title: Transgenerational transcriptomic and DNA methylome profiling of mouse fetal testicular germline and somatic cells after exposure of pregnant mothers to tributyltin, a potent obesogen

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

summary: Obesogens such as tributyltin (TBT) are xenobiotic compounds that promote obesity, in part by distorting the normal balance of lipid metabolism. The obesogenic effects of TBT can be observed in directly exposed (F1 and F2 generations) and also subsequent generations (F3 and beyond) that were never exposed. To address the effects of TBT exposure on germ cells, we exposed pregnant transgenic OG2 mouse dams (F0), which specifically express EGFP in germline cells, to an environmentally relevant dose of TBT throughout gestation through drinking water. When fed with a high fat diet (HFD), F3 male offspring of TBT-exposed F0 dams (TBT-F3) accumulated much more body fat than did Control-F3 males. TBT-F3 males also lost more body fluid and lean compositions than did Control-F3 males. Expression of genes involved in transcriptional regulation or mesenchymal differ-entiation was upregulated in somatic cells of TBT-F1 (but not TBT-F3) E18.5 fetal testes, and promoter-associated CpG islands were hyper-methylated in TBT-F1 somatic cells. Global mRNA expression of protein-coding genes in F1 or F3 fetal testicular cells was unaffected by F0 exposure to TBT; however, expression of a subset of endogenous retroviruses was significantly affected in F1 and F3. We infer that TBT may directly target testicular somatic cells in F1 testes to irreversibly affect epigenetic suppression of endogenous retroviruses in both germline and somatic cells.

overall_design: Mouse E18.5 fetal testicular cells were separated to germline cells (P4 and P5 populations) and somatic (P6) cells and then subjected to RNA-sesq (transcriptomic profiling) or MBD-seq (DNA methylation analysis).

first: Keiko

first: Junko

last: Odajima

first: Bruce

last: Blumberg

first: Toshi


title: Superoxide dismutase-3 downmodulates laminin α5 expression in endothelial cells via Nuclear Factor kappa B signaling inhibition

status: Public on Mar 02 2022

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: The balance between laminins containing the α5 (LAMA5) or the α4 (LAMA4) subunits is determinant for the diapedesis of different leukocyte subtypes in inflammatory conditions. We have shown that the extracellular superoxide dismutase (SOD3) is a positive regulator of LAMA4, and this was associated with enhanced intratumor T cell infiltration in experimental and primary human cancers. Here we show that SOD3 overexpression in neoplastic or endothelial cells (ECs) downmodulates LAMA5 levels in implanted tumors. The inhibitory effect of SOD3 on LAMA5 expression occurs at the transcriptional level and is specific for SOD3, since LAMA5 levels are not changed by in SOD1-overexpressing cells. Global transcriptomic analyses revealed that SOD3 overexpression changes the transcription of 1,682 genes in ECs exposed to tumor secreted factors, being the canonical and non-canonical Nuclear Factor kappa B (NF-κB) pathways major SOD3 targets. Indeed, SOD3 reduced the transcription of well-known NF-κB target genes as well as the NF-κB-driven promoter activity in endothelial cells stimulated with tumor necrosis factor (TNF)-α, an inducer of NF-κB signaling

overall_design: Total RNA from two cell types (1G11-mock and 1G11-SOD3), with three biological replicates per cell type, were hybridyzed to mouse Agilent microarrays (one color per slide).

first: Lorena

last: Carmona-Rodríguez

first: Diego

last: Martínez-Rey

first: Paula

last: Martín-González

first: Mònica

last: Franch

first: Lydia

last: Sorokin

first: Emilia

last: Mira

first: Santos

last: Mañes


title: Qingda granule（QDG） treatment lower Angiotensin-II-induced blood pressure

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

country: China

institute: Fujian University of Traditional Chinese Medicine

type: Expression profiling by high throughput sequencing

summary: The goals of this study is to compare the differently expressed genes in renal tissue of C57BL/6 WT mice with or without Angiotensin II (AngII) treatment as well as differently expressed genes in the  renal tissue  of WT mice with AngII treatment with or without Qingda granule（QDG）treatment. The mice (n=15) were randomly divided into 3 groups: control, AngII,AngII+ QDG (n=5 for each group). Mice in Control and AngII groups were infused with saline or 500 ng/kg/min of AngII respectively, and  intragastrically with double distilled water (dd H2O); while mice in AngII + QDG groups were infused with AngII (500 ng/kg/min) and  intragastrically with 1.145 g/kg/D of QDG for 4 weeks.  Then the renal tissue were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with renal tissue of  mice in 3 groups: control, AngII, Qingda granule（QDG） treated (n=5 for each group) to identify the differently expressed genes and related pathway.

first: Aling

last: Shen

first: Linzi

last: Long

first: Xiuli

last: Zhang


title: Maelstrom functions in the production of Siwi-piRISC capable of regulating transposons in Bombyx germ cells

city: Tokyo

first: Yurika

last: Namba

state: --- Select a state ---

address: 2-11-16 Yayoi, Bunkyo-ku

department: Department of Biological Sciences, Graduate School of Science

country: Japan

institute: The University of Tokyo

summary: PIWI-interacting RNAs (piRNAs) bind to PIWI proteins to assemble the piRISC, which represses germline transposons. Maelstrom (Mael) is necessary for piRISC biogenesis in germ cells, but its function remains unclear. Here, we show that Mael interconnects Spindle-E (Spn-E), a key piRISC biogenesis factor, with unloaded Siwi, one of two silkworm PIWI members. Mael also assembles a subset of nuage, a non-membranous organelle involved in piRISC biogenesis. Loss of Mael abrogated the Spn-E–Siwi interaction and Ago3-piRISC biogenesis, but Siwi-piRISC was produced. Bioinformatic analysis showed that Siwi-bound piRNAs in Mael-lacking cells were rich in transposon-targeting piRNAs as in normal cells but were biased toward transposons that are marginally controlled by Siwi-piRISC. This explains the impairment in Ago3-piRISC production because transposon mRNAs cleaved by Siwi are the origin of Ago3-loaded piRNAs. We argue that Mael plays a role in the production of primary Siwi-piRISC capable of regulating transposon expression in germ cells.

overall_design:
Six smRNA-seq libraries: PIWI-associated small RNA libraries were prepared from small RNAs associated with Flag-Siwi immunoprecipitates with size selection at 22-35nt.
Six RNA-seq libraries: RNA libraries were prepared from total RNAs with poly-A selection.

first: Mikiko

middle: C

last: Siomi


title: Anatomical transcriptome atlas of the male mouse reproductive system during aging

city: Guangzhou

first: Yun

last: Xie

state: China

address: No. 58 Zhongshan 2nd Road, Yuexiu District, 0080, China.

institute: sun yat-sen university

summary: The testis, efferent ductules, epididymis, and vas deferens, constituting the majority of male reproductive tract, are the regions for testosterone production, spermatogenesis, and sperm maturation, storage and discharge, but whether these regions change during aging is unknown. Here, we addressed this by investigating the adult (3-month) and aged (18-month) transcriptomes from seven regions of male mouse reproductive tract：the testis, efferent ductules, initial segment, caput, corpus and cauda epididymis, and vas deferens. We identified various of region-specific genes across different regions of male mouse reproductive tract. Moreover, we identified region-dependent changes of transcripts at an anatomic resolution. This study provides a framework for futher studies on male reproducitve aging.

overall_design: The tissues (testis, efferent ductules, initial segment, caput, corpus and cauda epididymis, and vas deferens) were dissected from the 3 months (n = 4) and 21 months old mice (n = 4). After total RNA extraction and library  preparation, high throughput RNA sequencing was performed using Illumina novaseq 6000. Reads were aligned with Hisat2 to the mouse genome (Ensemble Mouse GRCm38).

first: Yang-Ping

last: Huang

first: Qi-Yun

last: Yang

first: Chun-Hua

last: Deng


title: miRNA sequencing from exosomes derived from M1-or M2-polarized bone-marrow derived macrophages (BMDMs).

city: Baltimore

first: Gijung

last: Kwak

state: Maryland

address: 400 N. Broadway

department: School of Medicine

country: USA

institute: Johns Hopkins University

type: Non-coding RNA profiling by high throughput sequencing

summary: We reported exosome-guided phenotype switches between M1- and M2-polarized BMDMs. M1- or M2-polarized BMDMs were successfully reprogrammed to M2- or M1-phenotype via the treatment of exosomes obtained from M2- or M1-polarized BMDMs. In this uploaded information, the exosomes from M1- and M2-polarized BMDMs were analyzed by high-throughput sequencing.

overall_design: Examination of 2 different exosomes derived from M1- and M2-polarized BMDMs.

first: Sun Hwa

last: Kim


title: Gene expression profile of breast cancer cell line MDA-MB-231 xenograft - discovery set

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: Progression to stage IV disease remains the main cause of breast cancer-related deaths. Increasing knowledge of the hematogenous phase of metastasis is key for exploiting the entire window of opportunity to interfere with early dissemination and to achieve a more effective disease control. On the hypothesis that the distinguishing molecular features of circulating tumor cells (CTCs) reveal useful information on metastasis biology and disease outcome, we compared the transcriptomes of CTCs and solid primary/secondary lesions of the MDA-MB-231 xenograft model and provided evidence that blood-borne dissemination is regulated by numerous genes. Our new CTC-specific signature improved CTC detection and outcome prognostication in early-stage breast cancer patients compared to conventional CTC markers, and shed light on the metastatic process by highlighting the role of two genes.

overall_design: We injected MDA-MB-231 breast cancer cells in the mammary fat pad of NOD scid female mice and ran two independent gene expression profile experiments using tissues from three animals each. Sample profiling was carried out through the Whole-Genome DASL HT Assay. We first demonstrated that query oligos detect human and not murine RNA sequences, and compared the transcriptomes of (i) frozen sections of primary tumor nodules, lymph-nodes and lungs (solid lesions), (ii) circulating tumor cells isolated from blood samples (CTC), (iii) tumor cells disseminated to bone marrow flushed out from femur bones (DTC), and (iv) in vitro cultured MDA-MB-231 cells (parental cell line). A universal Mouse RNA reference was used as negative control (CG96_UMR).

first: Emanuela

last: Fina

first: Vera

last: Cappelletti


title: Epigenetic marks imply a common cellular origin of virus- and UV-associated Merkel cell carcinoma (MCC)

city: Essen

first: Jan

last: Gravemeyer

address: Universitätstraße 1

country: Germany

institute: DKZF

summary: Differences in DNA-methylation between VP- and UV-MCCs mainly refer to heterogeneity in carcinogenesis rather than an origin in utterly different cell types. Indeed, a principal component derived scoring suggest an epithelial for UV-MCC as well as VP-MCC cell lines.

overall_design: This study compared the DNA methylation patterns of virus- (VP-MCC) and UV-light associated (UV-MCC) Merkel cell carcinoma cell lines

first: Jürgen

last: Becker


title: Expression data from Hela cells stably expressing the wild-type HBx and the four mutant HBx

