title: RT² Profiler PCR Array analysis of different human HCT116 cell lines [Epithelial to Mesenchymal Transition]

city: Erlangen

first: Pablo

last: Lindner

address: Universitaetsstr. 22

department: Pathology

country: Germany

institute: Universityclinic Erlangen

summary: Two HCT116 cell lines (HCT WT, HCT p21-/-) were analyzed by RT-qPCR array analysis for genes associated with Epithelial to Mesenchymal Transition (EMT) to identify potential target genes, that depend on the cell cycle regulator p21. HCT116 cell lines (HCT WT, HCT p21-/-) were cultured at 37°C in a humidified atmosphere with 5% CO2. Cells were harvested at a confluency of ~60-80% and RNA was isolatd using QIAzol an Rneasy Kits from Qiagen. cDNA was produced from equal amounts of RNA using the RT² First Strand Ki from Qiagen and RT-qPCR analysis was performed following the manufacturer's instructions using the Epithelial to Mesenchymal Transition RT² Profiler PCR Array from Qiagen. The CFX96TM Real-Time System and the C1000TM Thermal Cycler from Bio-Rad were used to perform the RT-PCR runs. The two different cell lines were analyzed in three biological triplicates. The mean expression Ct values of the target genes were normalized against the mean Ct value for B2M to calculate the Fold Change values. The Raw Data was processed using the RT² Profiler PCR Array Data Analysis version 3.5 software from SABiosciences.

overall_design: RT² Profiler PCR Array analysis of different HCT116 cell lines (HCT WT, HCT p21-/-) for expression patterns of genes associated with Epithelial to Mesenchymal Transition (EMT).

first: Regine

last: Schneider-Stock


title: miRNA profiling of Hepa1-6-bearing mouse model

status: Public on Dec 29 2019

city: Shanghai

first: Qilong

last: Chen

address: 1200, Cailun Road

country: China

institute: TCM center

summary: the Hepa1-6-bearing C57 BL/6 mouse model was utilized to explore the therapeutic efficacy of Ganoderma lucidum extract (GLE), documenting that it could effectively inhibit tumor growth. Furthermore, the microRNA (miRNA) profiles of GLE-treated and untreated mice were detected, and 25 differential expressed (DE) miRNAs were determined, including 24 up-expressed and one down-expressed miRNAs., documenting that it could effectively inhibit tumor growth. Furthermore, the microRNA (miRNA profiles of GLE-treated and untreated mice were detected, and 25 differential expressed (DE miRNAs were determined, including 24 up-expressed and one down-expressed miRNAs.

overall_design: 6 samples, including 3 GLE treated Hepa1-6-bearing C57 BL/6 mice and 3 GLE untreated Hepa1-6-bearing C57 BL/6 mice were performed to analyze

first: Ruolin

last: Zhao


title: Transcriptome of elt-2 for the nematode Caenorhabditis elegans

status: Public on Dec 31 2019

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

type: Expression profiling by high throughput sequencing

summary: In the past decade, the paradigm which claimed that invertebrate immune systems lack specificity has been reconsidered. Accumulating evidence supports that invertebrate immune systems are able to mount specific responses to the pathogen species-, and even to the pathogen strain-level. However, the underlying molecular mechanisms behind invertebrate immune specificity remain mostly unknown. Studying the molecular basis of invertebrate immune specificity in a genetically tractable model, such as the nematode Caenorhabditis elegans, has the potential to reveal insights into the immune systems of other metazoans, including humans. We chose to study the mechanisms of specific immune responses of the worm to two different pathogenic strains of the Gram-positive bacterium Bacillus thuringiensis (MYBY18247 and MYBT18679), because there is phenotypic evidence of specific genotype-genotype interactions between this host-pathogen pair. We did an initial RNA-Seq experiment upon pathogen exposure and found that 9% of the differentially expressed genes change their expression in different ways when comparing the two pathogen strains. Through promoter region motif enrichment analysis, we found the GATA transcription factor ELT-2 is responsible for the pathogen strain-specific transcriptomic response. Upon elt-2 knockdown worms exposed to MYBT18679 display lower survival rate coupled with higher intestinal damage than non-infected controls. Additionally, by performing further genetic analysis using gene knockdown and knockout, we found that the p38 MAPK pathway acts likely in parallel to elt-2 and the transcription factor skn-1 cooperates with elt-2 to promote resistance to MYBT18679. On the other hand, elt-2 knockdown leads to a substantially higher survival rate, together with lower intestinal tissue damage compared to control worms, upon exposure to MYBT18247, another pathogenic Bacillus thuringiensis strain. The MYBT18247 pathogen load of elt-2(RNAi) worms compared to control worms remained unchanged, suggesting the elt-2 negatively regulates tolerance towards MYBT18247. We found that tolerance to MYBT18247 was positively regulated by the transcription factors: FOXO daf-16, bZip zip-2, nhr-99 and nhr-193. To identify elt-2 negatively-regulated downstream targets that could promote tolerance to MYBT18247, we performed a second RNA-Seq experiment, this time including elt-2(RNAi) worms exposed to both pathogenic strains. We found four genes negatively regulated by elt-2: cdr-2, poml-3, dhs-30 and tre-3, with putative function in detoxification and lipid metabolism, which can mediate tolerance to MYBT18247. We conclude that ELT-2 coordinates strain-specific immune responses in this invertebrate host and promotes resistance upon exposure to MYBT18679, while it negatively regulates tolerance to MYBT18247. The response is likely to be specific to the crystal pore-forming toxins produced by this pathogen.

