title: Chromosome 8p-engineering and CRISPR-Cas9 viability screening reveal increased  metastatic capacity of liver cancer cells targetable by patient-specific synthetic lethality [Cas9]

overall_design: Small interfering RNA-mediated knockdown of NUDT17 alone, NUDT18 alone, combination of NUDT17 and NUDT18 or transfected with Control siRNAs. All four different treatments were performed in triplicates.


title: Human vascular endothelial cells display different gene expression patterns and response to EGF

status: Public on Dec 27 2023

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

country: Germany

institute: Martin Luther University - Halle-Wittenberg

type: Expression profiling by high throughput sequencing

summary: RNA sequencing was performed for human primary aortic (HAoEC) and coronary artery (HCAEC) endothelial cells from female donors, after incubation with or without EGF.

overall_design: HAoEC and HCAEC were incubated for 48h with 10 µg/L EGF (N=8).

first: Michael

last: Gekle

first: Gerald

last: Schwerdt

first: Barbara

last: Schreier

last: Kopf

first: Sigrid

last: Mildenberger


title: Melanoma Differentiation Associated Gene-9/Syndecan Binding Protein (MDA-9/SDCBP) Promotes Hepatocellular Carcinoma (HCC)

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

country: USA

institute: Virginia Commonwealth University

summary: The oncogene Melanoma differentiation associated gene-9/syndecan binding protein (MDA-9/SDCBP) promotes tumorigenesis and metastasis in many cancers. However, the role of MDA-9 in regulating HCC has not been well-studied. To unravel the function of MDA-9 in HCC we generated a transgenic mouse with hepatocyte-specific overexpression of MDA-9 (Alb/MDA-9). Alb/MDA-9 mice demonstrated significantly higher incidence of N-nitrosodiethylamine/phenobarbital-induced HCC compared to WT littermates. To check what genes are regulated by MDA-9 to promote HCC, RNA-seq was performed in naïve WT and Alb/MDA-9 hepatocytes.

overall_design: mRNA from naïve WT and Alb/MDA-9 hepatocytes.

first: Debashri

last: Manna

middle: G

first: Devanand

last: Sarkar


title: Identification of differences in CD4+ T-cell gene expression between people with asthma and healthy controls

city: Manchester

first: Mauro

last: Tutino

address: Oxford road

country: United Kingdom

institute: University of Manchester

summary:
Background: Functional enrichment analysis of genome-wide association study (GWAS)-summary statistics has suggested that immune cell-types, and especially CD4+ T-cells, play an important role in asthma pathogenesis. Despite this, CD4+ T-cells are under-represented in asthma transcriptome studies.
Objective: To identify differences in gene expression between asthmatics and healthy controls in CD4+ T-cells.
Methods: CD4+ T-cells were isolated within 2 hours from collection from peripheral blood from people with well-established asthma (n=33) and healthy controls (n=12). 3'-RNA-Seq was used to generate gene expression data. Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify sets of co-expressed genes (modules). The asthma-associated modules were tested for enrichment of GWAS-identified asthma genes and gene ontology (GO) biological processes. For the genes in the asthma-associated modules, integration of eQTL and GWAS summary statistics (colocalisation), and protein-protein interaction (PPI) data was used to identify master regulators.
Results: After quality control, 43 samples were available for the analysis. WGCNA identified three modules associated with asthma, which are strongly enriched for GWAS-identified asthma genes, antigen processing/presentation and immune response to viral infections. Colocalisation analysis of eQTL and GWAS summary statistics, together with PPI data, identified PTPRC as a master regulator of asthma gene-expression profiles in CD4+ T-cells.
Conclusion: Unstimulated CD4+ T-cells from peripheral blood from asthmatics have different expression profiles, compared to healthy controls, for sets of genes involved in immune response to viral infections and antigen processing/presentation . Integration of genetic and protein-protein interaction data identified PTPRC as a master regulator of genes in asthma.

overall_design: 3'UTR RNA-seq from CD4+ T cell from asthmatics and healthy controls

first: Jenny

last: Hankinson

first: Clare

last: Murray

first: Lesley

last: Lowe

first: Gina

last: Kerry

first: Magnus

last: Rattray

first: Adnan

last: Custovic

first: Sebastian

middle: L

last: Johnston

first: Chenfu

last: Shi

first: Gisela

last: Orozco

first: Stephen

last: Eyre

first: Paul

last: Martin

first: John

last: Curtin

first: Angela

last: Simpson


title: Whole genome mRNA  expression profiling during Candida albicans growth in complete human serum and butanol

city: New Delhi

first: Agam

middle: Prasad

last: Singh

state: Delhi

address: Aruna Asaf Ali Marg

department: IDL

country: India

institute: NII

summary: In order to get an insight into the complex interplay of mRNAs during the growth in complete human serum supplemented with butanol, the total RNA population of Candida albiacns NCCPF 400034 extracted at 20, 45, and 120 minutes was sequenced by Next Generation sequencing techniques. The control RNA was extracted from Candida cells placed in YPD medium for 18 hrs at 37 ° C and was also sequenced using the next generation sequenicng technique.

overall_design: Total RNA extraction from samples grown in YPD as control (02 samples) or complete human serum + butanol (06 samples: 02replicates each time point ) and library preparared using Illumina kits. Sequenicng was performed using next generation sequencing platform.

first: Rajesh

last: Anand

first: Mohammad

last: Kashif

first: Awadhesh

last: Pandit

middle: P


title: Whole genome mRNA  expression profiling during Candida albicans growth in complete human serum

summary: In order to get an insight into the complex interplay of mRNAs during the growth in complete human serum, the mRNA polulation of Candida albiacns NCCPF 400034 taken at 0, 20, 45, and 120 minutes was extracted and sequenced by Next Generation sequencing techniques.

overall_design: Total RNA extraction from samples grown in YPD as control (02 samples) or complete human serum (06 samples: 02 replicates each time point ) and library preparared using Illumina kits. Sequenicng was performed using next generation sequencing platform.


title: Genetic selection shaped the gene expression patterns of mRNA and protein in rice subspecies

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

country: China

institute: Peiking University

summary: Eukaryotes gene expression of mRNA and protein is a basic cellular activity and regulated by multiple process, yet the expression patterns at these two levels and their genetic and evolutionary determinants remain undefined in plants. Here, using RNA-sequencing and TMT labeled LC-MS/MS analysis, we investigated the genome-wide variation of mRNA and protein expression in rice subspecies japonica C92, indica MH63 and their F1 hybrid. Different expression patterns of mRNA and protein between C92 and MH63 were linked to distinct functional categories. Genes with consistent divergence of mRNA and protein expression between subspecies tend to be regulated by cis effect and had higher sequence variation in nonsynonymous sites. Population differentiation (FST) analysis showed that genes with conserved expression of either mRNA or protein in C92 and MH63 were more likely to be under purify selection, while genes with consistent divergence in mRNA or protein expression were more likely to be under positive selection, especially in their nonsynonymous site have high frequency of positive selected genes that changed their protein sequence by nonsynonymous mutation. Furthermore, oxidative stress response genes were enriched in genes with consistent divergence of expression, and showed higher sequence variation in nonsynonymous sites and are more likely to be positive selected in evolution. These results suggested that cis-regulation with high nonsynonymous-variation was evolutionarily important feature to shape divergent expression patterns of mRNA and protein and may contribute to diversity in oxidative stress response between rice subspecies.

sample_organism: Oryza sativa Indica Group x Oryza sativa Japonica Group

overall_design: Total RNA was isolated from the 14-day-old rice seedlings for three biological replicates RNA sequencing.

first: Mei

last: Yang

first: Guangming

last: He

first: Xing

middle: W

last: Deng


title: A unique epigenomic landscape defines CD8+ tissue-resident memory T cells [Perturb-seq]

status: Public on Dec 26 2023

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: scATAC-seq datasets of CD8+ T cells in LCMV and HSV infections

overall_design: 10 libraries (5 populations x 2 cohort replicates) were created for Perturb-seq, pairing gene expression and sgRNA counts per cell in a massively-parallel assay.

first: Frank

middle: A

last: Buquicchio

first: Raissa

last: Fonseca

first: Ansuman

middle: T

last: Satpathy

first: Laura

middle: K

last: Mackay


title: Bulk RNA-seq of in vivo expanded and franformed human IgM-producing tumor cells

city: Seattle

first: Rene

last: Cheng

state: WA

address: 1900 9th AVE

institute: Seattle children research institute

summary: We are trying to quantify differences between the transformed in vivo-expanded cells and non-transformed ex vivo plasma cells isolated from paired donors. we observed strong enrichment for several pathways in EBV+IgM+ B cells including nuclear factor kappa B (NF𝛋B) activation and Myc targets. And, Genes associated with BCR-regulated pathways were upregulated in EBV+IgM+ B cells.

overall_design: Enriched hCD45+ in vivo expanded tranformed human B cells derived from NSG mice receiving human differentitated B cells

middle: Y

first: Richard

last: James

first: Tingting

last: Zhang


title: N6-methyladenosine modification of lnc-CCKAR-5 regulates autophagy in human umbilical cord mesenchymal stem cells by destabilizing LMNA and inhibits diabetic wound healing

city: xuzhou

first: qiang

last: li

address: No. 99 Huaihai West Road, Xuzhou City

institute: Xuzhou Medical University

summary: Long noncoding RNAs(lncRNAs) are pivotal contributors to the development of human diseases. However, their significance in the context of diabetic wound healing regulated by human umbilical cord mesenchymal stem cells(hUCMSCs) remains unclear. This study sheds light on the involvement of lncCCKAR5 in this process. We found that hUCMSCs exposed to high glucose conditions exhibited a significant downregulation of lncCCKAR5 expression, and lncCCKAR5 played a critical role in modulating autophagy, thus inhibiting apoptosis in hUCMSCs. Additionally, the reduction of LncCCKAR5 in cells exposed to high glucose effectively thwarted cellular senescence and facilitated filopodium formation. Mechanistically, LncCCKAR5 served as a scaffold that facilitated the interaction between MKRN2 and LMNA, a key regulator of cytoskeletal function and autophagy. The LncCCKAR5/LMNA/MKRN2 complex played a pivotal role in promoting the ubiquitin-mediated degradation of LMNA, with this effect being further augmented by N6-adenosine methylation of LncCCKAR5. Consequently, our findings underscore the critical role of LncCCKAR5 in regulating the autophagic process in hUCMSCs, particularly through protein ubiquitination and degradation. This intricate regulatory network presents a promising avenue for potential therapeutic interventions in the context of diabetic wound healing involving hUCMSCs.

overall_design: RNA-seq libraries were constructed by NewCore Biotech (Shanghai, China). Firstly, RNA was isolated with TRIZOL reagent (Invitrogen, Grand Island, NY), total RNA was purified by the Qiagen RNeasy mini kit (Qiagen, Valencia, CA). Purified RNA was analyzed on an ND-8000 spectropho tometer (Nanodrop Technologies, Wilmington, DE). High quality total RNA was used as the starting material. Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer’s instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies,Inc., USA). Library sequencing was performed on an Illumina NovaSeq 6000 instrument with 151 bp paired end reads.