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

institute: Second Military Medical University

summary:
In large cohort studies, several HBx mutants were identified as independent risk factors for HCC risk.In order to study the carcinogenic mechanism between different mutants, HeLa cell lines expressing wild type and different mutated HBx proteins were constructed.
We used microarrays to describe gene expression in HeLa cells  stably expressing the wild-type HBx and the four mutant HBx, and to identify distinct classes of up-regulated genes.

overall_design: HBV DNA extracted from HCC patients was used as a template to amplify HBx gene fragments and construct corresponding lentiviruses. Lentiviral vectors expressed different HBx mutant proteins in Hela cells. Microarray analysis was performed on the constructed cells.

first: Wenbin

last: Liu

first: Xinyu

last: Zhou


title: Evaluation the targeted nanobubbles mediated LND against hepatocellular carcinoma by sonodynamic therapy with RNA-Seq

city: Harbin

first: shang

last: haitao

address: Haping road

department: ultrasound department

institute: Harbin Medical University Cancer Hospital

summary: Sonodynamic therapy is an important approach in the treatment of hepatocellular carcinoma. A novel targeted nanobubbles loaded with HMME and LND was structured as sensibilizer, characterized the properties, and studied therapeutic effect on hepatocellular carcinoma. Next-generation high throughput RNA sequencing (RNA-Seq) was performed to accurately analyze the differential expression of mRNAs and lncRNA targets in hepatocellular carcinoma after sonodynamic therapy.

overall_design: HepG2  cells and Huh7 cells were used for the research. The cells were transfected using the nanoparticles with the aid of low-frequency ultrasound (LFUS) exposure. Two groups of  cells were analyzed using high-throughput RNA sequencing.

first: Haitao

last: Shang

first: Yichi

first: Bolin

last: Wu

first: Chunyue

last: Wang

first: Wen

last: Cheng


title: Transcriptomic and GC-MS metabolomic analysis to provide insight into aroma volatile compounds of ‘Granny Smith’ and ‘Jonagold’ apples (Malus domestica)

city: Yangling

first: Zhengyang

last: Zhao

address: Taocheng Road

institute: Northwest A&F university

summary: In order to know more about the expression levels of aroma-related genes involved in the metabolic pathways, transcriptome sequencing of Granny Smith and Jonagold apples was conducted utilizing the Illumina platform. Our study provides new insights on the understanding of transcriptional regulatory mechanisms associated with aroma volatiles formation in apples.

overall_design: Two samples of Granny Smith and Jonagold apples are analyzed and three biological replicates are included.

first: Shunbo

last: Yang


title: RNA sequencing of polymerase II-associated factor 1 complex (PAF1c) mutants at 10°C and 23°C  under LD conditions

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

summary: We sequenced mRNA of WT (Col-0) and PAF1c single mutants (php, elf7, vip3, vip4, vip5, and vip6) grown at 10°C and 23°C  under LD conditions. RNA was extracted from seedlings of 1.02 developmental stage at both temperatures and proceeded for library preparation

overall_design: RNA extracted followed by high-throughput transcriptome sequencing of WT (Col-0) and PAF1c single mutants (php, elf7, vip3, vip4, vip5, and vip6) grown at 10°C and 23°C  under LD conditions

first: Ji

middle: H

last: Ahn


title: Expression data of endometrium from patients with recurrent implantation failure and normal women

city: Beijing

first: Feiyan

state: Beijing

address: Yaojiayuan Road No.251

institute: Beijing Obstetrics and Gynecology Hospital, Capital Medical University

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

summary:
Recurrent implantation failure (RIF) is a challenge in the field of reproductive medicine. The dysfunction of endometrium is one of the pathogenesis of implantation failure.
We used microarrays to detail the global programme of gene expression underlying the molecular pathogenesis of implantation failure.

overall_design: Endometrium tissues from five RIF and five control women were obtained for RNA extraction and hybridization on Agilent microarrays. We aimed to select differentially expressed RNA in the RIF patients.

first: Tong


title: Spatial transcriptome profiling identifies CREB1 as a regulator of core transcriptional programs in idiopathic pulmonary fibrosis

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 300 Cedar St

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale School of Medicine

summary: A defining feature of idiopathic pulmonary fibrosis is the regional heterogeneity of the lung pathology. Here we established methodology to study the transcriptome of spatially discrete morphological areas in IPF lung tissue through the integration of laser capture microdissection of formalin fixed paraffin embedded lung tissue with low input RNA-Seq. We applied this methodology to obtain an in situ transcriptome for fibroblast foci and alveolar septae from IPF tissue as well as alveolar septae from age sex-matched control lung tissue. Differential gene expression analysis was performed between IPF alveolar septae vs control alveolar septae and between IPF fibroblast foci vs alveolar epithelium. Metacore TM was used for gene enrichment analysis of significantly differentially expressed genes, for transcription factor (TF) network analysis to identify predicted TF from human TF-target gene interaction.

overall_design: Laser capture microdissection was performed upon formalin fixed paraffin embedded (FFPE) control non-fibrotic lung tissue (alveolar septae (n=10)) and UIP/IPF FFPE lung tissue (myofibroblast foci, (n=10) and adjacent non-affected alveolar septae (n=10)).

first: Milica

last: Vukmirovic

first: Xiting

last: Yan

first: Mark


title: Small RNA-sequencing in primary breast fibroblasts treated and not-treated with breast cancer exosomes

city: Naples

first: Gerolama

last: Condorelli

address: Via Pansini,5

department: Department od Molecular Medicine and Medical Biotechnology

institute: University of Naples "Federico II"

summary: We report the application of small-RNA-sequencing technology for high-throughput profiling of  microRNAs in primary mammalian fibroblasts upon breast cancer-derived exosome treatment. We generated microRNA expression profile by obtaining 928(?) microRNA sequences diffrentially expressed between fibroblasts incubated with exosomes and with PBS (NT,negative control).  Among  14 (?) microRNAs significantly upregulated in primary fibroblasts after exosome treatment, we demonstrated that microRNA-185-5p, microRNA-652-5p, and microRNA-1246 were actively involved in fibroblasts functional activation, thus corroborating our initial hypothesis.

overall_design: Examination of miRNAs differentially expressed in fibroblasts treated with breast cancer exosomes compared to not-treated fibroblasts


title: Single-cell RNA-sequencing of skin immune cells uncover a role for Angptl4-mediated ifi20b expression in monocyte cell fate differentiation during wound healing

city: Singapore

first: Hong Sheng

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine,

country: Singapore

institute: Nanyang Technological University

summary: Angiopoietin-like protein 4 (Angptl4) is a matricellular protein that associates with extracellular matrix proteins, mediating complex cell-cell, and cell-matrix interactions. It has been implicated in various inflammation-associated diseases, including wound healing, but very few reports describe a direct role for Angptl4 in the immune landscape of wound microenvironment. Here, we studied whether Angptl4 regulates the immune response during wound healing. Using single-cell RNA sequencing to examine the temporal changes in the immune cell landscape of excisional wounds from wild type and Angplt4-knockout (Angplt4-/-) mice revealed that Angptl4-/- wounds had a stalled inflammatory phase. Infiltrated neutrophils remained elevated in the Angptl4-/- wounds due to an impaired monocyte to macrophage differentiation needed for clearance. The impaired monocyte differentiation was also validated in wounds using multi-color flow cytometry. Pairwise comparisons of differentially expressed genes from wound-derived and bone-marrow derived macrophages demonstrated few differences, suggesting that Angptl4 has a confined regulome. We identified interferon activated protein 202B (ifi202b) to be consistently upregulated in Angptl4-/- macrophages. . Pathway analysis further confirmed that ifi202b significantly impacted multiple gene networks involved in the cell fate of monocytes and the functions of monocyte-derived macrophages. Taken altogether, we conclude that Angptl4 orchestrates the inflammatory state, innate immune landscape, and healing process in the wound microenvironment via its transcriptional regulation on ifi202b.

overall_design: Single cell RNA-sequencing of the immune cells isolated from excisional wounds on wildtype and Angptl4-knockout mice at 1- and 5-days post wounding

first: Wei

middle: J

last: Wee

first: Nguan

middle: S

last: Tan


title: Ultra-Efficient Exosome-Guided Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes [miRNA-Seq]

city: SEOUL

first: HYOSUK

last: KIM

address: 5, Hwarang-ro 14-gil, Seongbuk-gu

institute: Korea Institute Science and Technology

summary: Direct lineage conversion holds great promise in the regenerative medicine field for restoring damaged tissues using functionally engineered counterparts. However, current methods of direct lineage conversion, even those employing virus-mediated transgenic expression of tumorigenic factors, are extremely inefficient (~25%). Thus, advanced methodologies capable of revolutionizing efficiency and addressing safety issues are key to clinical translation of these technologies. Here, we propose an exosome-guided, non-viral, direct-lineage conversion strategy to enhance transdifferentiation of fibroblasts to induced cardiomyocyte-like cells (iCMs). Exosomes produced during the cardiac differentiation process of embryonic stem cells (ESCs) are able to achieve extremely high reprogramming efficiency (>60%) by generating functional iCMs from mouse embryonic fibroblasts via a cardiac precursor-like stage rather than a pluripotent state. The resulting iCMs possess typical cardiac Ca2+ transients and electrophysiological features, and exhibit global gene expression profiles similar to those of cardiomyocytes. The optimized reprogramming conditions produce beating iCM clusters ~3-fold more efficiently than conventional methods. This is the first demonstration of the use of exosomes derived from ESCs undergoing cardiac differentiation as biomimetic tools to induce direct cardiac reprogramming with greatly improved efficiency, establishing a general, more readily accessible platform for broadly generating a variety of specialized somatic cells through direct lineage conversion.

overall_design: microRNA sequencing for exosome analysis of MEF, iCMs at day 15, iCMs at day 30 and nCMs

first: Hyosuk

last: Kim


title: Ultra-Efficient Exosome-Guided Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes [Quant-seq]

overall_design: Quant-seq 3’ mRNA sequencing for gene expression analysis of MEF, iCMs at day 15, iCMs at day 30 and nCMs


title: Phenotypic convergent evolution towards fosfomycin collateral sensitivity of Pseudomonas aeruginosa antibiotic resistant mutants

first: Juan

last: Oliveros

summary: In this work we describe a robust fosfomycin collateral sensitivity phenotype of Pseudomonas aeruginosa resistant mutants selected by antibiotics from different structural families. The underlying mechanism was the reduced expression of the genes encoding the peptidoglycan-recycling pathway, which preserves the peptidoglycan synthesis in situations where the de novo synthesis is blocked, and of fosA, encoding a fosfomycin-inactivating enzyme.

overall_design: Transcriptomic analysis of P. aeruginosa antibiotic resistant mutants (here dubbed Tgc5d, Tob5d and Caz5d) compared to wild-type PA14 strain

first: Pablo

last: Laborda

first: Sara

last: Hernando-Amado

first: José

middle: L

last: Martínez


title: Dissecting the Balance between Metabolic and Oncogenic Functions of Astrocyte Elevated Gene-1/Metadherin (AEG-1/MTDH)

