title: The N6-methyladenosine RNA landscape in aged mouse hippocampus [meRIP-seq]

summary:
Aged brain is associated with an inevitable decline in cognitive functions and increased vulnerability to neurodegenerative disorders. Multiple molecular hallmarks have been associated with the aging nervous system through transcriptomics and proteomic studies. Recently, the field of epitranscriptomics highlights the role of RNA chemical modification in various biological processes. In particular, N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic mRNAs, has been functionally linked to multiple aspects of RNA processing.
Importantly, the functional roles of m6A in neurophysiology, such as in the process of learning and memory, have led to our current investigation of how m6A-transcriptomic landscape is shaped during aging. Using the inbred C57Bl/6 line, we compared the m6A-transcriptomic profiles from the hippocampi of young (3-month-old) and aged (20-month-old) mice. The methylated RNA immunoprecipitation (MeRIP)-sequencing analysis revealed hyper- and hypo-methylation in 426 and 102 genes, respectively, in the aged hippocampus (fold-change >1.5, FDR<0.05).
By correlating the methylation changes to their steady state transcript levels in the RNA-seq, we found a significant concordance between m6A and transcript levels in either direction.

overall_design: Measure m6A-transcriptomic profiles from the hippocampi of young (3-month-old) and aged (20-month-old) mice.

first: Renhua

last: Song

first: Justin

last: Wong

first: Victor

last: Anggono

first: Jocelyn

last: Widagdo


title: Whole-transcriptome analyses of sheep embryonic testicular cells infected with bluetongue virus [miRNA-Seq]

status: Public on Nov 28 2022

city: Kunming

first: Zhuoran

last: Li

state: Yunnan

address: Fengyu Road

department: Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory

country: China

institute: Yunnan Animal Science and Veterinary Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: To comprehensively understand the characterization of bluetongue virus (BTV)-host interactome, and BTV infection and pathogenic mechanisms, RNA-seq was performed with BTV serotype 1 Y863 strain-infected and mock-infected sheep embryonic testicular cells (OA3.Ts) at 24 hours post-infection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bluetongue virus serotype 1 (BTV-1)-infected and mock-infected sheep embryonic testicular cells (OA3.Ts).


title: The tomato receptor-like cytoplasmic kinase Fir1 is involved in flagellin signaling and regulates pre-invasion immunity

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

type: Expression profiling by high throughput sequencing

summary: Detection of bacterial flagellin by the tomato receptors Flagellin sensing 2 (Fls2) and Fls3 triggers activation of pattern-triggered immunity (PTI). We identified a tomato Fls2/Fls3-interacting receptor-like cytoplasmic kinase, Fir1, that is involved in PTI triggered by flagellin perception. Fir1 localized to the plasma membrane and interacted with Fls2 and Fls3 in yeast and in planta. CRISPR/Cas9-generated tomato fir1 mutants were impaired in several immune responses induced by the flagellin-derived peptides flg22 and flgII-28, including resistance to Pseudomonas syringae pv. tomato (Pst) DC3000, production of reactive oxygen species, and enhanced PR1b gene expression, but not MAP kinase phosphorylation. Remarkably, fir1 mutants developed larger Pst DC3000 populations than wild-type plants, whereas no differences were observed in wild-type and fir1 mutants plants infected with the flagellin deficient Pst DC3000deltafliC. fir1 mutants failed to close stomata when infected with Pst DC3000 and Pseudomonas fluorescens, and were more susceptible to Pst DC3000 than wild-type plants when inoculated by dipping, but not by vacuum-infiltration, indicating involvement of Fir1 in pre-invasion immunity. RNA-seq analysis detected fewer differentially expressed genes in fir1 mutants and altered expression of jasmonic acid (JA)-related genes. In support of JA response deregulation in fir1 mutants, these plants were similarly susceptible to Pst DC3000 and to the coronatine deficient Pst DC3118 strain, and more resistant to the necrotrophic fungus Botrytis cinerea following PTI activation. These results indicate that tomato Fir1 is required for a subset of flagellin-triggered PTI responses and support a model in which Fir1 negatively regulates JA signaling during PTI activation.

overall_design: To better understand the part Fir1 plays in activating plant defense we sought to analyze the effect of a Fir1 mutation on gene transcription using RNA-seq. Here, we investigated the involvement of tomato Flagellin-sensing 2/3 interacting RLCK 1 (Fir1) in PTI triggered by perception of Pseudomonas fluorescens A506. Fir1 localized to the plasma membrane and interacted in yeast and in planta with the flagellin receptors Fls2 and Fls3.

first: Guy

last: Sobol

first: Bharat

last: Bhusan Majhi

first: Ning

last: Zhang

first: Holly

middle: M

last: Roberts

first: Gregory

middle: B

last: Martin

first: Guido

last: Sessa


title: Chromatin binding alteration after enzalutamide treatment

city: Rochester

first: Liewei

last: Wang

state: Minnesota

address: 200 First Street SW

department: Molecular Pharmacology and Experimental Therapeutics department

country: USA

institute: Mayo Clinic

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
In this study, we found the efficacy of AR-targeting drugs largely depended on the context of AR (Androgen Receptor) and ERα (Estrogen Receptor) status. Enzalutamide, an AR blocker, had a better inhibition effect on ER+ cells with lower AR expressed compared to cells expressed higher AR. To explore the mechanism of action of Enzalutamide, we performed ChIP-seq to illustrate the AR and ER genomic bindings after Enzalutamide treatment in both MCF7 and MCF7 with AR over expression (AROE) cells.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for androgen receptor (AR) and Estrogen receptor (ER) after Enzalutamide treatment in MCF7 and MCF7 AROE cells

overall_design: AR and ER ChIP-seq were performed under four conditions, DMSO treatment in parental MCF7 cells, Enzalutamide treatment in parental MCF7 cells, DMSO treatment in AROE MCF7 cells and Enzalutamide treatment in AROE MCF7 cells.


title: Gene expression change after Enzalutamide treatment in MCF7 cells

summary:
To explore the mechanism of action of Enzalutamide, we performed RNA-seq to investigate gene expression difference after Enzalutamide treatment in both MCF7 and MCF7 with AR over expression (AROE) cells.
RNA-sequencing (RNA-seq) of  MCF7 and MCF7 AROE cells with DMSO or Enzalutamide treatment

overall_design: RNA-seq were performed under four conditions, DMSO treatment in parental MCF7 cells, Enzalutamide treatment in parental MCF7 cells, DMSO treatment in AROE MCF7 cells and Enzalutamide treatment in AROE MCF7 cells.


title: The N6-methyladenosine RNA landscape in aged mouse hippocampus [RNA-seq]

city: Brisbane

first: He

last: Huang

state: QUEENSLAND

address: THE UNIVERSITY OF QUEENSLAND, ST LUCIA

country: Australia

institute: The University of Queensland

overall_design: Measure RNA abundance and splicing level changes of hippocampi of young (3-month-old) and aged (20-month-old) mice.

middle: J


title: KSHV infection of Endothelial Colony Forming Cells

city: Seattle

first: Terri

last: DiMaio

state: WA

address: 750 Republican St.

department: Microbiology

institute: University of Washington

summary: We performed high throughput RNA-sequencing on KSHV-infected blood and lymphatic Endothelial Colony-Forming Cells at 48hpi to identify differences in gene expression induced by KSHV in these two cell types.

overall_design: RNA was isolated from 2 blood-specific ECFC cell lines and 2 lymphatic-specific ECFC cell lines 3 separate times each

first: Michael

last: Lagunoff


title: Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

institute: Institute of Crop Sciences

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

overall_design: Refer to individual Series


title: HU308 Mitigates Osteoarthritis by Stimulating Sox9-Related Networks of Carbohydrate Metabolism

status: Public on Nov 27 2022

city: jerusalem

first: lital

last: zecharyahu

address: Campus Ein Kerem

institute: hebrew university

summary: Osteoarthritis (OA) is characterized by progressive, irreversible erosion of articular cartilage accompanied with severe pain and immobility. This study aimed to assess the effect and mechanism of action of HU308- a selective cannabinoid receptor type 2 (CB2) agonist, in potentially preventing OA-related joint damage. To test this assumption, Cn2r null mice and WT mice were aged to reach 20 months, and analyzed for joint structural  features.  OA was induced in Wild type (WT) mice via ageing or post-traumatic procedure, followed by HU308 systemic (intraperitoneal) or local (intra-articular) administration, respectively.  Additional analysis of time and dose courses for HU308 were carried out in human primary chondrocytes, analyzed by RNA-sequencing, RT-PCR, ChIP and immunoblotting. Our results show that Cnr2r null mice exhibited enhanced age-related OA severity and synovitis compared to age-matched WT mice.  Systemic administration of HU308 to 16-month mice improved pain sensitivity and maintained joint integrity, which was consistent with the intra-articular administration of HU308 in post-traumatic OA mice. When assessing human chondrocytes treated with HU308, we uncovered a dose- and time related increase in ACAN and COL2A1 expression, which was preceded by increased SOX9 expression due to pCREB transcriptional activation of the SOX9 gene. Finally, transcriptomic analysis of patient-derived human chondrocytes, identified HU308 populations exhibiting enhanced SOX9 expression, accompanied by enriched gene networks related to carbohydrate metabolism. Collectively, the results show that HU308 reduced trauma and age-induced OA, via CB2-pCREB dependent activation of SOX9, contributing to augmented genes networks related to metabolism.

overall_design: mRNA was extracted from human chondrocytes from OA-derived cartilage either treated with vehicle (i.e, untreated), or with 100nM HU308 for 4h or 48h.

first: Mona

last: Dvir-Ginzberg

first: Idan

last: Carmon

first: Lital

last: Zecharyahu


title: Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [ATAC-seq]

summary: Expression divergence caused by genetic variation and crosstalks among subgenomes of the allohexaploid bread wheat (Triticum aestivum. L., BBAADD) is hypothesized to increase its adaptability and/or plasticity. However, the molecular basis of expression divergence remains unclear. Squamosa promoter-binding protein-like (SPL) transcription factors are critical for a wide array of biological processes. In this study, we constructed expression regulatory networks by combining DAP-seq for 40 SPLs, ATAC-seq, and RNA-seq. Our findings indicate that a group of low-affinity SPL binding regions (SBRs) were targeted by diverse SPLs and caused different sequence preferences around the core GTAC motif. The SBRs including the low-affinity ones are evolutionarily conserved, enriched GWAS signals related to important agricultural traits. However, those SBRs are highly diversified among the cis-regulatory regions (CREs) of syntenic genes, with less than 8% SBRs coexisting in triad genes, suggesting that CRE variations are critical for subgenome differentiations. Knocking out of TaSPL7A/B/D and TaSPL15A/B/D subfamily further proved that both high- and low-affinity SBRs played critical roles in the differential expression of genes regulating tiller number and spike sizes. Our results have provided baseline data for downstream networks of SPLs and wheat improvements and revealed that CRE variations are critical sources for subgenome divergence in the allohexaploid wheat.

overall_design: To systematically study the regulatory networks mediated by wheat SPLs, we performed DAP-seq for 40 wheat SPLs (SPLs), ATAC-seq and RNA-seq seq for four tissues (leaves, roots, axillary buds and shoot apices) of wheat (Triticum aestivum L.).


