title: Transcriptome profiling in early-stage luminal breast cancer

city: Prague

first: Petr

last: Holý

address: Šrobárova 48/49

country: Czech Republic

institute: National Institute of Public Health


title: Integrative analysis of mRNA-miRNA expression profiles and somatic variants in oxysterol signaling in early-stage luminal breast cancer

status: Public on Aug 02 2023

type: Expression profiling by high throughput sequencing

summary: Oxysterols, oxidized derivatives of cholesterol, act in breast cancer (BC) as selective estrogen receptor modulators and affect cholesterol homeostasis, drug transport, nuclear and cell receptors, and other signaling proteins. Using overlapping data from patients with early-stage estrogen receptor-positive BC—high-coverage targeted DNA sequencing (99 patients, 113 genes), mRNA sequencing (67 patients), and full miRNome by microarrays (123 patients)—we describe complex mRNA-miRNA and miRNA-miRNA interaction (correlation) networks, with validation in two carefully curated public datasets (n=538 in total) and 11 databases. The ESR1-CH25H-INSIG1-ABCA9 axis was the most prominent, being interconnected through hsa-miR-125b-5p, but also hsa-miR-99a-5p, hsa-miR-100-5p, hsa miR 143 3p, hsa-199b-5p, hsa-miR-376a-3p, and hsa-miR-376c-3p. Mutations in SC5D, CYP46A1, and its functionally linked gene set were associated with multiple differentially expressed genes. STARD5 was upregulated in patients with positive lymph node status. High expression of miR-19b-3p was weakly associated with poor survival in multiple datasets. This is the first detailed dedicated study of interactions between DNA variation and mRNA expression of oxysterol-related genes, the miRNA transcriptome, and clinical factors in BC.

overall_design: Total RNA samples from tumors of 67 breast cancer patients had their transcriptome sequenced. Panel of oxysterol-related genes was extracted from the data in order to study mRNA expression correlation with miRNome expression and somatic mutation status of the same genes based on targeted DNAseq.

last: Holy


title: miRNA transcriptome profiling in early-stage luminal breast cancer

overall_design: Tumor samples, 1 each for every patient (125 in total). Measured in two batches - 101 and 24. No replicates. No control samples. The purpose was to assess overall miRNome trends of the cohort.

first: Veronika

last: Brynychova

first: Vojtech

last: Hanicinec


title: Expression data from ALDH− and ALDH+ shXIst0SUM159 cells treated with or without DOX

city: WUhan

first: Yuxi

last: Ma

address: Jiefang Avenue

country: China

institute: Huazhong University of Science and Technology

summary: We used microarrays to identify differentially expressed miRNAs in ALDH− and ALDH+ cells treated with or without DOX

overall_design: To identify potential miRNAs directly targeted by XIST, ALDH− and ALDH+ BCCs from DOX-untreated SUM159-shXIST cells were sorted, replated, and treated with or without DOX for 3 days, and subjected to GeneChipTM miRNA Array analysis

first: Max

middle: S

last: Wicha

first: Ming

last: Luo


title: Identifying splicing targets of CLAMP by mRNA-sequencing

city: Providence

first: Erica

last: Larschan

state: RI

address: Sidney Frank Hall 367, 185 Meeting Street

department: MCB

country: USA

institute: Brown University

summary: CLAMP is a GA-repeat motif binding transcription factor that regulates gene expression. We hypothesized that CLAMP also regulates RNA processing, specifically alternative splicing that occurs co-transcriptionally because CLAMP is bound to intronic regions that are rich in polypyrimidine tracts which contain GA-rich sequences. Furthermore, GA-rich repeat sequences are thought to have evolved from polypyrimidine tracts that regulate splicing. Also, MALDI-mass spectrometry data identifying putative CLAMP interactors found association with 33 RNA binding proteins, including 6 that regulate alternative splicing. Thus, to test our hypothesis that CLAMP shapes transcriptome diversity by regulating RNA transcript splicing, we performed mRNA-sequencing in the presence and absence of CLAMP in Kc (female) and S2 (male) cell lines and used a SUPPA based pipeline called time2splice (https://github.com/ashleymaeconard/time2splice) to analyze the sequencing data. Using both cell lines helped us to identify female (Kc) and male (S2) specific splicing events. We identified 452 genes differentially spliced beetween Kc and S2 cells. There are 46 and 113 CLAMP-dependent splicing events in Kc and S2 cells, respectively. Interestingly, 45 CLAMP-dependent events (belonging to 42 genes) are specific to Kc cells, i.e female-specific, whereas 112 CLAMP dependent events (belonging to 100 genes) in S2 cells are specific to S2 cells, i.e male-specific. Therefore, we identified a new role for the transcription factor CLAMP in regulated sex-specific splicing events in Kc and S2 cells.

overall_design: dsRNA for CLAMP was used to deplete CLAMP from cell lines (Kc and S2), validated using qRT-PCR for CLAMP mRNA transcript. Total RNA was extracted from control (GFPRNAi) and experimental (CLAMPRNAi) Kc and S2 cell lines to make cDNA libraries and sequenced. Sequencing data was analyzed for changes in splicing events between control and experimental groups. Three replicates for each categories was performed.

first: Jennifer

last: Urban

first: Pranav

last: Mahableshwarkar

first: Mukulika

last: Ray


title: Effect of loss of transcription factor CLAMP on sex-specific splicing in Drosophila third instar larvae (L3) stage

summary: CLAMP transcription factor is a GA binding protein that recruits the male dosage compensation complex MSL to male X-chromosome, thus upregulating transcription level twice that of female X-chromosomes. Interestingly, CLAMP is essential for survival of both male and female individuals. However, what function it plays at the autosomes, especially in females is not known. It is well establised that GA-rich sequences to which CLAMP bind have evolved from polypyrimidine tracts that regulate splicing. Also, MALDI-MS data shows that CLAMP binds to RNA binding proteins involved in sex-specific splicing like, Squid. Furthermore, as part of MSL complex CLAMP interacts with MLE, a RNA helicase which is a known component of spliceosome complex conserved from flies to humans. Thus, we hypothesized that CLAMP plays a role in sex-spcific splicing. Given that CLAMP is a transcription factor, understanding mechanism of how it regulates splicing will add to our understanding about how regulators of gene expression shape the transcriptome differentially between males and females. We tested our hypothesis by identifying CLAMP dependent female  and male sex-specific splicing events by analysing RNA-seq data from control as well as clampnull mutant male and female third instar larvae (L3) using suppa based time2splice pipeline (https://github.com/ashleymaeconard/time2splice). We identified 189 and 211 CLAMP dependent splicing events in female and male L3. Out of these 139 were female sex-specific splicing whereas 161 was male-sex-specific splicing. 50 splicing events identified as CLAMP dependent were non-specific to any particular sex, and were affect in both the sexes. Interestingly, we identified splicing of master regulator of sex-determination sxl affected by absence of CLAMP in females whereas splicing of one of the sex-determination pathway effectors, tra regulated by CLAMP in males. These findings indicate CLAMP plays important role in determining sex-specific transcript diversity in Drosophila.

overall_design: Total RNA extracted from control (yw) and CLAMP mutant (yw;Clampnull) male and female third instar larvae (3 each)  for RNA-sequencing. The sequenceing data was run through SUPPA based time2splice pipeline to identify CLAMP dependent sex-specific splicing events

first: Joseph

last: Aguilera


title: Pannexin-1 channels promotes CD8+ T cell effector and memory responses through distinct metabolic pathways

city: Scottsdale

first: Henrique

last: Borges da Silva

state: Arizona

address: 13400 E Shea Blvd, 3-364 (Office)

department: Immunology

institute: Mayo Clinic Arizona

summary: Sensing of extracellular metabolites controls CD8+ T cell function. Their accumulation can occur through export by specialized molecules, such as the release channel Pannexin-1 (Panx1). Here, we report that T cell-specific Panx1 is needed for efficient CD8+ T cell responses to viral infection and cancer. Panx1 favors both the expansion of effector CD8+ T cells and the survival of memory CD8+ T cells. Our data suggests that, while memory CD8+ T cells require Panx1 for mitochondrial function, Panx1 promotes the glycolytic pathway in effector CD8+ T cells. Panx1 promotes memory CD8+ T cell survival together with the eATP sensor P2RX7. However, Panx1 induces effector CD8+ T cells independently of eATP. Rather, we found an unexpected link between Panx1, sodium lactate export and the activation of effector CD8+ T cells. Therefore, Panx1 regulates effector and memory CD8+ T cells through export of distinct metabolites and by engaging different intracellular pathways.

overall_design: WT CD8 T cells versus Panx1-KO (KO) CD8 T cells, in vitro activated for 72h (72h WT, 72h KO; three replicates each) or further polarized with IL-15 (IL-15 WT, IL-15 KO; two replicates each).


title: RNA sequencing analysis and comparison of scr and CSE knockdown in non-senescent and senescent conditions in A549 cells

city: BANGALORE

first: DEEPAK

last: SAINI

state: KARNATAKA

address: GA-06,MRDG DEPARTMENT, IISC

department: MRDG

country: India

institute: INDIAN INSTITUTEOF SCIENCE

summary: Using an optimized analysis data workflow, we identified 3945 genes were upregulated and 510 genes were downregulated in scr senescent cells as compared to scr non-senescent cells. CSE knockdown cells also showed huge differences in gene expression as compared to scr cells in both non-senescent and senescent conditions. For analysis purposes, all samles were used in duplicates.

overall_design: Examination of scr and CSE knockdown cells in both non-senescent and senescent conditions

first: K

last: Gupta

first: D

middle: K

last: Saini


title: p16 epimutation modulates the tumor microenvironment and promotes malignancy  of Apc-mutant colon cancer (RNA-Seq)

city: Houston

first: Lanlan

last: Shen

state: Texas

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

summary: Using a mouse model of engineered p16 promoter hypermethylation (p16cis/cis), we found that p16 epimutation cooperates with mutant Apc to promote colon cancer development. Therefore, we performed RNA-seq analysis to identify genes regulated by p16 epimutation that contribute to intestinal carcinogenesis.

overall_design: Comparative transcriptome profiles of colonic mucosa from ApcMin/+; p16cis/cis mice with those from ApcMin/+ mice at 15 wk of age.

first: Li

last: Yang


title: p16 epimutation modulates the tumor microenvironment and promotes malignancy of Apc-mutant colon cancer (scRNA-Seq)

summary: Methylation of p16 promoter resulting in epigenetic gene silencing- known as p16 epimutation- is common in human colorectal cancer (CRC). Using mouse models, we demonstrated that p16 epimutation cooperates with mutant Apc to promote colon cancer development. To comprehensively characterize immune function within the tumor microenvironment (TME), we performed single-cell RNA sequencing (scRNA-seq) of colon tumors in these animals.

overall_design: As a control, we analyzed cells from adjacent normal colonic mucosa. Colon tumors were divided into two groups: small, early-stage lesions (median diameter = 1.7 mm) and larger, late-stage larger tumors (median diameter = 4.0 mm).