overall_design: mRNA profiles of wild type (WT) and elt-2 (RNAi) C.elegans exposed to either Bacillus thuringiensis B-18247, B-18679 and B-18407 at 6h or 12h were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Alejandra

last: Zarate-Potes

first: Katja

last: Dierking


title: A Zebrafish JAK1-A634D Gain-of-Function Model Provides New Insights into the Pathogenesis of Familial Hypereosinophilia

status: Public on Dec 27 2019

city: Ottawa

first: Sergey

last: Prykhozhij

state: ON

address: Room 318/319 | CAREG, 20 Marie-Curie Private

country: Canada

institute: CHEO Research Institute/University of Ottawa

summary: JAK1 plays an important role during zebrafish development as hematopoietic regulator with a specific impact in the myeloid lineage, from where the eosinophils arise. Several genes in the JAK-STAT pathway are elevated in the transgenic mutants (STAT1B, SOCS3A, SOCS3B, PIAS2) as well as patways involved in hematopoiesis, immunity, response to interferon and response to biotic stimuli.

overall_design: Total RNA from casper, JAK1-WT and JAK1-A634D zebrafish embryos at 28 and 36 hours post-fertilization was extracted to characterize the transcriptomic effects of the JAK1-A634D gain-of-function mutation

first: Anna

last: Cordeiro-Santanach

middle: V

first: Adam

middle: P

last: Deveau

first: Gabriel

last: Wajnberg

first: Nicolas

last: Crapoulet

first: Stuart

middle: E

last: Turvey

first: Jason

middle: N

last: Berman


title: Bazedoxifene and conjugated estrogen combination improves gut-liver axis health [microbiota]

status: Public on Dec 28 2019

city: Urbana

first: Karen

state: IL

address: 1201 W Gregory St

department: Division of Nutritional Sciences

country: USA

institute: University of Illinois at Urbana-Champaign

summary: Bazedoxifene and conjugated estrogens (CE+BZA) combination has been shown to prevent visceral adiposity and weight gain after menopause. However, its interaction with the microbiota has yet to be examined. In the present study, we use several –omics technologies to characterize the effects of various estrogens on the health of gut-liver axis. As reported in previous studies, CE+BZA combination is very effective at preventing ovariectomy-induced weight gain in mice fed a high-fat diet. Additionally, CE+BZA induces unique liver transcriptomic and blood metabolite profiles compared to estradiol, conjugated estrogens alone, and bazedoxifene alone. Several pathways and metabolites influenced are associated with lower rates of inflammation and overall benefits to gut and liver health. Finally, microbiome analysis shows that several bacterial species that potentially metabolize estrogens and affect their half-life in the body were significantly changed in CE+BZA treated mice. Our findings indicate a possible link between certain estrogens and gut microbiome and suggest a metabolic benefit of estrogens through manipulation of the gut-liver axis.

overall_design: Cecal and Fecal bacteria

first: Zeynep

last: Madak-Erdogan


title: Genome-wide screening of N6-methyladenosine modification pattern in clear cell renal cell carcinoma (ccRCC)

city: Changzhou

first: Yimeng

state: Jiangsu

address: No.185, Juqian Street

institute: The Third Affiliated Hospital of Soochow University

summary: m6A modification patterns in ccRCC and normal tissues were described via m6A-sequencing and RNA-sequencing, followed by bioinformatics analysis. m6A-related RNAs were immunoprecipitated by anti-m6A antibody-coupled beads, and validated by qPCR.

overall_design: Examing clear cell renal cell carcinoma tissues and tumor-adjacent normal tissues, each with 3 replicates

first: Dong

last: Xue


title: Replication timing alterations in leukemia reflect stable clinically-relevant changes in genome architecture

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

type: Genome variation profiling by genome tiling array

type: Genome variation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Capture-C analysis of RCC-susceptibility loci in 786O renal cancer cell line

city: Oxford

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

summary: Analysis of chromatin looping identies gene promoters that interact with enhancers and HIF-binding sites at kidney cancer-associated susceptibility loci

overall_design: We utilised Capture-C to study chromatin looping from enhancers and HIF binding sites that overlap kidney cancer-associated polymorphisms identifed in a meta-analysis of kidney cancer GWAS

middle: R

first: Veronique

last: Lafleur


title: Partial replacement of glucose with galactose in the post-weaning diet positively affects markers of liver health

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: Previous research showed a beneficial programming effect of replacting glucose in the post-weaning diet with galactose on later life adiposity. Here, we studied the direct effect of the diets in the postweaning phase in female mice.  In this study, female mice were fed a glucose diet (32 en% glucose; GLU) or a glucose+galactose diet (16 en% glucose and 16 en% galactose; GLU+GAL) postweaning for three weeks, from postnatal day (PN) 21 till PN42. We observed lower circulating insulin levels and lower hepatic triglyceride levels in the females on the GLU+GAL diet. The body weight, fat mass, liver weight and liver glycogen content did not differ between the groups. We next studied hepatic gene expression profiles, because of the altered hepatic triglyceride levels and since the liver is considered the primary site of galactose metabolism. However, detailed analyses including pathway analysis, showed mainly inflammation being reduced by the GLU+GAL treatment. This was confirmed by qPCR of liver tissues and focussed serum protein analysis.

overall_design: The C57BL/6JRcc female mice (3 weeks old) were individually housed (12h light–dark cycle, 23±1°C, 55±15% humidity), with ad libitum access to feed and water. A semi-synthetic diet (16% energy from fat, 20% energy from protein, 32% energy from starch, and 32 en% from monosaccharides: either glucose only (GLU) or glucose and galactose in a 1:1 ratio (called GLU+GAL). After three weeks on the diets, animals were sacrificed at PN42 in a food-deprived state in the light phase.