first: Jian

first: Wang

last: Xiaotian

first: Feifei

last: Chen

first: Ning

last: Qianqian


title: RNA-seq of Snu-449 cells treated with Ezetimibe or control

status: Public on Dec 25 2023

city: Guangzhou

first: yuting

last: Yin

state: China

address: Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, China 510060.

institute: Sun Yat-sen University Cancer Center (SYSUCC)

summary: purpose:different gene enrichment

overall_design: Snu-449 cells were treated with Ezetimibe for 24h

first: Yuting

last: YIN


title: RNA-sequencing signatures of liver endothelial cells from iron-adequate and iron-loaded mice

city: Boston

first: Allison

last: Fisher

state: MA

address: 50 Blossom Street, Thier Research Building, 1117A

institute: Massachusetts General Hospital, Harvard Medical School

summary: Iron induces hepcidin by activating bone morphogenetic protein (BMP)6-SMAD signaling, which is critical for regulation of systemic iron homeostasis. High iron levels induce BMP6 production in liver endothelial cells, but the molecular mechanisms by which iron regulates BMP6 are incompletely understood. To address this, we performed RNA-sequencing on sorted liver endothelial cells from iron-adequate and iron-loaded mice.

overall_design: Liver endothelial cells were isolated by fluorescence-activated cell sorting from 7-week-old wild-type 129S6/SvEvTac male mice fed purified iron-adequate diet (37 ppm iron as ferric citrate) or iron-loaded diet (10,000 ppm carbonyl iron) for 4 weeks. Total RNA from liver endothelial cells was isolated and subjected to RNA-Seq. For each group we have 3 biological replicates for a total of 6 samples.

first: Chia

last: Wang

first: Yang

last: Xu

first: Sydney

last: Phillips

first: Joao

last: Paulo

first: Beata

last: Małachowska

first: Xia

last: Xiao

first: Wojciech

last: Fendler

first: Joseph

middle: D

last: Mancias

first: Jodie

last: Babitt


title: Rpb9 plays a critical role in global co-transcriptional splicing (Time-course GRO-seq)

city: San Diego

first: Yajing

last: Hao

state: CA

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

summary:
To investigate the question that whether Rpb9 affects elongation velocity, thereby indirectly affecting splicing the regulation, we performed time-course GRO-seq after DRB release.
In this assay, DRB was first used to block transcription elongation, which caused Pol II to accumulate at TSSs.  Upon DRB wash-off, we performed GRO-seq at 0, 10, 20, and 30min to determine the movement of Pol II wave toward gene 3’ end.Based on the hidden Markov model established earlier, we detected a marked reduction of Pol II re-initiation upon DRB removal in response to Rpb9 knockdown (KD) in HeLa cells. This is consistent with the role of Rpb9 in transcription initiation.  By determining the mean elongation rate between 10 and 20min and between 20 and 30m, we found accelerated Pol II elongation, as reported earlier, and interestingly, Rpb9 knockdown appeared to have slightly decreased, rather increased, the rate of transcription.
We divided all impacted splicing events 4 equal bins and then asked if a higher degree of induced exon skipping tends to occur on genes with faster Pol II movement, finding that this is not the case. Conversely, we divided Rpb9 KD-altered Pol II rate into 4 equal binds and asked whether splicing shows any correlation to Pol II Rpb9 KD-altered Pol II elongation rate, and again, we detected no correlation. We conclude from these data that Rpb9 KD has some minor impact on the Pol II elongation rate in vivo, and importantly, whatever measurable changes in Rpb9 KD-induced Pol II elongation rate are not linked to changes in Rpb9 KD-induced co-transcriptional splicing.

overall_design: Compare the transcriptional wave in negative control and RPB9 knockdown samples. Then check whether the changes of transcriptional wave could affect the co-transcriptional splicing.

first: Changwei

last: Shao

first: Xiang-Dong

last: Fu


title: Identification of N6-Methyladenosine associated genes in osteoarthritis

city: zhengzhou

last: Yu

address: jianshe road

department: Department of orthopedics

institute: the First Affiliated Hospital of Zhengzhou University

type: Methylation profiling by high throughput sequencing

summary: Our study aimed to identify common m6A features in OA. We identified 8511 genes with 25295 peaks in the OA sample and 7541 genes with 17474 peaks in the control sample, indicating an overall hypermethylated level in the OA cartilage.

overall_design: We collected three OA knee cartilage tissues and three normal knee cartilage tissues to obtain the transcriptome-wide m6A modification profile of genes in OA by methylated RNA immunoprecipitation next-generation sequencing (MeRIP-seq).

first: Shitao

last: Lu

first: Yu

last: Li

first: Jianzhong


title: Loss of Su(var)3-9 and SetDB1 disrupts late stages of larval development of Drosophila

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

summary: Methylation of H3K9 histone residue is a marker of gene silencing in eukaryotes. Three enzymes responsible for adding this modification – G9a, SetDB1/Egg, and Su(var)3-9 – are known in Drosophila. To understand how simultaneous mutations of SetDB1 and Su(var)3-9, or all three proteins may affect the fly development, appropriate combinations were obtained. Double mutants egg; Su(var)3-9 displayed pronounced embryonic lethality, slower larval growth and died before or during metamorphosis. Analysis of transcription in larval salivary glands and wing imaginal disks indicated that the effect of double mutation is tissue-specific. In salivary gland chromosomes, affected genes display low H3K9me2 enrichment and are rarely bound by SetDB1 or Su(var)3-9. We suppose that each of these enzymes directly or indirectly controls its own set of gene targets in different organs, and double mutation results in an imbalanced developmental program. This also indicates that SetDB1 and Su(var)3-9 may affect transcription via H3K9-independent mechanisms. Unexpectedly, in double and triple mutants, amount of di-and tri-methylated H3K9 is drastically reduced, but not completely absent. We hypothesize that this residual methylation implies the existence of additional H3K9-specific methyltransferase in Drosophila.

overall_design: Examination of differential expression of genes in salivary glands or wing imaginal discs of oregon flies versus SetDB1 and Su(var)3-9 double mutants

first: Stanislav

middle: E

last: Romanov

first: Viktor

middle: V

last: Shloma

first: Dmitry

last: Koryakov


title: Effect of PD-1 knockout on Mtb infection

city: Wuhan

first: Bing

last: Yang

state: Hubei

address: No.1 Shizishan Street, Hongshan District

department: College of Vetirinary Medicine

institute: Huazhong Agricultural University

summary: To investigate the effect pf PD-1 knockout during Mtb infection, wild type mice and PD-1 knockout mice were infected with Mtb and BMDC were isolated for the transcriptome analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BMDC of wild type and PD-1 knockout mice infected/uninfected with Mtb.

first: Xiaojian

last: Cao


title: RNA-sequencing of estradiol inducible DOF6 overexpression (DOF6ioex) and rgl2-13 DOF6ioex  seeds imbibed in mock or 50µM estradiol for 8h

city: Singapore

first: Prakash

last: Kumar

state: Singapore

address: 14 Science Drive 4

department: DBS

country: Singapore

institute: NUS

summary: The DELLA protein RGA-LIKE2 (RGL2) is a key transcriptional repressor of gibberellic acid (GA) signaling that regulates seed germination.RGL2 lacks a DNA binding domain and requires a transcription  factor to induce GATA12 expression. Our data show that this RGL2-containing protein complex includes DNA BINDING1 ZINC FINGER6 (DOF6), which is a known negative regulator of germination in freshly harvested seeds. The RGL2-DOF6 complex regulates primary seed dormancy in Arabidopsis by regulating downstreming targets.

overall_design: Differential gene expression in freshly harvested DOF6ioex and rgl2-13 DOF6ioex  seeds imbibed in mock or 50µM estradiol at room temperature for 8h

first: Pratibha

last: Ravindran

first: Pannaga

last: Krishnamurthy

first: Chong

middle: S

last: Ney


title: Small RNAs in anti-tuberculosis drug-induced liver injury

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

type: Non-coding RNA profiling by high throughput sequencing

summary: The antimicrobials isoniazid and pyrazinamide, used for the treatment of tuberculosis are known to cause drug-induced liver injury in humans. This limits the effectiveness of tuberculosis treatment, resulting in incomplete cure, relapse and the development of antimicrobial resistance. MicroRNAs are known to be good biomarkers of disease, with the microRNA miR-122 being diagnostic for liver injury. In this study zebrafish larvae were exposed to the anti-tuberculosis drugs isoniazid and pyrazinamide at concentrations which demonstrated liver injury by microscopy and histology. The aim of this study is to understand small RNA changes occurring in anti-tuberculosis drug-induced liver injury and to attempt to identify novel microRNA biomarkers of liver injury.

overall_design: Zebrafish larvae were exposed to 6 mM pyrazinamide or 10 mM isoniazid for 24 hours from 4 to 5 days post fertilisation. Control zebrafish larvae were maintained in system water. After drug exposure, larvae were anaesthetised and RNA collected for small RNA sequencing. A total of 24 samples were analysed, 8 in each treatment group. A total of 30 zebrafish larvae were pooled for each sample.

first: James

last: Dear

first: Sarah

last: Stedman

middle: C


title: Introducing cellular senescence in human induced pluripotent stem cells and differentiated neural lineage for modeling of age-associated diseases

city: Worcester

first: Hong

last: Zhang

address: 55 Lake Avenue North

department: Pediatrics

institute: University of Massachusetts Chan Medical School

summary: Reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) resets the epigenetic landscapes that mark the aging clock, and consequently cells differentiated from iPSCs resemble fetal cells rather than adult or aged cells. The lack of proper cellular aging in cells differentiated from iPSCs presents a significant problem in iPSC-based disease models to investigate the pathological progression of age-associated diseases such as neurodegeneration. To address this caveat, we introduced cellular senescence into iPSC-based cell models in this study, as senescence has been shown to play a critical role not only in aging but also in neurodegeneration. We created an inducible CRISPR interference (CRISPRi) targeting TERF2, a major component of the telomere protecting Shelterin complex. We demonstrated that suppression of TERF2 robustly activated DNA damage response, the p53/p21 signaling, cellular senescence and inflammatory response in iPSCs. The inducible approach allows the temporal control of senescence activation over the course of differentiation of iPSCs to desired cell types. We applied the CRISPRi-TERF2 system to differentiation of iPSCs into neural progenitor cells (NPCs) and showed that suppression of TERF2 efficiently activated DNA damage response, the p53/p21 signaling and senescence in differentiated NPCs. The inducible cell model of cellular senescence generated in this study has broad application in investigation of cellular senescence in the progression of age-related diseases and improvement of disease modeling with a proper cellular aging context to facilitate drug discovery.

overall_design: To investigate the consequence of TERF2 suppression in activation of senescence, we established human iPSC lines with an inducible CRISPRi targeting TERF2. Two iPSC lines and two gRNAs were used. Cells were treated with or without doxycycline (DOX) for 4 or 6 days. We performed gene expression profiling analysis of RNA-seq data obtained from untreated and Dox-treated iPSCs at two different treatment points with 16 samples in total.