title: p16 epimutation modulates the tumor microenvironment and promotes malignancy of Apc-mutant colon cancer

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

overall_design: Refer to individual Series


title: Pannexin-1 channels promotes CD8+ T cell effector and memory responses through distinct metabolic pathways.

overall_design: WT CD8 T cells versus Panx1-KO (KO) CD8 T cells, antigen-specific (gp33-tetramer+), sorted from mice infected with LCMV-Armstrong at d7 post-infection; terminal effectors (TE; CD127-KLRG1+) and memory precursors (MP; CD127+KLRG1-) were separated; three replicates each sample.

last: .Borges da Silva


title: Development of Plasmodium falciparum liver stages in human fetal hepatocyte organoid cultures

city: Würzburg

first: Kai

last: Kretzschmar

address: Josef-Schneider-Str. 2

country: Germany

institute: University Hospital Würzburg

summary: Plasmodium falciparum (Pf) parasite development in liver represents the initial step of the life-cycle in the human host after a Pf-infected mosquito bite. While an attractive stage for life-cycle interruption, understanding of parasite-hepatocyte interaction is inadequate due to limitations of existing in vitro models. We explore the suitability of hepatocyte organoids (HepOrgs) for Pf-development and show that these cells permitted parasite invasion, differentiation and maturation of different Pf strains. Single-cell messenger RNA sequencing (scRNAseq) of Pf-infected HepOrg cells has identified more than 80 Pf-transcripts upregulated on day 5 post-infection. Transcriptional profile changes are found involving distinct metabolic pathways in hepatocytes with Scavenger Receptor B1 (SR-B1) transcripts highly upregulated. A novel functional involvement in schizont maturation is confirmed in fresh primary hepatocytes. Thus, HepOrgs provide a strong foundation for a versatile in vitro model for Pf liver-stages accommodating basic biological studies and accelerated clinical development of novel tools for malaria control.

overall_design: We generated single-cell transcriptome data from single cells purified from human hepatocyte organoids and human red blood cells that were exposed to Malaria parasite Plasmodium falciparum

first: Annie

first: Devanjali

last: Dutta

first: Delilah

last: Hendriks

first: Jens

last: Puschhof

first: Huili

last: Hu

first: Kim

middle: E

last: Boonekamp

first: Youri

last: van Waardenburg

first: Susana

middle: M

last: Chuva de Sousa Lopes

first: Geert-Jan

last: van Gemert

first: Johannes

middle: H

last: de Wilt

first: Teun

last: Bousema

first: Robert

middle: W

last: Sauerwein

first: Hans

last: Clevers


title: Nanopore sequencing combining AlphaFold2 identifies alternative splicing derived putative neoantigens in uveal melanoma

city: Shanghai

first: Nestor

last: Zhang

address: Dongchuan Road

institute: Shanghai Jiao Tong University

summary: We employed a hybrid method based on Oxford Nanopore long-read sequencing and Illumina sequencing to characterize the AS landscapes, and to identify AS-derived neoantigens. Furthermore, we used the AlphaFold2 algorithm to analyze the structure of these putative neoantigens, thus offering structural insights for further drug development. These results lay the foundation for the development of therapies targeting UM-specific, AS-derived neoantigens.

overall_design: We performed Nanopore sequencing using high quality fresh UM patient samples to understand the overall AS landscape.

first: Jianfeng

first: Zhe


title: Genome-wide analysis of planarian piRNAs

city: Bayreuth

first: Andreas

last: Pittroff

address: Universitätsstr. 30

department: BIOmac Research Center, NW1

institute: University of Bayreuth

type: Non-coding RNA profiling by high throughput sequencing

summary: Sample dataset for the described bioinformatic pipeline (piRNAnalyzer) comprising  epidermal piRNA libraries of Schmidtea mediterranea

overall_design: Three biological replicates of piRNA libraries from Schmidtea mediterranea were sub-sampled to 1.5 million reads each in order to provide a sample dataset for the described bioinformatic pipeline piRNAnalyzer

first: Iana

middle: V

last: Kim

first: Tim

last: Demtröder

first: Claus-D

last: Kuhn


title: Single cell analysis reveals transcriptional changes underlying neurological complications in tuberculous meningitis

first: Feng

last: Li

address: No.2901, Caolang Road

department: Department of Respiratory Disease and Critical Care Medicine

institute: Shanghai Public Health Clinical Center, Fudan University

summary: Tuberculous meningitis (TBM) is the most severe and deadly manifestation of tuberculosis. Neurological complications, e.g., hydrocephalus are observed in up to 50% of patients affected. The study of TBM pathogenesis is hampered, at least partially, by a lack of experimental models that recapitulate all clinical features of the human disease. With single-cell transcriptome of blood in tuberculosis revealed, the single cell transcriptome atlas in TBM brain remains yet to be explored. Here, a TBM model was built and then whole brain was dissected for single cell sequencing. Transcriptional changes were observed in all cell types, suggesting a complex biology in TBM pathogenesis. As a result, pervasive immune response was activated by transcription factors Stat1 and IRF1 in macrophages and microglia. For neurons, decreased oxidative phosphorylation activity in neurons links TBM with neurodegenerative diseases. Finally, Ependymal cells show most remarkable transcriptional changes, and decreased Frmd4a may contribute to hydrocephalus and neurodegenerative disorders. We first revealed a comprehensive transcriptome map in TBM mouse model with ScRNA-Seq, and link the cell types, transcriptional genes with regulons and functional processes with neurological complications. These identified cellular and molecular changes offer an unprecedented clue for inspiring the clinical diagnosis and therapeutics of TBM.

overall_design: All twenty-four 6-week C57BL6 mice were used in TBM model and control groups. To acquire a representative TBM expression of each group, 6 mice were pooled together for the folleowing examinations. Each group were composed of two pooled samples: Control group (Ctrl-brain-1 and Ctrl-brain-2) and TBM group (TBM-brain-1 and TBM-brain-2)

first: Xiaolin


title: Targeted transcriptome analysis of isolated intestinal epithelial cells from mice with constitutive Ptpn2-deficiency [Proximal colon]

city: RIVERSIDE

first: Declan

last: McCole

state: CA

address: 3401 Watkins Drive

department: Biomedical Sciences

institute: University of California Riverside

summary: Loss-of-function variants in the protein tyrosine phosphatase non-receptor type 2 (PTPN2) gene are associated with increased risk of inflammatory bowel disease (IBD). PTPN2 encodes T cell protein tyrosine phosphatase (TCPTP), a negative regulator of several intracellular signaling pathways including JAK-STAT. It has been shown that Ptpn2 is critical for intestinal epithelial cell (IEC) barrier maintenance, IEC-macrophage communication, and modulation of the gut microbiome in mice. However, the mechanisms by which Ptpn2 influences the intestinal flora are unknown. In this study, we aimed to identify how Ptpn2-loss affects the expression of genes associated with function/differentiation of IECs in the small and large intestines that could contribute to higher susceptibility to infection.

overall_design: Intestinal epithelial cells were isolated from 21 days old mice (littermates) as Ptpn2-KO mice are normal at birth but die within 3-5 weeks of age. Total RNA was used. Results of two separate panels with a predefined set of targets ('AutoImmune Profiling’ and ‘PanCancer Pathways') from the same intestinal segment were combined for analysis, with the addition of 30 customized targets to each panel comprising of IEC markers, function and differentiation factors, host-bacteria interaction, autophagy, immune response and iron transport, totaling >1500 targets. Data from each panel was normalized separately and then consolidated using the MultiRLF function in the nSolver Analysis Software 4.0.

first: Vinicius

last: Canale

first: Ali

last: Shawki

first: Marianne

middle: R

last: Spalinger

middle: F


title: RNA sequencing of adult mouse ventricular cardiomyocytes incubated in normal growth medium or medium conditioned by CCR2+ cardiac macrophages

city: Toronto

first: Andrew

last: Advani

state: Ontario

address: 6-151 61 Queen Street East

department: Medicine

country: Canada

institute: St. Michael's Hospital

summary: RNA-sequencing of primary cultured adult mouse cardiomyocytes under control conditions or cultured for 24h with medium conditioned by CCR2+ macrophages isolated from pressure overloaded mouse hearts

overall_design: Ccr2/gfp macrophages were FACS sorted from mouse hearts four weeks after transverse aortic constriction (TAC) surgery. Cardiomyocytes were isolated from C57BL/6 mouse hearts and were incubated for 24h with control medium or medium conditioned by CCR2+ cardiac macrophages

first: Veera

middle: G

last: Yerra

first: Sri

middle: N

last: Batchu


title: Targeted transcriptome analysis of isolated intestinal epithelial cells from mice with constitutive Ptpn2-deficiency [Distal Colon]


title: RNA-seq in HCT116 cells with LINC01534 knockdown

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: To obtain a detailed view of genes and pathways regulated by LINC01534 (Long Intergenic Non-Protein Coding RNA 1534) in the HCT116 cells, we carried out global RNA-seq in HCT116 cells with LINC01534 knocked down.

overall_design: We performed RNA-sequencing analysis using samples of parent and siLINC01534 cells.

first: Momoko

last: Ichihara

first: Yuhki

last: Yokoyama

first: Hirofumi

last: Yamamoto


title: Targeted transcriptome analysis of isolated intestinal epithelial cells from mice with constitutive Ptpn2-deficiency [Cecum]


title: Effect of depletion of p38α and p38beta on gene expression in primary effector CD8+ T cells

status: Public on Aug 01 2023

city: Xiamen

first: Lichen

last: Hu

state: Fujian

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District

department: School of Life Sciences

institute: Xiamen University

summary: p38 MAPK is activated during CD8+ T cell primary response. p38 activation promotes effector CD8+ T cell terminal differentiation but represses MPEC formation. p38α/beta deficient mice possess a similar number of virus-specific effector CD8+ T cells as wildtype counterparts. Meanwhile p38α/beta deletion doesn’t influence the clearance of LCMV although it impairs the cytolytic activity of CD8+ T cells. Loss of p38α/beta significantly enhances IL-2-producing Tcm accumulation in mouse spleen with no impact on total memory CD8+ T cell numbers yet. And in line with this, more robust proliferation of memory CD8+ T cells in the secondary response and stronger antigen-specific killing ability in rechallenged mice are resulted from p38α/beta deficiency. These results establish a pivotal role for p38α/beta in skewing MPEC formation toward SLEC differentiation, as well as in suppressing Tcm formation, and thus affecting the recall response.

overall_design: To investigate the cooperative function of p38α and p38beta in effector CD8+ T cell differentiation, we immunized p38αfl/flp38betafl/fl and p38αfl/flp38betafl/flGzmBcre mice with LCMV. At 8th day, splenic Db-GP33-41-tetramer+ CD8+ T cells were sorted by flowcytometry. We then performed gene expression profiling analysis using data obtained from RNA-seq of 8 different mice. Comparative gene expression profiling analysis of RNA-seq data  for WT cells and its KO counterparts (p38α-/-p38beta-/-).