first: Lianne

last: Bouwman

first: Inge

last: van der Stelt

first: Jaap

last: Keijer


title: RNA-Seq provides insight to the body size evolution from comparative analyses of three Asia Sisoridae catfish

city: Kunming

first: Wansheng

last: Jiang

state: Yunnan

address: 32# East Jiaochang Road

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

summary: We sampled three catfishes from the Mekong River that belonging to the same Asia Sisoridae family but possessing extremely body size variations. We used RNA-Seq to compare the gene expression and sequence differences of these three sympatric species at their relatively early lives  to search the possible genetic clues that equally response to growth. We found two crucial growth related candidate genes (AKT3 and SH2B1) were consistently up-regulated in BY when compared with both GM and OS at brain, liver and muscle respectively. The adaptor protein SH2B1 can bind to dozens of signaling molecules in response to a variety of extracellular growth signals, and the AKT3 can mediate a broad of intracellular cellular responses. The SH2B1 to AKT3 pathway could regulate growth, proliferation and biosynthetic processes at multiple levels through the AKT crosstalking effects, such as the overall enhancement of ribosome biogenesis we revealed from the multistep analyses strategy. Both the up-regulated DEGs and PSGs of BY converged to pyruvate metabolic process and cell cycle, which would also be critical for BY to accumulate cell growth and proliferation more actively to conduct the final big size. The different gene expression patterns would guide the further studies about body size evolution, and therelated candidate geneshighlighted in this study worth to be tested in the future.

sample_organism:
Bagarius yarrelli
Glyptothorax macromaculatus
Oreoglanis setiger

overall_design: Sequencing a total of 27 samples; including three catfish species, each species has three individuals as replicates, and each individual uses three tissues (brain, liver and muscle).

first: Yicheng

last: Guo


title: Replication timing alterations in leukemia reflect stable clinically-relevant changes in genome architecture [Repli-Seq]

summary: Human B-lineage precursor acute lymphoid leukemias (BCP-ALLs) comprise a group of genetically and clinically distinct disease entities with features of differentiation arrest at known stages of normal B-lineage differentiation. We previously showed BCP-ALL cells display unique and clonally heritable DNA-replication timing (RT) programs; i.e., programs describing the variable order of replication and sub-nuclear 3D architecture of megabase-scale chromosomal units of DNA in different cell types. To determine the extent to which BCP-ALL RT programs mirror or deviate from specific stages of normal human B-cell differentiation, we transplanted immunodeficient mice with quiescent normal human CD34+ cord blood cells and obtained RT signatures of the regenerating B-lineage populations. We then compared these with RT signatures for leukemic cells from a large cohort of BCP-ALL patients of varied genetic subtype and outcome. The results identify BCP-ALL subtype-specific features that resemble specific stages of B-cell differentiation and features that appear associated with relapse. These results suggest the genesis of BCP-ALL involves alterations in RT that reflect biologically significant and clinically relevant leukemia-specific epigenetic changes that have potential as a novel genre of prognostic biomarkers.

overall_design:
Genome-wide replication timing profiles were constructed from leukemia patients cells and normal differentiation stages of B-cell differentiation

Please note that the processed data 'BALLanBlood_Alldata.txt' was generated from both array and HTS data (GSE130372 and GSE130373).


title: TNF deficiency causes changes in the spatial organization of neurogenic zones and the number of microglia and neurons in the cerebral cortex

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

summary:
Background: Although TNF inhibitors are used to treat chronic inflammatory diseases, there is little information about how long-term inhibition of TNF affects the homeostatic functions that TNF maintains in the intact CNS. TNF is known to modulate neurogenesis by decreasing cell proliferation, increasing apoptosis of precursor cells, and impairing neuronal differentiation. TNF can also influence the formation of the hippocampus, with long-lasting effects on cognition. Materials and methods: To clarify whether developmental TNF deficiency causes alterations in the naïve CNS, we estimated the number of proliferating cells, microglia, and neurons in the brains of E13.5, P7, and adult TNF +/+ and TNF-/- mice and measured changes in gene and protein expression and monoamine levels in adult TNF+/+ and TNF-/- mice. To evaluate long-term effects of TNF inhibitors, we treated healthy adult C57BL/6 mice with either saline, selective soluble TNF inhibitor XPro1595, or nonselective TNF inhibitor etanercept. We estimated changes in cell number and protein expression after two months of treatment. We assessed the effects of TNF deficiency on cognition by testing adult TNF+/+ and TNF-/- mice and anti-TNF treated mice with behavioral tasks.
Results: TNF deficiency initially decreased the number of proliferating cells and microglia, but subsequently increased the number of neurons. At the same time, TNF deficiency decreased the expression of WNT signaling-related proteins, specifically Collagen Triple Helix Repeat Containing 1 (CTHRC1) and Frizzled receptor 6 (FZD6). In contrast to XPro1595, longterm inhibition of TNF with etanercept in adult C57BL/6 mice decreased the number of proliferating cells in the granule cell layer of the dentate gyrus. Etanercept, but not XPro1595, also impaired spatial learning and memory in the Barnes maze memory test. Conclusion: TNF deficiency impacts the organization of neurogenic zones and alters the cell composition in brain. Long-term inhibition of TNF with the nonselective TNF inhibitor etanercept, but not the soluble TNF inhibitor XPro1595, decreases neurogenesis in the adult mouse hippocampus and impairs learning and memory after two months of treatment.