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

summary: Obesity is an enormous global health problem and obesity-induced non-alcoholic steatohepatitis (NASH) is contributing to a rising incidence and mortality for hepatocellular carcinoma (HCC). Increase in de novo lipogenesis (DNL) and decrease in fatty acid -oxidation (FAO) underlie hepatic lipid accumulation in NASH. Astrocyte elevated gene-1/metadherin (AEG-1/MTDH) overexpression contributes to both NASH and HCC. AEG-1 harbors an LXXLL motif through which it blocks activation of peroxisome proliferator activated receptor  (PPAR), a key regulator of FAO. To better understand the role of LXXLL motif in mediating AEG-1 function, using CRISPR/Cas9 technology, we have generated a novel mouse model (AEG-1-L24K/L25H) in which the LXXLL motif in AEG-1 was mutated to LXXKH. We observed increased activation of PPAR in AEG-1-L24K/L25H livers providing partial protection from high fat diet (HFD)-induced steatosis. Interestingly, even with equal gene dosage levels, compared to AEG-1-WT livers, AEG-1-L24K/L25H livers exhibited increase in levels of lipogenic enzymes, mitogenic activity and inflammation which are attributes observed when AEG-1 is overexpressed. These findings indicate that while LXXLL motif favors steatotic activity of AEG-1 it keeps in check inflammatory and oncogenic functions thus maintaining a homeostasis in AEG-1 function. Conclusion: AEG-1 is being increasingly appreciated as a viable target for ameliorating NASH and NASH-HCC and as such in-depth understanding of the functions and molecular attributes of this molecule is essential. The present studies unravel the unique role of the LXXLL motif in mediating the balance between the metabolic and oncogenic functions of AEG-1.

overall_design: mRNA from AEG-1-WT, AEG-1-L24K/L25H hepatocytes, treated vs. untreated with PPARalpha-agonist CP775146

first: Yetirajam

last: Rajesh

first: Saranya

last: Reghupaty

first: Rachel

last: Mendoza

first: Debashri

last: Manna

last: Subler

first: Dawn

last: Garcia

first: Zhao

last: Lai

first: Shah

last: Giashuddin

first: Paul

middle: B

last: Fisher

first: Arun

last: Sanyal

middle: G

first: Jolene

last: Windle

first: Devanand

last: Sarkar


title: Response of LUAD cells to LCS3

city: Vancouver

first: William

last: Lockwood

state: British Columbia

address: 675 West 10th Avenue

department: Integrative Oncology

country: Canada

institute: BC Cancer

summary: High-throughput phenotype-based screening of large libraries of compounds can identify small molecules that elicit a desired cellular response, but additional approaches are required to find and characterize their targets and mechanisms of action. Here we show that a compound termed lung cancer screen 3 (LCS3), previously selected for its ability to impair the growth of human lung adenocarcinoma (LUAD) cell lines, but not normal lung cells, induces oxidative stress and activates the NRF2 signaling pathway by generating reactive oxygen species (ROS) in sensitive LUAD cell lines. To identify the effector that mediates this effect, we applied thermal proteome profiling (TPP) and uncovered the disulfide reductases GSR and TXNRD1 as LCS3 targets. Through enzymatic assays using purified protein, we confirmed that LCS3 inhibits disulfide reductase activity through a reversible, uncompetitive mechanism. Further, we demonstrate that LCS3-sensitive LUAD cells are correspondingly sensitive to the synergistic inhibition of glutathione and thioredoxin pathways. Lastly, a genome-wide CRISPR screen identified the loss of NQO1 as a mechanism of LCS3 resistance. This work highlights the power of TPP to uncover targets of small molecules identified by high-throughput screens and demonstrates the potential utility of inhibiting disulfide reductases in treatment of LUAD.

overall_design: Two LUAD cell lines (H1650 and H23) sensitive to LCS3 were treated with the 3uM LCS3 or DMSO (0.1%)  and RNA harvested at the points indicated for expression analysis using Affymetrix arrays. In total, two biological replcates were analyzed for each cell line for each treatment condition/time point.

middle: W

first: Fraser

last: Johnson


title: Transcriptome alterations in prostates from Trp53 R270H mutant mice following irradiation

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: Our group previously demonstrated that the Trp53 R270H mutation can drive prostate cancer (CaP) initiation in a genetically engineered mouse model (FVB.129S4(Trp53tm3Tyj/wt);FVB.129S(Nkx3-1tm3(cre)Mmswt)). The objective of the current study was to identify molecules that may facilitate Trp53 R270H-mediated prostate carcinogenesis. Mice that harbor a Trp53 R270H germline mutation (B6.129S4-Trp53tm3.1Tyj/J) were used for the current study. Wildtype (Trp53WT/WT), heterozygous (Trp53R270H/WT), and homozygous mice (Trp53R270H/R270H) were exposed to 5 Gy radiation to activate and stabilize p53 and thereby enhance our ability to identify differences in transcriptional activity between the 3 groups of mice. Mouse prostates were harvested 6 hours post-irradiation and either processed for histological/immunohistochemistry (IHC) analysis or snap-frozen for RNA extraction and transcriptome profiling with RNA-Sequencing (RNA-Seq) analysis. IHC was used to assess cell proliferation (Ki67) and apoptosis (activated caspase 3). PIN lesions were observed in heterozygous and homozygous mice as early as 3 months, thereby validating our prior finding that the Trp53 R270H mutation can drive CaP initiation. RNA-Seq analysis identified 1,378 differentially expressed genes, including multiple wildtype p53 target genes (E.g. Cdkn1a, Bax, Bcl2, Kras, Mdm2), p53 gain-of-function (GOF) genes (Mgmt, Id4), and CaP-related genes (Cav-1, Raf1, Kras). Our combined data validate a role for the Trp53 R270H mutation in CaP initiation, and identify molecules that may contribute to Trp53 R270H-mediated prostate carcinogenesis.

overall_design: The study consisted of 3 groups of mice with duplicate sampels in each. Mice that were homozygous (Trp53+/+) for wild type Trp53 served as the control group. The experimental groups consisted of mice that were heterozygous (Trp53R270H/+) or homozygous (Trp53R270H/R270H) for the Trp53 R270H mutation.  At ~3 months of age, mice were exposed to 5 Gy whole body irradiation. Mouse prostates were harvested 6 hours post-irradiation and snap-frozen for subsequent RNA extraction and transcriptome profiling with RNA-Sequencing (RNA-Seq) analysis.

first: Ruth

last: Vinall


title: Peroxisomes are dispensable for normal renal function.

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

summary: Peroxisomes are highly abundant in proximal tubules where peroxisomal enzymes have been proposed to play an important role in a variety of metabolic and antioxidant functions. This hypothesis was supported by human genetic studies that identified mutations leading to peroxisomal biogenesis deficiency, resulting in severe multi-organ damage (Zellweger’s spectrum disorders (ZSD)), including renal impairment. However, the role of proximal tubule peroxisomes in renal (patho)physiology remains uninvestigated. We addressed this question in mice with conditional ablation of peroxisomal biogenesis in the renal tubule. Our results demonstrate that renal tubular peroxisomes are dispensable for normal renal function and suggest that renal damage in ZSD patients is of extrarenal origin.

overall_design: Peroxisome biogenesis in the renal tubule was disrupted through conditional inactivation of Pex5 encoding cytosolic peroxisome targeting signal 1 (PTS1) receptor essential for import of PTS1 motif-containing proteins into peroxisomes. The Pex5 deletion in the renal tubule of adult mice was induced by 2-week treatment with DOX of 8-week-old Pex5lox/lox/Pax8-rtTA/LC1 male and female mice. In parallel, the same DOX treatment was provided to their littermate controls (Pex5lox/lox mice). All experiments on adult mice were performed 4 weeks after the end of DOX treatment.

first: Camille

last: Ansermet

first: Gabriel

last: Centeno

first: Andy

first: Yohan

last: Bignon

first: Dmitri

last: Firsov


title: Nanostring nCounter Bovine Arrival BRD 60 Panel v1.0

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

summary: The objective of this study was to corroborate the findings of previous BRD-associated transcriptome experiments, utilizing multiple independent populations of high-risk beef cattle.

overall_design: Blood samples were utilized from 240 cattle at facility arrival, across seven independent populations. Samples were randomly selected from cattle never having received clinical treatment for bovine respiratory disease (Healthy, n=116) and those having been treated at least one time in the 28 days post-arrival (BRD, n=124). BRD samples were further stratified into disease severity cohorts, based on frequency of treatment and mortality (Treated_1, n=91; Treated_2+, n=33). Samples were profiled for mRNA expression with the NanoString nCounter SPRINT Profiler, selecting 56 genes plus four internal controls. Quality control and differential expression was analyzed with nSolver v4.0. Six samples were removed from further analysis due to poor quality assessment and/or flagged normalization values.

middle: A


title: Spatial transcriptomic and single-nucleus analysis reveals heterogeneity in a gigantic single-celled syncytium

city: Heidelberg

first: Tobias

last: Gerber

address: Meyerhofstr. 1

department: Developmental Biology

institute: EMBL Heidelberg

summary: In multicellular organisms, the specification, coordination, and compartmentalization of cell types enable the formation of complex body plans. However, some eukaryotic protists such as slime molds generate diverse and complex structures while remaining in a multinucleated syncytial state. It is unknown if different regions of these giant syncytial cells have distinct transcriptional responses to environmental encounters, and if nuclei within the cell diversify into heterogeneous states. Here we performed spatial transcriptome analysis of the slime mold Physarum polycephalum in the plasmodium state under different environmental conditions, and used single-nucleus RNA-sequencing to dissect gene expression heterogeneity among nuclei. Our data identifies transcriptome regionality in the organism that associates with proliferation, syncytial substructures, and localized environmental conditions. Further, we find that nuclei are heterogenous in their transcriptional profile, and may process local signals within the plasmodium to coordinate cell growth, metabolism, and reproduction. To understand how nuclei variation within the syncytium compares to heterogeneity in single-nucleated cells, we analyzed states in single Physarum amoebal cells. We observed amoebal cell states at different stages of mitosis and meiosis, and identified cytokinetic features that are specific to nuclei divisions within the syncytium. Notably, we do not find evidence for predefined transcriptomic states in the amoebae that are observed in the syncytium. Our data shows that a single-celled slime mold can control its gene expression in a region-specific manner while lacking cellular compartmentalization, and suggests that nuclei are mobile processors facilitating local specialized functions. More broadly, slime molds offer the extraordinary opportunity to explore how organisms can evolve regulatory mechanisms to divide labor, specialize, balance competition with cooperation, and perform other foundational principles that govern the logic of life.

overall_design: Bulk RNA-seq measurements of 719 spatially resolved Physarum polycephalum plasmodium parts, single-cell RNA-seq data of haploid amoeba and single-nucleus RNA-seq data of single-celled multinucleated plasmodia were acuired to describe and understand the molecular processes guiding complex behaviors and shapes in a multinucleated syncyctium.

first: Barbara

last: Treutlein

first: Gray

last: Camp


title: Single-cell analysis of colonic epithelium reveals unexpected shifts in cellular composition and molecular phenotype in treatment-naïve adult Crohn’s disease