title: A Natural Biological Adhesive from Snail Mucus for Wound Repair

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: The discovery of the natural adhesion phenomena and mechanisms has advanced the information and development of a new generation of tissue adhesives in recent decades. In this study, we developed a natural biological adhesive from snail mucus consisting of a positively charged protein network and a polyanionic glycosaminoglycan network. The malleable bulk adhesive matrix could adhere to wet tissue through multiple interactions. The biomaterial exhibited excellent hemostatic and tissue adhesion properties in vitro and in vivo, and was also effective in accelerating the healing of full-thickness skin wounds in both normal and diabetic rats. The natural biomaterial effectively promoted the polarization of macrophages toward the anti-inflammatory M2 phenotype, alleviated inflammation in chronic wounds, and significantly improved epithelial regeneration and angiogenesis. Its abundant heparin-like glycosaminoglycan component was indispensable. These findings provide theoretical and material insights into bio-inspired tissue adhesives and bioengineered scaffold designs.

overall_design: RNA sequencing was performed in four groups  diabetic rats to evaluate the chronic wound healing ability

first: Tuo

last: Deng

first: Dongxiu

last: Gao

first: Xuemei

last: Song

first: Zhipeng

last: Zhou


title: Integrative analysis of multiple genomic data from intrahepatic cholangiocarcinoma organoids enables tumor subtyping

status: Public on Nov 26 2022

city: SEOUL

first: Hee Seung

last: Lee

state: --- Select ---

address: SEOUL

country: South Korea

institute: Yonsei University

summary: As genomic analysis technology has advanced, it has become possible to sub-classify intrahepatic cholangiocarcinoma (ICC) at the histological or molecular level. However, there are no truly representative models of ICC subtypes for use in studying developmental differences, carcinogenesis, and personalized drug response. Here, we sought to verify recent suggested two subgroup of ICC in organoids model, compare the characteristics between LD and SD type of ICC, and find the type-specific gene expression profile and targetable pathway as a therapeutic target. ICC organoids from 16 patients pathologically diagnosed with cholangiocarcinoma were prepared according to a previously established organoid culture protocol. ICC patients were subclassified into small-duct (SD) type and large-duct (LD) type according to histological characteristics and S100P, N-cadherin, and CD56 expression. ICC organoids were successfully established within one month and exhibited a morphology similar to that of their matching primary cancer. LD- and SD-type organoids exhibited histologic phenotypes and staining patterns characteristic of the corresponding ICC subtypes. ICC organoids showed high concordance of somatic mutations with primary tumors. Unsupervised principal component analysis clustering effectively separated each type of ICC. Differential gene expression revealed significant enrichment on KRAS, TGFβ and ERBB2 signaling pathways in LD-type compared with SD-type ICC (P<0.05). Gene set enrichment analysis further demonstrated that the cholangiocarcinoma class 2 signature, defined by Andersen et al., was significantly enriched in the LD-type (enrichment score=2.19, P<0.001). A protein-protein interaction network analysis identified ZNF217 as a significant hub protein (odds ratio=4.96, P=0.0105). We successfully performed prospective modeling of histological subtype specification using patient-derived ICC organoids. Moreover, gene expression profiling of ICC organoids enabled identification of type-specific targetable pathways.

overall_design: 13 Cancer tissues were obtained from patients who were pathologically diagnosed with cholangiocarcinoma and they were analyzed for RNA sequencing.

first: Hee

middle: S

first: Jun

middle: Y

last: Park


title: UHRF2 Commissions the Accomplishment of DNA Demethylation through Allosteric Activation by 5hmC and K33-linked Ubiquitination of XRCC1

first: Yu

last: Zhang

address: Xueyuan Road

institute: Peking University Health Science Center

summary: The transition of oxidized 5-methylcytosine (5mC) intermediates into base excision repair (BER) pipeline to complete DNA demethylation remains enigmatic. We report here that UHRF2, the only paralog of UHRF1 in mammals that is neither able to maintain 5mC nor to rescue Uhrf1-/- phenotype, is physically and functionally associated with BER. UHRF2 is allosterically activated by 5-hydroxymethylcytosine (5hmC) and acts as a ubiquitin E3 ligase to catalyze K33-linked polyubiquitination of XRCC1, a core subunit of the BER complex. This nonproteolytic action stimulates the interaction of XRCC1 with the ubiquitin binding domain-bearing RAD23B, leading to the formation of the TDG-RAD23B-BER complex amenable to complete DNA demethylation. Integrative epigenomic analysis in mouse embryonic stem cells reveals that the Uhrf2-coordinated TDG-RAD23B-BER complex functionally links to the completion of DNA demethylation at promoters, and that during neuronal commitment, Uhrf2-associated and H3K4me1-marked latent enhancers undergo poised-to-active transition accompanied by H3K27ac acquisition. Accordingly, Uhrf2 ablation impairs DNA demethylation and abolishes neuronal differentiation. Together, these observations highlight the essentiality of 5hmC-switched UHRF2 E3 ligase activity in commissioning the accomplishment of active DNA demethylation.

overall_design: We examined the binding profiles of Uhrf2 in mouse embryonic stem (mES) cell line R1.

first: Bosen

last: Xu


title: Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [RNA-seq]


title: Epigenome analysis of a pheochromocytoma sample carrying co-ocurrent mutations in NF1 and DLST.

status: Public on Nov 25 2022

city: Madrid

first: Alberto

last: Cascón

address: Melchor Fernández Almagro 3

department: Human Cancer Genetics Program

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

summary: Genome wide DNA methylation profiling of a pheochromocytoma sample carrying co-ocurrent mutations in NF1 and DLST. The Illumina Infinium EPIC Human DNA methylation Beadchip v1.2 was used to obtain a DNA methylation profile across approximately 850,000 CpGs. The main goal of this project was to gain insight into the role of these events in tumour development.

overall_design: Bisulphite converted DNA from the tumor sample was hybridised to the Illumina Infinium EPIC Human Methylation Beadchip

first: Mellid

last: Sara

first: Robledo

last: Mercedes

first: Cascon

last: Alberto


title: Analysis of pheochromocytoma samples carrying co-occurrent mutations in NF1 and DLST


title: Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [DAP-seq]

first: Zefu

last: Lu


title: Gene expression analysis of pheochromocytoma samples carrying co-occurrent mutations in NF1 and DLST.

summary: We performed gene expression profiling analysis using data obtained from RNA-seq of two pheochromocytoma samples carrying co-occurrent mutations in NF1 and DLST. The main goal of this project was to to gain insight into the role of these events in tumour development.

overall_design: Gene expression profiling of RNA-seq data from pheochromocytoma samples carrying the co-occurrent mutations in NF1 and DLST.

first: Cascón


title: ChIP-seq of H3K18la in murine Th17-differentiated T cells

city: Marburg

first: Ho Ryun

last: Chung

address: Hans-Meerwein-Straße 6

department: Institute for Medical Bioinformatics and Biostatistics

country: Germany

institute: Philipps University of Marburg

summary: Increased lactate levels in the tissue microenvironment are a well-known feature of chronic inflammation. However, the role of lactate in regulating T cell function remains controversial. We here demonstrate that extracellular lactate predominantly induces deregulation of the Th17-specific gene expression program by modulating metabolic and epigenetic status of Th17 cells. Following lactate treatment, Th17 cells significantly reduced their IL-17A production and upregulated Foxp3 expression through ROS-driven IL-2 secretion. Moreover, we observed a broad pattern of histone lactylation at various genes in CD4+ T cells, with particularly highly enriched lactylation of histone H3 at the Foxp3 promoter regions in lactate-treated Th17 cells. These results indicate that lactate is capable of reprogramming pro-inflammatory T cell phenotype into regulatory T cells. Moreover, we show that high lactate concentrations suppress the Th17 pathogenicity during intestinal inflammation. Collectively, these findings have a potential therapeutic value for development of novel clinical strategies to target inflammatory and autoimmune diseases.

overall_design: Treatment of murine Th17 cells with vehicle or lactate for 24 h. ChIP with anti-H3K18la (L-lactylated lysine 18 on histone H3).

first: Alexandra

last: Lopez Krol

first: Till

last: Adhikary

first: Andrea

last: Nist

first: Thorsten

last: Stiewe


title: TDP-43 condensates and lipid droplets regulate the reactivity of microglia and regeneration after traumatic brain injury

city: Planegg-Martinsried

first: Jovica

last: Ninkovic

state: Bayern

address: Großhaderner Straße 9

department: Department for Cell Biology

institute: LMU München

summary: Decreasing the activation of pathology-activated microglia is crucial to prevent chronic inflammation and tissue scarring. In this study, we used a stab wound injury model in zebrafish and identified an injury-induced microglial state characterized by the accumulation of lipid droplets and TAR DNA-binding protein of 43 kDa (TDP-43)+ condensates. Granulin-mediated clearance of both lipid droplets and TDP-43+ condensates was necessary and sufficient to promote the return of microglia back to the basal state and achieve scarless regeneration. Moreover, in postmortem cortical brain tissues from patients with traumatic brain injury, the extent of microglial activation correlated with the accumulation of lipid droplets and TDP-43+ condensates. Together, our results reveal a mechanism required for restoring microglia to a nonactivated state after injury, which has potential for new therapeutic applications in humans.

overall_design: Single-cell RNA sequencing of telencephalic cells from wildtype (Wt) and grna-/-;grnb-/- (Mutant) animals. Intact, 3 days post injury (dpi) and 7 dpi are used as time points. Animals were from 3 to 5 months old.

first: Alessandro

last: Zambusi

first: Klara

middle: T

last: Novoselc

first: Saskia

last: Hutten

first: Sofia

last: Kalpazidou

first: Christina

last: Koupourtidou

first: Rico

last: Schieweck

first: Sven

last: Aschenbroich

first: Lara

last: Silva

first: Ayse

last: Yazgili

first: Frauke

middle: v

last: Bebber

first: Bettina

last: Schmid

first: Gabriel

last: Möller

first: Clara

last: Tritscher

first: Christian

last: Stigloher

first: Claire

last: Delbridge

first: Swetlana

last: Sirko

first: Zeynep

middle: I

last: Günes

first: Sabine

last: Liebscher

first: Jürgen

last: Schlegel

first: Hananeh

last: Aliee

first: Fabian

last: Theis

first: Silke

last: Meiners

first: Michael

last: Kiebler

first: Dorothee

last: Dormann


title: Next Generation Sequencing Facilitates Quantitative Analysis of  ribo-tag pulled down Transcriptomes in renal proximal tubule epithelial cells from Plasmodium Chabaudi Chabaudi infected Egfp.l10Pepck and Egfp.l10PepckSlc40a1Pepckdelta/delta mice