overall_design: We first characterized the possible effects of developmental TNF deficiency and long-term inhibition of TNF in adulthood on gene and protein expression, monoamine levels, neurogenesis, and cell composition in the brain, and on the function and permeability of the blood-brain barrier (BBB). We then investigated the effect of TNF deficiency on cognitive functions. Adult male TNF+/+ and TNF-/- brain lysates were used for RNA isolation. Isolated RNA was quality assessed using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA) with an Agilent 2100 bioanalyzer (Agilent Technologies). Isolated RNA was hybridized to the Affymetrix GeneChip Mouse Gene 1.0 ST Array according to the manufactorer protocol (Thermo Fisher Scientific, Waltham, MA, USA). We used the Significance Analysis of Microarray (SAM) method to identify probe sets with target in transcripts that were significantly differentially expressed between TNF+/+ and TNF-/- mice (Tusher et al., 2001). SAM analysis was performed using MultiExperimentViewer Software v. 4.5.1. (Dana- Farber Cancer Institute, Boston, MA, USA), 70 unique permutations and an s0 value selected by Tusher’s method (Saeed et al., 2006; Saeed et al., 2003; Tusher et al., 2001). A false discovery rate (FDR) < 5% was considered evidence of statistical significance.

first: Minna

last: Yli-Karjanmaa

first: Kathrine

last: Solevad Larsen

first: Christina

last: During Fender

first: Lotte

last: Kellemann Kristensen

first: Nallie

middle: A

last: Martin

first: Peter

last: Toft Jensen

first: Alexandre

last: Breton

first: Stephanie

last: Lindemann Carlsen

first: Jan

middle: B

last: Gramsbergen

first: Bente

last: Finsen

first: Jane

last: Stubbe

first: Lars

last: Frich

first: Helen

last: Stolp

first: Roberta

last: Brambilla

first: Daniel

last: Anthony

first: Morten

last: Meyer

first: Kate

last: Lambertsen


title: Proteogenomic characterization and comprehensive integrative genomic analysis of human colorectal cancer liver metastasis

first: DA

last: FU

state: Shanghai

address: Middle 301 Yanchang Road

institute: Shanghai Tenth People's Hospital

summary: Colorectal cancer (CRC) is the third most common cancer worldwide and liver metastasis remains the major cause of death in CRC. Extensive genomic analysis provided valuable insight into the pathogenesis and progression of CRC. However, the major proteogenomic characterization of CRC liver metastasis is still unknown. We investigated proteogenomic characterization and performed comprehensive integrative genomic analysis of human colorectal cancer liver metastasis.

overall_design: Here we performed SNP array profiling for 2 triplets, each comprising normal colorectal tissue, primary colorectal carcinoma, and its synchronous matched liver metastasis

first: Yu

middle: S

last: Ma

first: Zhong

middle: W

last: Lv

first: Tao

last: Huang

first: Xian

middle: L

last: Cong

first: Da

last: Fu


title: Genome-wide methylation in alcohol use disorder subjects: implications for an epigenetic regulation of the cortico-limbic glucocorticoid receptors (NR3C1)

city: Chicago

first: Subhash

middle: C

last: Pandey

address: 1601 West Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago & Jesse Brown VA Medical Center

type: Methylation profiling by genome tiling array

summary: Environmental factors, including substance abuse and stress, cause long-lasting changes in the regulation of gene expression in the brain via epigenetic mechanisms, such as DNA methylation. We examined genome-wide DNA methylation patterns in the prefrontal cortex (PFC, BA10) of 25 pairs of control and individuals with AUD, using the Infinium® MethylationEPICBeadChip. We identified 5,254 differentially methylated CpGs (pnominal<0.005). Bioinformatic analyses highlighted biological processes containing genes related to stress adaptation, including the glucocorticoid receptor (encoded by NR3C1). Considering that alcohol is a stressor, we focused our attention on differentially methylated regions of the NR3C1 gene and validated the differential methylation of several genes in the NR3C1 network. We observed that chronic alcohol drinking results in a significant increased methylation of the NR3C1 exon variant 1H, with a particular increase in the levels of 5-hydroxymethylcytosine over 5-methylcytosine. These changes in DNA methylation were associated with reduced NR3C1 mRNA and protein levels in PFC as well as other cortico-limbic regions of AUD subjects when compared to controls. Furthermore, we show that the expression of several stress-responsive genes (e.g., CRF, POMC, FKBP5) is altered in the PFC of AUD subjects. These stress-response genes were also changed in the hippocampus, a region that is highly susceptible to stress. These data suggest that alcohol-dependent aberrant DNA methylation of NR3C1 and consequent changes in other stress-related genes might be fundamental in the pathophysiology of AUD and lay the groundwork for treatments targeting the epigenetic mechanisms regulating NR3C1 in AUD.

overall_design: Compare CpG in BA10 of 23 control and 23 AUD subjects

first: Eleonora

last: Gatta

first: Dennis

last: Grayson

first: James

last: Auta

first: Vikram

last: Saudagar

first: Erbo

last: Dong

first: Ying

last: Chen

first: Harish

last: Krishnan

first: Jenny

last: Drnevich

first: Alessandro

last: Guidotti


title: Genome-wide maps of chromatin state in immune cells derived from IBD patients

city: tyuo-ku

first: noriko

last: nishi

state: Tokyo

address: 5-11 hakozaki 5F Yunibasaru Bldg

country: Japan

institute: Axiohelix Co. Ltd.