first: Kashfia

last: Neherin

first: Kristopher

last: Holloway

first: Yingduo

last: Song

first: Kazuhito

last: Sato

first: Andrew

last: Houston

first: Feng

last: Chen

first: Li

last: Ding


title: Transcriptome and metabolome profiling reveals key pathways and metabolites involved in defense response of upland cotton against Verticillium dahliae

first: yuzhi

last: zhang

state: henan

address: No. 218, Ping'an Avenue, Zhengdong New District, Jinshui District, Zhengzhou City, Henan Province

department: agronomy

institute: Henan Agricultural University

summary: Cotton is the main source of natural fiber in the textile industry, making it one of the most economically important fiber crops in the world. Verticillium wilt, caused by the pathogenic fungus Verticillium dahlia, is one of the most damaging biotic factors limiting cotton production. Mechanistic details of cotton defense responses to verticillium wilt remain unclear. In this study, GFP-labeled strain of V. dahlia was used to track colonization in cotton roots, and clear conidial germination could be observed at 48 hours post-inoculation (hpi), marking this as a crucial time point during infection. Transcriptome analysis identified 1,523 and 8,270 differentially expressed genes (DEGs) at 24 hpi and 48 hpi, respectively. Metabolomic screening found 78 differentially accumulated metabolites (DAMs) at 48 hpi. Conjoint analysis indicated that the phenylpropanoid biosynthesis pathway was activated in cotton infected with V. dahliae. The five metabolites in the phenylpropanoid biosynthesis pathway, including caffeic acid, coniferyl alcohol, coniferin, scopoletin and scopolin, could significantly inhibit V. dahlia growth in vitro, implicating their roles in cotton resistance to Verticillium wilt. The findings expand our understanding of molecular mechanisms underlying the pathogen defense response against V. dahlia infection in upland cotton, which may lead to future insights into controlling Verticillium wilt disease.

overall_design: Treatment with V592-GFP for 24 and 48 hours

first: Yu-Zhi

first: Zong-Bin

last: Ma

first: Wen-Hao

last: Li

first: Wei

last: Liu


title: Human Fungiform Papilla Transcriptome and Proteome Reveal Sex Differences in Long Intergenic Noncoding RNA, Immune Response and Metabolism Genes [RNA-Seq]

city: Baltimore

first: Josephine

middle: M.

last: Egan

state: MD

address: BRC Suite 100, 251 Bayview Boulevard

department: Laboratory of Clinical Investigation

institute: National Institute on Aging - NIH

summary: Fungiform papillae (FP) are visible protrusions on the anterior tongue surface that contain taste buds, their nerves, and capillaries, epithelial cells, stromal cells, and immune-surveilling cells. As FP are easily biopsied in a minimally invasive procedure and have been shown to regrow, we compared three different mechanical methods of FP protein extraction and found that mechanical disruption of FP under liquid nitrogen or bead beating were more efficient than mincing in terms of yield and proteomic profile. A successful protocol to extract RNA from individual FP using bead beating was employed for transcriptomic analysis by RNA sequencing and microarray. Relative to female FP, male FP proteomes and transcriptomes showed predominant expression of Y chromosome-encoded Y antigens, such as EIF1AY, DDX3Y, SMCY, NLGN4Y, UTY, and PCDH11Y, validating our findings. We further found significantly higher levels of Human Leucocyte Antigen (HLA)-associated transcripts and HLA-A protein levels in males than in females. Several long intergenic non-coding (LINC) RNAs exhibit sex-specific expression, in particular LIN02888 with unknown function is more highly expressed in female relative to male FP.  Transcripts in the interferon response pathway a key element of the innate immune system’s defense against pathogens exhibits differential regulation between the sexes. This indicates that FP biopsy is a minimally invasive method to obtain human tissue in order to study, for example, age-related and sex specific changes of interest, while allowing for dynamic investigation of interindividual differences over time in the context of both health and disease

overall_design: Comparative gene expression profiling analysis of RNA-seq data  from human fungiform papillae obtained from young males (n=4) and females (n=4)

first: Gayan

last: Premaratne

first: Hasitha

middle: U

last: Premathilake

first: Ceereena

last: Ubaida-Mohien

first: Alexey

last: Lyashkov

first: Elin

last: Lehrmann

first: Qing-Rong

first: Yongqing

first: Ashley

last: Appleton

first: Chee

last: Chia

middle: M

first: Máire

last: Doyle


title: Saracatinib Promotes Definitive Endoderm Differentiation by Inhibition of FAK-YAP Signaling Axis

status: Public on Dec 24 2023

city: Xi’an

first: Xiaoming

address: 277 Yanta west Rd.

institute: The First Affiliated Hospital of c Jiaotong University

summary: Optimizing the efficiency of definitive endoderm differentiation is significant for the generation of diverse organ-like structures. In this study, we utilized saracatinib to enhance definitive endoderm differentiation in pluripotent stem cells. We found saracatinib significantly improved the definitive endoderm differentiation at low concentrations. To investigate the impact of 0.5 μM saracatinib on definitive endoderm differentiation of ESC H1 cells, we conducted RNA-seq analysis with differentiated cells with or without 0.5 μM saracatinib treatment.

overall_design:
To investigate the role of saracatinib in definitive endoderm (DE) differentiation, we treated differentiating embryonic stem cells. Initially, the cells were cultured for three days to induce DE differentiation. Embryonic stem cells were seeded at a density of 1×10^6 cells per well on Matrigel-coated 6-well plates. The differentiation medium used was DMEM supplemented with B27, Glutamax, 50 ng/mL Activin A, and 2.5 μM CHIR99021 for 24 hours. Subsequently, CHIR99021 was removed from the medium for the following two days.
The experimental group comprised the treatment group, where 0.5 μM saracatinib was added to the cells throughout the differentiation period (3 days). As a control group, an equal volume of DMSO was added to the cells to serve as a volume control.


title: Small RNAs report early heart injury after cardiac surgery

first: Alasdair

last: Ivens

summary: Study aims to identify circulating small RNAs that report early heart injury after cardiac surgery with a view to translating them to the early diagnosis of myocardial infarction

overall_design: Serum samples were taken from 15 human subjects: once before and once after cardiac surgery, yielding a total of 30 samples.

first: James

last: Dear

first: Kathleen

last: Scullion


title: Chromatin interactions of the EVI1 oncogene in myeloid leukaemia (ChIP-Seq)

city: London

first: Niklas

last: Feldhahn

address: The Commonwealth Building, Hammersmith Hospital, Du Cane Road

department: Department of Medicine

institute: Imperial College London

type: Genome binding/occupancy profiling by high throughput sequencing

summary: EVI1 expression is associated with poor prognosis in myeloid leukaemia. Aberrant expression can result from Chr.3q alterations, which cause juxtaposition of enhancers that induce EVI1 activation via long-range chromatin interactions. More often, however, EVI1 expression occurs unrelated to 3q alterations, and it is unclear if its expression underlies similar dependencies as 3q+ cells. As enhancers regulate promoters by physical interaction/chromatin looping, we explored if the EVI1 promoter in EVI1+3q- cells interacts with distally located chromatin and if these intereactions promote EVI1 expression. To monitor if these interactions involve active chromatin, we further performed H3K27ac-ChIP-Seq.

overall_design: For this sample set, we performed ChIP-Seq using H3K27ac antibodies (abcam ab4729) as previously described (Boulianne et al, doi:10.1016/j.celrep.2017.01.057) using formaldehyde crosslinked DNA from CML patients' leukaemia cells.

first: Philippa

last: May

first: Mark

last: Robinson


title: Chromatin interactions of the EVI1 oncogene in myeloid leukaemia (ATAC-Seq)

summary: EVI1 expression is associated with poor prognosis in myeloid leukaemia. Aberrant expression can result from Chr.3q alterations, which cause juxtaposition of enhancers that induce EVI1 activation via long-range chromatin interactions. More often, however, EVI1 expression occurs unrelated to 3q alterations, and it is unclear if its expression underlies similar dependencies as 3q+ cells. As enhancers regulate promoters by physical interaction/chromatin looping, we explored if the EVI1 promoter in EVI1+3q- cells interacts with distally located chromatin and if these intereactions promote EVI1 expression. To monitor TF binding sites at interactions involving active chromatin, we performed ATAC-Seq.

overall_design: ATAC-Seq was performed on CML/AML cell lines according to the Omni-ATAC-seq protocol (https://doi.org/10.1038/protex.2017.096).


title: Detect R-loop signal by DRIP-seq in PA1 cell line

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: DRIP-seq of PA1 cells

overall_design: DRIP-seq of PA1 cells

first: Xiang

last: Li

first: Yun-Ni

last: Lei

first: Fang

first: Ling-Ling

last: Chen


title: Ablation of macrophage transcriptional factor FoxO1 protects against ischemia-reperfusion injury-induced acute kidney injury

city: Beijing

first: Yao

last: He

address: 38 Xueyuan Road, Haidian District

department: Pharmacology

institute: Peking University

summary: Acute kidney injury (AKI) has high morbidity and mortality, but effective clinical drugs and management are lacking. Previous studies have suggested that macrophages play a crucial role in the inflammatory response to AKI and may serve as potential therapeutic targets. Emerging evidence has highlighted the importance of forkhead box protein O1 (FoxO1) in mediating macrophage activation and polarization in various diseases, but the specific mechanisms by which FoxO1 regulates macrophages during AKI remain unclear. The present study aimed to investigate the role of FoxO1 in macrophages in the pathogenesis of AKI.By generating myeloid-specific FoxO1-knockout mice, we observed that the deficiency of FoxO1 in myeloid cells protected against ischemia-reperfusion (I/R)-induced AKI. Furthermore, our study provided evidence of FoxO1's pivotal role in macrophage chemotaxis, inflammation, and migration.

overall_design: To investigate the funtion of FoxO1 in the regulation of macrophage during ischemia-reperfusion injury-induced acute kidney injury, we established ischemia-reperfusion injury model in mice with myeloid-specific FoxO1-knockout.

first: Xue

first: Qian

last: Liu

first: Lu

last: Tie


first: Zhenxing

last: Liang

state: Guangdong

address: 26 Yuancun Erheng Rd

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

summary: We performed Next Generation Sequencing of normal human intestinal epithelial cell lines, CRC cell lines and CRC cell lines with hypoxia treatment to identify the differentially expressed non-coding RNAs.

overall_design: Next Generation Sequencing to find the change of non-coding RNAs

first: Ping

last: Lan


title: Chromatin interactions of the EVI1 oncogene in myeloid leukaemia (4C-Seq)

summary: EVI1 expression is associated with poor prognosis in myeloid leukaemia. Aberrant expression can result from Chr.3q alterations, which cause juxtaposition of enhancers that induce EVI1 activation via long-range chromatin interactions. More often, however, EVI1 expression occurs unrelated to 3q alterations, and it is unclear if its expression underlies similar dependencies as 3q+ cells. As enhancers regulate promoters by physical interaction/chromatin looping, we explored if the EVI1 promoter in EVI1+3q- cells interacts with distally located chromatin and if these intereactions promote EVI1 expression.

overall_design: For this sample set, we performed 4C-Seq using EVI1 promoter specific baits on leukaemic cells from CML patients and AML/CML cell lines. 4C-Seq was performed as previously described by Stadhouders, R. et al. (doi:10.1038/nprot.2013.018).


