title: Endothelial H2S-AMPK dysfunction upregulates the angiocrine factor PAI-1 and contributes to lung fibrosis

status: Public on Jan 31 2024

city: chengdu

first: Xiangqi

last: Chen

state: China

address: No.17, Section 3, Renmin South Road

country: China

institute: Sichuan University Huaxi Second Hospital

type: Expression profiling by high throughput sequencing

summary: Dysfunction of the vascular angiocrine system is critically involved in regenerative defects and fibrosis of injured organs. Previous studies have identified various angiocrine factors and found that risk factors such as aging and metabolic disorders can disturb the vascular angiocrine system in fibrotic organs. One existing key gap is what sense the fibrotic risk to modulate the vascular angiocrine system in organ fibrosis. Here, using human and mouse data, we discovered that the metabolic pathway hydrogen sulfide (H2S)-AMP-activated protein kinase (AMPK) is a sensor of fibrotic stress and serves as a key mechanism upregulating the angiocrine factor plasminogen activator inhibitor-1 (PAI-1) in endothelial cells to participate in lung fibrosis.

overall_design: In order to investigate the specific mechanisms underlying the regulation of pulmonary fibrosis by AMPK in vascular endothelial cells, we utilized lentiviral-mediated short hairpin RNA (shRNA) to knockdown PRKAA1 in human umbilical vein endothelial cells (HUVECs). Subsequently, HUVECs were stimulated with TGFβ for 24 hours and samples were collected for bulk RNA sequencing (n=3).

first: Xiaoqiang

last: Tang

first: Bi-Sen

last: Ding


title: Gene expression of myeloma cell lines with miR-7 transduction

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

country: Japan

institute: Akita univ.

summary: Gene expression of myeloma cell lines (MM.1S and KMS-11) transiently transduced with miR-7 and cultured for 48 h.

overall_design: We performed comprehensive gene expression analysis on the miR-7-5p transduced MM.1S and KMS-11 myeloma cell lines and extracted several genes that have decreased expression by miR-7-5p


title: Role of quorum sensing of Hafnia alvei H4 in co-culture with Pseudomonas fluorescens ATCC13525 analyzed by biological and transcriptomic

city: Dalian

first: Yanan

last: Wang

state: Liaoning

address: Ganjingzi District

institute: Dalian Polytechnic University

summary: transcriptomics was used to explore the regulation mechanism of QS in dual-species spoilage at mRNA molecular level.

sample_organism:
Pseudomonas fluorescens
Hafnia alvei

platform_organism:
Pseudomonas fluorescens
Hafnia alvei

overall_design: The cocultures formed by duo-species (H. alvei H4 WT + P. fluorescens ACTT13525) and duo-species (H. alvei H4 ΔluxI +P. fluorescens ACTT13525) underwent RNA-seq.

first: Xue

last: Li

first: Hongman

last: Hou


title: Single-cell transcriptome analysis reveals effector CD8+ T cells may play an important role in residual chronic immune activation and inflammation in HIV-1 infected patients

city: Wuhan

first: Guo

address: No. 169, East Lake Road, Wuchang District

institute: Zhongnan Hospital of Wuhan University

summary: Despite antiretroviral therapy (ART) suppressed viremia and reduced mortality in HIV-1 infected patients, residual chronic immune activation and inflammation in these patients can lead to an increased risk of non-communicable diseases, while the mechanism is still not clear. Harnessing scRNA-seq of PBMC of HIV-1 patients receiving ART and public avaialable scRNA-seq data, we found that the proportion of CD4+ T cells, CD8+ T cells, monocytes, and B cells showed variation in these patients. Through cluster analysis, it was found that effector CD8+ T cells were significantly decreased in HIV infected patients and lsATR, but increased in fsART, migration inhibitory factor (MIF) signaling was significantly increased in fsART.

overall_design: We used single-cell transcriptome sequencing (scRNA-seq) of peripheral blood mononuclear cells from 2 HIV-1 infected patients with virus fully suppressed, and analyzed the scRNA-seq data of 16 HIV-1 infected patients from public data


title: Lysine tRNA fragments and miR-194-5p co-regulate hepatic steatosis via β-Klotho and Perilipin 2 (small RNA I)

city: Jerusalem

first: Yonat

last: Tzur

address: Givat Ram Campus

country: Israel

institute: Hebrew University of Jerusalem

type: Non-coding RNA profiling by high throughput sequencing

summary: Non-alcoholic fatty liver disease (NAFLD) involves hepatic accumulation of intracellular lipid droplets via incompletely understood processes. Here, we report distinct and cooperative NAFLD roles of LysTTT-5’tRF transfer RNA fragments and microRNA miR-194-5p. Unlike lean animals, dietary-induced NAFLD mice showed concurrent hepatic decrease of both LysTTT-5’tRF and miR-194-5p levels, which were restored following miR-132 antisense oligonucleotide treatment which suppresses hepatic steatosis. Moreover, exposing human-derived Hep G2 cells to oleic acid for 7 days co-suppressed miR-194-5p and LysTTT-5’tRF levels while increasing lipid accumulation. Importantly, transfecting fattened cells with a synthetic LysTTT-5’tRF mimic elevated mRNA levels of the metabolic regulator β-Klotho while decreasing triglyceride amounts by 30% within 24 hours. In contradistinction, antisense suppression of miR-194-5p induced accumulation of its novel target, the NAFLD-implicated lipid droplet-coating PLIN2 protein. Further, two out of 15 steatosis-alleviating screened drug-repurposing compounds, Danazol and Latanoprost, elevated miR-194-5p or LysTTT-5’tRF levels. The different yet complementary roles of miR-194-5p and LysTTT-5’tRF offer new insights into the complex roles of small non-coding RNAs and the multiple pathways involved in NAFLD pathogenesis.

overall_design: We assessed the expression of short noncoding RNAs (microRNAs ans transfer RNA fragments)  in hypothalamus samples from diet-induced obese mice after anti-miR-132-treatment, which showed reduced liver steatosis and control animals (treated with inert miR molecule and lean animals on regular chow diet). C57Bl/6J mice were fed a regular chow diet (RCD) or a high fat diet (Harlan Teklad, Madison, Wisconsin, USA) for 11 weeks to reach diet-induced obesity (DIO). Injected oligonucleotides were modified by locked nucleic acid protection and complementary to mature miR-132 (AM132, 16-mer) or to mature primate-specific miR-608 (AM608, 15-mer, as a control with no predicted complementary sequences in mice) (LNA, Exiqon, Qiagen). DIO mice were injected intravenously with 3.3 mg/kg oligonucleotide for three consecutive days and were sacrificed  7 days post-treatment. Liver and hypothalamus samples were collected, snap frozen in liquid nitrogen, and stored at -80°C. Age matched RCD mice were sacrificed and samples collected as above

first: Hermona

last: Soreq


title: Increased perfluorooctanesulfonic acid (PFOS) toxicity and accumulation is associated with perturbed DHA and prostaglandin metabolism and increased OATP-transporter expression

city: Central

first: Lanie

last: Williams

state: SOUTH CAROLINA

address: 1980 West Main Street, Unit 67

department: Biological Sciences

country: USA

institute: Clemson University

summary: Perfluorooctanesulfonate (PFOS) is a widespread environmental pollutant with a long half-life and clearly negative outcomes on metabolic diseases such as fatty liver and diabetes. Male and female Cyp2b-null and humanized CYP2B6-transgenic (hCYP2B6-Tg) mice were treated with 0, 1, or 10 mg/kg/day PFOS for 21 days, and surprisingly it was found that PFOS was retained at greater concentrations in the serum and liver of hCYP2B6-Tg mice than Cyp2b-null mice with greater differences in the females. Thus, Cyp2b-null and hCYP2B6-Tg mice provide new models for investigating individual mechanisms for PFOS bioaccumulation and toxicity. Overt toxicity was greater in hCYP2B6-Tg mice (especially females) as measured by mortality; however, steato-sis occurred more readily in Cyp2b-null mice despite the lower PFOS liver concentrations. Tar-geted lipidomics and transcriptomics from PFOS treated Cyp2b-null and hCYP2B6-Tg mouse livers were performed and compared to PFOS retention and serum markers of toxicity by PCA. Several oxylipins, including prostaglandins, thromboxanes, and docosahexaenoic acid metabo-lites are associated or inversely associated with PFOS toxicity. Both lipidomics and tran-scriptomics indicate PFOS toxicity is associated with PPAR activity in all models. GO terms as-sociated with reduced steatosis were sexually dimorphic with lipid metabolism and transport increased in females and circadian rhythm associated genes increased in males. However, we can rule out that steatosis was initially protective from PFOS toxicity. Moreover, several transporters are associated with increased retention probably due to increased uptake. The strongest associa-tions are the organic anion transport proteins (Oatp1a4-6) genes and a long-chain fatty acid transport protein (fatp1), enriched in female hCYP2B6-Tg mice. PFOS uptake was also reduced in cultured murine hepatocytes by OATP inhibitors. The role of OATP1A6 and FATP1 in PFOS transport has not been tested. In summary, Cyp2b-null and hCYP2B6-Tg mice provided unique models for estimating the importance of novel mechanisms in PFOS retention and toxicity.

overall_design: The goal of this experiment was to determine the gene expression differences between our Cyp2b-null and hCYP2B6-Tg mouse models that led to increased PFOS retention in the livers of hCYP2B6-Tg mice. The Cyp2b-null mouse model was generated via Crispr-Cas9 knockout, and the hCYP2B6-Tg mouse was generated on the null background by breeding it with a CYP2B6/2A13/2F1-transgenic mouse (Wei, 2012). Male and female Cyp2b-null and hCYP2B6-Tg mice were treated with 0, 1, or 10 mg/kg/day PFOS, and greater PFOS retention was observed in the hCYP2B6-Tg mice livers. Total RNA was then extracted  from 4 mouse livers in each group for RNA-seq. Differential gene expression analysis was performed to compare expression profiles betwen PFOS treatments within a genotype and across genotypes at each particular PFOS concentration.