title: FMRP iCLIP and miCLIP in Mettl3 knockout MEFs

city: New York

first: Brian

middle: Frederick

last: Pickering

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

summary: FMRP binding sites were determined by iCLIP in wild-type or Mettl3-/- MEFs as well as HEK293.

overall_design: iCLIP, miCLIP, RNAseq

first: Samie

last: Jaffrey


title: Allosteric inhibition of proteolytic and ATPase activities of the proteasome by the BTK inhibitor CGI-1746

city: AUBURN

first: Amit

middle: Kumar

last: Mitra

state: AL

address: HARRISON COLLEGE OF PHARMACY

department: DRUG DISCOVERY AND DEVELOPMENT

institute: AUBURN UNIVERSITY

summary: Bruton’s tyrosine kinase (BTK) inhibitor Ibrutinib has been shown to synergize in vitro with proteasome inhibitors (PIs) in reducing the viability of cells derived from B-cell malignancies, but the mechanism is not known. We report here that an off-target effect of Ibrutinib causes synergy because not all BTK inhibitors exhibited the synergistic effect, and those that synergized did so even in cells that do not express BTK. The allosteric BTK inhibitor CGI-1746 showed the strongest synergy. Co-treatment of cells with CGI-1746 increased PI-induced expression of heat shock proteins and accumulation of ubiquitin conjugates. The CGI-1746 inhibited the degradation of a model substrate by a purified 26S proteasome. CGI-1746, but not other BTK inhibitors, allosterically inhibited ATPase activity and 2 and 1 peptidase activities of the 26S proteasomes. Although the effect is unlikely to contribute to the anti-neoplastic activity of BTK inhibitors in multiple myeloma and mantle cell lymphoma, it demonstrates a conceptually novel mode of inhibition that may aid the development of more potent proteasome inhibitors and improve response in solid tumors clinically.

overall_design: MDA-MB-231 cells were treated for four hours with CGI-1746, LU-102, a combination of the two, or bortezomib as a control for pathways changed by proteasome inhibition. RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer’s protocol, frozen, and shipped on dry ice to LCSciences (Houston, TX) for total RNA sequencing (150 bp PE, 40 million reads per sample).

first: Alexei

last: Kisselev

first: Olasubomi

last: Akintola


title: Modification of liver transcriptome under the influence of ascites triggered by cold ambient temperature

city: Tabriz

first: Karim

last: Hasanpur

state: Azarbaijan

address: Jam-e-jam

country: Iran

institute: university of Tabriz

summary: Ascites syndrome in both human and chicken has been traditionally known as a metabolic disorder. However, recent scientific findings have suggested a genetic base for the susceptibility to develop AS. The complexity of molecular mechanisms underlying the influence of AS on chicken main organs has not been comprehensively elucidated. In this work, after precise differentiating the ascitic chickens from those healthy ones, we conducted a transcriptome profile comparison between the ascitic and healthy chickens within both males and females using high-throughput RNA-seq data. The results revealed a total of 1,152 differentially expressed genes (DEGs; 669 up- and 483 down-regulated) in males and 1,803 DEGs in females (489 up- and 1,314 down-regulated) between the ascitic and healthy chickens. There were 450 DEGs in common in both males and females.

overall_design: Comparative gene expression profiling analysis of liver RNA-seq data between the ascitic and healthy meat-type chickens


title: Expansion of Interleukin-22-producing Innate Lymphoid Cells in Tristetraprolindeficient mice protects against Dextran Sulfate Sodium-induced Colitis

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: Tristetraprolin (TTP, encoded by Zfp36) is an RNA-binding protein that plays a major role in the control of inflammation. Zfp36 -/-mice spontaneously develop a complex multi-organ inflammatory syndrome that shares many features with spondyloarthritis. Herein, we show that Zfp36 -/-mice are paradoxically protected from Dextran Sulfate Sodium (DSS)-induced colitis. This effect was maintained on a Rag2 -/- background but was lost in Rag2 -/-Il2rg -/-Zfp36 -/-mice that lack innate lymphoid cells (ILCs). Furthermore, we observed a local expansion of type 3 ILCs in the lamina propria of Zfp36 -/-mice. These cells produced large amounts of Interleukin (IL)-22 and were expanded in response to systemic inflammation. Finally, we show that IL-22 contributed to protection of Zfp36 -/-mice against DSSinduced colitis but had a minor impact on their spontaneous inflammatory syndrome. Taken together, these data highlight the complex role of TTP in the control of organ-specific inflammation.

overall_design: Zfp36-deficient mice (Zfp36-/-), LoxP-flanked Zfp36 mice (Zfp36 flox/flox) and Zfp36-V5 knock-in mice on a C57BL/6 background were used to assess inflammatory response mediated by innate lymphoid cells (ILCs).

first: Bérengère

last: De Toeuf

first: Caroline

last: La

first: Villanueva

last: Alcantara

first: Vincent

last: Martens

first: Céline

first: Ingrid

middle: D

last: Vedrenne

first: Sylvie

last: Velde

first: Lara

last: Meyer

first: Muriel

last: Nguyen

first: Séverine

last: Thomas

first: Frédérick

last: Libert

first: Laure

last: Dumoutier

first: Perry

last: Blackshear

first: Stanislas

last: Goriely


title: Comparison of wildtype and Fmr1 knock-out adult mouse gene expression in the cochlear nucleus

city: Seattle

first: Hitomi

last: Sakano

state: WA

address: 1902 Columbia Rd, CHDD, Rm CD176, Box357923

department: Otolaryngology

institute: University of Washington

summary: Fragile X Syndrome (FXS) is a hereditary form of autism spectrum disorder. It is caused by a trinucleotide repeat expansion in the Fmr1 gene, leading to a loss of Fragile X Protein (FMRP) expression. The loss of FMRP causes auditory hypersensitivity: FXS patients display hyperacusis and the Fmr1- knock-out (KO) mouse model for FXS exhibits auditory seizures. FMRP is strongly expressed in the cochlear nucleus and other auditory brainstem nuclei. We hypothesize that the Fmr1-KO mouse has altered gene expression in the cochlear nucleus that may contribute to auditory hypersensitivity.

overall_design: Cochlear nuclei (containing both ventral and dorsal portions) were dissected from Fmr1-KO and WT mice (n=3 each), at age two months. Gene expressions were compared between the two genotypes.

first: Michael

last: Castle

first: Paromita

last: Kundu


title: Resolving therapy resistance mechanisms in multiple myeloma by multiomics subclone analysis

city: Heidelberg

first: Alexandra

last: Poos

address: Im Neuenheimer Feld 410

institute: University Hospital Heidelberg

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Intratumor heterogeneity as a clinical challenge becomes most evident after several treatment lines, when multidrug-resistant subclones accumulate. To address this challenge, the characterization of resistance mechanisms at the subclonal level is key to identify common vulnerabilities. In this study, we integrate whole-genome sequencing, single-cell (sc) transcriptomics (scRNA sequencing), and chromatin accessibility (scATAC sequencing) together with mitochondrial DNA mutations to define subclonal architecture and evolution for longitudinal samples from 15 patients with relapsed or refractory multiple myeloma. We assess transcriptomic and epigenomic changes to resolve the multifactorial nature of therapy resistance and relate it to the parallel occurrence of different mechanisms: (1) preexisting epigenetic profiles of subclones associated with survival advantages, (2) converging phenotypic adaptation of genetically distinct subclones, and (3) subclone-specific interactions of myeloma and bone marrow microenvironment cells. Our study showcases how an integrative multiomics analysis can be applied to track and characterize distinct multidrug-resistant subclones over time for the identification of molecular targets against them.

overall_design:
Single cell ATAC-sequencing of relapsed/refractory multiple myeloma patients.
Submitter states that raw data has been deposited at the European Genome-phenome Archive under the accession number EGAS00001006538.

first: Niels

last: Weinhold

first: Karsten

last: Rippe

first: Nina

last: Prokoph

first: Jan-Philipp

last: Mallm


title: Neuroprotective effect of a medium-chain triglyceride ketogenic diet on MPTP-induced Parkinson’s disease mice: A combination of transcriptomics and metabolomics in the substantia nigra and fecal microbiome

city: Guangzhou

first: Chen

last: Shiyu

state: Guangdong

address: 253 Gongye Middle Ave

institute: Zhujiang Hospital

summary: To explore effect of medium-chain triglyceride KD (MCT-KD) in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD mouse model, we profiled substantia nigra pars compacta tissues from control group, MPTP group and MPTP + KD mice by RNA sequencing (RNA-seq).

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of control (Ctrl), MPTP and MPTP-KD mice.

first: Wenlong

last: Zhang

first: Shiyu

last: Chen

first: Xingting

last: Huang

first: Lingli

last: Lu


title: BRD4 inhibition sensitizes diffuse large B-cell lymphoma cells to ferroptosis

city: Münster

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

summary: Diffuse large B-cell lymphoma (DLBCL), the most common form of non-Hodgkin lymphoma, is characterized by an aggressive clinical course. In approximately one-third of DLBCL patients, first-line multi-agent immunochemotherapy fails to produce a durable response. Molecular heterogeneity and apoptosis resistance pose major therapeutic challenges in DLBCL treatment. To circumvent apoptosis resistance, the induction of ferroptosis might represent a promising strategy for lymphoma therapy. Here, a compound library targeting epigenetic modulators was screened to identify ferroptosis-sensitizing drugs. Strikingly, bromodomain and extra-terminal domain (BET) inhibitors sensitized cells of the germinal center B cell-like (GCB) subtype of DLBCL to ferroptosis induction and the combination of BET inhibitors with ferroptosis inducers, such as dimethyl fumarate (DMF) or RSL3, synergized in the killing of DLBCL cells in vitro and in vivo. On the molecular level, the BET protein BRD4 was found to be an essential regulator of ferroptosis suppressor protein 1 (FSP1) expression and to thus protect GCB DLBCL cells from ferroptosis. Collectively, we identified and characterized BRD4 as an important player in ferroptosis suppression in GCB DLBCL and provide a rationale for the combination of BET inhibitors with ferroptosis-inducing agents as a novel therapeutic approach for DLBCL treatment.

overall_design: For gene expression profiling, we performed RNA-sequencing of the cell line DOHH2 after 24 hours of JQ-1 treatment at 0.250 µM, compared to solvent treated controls. Statistics investigating specific down- and upregulation were computed over four biological replicates.