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We generated genome-wide chromatin-state maps of  immune cells purified from LPMC of IBD and non-IBD patients by using next generation sequencing.

overall_design: Examination of 3 different histone modifications in 2 cell types.

first: Takeshi

last: Otsubo

first: Kenshiro

last: Oshima

first: Masahira

last: Hattori

first: Taeko

last: Dohi

first: Yuki

middle: I

last: Kawamura


title: Large-scale Production of Human Liver Organoids with Improved Hepatocyte Differentiation

status: Public on Dec 26 2019

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

institute: Utrecht University

summary: The establishment of a new method for the expansion of human adult stem cell-derived liver organoids in spinner flasks which results in a highly efficient method for culturing large numbers of organoids applicable for transplantation.

overall_design: Whole transcriptome data of human liver organoids cultured in spinner flasks or Matrigel produced on Illumina NextSeq500 using a single-end 75 bp configuration

first: Kerstin

last: Schneeberger

first: Natalia

last: Sánchez-Romero

middle: G

first: Loes

last: Oosterhoff

first: Iris

last: Palacin

first: Chen

first: Monique

last: van Wolferen

first: Gilles

last: van Tienderen

first: Ruby

last: Lieshout

first: Imre

last: Schene

first: Ruurdtje

last: Hoekstra

last: Verstegen

first: Luc

middle: J

last: van der Laan

first: Louis

last: Penning

first: Sabine

last: Fuchs

first: Hans

last: Clevers

first: Pedro

last: Baptista

first: Bart

last: Spee


title: Dissecting heterogeneity in epithelial sinonasal cancer

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Epithelial, non-glandular sinonasal cancers (SNCs)  is a rare disease, with a global dismal prognosis. There are no recognized targeted treatments and the knowledge of molecular mechanisms involved in the resistance to available therapies is limited. Dissecting the heterogeneity of paranasal sinus cancersSNCs and providing valuable information on the biology of the malignancy is eagerly needed to improve therapeutic approaches.

overall_design: We selected a retrospective cohort of 47 SNCs including: i) non keratinizing squamous cell cancer (NKSCC, n=21); ii) sinonasal neuroendocrine cancer (SNEC, n=13); iii) sinonasal undifferentiated cancer (SNUC, n=13). Main tumor subsite was the ethmoid sinus (62%), followed by nasal cavity (26%), maxillary sinus and other subsites (6% each).  Locally advanced stages were the most represented (stage III and IV 91%), mainly due to advanced T stage (T4a 19%; T4b 53%). Treatment modality was multimodal, comprising surgery followed by adjuvant radiation (with or without concomitant chemotherapy) in 70% of the cases and curative chemoradiation, with or without induction chemotherapy, in 30% of the patients.


title: RNA-seq in liver cancer cell and cinobufagin treatment cells

city: Tianjin

first: Zhongwei

last: Xu

state: Tianjin

address: No.1 Huizhi Huan Road , DongLi district, Tianjin City, China, Shuguang Zhou

institute: Logistics University of Chinese People’s Armed Police Force

summary: Cinobufagin, belonged to a kind of cardiotonic steroids (CSs), derived from the extracts of toad venom, which presented the significant anticancer properties as inhibitors of Na+/K+-ATPase (NKA) in many cancer cells. Nowadays, cinobufagin was usually used to apply for clinical treatments of patients in advanced stage of cancer, and improved their quality of life and prolonged their survival period. Unfortunately, long-term drug treatment had also led to multi-drug-resistance (MDR) likely other chemotherapy drugs. However, this detailed mechanism was not still clear. In the present study, we noticed that cinobufagin could trigger the protective autophagy to suppress cells apoptosis in liver cancer HepG2 and Huh-7 cells by inhibition of PI3K-AKT-mTOR pathway using RNA-seq method. We also confirmed that cinobufagin could inhibit cells proliferation and induce cells apoptosis, and generated cells autophagy by up-regulation expression of LC3B-II, Beclin 1 and Atg12-atg5. More importantly, autophagy inhibitor (MRT68921) enhances the anti-proliferation and pro-apoptosis effects of cinobufagin in HCC cells. Therefore, we thought that a combination of cinobufagin and autophagy inhibitors may be a potential effective strategy in treatment of HCC.

overall_design: Examination of cinobufagin treatment for 0, 12, and 24 h in 2 cell types.


title: A compositional change in exomiRs during normal fibroblast to cancer-associated fibroblast transition.

city: Seoul

first: Baek Gil

last: Kim

address: 50-1 Yonsei-Ro

country: South Korea

institute: Yonsei University

summary: To understand the role of stromal exomiRs on tumor progression, the count values of exomiRs was compared between the normal and cancer-associated fibroblasts derived from an invasive ductal carcinoma patient.

overall_design: Cancer-associated fibroblasts were isolated from the tumor tissue of an invasive ductal carcinoma patient. Normal fibroblasts were isolated from the stromal tissue 10 mm away from the margin of the tumor tissue. Microarray was performed in triplicates with separately prepared samples.

first: Baek

first: Nam

middle: H

last: Cho


title: Transcriptome Analysis of immune cells derived from IBD patients by using Next Generation Sequencing

first: noriko

last: nishi

summary: We obtained transcriptome profiling (SAGE-seq) of immune cells purified from LPMC of IBD and non-IBD patients by using next generation sequencing.

overall_design: Comparison of expression pfofiles in 2 cell types between IBD and non-IBD patients.

first: Takeshi

last: Otsubo

first: Kenshiro

last: Oshima

first: Masahira

last: Hattori

first: Taeko

last: Dohi

first: Yuki

last: Kawamura


title: Plasmacytoid dendritic cell heterogeneity is defined by CXCL10 expression following TLR7 stimulation

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: We have used chemokine reporter mice to investigate down-stream effectors of type I IFN signaling, the chemokines of the CXCR3 family. We show that pDCs and conventional DCs display unique chemokine expression profiles that are dependent on IFNAR1 signaling. We go onto show that, following stimulation, pDCs form two stable and transcriptionally distinct populations based on their expression of CXCL10.

overall_design: Transcriptional profiling of CXCL10+BFP+ and CXCL10-BFP- pDC populations following IMQ stimulation in vitro

first: Joanna

last: Groom

first: Yifang

last: Hu

first: Yang

last: Liao


title: Genome-wide transcriptome analysis of a specific brain region (ICo) in chickens

city: Fuchu-shi

first: Tsuyoshi

last: Shimmura

address: 3-8-1 Harumi-cho

institute: Tokyo University of Agriculture and Technology

summary: We compared the gene expression of ICo (center of rooster crowing) using RNA-seq between the two comparison groups showing and not showing crowing and uncovered the molecular basis on animal vocalization.