middle: A

first: Matthew

middle: C

last: Hamilton

middle: L

last: Edin

first: Jazmine

last: Eccles-Miller

first: Fred

middle: B

last: Lih

first: Nishanth

last: Tharayil

first: Elizabeth

last: Leonard

first: William

middle: S

last: Baldwin


title: Lysine tRNA fragments and miR-194-5p co-regulate hepatic steatosis via β-Klotho and Perilipin 2 (small RNA II)

overall_design: We assessed the expression of short noncoding RNAs (microRNAs ans transfer RNA fragments)  in liver samples from diet-induced obese mice after anti-miR-132-treatment, which showed reduced liver steatosis and control animals (treated with inert miR molecule and lean animals on regular chow diet). C57Bl/6J mice were fed a regular chow diet (RCD) or a high fat diet (Harlan Teklad, Madison, Wisconsin, USA) for 11 weeks to reach diet-induced obesity (DIO). Injected oligonucleotides were modified by locked nucleic acid protection and complementary to mature miR-132 (AM132, 16-mer) or to mature primate-specific miR-608 (AM608, 15-mer, as a control with no predicted complementary sequences in mice) (LNA, Exiqon, Qiagen). DIO mice were injected intravenously with 3.3 mg/kg oligonucleotide for three consecutive days and were sacrificed  7 days post-treatment. Liver and hypothalamus samples were collected, snap frozen in liquid nitrogen, and stored at -80°C. Age matched RCD mice were sacrificed and livers collected as above


title: E3 ubiquitin ligase FBXO38 maintains antitumor function of NK cells through sustaining IL-15R signaling

city: Hefei

first: Shi

last: Yongjing

address: Jinzhai

institute: University of Science and Technology of China

summary: Natural killer (NK) cells are the main innate antitumor effector cells and can be constrained in the tumor microenvironment (TME). It has been reported that E3 ligase FBXO38 accelerates PD-1 degradation of tumor-infiltrating T cells to unleash their cytotoxic function. In this study, we found that FBXO38 transcripts were significantly lower in intra-tumoral NK cells than in peri-tumoral regions using specimens from cancer patients in The Cancer Genome Atlas (TCGA). Conditional knock-out (cKO) of FBXO38 in NK cells accelerated tumor growth and increased tumor metastasis. However, FBXO38 deficiency did not show an effect on the cytotoxic function of tumor-infiltrating NK (TINK) cells, but decreased proliferation and survival of TINK cells. Mechanically, FBXO38 deficiency led to TINK cell hyporesponsiveness to IL-15 by reducing the expression of IL-15Rβ and IL-15Rγc, which accounted for the reduced expansion of FBXO38-deficient TINK cells in TME. Furthermore, human NK-92 cells proliferated more rapidly when FBXO38 was overexpressed and exerted greater antitumor efficacy in xenograft mouse models. Conversely, the removal of FBXO38 led to a dramatic decrease in NK-92 cell proliferation. In conclusion, our results suggest that FBXO38 strongly sustains NK cell expansion in the antitumor immunity response.

overall_design: For bulk RNA sequencing, splenic and tumor-infiltrating NK cells from control and cKO mice were sorted.


title: Lysine tRNA fragments and miR-194-5p co-regulate hepatic steatosis via β-Klotho and Perilipin 2 (RNA)

overall_design: RNA was extracted from steatotic cells treated with LysTTT-5'tRF mimic or NC (two replicates per treatment). 150,000 cells/ml were plated and 24 hours later medium was replaced with oleic acid (OA)-rich medium prepared as described in the manuscript. 24 hours after this cells were transfected with tRF mimic oligonucleotide or negative control (IDT, Syntezza Bioscience) using HiPerFect transfection reagent (Qiagen, 301705) and harvested after an additional 24 hours.


title: Single-cell RNA sequencing of the liver cells from 2-month-old A/A and S/S mice with or without TNF challenge.

city: Oklahoma City

first: Huiping

last: Shi

state: Oklahoma

address: 825 NE 13th St

institute: Oklahoma Medical Research Foundation

summary: To gain insights into the liver transcriptomic profiles, we performed single-cell RNA sequencing of the liver single cells isolated from four groups of 2-month-old mice that included: A/A and S/S mice at baseline (n = 2 mice/genotype), and A/A and S/S mice after TNF challenge (n = 2 mice/genotype). TNF challenge (500 ng/mouse) is an established method to induce vaso-occlusive episode in S/S mice.

overall_design: The experiment goal is to dissect the effects of genotype and TNF challenge on the liver transcriptomic profiles. Therefore, four groups (total n = 8) of 2-month-old mice were included: A/A and S/S mice at baseline (n = 2 mice/genotype), and A/A and S/S mice after TNF challenge (n = 2 mice/genotype). For each group, the liver single cells of two mice were pooled together for single-cell RNA sequencing analysis. For TNF challenge, each mouse was intraperitoneally injected with 500 ng TNF and liver single cells were collected at 3 h after injection.

first: Liang

last: Gao

first: Nicole

last: Kirby

first: Bojing

last: Shao

first: Xindi

last: Shan

first: Mariko

last: Kudo

first: Robert

last: Silasi

first: John

middle: M

last: McDaniel

first: Meixiang

last: Zhou

first: Samuel

last: McGee

first: Wei

last: Jing

first: Florea

last: Lupu

first: Audrey

last: Cleuren

first: James

middle: N

last: George

first: Lijun

last: Xia


title: Characterisation of ER-beta functions in prostate cancer (ATAC-Seq)

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate the effect of a novel ER-beta selective ligand alone and with Enzalutamide on chromatin accessabilty in prostate cell lines

overall_design:
Cells were treated cells in the presence of OSU-ERb-12 alone (100 nM) or E2 alone (100nM), Enza (1 microMolar) or the combinations for 6h. Briefly, 50x103 cells were resuspended in 50ul of ATAC-resuspension buffer (ATAC-RSB - 10mM Tris-HCl, 10mM NaCl, 3mM MgCl2) containing (0.1% NP-40, 0.1% tween-20, and 0.01% digitonin) and pipetted up and down 3 times. Further, 1ml of ATAC-wash-resuspension buffer (ATAC-RSB + 0.1% tween 20) was used to pellet down the nuclei. The nucleic were further resuspended in transposition mix (2X TD buffer, 1X PBS, Digitonin 0.01%, tween 20 0.1%, NFW 5ul, and Illumina transposase 2.5ul). Mixing, cleanup and library preparation, quantification and sequencing was performed using NovaSeq6000 S1 PE150bp Sequencing as per protocol51 (28846090). (ATAC-Seq data were separated into nucleosome free (NF), mono-, di- and tri-nucleosome compartments (ATACSeqQC).
Comparative chromatin accessability analsyes by ATAC-seq analsyes of prostate cancer cells lines treated in triplicate with either vehicle, OSU-ERb-12 alone (100 nM) or E2 alone (100nM), Enza (1 microMolar) or the combinations for 6h

first: Campbell

last: Moray


title: Coordinated and contrasting maturation of phenotypically distinct strains of Eimeria maxima

city: Bradenton

first: Matthew

last: Tucker

state: Florida

address: 5000 Lakewood Ranch Blvd.

institute: LECOM

summary: Intraspecific phenotypic variation markedly influences the damage that parasites inflict on their hosts. Such is the case for strains of Eimeria maxima, a costly enteric parasite of poultry, where strain APU-1 exhibits greater pathogenicity than APU-2. Here, we examined how these strains differ as oocysts mature to the fully-sporulated stage. We performed mi-croscopy and RNA-Sequencing on oocysts at regular intervals (6-12 hours) during sporulation. Although each strain underwent parallel development, APU-1 initially approached maturation more slowly. Each strain achieved full sporu-lation and similar transcription profiles by hour 36, after which strains appeared to diverge. These differences may in-fluence subsequent virulence. Candidate biomarkers of oocyst viability include 58 genes contributing at least 1,000 Transcripts Per Million throughout sporulation. Many genes resemble constitutively expressed genes also important to Eimeria acervulina. Mature and immature oocysts differentially express certain genes. Expression of some such bi-omarkers appears strain-specific. These data illuminate processes that may generally underlie sporulation in Eimeria and related genera, such as Cyclospora, and identify biological processes which differentiate among them. Drivers of devel-opment and senescence may provide tools to assess the viability of oocysts, which would greatly benefit the poultry industry and food safety applications.

overall_design: To investigate transcriptional changes during oocyst development that may differentiate pathogenically distinct strains of E. maxima, oocysts from chickens (replicates) were collected every 6-12 hours over a 48 hour sporulation time course for RNA-Sequencing

first: Mathew

first: Celia

last: O'Brien

first: Alexis

last: Johnson

first: Jitender

middle: P

last: Dubey

first: Benjamin

last: Rosenthal

first: Mark

last: Jenkins


title: Analysis of changes in the BLA and vmPFC brain region of control mice and global cerebral ischemia mice after acute stress

city: qingdao

first: xufeng

last: xu

address: No. 16 Jiangsu Road

institute: qingdao university

summary: It is known that the eCB 2-AG is synthesized in postsynaptic cells and released into synaptic clefts when needed. As we observed that acute stress prominently increased eCBs in vmPFC-BLA synapses and that inhibited expression of 2-AG synthase gene Dagla in vmPFC-BLA synapses blocked stress-induced PGCID, we plausibly hypothesized that transient GCI increased 2-AG biosynthesis in BLA neurons, leading to stress-induced increase of 2-AG release into vmPFC-BLA synapses. To test this hypothesis, we employed single-cell sequencing to examine whether GCI mice, in comparison with sham mice, showed increased mRNA expression of the Dagla in c-fos positive BLA and vmPFC cells of acute stress-treated mice

overall_design: Seven days after global cerebral ischemia, forced swimming stress was performed, and then BLA and vmPFC were taken for single-cell sequencing analysis

first: Xufeng

last: Xu

first: Yu

last: Qu


title: The CD27/CD70 pathway negatively regulates visceral adipose tissue resident Th2 cells and controls metabolic homeostasis

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: The adipose tissue homeostasis relies on the interplay between several regulatory lineages, such as ILC2, Th2, Treg, eosinophils and type 2 macrophages. Among them, ILC2 are numerically the dominant source of type 2 cytokines and are considered as major regulators of adiposity. Despite the overlap in immune effector molecules and sensitivity to alarmins (TSLP, IL-33) between ILC2 and resident memory Th2 lymphocytes, the role of the adaptive axis of type-2 immunity remains unclear. We show that mice deficient for CD27, a member of the TNF receptor superfamily, are more resistant to obesity and associated disorders. A comparative analysis of the CD4 compartment of both strains revealed higher numbers of fat resident memory Th2 cells in the adipose tissue of CD27KO mice, which correlated with decreased PD-1-induced apoptosis. Our data point to a non-redundant role for Th2 lymphocytes in obesogenic conditions.

overall_design: C57Bl/6 mice were crossed with CD11c-Cd70tg;CD27-/- or CD27-/- to generate CD11c-Cd70tg;CD27+/- mice and CD27+/- control mice. Stromal vascular fractions of VAT of 10 WT or CD27-/- mice were pooled and TCR+ CD4+ cells were subsequently FACS-sorted. Cells were next loaded on the Chromium Controller (10x Genomics) and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ v3.1 Reagent Kit (10x Genomics) according to manufacturer’s user guide CG000206.

first: Kevin

last: Englebert

first: Anaelle

last: Taquin

last: Azouz

first: Valérie

last: Acolty

first: Sylvie

middle: V

last: Velde

first: Marie

last: Vanhollebeke

first: Hadrien

last: Innes

first: Louis

last: Boon

first: Thibaut

last: Keller

first: Oberdan

last: Leo

first: Stanislas

last: Goriely

first: Muriel

last: Moser

first: Guillaume

last: Oldenhove


title: Identification of genes regulated by mechanical tension in Xenopus laevis explants by transcriptome comparison

city: Moscow

first: Fedor

last: Eroshkin

address: 16/10 Miklukho-Maklaya str.

country: Russia

institute: IBCH RAS

summary: During gastrulation and neurulation, the chordamesoderm and overlying neuroectoderm of vertebrate embryos converge under the control of a specific genetic programme to the dorsal midline, simultaneously extending along it. However, whether mechanical tensions resulting from these morphogenetic movements play a role in long-range feedback signalling that in turn regulates gene expression in the chordamesoderm and neuroectoderm is unclear. In the present work, by using a model of artificially stretched explants of Xenopus midgastrula embryos and full-transcriptome sequencing, we identified genes with altered expression in response to external mechanical stretching. Importantly, mechanically activated genes appeared to be expressed during normal development in the trunk, i.e., in the stretched region only. By contrast, genes inhibited by mechanical stretching were normally expressed in the anterior neuroectoderm, where mechanical stress is low. These results indicate that mechanical tensions may play a role of a long-range signalling factor that regulates patterning of the embryo, serving as a link coupling morphogenesis and cell differentiation.

