evasion that predict clinical immunotherapy responses

city: Pamplona

first: Jose A.

state: Navarra

address: Avda. Pio XII, 55

department: Division of Hemato-Oncology

institute: Center for Applied Medical Research CIMA and School of Medicine, University of Navarra

summary: Data from engineered fifteen mouse strains fully encompassing MM genetic heterogeneity that recapitulate the key pathogenic elements in human MM development and multiple myeloma patients.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
RNA-seq was performed in isolated BM GFP+CD138+B220- PCs from mice at MGUS (n=25) and MM (n=40) stages, and in BM CD38+CD138+ PCs from patients with newly diagnosed MGUS (n=9) and MM (n=43). As controls, BM PCs and spleen B220+CD38-FAS+ germinal center B cells were isolated from T-cell immunized 6 month-old YFP+cγ1-cre mice (n=6). In addition, human CD38+CD138+ PCs were isolated from BM aspirates in healthy donors (n=7).
***Raw data for human samples are unavailable due to legal restrictions***

first: David

last: Gomez-Cabrero


title: A hyper-quiescent chromatin state formed during aging is reversed by regeneration

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Epigenetic alterations are a key hallmark of aging but have not been extensively explored in tissues. Here, using naturally aged murine liver as a model and extending study to other quiescent tissues, we find that aging is driven by temporal chromatin alterations that promote a refractory cellular state and compromise cellular identity. Using an integrated multi-omics approach and the first direct visualization of aged chromatin, we find that old cells show global H3K27me3-driven broad heterochromatinization and transcription suppression. At the local level, site-specific loss of H3K27me3 from promoters of genes encoding developmental transcription factors leads to expression in liver of non-hepatocyte markers. Interestingly, liver regeneration reverses H3K27me3 patterns and rejuvenates multiple molecular and physiological aspects of the aged liver.

overall_design: meDIP-seq in 4 young (12-18 weeks) and 4 old (81-90 weeks) mouse livers

last: Yang

first: Payel

last: Sen


title: Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B [polyA capture]

first: Ashish

last: Lal

address: 37 Convent Drive, Room 6134

department: NCI

institute: NIH

summary:
Purpose: Matrin3 (MATR3) is a DNA and RNA-binding protein and one of the major components of the nuclear matrix. Matrin3 is upregulated in colorectal cancer (CRC) compared to normal tissues, indicating potential oncogenic function in CRC. We found that depletion of Matrin3 results in decreased proliferation and colony formation in two CRC cell lines. To understand the molecular mechanism(s) by which Matrin3 mediates these effects, we aimed to find Matrin3 direct RNA targets and the effects of Matrin3 on them.
Methods: We performed PAR-CLIP for endogenous Matrin3 and RNA-seq after Matrin3 silencing in HCT116 cells, a colorectal cancer cell line.
Results: We uncovered Matrin3-mediated regulation of spindle dynamics in colorectal cancer (CRC) cells. We identified bound and regulated Matrin3 target RNAs transcriptome-wide in CRC cells, and found that Matrin3 broadly regulates alternative splicing. Among the top Matrin3 targets, we focused on CDC14B and found that Matrin3 loss resulted in misprocessing of the CDC14B transcript that has a premature termination codon and simultaneous down-regulation of the standard CDC14B transcript in our model. Selective knockdown of the CDC14B standard variant phenocopied the loss of Matrin3 and resulted in reduced CRC cell proliferation, stabilized microtubules, and defects in mitotic spindle formation with tumbled mitotic spindles, suggesting that CDC14B is a key downstream effector of Matrin3.
Conclusions: Our data show that by regulating the abundance of CDC14B standard variant, Matrin3 contributes to maintenance of microtubules dynamics, spindle morphology and proper mitotic spindle orientation and suggest that defects in this pathway may contribute to the reduced proliferation of cells after depletion of Matrin3.