city: Oeiras

first: Rui

last: Martins

address: Rua da Quinta Grande 6

department: Inflammation

country: Portugal

institute: Gulbenkian Institute for Molecular Medicine

summary:
Purpose: Next-generation sequencing (NGS) is emmerged as a highthrough-put technique to analyze cellular pathways. The goals of this study are to profile NGS-derived renal proximal tubule epithelial cells (RPTEC) transcriptome (RNA-seq), to identify transcription signature in RPTEC upon Plasmodium Chabaudi Chabaudi (Pcc) infection and steady state (NI). We also would like to understand how iron export affect the transcriptome in this cell compartment. Therefore, we will compare the transcriptome between Pcc infected (or steady state) Egfp.l10Pepck and Egfp.l10PepckSlc40a1Pepckdelta/delta mice.
Methods: TRAP (Translating Ribosome Affinity Purification) were performed in the kidneys of Pcc infected (or steady state) 10-16 weeks Egfp.l10Pepck and Egfp.l10PepckSlc40a1Pepckdelta/delta mice. RPTEC TRAP mRNA profiles were generated by next generation sequencing, in triplicate, using Illumina High output kit v2.5 and NextSeq500 sequencer.
Results: Using an optimized data analysis workflow, we mapped an average 32.54 million sequence reads per sample to the mouse genome (build mm39) and identified 19,052 transcripts in the TRAP mRNA of  in the kidneys of Pcc infected or steady state 10-16 week old Egfp.l10Pepck and Egfp.l10PepckSlc40a1Pepckdelta/delta mice. Differential gene expression was performed using the DESeq2 R package (v.1.32) and gene expression was modeled by genotype and condition. Differentially expressed genes were considered for genes with an adjusted p-value<0.05 and an absolute log2 fold change>0.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

first: Qian

last: Wu

first: Euclides

last: Sacomboio

first: Lara

last: Sousa

first: Sílvia

last: Cardoso

first: Temitope

middle: W

last: Ademolue

first: Tiago

last: Paixão

first: Ana

last: Domingos

first: Günter

last: Weiss

first: Susana

last: Ramos

first: Miguel

middle: P

last: Soares


title: A Cdh3 - b-Catenin - Laminin signaling axis by a subset of breast tumor leader cells controls leader cell polarization and directional collective migration

city: St. Louis

first: Greg

last: Longmore

state: MO

address: BJCIH, South Euclid Ave.

department: Medicine

institute: Washington University, St. Louis

summary: Carcinoma dissemination can occur when heterogeneous tumor and tumor stromal cells clusters migrate together via collective migration. Cells at the front lead and direct collective migration, yet how these leader cells form and interact with the microenvironment to direct migration are not fully appreciated. From live videos of primary mouse and human breast tumor organoids in a 3D microfluidic system that mimics native breast tumor microenvironment, we developed 3D computational models which hypothesize that leader cells generate high protrusive forces and overcome extracellular matrix (ECM) resistance. Using single cell sequencing, we reveal leader cells are heterogeneous, and we identify and isolate a unique Cadherin-3 (Cdh3) positive leader cell subpopulation necessary and sufficient to lead migration. Cdh3 controls leader cell protrusion dynamics and local production of Laminin-332 which is required for integrin/focal adhesion function. Our findings highlight how a subset of leader cells interact with the microenvironment to direct collective migration.

overall_design: Primary tumor organdoids from K14-Actin.GFP; MMTV-PyMT mice (pure FVB/n background) were isolated, cultured in a microphysiological system, migration was induced (biochemical or biomechanical), organoids were isolated and analyzed using scRNAseq.

first: Gregory

middle: D

first: Priscilla

last: Hwang


title: LncRNAs expression profiles in renal tissues from patients with diabetic nephropathy

status: Public on Nov 24 2022

city: Guangzhou

first: Xiaoyan

last: Bai

address: No. 106, Zhongshan 2nd Road Yuexiu District Guangzhou

department: Nephrology

institute: Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences

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

summary: In order to more accurately and objectively clarify the biological role of lncRNAs in diabetic nephropathy, we detected their expression profiles in renal tissues from patients with diabetic nephropathy.

overall_design: Renal tissues from six patients were utilized for analysis. In detail, three were from patients with diabetic nephropathy while three were normal kidney tissues obtained from patients with renal tumor at the time of nephrectomy which were unaffected by tumor. All patients are diagnosed by renal pathological examination.

first: Ting

last: Zhang


title: MDC1 maintains active elongation complexes of RNA polymerase II

city: København

first: Lea

middle: Haarup

last: Gregersen

address: Blegdamsvej 3B,

department: ICMM

country: Denmark

institute: University of Copenhagen

summary: The role of MDC1 in the DNA damage response has been extensively studied, however, its impact on other cellular processes is not well understood. Here, we describe a role for MDC1 in transcription by regulating the activity of the RNAPolymerase II (RNAPII). Depletion of MDC1 caused a genome-wide reduction in the abundance of actively engaged RNAPII elongation complexes throughout the gene body of protein coding genes under unperturbed conditions. Decreased engaged RNAPII subsequently alters the assembly of the spliceosome complex on chromatin, leading to defects in pre-mRNA splicing. Mechanistically, the S/TQ domain of MDC1 modulates RNAPII-mediated transcription. Upon genotoxic stress, MDC1 promotes the abundance of engaged RNAPII complexes at DNA breaks, thereby stimulating nascent transcription at the damaged sites. Of clinical relevance, cancer cells lacking MDC1 display hypersensitivity to RNAPII inhibitors. Overall, we unveil a previously uncharacterized role of MDC1 in RNAPII-mediated transcription with potential implications for cancer treatment.

overall_design: To study the RNAPII elongation rate in control and siMDC1 treated cells we performed DRB/Ttchem-seq as desribed in Gregersen et al. 2020 Nature Protocols.

first: George

last: Pappas

first: Quentin

last: Thomas

middle: H

first: Panagiotis

last: Galanos

first: Jiri

last: Bartek


title: POLR3A  ChIPseq

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

summary: POLR3A ChIPseq in MDA-231 and MDA-LM2 cells

overall_design: Differential RNA Polymerase III was assessed by performing POLR3A ChIP-seq in MDA-MB-231 and MDA-LM2 cells

first: L

last: Noble

first: H

first: S

middle: F

last: Tavazoie


title: Effects of urolithin B treatment on gene expression of IAPP-expressing yeast cells

city: Lisboa

first: Regina

last: Menezes

address: Campo Grande 376

institute: Universidade Lusófona de Humanidades e Tecnologias

summary:
To investigate the effects of ppIAPP-GFP expression and urolithin B treatment in the gene expression of Saccharomyces cerevisiae cells,
we compared different cells: cells expressing the empty vector, cells expressing ppIAPP-GFP, cells expressing the empty vector treated with urolithin B, cells expressing ppIAPP-GFP treated with urolithin B

overall_design: Comparative gene expression profiling analysis of RNA-seq data for yeast cells expressing the empty vector or ppIAPP-GFP (under the control of a galactose inducible promoter) for 12 h and/or receiving urolithin B treatment

first: Ana

last: Raimundo

first: Sofia

last: Ferreira

first: Vânia

last: Pobre

first: Mafalda

last: Lopes-da-Silva

first: José

middle: A

last: Brito

first: Nuno

last: Saraiva

first: Cláudia

middle: N

last: Santos


title: Structure of the human DICER-pre-miRNA complex in a dicing state I

status: Public on Nov 23 2022

city: Seoul

first: Haedong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

institute: Seoul National University

summary: Dicer plays a key role in small RNA biogenesis by processing double-stranded RNAs (dsRNAs). Human DICER (hDICER) is specialized in processing of small hairpins such as pre-microRNAs (pre-miRNAs) with a limited activity towards long dsRNAs, unlike its homologs in lower eukaryotes and plants which cleave long dsRNAs. While the mechanism of long dsRNA cleavage has been well documented, our understanding of pre-miRNA processing is limited due to lack of the structure of hDICER in a catalytic state. Here we report the cryo-electron microscopy structure of hDICER bound to pre-miRNA in a dicing state, uncovering the structural basis for pre-miRNA processing.

overall_design: AQ-seq (bias-minimized sRNA-seq) libraries were constructed using total RNAs as described in our previous study (Kim et al., 2019).

first: Young-Yoon

last: Lee

first: Hansol

first: V

first: Soung-Hun

last: Roh


title: NuRD independent Mi2 activity represses ectopic gene expression during neuronal maturation

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

summary: During neuronal development, extensive changes to chromatin states occur to regulate lineage-specific gene expression. The molecular factors underlying the repression of non-neuronal genes in differentiated neurons are poorly characterised. The Mi2/NuRD complex is a multiprotein complex with nucleosome remodelling and histone deacetylase activity. Whilst NuRD has previously been implicated in the development of nervous system tissues the precise nature of the gene expression programmes that it coordinates are ill-defined. Furthermore, evidence from several species suggests that Mi-2 may be incorporated into multiple complexes that may not incorporate histone deacetylase activity. Here, we show that Mi-2 activity is required for suppressing the ectopic expression of germline genes in neurons independently of HDAC1/NuRD, whilst components of the NuRD complex including Mi-2 regulate neural gene expression to ensure proper development of the larval nervous system. We find that Mi-2 and NuRD-associated repression of ectopic gene expression is restricted to the early stages of neuronal development, indicating that newly derived neurons are more sensitive to epigenetic perturbations.

overall_design: We performed targeted DamID (TaDa) experiments to determine NuRD component chromatin association in multiple cell types in the developing Drosophila brain. RNA-seq was also performed on brains in which Mi2 was knocked down by RNA interference.

first: Gabriel

last: Aughey


title: Effects of ATV:TREM2 and pro-inflammatory stimuli on transcriptome of WT iPSC-derived microglia

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: ATV:TREM2 induces robust G2M checkpoint geneset and is differentiated from pro-inflammatory or mitogenic signatures induced by LPS, TGFb, and IFNg

overall_design: iPSC microglia were dosed for 4 days with antibody or stimuli, RNA was extracted and analyzed by bulk RNA-seq

first: Bettina

last: van Lengerich

first: Lihong

last: Zhan

first: Steve

last: Lianoglou

first: Connie

last: Ha


title: Longitudinal scRNA-seq analysis of primary microglia from mice treated with ATV:4D9 and controls

summary: This study employs single-cell RNAseq (10X Genomics platform) to determine the transcriptional effects of ATV:4D9 treatment on primary mouse microglia in a longitudinal study.

overall_design: Single dose of 10 mg/kg ATV:4D9 or 10 mg/kg ATV:RSV (control) treatments in hTfR knock-in animals were sacrificed at day 1, day 7, day 14 and day 28 post-dose for ex vivo analysis.

first: Dan

last: Xia

first: Elliot

last: Thomsen


title: Longitudinal analysis of DNL919 on microglia transcriptomics in the TB36 mouse model

summary: DNL919 induces durable response in microglia evidenced by mild-to-strong activation of DAM, cell cycle, and immune related pathways at day 7.

overall_design: TB36; hTfR KI mice were administrated with a single dose (10mg/kg) of DNL919 or ATV:DNP02 or vehicle at Day 0 and taken down 1, 4 , and 7 days post dose. Microglia were FACS-sorted from the brains for microglia RNAseq analysis.