overall_design: Three independent biological replicates were analyzed for 2 conditions (stretched and control (not stretchd) neuroectoderm explants)

first: A

middle: G

last: Zaraisky

first: F


title: The impact of knocking down METTL3 and METTL14 on the gene expression profile of EC109 esophageal squamous cell carcinoma cells.

city: changzhi

first: Pu

last: wang

state: shanxi

address: jiefang road 163

institute: changzhi medical college

summary: METTL3 and METTL14 are considered to faithfully form the m6A writing complex in a 1:1 ratio, regulating the fate of mRNA by adding m6A modifications. However, recent studies have shown inconsistent expression and prognostic value of METTL3 and METTL14 in some tumors, suggesting that they may not be faithful in tumors. Pan-cancer analysis based on TCGA data reveals significant differences in expression, function, tumor burden correlation, and immune correlation between METTL3 and METTL14, especially in esophageal squamous cell carcinoma (ESCC). Knockdown of METTL3 significantly inhibits the cell proliferation in vitro and in vivo in ESCC EC109 cells, while the impact of METTL14 knockdown on proliferation is limited, and it cannot abolish the expression of METTL3 protein. mRNA-seq results indicate that METTL3 independently regulates the expression of 1615 genes, while only 776 genes are co-regulated by METTL3 and METTL14. Furthermore, through immunofluorescence co-localization, it is observed that METTL3 and METTL14 have certain inconsistencies in cellular localization. HPLC-MS results show that METTL3 independently binds to the Nop56p-associated pre-rRNA complex and mRNA splicing complex, separate from METTL14. Through bioinformatics and various omics studies, we have preliminarily discovered that METTL3 independently regulating tumor cell proliferation, and the participation in mRNA splicing may be a critical molecular mechanism.

overall_design: In order to study the effect of METTL3/METTL14 on the cell gene expression profile, we used siRNA to knock down METTL3/METTL14. After 24 hours of siRNA treatment, the cells were harvested and treated with Trizol.


title: MYC-driven increases in mitochondrial DNA copy number occur early and persist throughout prostatic cancer progression

city: Baltimore

first: Angelo

last: De Marzo

state: Maryland

address: 1550 Orleans Street, CRB II RM 138

institute: Johns Hopkins University School of Medicine

summary: Increased mitochondrial function may render some cancers vulnerable to mitochondrial inhibitors. Since mitochondrial function is regulated partly by mitochondrial DNA copy number (mtDNAcn), accurate measurements of mtDNAcn could help reveal which cancers are driven by increased mitochondrial function and may be candidates for mitochondrial inhibition. However, prior studies have employed bulk macrodissections that fail to account for cell type-specific or tumor cell heterogeneity in mtDNAcn. These studies have often produced unclear results, particularly in prostate cancer. Herein, we developed a multiplex in situ method to spatially quantify cell type specific mtDNAcn. We show that mtDNAcn is increased in luminal cells of high-grade prostatic intraepithelial neoplasia (HGPIN), is increased in prostatic adenocarcinomas (PCa), and is further elevated in metastatic castration-resistant prostate cancer. Increased PCa mtDNAcn was validated by two orthogonal methods and is accompanied by increases in mtRNAs and enzymatic activity. Mechanistically, MYC inhibition in prostate cancer cells decreases mtDNA replication and expression of several mtDNA replication genes, and MYC activation in the mouse prostate leads to increased mtDNA levels in the neoplastic prostate cells. Our in situ approach also revealed elevated mtDNAcn in precancerous lesions of the pancreas and colon/rectum, demonstrating generalization across cancer types using clinical tissue samples.

overall_design:
Fresh frozen prostate tissues were placed in OCT and sections were cut at 7 μm thickness and mounted onto membrane slides. Laser capture microdissection (LCM) of regions of interest was performed using Leica LMD 7000 Microscope in which study pathologists were careful to exclude areas with overt inflammatory infiltrates, carcinoma, and high grade PIN when isolating normal appearing regions. 115 patients with paired adjacent normal and tumor tissues were analyzed with RNAseq.
---------------------------
Authors state "the raw data will be deposited in dbGaP due to patient privacy concerns".

first: Jiayu

last: Chen

first: Srinivasan

last: Yegnasubramanian

first: Anuj

last: Gupta


title: Characterisation of ER-beta functions in prostate cancer  (RNA-Seq)

first: Moray

last: Campbell

summary: To investigate the effect of a novel ER-beta selective ligand alone and with Enzalutamide  on RNA expression in prostate cancer cell lines

overall_design: LNCaP, LNCaP C4-2 and 22Rv1 cells in triplicate were treated with either vehicle, OSU-ERb-12 alone (100 nM) or E2 alone (100nM), Enza (1 microMolar) or the combinations for 12h and RNA-Seq was undertaken. . Sequencing libraries prepared with the TruSeq Stranded Total RNA kit (Illumina Inc), from 1ug total RNA. Alignment of raw sequence reads to the human transcriptome (hg38) was performed via Rsubread and transcript abundance estimates were normalized and differentially expressed genes (DEGs) identified using a standard edgeR pipeline.

first: Campbell

last: Moray


title: Aryl Hydrocarbon Receptor suppresses STING-mediated Type I IFN expression in Triple-Negative Breast Cancer

city: Buffalo

first: Spencer

last: Rosario

address: Elm & Carlton Sts

institute: Roswell Park Comprehensive Cancer Center

summary: Triple-negative breast cancer (TNBC) is one of the most aggressive types of cancer. Despite decades of intense investigation, treatment options remain limited and rapid recurrence with distant metastases remains a significant challenge in the clinic. Cancer cell-intrinsic production of cytokines such as type I interferons (IFN-I) is a known potent modulator of response to therapy in many cancers, including TNBC, and can influence therapeutic outcome. Here, we report that in TNBC systems the aryl hydrocarbon receptor (AhR) suppresses IFN-I expression via inhibition of Stimulator of Interferon Genes (STING), a key mediator of interferon production. Intratumoral STING activity is essential in mediating the efficacy of PARP inhibitors (PARPi) which are used in the treatment of cancers harboring BRCA-1 deficiency. We find that, in TNBC cells, PARPi treatment activates AhR in a BRCA1 deficiency-dependent manner, thus suggesting the presence of a negative feedback loop aimed at modulating PARPi efficacy. Importantly, our results indicate the combined inhibition of PARP and AhR is superior in elevating IFN-I expression as compared to PARPi-alone. Thus, AhR inhibition may allow for enhanced IFN-I production upon PARPi in BRCA1-deficient breast cancers, most of which are of TNBC origin, and may represent a therapeutically viable strategy to enhance PARPi efficacy.

overall_design: To investigate the effects of AHR, we have established MDA-MB-231 cells with either GFP-PLKO or shAHR knockdowns of AHR, using 2 different constructs.

first: Anna

last: Bianchi-Smiraglia

first: Jeffrey

last: Martin

middle: R


title: Effect of Ep300 silencing on gene expression of RAW264.7

first: Yanshuo

last: Han

address: No.2 Dagong Road

institute: Dalian University of Technology

summary: Differentially expressed genes were identified by comparing the gene expression profiling of RAW264.7 of Ep300 silencing with that of control. Results provide important information to indicate Effect of Ep300 silencing on RAW264.7.

overall_design:
To investigate the effect of EP300 on macrophages, we established RAW264.7 cell lines in which Ep300 has been silenced by si_Ep300.
Then, we added si_nc to another cell line of the same generation as a control and performed the gene expression profiling analysis of these two different cells.
Comparative gene expression profiling analysis using data for RAW264.7 with Ep300 silencing.


title: The function of  Oxytocin Receptor in the Tumorigenesis of Hepatocarcinoma

city: xinxing

first: huijie

last: yang

address: Hongqi District, Xinxiang City

institute: Xinxiang Medical University

summary: To investigate the  function of  Oxytocin Receptor in the Tumorigenesis of Hepatocarcinoma.

overall_design: SNU449 cell mRNA samples were summarized in six samples, divided into two groups, siControl and siOXTR. Comparative gene expression profiling analysis of RNA-seq data for SNU449 cells treated with siControl and siOXTR.


title: Characterisation of ER-beta functions in prostate cancer

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

overall_design: Refer to individual Series


title: Lysine tRNA fragments and miR-194-5p co-regulate hepatic steatosis via β-Klotho and Perilipin 2

first: Yonat

last: Tzur

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: The R1441C-LRRK2 mutation induces myeloid immune cell exhaustion in an age- and sex-dependent manner

city: Atlanta

first: Karen

last: McFarland

state: GA

address: 100 Woodruff Circle

department: Pharmacology

institute: Emory University

summary: Considering age is the greatest risk factor for many neurodegenerative diseases, aging, in particular aging of the immune system, is the most underappreciated and understudied contributing factor in the neurodegeneration field. Genetic variation around the LRRK2 gene affects risk of both familial and sporadic Parkinson's disease (PD). The leucine-rich repeat kinase 2 (LRRK2) protein has been implicated in peripheral immune signaling, however, the effects of an aging immune system on LRRK2 function have been neglected to be considered. We demonstrate here that the R1441C mutation induces a hyper-responsive phenotype in macrophages from young female mice, characterized by increased effector functions, including stimulation-dependent antigen presentation, cytokine release, phagocytosis, and lysosomal function. This is followed by age-acquired immune cell exhaustion in a Lrrk2-kinase-dependent manner. Immune-exhausted macrophages exhibit suppressed antigen presentation and hypophagocytosis, which is also demonstrated in myeloid cells from R1441C and Y1699C-PD patients. Our novel findings that LRRK2 mutations confer immunological advantage at a young age but may predispose the carrier to age-acquired immune exhaustion have significant implications for LRRK2 biology and therapeutic development. Indeed, LRRK2 has become an appealing target in PD, but our findings suggest that more research is required to understand the cell-type specific consequences and optimal timing of LRRK2-targeting therapeutics.

overall_design: The primary objective of this research was to investigate the effects of the R1441C LRRK2 pathogenic variant on myeloid cell effector function in a sex- and age-dependent manner. We hypothesized that a biphasic, age-dependent effect of the R1441C pathogenic variant would be observed, affecting antigen presentation, cytokine release, phagocytosis and lysosomal function in macrophages. To explore our hypothesis, we used R1441C knock-in mice and B6 controls and assessed myeloid cell effector function both ex vivo and in vivo, in males and females at 2-3 months and 18-21 months. All studies were performed by investigators blinded to genotype and treatment groups at the University of Florida, USA. Power analyses based on the labs pilot and published data indicated that n = 12 per group for flow-cytometry and cytokine release assays, and n = 6 for imaging based immunophenotyping and immunoblotting would be needed to yield 80% power with a α set to 0.05. The study used human PBMCs received from collaborators at University Hospital Schleswig-Holstein, University of Luebeck, Germany and the University Hospital Eppendorf, Hamburg, Germany. Samples were received at the University of Florida and investigators were unblinded after completion of analysis. Deidentified data provided included sex, age at collection, age of diagnosis, clinical diagnosis and genetic status.

first: Rebecca

last: Wallings

first: Malu

last: Gamez Tansey


title: miRNA expression of myeloma cell lines cultured with HDAC inhibitors panobinostat and vorinostat

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

institute: Akita univ.

summary: miRNA expression of myeloma cell lines (MM.1S and KMS-11) cultured with HDAC inhibitors (10 nM panobinostat and 1 uM vorinostat) for 48h.