overall_design: mRNA profiles from HCT116 upon siCTRL, or siMatrin3 after 72 + 48 hours of transfection

first: Bruna

middle: R

last: Muys

first: Roshan

middle: L

last: Shrestha

first: Dimitrios

last: Anastasakis

first: Lorinc

last: Pongor

first: Xiao

last: Li

first: Ioannis

last: Grammatikakis

first: Ahsan

last: Polash

first: Raj

last: Chari

first: Myriam

last: Gorospe

first: Curtis

last: Harris

first: Mirit

last: Aladjem

first: Munira

last: Basrai

first: Markus

last: Hafner


title: Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B [Iso-Seq]

overall_design: Iso-seq of HCT116 cell line

middle: C


title: Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B

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


title: H3K4me2/3 modulate the stability of RNA polymerase II pausing

first: Aixia

last: Song

address: Dong'an Road


title: Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B [Ribo-deplete]

overall_design: RNA total profiles from HCT116 upon siCTRL, or siMatrin3 after 48 hours of transfection


title: Notch signaling pathway in tooth shape variations throughout evolution

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Evolutionary changes in vertebrates are linked to genetic alterations that often affect tooth-crown shape, which is a criterion of speciation events, especially in mammals. The Notch pathway is highly conserved between species and controls morphogenetic processes in most developing organs, including teeth. Epithelial loss of the Notch-ligand Jagged1 in developing mouse molars affects the location, size and interconnections of their cusps that lead to minor tooth-crown shape modifications convergent to those observed along Muridae evolution. RNA sequencing analysis revealed that these alterations are due to the modulation of more than 2000 genes and that Notch signaling is a hub for significant morphogenetic networks, such as Wnts and Fibroblast Growth Factors. The modeling of these tooth-crown changes in mutant mice, via a three-dimensional metamorphosis approach, allowed prediction of how Jagged1-associated mutations in humans could affect the morphology of their teeth. These results shed new light on Notch/Jagged1-mediated signaling as one of the crucial components for dental variations in evolution.

overall_design: We compared the global gene expression in lower first molars from n = 4 E18.5 K14cre; Jagged1fl/fl embryos and n = 4 Jagged1fl/fl control littermates. Left and right lower first molars from the same animal were pooled. RNA was isolated using the RNeasy Plus Mini Kit (Qiagen AG, Switzerland) and subsequently purified by ethanol precipitation

first: Pierfrancesco

last: Pagella

first: Thimios

last: Mitsiadis


title: The infusion of ex vivo, interleukin-15 and -21-activated donor NK cells after haploidentical HCT in high-risk AML and MDS patients—a randomized trial

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

institute: KAIST

summary: To understand the cellular landscape of PBMCs of the AML patients after DNKI therapy, we analyzed a totally longitudinal (before DNKI, after 1 and 3 months DNKI therapy) 55,398 PBMC single cells from 4 AML patients by single cell RNA-seq

overall_design: 12 single-cell RNA-sequencing data consists of longitudinal (before DNKI, after 1 and 3 months DNKI therapy) PBMCs from 4 AML patients with DNKI therapy

first: Kyoo-Hyung

last: Lee

first: Eun-Ji

last: Choi

first: Inpyo

first: Mirang

last: Kim

first: Jeong-Hwan

first: Suk

last: Yoon

first: Haiyoung

last: Jung

first: Jae-Eun

last: Byun

first: Hanna

first: Kwang-Hyun

last: Cho

first: Hoon-Min


title: Deciphering a distinct regulatory network of TEAD4, CDX2 and GATA3 in humans for trophoblast transition from embryonic stem cells

city: Guangzhou

first: Lu

last: Xiao

address: Guangzhou North Avnue

institute: Nanfang Hospital, Southern Medical University

summary: In this study, we perform multiple gain- and loss-of-function of TEAD4, CDX2 or GATA3 to study their roles in the trophoblast transition from BMP4-treated human embryonic stem cells (hESCs). Although hESCs with TEAD4 deletion maintain in pluripotency, their potential of trophoblast transition is attenuate. We then performed large-scale transcriptome analysis to explore more information.

overall_design: Two TEAD4 knockout human embryonic stem cell clones and the wild type cells were induced towards trophoblast differentiation under BAP treatment. Cells were collected on day9 after transition for the transcriptome analysis.