first: David

last: Tatarakis


title: G-quadruplexes sense natural porphyrin metabolites for regulation of gene transcription and chromatin landscapes

first: Yin

last: Zhinang

address: Donghu road 185

institute: Wuhan University

summary: G-quadruplexes (G4s) are unique noncanonical nucleic acid secondary structures, which could interact with transcription factors and chromatin remodelers to regulate cell type-specific transcriptome and shape chromatin landscapes. Based on the direct interactions between G4 and natural porphyrins, we established an in situ capture sequencing approach combining synthesized biotin-PEG4-Hemin and Cleavage Under Targets and Tagmentation (CUT&Tag) strategy to profile the Hemin binding sites in the human genome. We found that a proportion of G4s overlapped with Hemin binding sites and Hemin promoted genome-wide G4 formation at Hemin binding sites. Hemin treatments impaired gene transcription initiation and altered chromatin landscape with decreased H3K27ac and H3K4me3 modifications. Interestingly, G4 was not involved in the canonic Hemin-BACH1-NRF2-mediated enhancer activation process, highlighting an unprecedented G4-dependent mechanism for metabolic regulation of transcription. Furthermore, Hemin induced specific gene expression profiles in mouse primary hepatocytes, and block of Hemin degradation in mice by Hmox1 knockdown resulted in hepatic injury, providing in vivo insights for metabolic control of gene transcription by porphyrins.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Determination of hemin binding sites in the human genome, Determination of G4-CUT&Tag, R-loop-CUT&Tag, PRO-seq, ChIP-seq and RNA-seq in HEK293T or primary hepatocytes

first: Kaiwei

last: Liang


title: T Cell Infiltration in Central Nervous System and Their Association with Brain Calcification in Slc20a2-deficient Mice

city: Harbin

first: Zhang

last: Yi

address: xiangan street num 766

institute: The Fourth Affiliated Hospital of Harbin Medical University

summary: Primary familial brain calcification (PFBC) is a rare neurodegenerative and neuropsychiatric disorder characterized by bilateral and symmetric brain calcification along the microvessels or inside neuronal cells in the basal ganglia, thalamus, and cerebellum. Neurological symptoms typically include movement disorders, cognitive impairment, and neuropsychiatric signs. Slc20a2 homozygous (HO) knockout mice can simulate the phenotype of brain calcification observed in humans. However, the cellular and molecular mechanisms associated with brain calcification, particularly at an extremely early stage (before calcification emerges), remain largely unknown.    Herein, we quantified central nervous system (CNS)-infiltrating immune cells in different age groups and found that CD45+CD3+ T cells were significantly increased in the brain parenchyma even in the pre-calcification stage of 1-month-old Slc20a2-HO mice. Further immunophenotyping demonstrated that CD3+CD4-CD8- and CD3+CD4+ T cells were the two main subtypes increased in the brain. The accumulation of total T cells appears to be associated with the severity of brain calcification. Paracellular and transcellular permeability of the blood-brain barrier increased in endothelial cells of brain microvessels in Slc20a2-HO mice. The expression of endothelial cell adhesion molecules was increased, while that of tight and adherens junction proteins was decreased, reflecting the molecular basis of T cell recruitment to endothelial cells and paracellular migration into the brain. IgG and albumin assays revealed an increased leakage of endothelial cells and the process of T cell transcellular migration was captured by immunoelectron microscopy, suggesting the enhancement of transcytosis or endocytosis in brain endothelial cells of Slc20a2-HO mice. The sphingosine 1-phosphate receptor modulator, FTY720, could significantly inhibit brain calcification, probably by reducing the CNS infiltration of T cells, subsequently modulating neuroinflammation, and enhancing the phagocytosis of CNS resident immune cells.    This study demonstrated that CNS-infiltrating T cells were associated with the progression of brain calcification and suggested that the impairment of blood-brain barrier permeability, which was closely related to T cell invasion into the CNS, could be explained by an increase in the paracellular and transcellular pathways of brain endothelial cells in Slc20a2-HO mice. Moreover, FTY720 was a potential drug that could be used to treat patients with PFBC in the future

overall_design: Comparative gene expression profiling analysis of RNA-seq data between FTY720-treated Slc20a2-HO mice and the placebo group

first: Yi

last: Zhang

first: Yaqiong

last: Ren

first: Yueni

first: Ying

last: Li

first: Chao

last: Xu

first: Ziyue

last: Peng

last: Jia

first: Zitong

first: Shupei

last: Qiao

first: Lei

last: Shi


title: effects of microbiome dysbiosis on murine dystrophic muscle

status: Public on Nov 22 2022

city: Cincinnati

first: Mattia

last: Quattrocelli

state: OH

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: Duchenne muscular dystrophy (DMD) is a progressive severe muscle-wasting disease caused by mutations in DMD encoding dystrophin that leads to loss of muscle function with cardiac/respiratory failure and premature death. Since dystrophic muscles are sensed by infiltrating inflammatory cells and gut microbial communities can cause immune dysregulation and metabolic syndrome, we sought to investigate whether intestinal bacteria may support the muscle immune response in mdx dystrophic animal model. We assess this question here through unbiased profiling of muscle transcriptome through RNAseq. We found that the absence of gut microbes through the generation of a mdx GF animal model as well as modulation of the microbial community structure by antibiotic treatment revealed the ability of the dystrophic-associated intestinal microbiota to modulate immunity and secondary muscle pathogenetic mechanisms of DMD, including inflammation, fibrosis, and atrophy.

overall_design: 3 male mdx mice (3mo); 3 male mdx mice germ-free (3mo); 3 male mdx mice with antibiotics (3mo); 3 male WT mice (3mo); 3 male mdx mice (9mo); 2 male mdx mice germ-free (9mo); 3 male mdx mice with antibiotics (9mo).

first: Andrea

last: Farini

first: Yvan

last: Torrente


title: A genetic disorder reveals a hematopoietic stem cell regulatory network co-opted in leukemia [bulk RNA-seq]

city: Cambridge

first: Liming

last: Tao

address: 415 Main Street

institute: Broad Institute of Harvard and MIT

summary: we uncover a key transcriptional network involving hundreds of genes that is required for HSC self-renewal.

overall_design: MECOM impact on the hematopoietic stem cells

first: Richard

last: Void

first: Fulong

last: Yu

first: Vijay

middle: G

last: Sankaran

first: Regev

last: Aviv


title: Lineage tracing and single nuclear multiomics reveal novel features of adaptive and maladaptive repair after acute kidney injury

city: Los Angeles

first: Kari

middle: Ann

last: Koppitch

address: 1425 San Pablo Street, BCC 312

department: Stem Cell

institute: USC

summary: We combined lineage tracing of cycling (Ki67+) cells with single nuclear multiomics (single nucleus RNA-seq + single nucleus ATAC-seq) to characterize the long-term (4 weeks and 6 months) outcome of cells that initiate proliferation early after acute kidney injury (AKI). The data document a broad proliferative response to injury in epithelial and non-epithelial kidney cell types, identify novel transcription factors governing the adaptive and maladaptive proximal tubule cell state and highlight the importance of enhancer dynamics in determining cell states. Comparison of lineage traced with control proximal tubule cells reveals long-term effects of AKI on proximal tubule cells, even following adaptive repair.

overall_design: Ki67 is expressed by cells in the cell cycle. We injected Tamoxifen into Ki67cre/ERT2; INTACT mice on day 2 and 3 after ischemia-reperfusion injury (IRI) to induce nuclear membrane green fluorescent protein (GFP) labeling of all cells in the cell cycle at the induction of renal repair and enable tracking of these cells until 4 weeks and 6 months post IRI. At collection GFP+ and GFP- nuclei were separated by fluorescence-activated cell sorting (FACS) and combined snRNA- and snATAC-seq was performed using the 10X Chromium multiome ATAC + gene expression kit. Sham operated and non-surgery mice were used as controls. In total 12 samples were processed: 3 GFP+ samples (AKI_GFP+_4weeks) and 1 GFP- sample AKI_GFP-_4weeks) at 4 weeks post IRI; 4 GFP+ samples (AKI_GFP+_6months) and 1 GFP- sample AKI_GFP-_6months) at 6 months post IRI; 2 controls at 4 weeks (Ctrl_4weeks) and 1 control at 6 months (Ctrl_6months) (for controls no separation of GFP+ and GFP- nuclei by FACS was performed).

first: Louisa

middle: M

last: Gerhardt

first: Jordi

last: van Gestel

first: Jinjin

last: Guo

first: Sam

last: Cho

first: Yuhei

last: Kirita

first: Benjamin

last: Humphreys

first: Andrew

last: McMahon


title: Effect of Ube3d knockout on gene expression in 3T3-L1 preadipocytes

city: Boston

first: Daniel

last: Heller-Trulli

state: MA

address: 136 Harrison Ave

department: Developmental, Molecular, and Chemical Biology

institute: Tufts University School of Medicine

summary:
To investigate the effect of UBE3D loss on 3T3-L1 differentiation, we generated Ube3d-KO 3T3-L1 cells.
We then performed RNA sequencing on undifferentiated WT and KO cells to assess gene expression changes and alterations in RNA 3' end processing.

overall_design: Sequencing of rRNA-depleted RNA from undifferentiated WT and Ube3d-KO 3T3-L1 cells grown in log phase.

first: Huiyun

last: Liu

first: Srimoyee

last: Mukherjee

first: Claire

middle: L

last: Moore


title: A transcriptomic atlas of drug-induced endothelial dysfunction in human endothelial cells

status: Public on Nov 21 2022

city: Palo Alto

first: Yu

address: 1215 Welch Road

department: CVI

institute: Stanford University

summary: We report the RNA-Sequencing of iPSC-ECs or primary aorta ECs treated with 8 clinically-relevant compounds and DMSO for 24 hrs or 72 hrs.

overall_design: Transcriptomic profiles of 72 samples (4 cell lines, 9 conditions and 2 time points)

first: Chengyi

last: Tu

first: Joseph

middle: C

last: Wu


title: Next Generation Sequencing Facilitates Quantitative Analysis of primary cultured astrocytes Transcriptomes from neonatal wild type and Spp1 KO retina and optic nerve.

first: Tatjana

last: Jakobs

address: 20 Staniford Street

department: Howe Laboratory of Ophthalmology

institute: Massachusetts Eye and Ear Infirmary

summary:
Purpose: The goals of this study are to investigate differential genes expression with RNA-seq between wild type and Spp1 KO retinal and optic nerve astrocytes and then to identify the effected genes after Spp1 knockout
Methods: Total RNA was extracted from cultured astrocytes isolated from either C57BL/6 wild-type or Spp1 KO neonatal mice using the RNeasy Plus Micro Kit (Qiagen; 74034). mRNA profiles were generated by deep sequencing using Illumina   NovaSeq 6000. The sequence reads that passed quality filters were aligned to the mouse reference genome (GRCm38) using the STAR software package. Differential expression analysis were performed using the R package DESeq2. qPCR validation was performed using SYBR Green assays.
Results: After quality control and data filtering, about 40 million raw reads per sample were obtained. We mapped sequence reads per sample to the mouse reference genome (GRCm38) and identified 35825 transcripts in astrocytes of wild type and Spp1−/− mice. A total of 3624 differentially expressed genes (DEGs) were identified between wild type and Spp1−/− astrocytes, with a fold change ≥1.5 and p value <0.05. Among DEGs, 1991 were upregulated and 1633 were downregulated in the Spp1−/− astrocytes. Hierarchical clustering heat map, pathway enrichment and analysis of DEGs were performed.
Conclusions: Our RNA-seq dataset represents the differentially expressed genes in theSpp1 KO astrocytes.