overall_design: Compasison of gene expression of ICo between the two comparison groups showing and not showing crowing (roosters versus hens, and T-administrated chicks versus chicks)

first: Takashi

last: Yoshimura


title: Gene expression profile of sheep following dietary iodide supplementation

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

summary: In the present study, we studied the effect of dietray iodide (IOD) supplementation on the transcriptome's profile of sheep. The main objective was to evaluate the effect of IOD-supplementation on the overall transcriptome of sheep, the altered pathways, and the biological processes related to it . A previously custom-designed oligo microarray platform (GPL20576) was used to profile the transcriptome of 10 ewes at two time points [T0 (before supplementation) and T40 (after 40-days supplementation period). The Isolated and purified total RNAs were individually hybridized to the custom (4x44k) DNA microarray. The comparison of unsupplemented and supplemented animals' transcriptome revealed a large set of differentially expressed genes. Functional analysis showed several pathways and biological processes that have been altered following IOD-supplementation to the diet.

overall_design: Fifteen sheep were used in this study. Animals were randomly divided into two groups, where the first group was used as a control (CTRL; n = 5), and the second group (n = 10) was supplemented for 40 days with 28 mg iodide (IOD) per animal/day and served as a experimental group. Following completion of the treatment, blood samples were collected from each individual animal directly into Paxgene blood collection tubes, processed and stored at -20˚C till further analyses. All samples yielded high quality RNA that was tested prior the microarray setup.

first: Mery

last: Giantin

first: Mauro

last: Dacasto

first: Federica

last: Castellani

first: Lisa

last: Grotta

first: Fiorentina

last: Palazzo

first: Giuseppe

last: Martino


title: Gene expression profiles of subjects exposed to Arsenic through drinking water in Pakistan

city: Islamabad

first: Muhammad Yasir

last: Abdur Rehman

state: ICT

department: Environmental Sciences

country: Pakistan

institute: Quaid-i-Azam University

summary: Ground water Arsenic toxicity is the global problem and millions of people are exposed to elevated levels through drinking water than WHO permiscible limit of 10µg/L. The exposure is associated with various cancerous and non-cancerous diseases. It may alter the gene expression profile of invidual and suppress the activity of various genes giving rise to different diseases. Pakistan, a developing country in South Asian region, also have different areas reported to have elevated Ground water As. levels since 2005. The Present Study aimed to investigate Transcriptome profile of the exposed subjects in two districts of Punjab Province Pakistan. i.e Lahore and Kasur. The population was stratified into three exposure groups comprising Low, Medium and High exposure based on their urinary arsenic levels. We used Agilent Microarrays platform for Transcriptomics analysis and Linear mixed model was used to find differential gene expression associated with Arsenic exposure

overall_design: Whole blood samples stored in RNA later were collected form the respected exposure groups and transported to Department of Toxicogenomics Maastricht University, The Netherlands for further analysis. Total RNA was Isolated using Ribopure Blood RNA kit. Agilent one colour Microarrays protocol was used for Labeling, Hybridization and scanning.

first: Muhammad

middle: Y

last: Rehman

first: Jos

last: Kleinjans

first: Jacco

last: Briede

first: Marcel

last: van Herwijnen

first: Julian

last: Krauskopf

first: Danyel

last: Jennen

first: Abida

last: Farooqi

first: Riffat

last: Malik


title: Role of Sting in a lupus mouse model of Fcgr2b-deficient mice

status: Public on Dec 25 2019

city: Bangkok

first: Arthid

last: Thim-uam

address: Rama IV

department: Biomedical science

country: Thailand

institute: Chulalongkorn University

summary:
To determine the role of Sting pathway involving in the pathogenesis of SLE in a lupus mouse model of Fcgr2b-deficient mice.
To identify mechanisms of the Sting signaling that contributes to SLE development

overall_design: To better understand the effects of Sting in lupus pathogenesis, the Sting- deficient mouse were breed together with Fcgr2b-deficient lupus mouse model and explain the mechanism if Sting participates in this mouse model.

first: Prapaporn

last: Pisitkun


title: MicroRNA-18a promotes cancer progression through SMG1 suppression and mTOR pathway activation in nasopharyngeal carcinoma

city: Guangzhou

first: HAIDE

last: QIN

state: Guangdong  Province

address: No. 135, Xingang Xi Road

department: Sun Yat-sen Memorial Hospital

institute: SUN YAT-SEN UNIVERSITY

summary: To search for molecular processes underlying miR-18a-mediated oncogenesis in nasopharyngeal carcinoma(NPC) cells, whole-genome mRNA microarray analysis was performed using the HumanGene Expression 4 x 44k v2 Microarray Kit (Agilent Technologies) in 6-10B cells with stable miR-18a overexpression and in 5-8F cells with transient silencing of miR-18a by siRNA. Differentially expressed genes in miR-18a-overexpressing cell and differentially expressed genes in miR-18a knockdown cells were analyzed.

overall_design: Nasopharyngeal carcinoma(NPC) cell line 6-10B cells with stable miR-18a overexpression, and NPC cell line 5-8F with transient silencing of miR-18a by siRNA were subjected to gene expression profiling using the HumanGene Expression 4 x 44k v2 Microarray Kit (Agilent Technologies). Differentially expressed genes were analyzed by by comparison of the treated cell lines with their corresponding untreated parental cell lines.