first: Lishi

last: Ma

first: Yongli

last: Shan

first: Zhijian

last: Wang

first: Yanhong

last: Yu

first: Stephen

middle: J

last: Lye

first: Yanxing

last: Wei


title: Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B [PAR-CLIP]

first: Ashish

last: Lal

overall_design: RNA binding profile of Matrin3

first: Bruna

last: Muys

first: Roshan

last: Shrestha

first: Dimitrios

last: Anastasakis

first: Lorinc

last: Pongor

first: Xiao

last: Li

first: Ioannis

last: Grammatikakis

first: Ahsan

last: Polash

first: Raj

last: Chari

first: Myriam

last: Gorospe

first: Curtis

last: Harris

first: Mirit

last: Aladjem

first: Munira

last: Basrai

first: Markus

last: Hafner


title: RNA sequencing of murine ESC-derived cardiac progenitor cells treated with screening hit compound Cucurbitacin I Hydrate

first: Alice

last: Tang

state: NY

address: 1300 York Ave

department: Surgery

summary: Cucurbitacin I Hydrate promotes selection towards atrial cardiac fate when cardiac progenitor cells are treated with the compound. RNA sequencing was performed to assess transcript expression of signaling pathways or regulators of atrial or ventricular cardiac differentiation.

overall_design: For RNA-Sequencing total RNA was isolated using Qiagen RNeasy Extraction Kit from murine ESC-derived cardiac progenitor cells cultured for two days in DMSO (0.1% in culture medium) or 10 μM Cucurbitacin I Hydrate (n=2 each).

first: Todd

last: Evans


title: Regualtion of 5hMC during Twist-indced EMT

status: Public on Mar 16 2023

city: Lexington

first: Ren

last: Xu

state: KENTUCKY

address: 741 S. Limestone Rd

institute: University of Kentucky

summary:
EMT is associated with profound epigenetic regualtion. 5hMC is the first product of TET-dependent DNA methylation product. chromatin immunoprecipitation-sequencing (ChIP-seq) provide a tool to define the changes of 5hmC at the genome level.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for 5hMC in HMLE cells.

overall_design: Xu, Ren

first: Chen

last: Jie

first: Active

last: Motiff

first: Liu

last: Jinpeng


title: Comprehensive Analysis of N6-Methyladenosine (m6A) Methylation in human Calcific Aortic Valve Tissues by High-Throughput m6A Sequencing

city: Meizhou

first: Jingyuan

last: Hou

state: CHINA

address: No. 63 Huangtang Road, Meijiang District, Meizhou

institute: Meizhou People's Hospital

summary: Background: Recent research shows cardiovascular diseases have been strongly linked to N6-methyladenosine (m6A) methylation. However, there is still much to learn about the specific changes in m6A RNA methylation in patients with calcified aortic valve dBackground: Recent research shows cardiovascular diseases have been strongly linked to N6-methyladenosine (m6A) methylation. However, there is still much to learn about the specific changes in m6A RNA methylation in patients with calcified aortic valve disease (CAVD).  Methods: In this study, high-throughput methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were performed to identify the differentially expressed m6A methylation pattern in human calcified valves tissue for the first time.  Results: A total of 7,412 significantly changed m6A methylation peaks and 2,380 differentially expressed genes were identified. MeRIP-seq and RNA-seq analyses screened out 131 genes with significant m6A methylation and expression changes. Gene Ontology (GO) analysis also revealed a relationship between m6A methylated genes and inflammatory responses, calcium ion binding, extracellular matrix organization, and cell adhesion, among other. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that these genes had an increased role in focal adhesion. Using real-time qPCR, we also confirmed the presence of 4 genes involving the focal adhesion signaling pathway (SPP1, COL1A1, ITGA8, and MYL9).  Conclusions: Taken together, our study firstly revealed the distinct m6A methylation profiles in calcified valve tissue and associated biological roles and signaling pathways. The information in this study will be useful for future mechanism research and for developing new treatment targets for patients with CAVD.