title: Identification of long-range chromatin interactions on K562 cells using PCHiC

summary: Gene-regulatory elements, such as enhancers, regulate the expression of genes by physical interaction with their promoters and as such play a major role in development and disease. As enhancers not necessarily regulate the most proximal gene and are further often located in large distances to the gene they regulate, it is important to define their interaction partners to inform on their regulatory potential. To do so, we used a 3C based method called PCHIC on the myeloid leukaemia (CML) cell line K562, which is one of the most studied cell lines with much publicly available data that our data can be compared to. The knowledge obtained can be used with regards to transcriptional regulation in CML cells as well as for comparison to other leukaemias.

overall_design: K562 cells were first treated with either DMSO or ponatinib. Subsequently, the cells were fixed and processed with the promoter capture HiC protocol as described in Schoenfelder et al (doi:10.3791/57320).

first: Han

last: Ng


title: Role of the Tudor-knot domain of the TIP60 lysine acetyltransferase [ChIP-seq]

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: The histone lysine acetyltransferase TIP60 is the main enzyme that catalyzes histone H4 acetylation in cells. Domains on TIP60 regulate its enzymatic activity from different aspects. Here we use a CRISPR-Cas9 tiling screen to scan for essential domains on TIP60 protein and found that the Tudor-knot domain is essential for cell survival and intercellular H4 acetylation. We performed in-vitro biochemical assays and demonstrated Tudor-knot domain is not a histone reader. And deficiency of the Tudor-knot domain has mild effects on TIP60 intracellular localization, as well as the TIP60 complex’s constitution. But Tudor-knot deficiency significantly reduces TIP60 HAT activity both in vivo and in vitro. By comparing the catalytic efficiency of nucleosome substrate and histone octamer substrate, as well as TIP60 protein alone or TIP60 complex, we found the nucleosomal structure and other TIP60 complex components are required for Tudor-knot relative HAT activity regulation. We propose that the Tudor-knot domain function to increase nucleosome accessibility. Finally, we show that the Tudor-knot domain is required for TIP60-dependent transcription regulation. Altogether, our study reveals a mechanism that the Tudor-knot domain that regulates TIP60-dependent transcription through the regulation of TIP60 substrate catalytic efficiency.

overall_design: We performed ChIP-seq experiments of histone H4ac and HA-KAT5 in H1299 cell lines that overexpress HA-KAT5-FL, HA-KAT5-Y47A, and HA-KAT5-dN. Histone H4 pan-acetyl (Active Motif, catalog 39925, lot 12517004), and  HA tag (clone C29F4) (Cell Signaling Technology, catalog 3724S, lot 8) were used.

first: Fan

last: Xuan

first: Hongwen


title: Role of the Tudor-knot domain of the TIP60 lysine acetyltransferase [RNA-seq]

overall_design: RNA profiles of TIP60 KO and rescue with Tip60-FL, Y47A, and dN in H1299 cells.


title: Tudor-knot domain mutation in KAT8/MOF impede nucleosome interaction and histone acetylation [RNA-Seq]

summary: KAT8 is a lysine acetyltransferase and is involved in multiple important biological processes including cancer. The well-known function of KAT8 is catalyzing acetylation on histone H4, which regulates gene expression and chromatin decompaction. Besides catalytic HAT domain, the function of Tudor-knot domain of KAT8 remains largely unclear. Here, we report a novel function of Tudor-knot domain in facilitates histone acetyltransferase activity on H4K16ac. One hot-spot cancer mutation on Tudor-knot domain of KAT8 inhibits its interaction with nucleosome and reduces H4K16ac level both in vitro and in cells without altering the chromatin occupancy. Interestingly, this Tudor-knot mutation does not influence acetylation activity of KAT8 on p53, a non-histone substrate, suggests the important function of KAT8 Tudor-knot domain in the substrate specific catalytic regulation.

overall_design: RNA profiles of KAT8 WT and R98W OE in A549 cells.


title: Tudor-knot domain mutation in KAT8/MOF impede nucleosome interaction and histone acetylation

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

overall_design: Refer to individual Series


title: Tudor-knot domain mutation in KAT8/MOF impede nucleosome interaction and histone acetylation [ChIP-Seq]


title: Effect of knockout of GUN1 or NAC103 on gene expression in roots of the WT or rab8d-2

city: Jinan

first: Pengcheng

address: 202 Gongye North Road

institute: Shandong Academy of Agricultural Sciences

summary: We analyzed the root transcriptome profiles in WT, gun1-101, nac103-11, rab8d-2, gun1-101 rab8d-2, and nac103-11 rab8d-2. Our analysis showed that, compared to WT, approximately 108 genes were misregulated in gun1-101, while 78 genes were affected in nac103-11. Only two genes were influenced by both gun1-101 and nac103-11. In contrast, in the rab8d-2 background, blocking the function of GUN1 (gun1-101 rab8d-2) or NAC103 (nac103-11 rab8d-2) significantly altered the expression levels of approximately 948 and 267 genes, respectively. Importantly, over 72% (about 193) of the misregulated genes in nac103-11 rab8d-2 overlapped with those in gun1-101 rab8d-2, indicating a convergence of the GUN1- and NAC103-dependent signaling pathways in rab8d-2.

overall_design: To evaluate the roles of GUN1 and NAC103 on root development in rab8d-2, a mutant with functional deficiency of plastid EF-Tu, we extracted total RNA from roots of WT, rab8d-2, gun1-101, nac103-11, gun1-101 rab8d-2, and nac103-11 rab8d-2 at the 3-day-old seedling stage.

first: Xingjun

last: Wang


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of U251 cells transfected with negative control plasmids and U251 cells transfectet with STING overexpression plasmids

city: guangzhou

first: xinrou

last: lin

address: yanjiang Road

institute: Sun Yat-sen Memorial Hospital

summary: To investigate the effect of overexpression of STING in U251 cells, we then performed gene expression profiling analysis using data obtained from RNA-seq of two groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U251 cells transfected with negative control plasmids or STING overexpression plasmids .

first: Xinrou

last: Lin

first: Ying

last: Peng


title: Ago2-CLASH reveals a wide repertoire of small RNA mediated regulation

city: Brno

first: Vaclav

last: Hejret

address: Kamenice 5

country: Czech Republic

institute: Masaryk University


title: Ago2-CLASH reveals a wide repertoire of small RNA mediated regulation [CLASH-seq]

summary: Here we present the CLASH analysis of AGO2 in HEK293 cells to address the small RNA repertoire and uncover their physiological targets. We developed an optimized bioinformatics approach of chimeric read identification to detect chimeras of high confidence.  We report thousands of Ago2 target sites driven by microRNAs, but also a substantial number of Ago2 ‘drivers’ derived from fragments of other small RNAs such as tRNAs, snoRNAs, rRNAs and others. Target validation of several miRNAs delivered by 3’ Quantseq RNA-Seq.

overall_design: CLASH analysis of AGO2 in HEK293 cells in 3 replicates

first: Nandan

last: Varadarajan

first: Eva

last: Klimentova

first: Katarina

last: Gresova

first: Ilektra-Chara

last: Giassa

first: Stepanka

last: Vanacova

first: Panagiotis

last: Alexiou


title: Ago2-CLASH reveals a wide repertoire of small RNA mediated regulation [RNA-Seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data of antimir assays for miR-484, miR-92 and miR-320 to their wildtypes (each in 4 replicates)


title: DNA methylation of fibroblasts from Cockayne syndrome and UV-sensitivity syndrome patients

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

country: Italy

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

type: Methylation profiling by genome tiling array


title: DNA methylation of fibroblasts from Cockayne syndrome and UV-sensitivity syndrome patients [EPIC]

summary: Cockayne syndrome (CS) is a rare genetic disorder caused by mutation of the DNA repair and chromatin remodelling proteins CSA or CSB. Increasing evidences indicate that the progeroid phenotype of CS cannot be solely ascribed to impaired DNA repair, and UV-sensitivity syndrome (UVSS) patients that are also mutated for CSA or CSB do not age prematurely. Epigenetic modifications constitute a hallmark of ageing. We assessed genome-wide DNA methylation (DNAm) at single-nucleotide resolution on fibroblasts derived from CS versus UVSS patients and healthy donors.

overall_design: 1 µg of DNA was bisulfite-converted using the EZ DNA Methylation kit (Zymo Research) and analysed using the Infinium HumanMethylation450 or the HumanMethylationEPIC BeadChip (Illumina) following manufacturer's instructions

first: Clément

last: Crochemore

first: Alain

last: Sarasin

first: Miria

last: Ricchetti


title: Rna_seq analysis of muscle in click and EDC treated mouse

status: Public on Dec 23 2023

first: fei

last: sun

state: Shanghai

address: Laboratory of Biotechnology, School of Life Science, Baoshan Campus, Shanghai University, Dachang Town, Baoshan District, Shanghai

institute: Shanghai University

summary: First, two groups of mice were subjected to hindlimb ischemic modeling. Then, peptide hydrogels synthesized by EDC reaction and click reaction were injected into the ischemic limbs of each group of mice, respectively. Several days later, RNA-seq analysis was performed on the ischemic limb muscles of both groups of mice.

overall_design: Three click response-treated c57b6l mice and three EDC esponse-treated c57b6l

first: Xuelin

first: Jia

last: Jia

first: Tongying

last: Xing

first: Fei

last: Sun


title: DNA methylation of fibroblasts from Cockayne syndrome and UV-sensitivity syndrome patients [450k]


title: Establishment of ganglioside GD2-expressing extranodal NK/T-cell lymphoma cell line with scRNA-seq analysis

city: Bunkyo

first: Miki

last: Ando

state: Tokyo

address: Hongo 2-1-1

department: Hematology

country: Japan

institute: Juntendo University

summary: Extranodal natural killer (NK)/T-cell lymphoma, nasal type (ENKL), known for its poor prognosis and association with Epstein-Barr virus, has a new development with the establishment of the ENKL-J1 cell line. Derived from a patient's bone marrow, ENKL-J1 cells express the ganglioside GD2, making them targets for GD2-directed chimeric antigen receptor T cells. This discovery positions GD2 as a potential therapeutic target. Genetic analysis of ENKL-J1 revealed variants in TP53 and TET2. Single-cell RNA sequencing indicated high expression of genes in key oncogenic pathways such as JAK-STAT, NF-κB, and MAPK, along with genes linked to multidrug resistance, tumor suppression, and anti-apoptosis. In vitro, molecular targeting agents like eprenetapopt, tazemetostat, and vorinostat effectively induced apoptosis in these cells, with GD2-directed T cells also showing cytotoxicity in vivo. The ENKL-J1 cell line, therefore, provides valuable insights for developing treatments for ENKL, especially in advanced stages.

overall_design: We performed single-cell RNA sequencing (scRNA-seq) to better capture the characteristics of ENKL-J1.

first: Shoko

last: Sato

first: Shintaro

last: Kinoshita


title: (CA)n oligonucleotides correct RNA mis-splicing in TDP-43 pathology

city: Basel

first: Marco

last: Terrigno

address: Grenzacherstrasse 124

department: Neuroscience

country: Switzerland

institute: F. Hoffmann-La Roche AG


title: (CA)n oligonucleotides correct RNA mis-splicing in TDP-43 pathology (II)

summary: The occurrence of extensive cryptic splicing following the depletion of nuclear TDP-43 results in impaired neuronal function and degeneration. Here, we show that oligonucleotides containing CA-repeat sequences can mimic TDP-43 pre-mRNA binding and broadly repress cryptic splicing events, reverse protein loss, and restore neuronal activity in TDP-43-depleted neurons. Our results indicate that (CA)n oligonucleotides are potential therapeutic agents to address global mis-splicing in TDP-43 proteinopathies.