first: S

last: Hailfinger

first: G

last: Lenz


title: Huaier Enhances the Antitumor Activities of Black Phosphorus and Alleviates Nephrotoxicity by Regulating Mitophagy and Autophagy

city: China

first: Shengwei

last: Jiang

address: Xueyuan road 1098

department: Shenzhen University General Hospital

institute: Shenzhen University

summary: Black phosphorus (BP) has shown promise as a nanomaterial for cancer therapy, but its nephrotoxicity limits its use. To improve BP anti-tumor effects and reduced toxic side effects, this study presents a novel approach to cancer therapy by combining BP with the traditional Chinese medicine Trametes robiniophila Murr (Huaier) to improve the treatment outcome for pancreatic cancer, a highly fatal malignancy. In 2D/3D cell lines, patient-derived organoids (PDOs) and mouse model, Huaier extraction is demonstrated to the antitumor effects of BP and mitigates BP-induced nephrotoxicity. RNA-sequencing analysis revealed that the combination of BP and Huaier enriched the mitophagy and ferroptosis pathways. While BP activates the mitophagy pathway to recycle damaged mitochondria, Huaier accelerates BP-induced mitochondrial dysfunction, leading to a mitochondrial burst and ultimately activating ferroptosis in PAAD cells. Furthermore, Huaier mitigates BP-induced nephrotoxicity and recovers cell viability by modulating the level of autophagy in proximal tubule epithelial cells. By synergizing BP with Huaier, we have achieved more potent antitumor activities with lower nephrotoxicity. These findings provide a promising strategy for treating PAAD in in vitro and in vivo models.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MIAPaCa-2 cells treated with BP or BP+Huaier

first: Huan

last: Cheng

first: Dan

last: Shi


city: Mobile

first: Justin

last: Roberts

address: 5851 USA Drive North, MSB 3370

institute: University of South Alabama

summary:
We hypothesized that PFKFB3 inhibits fructose metabolism in pulmonary microvascular endothelial cells (PMVECs) and found that PFKFB3 knockout cells survive better than wild type cells in fructose-rich media, more so under hypoxia.
Our findings indicate that PFKFB3 is a molecular switch that controls glucose versus fructose utilization in glycolysis and help to better understand lung endothelial cell metabolism during respiratory failure.

overall_design: We performed RNA-seq on wild-type and PFKFB3 knockout cells after 24 hours of incubation in glucose or fructose media, in both normoxic and hypoxic conditions.

middle: T

first: Ji

middle: Y

last: Lee


title: Embryonic renal tumor cells sensitive to the small molecule inhibitor QC6352 display depletion of KDM4 levels and disruption of ribosome biogenesis-associated pathways

city: MEMPHIS

first: Andrew

middle: Jackson

last: Murphy

state: TN

address: 262 DANNY THOMAS PLACE, MS 133 DEPARTMENT OF SURGERY

department: Surgery

institute: St. Jude Children's Research Hospital

summary: To investigate the effects of the KDM4 inhibitor QC6352 on embryonic renal tumor cells, we treated WiT49 anaplastic Wilms tumor cells and tumor-forming HEK293 human embryonic kidney cells with 25 nM QC6352 for 72 hours

overall_design: We performed differential gene expression analysis using data obtained from RNA-seq

middle: J

first: Prahalathan

last: Pichavaram


title: GDF15-GFRAL orchestrates glutathione synthesis via NRF2-elicited GCLC activation to impedes cuproptosis

city: Beijing

first: Yabing Nan

last: Yabing Nan

address: 17 Panjiayuan Nanli, Chaoyang Diistrict

institute: Cancer Hospital Chinese Academy of Medical Sciences

summary:
This study identified a non-canonical function of GDF15-GFRAL pathway that plays oncogenic roles and modulates cuproptosis by mediating GSH addiction in SCC.
To identify the critical regulatory of cuproptosis, we performed RNA-seq in parental and DTP (EC) cells.

overall_design: RNA-seq of parental and drug tolerant persister (DTP) KYSE450 cells

first: Yabing


title: Expression data of glutathione-fed Arabidopsis thaliana

city: Kibichuo

first: Kenji

last: Henmi

state: Okayama

address: 7549-1 Yoshikawa

institute: Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Research Institute for Biological Sciences

summary: To comprehensively investigate the effects of glutathione on the gene expression, the microarray analysis was performed in the glutathione-fed wild-type Arabidopsis thaliana.  Wild-type Arabidopsis (ecotype Columbia-0) were fed with 1 mM oxidized glutathione (GSSG) and 2 mM reduced glutathione (GSH) for comparison at equal nitrogen equivalents. To examine the effects of glutathione other than nitrogen at equal nitrogen equivalents, plants were fed with 3 mM NH4NO3. Plants grown by water were used as a control.

overall_design: From the first week to the fifth week after sowing, a 25 ml of 1 mM oxidized glutathione (GSSG), 2 mM reduced glutathione (GSH) and 3 mM NH3NO4 aqueous solution per pot were applied by subirrigation once a week. Plants grown by water were used as control. The aerial parts including the shoot apical were harvested 3 weeks after sowing, and the second and third leaf blades from the top of the fully expanded leaves were harvested 4 and 5 weeks after sowing. Twelve samples. Two replicates for each samples.

first: Aya

last: Hatano-Iwasaki

first: Ken’ichi

last: Ogawa


title: RNAPII-dependent ATM signaling at collisions with replication forks [DSBCapture]

city: Tübingen

first: Elias

last: Einig

address: Otfried-Müller Straße 14

department: Medical Oncology and Pulmonology

institute: University Hospital Tübingen

summary: Deregulation of RNA Polymerase II (RNAPII) by oncogenic signaling leads to collisions of RNAPII with DNA synthesis machinery (transcription-replication conflicts, TRCs). TRCs can result in DNA damage and underlie genomic instability in tumor cells. Here we provide evidence that elongating RNAPII promotes activation of the ATM kinase at TRCs to drive DNA repair. We show the ATPase Wrnip1 that binds and protects stalled replication forks, associates with RNAPII and limits ATM activation. Wrnip1 binding to elongating RNAPII requires catalytic activity of the ubiquitin ligase Huwe1. Mutation of Huwe1 promotes the transfer of Wrnip1 onto replisome and induces TRCs stimulating ATM activation on RNAPII. This mechanism is evoked early upon replicative stress to induce Wrnip1 translocation and ATM signaling at TRCs. Thus, although primarily considered as genotoxic events, TRCs can provide a mechanism to maintain genome stability under replicative stress.

overall_design: DSBCapture in HCT116 cells harbouring the HUWE1 control (HUWE1-WT) or C4341S (HUWE1-CS) sequence expressing shCtrl or shWRNIP1.

first: Nikita

last: Popov


title: Effect of TWIST1 overexpression on human mesenchymal stem cell (MSC) gene expression.

city: Jupiter

first: Christopher

middle: Lee

last: Haga

state: Florida

address: 130 Scripps Way, BldgA261A

department: Molecular Medicine

institute: UF Scripps Biomedical Research

summary: To investigate the effects of TWIST1 expression on mesenchymal stem cells, we established a retrovirally transduced MSC line overexpressing TWIST1.

overall_design: Comparative gene expression analysis of TWIST1 overexpressing MSCs versus empty vector control MSCs

middle: L

first: Cori

last: Booker

first: Donald

last: Phinney


title: Analysis of gene-targeted DNA methylation patterns through the annual cycle in clonal epitypes of Norway spruce

city: Ås

first: Igor

last: Yakovlev

state: --- Select a state ---

address: Hogskoleveien 8

country: Norway

institute: Norwegian Institute of Bioeconomy Research

type: Methylation profiling by high throughput sequencing

summary: Main goal of the study is to distinguish stable DNA methylation differences from dynamic changes during the annual cycle in different epitypes. We examined whether the extant epigenetic marks created during embryogenesis under EpI-temperature conditions are maintained in the resulting epitype trees. We used unique well-defined clonal epitypes with a stable epigenetic memory of the temperature sum experienced during embryogenesis impacting bud phenology. Due to the massive size of the Norway spruce genome (Nystedt et al., 2013), we used a targeted approach to address the DNA methylation status at a single-base resolution in specific target gene regions of selected genes involved in the epigenetic machinery and adaptive traits formation. From these we have characterized DNA methylation patterns in apical buds for 10 time points throughout the year to observe the differences between epitypes and its dynamics through the annual cycle of development.

overall_design: 60 pooled captured bisulfite-converted DNA libraries were sequenced at the BGI Genomics (Hong Kong, China) using DNBSEQ (G-400) sequencing platform with 150PE with 40% in lane control sequencing.

first: Torstein

last: Tengs

first: Marcos

last: Somoano

first: Jorunn

middle: E

last: Olsen

first: Carl

last: Fossdal


title: Effect of depletion of FOXO3A on gene expression  of U-937 cells

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

summary:
To explore the underlying molecular mechanisms of FOXO3A-regulated AML cell function
To determine the impact of FOXO3A deficiency on AML cells, we generated knock-out (KO) cells of FOXO3A using small guide RNAs (sgRNAs)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U-937 cells and its KO derivatives (sgFOXO3A).


title: Genome-wide Maps of FOXO3A in leukemia cells.

summary: To explore the underlying molecular mechanisms of FOXO3A-regulated AML cell function

overall_design: To search the direct targets of FOXO3A, we profiled the genome-wide FOXO3A binding site utilizing FOXO3A Cleavage Under Targets and Tegmentation (CUT&Tag) strategy.


title: Transcriptomic changes in aortic endothelial cells and heart tissue in Hmox2-/- mice.

city: Chicago

first: Rengul

last: Cetin-Atalay

address: 5841 S. Maryland Avenue

institute: The University of Chicago

summary: Hemeoxygenase 2 (Hmox2-/-) plays key roles in oxygen sensing in carotid body and  exhibit spontaneous apneas during sleep and elevated levels of catecholamines. Here  we investigated the transcriptomic changes with RNA-sequencing in aortic ECs and heart tissue to understand the changes that occur in Hmox2-/- mice.

overall_design: Matched pair of aortic EC and Heart Tissue from Hmox2+/+ and Hmox2-/- mice

first: Gokhan

middle: M

last: Mutlu

first: Angelo

last: Meliton

first: Kaitlyn

last: Sun


title: RNAPII-dependent ATM signaling at collisions with replication forks [DSB]

overall_design: DSBCapture experiments in HCT116 cells treated with hydroxyurea (HU) and/or CdK9 inhibitor AZD4573.


title: RNAPII-dependent ATM signaling at collisions with replication forks [CUT&RUN]

overall_design: CUT&RUN experiment using a WRNIP1 antibody in HUWE1-WT (WT) and HUWE1-CS (CS) cells.


title: Tregs promote benefitial effects of exercise by reining in interferon-mediated damage to muscle mitochondria

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Exercise is a salubrious activity: it enhances physical performance and reduces the risk of modern afflictions such as cardiovascular disease, type 2 diabetes, and cancer. Exercise characteristically incites an inflammatory response, notably in skeletal muscles. While some key innate and adaptive effector immunocytes have been identified, counteracting regulatory elements remain obscure. We have addressed the roles of Foxp3+CD4+ regulatory T cells (Tregs) in the healthful activities of exercise via immunologic, transcriptomic, histologic, metabolic, and biochemical analyses of acute and chronic exercise models. Exercise rapidly induced expansion of the muscle Treg compartment, thereby guarding against over-exuberant production of interferons and consequent metabolic disruptions, particularly mitochondrial aberrancies. Importantly, typical performance enhancements resulting from exercise training were dampened in the absence of Tregs. Thus, exercise is a natural Treg booster with therapeutic potential in disease and aging contexts.