first: Shi-Juan

last: Mai

first: Xiao-Min

last: Zhou

first: Ruo-Wen

last: Xiao

first: Lu

last: Shi

first: Hai-De

last: Qin


title: STARR-seq based mutagenesis of transcription factor binding sites

city: Huntsville

first: Ryne

last: Ramaker

state: AL

address: 601 Genome Way

department: Genetics

institute: University of Alabama at Birmingham

summary: We performed a STARR-seq based, massively parallel reporter assay on reference genome and mutation-containing oligonucleotide sequences from regions associated with a large number of transcription factor ChIP-seq peaks or DHS-footprinted motifs.

overall_design: The data set includes a plasmid DNA oligo library reference sample and 6 replicate RNA samples isolated from the HepG2 cell line. 92,000 170bp oligonucleotides were cloned in parallel into the STARR-seq reporter vector and transfected into HepG2 in 6 replicates. RNA was harvested from these 6 replicates after 48 hours and oligonucleotide expression levels were compared to their representation in the original plasmid DNA pool.

first: Andrew

last: Hardigan


title: Comparative transcriptomic analysis between ‘Sanbenti’ and its bud sport ‘11-06-25’ during grape berry development stages

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

institute: Yangzhou University

summary: Taste and color, which are important organoleptic qualities of grape berry, undergo rapid and substantial changes during development and ripening. In this study, we use two cultivars ‘Sanbenti’ and its bud sport ‘11-06-25’ to explore expression profiles differences and identify genes associated with total soluble solid (TSS) and total anthocyanins during grape berry development stages using RNA sequencing.

overall_design: Transcriptome sequencing intwo cultivars ‘Sanbenti’ and its bud sport ‘11-06-25’ of grape berry

first: Feng

last: Leng


title: Transcriptomic profiling by RNA-Seq of MCF-7 cells edited by CRISPR/Cas9 in the FASN locus

city: Monterrey

first: Victor

last: Trevino

state: Nuevo León

address: Ave. Eugenio Garza Sada 2501 Sur

department: Investigación e Innovación

country: Mexico

institute: Tecnológico de Monterrey

summary: We report a preliminary RNA-Seq data of MCF-7 cells edited in the FASN locus using CRISPR/Cas9. MCF-7 cells were edited by CRISPR/Cas9, screened by Surveyor assay, purified by limiting dilutions, validated by sanger sequencing, and characterized by diverse cellular analyses. Then, RNA from edited cells and non-edited controls were processed by TruSeq-RNA-Library-Prep-Kit and sequenced in a illumina equipment. Reads were aligned to hg38 in Galaxy using RNA-Star and transcripts were counted by FeatureCounts.

overall_design: A CRIPSR/Cas9 edited clone and a edited-negative cells as control.

first: Fernando

last: Gonzalez-Salinas

first: Jessica

last: Herrera-Gamboa


title: Bisulfite sequencing of medaka PGCs methylomes

city: Greensboro

first: Ramji

middle: Kumar

last: Bhandari

state: NC

address: 321 McIver St

institute: University of North Carolina Greensboro

type: Methylation profiling by high throughput sequencing

summary: Medaka PGCs methylomes were sequenced using whole genome bisulfite sequencing (WGBS)

overall_design: Three biological replicates for each stage

middle: K


title: ANKRD31 anchors meiotic double-strand break formation as a direct partner of REC114

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

summary: Homologous recombination initiated by double-strand breaks (DSBs) is crucial for chromosome pairing and segregation during meiosis. Here we unveil mouse ANKRD31 as a lynchpin controlling DSB formation. Spermatocytes lacking ANKRD31 have altered DSB locations and fail to target DSBs to X and Y pseudoautosomal regions (PAR). They also have delayed and fewer recombination sites but, paradoxically, more total DSBs, indicating DSB dysregulation. Unrepaired DSBs and pairing failures—stochastic on autosomes, nearly absolute on X and Y—cause meiotic arrest and male sterility, while Ankrd31-deficient females have reduced oocyte reserves. A crystal structure defines direct ANKRD31–REC114 molecular contacts and reveals a surprising pleckstrin homology domain in REC114. In vivo, ANKRD31 recruits REC114 to the PAR and elsewhere. Our findings inform a model that ANKRD31 is a scaffold anchoring REC114 and other factors to specific genomic locations, promoting efficient and timely DSB formation but also suppressing formation of clustered DSBs.

overall_design: For ssDNA sequencing: Three samples of juvenile mice from same breeding colony (Ankrd31 knocknout, heterozygote, and wild type control); one sample of Ankrd31 knockout adult; one sample of wild type adult; two samples of wild type adult (one of which is a control using an irrelevant-antibody); and one sample from Prdm9 knockout adult. For H3K4me3 ChIPseq: two biological replicates each of wild type and Ankrd31 knockout.

first: Michiel

last: Boekhout

first: Mehmet

middle: E

last: Karasu

first: Juncheng

first: Laurent

last: Acquaviva

first: Florencia

last: Pratto

first: Diana

last: Eng

first: R

middle: D

last: Camerini-Otero

first: Dinshaw

last: Patel

first: Scott

last: Keeney


title: HNRNPM-regulated splicing dependencies in prostate cancer [RNA-Seq]

city: Singapore

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: Cancer cells are differentially dependent on the splicing machinery compared to normal untransformed cells. The splicing machinery thus presents a potential therapeutic target in cancer.  To identify splicing factors important for prostate cancer cell (PCa) growth, we performed an unbiased pooled shRNA screen in in vitro passaged cells and in vivo xenografted PCa tumors. Our screen revealed HNRNPM as a potential regulator of PCa cell growth. RNA- and eCLIP- sequencing data suggest that HNRNPM is bound to key homeostatic genes, and that loss of HNRNPM binding in a subset of these genes results in aberrant exon inclusion and exon back-splicing events in target transcripts. In mis-spliced transcripts, HNRNPM appears to preferentially bind to GU-rich elements in long flanking proximal introns. Mimicry of HNRNPM dependent splicing events using antisense oligonucleotides was sufficient to inhibit cell growth in HNRNPM expressing cells, suggesting that inhibition of cell growth in HNRNPM deficient cells likely has a multi-genic component. Taken together, our data reveal a role for HNRNPM in regulating PCa cell growth, and also as a potential therapeutic target in PCa.