overall_design: The m6A methylation profiles of calcified valve tissues and non-calcified valve tissues

first: Zhixiong

last: Zhong

first: Wei

first: Qunkai

last: Yuan


title: Functional and phenotypic characterizations of common  syngeneic tumor cell lines as estrogen receptor positive breast cancer models

city: Melbourne

first: Emily

last: Gruber

state: VIC

address: 305 Grattan St

institute: Peter MacCallum Cancer Centre

summary: Estrogen receptor positive breast cancers (ER+ BCas) are the most common form of BCa and is increasing in incidence largely due to changes in reproductive practices in recent decades. Tamoxifen is prescribed as a component of standard of care endocrine therapy for treatment and prevention of ER+ BCa.  However, it is poorly tolerated leading to low uptake of the drug in the preventative setting.  Alternative therapies and preventatives for ER+ BCa are needed but development is hampered due to a paucity of syngeneic ER+ preclinical mouse models that allow pre-clinical experimentation in immunocompetent mice. Two ER positive models, J110 and SSM3, have been reported in addition to other tumor models occasionally shown to express ER (for example 4T1.2, 67NR, EO771, D2.0R and D2A1). Here we have assessed ER expression and protein levels in seven mouse mammary tumor cell lines and their corresponding tumors in addition to their cellular composition, tamoxifen sensitivity and molecular phenotype. By immunohistochemical assessment, SSM3 and to a lesser extent 67NR cells are ER+. Using flow cytometry and transcript expression we show that SSM3 cells are luminal in nature whilst D2.0R and J110 cells are stromal/basal. The remainder are also stromal/basal in nature; displaying a stromal or basal Epcam/CD49f FACS phenotype and stromal and basal gene expression signatures are overrepresented in their transcript profile. Consistent with a luminal identity for SSM3 cells, they also show sensitivity to tamoxifen in vitro and in vivo. In conclusion, the data indicates that the SSM3 syngeneic cell line is the only definitively ER+ mouse mammary tumor cell line widely available for pre-clinical research.

overall_design: Gene expression profiling analysis of RNA-seq data for J110 and SSM3 cells

first: Kara

last: Britt


title: Next Generation Sequencing and Analysis of the Transcriptomes of RAW264.7 cells pretreated with PEP and PBS.

city: Beijing

first: Lu

last: Zhao

address: Dongdan Santiao 5

institute: Peking Union Medical College&Chinese Academy of Medical Sciences

summary: We demonstrate that phosphoenolpyruvate (PEP) generally inhibits viral infection in vitro and in vivo. In order to further explore whether PEP controls viral replication through a  general mechanism such as enhancing innate response, and if not, what's the critical downstream target(s) of PEP, we performed RNA sequencing (RNA-seq) analysis on the RAW264.7 cells that were pretreated with 250 μM PEP or PBS for 2 hours, and then infected with or without vesicular stomatitis virus (VSV) for 8 hours.

overall_design: Transcriptomes profiles of gene expression changes in RAW264.7 cells pretreated with 250 μM PEP and PBS for 2 hours, followed by VSV infection for 8 hours or  without infection. Three biological replicates.


title: Two opposing gene expression patterns within ATRX aberrant neuroblastoma

city: Utrecht

first: Michael

last: van Gerven

state: Utrecht

address: Heidelberglaan 25

department: Oncology

institute: Princess Maxima Center

summary: To study the role of distinct ATRX aberrations in neuroblastoma we created isogenic ATRX aberrant models using CRISPR-Cas9 in several neuroblastoma cell lines and one tumoroid. We created ATRX knock-out models, ATRX in-frame exon 2-10 deletions and ATRX in-frame exon 2-13 deletions. Additionally, we included patient-derived models data (i.e. cell line data and one tumoroid).

overall_design:
We performed gene expression profiling analysis using data obtained from total RNA-sequencing. We compared each of the distinct ATRX aberrant isogenic models with the corresponding wild-type clones. Additionally, we compared the patient-derived ATRX aberrant models with the patient-derived ATRX wild-type models (i.e. CHLA-90+SKNMM+AMC772T2 versus GIMEN+SKNAS+SKNSH+LAN6+SJNB12; patient-derived model data except AMC772T2 is available at ENA accession number PRJEB55331).