overall_design: We performed comprehensive miRNA expression analysis myeloma cell lines (MM.1S and KMS-11) cultured with HDAC inhibitors (10 nM panobinostat and 1 uM vorinostat) for 48h, and found commonly downregulated miR-7-5p.


title: Transcriptomic Analysis Identifies Dysregulated Aortic Ceramide Metabolism in a Miniature Pig Model of Atherosclerosis

city: Hangzhou

first: zhaowei

last: cai

state: Zhejiang

address: Binwen road 548

department: Laboratory Animal Research Center

institute: zhejiang chinese medical university

summary: Dysregulation of lipid metabolism is the pathological basis of the occurrence and development of  atherosclerosis.The pig is an ideal animal to study human cardiovascular diseases. However, the specific changes of lipid metabolism in its atherosclerotic plaques, as well as the underlying mechanisms, remain to be elucidated. To investigate the alterations of lipid metabolism related pathways, especially ceramide synthesis related genes, in the abdominal aorta of atherosclerotic pigs induced by high-fat, high-cholesterol, and high-fructose (HFCF) diet, we performed RNA-Seq on abdominal aorta tissue from Wuzhishan pigs fed either normal chow diet or HFCF diet for six months.

overall_design: Aorta mRNA profiles of Wuzhishan pigs fed either normal chow diet or  high fat, high cholesterol and high fructose diet were generated by deep sequencing, in triplicate, using Illumina NovaSeq.

first: Zhaowei

last: Cai


title: Comparative genomics reveals intra and inter species variation in the pathogenic fungus Batrachochytrium dendrobatidis

city: Riverside

first: Jason

last: Stajich

state: California

address: 900 Univeristy Avenue

department: Microbiology and Plant Pathology

institute: University of California, Riverside

summary: The Global Pandemic Lineage (GPL) of the amphibian pathogen Batrachochytrium dendrobatidis (Bd) has been described as a main driver of amphibian extinctions on nearly every continent. Near complete genome of three Bd-GPL strains have enabled studies of the pathogen but the genomic features that set Bd-GPL apart from other Bd lineages is not well understood due to a lack of high-quality genome assemblies and annotations from other lineages. We used long-read DNA sequencing to assemble high-quality genomes of three Bd-BRAZIL isolates and one non-pathogen outgroup species Polyrhizophydium stewartii (Ps) strain JEL0888, and compared these to genomes of previously sequenced Bd-GPL strains. The Bd-BRAZIL assemblies range in size between 22.0 and 26.1 Mb and encode 8495-8620 protein-coding genes for each strain. Our pan-genome analysis provided insight into shared and lineage-specific gene content. The core genome of Bd consists of 6278 conserved gene families, with 202 Bd-BRAZIL and 172 Bd-GPL specific gene families. We discovered gene copy number variation in pathogenicity gene families between Bd-BRAZIL and Bd-GPL strains though none were consistently expanded in Bd-GPL or Bd-BRAZIL strains. Comparison within the Batrachochytrium genus and two closely related non-pathogenic saprophytic chytrids identified variation in sequence and protein domain counts. We further test these new Bd-BRAZIL genomes to assess their utility as reference genomes for transcriptome alignment and analysis. Our analysis examines the genomic variation between strains in Bd-BRAZIL and Bd-GPL and offers insights into the application of these genomes as reference genomes for future studies.

overall_design: To investigate the effect of reference genome choice when aligning RNA from multiple Bd strains across two lineages

first: Mark

last: Yacoub

middle: E


title: All the regulated lncRNAs and mRNAs in BCSCs derived exosomes compared to non-BCSCs derived exosomes

city: xuzhou

first: Tingting

last: Tang

address: huaihai road 84

institute: xuzhou medical university

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

summary: Transcriptional landscapes between exosomes derived from BCSCs and non-BCSCs were compared using the LC Human ceRNA array V1.0 (4*180K, Design ID:085202) Microarray. Goal was to investigate potential lncRNAs involved in breast cancer progression through enveloping into exosomes.

overall_design: The total RNAs of 2 paired exosomes derived from BCSCs and non-BCSCs were extracted, and the global expression profile of lncRNAs and mRNAs was detected using the LC Human ceRNA array V1.0 (4*180K, Design ID:085202) Microarray.

first: Liang

last: Wei


title: Quantification of totalRNA expression in oral squamous cell carcinoma(OSCC)

city: Toon

first: Tomoko

last: Adachi

state: Ehime

address: Shitsukawa

department: Department of Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

summary:
Microarrays were used to compare the expression of oral squamous cell carcinoma in the high and low serum IL-6 groups.
The results of the analysis may also be used to understand the disease, such as whether patients with high serum IL-6 levels have a poor prognosis or nutritional and metabolic activity status.

overall_design: Human oral tissue samples were collected from 9 patients with high IL-6 levels and 9 patients with low IL-6 levels diagnosed with OSCC at the Oral Surgery Department of Ehime University hospital between December 2014 and December 2021.

first: Hiroyuki

last: Goda

first: Koh-ichi

last: Nakashiro


title: RNA-Sequencing Analysis of HP-AKI Murine Model

city: Rochester

first: Jessica

last: Hohenstein

state: MN

address: 200 1st St SW

institute: Mayo Clinic

summary: We studied a murine HP-AKI model.

overall_design: Kidney mRNA was studied at 1 day after sham or HP-AKI using an Illumina HiSeq 2000.

first: Karl

last: Nath


title: Maternal Western Diet Programs Cardiometabolic Dysfunction and Hypothalamic Inflammation via Epigenetic Mechanisms Predominantly in the Male Offspring [miRNA-seq]

city: New Orleans

first: Mona

last: Elgazzaz

state: LA

address: 533 Bolivar Street

department: Cardiovascular Center

institute: LSUHSC

summary: Maternal exposure during pregnancy is a strong determinant of offspring health outcomes. Such exposures induce changes in the offspring epigenome resulting in gene expression and functional changes. In this study, we investigated the effect of maternal Western hypercaloric diet (HCD) programming during the perinatal period and its effect on neuronal plasticity and cardiometabolic health in adult offspring. C57BL/6J dams were fed HCD for 1 month prior to mating with regular diet (RD) sires and kept on the same diet throughout pregnancy and lactation. At weaning, offspring were maintained on either HCD or RD for 3 months duration. Maternal programming resulted in male-specific hypertension and hyperglycemia, with both males and females showing increased sympathetic tone to the vasculature. Surprisingly, programmed male offspring fed on HCD exhibited lower glucose levels, less insulin resistance, and leptin levels compared to non-programmed HCD-fed male mice. Hypothalamic genes involved in glial and astrocytic differentiation were differentially methylated in programmed male offspring. Genes involved in inflammation and type 2 diabetes were targeted by differentially expressed miRNA in programmed male offspring. Methyl-seq data were supported by our findings of astrogliosis and microgliosis as well as increased microglial activation in programmed males in the paraventricular nucleus (PVN). Aligned with programming-induced protective effect in HCD male mice, we observed lower protein levels of hypothalamic TGFβ2, NF-κB2, NF-κBp65, Ser-pIRS1, and GLP1R compared to non-programmed HCD-fed male mice. In conclusion, our study shows that maternal HCD programs neuronal plasticity in the offspring and results in male-specific hypertension and hyperglycemia. On the other hand, we observed a compensatory role of programming potentially by priming metabolic pathways to handle excess nutrients in a more efficient way.

overall_design: These are miRNA-seq data driven from the hypothalamus of programmed mice with perinatal hypercaloric diet and non-programmed mice with either postnatal HCD or regular diet. First part of the name refers to maternal diet and the second part refers to offspring diet.


title: Characterisation of ER-beta functions in prostate cancer (ChIP-Seq)

city: WEST HOLLYWOOD

first: Moray

last: Campbell

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

summary: To investigate the effect of a novel ER-beta selective ligand alone and with Enzalutamide on AR, ARv7, MYC  genomic binding and H3K27ac distribution in prostate cancer cell lines

overall_design:
Cells were treated cells in the presence of OSU-ERb-12 alone (100 nM) or E2 alone (100nM), Enza (1 microMolar) or the combinations for 6h. Briefly, approximately cells were adsorbed to concanavalin A beads (Epicypher), and washed (150mM NaCl, 20mM HEPES, 0.01% Digitonin, 0.5mM Spermidine, protease inhibitor cocktail EDTA-free mini tab 1tab/10mL (Roche)) to permeabilize cells and nuclei. Samples were incubated overnight with antibodies against IgG (2729, Cell Signaling Technology), H3K27 (8173, Cell Signaling Technology), AR (5153, Cell Signaling Technology), ARv7 (ab198394, abcam), MYC (9402, Cell Signaling Technology) for 16 hours, and antibody bound DNA was then enzymatically cut with pAG-MNase (Epicypher). Samples were treated with Stop Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/mL RNase A, 50ug/mL Glycogen) to prevent further enzymatic activity. DNA fragments released into supernatant were collected and purified by Monarch PCR and DNA clean-up kit (New England Biosciences).
Comparative AR, ARv7, MYC and H3K27ac cistrome analsyes by ChIP-seq analsyes of prostate cell lines treated with OSU-ERb-12 alone (100 nM) or E2 alone (100nM), Enza (1 microMolar) or the combinations for 6h

first: Campbell

last: Moray


title: Deciphering Molecular Mechanism of Intermediate Secondary Growth and Internode Elongation of Castor Bean (Ricinus communis L.) by combined analysis of transcriptome and metabolome

city: Tongliao

first: Yujie

last: Chen

address: No.996 Xilamulun Street, Tongliao city, Inner Mongolia, China

institute: Inner Mongolia Minzu University

summary: The length of internodes is critical in determining the height of the castor plant (Ricinus communis L.), and is closely associated with internode elongation. However, the exact mechanisms underlying internode elongation, particularly in the main stem of the castor plant, remain uncertain. To investigate further, we conducted a study using the dwarf castor variety 071113, comparing it with the homologous high-stalk Zhuansihao as a control. Our research included cytological observation, physiological measurement, transcriptome sequencing, and metabolic determination. By integrating these findings, we discovered that the dwarf 071113 undergoes earlier main stem lignification development and has a more active lignin synthesis pathway in internode intermediate development. The plant hormone IAA also plays a role in this process. Furthermore, potential enzymes and regulators have been identified, including the auxin influx carrier AUX1 LAX, auxin response protein IAA13, ARF3, auxin-responsive protein SAUR50, peroxidase, and EXPs that regulate cell cycle, cell wall synthesis, as well as growth and development, were also. Based on these findings, we developed a model for castor internode elongation and gained a better understanding of the dwarfing mechanism of the 071113 variety. Our work lays a theoretical foundation for the future breeding of dwarf castor varieties.

overall_design: To investigate the mechanisms behind internode elongation in the development of castor bean stems, RNA-seq was conducted on two different varieties: the dwarf-stalk 071113 and the high-stalk Zhuansihao. Each variety was subjected to three biological replications. The short-stalk 071113 samples were labeled as D1, D2, and D3, while the high-stalk Zhuansihao samples were labeled as L1, L2, and L3.


title: Effect of deficiency of NLRP6 on hepatic lipids accumulation during non-alcoholic fatty liver disease in mice.