overall_design: Comparative alternative splicing analysis of RNA-seq data for hiPSC-derived glutamatergic neurons (FujiFilm Cellular Dynamics; Cat.R1034) after treatment with (CA)n oligonucleotides.

first: Congwei

last: Wang

first: Lars

last: Joenson

first: Meiling

last: Li

first: Manuel

last: Schröter

first: Bettina

last: Nordbo

first: Katarzyna

last: Chyzynska

first: Christian

last: Weile

first: Jessica

last: Bastien

first: Marianne

middle: B

last: Mogensen

first: Antonia

last: Seidel

first: Peter

middle: H

last: Hagedorn

first: Ravi

last: Jagasia

first: Jonas

last: Vikesaa


title: Eomes regulates mitochondrial function and promotes survival of pathogenic CD4+ T cells during chronic inflammation [ATAC-seq]

city: Toulouse

first: Anne

last: Dejean

state: Midi-Pyrenees

address: CHU Purpan – BP 3028

country: France

institute: Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)

summary: The tissue accumulation of T cells expressing the transcription factor Eomesodermin (Eomes) has been reported in several chronic inflammatory diseases, including multiple sclerosis. However, the mechanisms whereby Eomes controls this accumulation and strengthens inflammation remains ill-defined. Here, we show that Eomes deletion in antigen-specific CD4+ T cells is sufficient to protect against central nervous system (CNS) inflammation. We demonstrate that Eomes is dispensable for the initial priming of CD4+ T cells but is required for long-term maintenance of CNS-infiltrating CD4+ T cells. Our transcriptomic studies reveal that the impact Eomes on effector CD4+ T cell longevity is associated with sustained expression of multiple genes involved in mitochondrial organization and function. Accordingly, epigenetic studies demonstrate that Eomes supports mitochondrial function by direct binding to either metabolism-associated genes or mitochondrial transcriptional modulators. Besides, the significance of these findings was confirmed in both healthy donors and multiple sclerosis patients. CD4+ T cells expressing Eomes exhibit enhanced mitochondrial functions, which resulted in their increased capacity to survive upon prolonged in vitro stimulation. Together, our data reveal a new mechanism by which Eomes promotes severity and chronicity of inflammation via the enhancement of CD4+ T cell mitochondrial functions and resistance to stress-induced cell death.

overall_design: Naive CD4+ T cells were isolated from spleen and lymph nodes by negative selection using the « Naive CD4 T Cell Isolation Kit » according to the manufacturer’s instructions (Miltenyi Biotec, Cat: 130-104-453). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 2 mM L-glutamine, 100 U/mL penicillin/streptomycin and 50 μM β-mercaptoethanol in 96 well plates at a seeding concentration of 2x105 cells per well. Polyclonal naïve CD4+ T cells were stimulated with 2 ug/mL anti-CD3 antibody (Biolegend) and 1 ug/mL anti-CD28 (BD Biosciences) under non-polarizing conditions. After 48hrs of stimulation, viable CD4+ T cells (in triplicates, pool of 2 mice for Eomes-GFP+ CD4+ T cells and individual mice for Eomes-TKO) were flow-sorted according to GFP expression

first: Emeline

last: Joulia

first: Michaël

middle: F

last: Michieletto

first: Adeline

last: Chaubet

first: Nawad

last: Hakim

last: Lhuillier

first: Veronique

last: Adoue


title: Eomes regulates mitochondrial function and promotes survival of pathogenic CD4+ T cells during chronic inflammation [CUT&RUN]


title: To investigate the effect of TMAO intervention on fatty liver cells in vitro and potential genetic changes

first: Fulin

last: Nian

address: 2800 Gongwei Road, Pudong, Shanghai, China

institute: Department of Digestive, Shanghai Pudong Hospital, Fudan University Pudong Medical Center

summary: To construct the optimal fatty liver cell model in vitro and use TMAO intervention to observe its effect on fatty liver cells and identify potential key genes for change by transcriptomics.

overall_design: Comparative gene expression profiling of RNA-seq data between HepG2 fatty liver cells and HepG2 fatty liver cells with TMAO intervention, three samples in each group.

first: Xiaolan

last: Lu


title: Eomes regulates mitochondrial function and promotes survival of pathogenic CD4+ T cells during chronic inflammation


title: Genome-wide CRISPR screening identifies SEC31A as a regulator of alpha cell survival

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Impairment of the glucagon response to hypoglycemia is among the severe clinical consequences in patients with type 1 or advanced type 2 diabetes. However, an incomplete understanding of the stress-response mechanism(s) in alpha cells has limited the insights into the pathophysiology underlying the dysregulated glucagon response and precluded the development of therapeutics. In this study, we undertook an unbiased, genome-wide screening by transducing alpha cells with a CRISPR lentiviral library to identify potential proteins that regulate stress resistance in alpha cells. We identified SEC31A, a gene responsible for the ER-Golgi transportation system, as a critical mediator of cell survival in response to stress. To provide clinical relevance to these findings, we performed transcriptome analysis using pseudoislets generated from sorted and re-aggregated human alpha cells with a knockdown of SEC31A. Our study offers insights into the regulatory mechanism(s) underlying ER stress resistance in pancreatic alpha cells with implications for treating hypoglycemia in T1D and advanced T2D

overall_design: Comparative gene expression profiling analysis of RNA-seq data for re-aggregated human alpha and beta islet  cells and its KD derivatives (SEC31AKD).

first: Kimitaka

last: Shibue

first: Sevim

last: Kahraman

first: Rohit

middle: N

last: Kulkarni


title: Scavenger receptor A ameliorates acetaminophen induced hepatic inflammation

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

address: 203 E Cary St

institute: Virginia Commonwealth University

summary: Acetaminophen-induced liver injury (AILI) occurs frequently and can be life threatening. Although AILI is mainly caused by the direct drug cytotoxicity, increasing evidence suggests that the interplay between hepatocytes and immune cells can define this pathogenic process. To further understand the immunoregulatory role of SRA in AILI, we performed RNA-sequencing analysis using hepatic nonparenchymal cells (NPCs) derived from acetaminophen treated WT or SRA-/- mice to demonstrate hepatocyte-extrinsic mechanisms governed by the immune receptor SRA that maintains liver homeostasis upon drug insult.

overall_design: Wild type and SRA-/- mice were injected with Acetaminophen (400 mg/kg). Six hours after acetaminophen injection, total RNA was extracted from hepatic non-parenchymal cells (NPCs) and subjected to RNA sequencing. RNA from Wild type cells are used as reference.

first: Chunqing

last: Guo

first: Wenjie

last: Liu

first: Xixian

last: Jiang

first: Bei

last: Zhang

first: Jinze

first: Xiang-Yang

last: Wang


title: Super-enhancer trapping by the nuclear pore via intrinsically disordered regions of proteins in squamous cell carcinoma cells

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

summary: Master transcription factors such as TP63 establish super-enhancers (SEs) to drive core transcriptional networks in cancer cells, yet the spatiotemporal regulation of SEs within the nucleus remains unknown. The nuclear pore complex (NPC) may tether SEs to the nuclear pore where RNA export rates are maximal. Here, we report that NUP153, a component of the NPC, anchors SEs to the NPC and enhances TP63 expression by maximizing mRNA export. This anchoring is mediated through protein-protein interaction between the intrinsically disordered regions (IDRs) of NUP153 and the coactivator BRD4. Silencing of NUP153 excludes SEs from the nuclear periphery, decreases TP63 expression, impairs cellular growth, and induces epidermal differentiation of squamous cell carcinoma. Overall, this work reveals the critical roles of NUP153 IDRs in the regulation of SE localization, thus providing insights into a new layer of gene regulation at the epigenomic and spatial level.

overall_design: Comaprison between negative control cells and NUP153 knocked down cells. There is no biological replicates for each conditions.

first: Masaharu

last: Hazawa

first: Dini Kurnia

last: Ikliptikawati

first: Yuki

last: Iwashima

first: De-Chen

last: Lin

first: Yuan

first: Yujia

last: Qiu

first: Kei

last: Makiyama

first: Koki

last: Matsumoto

first: Akiko

last: Kobayashi

first: Goro

last: Nishide

first: Lim

last: Keesiang

first: Hironori

last: Yoshino

first: Toshinari

last: Minamoto

first: Takeshi

last: Suzuki

first: Isao

first: Makiko

last: Meguro-Horike

first: Yan-Yi

first: Takumi

last: Nishiuchi

first: Hiroki

last: Konno

first: Phillip

last: Koeffler

first: Hosomichi

last: Hosomichi

first: Atsushi

last: Tajima

first: Richard

middle: W

last: Wong


title: m6A-seq map of wild type P6497 and methyltransferase knockout mutant of Phytophthora sojae

first: Fan

last: Zhang

address: No.2 Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

summary: N6-methyladenosine (m6A) modification, as an important post-transcriptional regulator, is the most prevalent RNA modification in eukaryotes. However, the biological role of m6A in oomycetes remains unclear. Here, we characterized three m6A methyltransferases PsMETTL3A, PsMETTL3B, and PsMETTL16 that mainly affected the m6A levels in the CDS and 3’UTR in Phytophthora sojae. They play an important role in production of sporangia and oospores, mycelial growth, and virulence. PsMETTL3A/3B/16-mediated m6A positively regulated mRNA stability and translation efficiency of genes involved in chromatin remodeling and epigenetic regulation. Interestingly, PsMETTL3A, PsMETTL3B, or PsMETTL16 function in “independent” and “overlap” synergetic pattern. PsMETTL16 could interact with PsMETTL3A and PsMETTL3B to mediate m6A on some of the transcripts. Moreover, PsMETTL3A and PsMETTL3B positively regulated the expression of PsMETTL16 in an m6A-dependent manner. More importantly, m6A-modified PsBdf1 regulate chromatin accessibility to maintain DNA damage repair and tolerate host ROS stress in a PsMETTL3A/3B/16-dependent manner. Overall, these results indicate that m6A-mediated RNA metabolism are associated with development and pathogenicity of P. sojae, highlighting epigenetic variation as a mechanism of plant pathogenic oomycetes adaptive plasticity.

overall_design: We identified three major m6A methyltransferases PsMETTL3A, PsMETTL3B, and PsMETTL16 in Phytophthora sojae, and obtained their knockout mutants, respectively, in order to further analyze whether the downstream m6A modification mediated by different methyltransferases is different. We performed MERIP (m6A) -seq of the wild type P6497 of Phytophthora sojae and the three methyltransferase knockout mutants mentioned above.