overall_design: Astrocyes mRNA profiles of wild type  and Spp1 KO neonatal  mice

first: Song

last: Li


title: Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements [ChIP-seq]

city: Paris

first: Sebastian

last: Amigorena

state: --- Select a state ---

address: 26 rue Ulm

department: Center of Immunotherapy

country: France

institute: Curie Institute

summary: To analyze regulation of JET expression, we generated Setdb1-deficient MC38 and B16OVA cells, using lentivirus-based CRISPR/Cas9. Ctrl and KO cells lines were used to perform ChIP-seq against H3K9me3 and H3K9Ac, with 3 biological replicates.

overall_design: We analyzed H3K9me3 and H3K9Ac signals, in particular on loci involved in forming junctions between exons and TEs.

first: Marianne

last: Burbage

first: Derek

last: Rookhuizen

first: Mengliang

last: Ye


title: Next Generation Sequencing Facilitates Quantitative Analysis of primary cultured astrocytes treated with SB431542, Ro5-3335 and HLM006474 inhibitors.

summary:
Purpose: The goals of this study are to investigate differential genes expression with RNA-seq in primary cultured astrocytes treated with the Tgf-beta1 receptor inhibitor SB431542, the Runx1 inhibitor Ro5-3335 and the E2f1 inhibitor HLM006474.
Methods: Primary cultured astrocytes were isolated from either C57BL/6 wild-type neonatal mice. Total RNA was extracted from SB431542, Ro5-3335 and HLM006474-treated astrocytes with the RNeasy Plus Micro Kit (Qiagen; 74034). mRNA profiles were generated by deep sequencing using Illumina  NovaSeq 6000. The sequence reads that passed quality filters were aligned to the mouse reference genome (GRCm38) using the STAR software package. Differential expression analysis were performed using the R package DESeq2. qPCR validation was performed using SYBR Green assays.
Results: After quality control and data filtering, about 50 million raw reads per sample were obtained. We mapped sequence reads per sample to the mouse reference genome (GRCm38) and identified 35825 transcripts vehicle, SB431542, Ro5-3335 and HLM006474 group. Differentially expressed genes (DEGs) were analyzed with a fold change ≥1.5 and p value <0.05. A total of 748 DEGs were identified in SB431542 group with 347 upregulated genes and 401 downregulated genes. A total of 397 DEGs were identified in Ro5-3335 group with 82 upregulated genes and 315 downregulated genes. A total of 856 DEGs were identified in HLM006474 group with 216 upregulated genes and 640 downregulated genes. Hierarchical clustering heat map, pathway enrichment and analysis of DEGs were performed.
Conclusions: Our RNA-seq dataset represents the differentially expressed genes in the C57BL/6 astrocytes treated with SB431542, Ro5-3335 and HLM006474-treated astrocytes.

overall_design: Astrocyes mRNA profiles after treatment with SB431542, Ro5-3335 and HLM006474 inhibitors.


title: Field transcriptome analysis reveals a molecular mechanism of the cassava-flowering phenomena in a mountainous environment in Southeast Asia

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

summary: We report the sequencing data for time series profiling of cassava.This study provides transcriptome profile during floweing and non-flowering in cassava.

overall_design: mRNA profiles of leaf samples from cassava cultivating in general field (non flowering) and mountainous area (flowering) in Vietnam were generated by sequencing in illumina paired-end sequencing

first: Hiroki

last: Tokunaga

first: Motoaki

last: Seki

first: Yoshinori

last: Utsumi

first: Satoshi

last: Takahashi

first: Akihiro

last: Matsui

first: Hiroyuki

last: Tsuji


title: Effect of elevated CO2 concentraition in fennel (Foeniculum vulgare Mill.).

city: Wonju-si

first: Sun-Goo

last: Hwang

address: 83 Sangjidae-gil, Wonju-si, Gangwon-do, Korea

institute: Sangji University

summary:
To investigate the transcriptome changes by CO2 supply, we evaluated the transcriptional changes in fennel.
We then performed gene expression profiling analysis using data obtained from RNA-seq of fennel at two stress conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for fennel.


title: Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements [RNA-seq]

summary:
To study the expression of junctions between exons and transposable elements (TEs), we generated paired-end RNAseq from various mouse tumor cell lines, with several biological replicates (cultures from different days).
To analyse regulation of JET expression, we generated Setdb1-deficient B16F10 and B16OVA cells, using lentivirus-based CRISPR/Cas9. Ctrl and KO cells lines were used to generate paired-end RNAseq, with several biological replicates (cultures on different days).
We generated paired-end RNAseq from healthy female mouse tissues, to compare JET expression in healthy and tumor cells.

overall_design: We performed gene, TE and JET expression analyses on these datasets.

first: Marine

last: Gros

first: Ares

last: Rocañin-Arjo

first: Christel

last: Goudot


title: Horizontal transfer of bacteriocin biosynthesis genes requires metabolic adaptation to improve compound production and cellular fitness

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

summary: Biosynthetic gene clusters (BGCs) encoding the production of bacteriocins are widespread amongst bacterial isolates and are important genetic determinants of competitive fitness among bacterial lineages within a given habitat. Staphylococci produce a tremendous diversity of compounds and the corresponding gene clusters (Staphylococcal Antibiosis Islands - SAbIs) are frequently associated with mobile genetic elements, suggesting acquisition and loss of biosynthetic capacity. Pharmaceutical biology has shown that compound production in heterologous hosts is often challenged by the lack of optimal precursor supplies. Accordingly, many recipients produce low compound amounts or show reduced growth rates. To assess whether transfer of SAbIs between closely related S. aureus strains has similar effects, we used as model the SAbI encoding the ribosomally synthesized and post-translationally modified peptide (RiPP) Micrococcin P1 (MP1). We found that acquisition of the SAbI by S. aureus RN4220 did allow immediate MP1 production but also imposed a metabolic burden. Adaptive evolution selected for strains with increased TCA-cycle activity, which enhanced metabolic fitness and levels of compound production. Metabolome analysis showed that the adaptive mutation increased the levels of central metabolites including citrate and α-ketoglutarate, and the increased availability of citrate turned out to be essential to overcome SAbI associated growth defects. Our results indicate that acquisition of SAbIs represents a blessing for the recipient strain as long as its genetic and metabolic predispositions allow integration of bacteriocin production into the cellular metabolism. This in turn may be crucial to ensure the competitive fitness of SAbI recipients within natural bacterial communities.

sample_organism: Staphylococcus aureus subsp. aureus RN4220

overall_design: Differential expression analysis between a wild type strain of RN4220 and two strains with plasmid pD4-19 of which one was altered using an adaptive evolution experiment.

first: Sophia

last: Krauss

first: Theresa

last: Harbig

first: Simon

last: Heilbronner


title: R14del RNA-seq

city: Barcelona

first: Malgorzata

middle: Ewa

last: Rogaska

address: C/ del Dr. Aiguader, 88

institute: CRG

summary: Arrhythmogenic cardiomyopathy (ACM) is characterized by life-threatening ventricular arrhythmias and sudden cardiac death and affects hundreds of thousands of patients worldwide. The deletion of Arginine 14 (p.R14del) in the phospholamban (PLN) gene has been implicated in the pathogenesis of ACM. PLN is a key regulator of sarcoplasmic reticulum (SR) Ca2+ cycling and cardiac contractility. Despite global gene and protein expression studies, the molecular mechanisms of PLN-R14del ACM pathogenesis remain unclear. Using a humanized PLN-R14del mouse model and human induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs), we investigated the transcriptome-wide mRNA splicing changes associated with the R14del mutation. We identified >200 significant alternative splicing (AS) events and distinct AS profiles were observed in the right (RV) and left (LV) ventricles in PLN- R14del compared to WT mouse hearts. Enrichment analysis of the AS events showed that the most affected biological process was associated with “cardiac cell action potential”, specifically in the RV. We found that splicing of 2 key genes, Trpm4andCamk2d, which encode proteins regulating calcium homeostasis in the heart, were altered in PLN-R14del mouse hearts and human iPSC-CMs.  Bioinformatical analysis pointed to the tissue-specific splicing factors Srrm4 and Nova1 as likely upstream regulators of the observed splicing changes in the PLN-R14del cardiomyocytes. Our findings suggest that aberrant splicing may affect Ca2+- homeostasis in the heart, contributing to the increased risk of arrythmogenesis in PLN- R14del ACM.

overall_design:
We knocked in the R14del allelePSCs by CRISPR-Cas9 mediated HDR, and report the gene expression and splicing changes in isogenic iPSC-CMs
2 isogenic cell lines; parental line, and R14del line

first: Ioannis

last: Karakikes

middle: E

last: Rogalska


title: Transcriptomic analyses identifies novel regulators of placental development

city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

summary:
The placenta is a transient organ that is repsonsible for multiple processes during pregnancy. Here we aim to study the development of the placenta using mouse models at embryonic day (e) e7.5, e8.5 and e9.5
by integrating RNA-seq data at the three timepoints to identify important genes, inferring their interaction networks, and predict novel regulators of placental development.

overall_design: Gene expression analysis of RNA-seq data for mouse placental tissues on embryonic day (e) e7.5, e8.5 and e9.5.

first: Ha TH

last: Vu


title: Proteasome inhibition silences oncogenic transcripts in multiple myeloma through HDAC3-mediated DNA condensation and gene relocation [CUT&RUN]

city: Houston

first: Laure

last: Maneix

state: TX

address: One Baylor Plaza, MS230, Alkek building, Room N830

department: Huffington Center on Aging

institute: Baylor College of Medicine

summary: This study provides a genome-wide map of changes in degradative ubiquitination in response to proteasome inhibition in the multiple myeloma cell line MM.1S. Following proteasome inhibition with lactacystin, CUT and RUN assays were carried out to determine the genomic locations of ubiquitin in multiple myeloma cells stably expressing a flagged version of ubiquitin (MM.1S-3XFlag Ubiquitin cells). In addition, we report the DNA binding locations of the transcription factor c-MYC in basal conditions in MM.1S parental cells.

overall_design: Multiple myeloma cells MM.1S were treated for three hours with the synthetic proteasome inhibitor lactacystin and compared to DMSO control-treated cells in CUT & RUN experiments. We performed sequencing for degradative ubiquitination marks (3XFlag-ubiquitin) and the transcription factor c-MYC.

first: Andre

last: Catic


title: Proteasome inhibition silences oncogenic transcripts in multiple myeloma through HDAC3-mediated DNA condensation and gene relocation

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

overall_design: Refer to individual Series


title: Lymphatic endothelial cell identity is controlled by a GATA2 bound enhancer (Microarray)

city: Adelaide

first: John

last: Toubia

address: Frome Rd

institute: Centre for Cancer Biology

summary: This study investigates the transcriptome of primary dermal lymphatic endothelial cells compared with blood vascular endothelial cells using samples isolated from wildtype embryos at defined points (E14.5, E16.5 and E18.5) during mouse embryonic development.

overall_design: Matching LEC and BEC samples from three litters( independent biological replicates) at each timepoint are compared by RNA microarraay analysis.