city: Xinxiang

first: Wei

last: Hong

state: Henan

address: Xiangyang road no.688

institute: Sanquan College Of Xinxiang Medical University

summary: Nonalcoholic fatty liver disease (NAFLD) is one of the main causes of liver diseases in the world. At present, the pathogenesis of NAFLD is not completely clear, and the regulatory role of inflammatory corpuscles in NAFLD-related metabolic diseases is increasingly prominent. NLRP6 is a member of the NLRs family of pattern recognition receptors and is related to the occurrence and development of NAFLD, but the specific mechanism is still unclear. We report here that NLRP6 is an important regulator of liver lipid metabolism, and its absence will affect the formation and accumulation of lipid droplets in the liver. In the HFD-induced NAFLD model group, NLRP6 deletion increased the mouse lipid content and aggravated hepatocyte steatosis by up-regulating the expressions of ADRP and CIDEC and down-regulating the expression of ApoB100.On the contrary, overexpression of NLRP6 in hepatocytes can significantly reduce intracellular lipid content and lipid droplets, and reduce the expression of ADRP and CIDEC. Indicated that NLRP6 can inhibit the accumulation of lipid droplets in hepatocytes by regulating the expression of ADRP, CIDEC and ApoB100, and thus alleviating the symptoms of NAFLD.

overall_design: To investigate the function of NLRP6 in the accumulation of lipid droplets in hepatocytes, we established NLRP6 knockout mice and determined that NLRP6 in hepatocytes was knocked out. Then, we performed transcriptmic analysis of liver gene sequencing for ND or HFD-treated wild type and NLRP6 knockout mice.

first: Lili

last: Yu


title: Role of FGF23 and DMP1 in osteoblasts

city: Chicago

first: Valentin

last: David

state: Illinois

address: 320 E Superior Street

department: Medicine

institute: Northwestern University

summary: Primary bone marrow cells from murine long bones were cultured in osteoblastic medium for 21 days. RNAseq and differential expression analyzes were used to highlight the importance of FGF23 and DMP1 in osteoblastogenesis

overall_design: mRNA profiles of differentiated Bone marrow stromal cells (BMSCs) from wild-type (WT) mice,  mice with an osteocyte-specific deletion of Fgf23,  harboring a floxed first exon of the Fgf23 gene and expressing a transgene containing a Cre recombinase sequence downstream of the Dmp1 promoter (Fgf23cKO), Dmp1 global knockout mice (Dmp1KO) and compound  Dmp1KO/Fgf23cKO mice.

first: Aline

last: Martin

first: Jane

middle: J

last: Thomas


title: TRAIL deletion in myeloid cells augments cholestatic liver injury

first: Alexander

middle: Quinn

last: Wixom

department: Quantitative Health Sciences

summary: Ductular reactive (DR) cells exacerbate cholestatic liver injury and fibrosis. In this study we posited that tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) emanating from recruited macrophages restrains DR cell expansion by apoptosis, thereby limiting cholestatic liver injury.  Cholestatic liver injury was induced in Wild type (WT), Trailfl/fl and in myeloid-specific Trail deleted (TrailΔmye) C57BL/6 mice using the DDC diet.  The DDC diet induced injury and hepatomegaly. However, parameters of liver injury, fibrosis, ductular reaction and inflammation were all increased in the TrailΔmye mice as compared to the WT and Trailfl/fl mice.  To better resolve the gene expression profile of cholangiocytes that may promote the recruitment of myeloid cells into the periportal neighborhood, we performed spatial transcriptomics on FPPE liver tissue sections from WT and TrailΔmye mice that were fed the control or DDC diet using the NanoString GeoMx DSP platform (Cat. No. 121401103, GeoMx NGS RNA WTA Mm).

overall_design: FPPE mouse liver tissue sections from wild type (WT) mice and TrailΔmye mice fed on control (CON) or DDC diets were examined post-cholestatic liver injury using Nanostring GeoMx DSP platform to identify differential gene expression in cholangiocytes and macrophages in periportal and parenchymal regions.

first: Gregory

last: Gores


title: Bulk RNA transcriptome sequencing of adipose stem cells from multiple white adipose tissue depots

city: Changsha

first: Limin

last: Xie

state: Hunan

address: No.139，Renmin Road Central Changsha, Hunan, China

institute: The second xiangya hospital of central south university

summary: We performed RNA sequencing on the sorted adipose stem cells (ASCs) from multiple white adipose tissue depots to analyze the differential expression and pathway enrichment analysis of adipose stem cells from different anatomical sites.

overall_design: We use flow cytometry to sort adipose-derived stem cells from Subcutaneous inguinal(SWAT), epididymal(EWAT), mesenteric(MWAT), and perirenal(NWAT) adipose tissue depots and then perform transcriptome sequencing for further analysis.

first: Tuo

last: Deng

first: Wanyu

last: Hu

first: Haowei

last: Zhang


title: Profile of mRNA bound to circular RNA BTBD7_hsa_circ_0000563 in coronary artery disease investigated via chromatin isolation by RNA purification followed by RNA sequencing

city: Nanjing

first: Enzhi

last: Jia

state: Jiangsu

address: Guangzhou Road 300

institute: The First Affiliated Hospital of Nanjing Medical University

summary:
Background: As a novel circRNA, BTBD7_hsa_circ_0000563 has not been fully investigated in coronary artery disease (CAD). Our aim is to reveal the possible functional role and regulatory pathway of BTBD7_hsa_circ_0000563 in CAD via exploring genes combined with BTBD7_hsa_circ_0000563.
Methods: A total of 45 peripheral blood mononuclear cell (PBMC) samples of CAD patients were enrolled. The ChIRP-RNAseq assay was performed to directly explore genes bound to BTBD7_hsa_circ_0000563. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted to reveal possible functions of these genes. The interaction network was constructed by the STRING database and the Cytoscape software. The Cytoscape software were used again to identify clusters and hub genes of genes bound to BTBD7_hsa_circ_0000563. The target miRNAs of hub genes were predicted via online databases.
Results: In this study, a total of 221 mRNAs directly bound to BTBD7_hsa_circ_0000563 were identified in PBMCs of CAD patients via ChIRP-RNAseq. The functional enrichment analysis revealed that these mRNAs may participate in translation and necroptosis. Moreover, the interaction network showed that there may be a close relationship between these mRNAs. Eight clusters can be further subdivided from the interaction network. RPS3 and RPSA were identified as hub genes and hsa-miR-493-5p was predicted to be the target miRNA of RPS3.
Conclusions: BTBD7_hsa_circ_0000563 and mRNAs directly bound to it may influence the initiation and progression of CAD, among which RPS3 and RPSA may be hub genes. These findings may provide innovative ideas for further research on CAD.

overall_design: To reveal the possible functional role and regulatory pathway of BTBD7_hsa_circ_0000563 in CAD, we explored RNAs bound to BTBD7_hsa_circ_0000563 via the ChIRP-RNAseq assay.

first: Ning

last: Guo

first: Hanxiao

last: Zhou

first: Qian

first: Yahong

last: Fu

first: Qiaowei

first: Xiongkang

last: Gan

first: Yanjun

last: Wang

first: Shu

last: He

first: Chengcheng

last: Li

first: Zhengxian

last: Tao

first: Jun

last: Liu


title: Intrinsic Homeostatic Plasticity in Mouse and Human Sensory Neurons

city: Richardson

first: Theodore

last: Price

state: TX

address: 800 W Campbell Rd.

institute: University of Texas at Dallas

summary: The nervous system has a tremendous capacity for experience-dependent plasticity. In response to changes in activity induced by environmental cues, many types of neurons undergo a process known as homeostatic plasticity, which serves to maintain overall network function in the face of mounting experience-dependent changes in synaptic strengths. Homeostatic plasticity involves both changes in synaptic scaling and regulation of intrinsic excitability. Increases in spontaneous firing and excitability of sensory neurons are evident in some forms of chronic pain in both animal models and in human patients. However, it is not known whether homeostatic plasticity is engaged in sensory neurons under normal conditions or whether dysfunction in these homeostatic mechanisms might contribute to the pathophysiology of chronic pain. To address these questions, we tested the impact of sustained depolarization on various measures of excitability in mouse and human sensory neurons. Depolarization induced by 30mM KCl induces a compensatory decrease in the excitability of both mouse and human sensory neurons. Moreover, we also find that voltage-gated sodium currents are robustly inhibited in mouse sensory neurons after chronic depolarization, thus contributing to the overall decrease in neuronal excitability and serving as a potential regulatory mechanism to drive intrinsic neuronal homeostatic control. Our results indicate that mouse and human sensory neurons undergo homeostatic regulation of intrinsic excitability in response to sustained depolarization. Decreased efficacy of these homeostatic mechanisms could potentially contribute to the development of pathological conditions, including chronic pain.

overall_design:
To investigate changes at whole transcriptome level for cultured human and mouse neurons after sustained depolarization.
We compared gene expression across 3 treatment conditions: 24h KCl, 24h KCl followed by 24h recovery in control media, and control media. Each condition has 3 replicates.

first: Lisa

last: McIlvried

first: John

last: Del Rosario

first: Melanie

middle: Y

last: Pullen

first: Andi

last: Wangzhou

first: Tayler

middle: D

last: Sheahan

first: Andrew

last: Shepherd

first: Richard

last: Silvicki

first: Bryan

last: Coptis

first: Robert

middle: W

last: Gereau IV


title: RBL2 represses the transcriptional activity of Multicilin to inhibit multiciliogenesis

city: Iowa City

first: Amy

middle: Leanne

last: Ryan

state: IA

address: 51 Newton Road

department: Anatomy and Cell Biology

institute: The University of Iowa

summary: A core pathophysiology underlying many respiratory diseases is multiciliated cell dysfunction leading to inadequate mucociliary clearance. Due to the prevalence and high variability of etiologies of MCC dysfunction in respiratory diseases, it is critical to understand the mechanisms controlling multiciliogenesis that may be targeted to restore functional mucociliary clearance. Multicilin, in complex with E2F4, is necessary and sufficient to drive multiciliogenesis in airway epithelium, however this does not apply to all cell types nor occur evenly across all cells in the same cell population. In this study we investigated we further investigate how co-factors regulate the ability of Multicilin to drive multiciliogenesis. Combining data in mouse embryonic fibroblasts and human bronchial epithelial cells we identify RBL2 as an inhibitor of the transcriptional activity of Multicilin. Both knockdown of RBL2 and phosphorylation of RBL2 driven by exposure to an air-liquid interface in the presence of Multicilin activated multiciliogenesis demonstrating a dynamic interaction regulating the differentiation of human airway epithelial cells. Identification of this mechanism has important implications for facilitating MCC differentiation in diseases where mucociliary clearance is impeded.

overall_design: Primary MEFs were plated with 10% FBS-DMEM for overnight then treated with 2% FBS-DMEM. Six hours after serum-reduced treatment, siRNAs were transfected into MEFs using Lipofectamine RNAiMAX (Invitrogen) according to manufacturer’s instructions. Eighteen hours later, the cells were washed with 2% FBS-DMEM then infected with pAd/CMV/V5 vector expressing pAd/CMV/V5 vector encoding 3xFLAG-Multicilin, NLS-6xmyc-E2f4ΔTA-VP16-T2A-3xFLAG-Multicilin, and NLS-6xmyc-E2f4WT-T2A-3x-FLAG-Multicilin. Adenovirus infection was performed by adding the adenovirus crude lysates to the MEF cells for four hours, washing with pre-warmed PBS once, then growing infected cells with 2% FBS-DMEM. The cells were subjected to RNA extraction 2 days after infection.

first: Erik

last: Quiroz

first: Seongjae

last: Kim

first: Lalit

middle: K

last: Gautam

first: Zea

last: Borok

first: Christopher

last: Kintner


title: Altered histone acetylation patterns in pancreatic cancer cell lines induce subtype-specific transcriptomic and phenotypic changes.