first: Xili

last: Liu

first: Borui

first: Tongshan

last: Cui


title: Eomes regulates mitochondrial function and promotes survival of pathogenic CD4+ T cells during chronic inflammation [RNA-seq]

first: Anne

last: Dejean

overall_design: Naive CD4+ T cells were isolated from spleen and lymph nodes by negative selection using the « Naive CD4 T Cell Isolation Kit » according to the manufacturer’s instructions (Miltenyi Biotec, Cat: 130-104-453). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 2 mM L-glutamine, 100 U/mL penicillin/streptomycin and 50 μM β-mercaptoethanol in 96 well plates at a seeding concentration of 2x105 cells per well. Polyclonal naïve CD4+ T cells were stimulated with 2 ug/mL anti-CD3 antibody (Biolegend) and 1 ug/mL anti-CD28 (BD Biosciences) under non-polarizing conditions. After 0, 12 or 24 hrs of stimulation, viable CD4+ T cells (in triplicates, pool of 2 mice for Eomes-TWT+ CD4+ T cells and Eomes-TKO) were flow-sorted and process for RNA-seq.

first: Emeline

last: Joulia

first: Michaël

last: Michieletto

first: Adeline

last: Chaubet

first: Nawad

last: Hakim

last: Lhuillier

first: Veronique

last: Adoue


title: Dynamic transcriptomic tracking directs the treatment for acute leukemia of ambiguous lineage

city: Dalian

first: Jinsong

last: Yan

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary: Acute leukemia of ambiguous lineage (ALAL) is a rare subtype of acute leukemia characterized by the lack of straightforward myeloid or lymphoid lineage commitment. Currently, no treatment guidelines are commonly-accepted for ALAL. Herein, we have established an molecular-guided therapeutic approach to classify ALAL as either possessing an transciptional profile with a tendency towards acute myeloid leukemia (AML) or acute lymphoblastic leukemia (ALL). A three and a half years perspective study saw an ALAL patient failed to respond to the ALL-like treatment recommended in most retrospective studies. However, RNA-seq profiling of this ALAL, together with indepth comparative analysis with AML, ALL and healthy bone marrow samples, demonstrated that the ALAL was transcriptomically more similar to AML, and correspondingly a complete molecular remission (CMR) was achieved with AML-like treatment regimen. Moreover, tracking of transcriptomic profile changes at nine time points throughout the treatment successfully detected tumor relapse seven months earlier than conventional approaches. Under the guidance of this Dynamic Transcriptomic Tracking (DTT) approach, we present a further ALAL patient that reached CMR with an AML-like treatment regimen. DTT maybe beneficial in other leukemias that do not possess recommended treatment guidelines. We propose that DTT is condidered for perspective trials.

overall_design: The direction of  treatment for acute leukemia of ambiguous lineage by combining multiple time points sampling and comprehensive transcriptomic similarity analysis

first: Zhigunag

last: Li

first: Xuehong


title: Expression profiles of transfer RNA-derived small RNAs in serum exosomes from breast cancer patients and healthy controls

status: Public on Dec 22 2023

city: Nanjing

first: Shanliang

last: Zhong

address: Baiziting 42

institute: The Affiliated Cancer Hospital of Nanjing Medical University

summary: To explore expression levels of tsRNAs in serumal exosomes, 4 serum specimens were chosen from patients with metastatic breast cancer and 4 samples from healthy subjects. The exosomes were isolated and sent for tsRNA-sequencing.

overall_design: The tsRNA expression levels in serum exosomes from breast cancer patients were compared to those from healthy controls.


title: Timp2 loss-of-function mutation and rTIMP2 treatment in murine lung cancer models: alteration of myeloid response and suppression of tumorigenesis

city: bethesda

first: David

last: Peeney

address: 10 Center Drive, Building 10, 6B05

institute: NCI

summary: TIMP2 inhibits metalloproteinase activity and possesses metalloproteinase-independent functions that regulate cell growth, invasion, and gene expression. Although mounting evidence suggests TIMP2 can reduce tumor burden and metastasis the demonstration of these effects using in vivo tumor models are lacking. In this study, we examine the effects of functional mutation of Timp2 and administration of recombinant TIMP2 in models of both orthotopic and heterotopic murine lung cancer using the syngeneic Lewis Lung carcinoma cells (LL/2-luc2). Mice harboring a functional mutation of TIMP2 (mT2) display a marked increase in tumor growth and mortality, enhanced tumor micro-vasculature, and greater infiltration of myeloid-derived cells compared to wt mice, suggesting that reduced TIMP2 function results in enhanced presence of pro-tumorigenic, immunosuppressive myeloid cells. Treatment with recombinant TIMP2 reduced primary tumor growth in both genotypes. Transcriptional profiling of lung tissues from non-tumor-bearing mice reveals minimal changes in mice. However, orthotopic, lung tumor-bearing mice demonstrate significant changes in gene expression that are genotype-dependent. In tumor-bearing wt mice TIMP2-treatment reduced the expression of upstream oncogenic mediators. In comparison, treatment of mT2 mice resulted in an immunomodulatory phenotype, as suggested by enhanced activity of Il4, Il2, and Ifng. A heterotopic model of LL/2 generating metastatic pulmonary tumors demonstrated that daily administration of recombinant TIMP2, while also reducing primary tumor growth, significantly altered transcriptional profiles in the lungs of wt mice, suggesting modification of the metastatic niche. These changes result in the downregulation of cell-stress responses, as evidenced by reduced expression of heat shock proteins. In summary, we describe how TIMP2 exerts novel, anti-tumor effects in a murine model of lung cancer and that rTIMP2 treatment supports a normalizing effect on the tumor microenvironment. These findings support the concept that TIMP2 displays homeostatic functions to reverse cell stress signaling in addition to inhibition of metalloproteinases.

overall_design: To assess the effects of Timp2 mutation on pulmonary tumor progression, and determine the therapeutic success of daily recombinant TIMP2 treatment in pulmonary tumor bearing mice.

first: Sarvesh

last: Kumar

first: William

middle: G

last: Stetler-Stevenson


title: Goat liver single-cell RNA sequencing

city: Yangling

first: Yue

last: Wang

address: No.22_Xinong Road

department: College of Animal science and Technology

institute: Northwest A&F University

summary: The difference in liver cell types from healthy, non-alcoholic steatohepatitis (NASH) and non-alcoholic steatohepatitis tolerance goats.

overall_design: A total of 15 liver samples from healthy, non-alcoholic steatohepatitis (NASH) and non-alcoholic steatohepatitis tolerance goats (n = 5). The 5 samples in each group were mixed well and made into a mixed sample.

first: Xiaodong

last: Chen

first: Shengru

last: Wu

first: Junhu

last: Yao


title: Transcriptomic profiling of purple winged bean pods

city: Nottingham

first: Fei

last: Sang

address: QMC

institute: Nottingham University

summary: Our study unravels the regulatory network and structural genes involved in the anthocyanin biosynthesis pathway.

overall_design: Four time point study as pod ripen, in triplicates

first: Niki

last: Tsoutsoura


title: The epigenetic effects induced by ectopic expression of Pax7 in 3T3-L1

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: We report the robustness and plasticity of the differentiation potential of 3T3L1 adipocytes in the aspect of genome-wide change of chromatin structure by ectopic expression of Pax7 and classifying the genes potentially responsible for facilitating or suppressing trans-differentiation of 3T3L1 in the aspect of epigenetic regulation..

overall_design: We performed RNA-seq and ChIP-seq in control or Pax7 stably expressed 3T3-L1 adipocytes during adipocyte differentiation.

first: Alaa

last: Elgaabari

first: Atsuko

last: Miyawaki-Kuwakado

first: Kosuke

last: Tomimatsu

first: Qianmei

first: Wakana

last: Izumi

first: Takahiro

last: Suzuki

last: Tokunaga

first: Judy

last: Anderson

first: Ryuichi

last: Tatsumi

first: Mako

last: Nakamura


title: Monocyte gene expression in adult-onset Still's disease

city: Shanghai

first: Jinchao

last: Jia

address: No. 197 Ruijin Second Road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Adult-onset Still’s disease (AOSD) is a rare autoinflammatory disease, characterized by fever, rash, arthritis and other systemic inflammatory manifestations like hepatosplenomegaly and serositis. One of the most serious complications AOSD is macrophage activation syndrome (MAS), a life-threatening condition caused by excessive activation of immune system and a cytokine storm. Clinical features of MAS include continuous high fever, hepatosplenomegaly, liver dysfunction, lymphadenopathy, hyperferritinemia, and hemophagocytosis. The prevalence of MAS in AOSD patients is estimated to be between 10–19%, but the mortality rate of AOSD-associated MAS is approximately 10–20%. The precise mechanism by which AOSD develops to MAS remains unclear. There is an unmet need to investigate the pathogenesis of MAS in AOSD in order to identify novel biomarkers and therapeutic targets to improve disease prognosis.

overall_design: Transcriptomes from peripheral blood monocytes of 12 treatment-naïve AOSD patients and 10 healthy controls

first: Qiongyi

last: Hu

first: Mengyan


title: (CA)n oligonucleotides correct RNA mis-splicing in TDP-43 pathology (I)

first: Marco

last: Terrigno

overall_design: Comparative alternative splicing analysis of RNA-seq data for hiPSC-derived glutamatergic neurons  (FujiFilm Cellular Dynamics; Cat.R1034) after treatment with TDP43 antisense gapmers and (CA)n oligonucleotides.

first: Congwei

last: Wang

first: Lars

last: Joenson

first: Meiling

last: Li

first: Manuel

last: Schröter

first: Bettina

last: Nordbo

first: Katarzyna

last: Chyzynska

first: Christian

last: Weile

first: Jessica

last: Bastien

first: Marianne

last: Mogensen

first: Antonia

last: Seidel

first: Peter

last: Hagedorn

first: Ravi

last: Jagasia

first: Jonas

last: Vikesaa


title: Parallel neural pathways control sodium consumption and taste valence

city: Pasadena

first: Tongtong

address: 1200 E California Blvd

institute: California Institute of Technology

summary: We performed single-cell RNA-seq (10x Chromium 3' v.3.1) on dissociated single cell suspensions from mouse (C57BL/6) osmosensory brain nuclei - subfornical organ (SFO) to determine transcriptomic cell types and neuronal activation patterns. By performing single cell RNA-seq based stimulus to cell-type mapping, we captured the endogenous immediate early gene expression triggered by distinct physiological state stimuli in SFO cells. We identified a unique excitatory neuron type in SFO that is uniquely tuned to sodium deficiency.

overall_design: For stimulus to cell-type mapping experiments we used 15-20 animals per condition. Both male and female animals were used in equal measure. All animals were 7-8 weeks of age. Prior to tissue extraction, animals were subjected to one of the following experimental treatments: a) wated satiation: ad libitum access to food and water); b) sodium depletion: intraperitoneal (i.p.) injection of furosemide at a dose of 50 mg/kg bodyweight followed by one day maintainance on a low-sodium diet.