first: Jan

last: Kazenwadel

first: Luis

last: Arriola


title: A blood-brain barrier transport vehicle improves brain biodistribution of a TREM2 antibody and enhances microglial metabolism via receptor clustering

first: Thomas

last: Sandmann

address: 161 Oyster Point Blvd

institute: Denali Therapeutics


title: Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements

first: Sebastian

last: Amigorena


title: The LHX2-OTX2 transcriptional regulatory module controls retinal pigmented epithelium differentiation and underlies genetic risk for age-related macular degeneration

city: Tel Aviv

first: Mai

last: Eshel

address: Klatzkin 35

department: Human Molecular Genetics and Biochemistry

institute: Tel Aviv University


title: Transcription factor antagonism regulates heterogeneity in embryonic stem cell states

first: Sofia

last: Hu

email: sofiahu@mit.edu, xsu@cpdr.org

address: 500 Main Street

institute: MIT

summary: Gene expression heterogeneity underlies the formation of cell states, and switching between states contributes to developmental robustness. While gene expression variation can arise from stochastic transcriptional processes, whether it can be regulated and coordinated by an underlying program is unclear. We characterize the regulatory program underlying heterogeneity and switching between murine embryonic stem cell (mESC) states. Using nascent transcriptome assays, we identified a subset of differentially active and transcribed enhancers (DATEs) across states. DATEs regulate variably expressed gene targets and contribute to cell state formation. Further, DATEs are distinguished by co-binding of Kruppel-like transcription factors Klf4 and Zfp281. In contrast to other transcription factors that form a positive feedback network stabilizing ES cell-type identity, Klf4 and Zfp281 drive opposing transcriptional and chromatin programs. Abrogation of their ability to bind DATEs dampens variation in gene expression and reduces heterogeneity. Single cell analysis reveals competing Klf4 and Zfp281 gene programs that define mESC state, consistent with a model whereby Klf4 and Zfp281 generate transcriptional heterogeneity through functional antagonism at DATEs. These results show how antagonistic circuits of TFs and enhancers contributes to gene expression variation and cell state, with potential implications for the generation of diverse cell types during mammalian development.

overall_design:
(1) Examination of nascent transcriptome by mPROseq in three mESC states defined by Nanog- and Sox2-defined subpopulations (States 1, 2, and 3) in three biological replicates;
(2) Examination of nascent transcriptome by mPROseq in WT, Klf4KO, Zfp281KO mESC in three biological replicates;
(3) Examination of steady state transcriptome by RNAseq in WT, Klf4KO, Zfp281KO mESC in nine biological replicates;
(4) Examination of chromatin accessibility by ATACseq in WT, Klf4KO, Zfp281KO mESC in three biological replicates;
(5) ChIPseq of Klf4 and Zfp281 in WT, Klf4KO, Zfp281KO mESC;
(6) Single cell RNA sequencing of two biological replicates each of WT, Klf4KO, Zfp281KO mESC
(7) CUT&RUN of Klf4 and Zfp281 in States 1, 2, and 3

first: Salil

last: Garg


title: Lymphatic endothelial cell identity is controlled by a GATA2 bound enhancer [ChIP-seq]

first: Natasha

last: Harvey

state: SA

address: UniSA CRI Building, North Terrace

summary: Transcriptional enhancer elements are responsible for orchestrating the temporal and spatial control over gene expression that is crucial for programming cell identity during development. Here, we describe a novel enhancer element important for regulating Prox1 expression in lymphatic endothelial cells. This evolutionarily conserved enhancer is bound by key lymphatic transcriptional regulators including GATA2, FOXC2, NFATC1 and PROX1. CRISPR-Cas9 genome editing of this enhancer element revealed that deletion of only 5 nucleotides encompassing the GATA2 binding site has a dramatic impact on lymphatic vascular development; mice homozygous for this deletion die soon after birth exhibiting profound lymphatic vascular defects. Lymphatic endothelial cells in enhancer mutant mice exhibit reduced levels of genes characteristic of lymphatic endothelial cell identity and acquire characteristics of hemogenic endothelium, including the capacity to generate hematopoietic cells. These data reveal the first transcriptional enhancer element important for regulating Prox1 expression and lymphatic endothelial cell identity and suggest that Prox1 is important for repressing hemogenic cell identity in the lymphatic endothelium.

overall_design: Genome wide investigation of transcription factor binding in human lymphatic endothelial cells using key TFs in lymphatic valve development


title: Transcriptomic analysis of donor matched primary human immature dendritic cells and monocyte-derived Langerhans cells

status: Public on Nov 20 2022

city: Debrecen

first: Attila

middle: Gábor

last: Szöllősi

address: Egyetem tér 1.

department: Department of Immunology

country: Hungary

institute: University of Debrecen

summary: Donor matched immature dendritic cells and Langerhans cells were generated from CD14+ monocytes to show the validity of our Langehans cell model.

overall_design: Transcriptomic profiling of immature dendritic cells and Langerhans cells in five biological replicates.

first: Akos

last: Nemeth

first: Shahrzad

last: Alimohammadi


title: Hippo signaling instructs ectopic but not normal organ growth [Liver YapTazKO+CCl4]

status: Public on Nov 19 2022

city: Leuven

first: Georg

last: Halder

address: Herestraat 49

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB-KU Leuven

summary: We conditionally deleted Yap/Taz from hepatocytes prior to induction of acute injury by injection of liver toxin carbon tetrachloride (CCl4).

overall_design: Differential gene expression analysis of samples of purified hepatocytes from Yap/Taz KO livers 48 hours after acute injury and corresponding control conditions: regenerating Yap/Taz KO hepatocytes (Yap/Taz KO + CCl4), regenerating control hepatocytes (ctrl + CCl4), uninjured Yap/Taz KO hepatocytes (Yap/Taz KO) and uninjured control hepatocytes (ctrl).

first: Weronika

last: Kowalczyk

first: Soheil

last: Soheily

first: Leticia

last: Sansores


title: Proteasome inhibition silences oncogenic transcripts in multiple myeloma through HDAC3-mediated DNA condensation and gene relocation [ChIP-seq]

first: Laure

last: Maneix

summary: This study provides a genome-wide map of changes in histone mark modifications and HDAC3 binding in response to protesome inhibition in the multiple myeloma cell line MM.1S. Chromatin immunoprecipitation assays were carried out to determine the genomic locations of histone modifications (H3K27ac, H3K4me1, H3K4me3) and histone deacetylase 3 (HDAC3) binding locations in multiple myeloma cells following proteasome inhibition with either lactacystin, bortezomib or carfilzomib. In addition, we report the effects of the overexpression of the E3-ubiquitin ligase Siah2 and the impact of HDAC3 knockdown on H3K27 acetylation levels in multiple myeloma cells treated with lactacystin. Our global ChIP-seq analysis of histone marks showed that enhancer and promoter marks (H3K4me1 and H3K4me3, respectively) present little response to proteasome inhibition, while the acetylation of histone H3K27 was significantly up- or down-regulated after three-hour treatment with proteasome inhibitors. Treatment of the cells with lactacystin, bortezomib or carfilzomib strongly increased HDAC3 recruitment at cell cycle and mitochondrial promoters, indicating that proteasome inhibition stabilized HDAC3 locally at the promoter of these genes to induce their repression. Furthermore, genome-wide ChIP-seq analysis of H3K27ac profiles showed that overexpression of Siah2 enhanced H3K27 acetylation levels at cell cycle and mitochondrial promoters.

overall_design: Multiple myeloma cells MM.1S were treated for three hours with the synthetic proteasome inhibitor lactacystin or the FDA-approved clinical proteasome inhibitors bortezomib or carfilzomib and compared to DMSO control-treated cells in ChIP-sequencing experiments. We performed ChIP-seq for histone modifications (H3K27ac, H3K4me1, H3K4me3) and the histone deacetylase HDAC3. We also studied the changes in H3K27 acetylation triggered by HDAC3 knockdown or Siah2 overexpression in MM.1S cells.

first: Andre

last: Catic


title: Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci [bulk RNA-seq]

city: Wuhan

first: Junpeng

last: Zhan

address: 1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: The anther-enriched phased, small interfering RNAs (phasiRNAs) play vital roles in regulating male fertility in grass species. The long non-coding precursors of phasiRNAs are products of RNA polymerase II and are likely regulated by transcription factors (TFs). A few putative transcriptional regulators of the 21- or 24-nucleotide phasiRNA loci (i.e., 21- or 24-PHAS loci) have been identified in maize (Zea mays), but whether any of the individual TFs or TF combinations are sufficient to activate the PHAS loci is unclear. Here, we identified the temporal gene coexpression networks (modules) associated with maize anther development, including two modules highly enriched for the 21- or 24-PHAS loci. Comparisons of these coexpression modules and gene sets dysregulated in several reported male sterile TF mutants revealed new insights into the timing of activities of the TFs, including antagonistic roles for OUTER CELL LAYER 4 and Male sterile 32. Trans-activation assays of individual TFs using bulk-protoplast RNA sequencing (RNA-seq) showed that two of the TFs coexpressed with 21-PHAS loci could activate several 21-nt phasiRNA pathway genes, but none was sufficient to activate 21-PHAS loci. Screens for combinatorial activities of these TFs and, separately, the recently reported putative transcriptional regulators of 24-PHAS loci using single-cell (protoplast) RNA-seq, did not detect reproducible activation of 21-PHAS or 24-PHAS loci. Collectively, our results suggest that the endogenous transcriptional machineries and/or chromatin states in the anthers are necessary to activate reproductive PHAS loci. Nonetheless, the single-cell RNA-seq approach shows potential for future studies of combinatorial activities of TFs.

overall_design: Gene expression profiling of maize leaf protoplasts ectopically expressing putative transcriptional regulators of anther-enriched, 21-nt reproductive phasiRNAs

first: Lily

last: O'Connor

first: D

middle: B

last: Marchant

first: Chong

last: Teng

first: Virginia

last: Walbot

first: Blake

last: Meyers


title: Hippo signaling instructs ectopic but not normal organ growth [Drosophila YkiHyper]

summary: In order to study how ectopic Yki drives tissue overgrowth in Drosophila imaginal discs, we overexpressed the constitutively active Yki3SA and deleted wts in clones of cells in the entire eye-antennal imaginal disc, as well as specifically in eye disc proper cells using Optix-Gal4. Using the MARCM system allowed us to compare the effects of Yki3SA  overexpression in wild-type and sd mutant clones.

overall_design: Differential gene expression analysis of samples of eye-antennal imaginal discs with Yki hyperactivation and their corresponding controls: 1) eyFLP wts KO and eyFLP control; 2) optix>Yki3SA and optix control; 3) eyFLP MARCM Yki3SA and eyFLP MARCM ctrl as well as eyFLP MARCM Yki3SA sd- and eyFLP MARCM sd- to measure the effects of Yki hyperactivation in sd mutant clones.


title: Single-cell RNA-seq of hiPSCs under 5iLAF naïve culture conditions

status: Public on Nov 18 2022

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

institute: CIMA

summary: We applied single-cell RNA sequencing, to define heterogenous cell populations present in human naïve 5iLAF cultures. Noteworthily, although Epiblast-like cells represented the main cell population, we detected a population with a trophectoderm-like gene expression profile which could be subclustered according to three different stages of early trophectoderm maturation.  Furthermore, we provided evidence for the existence of an 8-cell-like cell population, equivalent to the 8-cell human embryo. Thus, the 5iLAF naïve culture condition emerges as an excellent system to model gene regulation in the earliest stages of human embryogenesis, including zygotic genome activation..