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

summary: Background: Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed at advanced tumor stages with chemotherapy as the only treatment option. Large-scale gene expression studies have defined two major PDAC subtypes, a classical and basal-like, which differ in their response to chemotherapy. The transcriptional networks, which define the molecular PDAC subtypes, are regulated by epigenetic modifications. Given the reversible nature of the epigenome, we aim to determine if drug-induced epigenetic reprogramming of pancreatic cancer cells affects PDAC subtype identity and chemosensitivity.

overall_design: Steady-state RNA measurement in varous PDAC cell lines with and without treatment

first: Quan

last: Zhou

first: Svenja

last: Pichlmeier

first: Anna

last: Kirmayr

first: Nicole

last: Schreiner

first: Simone

last: Benitz

first: Julia

last: Wolff

last: Fahr

first: Maria

last: del Socorro Escobar Lopez

first: Jörg

last: Kleeff

last: Mayerle

first: Ujjwal

last: Mukund Mahajan

first: Ivonne

last: Regel


title: Profiling histone post-translational modifications in mouse adult hepatocytes, biliary epithelial cells and biliary reprogrammed cells from hepatocytes.

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

summary: Recent studies have demonstrated that hepatocytes can be reprogrammed into biliary epithelial cell-like cells under cholestatic liver injury. To investigate the changes in histone post-translational modification in hepatocyte-derived reprogramming cells, we performed Cleavage Under Targets and Tagmentation (CUT&Tag)-sequencing.

overall_design: Rosa26-LSL-Cas9-EGFP mice were injected with serotype 8 adeno-associated viruses (AAV8) packaged with TBG-Cre (AAV8-TBG-Cre) to genetically label adult hepatocytes. Mice were then treated with 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-containing diet to induce cholestatic liver injury for 8-9 weeks. Reprogrammed cells in early (EGFP+ CD24-), intermidate (EGFP+ CD24+ EPCAM-) and late stages (EGFP+ CD24+ EPCAM+) as well as and biliary cells (EGFP- EPCAM+) were harvested by FACS. Normal hepatocyts, as a control group, were harvested by the percoll density gradient method from mice maintained on normal diet.

first: Ben

middle: Z

last: Stanger


title: Maternal Western Diet Programs Cardiometabolic Dysfunction and Hypothalamic Inflammation via Epigenetic Mechanisms Predominantly in the Male Offspring [RNA-seq]

first: Mona

last: Elgazzaz

overall_design: These are mRNA-seq data driven from the hypothalamus of programmed mice with perinatal hypercaloric diet and non-programmed mice with either postnatal HCD or regular diet. First part of the name refers to maternal diet and the second part refers to offspring diet.


title: Transcriptomes analysis of COVID-19 Inactivated Vaccine and Protein Subunit Vaccine as Third Booster Dose in Elderly Adults over 70 Years of Age

city: Jinan

first: yuwei

last: Zhang

state: Shandong

address: No.16992 Jingshi Road

department: Pathogenobiology

institute: SDCDC

summary: To compare the effects of different types of SARS-CoV-2 vaccines in booster immunization in Elderly Adults, this study established a population cohort vaccinated with inactivated vaccine and protein subunit vaccine as the third booster vaccine in Elderly Adults over 70 Years of Age, respectively. We collected serum and PBMC samples from participants, and performed a systematic review of distinct antibody signatures and microtranscriptomics to provide data support for booster immunization.

overall_design: Comparative gene expression profiling of RNA-seq data from PBMC samples from a elderly adults cohort vaccinated with inactivated vaccine and protein subunit vaccine as a third booster vaccine.

first: Xiaolin

last: Jiang

first: Yuwei

first: Shanshan

last: Han

first: Lianxiang

last: Zhao

first: Mingxiao

last: Yao

first: Xiaomei


title: Dynamic histone modifications establish the two phase kinetics of glucosinolates against wounding stress in Arabidopsis plant

city: Anseong-si

first: Dasom

last: Choi

state: Gyeonggi-do

address: 4726, Seodong-daero

country: South Korea

institute: Chung-Ang University

summary: This study demonstrates that distinct composition of histone modifications between aliphatic and indolic GSL pathway genes contribute to the two phase activation of two different groups of GSL pathway genes in stress condition of Arabidopsis.

overall_design: Performed RNA-seq analysis between untreated control and wound-treated time course samples (harvested at 6 hrs, 12 hrs, 24 hrs, 3 days, 5 days after wounding treatment).

first: Sang

last: Lee

first: Dong

middle: H

last: Kim


title: G207 and PVSRIPO treatment of medulloblastoma and pediatric high grade glioma

city: 5841 S Maryland Ave. MC3026

first: Eric

last: Thompson

state: IL

institute: The University of Chicago

summary: HSV G207 and polio:rhinovirus PVSRIPO are two different viral immunotherapies used to treat malignant brain tumors in children. While some patients experience durable survival with these viral immunotherapies, many children have no response. The purpose of this work is to explore these viral immunotherapies in pediatric high grade glioma (pHGG) and medulloblastoma in order to elucidate how tumor response to treatment and to identify putative biomarkers of response and therapeutic targets.

overall_design: Four different medulloblastoma cell lines treated with either G207 or PVSRIPO for 0, 8, or 24 hours. 2 different pediatric high grade glioma cell lines treated with G207 for 0, 8, or 24 hours.

first: Gregory

last: Friedman

first: Kevin

last: Stevenson


title: ChIP-seq using BrJMJ18-OX Par plants under NC and HS conditions

city: Beijing

first: Peirong

last: Li

state: Beijing

address: Zhanghualu No.50

institute: Beijing Academy of Agricultural and Forestry Sciences

summary: Using genome-wide pattern analysis and quantitative-trait-locus (QTL) mapping, we identified that a natural allele of BrJMJ18, BrJMJ18Par, encoding a novel H3K36me3/2 Jumonji demethylase, confers thermotolerance by delayed flowering and stimulated vegetative growth on B. rapa.To assess the downstream genes of BrJMJ18, we conducted a chromatin immunoprecipitation (ChIP) seq experiment using a polyclonal antibody recognizing BrJMJ18 in Par plants under normal conditon (LD, 21℃) and high temperature condiation (LD, 28℃), respectively.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for BrJMJ18-GFP in BrJMJ18 overexpresing Par plants. Par plants overexpressing tow allels of BrJMJ18, BrJMJ18WT (H1) and BrJMJ18Par (H2) were grown under low temperature (L, 21℃) for 5 weeks or low temperature (L, 21℃) for 4 weeks following with 1 week under high temperature (H, 28℃), respectively. And wildtype Par plant was used as control (CK). The young and health leaves were collected for ChIP-seq. Two biological replicates were performed for each sample.

first: Tongbing

last: Su

first: Xiaoyun

last: Xin

first: Shuancang

last: Yu


title: Mechanism of RUNX1 targeted AKT3 regulated alveolar procoagulant fibrinolytic inhibition in ARDS

city: Changchun

first: Tongjian

address: 1266 Fujin Road

institute: School of Pharmaceutical Sciences, Jilin University

summary: Acute respiratory distress syndrome (ARDS) is an acute inflammatory lung injury and one of the serious life-threatening forms of respiratory failure. Alveolar procoagulation and fibrinolytic inhibition constitute the core part of the pathophysiology of ARDS, RUNX1 plays an important role in this pathogenesis. We screened for AKT3, the target gene of RUNX1, using CHIP-seq and verified its binding target by a dual luciferase assay.

overall_design:
RLE-6TN cells were transfected with LV-RUNX1 to increase the expression level of RUNX1
We screened for AKT3, the target gene of RUNX1, using CHIP-seq and verified its binding target by a dual luciferase assay.

first: Chuan

last: Xiao


title: Perturbation of gene expression for increased protein secretion in yeast.

city: Heidelberg

first: Staffan Andreas

last: Johansson

address: Meyerhofstraße 1

institute: EMBL Heidelberg

summary: Study to identify genes for which a decrease or an increase in gene expression resulted in increased secretion of α-amylase.

overall_design: Perturbation of α-amylase secreting yeast cells using CRISPR/dCas9 plasmid activation or repression libraries, coupled with microfluidic screening for high secretion strains.

first: S

middle: A

first: Thierry

last: Dulermo

first: Cosimo

last: Jann

first: Justin

last: Smith

first: Anna

last: Pryszlak

first: Georges

last: Pignede

first: Daniel

last: Schraivogel

first: Didier

last: Colavizza

first: Thomas

last: Desfougères

first: Christophe

last: Rave

first: Alexander

last: Farwick

first: Christoph

last: Merten

last: Roy

first: Wu

last: Wei

first: Lars

last: Steinmetz


title: Glycogen Metabolism Drives Sensory Activation of Pomc Neurons

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

summary: In this study, we aimed at uncovering the molecular mechanisms underlying POMC neuron sensory activation and the mediated behavioral and metabolic processes. Unexpectedly, we found that glycogen metabolism is rapidly engaged in POMC neurons upon sensory food perception. Genetic deletion of glycogen synthase, the sole enzyme able to make glycogen in vivo, in POMC neurons impedes food-related sensory activation while causing impairments in food awareness, short-term food intake and insulin release. These perturbations associate with whole-body metabolic defects, including overweight and insulin resistance, that are exacerbated by high-dense diets or ageing. Collectively, our study identifies glycogen metabolism as an unanticipated mechanistic driver of POMC neuron sensory activation and provides paradigm-shift evidences of the importance of neuronal glycogen for physiology.

overall_design: POMCRiboTag mice were exposed to either an inaccessible nonedible object (NEO; wooden dowel pins in a wire mesh) or to sensory detection of food (SENS; standard chow in a wire mesh so that it could be seen and smelled but not consumed) for 10 minutes. The transcripts recruited to ribosomes specifically in POMC neurons were profiled through RNASeq.

first: Alicia

last: Gómez-Valadés

first: Elena

last: Eyre

first: Andrés

last: Vidal-Itriago

first: Macarena

last: Pozo

first: Mehdi

last: Boutagouga Boudjadja

first: Miriam

last: Toledo

first: Júlia

last: Fos

last: Beiroa

first: Maria

last: Milà-Guasch

first: Iñigo

last: Chivite

first: Arnaud

last: Obri

first: Sara

last: Ramírez

first: Roberta

last: Haddad-Tóvolli

first: Iassim

last: Tahiri

first: Giuseppe

last: D’Agostino

first: Rubén

last: Nogueiras

last: Duran

first: Joan

last: Guinovart

first: Marc

last: Claret


title: Ac4c modifications down-regulation in macrophages promotes suppressive tumor microenvironment in HCC

city: Hang Zhou

last: Xu

address: Huansha Roud

institute: Zhejiang University

summary:
To investigated how NAT10 inhibitor (Remodelin hydrobromide) affected the function of peritoneal macrophages , we treated peritoneal macrophages  IFN y，Remodelin hydrobromide and Remodelin hydrobromide with IFN y.
We then performed gene expression profiling analysis using data obtained from RNA-seq of peritoneal macrophages with four treaments

overall_design: Comparative gene expression profiling analysis of RNA-seq data for treated with IFNy,Remodelin hydrobromide and Remodelin hydrobromide with IFNy.