overall_design: To study the importance of immunomodulation, in particular Treg functions, to muscle transcriptional responses to exercise, mice were acutely exercised (Exer) or exercise-trained (EXT), and tibialis anterior (TA) and/or quadriceps (Qd) muscles were dissected and homogenized in TRIzol for RNA isolation, library construction, and whole-tissue RNA-seq. Exercised muscles were compared to muscles of sedentary (SED) controls. For loss-of-function experiments, Foxp3-expressing cells (i.e. Tregs) were punctually or continuously depleted via diphtheria toxin (DT)-mediated ablation of in Foxp3-IRES-GFP.hDTR (Foxp3DTR+). To uncover the importance of excessive IFN-gamma to impaired muscle properties in contexts of Treg-deficiency and aging, Foxp3DTR+ or 24-month-old mice were injected every other day with neutralizing anti-IFN-gamma (aIFNg) antibody or IgG for one week during EXT or rest.

first: Paul

middle: K

last: Langston

first: Diane

last: Mathis


title: Genomic context mediates position-dependent enhancer function at the Sonic hedgehog locus

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

institute: Berlin Institute of Health

summary: Enhancers can regulate their target promoters over large genomic distances for which spatial proximity between these elements is assumed to be necessary. Topologically Associating Domains (TADs) are thought to provide such a spatial environment for regulatory domains harboring multiple enhancers driving complex expression of developmental genes. However, how enhancer position within the TAD affects its function in vivo is not known. Here, we address this question by generating a series of genome-engineered mouse lines in which we systematically reposition the limb enhancer of Sonic hedgehog (Shh), ZRS, to various positions within and outside of its TAD to analyze positional effects on gene expression, chromatin folding, and limb phenotype. We find that the enhancer activates Shh only when located within the same TAD, however, its activity varies across intra-TAD positions. ZRS-driven Shh expression drops rapidly with increasing distance from the promoter but eventually plateaus irrespective of linear distance. Moreover, engineering of 3D enhancer-promoter contacts through integration of different CTCF sites reveals that increased contact frequencies do not directly translate into increased transcriptional output and may cause undesired consequences in vivo due to detrimental effects on Shh expression in other tissues. Finally, we show a selective ability of the ZRS enhancer to activate non-target genes in ectopic TADs. Our work highlights the importance of genomic context within TADs for enhancer function and our limited understanding of the interplay between regulatory sequences within these domains.

overall_design: Capture Hi-C experiments from wildtype and mutant E10.5 mouse limb buds

first: Despang

last: Alexandra

first: Schöpflin

last: Robert

first: Ibrahim

last: Daniel Murad


title: RNAPII-dependent ATM signaling at collisions with replication forks [RNA-seq]

first: Elias

last: Einig

overall_design: Comparative gene expression profiling analysis using RNA-seq for parental HCT116 cells (P), HUWE1-WT (WT) and HUWE1-CS (CS) cells.

first: Nikita

last: Popov


title: Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury.

city: Morgantown

first: Kate

last: Karelina

state: WV

address: 108 Biomedical Rd BMRC 322

department: Neuroscience

institute: West Virginia University

summary: In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males.

overall_design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000.

first: Brishti

middle: A

last: White

first: Julia

last: Ivey

first: Ruth

last: Velazquez-Cruz

first: Robin

last: Oliverio

first: Bailey

last: Whitehead

first: Mark

last: Pinti

first: John

last: Hollander

first: Li

last: Ma

first: Gangquin

last: Hu

first: Zachary

last: Weil


title: RNAPII-dependent ATM signaling at collisions with replication forks [ChIP-seq]

overall_design: ChIPseq analysis of indicated target proteins in HUWE1-WT (WT) and HUWE1-CS (CS) cells expressing a control shRNA or an shRNA targeting WRNIP1.


title: Small RNA sequencing of DROSHA-KO HCT116 cells transfected with DROSHA wild type and mutants

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

summary: The experiments were conducted to examine the effects of DROSHA mutations on miRNA biogenesis

overall_design: Small RNA sequencing libraries of the transfected DROSHA-KO HCT116 cells were generated using the NEBNext Small RNA Library Prep Set for Illumina kit.

first: Tuan

last: Anh Nguyen

first: Trung

last: Duc Nguyen

first: Thuy

last: Linh Nguyen


title: SoxC transcription factors shape the epigenetic landscape to establish competence for sensory differentiation in the mammalian organ of Corti

city: Los Angeles

first: Neil

last: Segil

state: CA

address: 1425 san pablo st, 503

department: DSR

institute: University of Southern California

summary: Understanding the molecular basis of competence acquisition by the lineage-specific progenitor cells can provide mechanistic insights into tissue development and regeneration. The sensory epithelium of the inner ear represents a convenient model to study this process, as only two cell types – the mechanosensory hair cells and their associated supporting cells – are specified from a single pool of progenitors in this lineage. Here we show that competence to respond to Atoh1, a transcriptional master regulator both necessary and sufficient for induction of mechanosensory hair cells, is established in the organ of Corti progenitor cells between E12.0 and 13.5. The transition to the competent state is rapid and is associated with extensive remodeling of the epigenetic landscape controlled by the SoxC group of transcription factors. Conditional loss of Sox4 and Sox11 – the two homologous family members transiently expressed in the inner ear at the time of competence establishment – blocks the ability of sensory progenitors to differentiate into hair cells. Mechanistically, we show that Sox4 binds to and establishes accessibility of early sensory lineage-specific regulatory elements, including ones associated with Atoh1 itself and its direct downstream targets. Consistent with these observations, overexpression of Sox4 or Sox11 prior to developmental establishment of competence precociously induces hair cell differentiation in the cochlear progenitors. Further, reintroducing Sox4 or Sox11 expression restores the ability of postnatal supporting cells to differentiate as hair cells in vitro and in vivo. Our findings demonstrate the pivotal role of SoxC family members as agents of epigenetic and transcriptional changes necessary for establishing competence for sensory receptor differentiation in the inner ear.

overall_design: 1. Cochlear duct epithelia from E13.5 wildtype and SoxC conditional double knockout animals were collected and analyzed using scRNA sequencing (10x);   2. ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) for cochlear duct epithelia from E13.5 wildtype and SoxC conditional double knockout animals;  3. Cut & Run ChIP-seq (Chromatin immunoprecipitation DNA-sequencing) for Sox4 transcription factor in FACS sorted E13.5 p27kip1 positive cochlea progenitor cells

first: Xizi

last: Wang

first: Litao

last: Tao

first: Talon

last: Trecek

first: Juan

last: Llamas

first: Welly

last: Makmura

first: Ksenia

last: Gnedeva


title: PDK1 coordinates mitochondrial dynamics and mitophagy to ensure mitochondrial maturation in post-natal cardiomyocytes

city: Nanjing

first: Wukui

last: Zhao

address: Hankou Road 22nd

institute: Nanjing University

summary: During early post-natal stage, cardiomyocytes undergo dramatic structural, metabolic, electrophysiological and cell cycle alterations towards maturation. Among them, the metabolic shift from carbohydrates to fatty acids metabolism is achieved along with mitochondrial biogenesis, dynamic switch and mitophagy. However, the regulatory mechanisms responsible for coordinated mitochondrial dynamics and mitophagy in mitochondrial maturation remain unclear. Here, we found that ablation of PDK1 in post-natal cardiomyocytes impairs mitochondrial maturation and metabolism, characterizing by arrest of mitochondria in neonatal stage, low levels of a subset of fatty acids and acylcarnitines. In addition, loss of PDK1 results in dysregulated mitochondrial dynamics and mitophagy. An imbalance of the AMPK-mTOR pathway and reduced phosphorylation of PDK1 substrates, including PKA and PKC family members, are observed. These results demonstrated that PDK1 ensures mitochondrial maturation and metabolic shift through kinase-dependent substrate phosphorylation and maintenance of the AMPK-mTOR axis to coordinate mitochondrial dynamics and mitophagy.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of wild type mouse heart at P0, P7 and P21, and PDK1 cKO hearts at P7 and P21.

first: Caoyu

last: Ji

first: Shan

last: Yu

first: Zhongzhou

last: Yang


title: Chromosome-level organization of the regulatory genome in the Drosophila nervous system [scRNA-seq]

city: Lausanne

first: Maria Cristina

last: Gambetta

address: Genopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

summary: We present evidence for a new level of genome folding, whereby distant domains megabases apart fuse to form meta-domains. Within meta-domains, certain gene promoters pair with structural intergenic elements in the distant TAD. These long-range associations occur in a large fraction of Drosophila neurons, but support transcription in only a subset of cells in the nervous system. Most of the associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. We used single cell RNA sequencing (scRNA-seq) to analyze gene misexpression genotypes after deleting intergenic meta-loop anchors.

overall_design: Drosophila melanogaster third instar larval central nervous systems (CNS) of wildtype animals or animals homozygous for a precise deletion of an intergenic meta-loop anchor were dissected and analyzed by scRNA-seq.

first: Giriram

last: Mohana

first: Julien

last: Dorier

first: Xiao

last: Li

first: Héléna

last: Malek

first: Marion

last: Leleu

first: Daniel

last: Rodriguez

first: Patrycja

last: Rosa

last: Mouginot

first: Pascal

last: Cousin

first: Christian

last: Iseli

first: Simon

last: Restrepo

first: Nicolas

last: Guex

first: Michael

middle: S

last: Levine

first: Aleksander

last: Jankowski

first: Maria

middle: C


title: The high-throughput pri-miRNA cleavage assays on 262144 variants

first: Duc

last: Nguyen

summary: Microprocessor (MP), DROSHA-DGCR8, processes primary miRNA transcripts (pri-miRNAs) to initiate miRNA biogenesis. The canonical cleavage mechanism of MP has been extensively investigated and comprehensively validated for two decades. However, this canonical mechanism cannot account for the processing of certain pri-miRNAs in animals. In this study, by conducting high-throughput pri-miRNA cleavage assays for approximately 260,000 pri-miRNA sequences, we discovered and comprehensively characterized a noncanonical cleavage mechanism of MP. This noncanonical mechanism does not need several RNA and protein elements essential for the canonical mechanism; instead, it utilizes previously unrecognized DROSHA dsRNA recognition sites (DRES). Interestingly, the noncanonical mechanism is conserved across animals and plays a particularly significant role in C. elegans. Our established noncanonical mechanism elucidates MP cleavage in numerous RNA substrates unaccounted for by the canonical mechanism in animals. This study suggests a broader substrate repertoire of animal MPs and an expanded regulatory landscape for miRNA biogenesis.

overall_design: ~260,000 pri-miRNA sequences were processed by D3∆belt-G2 or D3∆belt-G1-G4-dimer in vitro. The DNA dictionary, RNA original substrates, RNA cleaved products were cloned and sequenced.