first: Yameng

last: Zhang

first: Allan-Hermann

last: Pool

first: Yuki

last: Oka


title: Mapping of the master transcription factor MITF in prostate cancer

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

summary: “Mi” transcription family members such as TFE3 and TFEB, participate in the pathogenesis of a subgroup of renal cell carcinomas, whereas MITF is key in melanocyte development and also contributes to melanoma, behaving as an oncogene when amplified and facilitating tumor invasiveness and therapy resistance when MITF levels are low. In addition, MITF plays a role in the survival and growth of clear cell sarcoma and pancreatic cancer. In prostate cancer MITF through the regulation of the heat-shock protein CRYAB has been suggested to suppress tumor initiation. However, the role of MITF in advanced therapy resistant lethal stages of the disease remains unknown. To gain insight into the gene network regulated by MITF in prostate cancer, we mapped MITF genomewide in a human prostate cancer cell line (22Rv1) by chromatin immunoprecipitation followed by ultra high-throughput sequencing. This analysis revealed the genomewide locations of MITF in prostate cancer, including the promoter of eIF3B which we further functionally validated through ChIP-PCR and luciferase reporter assays. We propose that the master regulator MITF by regulating a distinct gene network may play key roles in suppressing lethal prostate cancer pathogenesis.

overall_design: MITF ChIP-Seq in human prostate cancer cell line 22Rv1

first: Sandra

last: Santasusagna

first: Shijia

last: Zhu

first: Vijayakumar

last: Jawalagatti

first: Liguo

first: Josep

last: Domingo-Domenech


title: Transcripts with H3K36me3 modification at differente stages of pancreas organogensis [CUT&Tag]

first: Ping

last: Lu

address: No 1630 Dongfang Road, Pudong New Area

institute: Shanghai Cancer Institute

summary: To find the genes with H3K36me3 modificaiton at different stages of pancreas development, we isolated the pancreatic epithelial cells  from E11.5, E13.5 and E15.5 fetal pancreas. Considering the low expression of H3K36me3 at E11.5, E11.5 samples worked as a "negantive" control. By compared with the peaks of E11.5, we was able to find genes under direct regulation of H3K36me3 at E13.5 and E15.5.

overall_design: Pancreatic epithelial cells were purified from fetal pancreas at E11.5, E13.3 and E15.5 mouse pancreas, labelled by EpCAM and then sorted by flow cytometry and finally were subject to H3K36me3 CUT&Tag seq.


title: The transcriptome of pancreatic epithelial cells at different stages during fetal organogenesis [RNA-seq]

summary: To investigate the transcriptome at different stages of pancreatic organogenesis, we sorted by flow cytometry the pancreatic epithelial from fetal murine pancreas.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of the pancreatic epithelium of  E11.5, E13.5, E15.5 and E18.


title: The opened-up transcriptome with H3K36me3 modification in murine fetal pancreatic epithelial cells

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

overall_design: Refer to individual Series


title: The chromatin accessibility in mouse pancreatic epithelial cells at E11.5, E13.5 and E15.5 during embryogenesis [ATAC-seq]

summary: To understand the chromatin  accessibility in mouse pancreatic epithelial cells at different stages during fetal development, we performed ATAC-seq in epithelial cells sorted from the pancreas tissues of E11.5, E13.5 and E15.5

overall_design: Epithelial cells of pancreas at indicated stages were labelleb with EpCAM, sorted by Flow cytometry and then underwent ATAC seq


title: Gene expression analysis of M and SM gastric cancer

city: Bunkyo-ku

first: Sayaka

last: Nagao

department: Gastroenterology

institute: The University of Tokyo

summary: The objective of this study was to identify genes and pathways involved in submucosal invasion of early gastric cancer through comprehensive gene expression analysis.

overall_design: 8 cases with intramucosal gastric cancer (M cancer) and 8 cases with early gastric cancer with submucosal invasion ≥ 500 μm (SM cancer) were enrolled in this study. Biopsies were taken from both tumor site and background normal mucosa.

first: Yu

last: Takahashi


title: Atlas of subcellular RNA localization in human embryonic stem cells and its flow during differentiation

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Peking Union Medical College

summary: The distribution of RNA in human embryonic stem cells (hESC) and the function of RNA localization in maintaining hESC pluripotency and differentiation are currently unknown. Here, by isolating five subcellular components of hESCs and differentiated cells, we uncovered the global subcellular RNA localization in hESC. For protein-coding mRNA, different transcripts of the same gene exhibit an “isoform switch” between subcellular components, which is regulated by localization cis-elements in their variable regions. For noncoding RNA, multiple sequence features such as polyA tail, length, and GC content jointly regulate their subcellular localization. In addition, we found that some developmental genes can be transcribed in advance and confined to chromatin in undifferentiated hESCs. Finally, we revealed significant changes in overall RNA distribution, mapped RNA dynamic localization atlas, and characterized different dynamic RNA localization patterns during hESC differentiation into mesoderm. The multiple RNA localization patterns we revealed will provide some new enlightenment for hESC stemness maintenance and differentiation.

overall_design: RNA localization profiling of RNA-seq data of subcellular components for hESCs and differentiated cells (Day3 and Day5).

first: Fanqi

last: Zhou

first: Puwen

last: Tan

first: Dong

last: Wang

first: Yanni

last: Ma


title: RNA array data of abdominal adipose tissue post duodenal-jejunal bypass (DJB)

first: Qingnan

last: Zhao

address: 650 XinSongjiang Rd

institute: Shanghai Jiao Tong University School of medicine affiliated Shanghai General Hospital

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

summary:
To analyze the mRNA, lncRNA, and circRNA expression profile in abdominal adipose tissues post DJB surgery, high-fat diet induced  typical diabetic mice were underformed sham surgery or DJB surgery. Two weeks post the surgery, mice were enthanized and the abdominal adipose tissues were collected for RNA array analysis.
To analyze the ceRNA networks regulated by DJB surgery

overall_design: After confirming that T-aFGL2 treatment induced long term suvival of GBM tumor bearing mice, and the formation of CD8+TRM in brain, the CD44+CD8+T cells from brain and dLNs were sorted and underwent TCR deep sequencing to analyze the TCR clone characteristics.

first: Yongjun

last: Liang


title: Role of MITF in advanced lethal prostate cancer

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary:
Great efforts have been made to identify key molecular aberrations that sustain growth and confer resistance to androgen deprivation therapy (ADT) in advanced prostate cancer (PC), and yet PC remains a lethal disease. Recent years have witnessed the discovery of several master regulator transcription factors that enhance lethal PC aggressiveness and provide actionable targets that may improve patient survival. Here we explore the role of the microphthalmia transcription factor (MITF) in lethal prostate cancer.  To identify the mechanisms through which MITF mododulates prostate cancer aggressiveness, we knock-down MITF in three prostate cancer cell lines to identify the MITF regulated effector gene network contributing to lethal prostate cancer.
Methods: We compared global transcription of three prostate cancer cell lines transduced with a siRNA control and 2 siRNAs targetting MITF by RNAseq.
Results:  RNA-seq of MITF knockdown prostate cancer cells uncovered a trasncriptional network of MITF regulated genes
Conclusions: MITF regulates a discrette gene network that contributes to prostate cancer aggressiveness

overall_design: To characterize the transcriptional program regulated by MITF, we performed RNA sequencing of three PC models, DU145, 22Rv1 and ARCaPM, after 48 hours of being transfected with siRNA control or two siRNAs targeting MITF (biological replicates of n = 3 for each condition).

first: Asim

last: Hassan


title: Atypical B cells consist of subsets with distinct effector functions

city: San Antonio

first: Evelien

last: Bunnik

address: 7703 Floyd Curl Drive

department: MIMG

institute: UT Health San Antonio

summary: Atypical B cells are a population of activated B cells that are commonly enriched in individuals with chronic immune activation, but are also part of a normal immune response to infection or vaccination. Prior studies to determine the function of these cells have yielded conflicting results, possibly due to functional heterogeneity among this B cell population. To better define the role(s) of atypical B cells in the host adaptive immune response, we performed single-cell sequencing of transcriptomes, cell surface markers, and B cell receptors in individuals with chronic Plasmodium falciparum exposure, a condition known to lead to accumulation of circulating atypical B cells. Our studies identified three previously uncharacterized populations of atypical B cells with distinct transcriptional and functional profiles, that separate into two differentiation pathways. We identified a set of cell surface markers to distinguish these atypical B cell subsets and confirmed their presence in malaria-experienced children and adults using flow cytometry. Plasmodium falciparum-specific cells were present in equal proportions within each of these atypical B cell populations, indicating that all three subsets develop in response to antigen stimulation. However, we observed marked differences among the three subsets in their ability to produce IgG upon T-cell-dependent activation. Collectively, our findings help explain the conflicting observations in prior studies on the functions of atypical B cells and provide a better understanding of their role in the adaptive immune response in chronic inflammatory conditions.

overall_design: Single cell sequencing analysis of B cells from 2 children at two time points following a malaria episode: 3 weeks after malaria (TP1) and 6 months later (TP2). For each sample, three libraries were constructed on the 10x Genomics platform: gene expression (GEX), cell surface marker expression (ADT), and antibody heavy and light chain variable regions (V(D)J).

first: Raphael

middle: A

last: Reyes

first: Gayani

last: Batugedara

first: Paramitta

last: Dutta

first: Ashley

last: Reers

first: Rolando

last: Garza

first: Isaac

last: Ssewanyana

first: Prasanna

last: Jagannathan

first: Margeret

last: Feeney

first: Bryan

last: Greenhouse

first: Sebastiaan

last: Bol

first: Ferhat

last: Ay


title: Regulation of Endogenous Retroviruses and Cellular Genes by HIV-1 Rev I

city: Charlottesville

first: Lou

last: Hammarskjold

state: VA

address: 1340 Jefferson Park Avenue

institute: University of Virginia

summary: A combination of bioinformatics, RNAseq, and cell-based functional assays were used to study the changes in host cell gene expression when HIV-1 Rev or Nef was expressed. These results suggest that HIV Rev and  Nef are capable of modulating gene and mRNA isoform expression, during HIV-1 infection.

overall_design: Investigation into host cell gene expression when HIV-1 Rev and HIV-1 Nef is expressed in T-lymphocyte cells.

first: Laurie

middle: R

last: Gray

first: David

last: Rekosh


title: Single cell seq of E13.5 and E15.5 pancreas of Setd2 WT and KO mice [scRNA-seq]

first: Ping

last: Lu

summary: To observe the difference in fetal pancreas between Setd2 WT and KO mice, we performed single cell seq to elucidate the discrapency.

overall_design: E13.5 and E15.5 pancreas of Setd2 WT and KO mice were harvest, digested sorted by flow cytometry and then analyzed by single cell sequence


title: Estrogen receptor agonism/antagonism in T47D cells

status: Public on Dec 21 2023

first: Thomas

last: Scott

address: 1340 Jefferson Park Ave, Pinn Hall 6225

department: Biochemistry and Molecular Genetics


title: Nascent RNA sequencing (PRO-seq) after various treatments in T47D cells

summary: This experiment identifies the primary estrogen response genes in T47D cells.

overall_design: T47D cells were hormone starved for 3 days and then treated with estrogen or a vehicle control for 1 hour.

first: Michael

middle: J

last: Guertin


title: Assay for transposase-accessible chromatin with sequencing (ATAC-seq) after various treatments in T47D cells

overall_design: T47D cells were either hormone starved for 3 days and then treated with estrogen or a vehicle control for 1 hour, or grown in complete media for 1 day and then treated with fulvestrant, raloxifene, tamoxifen, or a vehicle control for 1 hour.