overall_design: Single-cell RNA-seq of hiPSCs (G15.AO) cultured under 5iLAF naïve  conditions

first: Xabier

last: Aranguren

first: Marta

last: Moya-Jódar


title: Lymphatic endothelial cell identity is controlled by a GATA2 bound enhancer

first: John

last: Toubia


title: Targeting Xkr8 via nanoparticle-mediated in situ codelivery of siRNA and chemotherapy drugs for cancer immunochemotherapy

city: Pittsburgh

first: Song

last: Li

state: Pennsylvania

address: 335 Sutherland Drive, Salk Pavilion

institute: University of Pittsburgh

summary: Downregulation of specific proteins named scramblases might enhance tumour immunosuppression. In this paper the authors first show that the scramblase Xrk8 is overexpressed in tumour cells upon treatment with chemotherapeutics, and then developed a nanomedicine platform for co-delivery of a cancer pro-drug and of a siRNA directed against the Xrk8 gene, showing therapeutic effect and enhanced immune response in animal tumour models.

overall_design: BALB/c mice (n=3) bearing s.c. CT26 tumors (~200 mm3) received i.v. injection of FuOXP NPs (10 mg FuOXP/kg) with empty NPs as a control once every five days for three times. Tumors were harvested at 24 h after the last treatment.

first: Yuang

last: Chen

first: Zhangyi

last: Luo

first: Runzi

last: Sun


title: In-vitro response pattern of mesenteric lymph node (MLN) cells to specific gut commensal microbes

city: Wuxi

first: Sai

middle: sai

last: Feng

state: State/Province

address: Lihu Avenue No1800

department: School of Food Science and Technology

institute: Jiangnan University

summary: Gut microbiota plays a significant role in shaping gut and systematic immune and huge strain- and species- dependent differences exit. Using in-vitro MLN co-culture models, we want to initially uncover these differences. MLN cells were isolated from C57BL/6 mice and co-cultured with bacterial cells with or without anti-CD3 and anti-CD28 antibodies for three days. After that, IL-10 in cell supernatant was measured and RNA was extracted using Trizol reagent. RNA-seq was performed on Illumina Hiseq X ten. Raw sequenced data were filtered by fastp and clean data were mapped to reference genome (Mus_musculus, GRCm39). Data processing adopted featurecounts in subread, abundance_estimates_to_matirx.pl in Trinity, DEseq and ClusterProfiler. We found that all bacterial species activated the innate immunity response. However, only Akkermansia muciniphila and Clostridium butyricum had cognate T cell antigen and activated adaptive immunity responses even without stimulus.

overall_design: mRNA profiles of MLN cells isolated from C57BL/6 mice and colcultured with specifc gut microbes or stimulus in vitro for three days

first: Saisai

first: Qixiao

last: Zhai

first: Jin

first: Dingwu

last: Qu


title: Lymphatic endothelial cell identity is controlled by a GATA2 bound enhancer (RNA-Seq)

summary: This study investigates the impact on the transcriptome of lymphatic endotheial cells of a 5bp deletion (GATA2 binding site) in an enhancer element 11kb upstream of the Prox1 gene.

overall_design: Comparison of RNA from deletion mutant and wildtype lymphatic endothelial cells isolated directly from embryos at E14.5.  Also, to assess haematopoietic potential, comparison of the same samples after 7d co-culture on OP9 feeder cells.

first: Jan

last: Kazenwadel

first: Luis

last: Arriola


title: Actions of FGF2, LIF, and IGF1 on Embryo Survival and Conceptus Elongation following Slow-rate Freezing

city: Madison

last: Ortega

state: Wisconsin

address: 1675 Observatory Drive

department: Department of Animal and DairySciences

institute: University of Wisconsin

summary: Evaluation of FGF2, LIF, and IGF1 supplementation during embryo culture on conceptus development at day 15.

overall_design: Transcriptomic analyses of day 15 bovine conceptuses treated with FGF2, LIF, and IGF1 and control

first: Katy

middle: S

last: Stoecklein

first: MSofia

first: Randall

last: Prather

first: Alvaro

last: Garcia-Guerra

first: Benjamin

middle: J

last: Duran


title: Human CMV-specific vs IAV-specific CD8 T cells

city: Baltimore

first: Nan-Ping

last: Weng

address: 251 Bayview Blvd

department: LMBI

institute: NIA

summary: We compared CD8 T cells specific for a CMV epitope (pp65495-503) and an influenza A virus (IAV) epitope (M158-66) of the same healthy adults and identified genes whose expression are altered in CMV-specific compared to IAV-specific TCM cells

overall_design:
Transcriptional profiling of CMV-specific vs IAV-specific CD8 T cells from healthy human. Goal was to determine the differentially expressed genes between these two antigen-specific CD8 T cells.
CMV-specific vs IAV-specific CD8 T cells. Biological replicates: 4 CMV-specific replicates, 4 IAV-specific  replicates.

first: Guobing

first: Nan-ping


title: ARID2 mitigates hepatic steatosis via promoting the ubiquitination of JAK2

status: Public on Nov 17 2022

city: Shanghai

first: Jing-Jing

email: tide7@163.com, jjli@sinh.ac.cn

address: No. 320 Yueyang Road, Xuhui District

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

summary: Non-alcoholic fatty liver disease (NAFLD) has become a growing public health problem. However, the complicated pathogenesis of NAFLD contributes to the deficiency of effective clinical treatment. Here, we elucidated that liver-specific loss of Arid2 induced hepatic steatosis and this progression could be exacerbated by HFD. Mechanistic study revealed that ARID2 repressed JAK2-STAT5-PPARγ signaling pathway by promoting the ubiquitination of JAK2, which was mediated by NEDD4L, a novel E3 ligase for JAK2. ChIP assay revealed that ARID2 recruited CARM1 to increase H3R17me2 level at NEDD4L promoter and activated the transcription of NEDD4L. Moreover, inhibition of Jak2 by Fedratinib in liver-specific Arid2 knockout mice alleviated HFD-induced hepatic steatosis. Downregulation of ARID2 and the reverse correlation between ARID2 and JAK2 were also observed in clinical samples. Therefore, our study has revealed an important role of ARID2 in the development of NAFLD and provides a potential therapeutic strategy for NAFLD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for livers of Arid2 WT and LKO mice.

first: Huijun

last: Cao

first: Hao

last: Jiang

first: Dong

last: Xie

first: Jingjing


title: Lymphatic endothelial cell identity is controlled by a GATA2 bound enhancer [RNA-seq]

first: Natasha

last: Harvey


title: H3K36 methyltransferase NSD1 is essential for normal B1 and B2 cell development and germinal center formation

city: Nanjing

first: Xiaoming

last: Wang

state: jiangsu

address: 101 longmian avenue jiangning district

institute: Nanjing Medical University

summary: This study aims to illustrate the effect of H3K36 methyltransferase NSD1 in B2 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT B220+ B cells (Mb1-Cre+ NSD1+/+) and its NSD1 conditional knockout derivatives (Mb1-Cre+ NSD1fl/fl).

first: Zhenming

last: Cai

first: Yuliang


title: Single cell transcriptomic analysis and Epigenomic profiling of human Axioloids

city: Kyoto

first: Cantas

last: Alev

address: Medical Faculty Bldg. B, Yoshida-Konoe-cho, Sakyo-ku

department: Institute for the Advanced Study of Human Biology (ASHBi)

institute: Kyoto University

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

overall_design: Refer to individual Series


title: Epigenomic profiling of human Axioloids with CUT&Tag

summary: We have established a pluripotent stem cell (PSC)-based 3D model of human axial development, which recapitulates in vitro key features of the somitogenesis process including axial elongation, segmentation and sequential formation of epithelial somites with proper rostrocaudal pattering, and traveling wave-like gene expression dynamics associated with the segmentation clock. Initial molecular and functional analysis of these axially-organized embryonic tail-like structures, which we termed Axioloids, revealed the spatiotemporally controlled self-organization of somitogenesis associated human mesodermal cell populations. In order to gain a deeper understanding of this model, we performed CUT&Tag experiments using anti-H3K4me3 and anti-H3K27me3 antibodies to analyze the epigenomic landscapes in the Axioloids.

overall_design: CUT&Tag profiling for active (H3K4me3) and repressive (H3K27me3) epigenomic landscapes in human Axioloids

first: Yoshihiro

last: Yamanaka

first: Kumiko

last: Yoshioka-Kobayashi

first: AI

last: Mieda

first: Yuzuru

last: Kurokawa

first: Takuya

last: Yamamoto

first: Taro

last: Tsujimura


title: Hippo signaling instructs ectopic but not normal organ growth [Liver YapHyper]

first: Georg

last: Halder

summary: We conditionally activated Yap in hepatocytes of adult mice by two different methods: we deleted the Lats1/2 kinases via injecting AAV8-Cre into Lats1/2 double floxed mice (Lats1/2 KO) and we overexpressed YAP via doxycycline feeding of mice that expressed the tetracycline-activated transactivator (rtTA) under the hepatocyte-specific ApoE promoter and human YAP from a rtTA-responsive TetO promoter (Apo>YAP).

overall_design: Differential Gene Expression Analysis of Yap hyperactivation in adult hepatocytes including samples of purified hepatocytes from livers in the following condtions: Apo>Yap (ApoYap Dox) and untreated control (ApoYap ctrl); Lats1/2 KO and untreated control (Lats1/2 flox ctrl); BL/6 controls for the side effects of Doxycyline and AAV-Cre (BL/6 ctrl, BL/6 Dox, BL/6 AAV-Cre.

first: Weronika

last: Kowalczyk

first: Hanne

last: Hillen

first: Leticia

last: Sansores


title: Hippo signaling instructs ectopic but not normal organ growth  [Drosophila NonPupatingLarvae]

summary: We fed wildtype larvae a special diet that lacks precursor molecules necessary for the synthesis of the molting hormone ecdysone required for pupation, thus keeping animals in the larval stage. Importantly, in these larvae, the imaginal discs grow until their terminal size is reached but they do not proceed with differentiation as this requires a pulse of ecdysone. This method thus allowed us to directly compare actively growing discs with discs at the same developmental stage that terminated proliferation after reaching their proper size.

overall_design: Differential gene expression analysis of samples of eye-antennal imaginal discs from larvae raised on pupation-preventing food at two time points: 5 days after egg laying - before pupation would normally begin and eye discs are still actively growing ("actively growing"); 11 days after egg laying - after pupation would normally have begun and eye discs terminated proliferation after reaching their proper size ("growth completed").


title: MicroRNA signature to predict the response of adjuvant chemotherapy in patients with stage II & III colorectal cancer

status: Public on Nov 16 2022

city: Monrovia

first: Ajay

last: Goel

address: 1218 S. Fifth Avenue

department: Molecular Diagnostics and Experimental Therapeutics

institute: Beckman Research Institute of City of Hope

summary: The aim of our study was to identify a microRNA signature to predict the recurrence in stage II & III CRC patients who were treated with FOLFOX-based adjuvant chemotherapy after curative resection of tumors. We performed small RNA sequencing in 71 FFPE surgical specimens, and discovered differentially expressed microRNAs in patients who developed recurrence. Thereafter, selected microRNA biomarkers were validated in independent cohort using qRT-PCR assay.