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

summary: The intestinal epithelial barrier is comprised of a monolayer of specialized intestinal epithelial cells (IECs) that are critical in maintaining gut mucosal homeostasis. Dysfunction within various IEC fractions can increase intestinal permeability, resulting in a chronic and debilitating condition known as Crohn’s disease (CD). Defining the molecular changes in each IEC type in CD will contribute to an improved understanding of the pathogenic processes and the identification of potential therapeutic targets. Here we performed, for the first time at single-cell resolution, a direct comparison of the colonic epithelial cellular and molecular landscape between treatment-naïve adult CD and non-IBD control patients. Our analysis revealed that in CD patients there is a significant skew in the colonic epithelial cellular distribution away from canonical LGR5+ stem cells, located at the crypt-bottom, and toward one specific subtype of mature colonocytes, located at the crypt-top. Further analysis revealed unique changes to gene expression programs in every major cell type, including a previously undescribed suppression in CD of most enteroendocrine driver genes as well as L-cell markers including GCG. We also dissect a previously poorly understood SPIB+ cell cluster, revealing at least four sub-clusters that exhibit unique features. One of these SPIB+ sub-clusters expresses crypt-top colonocyte markers and is significantly up-regulated in CD, whereas another sub-cluster strongly expresses and stains positive for lysozyme (albeit no other canonical Paneth cell marker), which surprisingly is greatly reduced in expression in CD. Finally, through integration with data from genome-wide association studies, we show that genes implicated in CD risk exhibit heretofore unknown cell-type specific patterns of aberrant expression in CD, providing unprecedented insight into the potential biological functions of these genes.

overall_design: Single cell libraries were made from colonic epithelial-enriched suspensions and comparison of treatment-naïve and non-inflammatory bowel disease was performed.

first: Matt

last: Kanke


title: Meloidogyne incognita RNA-seq

city: Kunming

first: Chao-Jun

last: Lu

state: Yunnan

address: No. 2 Cuihu North Road

institute: Yunnan University

summary: We mainly descibed expression of genes of Meloidogyne incognita second stage juveniles under starvation stress

overall_design: second stage juveniles mRNA profiles of early stage and middle stage,both stages are in triplicate

first: Chao-jun

first: Ming-he

last: Mo


title: Ultra-Efficient Exosome-Guided Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes

first: HYOSUK

last: KIM

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

overall_design: Refer to individual Series


title: Addition of retinoic acid to kidney organoids

city: Parkville

first: Sean

last: Wilson

state: Victoria

address: 50 Flemington Road

country: Australia

institute: MCRI

summary: The addition of 5uM retinoic acid to kidney organoids at day 12 (day 7+5). This data is from the same experimental batch as data within GSE119561.

overall_design: Single-cell RNA-seq generated on a 10x Chromium genomics platform from iPSC-derived human kidney organoids. Each sample represents 6 pooled organoids derived from a single well of a transwell plate, generated from individual iPSC-derived reporter lines and harvested at either Day 18 (D18) or Day 25 (D25) of the differentiation protocol.

first: Jessica

last: Vanslambrouck

first: Sara

last: Howden

first: Melissa

last: Little


title: Next-generation sequencing reveals the regulatory mechanism of transcription factor Foxk1 in the liver (ChIP-seq)

status: Public on Mar 01 2022

city: Charlottesville

first: Shun

last: Fujinuma

state: Virginia

address: Jordan Hall, RM 4061B, 1340 Jefferson Park Ave

institute: University of Virginia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The goal of this study was to apply next-generation sequencing (NGS) analyses to identify genes and pathways regulated by the Foxk1 transcription factor in the liver and to see the effects of liver-specific Foxk1 deficiency in the diet-induced non-alcoholic steatohepatitis (NASH) model. Transcriptome and ChIP-seq analysis revealed that liver Foxk1 promotes the pathogenesis of NASH by regulating the expression of a series of molecules involved in hepatic lipid metabolism in an mTORC1-dependent manner.

overall_design: Foxk1 ChIP-seq analyses of mouse primary hepatocytes

first: S

first: H

last: Nakatsumi

first: K

last: Nakayama


title: Next-generation sequencing reveals the regulatory mechanism of transcription factor Foxk1 in the liver (RNA-seq)

overall_design: RNA-seq analyses of Alb-Cre/Foxk1(F/+) and Alb-Cre/Foxk1(F/F) mouse livers


title: Raw data of Stropharia rugosoannulata Transcriptome

first: CH

last: Dong

address: NO.3 Park 1, Beichen West Road, Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

summary: Detection of gene expression in mycelium stage, auxiliary genome

overall_design: Examination of 3 samples in mycelium stage,including replicates.

first: Cai

middle: h

first: Ying

last: Yang


title: Mutant GTF2I induces cell transformation and metabolic alterations in thymic epithelial cells

city: WASHINTON

first: IN-KYU

state: DC

address: 3970 RESERVOIR RD NW, New Research Bldg E212

department: Oncology

institute: Georgetown University Medical Center

summary: The pathogenesis of thymic epithelial tumors (TETs) is poorly understood. Recently we reported the frequent occurrence of a missense mutation in the GTF2I gene in TETs and hypothesized that GTF2I mutation might contribute to thymic tumorigenesis. Expression of mutant TFII-I altered the transcriptome of normal thymic epithelial cells and upregulated several oncogenic genes. Gtf2i L424H knockin cells exhibited cell transformation, aneuploidy, and increase tumor growth and survival under glucose deprivation or DNA damage. Gtf2i mutation also increased the expression of several glycolytic enzymes, cyclooxygenase-2, and caused modifications of lipid metabolism. Elevated cyclooxygenase-2 expression by Gtf2i mutation was required for survival under metabolic stress and cellular transformation of thymic epithelial cells. Our findings identify GTF2I mutation as a new oncogenic driver that is responsible for transformation of thymic epithelial cells.


title: RNA sequencing of Malus x domestica Borkh. with Botrytis cinerea

city: Leuven

first: Matthias

last: Naets

address: Willem de Croylaan 42

country: Belgium

institute: KU Leuven

summary: Apple is typically stored under low temperature and controlled atmospheric conditions to ensure a year round supply of high quality fruit for the consumer. During storage, losses in quality and quantity occur due to spoilage by postharvest pathogens. One important postharvest pathogen of apple is Botrytis cinerea. The fungus is a broad host necrotroph with a large arsenal of infection strategies able to infect over 1,400 different plant species. We studied the apple-B. cinerea interaction to get a better understanding of the defense response in apple. We conducted an RNAseq experiment in which the transcriptome of inoculated and non-inoculated (control and mock) apples was analyzed at 0, 1, 12 and 28 h post inoculation. Our results show extensive reprogramming of the apple's transcriptome with about 28.9 % of expressed genes exhibiting significant differential regulation in the inoculated samples. We demonstrate the transcriptional activation of pathogen-triggered immunity and a reprogramming of the fruit’s metabolism. We demonstrate a clear transcriptional activation of secondary metabolism and a correlation between the early transcriptional activation of the mevalonate pathway and reduced susceptibility, expressed as a reduction in resulting lesion diameters. This pathway produces the building blocks for terpenoids, a large class of compounds with diverging functions including defense. 1-MCP and hot water dip treatment are used to further evidence the key role of terpenoids in the defense and demonstrate that ethylene modulates this response.

sample_organism:
Malus domestica
Botrytis cinerea

platform_organism:
Malus domestica
Botrytis cinerea

overall_design: Three different treatments were applied: Control (no treatment), mock inoculation (wounded and inoculated with 2 µL 12 g/L potato dextrose broth), and Botrytis inoculated (wounded and inoculated with 12 g/L PDB containing 10^6 conidia/mL).  For each treatment 3 samples were analyzed. Each sample was pooled from 3 biological replicates.

first: Wendy

last: Van Hemelrijck

first: Willem

last: Gruyters

first: Pieter

last: Verboven

first: Bart

last: Nicolaï

first: Wannes

last: Keulemans

first: Barbara

last: De Coninck

first: Annemie

last: Geeraerd


title: Transcriptomic changes in response to 5/6 or 1/3 nephrectomy

city: Milwaukee

first: Alison

middle: J.

last: Kriegel

state: WI

address: 8701 Watertown Plank Rd.

department: Physiology

institute: Medical College of Wisconsin

summary: We report the changes in kidney mRNA abundance in response to 5/6 nephrectomy or 1/3 nephrectomy surgery when compared to sham operated controls.

overall_design: Ten week old male Sprague Dawley rats were subjected to the excision model of 5/6 nephrectomy (5/6Nx; right kidney + 2/3 of left kidney), 1/3 nephrectomy (1/3Nx; 2/3 of left kidney excised), or sham surgery (left kidney). Left kidney tissue was collected 6 weeks later for mRNA sequencing.

first: Amanda

last: Marks

first: Victoria

last: Nasci

first: Ryan

last: Adam

first: Pengyuan

last: Liu


title: Rbfox2 is necessary for cardiovascular development

city: Galveston

first: Muge

middle: N

last: Kuyumcu-Martinez

address: 301 University Blvd

department: Biochemistry and Molecular Biology

institute: University of Texas Medical Branch

summary:
Purpose: The goal of this study is to investigate the role of Rbfox2, an RNA binding protein in cardiovascular development.
Methods: RNA-Seq splicing analysis of mouse embryonic heart at embryonic day 9.5, isolated from control and genetic deletion of either one or both allels of Rbfox2 using Nkx2-5 Cre.

overall_design: Rbfox2 was deleted from early cardiovascular linease by crossing Rbfox2 floxed mice with Nkx2-5 Cre mice. Effect of Rbfox2 knock-down on alternative splicing and mRNA expression was compared between Control, heterozygous knock-out and homozygous knock-out.

first: Sunil

middle: K

last: Verma

first: Vaibhav

last: Deshmukh

first: Kaitlyn

last: Thatcher

first: Karryanne

last: Belanger

first: Alexander

middle: M

last: Rhyner

first: Shu

last: Meng

first: Michael

last: Bressan

first: James

middle: F

last: Martin

first: John

middle: P

last: Cooke

first: Joshua

middle: D

last: Wythe

first: Steven

last: Widen

first: Joy

last: Lincoln


title: Genome-wide gene expression of cancer-associated fibroblasts and normal fibroblasts from gastric cancer patients

city: Yushima, Bunkyo-ku

first: Yoshimi

last: Yasukawa

institute: national cancer center research institute, Japan

summary: Using CAFs or normal fibroblasts derived from scirrhous or non-scirrhous gastric cancer tissues, a genome-wide gene expression analysis was performed.

overall_design: Cy3-labeled cRNA was synthesized from total RNA, fragmented and hybridized to Microarray.