first: Tuan

last: Anh Nguyen

first: Trung

last: Duc Nguyen

first: Thuy

last: Linh Nguyen


title: Chromosome-level organization of the regulatory genome in the Drosophila nervous system

first: Maria Cristina

last: Gambetta

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

sample_organism:
Drosophila melanogaster
Drosophila virilis

overall_design: Refer to individual Series


title: RNAPII-dependent ATM signaling at collisions with replication forks

first: Elias

last: Einig


title: mTOR signaling pathway and targeting c-myc

city: 武汉

first: Yu

last: Hua

state: State...

address: 武汉大学医学部1舍2单元

institute: 武汉大学

summary:
Purpose: To investigate the tumor-promoting role of STIL in bladder cancer.
Method: We established the STIL knockout cell line in which the target gene was knocked out by sgRNA. RNA was extracted from cells using trizol reagent(Invitrogen)
Result: Through RNA-sequencing analysis of wild-type and STIL-deficient UMUC3 cell lines, the downstream signaling pathways that STIL may be involved in were determined. We found that the PI3K/AKT/mTOR signaling pathway and c-myc were significantly inactivated when STIL was knocked out in bladder cancer. Our RNA-sequencing analysis results showed that the downstream molecules of c-myc (MCM4, HSPD1, EIF2S2, DDX21, DDX18, CBX3, ABCE1) were significantly down-regulated in bladder cancer cells after knockout.
Conclusion: STIL enhances the PI3K/AKT/mTOR pathway, which consequently upgraded the expression of c-myc, ultimately promoting the occurrence and progression of bladder cancer C. STIL may suggest potential utility for bladder cancer therapy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for UMUC3 cells  (sgSTIL).

first: Hua

last: Yu

first: Feng

last: Tang

first: Tao

last: Liu

first: Jianping

last: Peng


title: Identification of BMP3b as a cardioprotective adipokine released by brown adipose tissue.

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Brown adipose tissue (BAT) has metabolic and endocrine effects to the whole-body, secreting molecules that target different tissues. Using transcriptomic analysis from isolated BAT from mice treated with isoproterenol in WT or UCP1-knockout mice, which have disfunctional BAT, we identified Bmp3b as an adipokine produced and secreted by activated BAT.

overall_design: To determine the activation of brown adipose tissue from isoproterenol-treated or saline-treated in WT and Ucp1-knockout mice. In these studies mice were implanted with Alzet minipumps for the infusion of isoproterenol (60 mg/kg/day for 3 days) to activate BAT.  WT and Ucp1-/- mice with minipumps infusing saline were used as controls. 3 days after minipumps implatantation, mouse brown adipose tissues were isolated to generate respective libraries for genome profiling.

first: Robrecht

last: Thoonen

first: Ingrid

last: Marti-Pamies

first: Marielle

last: Scherrer-Crosbie


title: HLA-DR is absent in primitive macrophages through epigenetic silencing of master regulator CIITA

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

summary: The earliest macrophages are generated during embryonic development from erythro-myeloid progenitors (EMPs) via primitive haematopoiesis. This process is poorly understood in humans and in the mouse is thought to be spatially restricted to the yolk sac. Human fetal placental macrophages, Hofbauer cells (HBC), arise during the primitive haematopoietic wave at ~18 days post conception. Here we identify a population of placental erythro-myeloid progenitors (PEMPs) in the early human placenta that give rise to HBC. PEMP are fetal CD34+CD43+ progenitors found exclusively at early gestational timepoints. Transcriptomic analyses reveal that PEMP have conserved features of primitive yolk sac EMPs, including the lack of HLF expression. Using in vitro single-cell culture experiments we show that PEMP generate HBC-like cells that completely lack HLA-DR expression  and demonstrate that this is a conserved feature of all macrophages generated by primitive haematopoiesis in humans. Finally, we demonstrate that the class II transactivator, CTIIA, the master regulator HLA-DR expression, is epigenetically silenced during primitive haematopoiesis, leading to HLA-DRneg macrophages. These findings demonstrate that HBC are derived locally from PEMP and establish the human placenta as an additional site of primitive haematopoiesis.

overall_design:
In this study we characterise CD34+CD43+ progenitors in human placental villi. We find that these placental CD34+CD43+ progenitors have conserved features with yolk sac erythro-myeloid progenitors (EMP), including a lack of HLF expression, a defining feature of EMP. Hence, we termed placental CD34+CD43+ progenitors, as placental EMP (PEMP).  We subsequently show that PEMP differentiate into primitive HLA-DRneg HBC-like macrophages in vitro. Finally, wWe demonstrate that a conserved feature of human primitive macrophages across embryonic tissues, as well as extra-embryonic tissues, is a complete of lack of expression of HLA Class II molecules. Analysis of methylation status of the class II transactivator, CTIIA,   reveals that CTIIA promoter is epigenetically silenced in primitive macrophages during the first trimester of pregnancy. With timeAs pregnancy progresses, primitive macrophages begin to express HLA-DR. Our data suggests that there is an erosion of epigenetic silencing throughout gestation, underpinnings the observed transition of HBC from an HLA-DRneg to HLA-DRpos state.

>>>Submitter states that raw data for this study are not publicly available due to patient privacy concerns. Raw data will be submitted for restricted access at EGA.<<<

first: Courtney

last: Hanna

first: Naomi

last: McGovern


title: Integrated analysis of transcriptome and small RNAome reveals the regulatory network for rapid growth in Mikania micrantha [sRNA-seq]

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

summary: M. micrantha has caused huge ecological damage and economic losses worldwide due to its rapid growth and serious invasion. However, the underlying molecular mechanisms of its rapid growth and environmental adaption remain unclear. Here, we performed transcriptome and small RNA sequencing with five tissues of M. micrantha to dissect miRNA-mediated regulation in M. micrantha. WGCNA and GO enrichment analysis of transcriptome identified the gene association patterns and potential key regulatory genes for plant growth in each tissue. The genes highly correlated with leaf and stem tissues were mainly involved in the chlorophyll synthesis, response to auxin, the CAM pathway and other photosynthesis-related processes, which promoted the fast growth of M. micrantha.  Importantly, we identified 350 conserved and 192 novel miRNAs, many of which displayed differential expression patterns among tissues. PsRNA target prediction analysis uncovered target genes of both conserved and novel miRNAs, including GRFs and TCPs, which were essential for plant growth and development. Further analysis revealed that miRNAs contributed to the regulation of tissue-specific gene expression in M. micrantha, such as mmi-miR396 and mmi-miR319. Taken together, our study uncovered the miRNA-mRNA regulatory networks and the potential vital roles of miRNAs in modulating the rapid growth of M. micrantha.

overall_design: Integrated analysis of transcriptome and small RNAome for M. micrantha flower, leaf, shoot apex, stem, and root tissues

first: Xiaowei

last: Mo

first: Haolang

last: Chen

first: Xiaolan

last: Yang

first: Beixin


title: Integrated analysis of transcriptome and small RNAome reveals the regulatory network for rapid growth in Mikania micrantha [RNA-seq]


title: Integrated analysis of transcriptome and small RNAome reveals the regulatory network for rapid growth in Mikania micrantha


title: Metabolomic and transcriptomic analyses identify quinic acid protecting eggplant from damage caused by western flower thrips

city: Baoding

first: yajing

address: Le Kai Nan StreetBaoding

department: College of Horticulture

institute: Hebei  Agricultural University

summary:
BACKGROUND: Western flower thrips are considered the major insect pest of horticultural crops worldwide, causing economic and yield loss to Solanaceae crops. The eggplant (Solanum melongena L.) resistance against thrips remains largely unexplored. This work aims to identify thrips-resistant eggplants and dissect the molecular mechanisms underlying this resistance using the integrated metabolomic and transcriptomic analyses of thrips-resistant and -susceptible cultivars.
RESULTS: We developed a micro-cage thrips bioassay to identify thrips-resistant eggplant cultivars, and highly resistant cultivars were identified from wild eggplant relatives. Metabolomic profiles of thrips-resistant and -susceptible eggplant were compared using the gas chromatography-mass spectrometry (GC-MS)-based approach, resulting in the identification of a higher amount of quinic acid in thrips-resistant eggplant compared to the thrips-susceptible plant. RNA-sequencing analysis identified differentially expressed genes (DEGs) by comparing genome-wide gene expression changes between thrips-resistant and -susceptible eggplants. Consistent with metabolomic analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs revealed that the starch and sucrose metabolic pathway in which quinic acid is a metabolic by-product was highly enriched. External application of quinic acid enhances the resistance of susceptible eggplant to thrips.
CONCLUSION: Our results showed that quinic acid plays a key role in the resistance to thrips. These findings highlight a potential application of quinic acid as a biocontrol agent to manage thrips and expand our knowledge to breed thrips-resistant eggplant.

overall_design: The RNAseq data from three biological replicates for thrip-resistant and -susceptible eggplants after feeding at 0 h, 4 h, 8 h, 12 h, 24 h and 48 h(36samples)

first: Yajing

first: Xuan

last: Wang

first: Xueping

first: Aixia

last: Gu

first: Wei

last: Ma


title: Inhibition of phospholipase D1 ameliorates NAFLD by reducing PPARγ/CD36 pathway mediated lipid accumulation in hepatocytes

city: Beijing

first: Huan

address: Yongan RD

institute: Capital Medical University

summary:
Objective：Phospholipase D1 (PLD1), a phosphatidylcholine-hydrolyzing enzyme, has been found to be involved in cellular lipid metabolism. However, how PLD1 involves in hepatocyte lipid metabolism and thus affects non-alcoholic fatty liver diseases (NAFLD) has not been explicitly explored.
Method: NAFLD is induced in hepatocyte-specific Pld1 knockout (Pld1(H)-KO) mice or control (Pld1-Flox) mice with a high fat diet (HFD) for 20 weeks. Plasma glucose and lipid levels, liver lipid and function parameters and inflammation- and fibrogenesis-related gene expression levels were studied. Changes in lipid composition of liver were detected by lipidomic analyses. Changes in gene expression profile were detected by mRNA sequencing. In vitro, alpha mouse liver 12 (AML12) cells were incubated with sodium palmitate (SP) to explore the mechanisms of PLD1 on development of NAFLD. The protein levels of PLD1 and CD36 were detected in the liver tissues of NAFLD patients. Finally, the therapeutic effect of NAFLD by inhibiting PLD with 5-Fluoro-2-indolyl deschlorohalopemide (FIPI) was examined.
Results: PLD1 expression levels were increased in the liver tissues of NAFLD patients and the hepatocytes of HFD-induced mice. Compared with Pld1-Flox mice, Pld1(H)-KO mice exhibited lower plasma glucose and lipids levels, and decreased lipid accumulation, inflammation and fibrosis related gene expression levels in the liver tissues after HFD feeding. Inhibition of hepatocyte PLD1 significantly altered lipid composition, especially phosphatidic acids (PA) and lyso-PAs (LPA) levels in the liver tissues after NAFLD. Transcriptomic analysis showed that hepatocyte specific deficiency of PLD1 mainly decreased CD36 expression levels in the NAFLD liver tissues, which was confirmed at the protein and gene expression levels. In vitro, inhibition of PLD1 markedly decreased CD36 expression and lipid accumulation in SP treated AML12 cells. Furthermore, PA, the downstream product catalyzed by PLD1, increased the expression levels of CD36 and lipid accumulation in vitro, which was reversed by PPARγ antagonist. These suggested that PPARγ played an important role in transcriptional regulation of CD36 expression after PA stimulation. Finally, PLD inhibitor FIPI had significant therapeutic effect on HFD-induced NAFLD.
Conclusion: Hepatocyte-specific deficiency of PLD1 ameliorates lipid accumulation and NAFLD development by inhibiting PPARγ/CD36 pathway conducted by PA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver of  hepatocyte-specific Pld1 knockout (Pld1(H)-KO) mice or control (Pld1-Flox) mice with a high fat diet (HFD) for 20 weeks.