** The submitter states that the raw data for the patient-derived tumoroid samples cannot be shared due to patient confidentiality concerns**

first: Linda

last: Schild

first: Jennemiek

last: van Arkel

first: Bianca

last: Koopmans

first: Luuk

last: Broeils

first: Loes

last: Meijs

first: Romy

last: van Oosterhout

first: Max

last: van Noesel

first: Jan

last: Koster

first: Sander

last: van Hooff

last: Molenaar

first: Marlinde

last: van den Boogaard


title: Mitochondrial fusion is a therapeutic vulnerability of acute myeloid leukemia [PDX shOPA1]

city: paris

first: Jerome

last: Tamburini

address: 22 rue mechain

institute: Cochin Institute

summary: Mitochondrial metabolism recently emerged as a critical dependency in acute myeloid leukemia (AML). The shape of mitochondria is tightly regulated by dynamin GTPase proteins, which drive opposing fusion and fission forces to consistently adapt bioenergetics to the cellular context. Here, we showed that targeting mitochondrial structure through the inhibition of mitochondrial fusion was a new vulnerability of AML cells, when assayed in patient-derived xenograft (PDX) models. Genetic depletion of mitofusin 2 (MFN2) or optic atrophy 1 (OPA1) or pharmacological inhibition of OPA1 (MYLS22) blocked mitochondrial fusion and had significant anti-leukemic activity, while having limited impact on normal hematopoietic cells ex vivo and in vivo. Mechanistically, inhibition of mitochondrial fusion disrupted mitochondrial respiration and reactive oxygen species production, leading to cell cycle arrest at the G0/G1 transition. These results nominate the inhibition of mitochondrial fusion as a promising therapeutic approach for AML.

overall_design: 12 conditions from patient-derived xenograft (PDX) AML samples (n=6, PDX1, PDX2, PDX3, PDX4, PDX5, PDX7) transduced with control (CTL) or anti-OPA1 shRNAs

first: Clement

last: Larrue

first: Sarah

last: Mouche

first: Shan

last: Lin

first: Federico

last: Simonetta

first: Nastassja

middle: K

last: Scheidegger

first: Laury

last: Poulain

first: Rudy

last: Birsen

first: Jean-Emmanuel

last: Sarry

first: Kimberly

last: Stegmaier


title: Mitochondrial fusion is a therapeutic vulnerability of acute myeloid leukemia [PDX shMFN2]

overall_design: 10 conditions from patient-derived xenograft (PDX) AML samples (n=5, PDX3, PDX4, PDX5, PDX7, PDX8) transduced with control (CTL) or anti-MFN2 shRNAs


title: Mitochondrial fusion is a therapeutic vulnerability of acute myeloid leukemia [Cell lines shCTL shMFN2]

overall_design: 12 conditions from 2 cell lines (MOLM-14 and OCI-AML2) transduced with doxycycline-inducible control (CTL) or anti-MFN2 shRNAs, in triplicate


title: Mitochondrial fusion is a therapeutic vulnerability of acute myeloid leukemia.

overall_design: Refer to individual Series


title: LIMK2 promotes melanoma tumor growth and metastasis through G3BP1-ESM1 pathway-mediated apoptosis inhibition

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: Melanoma is the leading cause of skin cancer-related deaths, and current melanoma therapies, including targeted therapies and immunotherapies, benefit only a subset of metastatic melanoma patients due to either intrinsic or acquired resistance. LIM domain kinase 2 (LIMK2) is a serine/threonine kinase that plays an important role in the regulation of actin filament dynamics. Here, we show that LIMK2 is overexpressed in melanoma, and its genetic or pharmacological inhibition impairs melanoma tumor growth and metastasis in both cell culture and mice. To determine the mechanism by which LIMK2 promotes melanoma tumor growth and metastatic progression, we performed a phosphoproteomics analysis and identified G3BP1 as a key LIMK2 target, which mirrored the effects of LIMK2 inhibition when inhibited. To further determine the role of G3BP1 downstream of LIMK2, we knocked down the expression of G3BP1, performed RNA-seq analysis, and identified ESM1 as a downstream target of G3BP1. G3BP1 was required for ESM1 mRNA stability, and ESM1 ectopic expression rescued LIMK2 or G3BP1 inhibition-induced suppression of melanoma growth and metastatic attributes. These results collectively identify the LIMK2→G3BP1→ESM1 pathway as a facilitator of melanoma tumor growth and metastasis and document that LIMK2 is a therapeutically tractable target for melanoma therapy.

overall_design: Total RNA was extracted from all cells, followed by poly-A selection and RNA-sequencing using Illumina Hi-Seq 2500 platform, with three biological replicates for each transformed sample.

first: Raj

last: Kumar