title: Regulation of Endogenous Retroviruses and Cellular Genes by HIV-1 Rev II

overall_design: Investigation into host cell gene expression when HIV-1 Rev or HIV-1 Nef is expressed in T-lymphocyte cells.


title: Aging and obesity prime the methylome and transcriptome of adipose stem cells for disease and dysfunction

city: West Lafayette

first: Dianne

last: Little

state: IN

address: 625 Harrison St

department: Basic Medical Sciences

institute: Purdue University


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Control and BRD9 Inhibitors-treated  Uterine Fibroid Cell Transcriptome

city: Chicago

first: Qiwei

last: Yang

address: 5841 S. Maryland Avenue

department: Obstetrics and Gynecology

institute: University of Chicago

summary: We report that BRD9 inhibition altered multiple biological pathways, including  cell cycle-related pathways in uterine fibroid cells

overall_design: Examine the transcriptome alteration in uterine fibroid cells with or without BRD9 inhibitors treatment

first: Ayman

last: Al-Hendy


title: Aging and obesity prime the methylome and transcriptome of adipose stem cells for disease and dysfunction [RNA-seq]

summary: The epigenome of stem cells occupies a critical interface between genes and environment, serving to regulate expression through modification by intrinsic and extrinsic factors. We hypothesized that aging and obesity, which represent major risk factors for a variety of diseases, synergistically modify the epigenome of adult adipose stem cells (ASCs). Using integrated RNA- and targeted bisulfite-sequencing in murine ASCs from lean and obese mice at 5- and 12-months of age, we identified global DNA hypomethylation with either aging or obesity, and a synergistic effect of aging combined with obesity. The transcriptome of ASCs in lean mice was relatively stable to the effects of age, but this was not true in obese mice. Functional pathway analyses identified a subset of genes with critical roles in progenitors and in diseases of obesity and aging. Specifically, Mapt, Nr3c2, App, and Ctnnb1 emerged as potential hypomethylated upstream regulators in both aging and obesity (AL vs. YL and AO vs. YO), and App, Ctnnb1, Hipk2, Id2, and Tp53 exhibited additional effects of aging in obese animals. Furthermore, Foxo3 and Ccnd1 were potential hypermethylated upstream regulators of healthy aging (AL vs. YL), and of the effects of obesity in young animals (YO vs. YL), suggesting that these factors could play a role in accelerated aging with obesity. Finally, we identified candidate driver genes that appeared recurrently in all analyses and comparisons undertaken. Further mechanistic studies are needed to validate the roles of these genes capable of priming ASCs for dysfunction in aging- and obesity-associated pathologies.

overall_design:
Paired Methyl-Seq and RNA-Seq on lean or obese, aged or young adipose-derived stem cells from C57BL6/J mice
Keywords:Affl; Cd44; Dusp6; Itih2; Nfatc2; diabetes; mesenchymal stem cell; multiomics; oncogenesis; osteoarthritis; tumorigenesis.

first: Shaojun

last: Xie

first: Sulbha

last: Choudhari

first: Jyothi

last: Thimmapuram

first: Chia-Lung

last: Wu

first: Karen

last: Abramson

first: Simon

last: Gregory

last: Corcoran

first: Farshid

last: Guilak


title: Development of a benzarone derivative as targeted therapy for SHH-medulloblastoma [Day 1]

city: Boston

first: Rosalind

last: Segal

address: 360 Longwood Ave.

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: Medulloblastoma is one of the most common malignant brain tumors of children, and 30% of medulloblastomas are driven by gain-of-function genetic lesions in the Sonic hedgehog (SHH) signaling pathway. Eyes Absent (EYA1), a haloacid dehalogenase (HAD) phosphatase and co-transcription factor, is critical for tumorigenesis and proliferation of SHH-medulloblastoma (SHH-MB). Benzarone and benzbromarone have been identified as allosteric inhibitors for the Eya proteins. Using benzarone as a point of departure, we developed a panel of 35 derivatives, and identified one new compound, DS-1-38, that functions as an Eya-antagonist, opposes SHH-signaling, inhibits SHH-MB growth in vitro and in vivo, shows excellent brain penetrance and increases the lifespan of mice predisposed to fatal SHH-MB. Our data suggest that DS-1-38 provides a path for developing targeted therapeutic for pediatric SHH-MB.

overall_design: Comparative analysis of MB21 cells after 5 days of treatment with a benzarone derivative, DS-1-38, and vehicle, DMSO

first: Grace

last: Hwang

first: Maria

last: Pazyra-Murphy


title: An engineered glioblastoma model yields macrophage-secreted drivers of invasion

city: Berkeley

first: Sanjay

last: Kumar

address: Stanley Hall, University Dr

department: Bioengineering

institute: University of California, Berkeley

summary: Glioblastomas (GBMs) are highly invasive brain tumors replete with brain- and blood-derived macrophages, collectively known as tumor-associated macrophages (TAMs). Targeting TAMs has been proposed as a therapeutic strategy but has thus far yielded limited clinical success in slowing GBM progression, due in part to an incomplete understanding of TAM function in GBM. Here, by using an engineered hyaluronic acid-based 3D invasion platform, patient-derived GBM cells, and multi-omics analysis of GBM tumor microenvironments, we show that M2-polarized macrophages stimulate GBM stem cell (GSC) mesenchymal transition and invasion. We identify TAM-derived transforming growth factor beta induced (TGFβI/BIGH3) as a pro-tumorigenic factor in the GBM microenvironment. In GBM patients, BIGH3 mRNA expression correlates with poor patient prognosis and is highest in the most aggressive GBM molecular subtype. Inhibiting TAM-derived BIGH3 signaling with a blocking antibody or small molecule inhibitor suppresses GSC invasion. Our work highlights the utility of 3D in vitro tumor microenvironment platforms to investigate TAM-cancer cell crosstalk and offers new insights into TAM function to guide novel TAM-targeting therapies.

overall_design: To investigate how M2-polarized THP-1-derived macrophage conditioned media (CM) alters the transcriptional profile of GSCs, we performed bulk RNA-sequencing (RNA-seq) on GSCs in hydrogels cultured in GSC maintenance (control) media or M2 CM. We utilized a previously developed microchannel invasion platform, which consists of a cylindrical cell reservoir channel embedded within a 3D hydrogel and enables the physical separation of highly invasive and non-invasive (core) cell fractions from a single device. We then performed Differentiaion Gene Expression Analysis between three samples (M2 CM invasive, M2 CM core, Control) collected at the same timepoint (28 day after start of invasion assay). Comparative Gene Expression profiling analysis of RNA-seq data for GSC-20 cells exposed to M2-polarized macrophage CM or Control media. Cells treated with M2 CM were further separated based on distance migrated in 3D invasion device (core = no invasion, invasive = invasive fraction).

first: Erin

last: Akins

first: Dana

last: Wilkins

first: Manish

middle: K

last: Aghi


title: Differential effects of plant- and animal fats on obesity-induced dyslipidemia and atherosclerosis

city: Leiden

first: Martine

last: Morrison

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

summary: Abstract  Cardiovascular disease (CVD) is closely associated with obesity through risk factors such as dyslipidemia and chronic low-grade inflammation, which may be affected by diet. Dietary fats have been extensively studied in relation to CVD risk, however these studies have not always yielded consistent results, most likely due to lack in control of experimental conditions and confounding factors. Here we studied the effects of different plant and animal fats on dyslipidemia, inflammation and atherosclerosis. Ldlr-/-.Leiden mice were fed isocaloric energy-dense diets with translational macronutrient composition for 28 weeks. The diets were identical apart from the type of fat they contained: either 1) a mixture of olive and rapeseed oil; 2) sunflower oil; 3) pork fat; 4) beef fat; or 5) milk fat. The fatty acid composition of the diets was determined and effects on circulating lipid and inflammatory risk factors and atherosclerosis were examined, complemented by adipose tissue histology and liver transcriptomics. While visceral fat mass, adipocyte size and adipose tissue inflammation were not differentially affected by the diets, atherosclerotic lesion load and severity was more pronounced with increasing dietary saturated fatty acid content and decreasing monounsaturated and polyunsaturated fatty acid content, and hence most pronounced with beef and milk fat. These differential effects were accompanied by increases in pro-atherogenic plasma lipids/lipoproteins (e.g., triglycerides, apolipoprotein B), activation of pro-atherogenic cytokine/chemokine signaling pathways in liver, and with circulating pro-atherogenic mediators of inflammation altogether providing a rationale for the differential effects of plant and animal fats.

overall_design: Ldlr-/-.Leiden mice were fed isocaloric energy-dense diets with translational macronutrient composition for 28 weeks. The diets were identical apart from the type of fat they contained: either 1) a mixture of olive and rapeseed oil; 2) sunflower oil; 3) pork fat; 4) beef fat; 5) milk fat. Additionally a control group was fed a standard chow diet as a healthy reference.

first: Bjørg

last: Egelandsdal

first: Silje

last: Harvei

first: Sérgio

middle: D

last: Rocha

first: Elsbet

last: Pieterman

first: Robert

last: Kleemann

first: Harald

last: Carlsen


title: Transcriptomic profile of hiPSC-derived myoblasts and myotubes coated on distinct substrates

city: Creteil

first: Joana

last: Esteves de Lima

address: 8 rue du general sarrail

department: IMRB INSERM U955

institute: INSERM

summary: Driving efficient and pure skeletal muscle cell differentiation from pluripotent stem cells has been challenging. Here, we report an optimized protocol that generates skeletal muscle progenitor cells with high efficiency and purity, in a short period of time. Human induced pluripotent stem cells (hiPSC) and mouse embryonic stem cells (mESC) were specified into the mesodermal myogenic fate using distinct and species-specific protocols. We used a specific Maturation Medium to promote terminal differentiation of both human and mouse myoblast populations, and generated myotubes associated with a large pool of cell cycle-arrested PAX7+ cells. We further show that myotube maturation is modulated by the dish coating properties, cell density and percentage of myogenic progenitor cells. Given the high efficiency in the generation of myogenic progenitors and differentiated myofibers, this protocol provides an attractive strategy for tissue engineering, modeling of muscle dystrophies and evaluation of new therapeutic approaches in vitro.

overall_design: Examining the transcriptomic profiles of hiPSC-derived myoblasts and myotubes

first: Reem

last: Bou Akar

first: Chéryane

last: Lama

first: Déborah

last: Aubin

first: Julien

last: Maruotti

first: Brigitte

last: Onteniente

first: Frederic

last: Relaix


title: Aging and obesity prime the methylome and transcriptome of adipose stem cells for disease and dysfunction [Methyl-seq]

first: Dianne

last: Little

overall_design: Paired Methyl-Seq and RNA-Seq on lean or obese, aged or young adipose-derived stem cells from C57BL6/J mice

first: Shaojun

last: Xie

first: Sulbha

last: Choudhari

first: Jyothi

last: Thimmapuram

first: Chia-Lung

last: Wu

first: Karen

last: Abramson

first: Simon

last: Gregory

first: David

last: Corcoran

first: Farshid

last: Guilak


title: Development of a benzarone derivative as targeted therapy for SHH-medulloblastoma [Day 5]

first: Rosalind

last: Segal

first: Grace

last: Hwang

first: Maria

last: Pazyra-Murphy


title: The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

overall_design: Refer to individual Series