first: Toshikazu

last: Ushijima


title: Epigenetic repression of STING by MYC promotes immune evasion and resistance to immune checkpoint inhibitors in triple negative breast cancer [RNA-seq]

city: Seoul

first: Kyung-min

last: Lee

address: 222 Wangsimni-ro

institute: Hanyang University

summary: The MYC oncogene is frequently amplified in triple negative breast cancer (TNBC). Here, we show that MYC suppression induces immune-related hallmark gene set signatures and tumor infiltrating T cells in MYC-hyperactivated TNBCs. Mechanistically, MYC repressed stimulator of interferon genes (STING) expression via direct binding to the STING enhancer region, resulting in downregulation of the T cell chemokines CCL5, CXCL10 and CXCL11. In primary and metastatic TNBC cohorts, tumors with high MYC expression or activity exhibited low STING expression. Using a CRISPR-mediated enhancer perturbation approach, we demonstrated that MYC-driven immune evasion is mediated by STING repression. STING repression induced resistance to PD-L1 blockade in mouse models of TNBC. Finally, a small molecule inhibitor of MYC combined with PD-L1 blockade elicited a durable response in immune-cold TNBC with high MYC levels, suggesting a strategy to restore PD-L1 inhibitor sensitivity in MYC-overexpressing TNBC.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mRNA profiles of indicated experimental conditions

first: Carlos

last: Arteaga


title: Single-Cell RNA-Seq of allogeneic and syngeneic heart grafts in mouse cardiac transplantation

city: Guangzhou

first: Yunhua

last: Tang

address: No. 58 Zhongshan Er Road, Guangzhou, China

institute: Sun Yat-sen University

summary: we present the first comprehensive analysis of the heterogeneity in gene expression and cell types in the allogeneic and syngeneic mouse heart grafts using scRNA-seq. We identify 21 distinct cell populations by performing dimensionality reduction and unsupervised cell clustering analysis in the allogeneic and syngeneic heart grafts.

overall_design: Single-cell transcriptional profiling using the 10x Chromium platform was performed on two allogeneic heart grafts and two syngeneic heart grafts.

first: Yixi

last: Zhang

first: Chenglin

last: Wu

first: Xiaoming

last: Shi


title: Epigenetic repression of STING by MYC promotes immune evasion and resistance to immune checkpoint inhibitors in triple negative breast cancer [CHIP-seq]

overall_design:
Profile of MYC interaction with chromatin in SUM159PT parental and Taxol-resistant cells
Please note that each processed data was generated from both ChIP and input sample, and is linked to the corresponding *_ChIP sample records.


title: GTF2I mutation induces metabolic alterations and cell transformation in thymic epithelial cells [II]

first: IN-KYU

last: KIM

summary: The molecular mechanisms underlying the pathogenesis of TETs are poorly understood. Recently we reported a common missense mutation on GTF2I gene in thymic tumors and hypothesized that GTF2I mutation might contribute to thymic tumorigenesis. Expression of mutant TFII-I altered the transcriptome of thymic epithelial cells and up-regulated several oncogenic genes. Using CRISPR/Cas9n, Gtf2i T1211A knock-in cells exhibited distinct features of cancerous cells including cell transformation, aneuploidy, tumor growth in xenograft, and survival after DNA damage or glucose deprivation. We also observed that Gtf2i mutation increased the expression of several glycolytic enzymes, cyclooxygenase-2, and altered lipid metabolism. Elevated COX-2 expression by Gtf2i mutation was required for survival under metabolic stress and cellular transformation of thymic epithelial cells. Our findings identify GTF2I mutation as a new oncogenic driver mutation that is responsible for transformation of thymic epithelial cells.

overall_design: We profiled transcriptome alteration following knock-in Gtfi2i T1211A mutation in immortalized mouse thymic epithelial cell line. Total RNA was prepared using the RNeasy Plus Mini Kit (QIAGEN), and microarray anlysis was performed using the Agilent SurePrint G3 mouse gene expression V2 8×60K microarray kit (design ID G4852B, Single color) according to the manufacturer's instructions. Data analysis was performed using DAVID functional annotation analysis.

first: In-Kyu

last: Kim

first: Guanhua

last: Rao

first: Xiaoliang

last: Zhao

first: Ruzong

last: Fan

first: Maria

last: Avantaggiati

first: Yisong

last: Wang

first: Yu-Wen

first: Giuseppe

last: Giaccone


title: Hippocampus RNA-sequencing of Q808 against PTZ-induced seizure model

city: Changchun

first: Wei

last: Li

state: Jilin

address: No 155 Chuangju Street

institute: Jilin Provincial Academy of Traditional Chinese Medicine

summary: The present study aimed to use RNA sequencing to reveal the gene transcriptomic profile of  PTZ-induced seizure rats and the difference of the PTZ model rat before and after treatment with Q808.

overall_design: Rats were randomly divided into vehicle control group (n=4), PTZ + vehicle group (n=5), and PTZ + Q808 group (n=5)

first: Xiang

first: Qing


title: GTF2I mutation induces metabolic alterations and cell transformation in thymic epithelial cells [I]

overall_design: We profiled transcriptome alteration by mutant (beta or delta) TFII-I expression under doxycycline-inducilble system in immortalized mouse thymic epithelial cell line (TEC100.4). Total RNA was prepared using the RNeasy Plus Mini Kit (QIAGEN), and microarray anlysis was performed using the Agilent SurePrint G3 mouse gene expression V2 8×60K microarray kit (design ID G4852B, Single color) according to the manufacturer's instructions. Data analysis was performed using DAVID functional annotation analysis.


title: Multimodal analyses of a non-human primate model harboring mutant amyloid precursor protein transgenes driven by the human EF1α promoter

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

institute: Keio University School of Medicine


title: Multi-omics evaluation of SARS-CoV-2 infected mouse lungs reveals dynamics of host responses

first: Xiao Xiao

address: No195,Dongfeng Xi Road

institute: Guangzhou Medical University

summary: Lung tissues from a mouse model sensitized to SARS-CoV-2 infection were serially collected at different time points for evaluation of transcriptome, proteome and phosphoproteome. We showed the ebb and flow of several host responses in the lung across viral infection. The signaling pathways and kinases regulating networks were alternated at different phases of infection. Our study not only revealed the dynamics of lung pathophysiology and their underlying molecular mechanisms during SARS-CoV-2 infection, but also highlighted some molecules and signaling pathways that might guide future investigations on COVID-19 therapies.

overall_design: mRNA profiles of mouse lung tissues collected at 2,4 and 6 days post infection (SARS-CoV-2-infected mice and control mice)

first: Xiao

middle: X


title: Transcriptome analysis of kidneys of acute-chronic (AC),  unilateral ureteral obstruction (UUO) mice and their respective controls

city: Jinhua

first: Weiqiang

last: Lin

state: Zhejiang

address: Shangcheng street N1

institute: The Fourth Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine

summary: Significant renal fibrosis and a significant increase in serum creatinine were observed in AC model mice and UUO model mice, and the same pattern of fibrosis was observed in the cortex and medulla. Compared with sham operation,  RNA-Seq detected  circRNAs that were differentially expressed in the two models.

overall_design: Examination of three different groups: euthanized mice and harvested kidneys 5 days after I/R, UUO and Sham-operated mice served as controls


title: Insufficiency of compound immune checkpoint blockade to overcome engineered T cell exhaustion in pancreatic cancer

city: Minneapolis

first: Ingunn

last: Stromnes

state: MN

address: 2101 6th St S

department: Microbiology & Immunology

institute: University of Minnesota

summary:
Achieving robust responses with adoptive cell therapy for the treatment of the highly lethal pancreatic ductal adenocarcinoma (PDA) has been elusive. We previously showed that T cells engineered to express a mesothelin-specific T cell receptor (TCR) accumulate in autochthonous PDA, mediate therapeutic antitumor activity, but fail to eradicate tumors in part due to acquisition of a dysfunctional exhausted T cell state.
Here, we investigated the role of immune checkpoints in mediating TCR engineered T cell dysfunction in a genetically engineered PDA mouse model. The fate of engineered T cells that were either deficient in PD-1, or transferred concurrent with antibodies blocking PD-L1 and/or additional immune checkpoints, were tracked to evaluate persistence, functionality, and antitumor activity at day 8 and day 28 post infusion. We performed RNAseq on engineered T cells isolated from tumors and compared differentially expressed genes to prototypical endogenous exhausted T cells.

overall_design: Mouse CD8+Thy1.1+ T cells were activated in vitro with anti-CD3+anti-CD28 + rIL-2, transduced with a high affinity mesothelin-specific murine TCR (clone 1045) and transferred into a tumor-bearing, genetically engineered KPC mouse model of pancreatic cancer. TCR engineered T cells were sorted from tumors on day 8 and day 28 post transfer and gene expression was compared to naive T cells and engineered T cells prior to transfer (effector) using microarray.


title: RNA-seq analysis of A549 cells treated with chrysin or nifurtimox

city: Beijing

first: Ying

last: Guo

address: 1 Xian Nong Tan Street

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

summary: The influences of 40 hours treatment of 30 μM chrysin (CAS No: 480-40-0) or  30 μM nifurtimox (CAS No: 23256-30-6) on A549 cell gene expression profile were examined by RNA sequencing.

overall_design: A549 cells were treated with chrysin or nifurtimox at a final concentration of 30 μM for 40 h. Vehicle controls were treated with 0.1% v/v DMSO. Both treatments and their own vehicle controls were performed in biological triplicate.

first: Yijing

last: Xin

first: Shubing

last: Chen


title: Multimodal analyses of a non-human primate model harboring mutant amyloid precursor protein transgenes driven by the human EF1α promoter [RNA-seq]

summary: Alzheimer’s disease (AD) is the first leading cause of dementia which afflicts tens of millions of people worldwide. Despite many scientific progresses to dissect the molecular basis of AD from studies on various mouse models, it has been suffered from evolutionary species differences between mice and humans. Here, we report generation of a non-human primate, common marmoset (marmoset; Callithrix jacchus) model that ubiquitously expresses Amyloid-beta precursor protein (APP) transgenes with the Swedish (KM670/671NL) and Indiana (V717F) mutations. We generated two female transgenic marmosets (TG1 and TG2), whose transgene integration was thoroughly investigated by genomic PCR, whole genome sequencing (WGS) and Fluorescence in situ hybridization (FISH) analyses. Using the reprogramming technology, we confirmed the validity of the transgene expression in induced neurons in vitro. Moreover, we discovered structural changes in specific brain regions of transgenic marmosets by magnetic resonance imaging (MRI) analysis, including in the entorhinal cortex and hippocampus. In postmortem histological analysis, we detected increased Aβ plaque formation in the TG1 cerebrum at the age of 7 years, although evident neuronal loss or glial inflammation was not observed. Thus, this study summarizes our attempt to establish a non-human primate model of AD, which may be beneficial for drug development and further disease modeling in combination with other genetically engineered models.

overall_design: RNA-seq of adult marmoset frontal cortex.

first: Tsukasa

last: Sanosaka

first: Hideyuki

last: Okano


title: Eutrophication and warming rapidly alter microbial community compositions in the mangrove sediment

first: Changyi

last: Xie

address: Qinghua yuan street

department: School of Environment

institute: Tsinghua University

summary: To study the responses of microbial communities to short-term nitrogen addition and warming,here we examine microbial communities in mangrove sediments subjected to a 4-months experimental simulation of eutrophication with 185 g m-2 year-1 nitrogen addition (N),  3oC warming (W) and nitrogen addition*warming interaction (NW).

overall_design: Samples were collected under four different nitrogen addition and warming treatment (CK,N,W and NW) in mangrove sediments, each treatment has 4 replicates.