first: Yushang

last: Zhao

first: Yuhualei

last: Pan

first: Aiting

first: Changying

last: Li

first: Song

first: Zhao

last: Dong

first: Guangyong

last: Sun

first: Yanbing

last: Zhu

first: Dong

last: Zhang


title: T Cell Intrinsic Responses to TGFβ Regulates Allergen Sensitization By Modulating Type 2 T Follicular Helper Cell Development

city: Bethesda

first: Tamara

last: Haque

state: MD

address: 10 Center Drive

institute: NIAID

summary: Immunoglobulin E (IgE) is a potent mediator of allergic diseases, but the mechanisms that regulate IgE responses to innocuous environmental and food antigens remain unclear. Patients with Loeys-Dietz syndrome (LDS) who have mutations in genes encoding the TGFβ receptor are predisposed to IgE-mediated disorders. Here, using patient samples and a mouse model, we demonstrate that LDS mutations lead to reduced canonical TGFβ signaling, elevated total and allergen-specific IgE, increased type 2 follicular helper T cells (Tfh2), and exaggerated germinal center activity that was not prevented by the presence of wild type T regulatory cells. T cell intrinsic defects in LDS mice resulted in spontaneous sensitization to orally administered OVA, and inhibition of mammalian target of rapamycin (mTOR) prevented the exaggerated Tfh and IgE responses to OVA. Thus, TGFβ limits human and mouse Tfh2 cell development via the phosphatidylinositol-3-OH kinase gamma (PI3Kg)/AKT/mTOR pathway, and disruption of this pathway promotes allergic inflammation.

overall_design: Differential expression analysis of Peyer’s patch CD4+CXCR5+PD1+ Tfh cells, Tgfbr1WT/mut vs WT littermates

first: Pamela

last: Guerrerio

first: Paul

last: Schaughency

first: Justin

last: Lack


title: Premature aging of skeletal stem/progenitor cells rather than osteoblasts causes bone loss with mechanosensation decline

city: Shanghai

first: Ruici

address: 320 Yue Yang Road

institute: Center for Excellence in Molecular Cell Science, CAS

summary: Distinct skeletal stem/progenitor cells (SSPCs) have been identified in the bone marrow, growth plate, and periosteum, which are indispensable for the maintenance and remodeling of the adult skeleton. However, the decline of which cell types are responsible for age-related bone loss and what characteristic changes of these cells during aging remain to be determined. Here, we constructed premature skeletal aging models by depleting metalloproteinase Zmpste24 (Z24) in mice and found that  Prx1-dependent, but not Osx-dependent, Z24 deletion caused significant bone loss. Single-cell RNA sequencing (scRNA-seq) revealed that Prx1-expressing cells in the periosteum (pSSPCs) and growth plate (gpSSPCs) significantly declined in progeria mice. Consistent with aggrecan (Acan) expression in gpSSPCs but not pSSPCs, Acan-linked Z24 depletion only caused trabecular bone loss. Chromatin and transcriptional profiling demonstrate that premature aged SSPCs gain apoptotic signaling pathway and mechanosensation decline. Moreover, SSPCs increased after physical exersice and Z24 depletion’s effects on cellular apoptosis and extracellular matrix expression were reverted by mechanical stimuli. Overall, this study identifies that Z24 deficiency-induced impairment of mechanosensation in SSPCs causes bone loss, shedding new insight on how physical exercise can be used to improve bone quality and prevent bone aging.

overall_design: Medium-intensity treadmill exercise was performed for 5 weeks at 8-week-old.Then bones of 13-week-old  exercised and sedentary mice after bone marrow was flushed were collected and ground with liquid nitrogen to extract the RNA.

first: Weiguo

last: Zou

first: Rui

last: Yue

first: Dandan

last: Cao


title: Single cell transcriptome of the mouse larynx

city: Madison

first: Zijian

last: Ni

address: 425 Henry Mall

institute: University of Wisconsin-Madison

summary: Microbiota play a critical role in training and development of major components of host innate and adaptive immune system. We present the cellular landscape of the upper airway, specifically the larynx, by establishing a reference single-cell atlas and dissected the role of microbiota in laryngeal cell development and functions at a single-cell resolution by comparing the transcriptomes of conventionally raised and germ-free mouse larynges.

overall_design: Single cell suspension of the mouse larynx was prepared for conventionally raised and germ-free mice and sequenced and analyzed following 10x genomics pipeline.

first: Ran

last: An

first: Yixuan

last: Xie

first: Federico

last: Rey

first: Christina

last: Kendziorski

first: Susan

last: Thibeault


title: A single-cell transcriptomic atlas of A. thaliana seed germination

city: Heidelberg

first: Quentin

last: Gouil

state: VIC

address: Studley Road

country: Australia

institute: Olivia Newton-John Cancer Research Institute

summary: Time-series single-cell transcriptome

overall_design: Duplicates of germinating seeds at three time points, dissociated into single cells. Triplicate of bulk controls at the same time points to account for dissociating treatment

first: Lim

last: Liew

first: Yue

last: You

first: Mathew

middle: G

last: Lewsey


title: Whole transcriptome analysis of human kidney cells after treatment with or without phosphoramidon

city: Taipei city

first: Hung-Jin

last: Huang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Taipei medical university

summary: The mechanism of autophagy can be triggered by phosphoramidon to ameliorate kidney fibrosis and inflammation. The precise targets of fibrosis and inflammation in chronic kidney disease (CKD) need further investigation. The purpose of this project is to development of potential therapeutic drugs for CKD treatment. The therapeutic targets might be identified from cellular signaling induced by phosphoramidon in the human kidney proximal tubular epithelial cell line (HK-2 cells).

overall_design: RNA sequencing of human kidney proximal tubular epithelial cell line (HK-2 cells) after treatment with phosphoramidon for 24 hours.

first: Yu-Jhe

last: Chiu

first: Hui-Wen


title: the peptide PDTLN1 induces the expression of a set of genes in P19 cells

first: Boshi

last: Yu

state: Please choose a State

address: No. 123 Tian Fei Xiang, Mo Chou Road, Nanjing 210004, Jiangsu Province, China

department: Pediatrics

institute: Womenʼs Hospital of Nanjing Medical University

summary:
In the present study, we disclose a new polypeptide corresponding to the sequence of human Talin-1 protein (named PDTLN1), which is highly expressed both in myocardial tissue and maternal peripheral blood of aborted fetuses with congenital heart disease (CHD).
The results shown that PDTLN1, but not the scrambled version, caused cardiac developmental defects in zebrafish and inhibited cellular viability, proliferation and promoted apoptosis of P19 cells via the inhibition of PI3K/AKT signaling pathway.
Our search may be helpful in gaining fresh perspective on the functions of human derived peptides and promote the detection of a novel class of diagnostic biomarkers in CHD. Further, to seek-and-find new targets for therapeutic intervention in CHD.

overall_design: Identification of differentially expressed mRNAs after PDTLN1 treatment in P19 cells

first: Shuwen

last: Yao

first: Linjie

last: Liu

first: Huimin

last: Li

first: Jingai

last: Zhu

first: Mengmeng

first: Shuping

last: Han

first: Zhangbin


first: Eric

last: Dang

state: Maryland

address: 9000 Rockville Pike

department: NIAID

institute: NIH

overall_design: The M318R allele previously identified in LDS patients was knocked into the mouse Tgfbr1 locus resulting in heterozygous TgfbrIWT/mut mice. Eight week old mice were orally gavaged once a week for 4 weeks with 5mg crude peanut extract and 10g Cholera Toxin from Vibrio cholera (Sigma) in 200uL water. One week after the last gavage, mice were bled from the submandibular cheek vein. OTII cells were purified from lymph nodes and spleen from OTII+/+RAG-/- mice that were WT or TgfbrIWT/mut, CD4+ bead purified (Miltenyi Biotec), and injected i.v. into CD45.1 WT mice. Hosts were fed water with 1.5% endotoxin-free OVA (Sigma Aldrich) for 7 days post-injection with normal mouse chow. In the rapamycin treatment experiments, mice were orally gavaged daily with vehicle or 125g rapamycin dissolved in DMSO and Kolliphor (Sigma) in a 3:1 ratio and then dissolved in water in a 1:25 ratio, on days 3-7. On day 8, the mesenteric lymph node and Peyer’s patches were collected, and smashed through 70M filters to make single-cell suspensions.

first: Tamara

last: Haque

first: Pamela

last: Guerrerio

first: Paul

last: Schaughency

first: Justin

last: Lack


title: Chromosome-level organization of the regulatory genome in the Drosophila nervous system [Hi-C]

first: Maria Cristina

last: Gambetta

summary: Here we present evidence for a new level of genome folding, whereby distant domains megabases apart fuse to form meta-domains. Within meta-domains, certain gene promoters pair with structural intergenic elements in the distant TAD. These long-range associations occur in a large fraction of Drosophila neurons, but support transcription in only a subset of cells in the nervous system. Most of the associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. Meta-domains are formed by diverse transcription factors that are able to pair over long and flexible distances. We present evidence that one of these factors, GAF, plays a direct role in this process.

platform_organism:
Drosophila melanogaster
Drosophila virilis

overall_design: Drosophila melanogaster and Drosophila virilis dissected central nervous systems (CNSs) or CNS cell types (neuroblasts, glia or neurons) isolated from staged Drosophila melanogaster embryos were subjected to Hi-C.