first: Shuai

last: Wang


title: Expression profiles of BMMs and osteoclasts

first: Chao

last: Song

state: Pennsylvania

address: 4141 Spruce St., Room 308

institute: Children's Hospital of Philadelphia

summary: To profile the overall transcriptomic changes, we performed RNA-seq with bone marrow macrophages (BMM) before and after osteoclast differentiation (day 0 vs day 4). To induce mature osteoclasts formation, BMM were seeded and culture with customized αMEM containing 1/50 CMG14-12 supernatant and 75 ng/ml RANKL for 4 days.

overall_design: Comparative gene expression analysis of RNA seq data for BMM (day0） and mature osteoclast (day4)

first: Fanxin

last: Long


title: A new adipocyte-specific long non-coding RNA engages impaired fatty acid sensing and dyslipidaemia in obese subjects (RNA-seq)

city: Barcelona

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: The relevance of adipose-derived long noncoding RNAs (lncRNAs) to the regulation of gene expression patterns related to the obese phenotype remains elusive. Here, the analysis of transcriptomes of adipose tissue before-after significant weight loss led to the identification of 496 putative lncRNAs (FDR p-values <0.05). Only the nonconserved linc-GALNTL6-4 displayed a fold-change above 2 plus adjusted p-value <0.0001. Exploration of additional omental and subcutaneous fat samples confirmed diminished linc-GALNTL6-4 in obese subjects, while lncRNA-mRNA co-expression analyses highlighted its association with fatty acid metabolism. Concurrently, the expression of this unique lncRNA towered in ex vivo isolated and in vitro differentiated adipocytes, being compromised under conditions that mimicked inflammation in obese adipocytes. On the other hand, the knockdown of linc-GALNTL6-4 in fat cell progenitors conveys impaired differentiation, fostering deranged expression patterns in differentiated adipocytes, including the increased expression of genes devoted to the transport of lipids, such as Apolipoprotein C1 (APOC1) and the intracellular fatty acid-binding protein FABP3. Conversely, overexpression of linc-GALNTL6-4 ameliorated adipocyte performance through the specific control of the short-chain fatty acid receptor FFAR3. Current data unveil the unforeseen relevance of linc-GALNTL6-4 as a modulator of fatty acid sensing in adipocytes deeply challenged by body weight and meta-inflammation.

overall_design:
To induce the adipogenic conversion of adipocyte progenitors, human preadipocytes (SP-F-1, Zen-Bio, Inc.) were led to grow as a monolayer in preadipocyte medium (PM-1) until reaching confluence, and then incubated with adipocyte differentiation medium (DM-2) for 7 days. This media is composed of DMEM / Ham’s F-12 (1:1), HEPES, FBS, biotin, pantothenate, insulin, dexamethasone, IBMX, PPARγ agonist, penicillin, streptomycin and amphotericin B. Thereafter, differentiating adipocytes were maintained in adipocyte maintenance medium (AM-1) for 7 additional days (DM-2 without dexamethasone, IBMX and PPARγ agonists). During this process, the shape of preadipocytes evolves from the flattened form to rounded cells containing abundant lipid droplets, and are thus considered differentiated, mature adipocytes (~12th day and thereafter). Once differentiated, we challenged these cultures of primary human adipocytes with the ectopic presence of synthetic small interfering (si-)RNAs directed against our lncRNA candidate.
8 samples were analysed (Control=4, siLINC2=4)

first: Francisco

last: Ortega

first: Aina

last: Lluch

first: Jèssica

last: Latorre

first: Núria

last: Oliveras-Cañellas


title: Ac4c modifications down-regulation in macrophages promotes suppressive tumor microenvironment in HCC (RIP-Seq)

summary:
Ac4C-binding RNAs were analyzed by imprinting RNA-sequencing of anti-Ac4C antibody-retrieved complexes from macrophages lysate.
We then performed gene expression profiling analysis using data obtained from RIP-seq of peritoneal macrophages incubated with IFN-G

overall_design: Examination of Ac4C-binding RNA from macrophages


title: Global gene expression analyses of channel catfish after being fed diets with inclusion of frass from black soldier fly larvae

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: Frass is the by-product of the larval meal industry and includes larval waste, exoskeleton sheds, and residual feed ingredients. Experimental frass was derived from the larvae of black solder flies (Hermetia illucens) fed distillers dried grains. A 10-week study was conducted to evaluate the effect of dietary levels of frass on the global gene expression of channel catfish, Ictalurus punctatus. Three diets containing 0, 50, and 300 g frass per kg diet were fed to channel catfish (5.24 ± 0.04 g) in quadruplicate aquaria to apparent satiation twice daily. Intestine (n=12 in pools of 3) and liver (n=12 in pools of 3) tissues were taken from fish at the end of the trial and processed for high-throughput Illumina RNA sequencing (RNAseq). Pairwise comparisons identified both up- and down-regulated genes in frass diets compared to no frass controls.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from channel catfish pooled liver and spleen tissues after being fed three different diets over a ten week period. Treatments include control diet (no frass inclusion) and two test diets with either 50mg frass inclusion (low frass) or 300mg frass inclusion (high frass). Tissues were pooled from three individuals; four pools were used for library creation and RNA-seq and treated as biological replicates.

first: Miles

last: Lange

first: Mediha

last: Aksoy

first: Rashida

last: Eljack

first: Benjamin

last: Beck

first: Nithin

last: Muliya Sankappa


title: A new adipocyte-specific long non-coding RNA engages impaired fatty acid sensing and dyslipidaemia in obese subjects (microarray)

first: Júlia

overall_design:
The increased expression of linc-GALNTL6-4 in primary in vitro differentiated human adipocytes was accomplished by means of a customized plasmid. To this end, the linc-GALNTL6-4 was first obtained and amplified from human liver cDNA, using specific primers with restriction sites for KpnI and FseI (Fwd, 5’-GGTAC* CCTTTTGCAGAAGTAGATGTGCG-3’; Rev, 5’-GGCCGG* CCATTCAAGTGGTTGTTTTATTGACA-3’). The resulting amplicon was purified and cloned into a modified pCMV6 vector (Origene, PS100001). Then, differentiated fat cells were transfected 1:3 with either our construct or an empty plasmid control using the FuGENE® HD Transfection Reagent (Promega).
10 samples were analysed (Control=5, LINC_OE=5)


title: Altered immune response and inflammation characterize patients with aortic valve sclerosis in acute myocardial infarction

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

summary: Background: Aortic valve sclerosis (AVSc) presents similar pathogenetic mechanisms to coronary artery disease (CAD) and is associated with both short- and long-term mortality. In the context of acute myocardial infarction (AMI), evidence of specific systemic mechanisms characterizing AVSc are currently lacking.  Objective: To evaluate the systemic pathophysiological landscape that might differentiate AVSc from non-AVSc subjects in AMI.  Methods: Whole-blood transcriptome of AVSc (n=44) and no-AVSc (n=66) patients with AMI was assessed by RNA-sequencing. A bioinformatic workflow, including feature selection, differential expression and enrichment analysis was performed to identify gene expression signatures discriminating AVSc from no-AVSc and infer functional association. Multivariable Cox regression analysis was used to estimate hazard ratio of AVSc versus no-AVSc patients.  Results: A signature of 100 informative genes allowed classifying AVSc from no-AVSc with 94% accuracy. Significant differences in 143 genes were also identified, 30 of which withstood association independently of age and previous AMI, or cardiac interventions. Functional inference unveiled significant association of AVSc with acute inflammatory and type I interferons (IFNs) response, platelet activation and hemostasis. AMI patients with AVSc showed a significantly higher incidence of adverse cardiovascular events within 10 years of follow-up with a full adjusted hazard ratio of 2.4 (95% CI 1.3–4.5).  Conclusions: During AMI, AVSc patients showed increased type I IFNs response and associated adverse cardiovascular outcomes at follow-up. Novel pharmacological therapies aiming to inhibit response to type I IFNs during or immediately after AMI might improve poor cardiovascular outcomes of AMI patients with AVSc.

overall_design:
A total of 110 whole-blood sample of AMI patients with AVSc or without AVSC have been used for RNA-sequencing. The population included 44 AMI with AVSc and 66 AMI without AVSc. A feature selection approach was used to identify a small set of informative genes to discriminate AVSc from no-AVSc patients. Differential expression and enrichment analysis were used to infer functional associations with the two sub-groups of patients.

Raw data for GSM6745956-GSM6745979 can be downloaded from PRJNA400456.

first: Mattia

last: Chiesa

first: Luca

last: Piacentini

middle: I

first: Paolo

last: Poggio


title: HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence

city: Suita

first: Mengying

last: Cui

institute: Osaka University

summary: Mitochondrial and lysosomal functions are intimately linked and are critical for cellular homeostasis, as evidenced by the fact that cellular senescence, aging, and multiple prominent diseases are associated with concomitant dysfunction of both organelles. However, it is not well understood how the two important organelles are regulated. Transcription factor EB (TFEB) is the master regulator of lysosomal function and is also implicated in regulating mitochondrial function; however, the mechanism underlying the maintenance of both organelles remains to be fully elucidated. Here, by comprehensive transcriptome analysis and subsequent chromatin immunoprecipitation sequencing (ChIP)-quantitative PCR (qPCR), we identified hexokinase domain containing 1 (HKDC1), which is known to function in the glycolysis pathway as a direct TFEB target. Moreover, HKDC1 was upregulated in both mitochondrial and lysosomal stress in a TFEB-dependent manner, and its function was critical for the maintenance of both organelles under stress conditions. Mechanistically, the TFEB–HKDC1 axis was essential for PINK1/Parkin-dependent mitophagy via its initial step, PINK1 stabilization. In addition, the functions of HKDC1 and voltage-dependent anion channels (VDACs), with which HKDC1 interacts, were essential for the clearance of damaged lysosomes and mitochondria-lysosome contact.Interestingly, the kinase regulated mitophagy and lysosomal repair independently from its function in glycolysis. Furthermore, loss function of HKDC1 accelerated DNA damage–induced cellular senescence with the accumulation of hyperfused mitochondria and damaged lysosomes. Our results show that HKDC1, a novel factor downstream of TFEB, maintains both mitochondrial and lysosomal homeostasis, which is critical to prevent cellular senescence.

overall_design: WT or TFEB KO or FLAG-expressing or TFEB-FLAG-expressing HeLa cells treated with or without valinomycin or CCCP or LLOMe

first: Shuhei

last: Nakamura

first: Tamotsu

last: Yoshimori


title: Evaluation of the specificity of transcriptional classifiers in larval Pimephales promelas exposed to toxic chemicals with different modes of action.

city: Cincinnati

first: John

middle: Walter

last: Martinson

state: Ohio

address: 26 W. Martin L. King Drive

department: ORD

summary:
RNA-seq expression assays were done in larval Pimephales promelas (Fathead minnow, FHM) exposed to either the pyrethroid pesticide Bifenthrin or copper sulfate.
Normalized gene expression profiles were used to identify genes differentially expressed between control samples and treated samples, and five machine learning methods were employed to predict the exposure status of the samples in a nested cross-validation framework in a binary manner with each treatment chemical.
Classifers trained with one chemical were tested against samples treated with the other chemical to evaluate the chemical specificity of the binary classifiers, and a random forest classifier trained with all three conditions (control, biefnethrin, copper) was also developed and used to predict sample class using a leave-one-out-cross-validation (LOOCV) approach.
Functional analysis based on canonical pathways represented by the genes differentially expressed in the two treatment groups was performed to find evidence that toxicant specific reponses were present in the two treatments.