first: Yunfeng

last: Yang

first: Guanghui

first: Jizhong

last: Zhou


title: SARS-CoV-2 produces a diverse small viral RNA landscape capable of targeting host transcripts

city: Santa Cruz

first: Jeremy

last: Sanford

address: 1156 High St

department: Molecular, Cell and Developmental Biology

institute: UC Santa Cruz

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease (COVID-19) in humans, which may be lethal. In this study, we used a comparative transcriptomics approach to investigate the effects of SARS-CoV-2 infection on the host mRNA and sRNA expression programs in two primate cell lines. Upon infection, we observed global changes in host gene expression and differential expression of dozens of host miRNAs, many with known links to viral infection and immune response. Unexpectedly, we also discovered an expanded landscape of more than a hundred SARS-CoV-2-derived small viral RNAs (svRNAs), predicted to interact with differentially expressed host mRNAs and miRNAs. svRNAs are derived from distinct regions of the viral genome and sequence signatures suggest they are produced by a non-canonical biogenesis pathway. Our data suggest that svRNAs may play a role in SARS-CoV-2 propagation and antagonization of these svRNAs has potential for use as a therapeutic target.

sample_organism:
Chlorocebus aethiops
Homo sapiens

platform_organism:
Chlorocebus aethiops
Homo sapiens

overall_design:
For Calu-3 cell experiment: 30 total samples, 5 time points, 3 SARS-CoV-2-infected and 3 control human lung epithelial cell replicates per time point.
For Vero-E6 cell experiment: 21 total samples, 7 time points, 1-2 SARS-CoV-2 infected and 1 control African green monkey kidney cell replicates per time point.

first: Zachary

middle: T

last: Neeb

first: Alexander

middle: J

last: George

first: Lokendra

middle: V

last: Chauhan

first: Sol

last: Katzman

first: Ian

last: Lipkin

first: Nischay

last: Mishra

middle: R


title: JUN ChIP-seq in injured nerve

city: Madison

first: John

last: Svaren

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

summary: ChIP-seq of c-JUN in injured rat peripheral nerve

overall_design: JUN ChIP samples were prepared from rat sciatic nerve at 8 day post-transection using both the distal stump of the injured nerve .

first: Ki

middle: H

last: Ma

first: Raghu

last: Ramesh


title: Changes of small non-coding RNAs by severe acute respiratory syndrome coronavirus 2 infection

first: Xiaoyong

last: Bao

address: 301 University Boulevard

department: Pediatrics

summary: The ongoing pandemic of coronavirus disease 2019 (COVID-19), which results from the rapid spread of the severe acute  respiratory syndrome coronavirus 2 (SARS-CoV-2), is a significant global public health threat, with molecular mechanisms  underlying its pathogenesis largely unknown. Small non-coding RNAs (sncRNAs) are known to play important roles in almost all  biological processes. In the context of viral infections, sncRNAs have been shown to regulate the host responses, viral replication,  and host-virus interaction. Compared with other subfamilies of sncRNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs  (piRNAs), tRNA-derived RNA fragments (tRFs) are relatively new and emerge as a significant regulator of host-virus interactions.  Using T4 PNK‐RNA‐seq, a modified next‐generation sequencing (NGS), we recently found that nasopharyngeal swabs (NPS) samples  from SARS-CoV-2 positive and negative subjects show a significant difference in sncRNA profiles. There are about 166 SARS-CoV-  2-impacted sncRNAs. Among them, tRFs are the most significantly affected and almost all impacted tRFs are derived from the 5’-end  of tRNAs (tRF5). Using a modified qRT-PCR, which was recently developed to specifically quantify tRF5s by isolating the tRF signals  from its corresponding parent tRNA signals, we validated that tRF5s derived from tRNA GluCTC (tRF5-GluCTC), LysCTT (tRF5-LysCTT),  ValCAC (tRF5-ValCAC), CysGCA (tRF5-CysGCA) and GlnCTG (tRF5-GlnCTG) are enhanced in NPS samples of SARS-CoV2 patients and  SARS-CoV2-infected airway epithelial cells. In addition to host-derived ncRNAs, we also identified several sncRNAs derived from the  virus (svRNAs), among which a svRNA derived from CoV2 genomic site 346 to 382 (sv-CoV2-346) has the highest expression. The  induction of both tRFs and sv-CoV2-346 has not been reported previously, as the lack of the 3’-OH ends of these sncRNAs prevents  them to be detected by routine NGS. In summary, our studies demonstrated the involvement of tRFs in COVID-19 and revealed new  CoV2 svRNAs.

overall_design: Nasopharyngeal swab small RNA profiles of SARS-CoV-2; 4 positive and 4 negative subjects

first: Wenzhe

last: Wu

first: Eunjin

last: Choi

first: Binbin

last: Wang

first: Ke

last: Zhang

first: Awadalkareem

last: Adam

first: Gengming

last: Huang

first: Leo

last: Tunkle

first: Philip

first: Rohit

last: Goru

first: Isabella

last: Imirowicz

first: Leanne

last: Henry

first: Inhan

last: Lee

first: Jianli

last: Dong

first: Tian


title: Epigenetic repression of STING by MYC promotes immune evasion and resistance to immune checkpoint inhibitors in triple negative breast cancer.

first: Kyung-min

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

overall_design: Refer to individual Series


title: Genome-wide identification of mRNAs involved in BCL2L2-PABNP1 regulation

city: Harbin

first: Jiyuan

last: Zhu

address: Xiangfang District, No. 600 Changjiang Road

department: College of Animal Science and Technology

institute: Northeast Agricultural University

summary: RNA-Seq technology was used to explore mechanisms of BP on adipogenesis in cells transfected with adenoviruses expressing BP at a condition of MOI 300 and 48 h which was predetermined with fluorescence microscope and qPCR analysis . A total of 3,074 DEmRs were obtained by RNA-Seq analysis, among which 1,476 were upregulated and 1,598 were downregulated in cells overexpressing BCL2L2–PABPN1 compared with control groups .

overall_design: The recombinant adenoviruses were constructed using the AdEasy system (Hanbio, Shang, China). BP CDS were inserted into the shuttle plasmid containing an enhanced green fluorescent protein (EGFP) and cyto-megalovirus promoters using Kpn Ⅰ and Xho Ⅰ sites, and homologous recombina-tion was performed in E. coli BJ5183 with adenoviral backbone pAdEasy 1. The recom-binant adenovirus plasmid was packaged in HEK-293A cells after linearized with Pac Ⅰ. Preadipocytes were infected with adenovirus virions at multiplicity of infection (MOI) of 300. At 48 h post-infection, cells were collected for RNA-Seq with Illumina NovoSeq 6000 platform (Illumina, San Diego, CA, USA) by Geneseeq Technology (Nanjing, China) using pair-end sequencing strategy according to the manufacturer’s protocols. Cells treated with empty adenovirus were used as a control. A total of six Ribo-Zero RNA-sequencing libraries including overexpressing and control groups were con-structed, each with three replicates.

first: Xiuqin

last: Yang


title: Identification of Genomic Safe Harbors in the Anhydrobiotic Cell Line, Pv11

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

institute: Juntendo University

summary: Genomic safe harbors (GSHs) are utilized as an ideal integration site for generating transgenic organisms and cells. Discovery of GSHs is one of the crucial factors for the advancement of basic and applied biology in the species. Such GSHs were discovered in Pv11 (Polypedilum vanderplanki) cell line, which can survive extreme desiccation. To identify the integration sites, high-molecular-weight genomic DNAs were extracted. The DNA libraries were prepared and sequenced with a Nanopore MinION sequencer. In the way to confirm that GSHs loci are localized in open chromatin regions we prepared ATAC-seq libraries, which were sequenced in Illumina HiSeq2500.

overall_design: Two libraries with Nanopore sequencing for GSHs and six libraries with ATACseq Illumina PE reads: 3 controls (K) and 3 trehalose treated Pv11 cells (T).

first: Yugo

last: Miyata

first: Shoko

last: Tokumoto

first: Tomohiko

last: Arai

first: Nurislam

last: Shaikhutdinov

first: Hiroto

last: Fuse

first: Natalia

last: Gogoleva

first: Sofya

last: Garushyants

first: Alexander

last: Cherkasov

first: Alina

last: Ryabova

first: Guzel

last: Gazizova

first: Richard

last: Cornette

first: Elena

last: Shagimardanova

first: Oleg

last: Gusev

first: Takahiro

last: Kikawada


title: Effect of TLR7/8 dual agonist 3M-052 on B cell response to melanoma

city: Houston

middle: Eric

last: Davis

address: 7455 Fannin Street

institute: MD Anderson Cancer Center

summary:
B cells potentially play a role in the immune response to melanoma, including during treatment with immune modulators. We profiled effects of 3M-052 on gene expression in draining lymph nodes of syngeneic mice bearing B16 melanoma tumors.
When B16 tumors reached 30-40 mm2 in size, they were injected intratumorally once with 3M-052 or vehicle control.

overall_design: Draining lymph nodes from 4 mice in each group (3M-052 vs. control) were harvested 4 days after intratumoral injection of 3M-052 or control.

first: Shubhra

last: Singh

first: Zhiqiang

last: Wang

middle: E

first: Willem

middle: W

last: Overwijk

first: Manisha


title: RNA sequencing of SF3B4 knockdown by siRNA in ovarian cancer cells

city: Jinan

first: Chen

last: Zhao

state: China

address: 107 Wenhua Xi Road

department: Department of Obstetrics and Gynecology

institute: Qilu Hospital, Shandong University

summary: In this study, SF3B4 was found to be upregulated in ovarian cancer patients and its high expression predicted poor prognosis. High expression of SF3B4 was involved in the malignant proliferation and mobility of ovarian cancer. SF3B4 could be a promising biomarker and effective therapeutic target for ovarian cancer.

overall_design: The assay was performed on three experimental triplictes of SF3B4 knockdown and control ovarian cancer cells.

first: Yuchao

last: Diao

first: Yingwei

last: Li


title: V. canescens comparison between sexual and asexual populations

city: Villeurbanne

first: Aurore

last: Gallot

address: 43 Bd du 11 novembre 1918

country: France

institute: Universite Lyon

summary: In the parasitic wasp Venturia canescens sexual and asexual populations coexist in sympatry and showed distinct foraging behaviours. By sequencing head transcriptome from sexual and asexual population, we assess transcriptomic divergence between the 2 populations.

overall_design: Female adult were decapited at emergence, their head were flask frozen. Pool of 30 heads constituted one sample. Sexual and asexual population were sequenced using 3 biological replicates each.


title: Genome-wide DNA methylation status of scirrhous CAF, non-scirrhous CAF, and GIST fibroblast

first: Yoshimi

last: Yasukawa

institute: national cancer center research institute, Japan

summary: Genome-wide DNA methylation was analyzed using the Infinium Human MethylationEPIC BeadChip.

overall_design: Bisulfite converted DNA from the 19 samples were hybridized to the Infinium Human MethylationEPIC BeadChip.

first: Toshikazu

last: Ushijima


title: Wild-type, Foxa2-/-, and Nkx2.2-/- mESCs at different time points of differentiation

city: Solna

first: Zhanna

last: Alekseenko

state: Stockholm

address: Solnavägen 9

department: CMB

country: Sweden

institute: Karolinska Institutet

summary: We report gene-expression profiling of different mouse embryonic stem cells (mESCs) mutant cell lines differentiating to neuronal lineages upon treatment with Retinoic Acid (RA) and Smoothened agonist (SAG). We generated genome-wide expression profiles of embryonic stem cells and neural progenitors at different differentiating time-points for different mutant cell lines and WT control mESCs. We find NKX2.2 and FOXA2 are key components of an intrinsic timer in neural stem cells founded on a negative feedback network that regulates the duration of motor neuron neurogenesis.