first: Giriram

last: Mohana

first: Julien

last: Dorier

first: Xiao

first: Héléna

last: Malek

first: Marion

last: Leleu

first: Daniel

last: Rodriguez

first: Patrycja

last: Rosa

last: Mouginot

first: Pascal

last: Cousin

first: Christian

last: Iseli

first: Simon

last: Restrepo

first: Nicolas

last: Guex

first: Michael

last: Levine

first: Aleksander

last: Jankowski

first: Maria


title: N-acetylcysteine and Vitamin C stimulate MYC binding to EGR1 and selectively stimulate apoptosis in B cell lymphoma

city: Huddinge

first: Martin

last: Bergo

address: MBE Group, Neo bldn. SE-141 83 Huddinge Sweden

department: BioNut

country: Sweden

institute: Karolinska Institutet

summary: Refractory and relapsed B cell lymphomas are often driven by MYC, a difficult-to-target oncogene due to its central role in normal transcription. Here we report that N-acetylcysteine (NAC) and vitamin C (VitC)—in doses that reduce reactive oxygen species levels levels—trigger apoptosis in human B lymphoma cells with high MYC expression. Intraperitoneal NAC and VitC injections dose-dependently reduced tumor growth in xenograft experiments, and combined NAC/VitC administration stopped tumor growth. Knockdown of MYC restored tumor growth in the presence of NAC and VitC and switching-on MYC expression in B cells rendered them sensitive to the compounds. The compounds stimulated MYC binding to Early growth response protein 1 (EGR1)—an interaction found to require Cys132 of MYC—which reduced MYC binding to promotors of cell cycle genes and increased binding to apoptotic genes; and thus, switched MYC’s transcriptional output from cell cycle to apoptosis gene expression. Short-term combined NAC/VitC administration into λMYC transgenic mice, an endogenous mouse model of B cell lymphoma, after tumor onset increased survival fourfold; and life-long oral administration of NAC and VitC stimulated apoptosis and reduced B cell progenitors in the spleen and measurably increased survival. The results provide a rationale with mechanistic understanding for evaluating the therapeutic efficacy of NAC and VitC in patients with MYC-driven B cell lymphoma.

overall_design: 2 cell lines, 3 treatments

last: Bergö


title: Gene expression profiling of response to Everolimus in a three-dimensional  (3D) model of oral mucosa

city: Miami

first: Dmitry

last: Velmeshev

state: FL

address: 1501 NW 10th ave, BRB 629

department: Psychiatry

institute: Universtiy of Miami

summary: We performed bulk RNA sequencing analysis of a 3D organoleptic model of human oral mucosa treated with everolimus. The 3D model (tissue) consisted of human normal keratinocytes grown on top of human fibroblasts and was histologically similar to buccal mucosa. The tissue was purchased from MatTek Corporation (Ashland, MA) and cultured in serum free media.  The 3D model was maintained for different times in the tissue culture (40 hours and 60 hours from the time received) and treated with different concentration of Everolimus (no drug (0 ng/ml), 32 ng/mL, 64 ng/mL).

overall_design: 3D model of oral mucosa, Everolimus treatment, bulk RNA-seq

middle: P

last: Lambros


title: RNA sequence analysis of hearts tissue after C57BL/6 mice subjected to transverse aortic constriction (TAC) and dioscin treatment

first: Zhiguang

last: Shi

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

institute: Nanjing Medical University

summary: To study the differient expression genes, heart tissues from TAC group and TAC treatment with dioscin group are performed to RNA sequence.

overall_design: Heart mRNA profiles of TAC and TAC treatment with dioscin for 4 weeks

first: Qiulun

last: Lu

first: Dayin


title: Chromosome-level organization of the regulatory genome in the Drosophila nervous system [scATAC-seq]

first: Maria Cristina

last: Gambetta

institute: University of Lausanne

summary: We present evidence for a new level of genome folding, whereby distant domains megabases apart fuse to form meta-domains. Within meta-domains, certain gene promoters pair with structural intergenic elements in the distant TAD. These long-range associations occur in a large fraction of Drosophila neurons, but support transcription in only a subset of cells in the nervous system. Most of the associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. We used single cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) to identify regions of open chromatin at single cell resolution.

overall_design: Drosophila melanogaster third instar larval central nervous systems (CNS) of wildtype animals were dissected and analyzed by scATAC-seq.

first: Giriram

last: Mohana

first: Julien

last: Dorier

first: Xiao

last: Li

last: Malek


title: Analysis of differential miRNA expression in mineralising DPCs treated with pharmacological epigenetic inhibitors.

status: Public on Jul 31 2023

city: Dublin

first: Michaela

last: Kearney

address: 2 Lincoln Place

country: Ireland

institute: Dublin Dental University Hospital

summary:
To establish a miRNA expression profile for DPCs undergoing epigenetically-mediated mineralisation, rodent DPCs were induced to mineralise and treated with a HDAC inhibitor, SAHA, and a DNMT inhibitor, 5-AZA-CdR.
RNA was then isolated from DPCs at day 4 of culture and subjected to RNA sequencing. Subsequent bioinformatic analysis identified differentially expressed miRNAs compared with untreated mineralising DPCs.

overall_design: Identification of differentially expressed miRNAs in mineralising rodent DPCs treated with epigenetic inhibitors compared with untreated mineralising DPCs and with non-mineralising DPCs.

first: Henry

middle: F

last: Duncan


title: Analysis of miRNA expression profile in unstimulated and anti-CD3 stimulated of T cells in WT and Cbl-b-/- mice

city: SUZHOU

first: Mengyun

last: Wu

address: 199 Renai Road, Industrial Park, Suzhou City, Jiangsu Province, China

institute: Soochow University

summary: In order to further explore the miRNAs expression in WT and Cbl-b-/- CD4+ T cells, we used anti-CD3 to activate CD4+ T cells, and then used microarray to detect the expression of miRNAs in unactivated and activated T cells from WT and Cbl-b-/- mice. The results showed that there were different expression of miRNAs in WT and Cbl-b-/- CD4+ T cells when activated or not.

overall_design: MiRNA profiles of unstimulated and stimulated CD4+ T cells from WT and Cbl-b-/- mice

first: Yuxu

last: Tang


title: Eviction of repressor PRC1 via RNA-binding of PHC1 promotes stress-induced transcription

city: Basel

first: Tommy

middle: Beat

last: Schlumpf

state: Basel-Stadt

address: Mattenstrasse 26

department: D-BSSE

institute: ETH Zürich

summary: Proteins of the Polycomb group (PcG) maintain cellular states through epigenetic control of gene expression. It is still heavily debated how RNAs modulate the function of these chromatin factors. To identify PcG RNA-binding proteins, we screened a library of HEK293T expressing PcG proteins for their binding potential using CLIP and PARCLIP. We find that RNA-binding is not as pervasive as suggested, but rather focused on few mostly core PcG proteins. Since the relationship between core-PRC1 and RNA has not been previously studied, we sequenced RNAs bound to PHC1, showing a 5’ enrichment at transcripts with lower expression. Drosophila mutants and overexpression of RNA-binding deficient PHC1, show binding to be essential to fast induction of response genes upon heat-shock and LPS/TNF treatment. ChIP at sequential time points reveals a lack of Polymerase S2 phosphorylation. Altogether, the RNA-PHC1-PRC1 axis aids rapid induction of immediate-early genes.

overall_design: We performed two replicates of PARCLIP on PRC1 member PHC1. From this we determined binding sites and strength in relation to two replicates of total nuclear RNA-Seq. As control, 2 replicates of RNAPII PARCLIP were used. To determine the functional mechanism of binding, we generated two replicates each of ChIP-Seq data of mutant and wt PHC1 as well as one replicate each of H3K27me3, H3K4me3, RNA Polymerase II and EZH2. All sequencing experiments were performed in HEK293T T-Rex cells.

middle: B

first: Tosca

last: Birbaumer

first: Fabienne

last: Leutwiler

first: Hind

last: Hashwah

first: Makiko

last: Seimyia

first: Renato

last: Paro


title: HDAC5 loss in pancreatic cancer induces enhanced arachidonic acid metabolism via overactivated GATA1-cPLA2 axis

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

summary: Unlike class I Histone deacetylase (HDAC) members (HDAC1, 2, 3, etc.), HDAC5, a class IIa HDAC member, is downregulated in multiple solid tumors, including pancreatic cancer, and its loss is associated with unfavorable prognosis. Additionally, HDAC5’s expression correlates negatively with arachidonic acid (AA) metabolism, which is highly implicated in inflammatory responses and cancer progression. This study aimed to elucidate the role of HDAC5 in AA metabolism and its prospect in the treatment of pancreatic cancer.

overall_design: RNA-seq were applied in BxPC-3 cells. GATA1 ChIP-seq were applied in control and HDAC5 knock-down PANC-1 cells.

first: Y

last: Zhou

first: H


title: Structural evolution of the tissue-specific U2AF paralog and alternative splicing factor LS2

city: Aurora

first: Matthew

last: Taliaferro

state: CO

address: 12801 E 17th Ave, RC1 South Room 10403D

department: Biology

institute: University of Colorado Anschutz Medical Campus

summary: To test the effects of mutations in the splicing factor LS2, we expressed GFP-LS2 fusions in Drosophila S2 cells. We then collected polyadenylated RNA and profiled it using high-throughput sequencing and alternative splicing analysis.

overall_design: Examination of specific mutations in the splicing factor LS2 on its ability to regulate alternative splicing

first: Michael

last: Sattler


title: Transcriptome profiling after reducing source-to-sink ratio in tomato plants reveals alterations in source leaf activity

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: Responses to altered source–sink balance have been characterized in many crops at the physiological level, but the underlying genetic and molecular mechanisms are largely unknown. Detailed transcriptional profiling was performed in partially defoliated and shaded tomato plants to explore the effect of reduced source-to-sink ratio on molecular changes in the remaining source leaves.  Transcription profiles of the remaining leaves 48 h after partial defoliation or partial shading were compared to leaves of control plants. Common significantly altered genes in the two treatments were assumed to be related to the reduced source-to-sink ratio. Sets of major genes in the abscisic acid, ethylene and gibberellin signal-transduction pathways were downregulated by both treatments. On the other hand, genes encoding cytokinin biosynthesis were upregulated. Most genes coding for transcription factors were also downregulated, especially those related to biotic and abiotic stress responses. Perhaps the most pronounced effect of reduced source-to-sink ratio was related to genes involved in the regulation of photosynthetic activity. Numerous genes coding for light-harvesting proteins, as well as those encoding plastocyanin, ferredoxin and ferredoxin NADP+ oxidoreductase were upregulated. Direct spectrophotometric analyses showed higher maximal potential activity of photosystem I with reduced source-to-sink ratio. As expected, the increased capacity for photosynthetic activity was associated with upregulation of almost all genes coding for the Calvin–Benson cycle and those encoding ATP biosynthesis in the mitochondria. Numerous transcriptional changes were observed 48 h after reducing source-to-sink ratio. Major genes in the photosynthetic-activity pathways were upregulated, whereas those in the pathways of defense mechanisms and responses to stress were downregulated. Genes involved in leaf senescence were also downregulated, suggesting that in addition to increased photosynthetic activity, the remaining leaves undergo a process of rejuvenation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3 biological replicates of partial shading, partial defoliation, and control tomato leaves.

first: Noga

last: Glanz-Idan

first: Nir

last: Keren

first: Shmuel

last: Wolf