overall_design: Comparative gene expression profiling analysis between controls and treated samples using RNA-seq data from statically exposed larval FHM larvae; untreated controls (n=11), 3.2 ug/L bifenthrin (n=10), or 40 ug/L CuSO4 (n=11).

first: Robert

last: Flick

first: Adam

last: Biales

first: David

middle: C

last: Bencic

first: Weichun

last: Huang

first: Mitchell

middle: S

last: Kostich


title: Melatonin alleviates LPS-induced abnormal pregnancy through MTNR1B regulation of m6A

first: Shisu

last: Zhao

address: No. 2 Yuanmingyuan West Road

institute: China Agricultural University

summary: In this study, the protective effect of melatonin and m6A on mouse pregnancy was studied by constructing an LPS-induced abnormal early pregnancy model in mice. Pregnant ICR mice were selected and intraperitoneal injection of LPS on D3 and D4 of pregnancy, melatonin was found to alleviated LPS-induced reductions in the number of implantation sites. Besides, melatonin alleviated the activation of inflammation, autophagy and apoptosis pathways, thereby protecting the pregnancy process of mice. We monitored m6A methylation by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and m6A-sequencing (m6A-seq), we found that melatonin regulated m6A methylation levels.

overall_design: m6A-seq of pregnant mouse uterus after treatment with LPS and Melatonin

first: Yanjun

last: Dong

first: Yuanyuan

last: Li

first: Zixu

last: Wang

first: Yaoxing

last: Chen

first: Yulan


title: Transcriptome-wide expression analysis of wild-type p53 and PANDAs in p53-null HCT116 cells

city: Shanghai

first: yangfei

last: Xing

state: Shanghai

address: 197 Rui Jin Er Road

department: Shanghai Institute of Hematology

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

summary: Our RNA-seq data suggested the different transcriptional profiles of wild-type p53 and PANDAs treated with or without ATO.

overall_design: Transcriptome-wide expression profiles of wild-type p53 and PANDAs in p53-null HCT116 cells.

first: Yangfei

first: Yigang

last: Tang

first: Yuntong

first: Min

last: Lu


title: Conservation of chromatin loops between mouse and human beta cells

city: Cleveland

first: Shanshan

last: Zhang

state: OH

address: 10900 Euclid Avenue

department: Department of Genome and Genetics

institute: Case Western Reserve University

summary: Studying the conservation and differences of regulation between human and mouse helps understand gene regulation on mouse models. Chromatin loop is an important gene regulatory mechanism to drive the 3D regulation between genes and their regulatory elements. Here, we performed eHi-C to profile genome wide contacts in mouse strains B6 and CAST islet beta cells, together with the loops identified in human islet alpha and beta cells from previous studies (GSE195523). The results show that the conserved chromation loop and open chromatin regions highlight the function of T2D risk loci and improve our understanding in islet biology.

overall_design: 3D genome structure mapping in beta cells from mouse starin B6 and CAST using easy Hi-C method

first: Xiaoxiao

last: Liu

first: Leina

first: Wanying

last: Xu

first: Mark

middle: P

last: Keller

first: Alan

last: Attie

first: Fulai

last: Jin

first: Yan


title: The DNA binding selectivity by wild-type p53 and PANDAs

summary: We performed ChIP-seq analysis of p53-null HCT116 cells stably expressed wild-type p53 or mutant p53 followed by ATO treatment (PANDAs) to identify p53 binding characteristics by wild-type p53 and PANDAs.

overall_design: Identification of the DNA binding characteristics by wild-type p53 and PANDAs


title: Discovery study in endometrial samples using RNA-HighSeq to build classifiers to differentiate between control patients and adenomyosis, ovarian endometriosis and deep infiltrating endometriosis

first: Xavier

last: Santamaria

state: Barcelona

address: Av. Diagonal 463 Bis Pl. 4

institute: Bioliquid Inovative Genetics SLU

summary: A discovery study using RNA-HighSeq from 37 endometrial biopsies was performed to build classifiers that differentiate between control patients and adenomyosis, ovarian endometriosis and deep infiltrating endometriosis. Total RNA was extracted from endometrial biopsies. We found an AUC of 0.97 where the classifier differentiated almost perfectly all three diseases together from the control group when including 11 phenotypic variables of the patients in the classifier.

overall_design: Transcriptome analysis by RNASeq of endometrial samples from control patients, women suffering from ovarian and deep infiltrating endometriosis as well women suffering from as adenomyosis.

first: Júlia

last: Vallvé-Juanico


title: Understanding the impact of KDM4 inhibition on host cell processes

city: Oxford

first: James

last: Harris

state: Oxfordshire

address: Old Road Campus, Roosevelt Drive

country: United Kingdom

institute: University of Oxford

summary: HepG2-NTCP cells were cultured in 1% oxygen or treated with a KDM4 inhibitor, QC6352, for 72 hours. RNA was extracted and the impact of treatment on the cellular transcriptome was investigated by RNA-sequencing.

overall_design: mRNA expression profiles of HepG2-NTCP cells cultured in 18% (control) or 1% Oxygen, or treated with 5uM QC6352 for 72 hours.

middle: M

first: Peter

last: Wing

first: Andrea

last: Magri

last: Balfe

first: Jane

last: McKeating


title: Single-cell Transcriptomics Dissects Premalignant Progression in Proliferative Verrucous Leukoplakia

city: Chengdu

first: Liang

last: Zhong

address: Renmin road

institute: Sichuan University

summary: Proliferative verrucous leukoplakia (PVL) is a potentially malignant disorder characterized by contiguous spread, a spectrum of clinicopathological features and high malignant transformation risk. Despite many efforts to describe the clinicopathological features of PVL progression, so far, there is still a lack of knowledge on the dynamic changes in molecular signature during this process. Hence, we applied single-cell RNA sequencing to 3 biopsy samples from a large PVL lesion. These samples exhibited the histopathological continuum of PVL lesions progression. By analysis for transcriptome profiling of 27,611 cells from these samples, we identified 10 major cell lineages and revealed the cellular remodeling occurring in the progression of PVL lesions, including epithelial, stromal and immune cells. The epithelial cells are shifted to pro-tumorigenic transcriptional cell states and secretory patterns at premalignant stage. Immune cells showed growing immunosuppressive phenotypes during PVL progression. Remarkably, two novel cell subtypes INSR+ endothelial cells and ASPN+ fibroblasts were discovered and may play a vital role in microenvironment remodeling, such as angiogenesis and stromal fibrosis, closely involved in the malignant transformation. Our work preliminarily describes the dynamic molecular properties of PVL lesions, enhances the systematic understanding of the premalignant evolution of PVL and attempts to provide the framework for future research.

overall_design: 3 samples taken from an  large lesion present a pathological continnum of oral proliferative verrucous leukoplakia

first: Hongxia

last: Dan

first: Fei

last: Wang

first: Dan

first: Wenjing

last: Kuang

first: Ning

last: Ji

first: Jing

last: Li

first: Xin

last: Zeng

first: Taiwen

first: Qianming

last: Chen


title: Gene expression changes in REH following STAT3 inhibition by shRNA

city: London

first: Luca

last: Gasparoli

address: 30 Guilford Street, Location 1B

department: Developmental Biology and Cancer

institute: UCL Great Ormond Institute of Child Health

summary: STAT3 (Signal transducer and activator of transcription 3) expression is associated with with t(12;21) acute lymphoblastic leukaemia (ALL) and it is crucial for the survival of the t(12;21) ALL . Our study investigated the STAT3 regulated pathways and discovered a novel STAT3-TP53 axis in B-ALL.  In order to determine the STAT3 regulated pathways in t(12;21) ALL cells, we performed RNAseq analysis on the Pre-B Acute Lymphoblastic Leukemia (ALL) cell line REH following shRNA-mediated STAT3 knockdown

overall_design: Total cellular RNA was purified from control scramble or shSTAT3 transduced REH samples from three independent experiments

first: Jasper

last: de Boer

first: Owen

last: Williams


title: Gene expression changes in REH following STAT3 pharmacological inhibition

summary: STAT3 (Signal transducer and activator of transcription 3) expression is associated with with t(12;21) acute lymphoblastic leukaemia (ALL) and it is crucial for the survival of the t(12;21) ALL . Our study investigated the STAT3 regulated pathways and discovered a novel STAT3-TP53 axis in B-ALL.  In order to determine the STAT3 regulated pathways in t(12;21) ALL cells, we performed RNAseq analysis on the Pre-B Acute Lymphoblastic Leukemia (ALL) cell line REH, treated with DMSO vehicle control in comparison to 50uM S3I-021, a specific STAT3 inhibitor

overall_design: Total cellular RNA was purified from DMSO and 50uM S3I-201 treated REH samples from three independent experiments


title: Sugar activates defense signaling in Arabidopsis

city: Kyoto

first: Akira

last: Mine

state: Kyoto

address: Kitashirakawaoiwake-cho

department: Graduate School of Agriculture

institute: Kyoto university

summary: Sugar is propose to be a signal molecules for defense in plants. Here, using RNA-seq, we revealed that the application of non-metabolizable glucose analogue 2-deoxy-d-glucose induces the expression of defense-related genes in Arabidopsis. In addition, loss of sugar transporters (STPs) leads to altered responsiveness to flg22, suggesting that sugar-mediated signaling contributes to plant defense.

overall_design: Seedlings of Col-0, stp1stp4stp13 and fls2 were treated with 1 μM flg22 or 1 mM 2-deoxy-d-glucose. Plants were harvested as a single biological replicates at 2, 10, 24 hours after flg22 application or at 24 hours after 2-deoxy-d-glucose application. To generate three biological replicates, three independent experimental trials were carried out.

first: Kohji

last: Yamada


title: Characterizing hookah smoking-induced transcriptional regulations in the human bronchial epithelial cell

city: Hsinchu City

first: Sing-Hang

last: Huang

address: Rm. 304, No.75, Bo’ai St., East Dist.

department: Institute of Bioinformatics and Systems Biology

country: Taiwan

institute: National Chiao Tung University

summary: Hookah smoking is becoming increasingly popular worldwide and recent epidemiological studies indicate that it is significantly associated with respiratory diseases, and could contain constituents more harmful than cigarette smoking. However, the gene expression alterations and mechanisms of disease development induced by the hookah constituents are still unclear. Here, we propose a new experimental design that compared the constituents of hookah smoking generated with different heating ways and w/wo tobacco, for studying the harmful effects on respiratory cells (30 samples among five conditions).

overall_design: BEAS-2B cells were exposed to various conditions of hookah smoking, including internal control (IC), charcoal with no shisha (C), charcoal with non-tobacco (herbal) shisha (CNT), charcoal with tobacco shisha (CT), and electronic heater with tobacco shisha (ET) for 30 min while on a rocker. The exposure concentration was measured as the highest that caused no toxicity at 24 hours, as assayed by LDH release. For each exposure group, three wells were treated with Trizol at 2 and 24 hours after exposure. Then, all of these samples were performed RNA-seq to analyze whole-genome transcriptome using Illumina HiSeq 2500 platform with 50 bp single-end reads (Illumina, USA).

first: Sing-Han

first: Yi-Hsuan

last: Chuang

first: Terry

last: Gordon

first: Hong

last: Sun

first: Lung-Chi

first: Jinn-Moon

last: Yang