overall_design: mRNA expression profiles of wild-type, Foxa2-/-, and Nkx2.2-/- mESCs at different time points of differentiation.

first: Johan

last: Ericson

first: Jose

last: Dias


title: Multimodal analyses of a non-human primate model harboring mutant amyloid precursor protein transgenes driven by the human EF1α promoter [WGS]

first: Sho

last: Yoshimatsu

overall_design: Whole genome sequencing of fibroblasts derived from transgenic marmosets.

first: Tsukasa

last: Sanosaka

first: Hideyuki

last: Okano


title: Epigenomic and proteomic changes in bovine viral diarrhea virus persistently infected fetal spleens: repercussions for the developing immune system, bone, brain, and heart.

city: New Haven

first: Hanah

last: Georges

state: Connecticut

address: 333 Cedar St

institute: Yale University

type: Methylation profiling by high throughput sequencing

summary: Reduced representation bisulfite sequencing of BVDV PI and controls fetal spleens, collected on day 245 of gestation (maternal inoculation at day 75 of gestation)

overall_design: Examination of methylation patterns from 3 PI fetal spleens and 4 control fetal spleens

first: Hana

last: Van Campen

first: Thomas

last: Hansen

first: Helle

last: Bielefeldt-Ohmann


title: Oppositional Poly(A) Tail Length Regulation by FMRP and CPEB1

city: Lyon

first: Kiran

last: Padmanabhan

address: 32-34 avenue Tony Garnier

department: IGFL

institute: ENS-Lyon

summary: Poly(A) tail length is regulated in both the nucleus and cytoplasm. One factor that controls polyadenylation in the cytoplasm is CPEB1, an RNA binding protein that associates with specific mRNA 3’UTR sequences to tether enzymes that add and remove poly(A). Two of these enzymes, the noncanonical poly(A) polymerases Gld2 (TENT2, PAPD4, Wispy) and Gld4 (TENT4B, PAPD5, TRF4, TUT3), interact with CPEB1 to extend poly(A). To identify additional RNA binding proteins that might anchor Gld4 to RNA, we expressed double tagged Gld4 in U87MG cells, which was used for sequential immunoprecipitation and elution followed by mass spectrometry. We identified several RNA binding proteins that co-precipitated with Gld4, among which was FMRP. To assess whether FMRP regulates polyadenylation, we performed TAIL-seq from WT and FMRP-deficient HEK293 cells. Surprisingly, loss of FMRP resulted in an overall increase in poly(A), which was also observed for several specific mRNAs. Conversely, loss of CPEB1 elicited an expected decrease in poly(A), which was examined in cultured neurons. We also examined polyadenylation in wild type (WT) and FMRP-deficient mouse brain cortex by direct RNA Nanopore™ sequencing, which identified RNAs with both increased and decreased poly(A). Our data show that FMRP has a role in mediating poly(A) tail length, which adds to its repertoire of RNA regulation.

overall_design: Identification of Poly(A) tail length for all transcripts in WT and FMRP Knock-out mice using direct RNA sequencing (PromethION)

first: Jihae

last: Shin

first: Ki

middle: Y

last: Paek

first: Hyeshik

last: Chang

first: Lies

last: Chikhaoui

first: Suna

last: Jung

first: SitharaRaju

last: Pony

first: Yutaka

last: Suzuki

first: V

last: Kim

first: Joel

last: Richter


title: Autocrine Canonical Wnt Signaling Primes for Noncanonical Signaling through ROR1 in Metastatic Castration-Resistant Prostate Cancer

city: Boston

first: Fen

last: Ma

state: MA

address: 3 Blackfan Circle

department: Hem/Onc

institute: BIDMC

summary: To identify genes and pathways downstream of Canonical WNT signaling in prostate cancer, we performed RNA sequencing to capture the transcriptional changes upon APC knockdown or RNF43 knockdown plus Wnt3a stimulation in VCaP cells. The global changes of gene expression were assessed by comparing APC knockdown with Control knockdown or RNF43 knockdown plus Wnt3a stimulation with RNF43 knockdown. By overlapping the genes differentially expressed under both conditions, we obtained a bona fide WNT/β catenin downstream effectors list in prostate cancer.

overall_design: Transcriptome profiling of mRNAs obtained from VCaP cells exposed for 72hrs with Control SiRNAs, SiAPC-2/3s, SiRNF43-3/4 and SiRNF43-3/4 with Wnt3a(100ng/ml) stimulation at the last 7hrs. Both APC and RNF43 knockdown were performed using twp independent SiRNAs. RNA sequencing was performed in biological duplicates for all samples. Differential gene expression was assessed by comparing APC versus control knockdown or RNF43i with Wnt3a stimulation versus RNF43 knockdown.

first: Manoj

last: Bhasin


title: Multi-omics comparisons between CFBE41o- cells stably expressing wide-type CFTR and F508del-mutant CFTR

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University


title: mRNA-Seq of WTBE and CFBE cells

summary: Cystic fibrosis (CF) is characterized by chronic inflammation and excessive cytokines secretion in the lung. Isogenic human CF bronchial epithelial (CFBE41o-) cell lines stably expressing wt-CFTR (WTBE) or F508del mutant (CFBE) are widely used tools in understanding responses to stimuli or drugs and CF pathogenesis in vitro. However, their intrinsic cellular differences in culture are unknown. Hence, we performed integrative analyses at protein, mRNA and chromatin levels on these isogenic cell lines cultured in submerged and transwell condition. CFBE and WTBE cells displayed different secretion patterns on IL-6, IL-8, CXCL1, CXCL10, and CCL5 . The ALI culture dramatically increased cytokines secretion in both cells. ATAC-seq results showed that CFBE cells exhibited higher genome-wide chromatin accessibility than WTBE cells in both culture methods, but the relative openness of cytokine genes between two cells varied individually. Differentially expressed genes between two cell lines from mRNA sequencing were highly concentrated in immunity-related pathways. While the mRNA stability of CXCL10 and CXCL1 exhibited the most significant differences between cell lines in SUB culture, most cytokines had comparable mRNA stabilities within same culture method. Moreover, polarization of cells via transwell culture remodeled the chromatin accessibility and transcriptome. This multilayered studies presents a comprehensive baseline activities of CFBE and WTBE cells, further facilitating their usage and data interpretation as CF cell models.

overall_design: transcriptome profile of WTBE and CFBE cells under different culture models.

first: Shiping

last: Lu

first: Kejing

last: Song


title: ATACseq of CFBE41o- stably expressing wild-type CFTR (WTBE) and F508del-CFTR (CFBE) cells

overall_design: Chromatin-accessibility profile of WTBE and CFBE cells under different culture models.


title: The global transcriptomic profile in the spermidine-stressed E. coli

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: To achieve extreme spermidine stress we used DspeG E. coli strain. We identified the pathways that are altered under spermidine stress. Among many changes spermidine altered the iron-sulfur cluster metabolism and redox balance in the cells. Therefore, we have shown that superoxide quencher, NAC and ascorbate mitigates spermidine stress. Overall our data explains the importaance of tight spermidine homeostasisin the cell.

overall_design: Organism : Escherichia coli , Agilent custom E.coli Gene Expression  8x15k Array (AMADID: 068043) designed by Genotypic Technology Private

first: Dipak

last: Dutta

first: Vineet

last: Kumar

first: Rajesh

last: Mishra

first: Amit

last: Arora


title: Serial transcriptomic analysis of mouse acute myocardial infarction

city: Oxford

first: Shoumo

last: Bhattacharya

address: Roosevelt Drive

department: RDM Cardiovascular Medicine

country: United Kingdom

institute: Wellcome Centre For Human Genetics, University of Oxford

overall_design: Changes in cardiac transcriptome following acute myocardial infarction

first: Hai

last: Fang

first: Gopala

last: Yakala

first: Jason

last: Lew

first: Craig

last: Lygate

first: Debra

last: McAndrew

first: Julian

middle: C

last: Knight


title: Expression data from normo- and hypoosmotic perfused rat liver [120min]

city: Düsseldorf

first: David

last: Schöler

address: Moorenstr. 5

institute: University Hospital Düsseldorf

summary: We used microarrays to detail differential gene expression in perfused rat liver after 180 min under normo- and hypoosmotic condition.

overall_design: Male wistar rat livers (Age 6-10 weeks) were perfused with normo- (305 mosm/L) or hypoosmotic (225 mosm/L) Krebs-Henseleit buffer for up to 180 min


title: Expression data from normo- and hypoosmotic perfused rat liver [180min]


title: Gene Expression of Fibroblasts Derived from Knee Tissue of Patients Undergoing Primary Total Knee Arthroplasty for Osteoarthritis

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Arthrofibrosis is characterized by excessive extracellular matrix (ECM) deposition that results in restricted joint motion after total knee arthroplasty (TKA). Current surgical and pharmacologic treatment options are limited.  Therefore, an in vitro model for joint myofibroblastogenesis is valuable to investigate the arthrofibrotic process and identify diagnostic biomarkers and treatment options. In this study,  we obtained intraoperative posterior capsule (PC), quadriceps tendon (QT), and suprapatellar pouch (SP) tissue from knees of four patients undergoing primary TKA for osteoarthritis and characterized primary outgrowth cells from these tissues in the absence and presence of transforming growth factor beta 1 (TGFβ1), a pro-myofibroblastic cytokine. Light microscopy of knee outgrowth cells revealed spindle-shaped cells while immunofluorescence (IF) established staining for the fibroblast-specific antigen TE-7 and Vimentin, which are characteristics of fibroblasts. These fibroblasts differentiate readily into myofibroblasts as highlighted by enhanced alpha smooth muscle actin (ACTA2) mRNA and protein expression and increased collagen mRNA (i.e., collagen type 1 (COL1A1) and collagen type 3 (COL3A1)) expression and collagenous matrix deposition in the presence of TGFβ1. Of note, these studies also revealed that knee-derived fibroblasts are more sensitive to TGFβ1-mediated myofibroblastogenesis than adipose-derived mesenchymal stem cells. Importantly, while outgrowth fibroblasts isolated from four patients and three anatomical regions exhibit similar gene expression profiles, these knee fibroblasts form a unique gene expression cluster within the fibroblast niche as revealed by RNA-sequencing analysis. In conclusion, our study provides a fibroblast/myofibroblast model of outgrowth knee cells derived from patients undergoing primary TKA that can be employed to assess myofibroblast-related processes and test novel pharmacological strategies in vitro for arthrofibrosis.