overall_design: Identify microRNAs differentially expressed in non-responders to adjuvant chemotherapy compared to responders in stage II & III CRC patients

first: Keisuke

last: Okuno


title: Epigenetic regulator Smarcd3 is required for established tumor growth in pancreatic cancer

city: San Diego

first: Diana

middle: C.

last: Hargreaves

address: 10010 North Torrey Pines Road

institute: The Salk Institute for Biological Studies

summary: Pancreatic ductal adenocarcinoma (PDAC) is a disease characterized by aggressive metastasis and resistance to therapy, making clinical management a significant challenge. As cancer progresses, developmental signals are often aberrantly re-activated, driving the self-renewal of cancer cells and malignant features of disease. Given the central role for epigenetic regulation in development, we hypothesized that epigenetic factors may be required to sustain the self-renewal of pancreatic cancer cells. Here, we used a functional screen to identify Smarcd3, a component of the SWI/SNF (BAF) nucleosome remodeling complex, as a novel functional dependency in PDAC. SWI/SNF coordinates context-specific gene regulation in development and is frequently dysregulated in cancer. However, Smarcd3 has not been linked to functions in PDAC and represents a new epigenetic mediator of cancer function. We found that Smarcd3 was uniquely up-regulated in PDAC stem cells and was required for the in vivo propagation of mouse and patient-derived tumors. Furthermore, using integrated RNA-seq, ChIP-seq, and network analysis we showed that Smarcd3 regulates global SWI/SNF binding and histone acetylation, driving the epigenetic regulation of lipid metabolic programs. Specifically, we found that Smarcd3 regulated genes converging on fatty acid metabolism, which has been directly implicated in stem signaling in PDAC. Collectively, these data identify Smarcd3 as a critical novel dependency and epigenetic regulator of lipid metabolism pancreatic cancer.

overall_design: ChIP-seq for Smarca4, Arid1a, H3K4me, H3K4me3 and H3K27ac in KPf/fC cells transduced with shControl or shSmarcd3; RNA-seq in KPf/fC cells transduced with shControl or shSmarcd3.

first: Jovylyn

last: Gatchalian

first: Lesley

middle: P

last: Ferguson

first: Tannishtha

last: Reya


title: Upregulation of MTHFD2 is associated with PD-L1 activation in bladder cancer via the PI3K/AKT pathway

city: Nanchang

first: Bin

last: Fu

state: Jiangxi

address: No.17, Yong Wai Zheng Street, Donghu Districtstrict,

department: department of urology

institute: The First Affiliated Hospital of Nanchang Universi

summary: Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) has been implicated in the etiology of various human malignant tumors, although its exact role in bladder cancer (BC) remains to be explored. The present study determined the upregulation of MTHFD2 in BC tissues using expression data from The Cancer Genome Atlas (TCGA), a commercial BC tissue microarray (TMA) and patients’ tissues collected by surgery. MTHFD2 expression in patients with BC was frequently associated with worse prognosis, tumor immune cell infiltration and programmed death-ligand 1 (PD-L1) expression. Next, using small interfering RNA, the expression of MTHFD2 in BC cell lines was knocked down, and the results revealed that the tumor cell proliferation and colony-formation abilities were greatly reduced, as well as the expression of PD-L1. In a xenograft nude mouse model, these findings were confirmed. Simultaneously, it was found that abnormal expression of MTHFD2 was closely associated with the PI3K/AKT signaling pathway in both RNA-sequencing and TCGA datasets. This observation was verified in vitro by detecting the protein expression of PI3K and AKT. The activation of PI3K and AKT was enhanced after stimulation with 740Y-P, a PI3K activator, and their cellular activities and PD-L1 expression levels were restored. Finally, it was found that the MTHFD2 levels were positively correlated with chemosensitivity to traditional BC chemotherapeutic agents and various PI3K-AKT-targeted drugs by analyzing the Genomics of Drug Sensitivity in Cancer (GDSC) database. Overall, the present findings revealed that elevation of MTHFD2 was associated with PD-L1 activation in BC via the PI3K/AKT signaling pathway, suggesting that it could be a promising marker of chemotherapy and immunotherapy for BC.

overall_design: The MTHFD2 gene was knocked out in bladder cancer cell lines, and the differentially expressed genes and regulated signaling pathways were analyzed by sequencing. Finally, the results were verified by in vitro experiments.

first: Xinxi

last: Deng

first: Xiaoqiang

last: Liu

first: Bing

last: Hu

first: Jianyun


title: ATAC-seq profiling of pancreatic endoderm derived from expanding ventral foregut progenitors

city: Edinburgh

first: Yatendra

last: Kumar

email: yaten2020@gmail.com, ykumar@ed.ac.uk

address: Crewe Road south

department: MRC HGU

institute: MRC Human Genetics Unit, The University Of Edinburgh

summary: This dataset is part of ERC funded HumEn project (http://www.hum-en.eu/). This dataset relates to standardization of genome wide DNase 1 hypersensitivity methods in the differentiation system developed in HumEn project.

overall_design: Methods: HUES4 human ESCs carrying a PDX1::eGFP knock-in transcriptional reporter (1) was maintained in DEF-CS system, with over 95% of SSEA3/4 double-positive cells as analysed by flow cytometry. These cells were differentiated to ADE cells and subsequently expanded in VFG culture, according to the protocol established by Cheng et al., 2012 (2). CXCR4/KIT double-positive endoderm cells from transient ADE population (day 5) and from passage 3 VFG culture (one month) were sorted by Fluorescence Activated Cell Sorting (FACS). 50000 sorted endoderm and hESC cells were subjected to ATAC-seq libraries preparation using Nextera DNA library preparation kit from Illumina (cat no; FC-121-1030) using a slight modification of protocol published by Buenrostro et al. 2015 (3).  1. Ameri J, Borup R, Prawiro C, Ramond C, Schachter KA, Scharfmann R, et al. Efficient Generation of Glucose-Responsive Beta Cells from Isolated GP2(+) Human Pancreatic Progenitors. Cell reports. 2017;19(1):36-49.  2. Cheng X, Ying L, Lu L, Galvao AM, Mills JA, Lin HC, et al. Self-renewing endodermal progenitor lines generated from human pluripotent stem cells. Cell stem cell. 2012;10(4):371-84.  3. Buenrostro, Jason et al. “ATAC-Seq: A Method for Assaying Chromatin Accessibility Genome-Wide.” Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] 109 (2015): 21.29.1–21.29.9. PMC. Web. 28 Dec. 2017.

first: Wendy

last: Bickmore

first: Joshua

last: Brickman

first: Yan

middle: F

last: Wong


title: Xrn2 substrate mapping identifies torpedo loading sites and extensive premature termination of RNA pol II transcription

city: Aurora

first: David

last: Bentley

state: Colorado

department: BMG

institute: UCD AMC

summary: The exonuclease torpedo Xrn2 loads onto nascent RNA 5’-PO4 ends and chases down pol II to promote termination downstream of polyA sites. We report that Xrn2 is recruited to pre-initiation complexes and “travels” to 3’ ends of genes. Mapping of 5’-PO4 ends in nascent RNA identified Xrn2 loading sites stabilized by an active site mutant, Xrn2(D235A). Xrn2 loading sites are ~2-20 bases downstream of where CPSF73 cleaves at polyA sites and histone 3’ ends. We propose that processing of all mRNA 3’ ends comprises cleavage and limited 5’-3’ trimming by CPSF73 followed by hand-off to Xrn2. A similar hand-off occurs at tRNA 3’ ends where co-transcriptional RNAseZ cleavage generates novel Xrn2 substrates. Exonuclease-dead Xrn2 increased transcription in 3’ flanking regions by inhibiting polyA site-dependent termination. Surprisingly, the mutant Xrn2 also rescued transcription in promoter-proximal regions to the same extent as in 3’ flanking regions. eNET-seq revealed Xrn2-mediated degradation of sense and anti-sense nascent RNA within a few bases of the TSS where 5’-PO4 ends may be generated by decapping or endonucleolytic cleavage. These results suggest that a major fraction of pol II complexes terminate prematurely close to the start site under normal conditions by an Xrn2-mediated torpedo mechanism.

overall_design: ChIP-seq of Xrn2 under various conditions in human and Drosophila cells, nascent RNA-seq in human cells expressing WT and exonuclease dead Xrn2

first: Benjamin

last: Erickson


title: Nonstructural protein 1 (nsp1) widespread RNA decay phenotype varies among Coronaviruses

city: Amherst

first: Mandy

last: Muller

address: 639 North Pleasant Street

department: Microbiology

institute: Univ of Massachusetts Amherst

summary: Extensive remodeling of host gene expression by coronaviruses nsp1 proteins is a well-documented and conserved aspect of coronavirus-host takeover. Using comparative transcriptomics we investigate the diversity of transcriptional targets between nsp1 proteins between α- and β- coronaviruses. Additionally, Affinity Purification Mass-Spectrometry was implemented to identify common and divergent interactors between the nsp1 proteins. While we detected widespread RNA destabilization between the different nsp1s, closely related nsp1 showed little similarities in clustering of targeted genes. Partial overlapping transcriptional targeting between α-CoV 229E and MERS nsp1 may suggest a shared similar targeting mechanism, as MERS nsp1 preferentially targets nuclear transcripts. Our interactome data shows great variance between nsp1 interactions, with 229E nsp1, the smallest tested here, interacts with the most host proteins, while MERS nsp1 only engaged with a few. While nsp1 is a rather well-conserved protein with consistent functions across different coronaviruses, its precise effects on host cells is virus-specific.

overall_design: Comparative gene expression profiling analysis of RNA-seq data comparing cells lentivirally transduced with one of four coronavirus nsp1 protein, with conditions being uninduced nsp1 expression vs induced nsp1 expression

first: Yahaira

last: Bermudez

first: Jacob

last: Miles

last: Mulles


title: Reevaluation of Piezo1 as a gut RNA sensor

city: Bethesda

first: Minh

middle: Q

last: Nguyen

state: MARYLAND

address: 9000, Rockville Pike

institute: NIDCR/NIH

summary: Piezo1 is a stretch-gated ion channel required for mechanosensation in many organ systems. Recent provocative findings describe a new role for Piezo1 in the gut, suggesting that it is a sensor of microbial single-stranded RNA (ssRNA) rather than mechanical force. If true, this would redefine the scope of Piezo biology. Here, we sought to replicate the central finding that fecal ssRNA is a natural agonist of Piezo1. While we observed that fecal extracts and ssRNA stimulate calcium influx in certain cell lines, this response was independent of Piezo1. Additionally, sterilized dietary extracts devoid of gut biome RNA showed similar cell line-specific stimulatory activity to fecal extracts. Together, our data highlight potential confounds inherent to gut-derived extracts, exclude Piezo1 as a receptor for ssRNA in the gut, and support a dedicated role for Piezo channels in mechanosensing.

overall_design: Nuclei from RIN14B cells were isolated using FACS and single nucleus RNA-seq were performed with 10x Genomics method.

first: Nickolls

last: Alec

first: Chesler

last: Alexander