overall_design: Intraoperative tissues were obtained from the posterior capsule (PC), quadriceps tendon (QT), and suprapatellar pouch (SP) of four patients undergoing primary TKA (patient numbers 030, 256, 565 and 797).  Cells were expanded by outgrowth culture in vitro and resulting cells were evaluated for unique fibroblast markers, morphology, myofibroblast differentiation, collagen production potential and gene expression fingerprint. Cell morphology at various cell densities and the fibroblast marker TE-7 and VIM, mesenchymal human connective tissue marker, were assessed by light microscopy and immunofluorescence (IF) microscopy, respectively.  Expression of ACTA2 (myofibroblast marker) assessed by IF, real time quantitative reverse transcription polymerase chain reaction (RT-qPCR), and western blotting (WB) in the absence or presence of TGFβ1 (10 ng/ml) to evaluate myofibroblast differentiation.  Expression of COL1A1 and COL3A1 genes and collagen deposition were evaluated in the absence or presence of TGFβ1 (10 ng/ml) by qPCR and picrosirius red staining respectively. RNA-seq analysis was employed for gene expression profiles of knee fibroblasts.

first: Banu

last: Bayram

first: Amel

last: Dudakovic

first: Matthew

last: Abdel


title: The Rim15p homolog RimO mediates starvation response and is required for secondary metabolite production in Aspergillus nidulans

city: Tulln

first: Harald

last: Berger

state: NOE

address: Konrad-Lorenzstraße 43

department: DAGZ

country: Austria

institute: Universität f. Bodenkultur Wien

summary: Depending on the prevailing environmental, developmental and nutritional conditions Aspergillus nidulans produces different combinations of secondary metabolites (SMs). To activate the biosynthetic gene cluster (BGC) for a given SM global, chromatin-based de-repression must be integrated with pathway-specific induction signals. Here we describe a new global regulator affecting the set of starvation-induced SMs. We found a hitherto uncharacterized putative PAS-domain containing kinase to be upregulated in SM-producing cultures. The predicted protein is highly similar to yeast Rim15 which transmits nutritional and stress signals to downstream effectors involved in chromatin regulation, stress and starvation response. The putative kinase – termed RimO – is required for the transcription of a number of starvation-induced SMs including sterigmatocystin (ST). RimO regulates the pathway-specific transcription factor AflR both at the transcriptional and post-translational level. In the absence of RimO aflR is barely transcribed under SM conditions and the protein is not retained in the nucleus. Genome-wide transcriptional profiling showed that cells lacking rimO fail to correctly respond to carbon and nitrogen starvation and continue to transcribe genes of the basic metabolism to a high level. Conversely, overexpression of the kinase made cells largely insensitive to glucose repression and led to overproduction of several secondary metabolites. We propose a model that positions RimO downstream of PKA being necessary to transmit the starvation signal to downstream targets, including chromatin and transcriptional regulators of SM gene clusters. Additionally, it may also regulate signaling modules required for recognizing the starvation response.

overall_design: 12 Samples of A. nidulans, 3 Types: wild type, rimO deletion and rimO over expression , 2 time points of harvest (17h and 48h or 54h post inocculation), all samples are replicated

first: Franz

last: Zehetbauer

first: Angelika

last: Seidl

first: Michael

last: Sulyok

first: Joseph

last: Strauss


title: Expression data from normo- and hypoosmotic perfused rat liver

overall_design: Refer to individual Series


title: Whole genome bisulfite sequencing of rumen, muscle, placenta, sperm tissues in cattle

city: Beltsville

first: George

middle: E.

last: Liu

state: Maryland (MD)

address: 10300 Baltimore Ave Bldg 306

institute: USDA-ARS

summary: In this study, we generated whole genome bisulfite sequencing data 4 tissues in cattle. We analyzed the variations of DNA methylation among tissues.

overall_design: Genomic DNA for each tissue was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA). The quality of DNA samples was evaluated using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) including degradation, and potential RNA contamination, and purity (OD260/OD280), and concentration using a spectrophotometer (NanoDrop Technologies, Rockland, DE) to meet the requirements for library construction. The qualified genomic DNA from somatic tissues and sperm were used to construct a library. The library different lanes of a HiSeq X Ten (Illumina, San Diego, CA, USA) to generate 150-bp paired-end reads by Novogene (Novogene, Beijing, China).

first: Shuli


title: Triple combination of BET plus pan-PI3K and NF-κB inhibitors exhibit synergistic activity in adult T cell leukemia/lymphoma

city: Bethesda

first: Anusara

last: Daenthanasanmak

state: MD

address: 10 Center Dr

department: Lymphoid Malignancies Branch

institute: National Institutes of Health

summary: We exploited the use of I-BET762, copanlisib, and bardoxolone methyl inhibitors as triple combination to understand the interactions between these three pathways in Adult T cell leukemia/lymphoma.

overall_design: Examination of ATL43Tb (-) tumor isolated from NSG mice treated with either vehicle or Triple combination of I-BET762, Copanlisib and bardoxolone methyl.

first: Thomas

middle: A

last: Waldmann

first: Philip

last: Homan


title: Signature of acquired resistance to fluvastatin

first: Anjana

last: Bhardwaj

state: Texas

address: 1515 Holcombe Blvd

department: Breast Surgical Oncology

institute: UT MD Anderson cancer Center

summary: Background:  Cholesterol pathway inhibition by statins prevents breast cancer development in mouse models of breast cancer but their efficacy is not very high (about 50%) . Therefore, the goal of this study is to investigate if the fluvastatin mediated upregulation in the steroid biosynthesis pathway genes limit the efficacy of statin chemoprevention.  Methods:  A published gene signature of statin resistance was validated in cell line-based models of inherent and acquired resistance during breast cancer.  These signatures were next validated in a mouse model of hormone receptor negative breast cancer.  Results: We found more than 70% of a published multi-gene fluvastatin resistance signature to be significantly upregulated in an inherently resistant cell line relative to fluvastatin sensitive cell line.  We found this inherent statin resistance gene signature to be also shared with the signature of acquired resistance to fluvastatin (13 / 23 total genes).  These 13 inherent resistance genes and 10 additional genes mapped to 2 of the top 3 deregulated pathways that are steroid-, and terpenoid backbone- biosynthesis pathway.  Next, we tested if one or multiple genes of statin resistance signature, could predict efficacy of statin chemoprevention in the SV40 C3TAg transgenic mouse model.  We found upregulation of a large number (19/24) of genes in the tumor bearing mammary glands, suggesting that upregulation of these pathways drives resistance to statin chemoprevention. A subset of 13-genes from this panel was significantly associated with response to statin treatment, as was the expression level of HMGCR alone in a mouse model of breast cancer.  Lastly, we studied if a 10-day period of fluvastatin treatment to SV40C3 TAg mice, can also trigger the upregulation of these genes and provide an early signal of statin resistance. These experiments showed that a 10-day period is insufficient to cause a feedback upregulation in steroid biosynthesis pathway genes and thus cannot be used as an early biomarker to detect resistance to fluvastatin. Conclusions:  High basal or restorative upregulation in the steroid biosynthesis pathway gene expression after fluvastatin treatment appears to be strongly associated with resistance to statin chemoprevention for breast cancer and may serve as a biomarker to identify patients that are most likely to respond to statins or develop resistance.

overall_design: Three replicates of the untreated MCF10.AT1 and three replicates of the MCF10.AT1-resistant cells were used for the clariom D array analysis.

first: Isabelle

last: Bedrosian


title: Propranolol reduces sarcoma growth and enhances the response to anti-CTLA4 checkpoint inhibitor therapy by modulating the tumor microenvironment

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: The nonselective beta blocker, propranolol, which for decades has been used for treatment of cardiovascular conditions, has recently been used successfully to treat metastatic angiosarcoma. These results have led to an orphan drug designation by the European Medicines Agency for the treatment of soft tissue sarcomas. The anti-tumor effects of propranolol are suggested to involve the reduction of cancer cell proliferation as well as angiogenesis. Here, we have investigated the anti-angiogenic properties of propranolol in the context of stimulating an anti-tumor immune response. We show that oral administration of propranolol delays tumor progression of MCA205 fibrosarcoma tumors and improves the survival rate of tumor bearing mice. Propranolol works by reducing tumor angiogenesis and facilitating an anti-tumoral microenvironment with increased T cell infiltration and reduced infiltration of myeloid-derived suppressor cells (MDSCs). Using T cell deficient mice, we demonstrate that the full anti-tumor effect of propranolol requires the presence of T cells. Flow cytometry-based analysis and RNA sequencing of FACS-sorted cells show that propranolol-treatment leads to an upregulation of PD-L1 on tumor-associated macrophages (TAMs) and changes in their chemokine expression profile. Lastly, we observe that the efficacy of anti-CTLA4 therapy is significantly enhanced by the co-administration of propranolol. Our results identify propranolol as an immune modulating agent, which can improve immune checkpoint inhibitor therapies in soft tissue sarcoma patients and potentially also in other cancers.

overall_design: Gene expression analysis of tumor-associated macrophages isolated from MCA205 tumors from control and propranolol treated mice.

first: Victor

last: Goitea

first: Daniel

last: Madsen


title: Genetic variation in feral hemp populations across the Nebraska climate gradient

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: The objective in this study was to develop and characterize the chemistry and genetics of a collection of feral hemp germplasm from across Nebraska for use in a hemp breeding program. An additional goal was to compare the chemistry and genetics of male and female flower structures. RNA was extracted from isolated, dissected flower tissue of one female and one male plant from each of three populations (total six samples). These plants were derived from seeds collected in Knox, Madison, and Merrick counties. Illumina reads were obtained from the RNA extracts, mapped onto a C. sativa reference genome, and gene expression levels were determined.

overall_design: mRNAs in female and male flower tissues

first: Lucas

last: Busta


title: Transcriptional profiling of NK cells sorted from lungs and axillary LNs from Cdh1F/F;Trp53F/F;Foxp3GFP-DTR mice bearing 100mm2  orthotopically transplanted mammary tumors, treated with difteria toxin (DT) or PBS [NK]

city: AMSTERDAM

first: Kevin

last: Kos

email: k.kos@nki.nl, k.d.visser@nki.nl

state: NOORD-HOLLAND

address: PLESMANLAAN 121

department: Immunology

country: Netherlands

institute: Netherlands Cancer Institute

summary: We studied the impact of DT treatment (Treg depletion)  on NK cells (CD3-, NKp46+, DX5+) in axillary TDLNs and lungs of tumor bearing Foxp3GFP-DTR mice . Here we generated RNAseq data from sorted NK cells from DT or PBS treated  Foxp3GFP-DTR mice  bearing 100mm2 mammary tumors from lungs, axillary TDLNs

overall_design: In this study, gene expression profiles of NK cells sorted from Cdh1F/F;Trp53F/F;Foxp3GFP-DTR mice bearing 100mm2 orthotopically transplanted mammary tumors, treated with difteria toxin (DT) or PBS were analysed. We generated 4 biological replicates per group (LN untreated, LN treated, lung untreated, lung treated). Samples were grouped according to tissue and treatment status. Comparisons were made between NK cells derived from DT/PBS treated mice.

first: Muhammad

last: Aslam

first: Max

last: Wellenstein

first: Wietske

last: Pieters

first: Antoinette

last: Weverwijk

first: Kim

last: Vrijland

first: Lisanne

last: Raeven

first: Sergio

last: Quezada

first: Rudy

last: Beyaert

first: Heinz

last: Jacobs

first: Karin

last: de Visser