overall_design: Experiment was performed in technical triplicates of RNA isolated LNCAP cells expressing either control non-targetting shRNA (SCR) or HNRNPM targetting shRNA (2B7 or 2B9)

last: Ho


title: HNRNPM-regulated splicing dependencies in prostate cancer

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

overall_design: Refer to individual Series


title: HNRNPM-regulated splicing dependencies in prostate cancer [eCLIP-Seq]

overall_design: Two biological replicates of LNCAP cells were harvested for eCLIP library preparation. An Input and HNRNPM antibody IP sample was included per replicate


title: Gene expression-based, individualized outcome prediction for exposure of rat ovarian tissue

city: Xiamen

first: Zhenghong

last: Zuo

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

department: School of Life Sciences, Xiamen University

institute: Xiamen University

summary:
Hierarchical clustering of the dysregulated genes from ovary of SD rat in different groups were successfully constructed through expression profiling，which suggested large sets of differentially regulated genes in rat ovaries in response to TBT or BPA exposure, and the combined group had more regulated genes. Though these differential expression genes, we can see the differentiation of agents of TBT and BPA. And according to these genes, we could farther study these related pathways to the PCOS.
Using the selection criteria (FC ≥ 2, p ≤ 0.05), 86 up-regulated genes and 71 down-regulated genes were identified in the TBT100 group. In the BPA50 group, 45 up-regulated genes and 95 down-regulated genes were identified using the same criteria. The TBT+BPA group had 258 up-regulated genes and 234 down-regulated genes.

overall_design:
There are three experimental groups and one control group. Each group has three sample replicates.From postnatal day 1 (PND1) to postnatal day 16 (PND16) , pups were injected TBT 100 ng/kg (TBT100), BPA 50μg/kg (BPA50) and TBT100 combined with BPA50 (TBT+BPA), which were administered by subcutaneous injection, whereas the control rats received an equal volume of vehicle (5 μL/g). All compounds were dissolved in ethanol and then sesame oil at a ratio of 10% ethanol and 90% oil. The vehicle was also prepared with this ratio. Actual dosing volumes were adjusted based on the body weights recorded every day.

Please note that each raw data file contains raw data for two samples as indicated in the corresponding sample title and description field.
For example, the 'Block_Column_Row' 1_1_1 to 1_272_194 (in the 1-1--2-1.gpr file) contains the first sample (i.e. [1-1]) raw data and the 'Block_Column_Row' 1_1_195 to 1_272_349 contains the second sample (i.e. [2-1]) raw data.

first: Zuo

last: Zhenghong


title: Replication timing alterations in leukemia reflect stable clinically-relevant changes in genome architecture [Repli-Chip]

city: Tallahassee

first: David

middle: M

last: Gilbert

address: 319 Stadium Drive

institute: Florida State University

summary: Human B-lineage precursor acute lymphoid leukemias (BCP-ALLs) comprise a group of genetically and clinically distinct disease entities with features of differentiation arrest at known stages of normal B-lineage differentiation. We previously showed BCP-ALL cells display unique and clonally heritable DNA-replication timing (RT) programs; i.e., programs describing the variable order of replication and sub-nuclear 3D architecture of megabase-scale chromosomal units of DNA in different cell types. To determine the extent to which BCP-ALL RT programs mirror or deviate from specific stages of normal human B-cell differentiation, we transplanted immunodeficient mice with quiescent normal human CD34+ cord blood cells and obtained RT signatures of the regenerating B-lineage populations. We then compared these with RT signatures for leukemic cells from a large cohort of BCP-ALL patients of varied genetic subtype and outcome. The results identify BCP-ALL subtype-specific features that resemble specific stages of B-cell differentiation and features that appear associated with relapse. These results suggest the genesis of BCP-ALL involves alterations in RT that reflect biologically significant and clinically relevant leukemia-specific epigenetic changes that have potential as a novel genre of prognostic biomarkers.

overall_design:
Genome-wide replication timing profiles were constructed from leukemia patients cells and normal differentiation stages of B-cell differentiation

Please note that the processed data 'BALLanBlood_Alldata.txt' was generated from both array and HTS data (GSE130372 and GSE130373).


title: Gastrointestinal tissue-specific chromatin accessibility and gene expression during development (ATAC-Seq)

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

institute: UNIV HEALTH NETWORK

summary: We used ATAC-Seq to profiling epigenomic changes and RNA-Seq to profiling gene expression changes during the embryonic development of gastrointestinal  tract.

overall_design: ATAC-Seq  of mouse embryonic tissues

first: Roshane

last: Francis

first: Musa

last: Ahmed

first: Theodora

last: Yung

first: Peter

last: Dirks

first: Housheng

last: He

first: Tae-Hee

last: Kim


title: Hypoxia and dimethyloxalylglycine (DMOG) downregulates tryptophan-2,3-dioxygenase (TDO2) expression in GBM cells

city: Heidelberg

first: Ahmed

last: Sadik

address: Im Neunheimer Feld 280

department: Metabolic Crosstalk in Cancer

institute: DKFZ

summary: The tryptophan degrading enzyme TDO2 is downregulated upon HIF1alpha stabilization by exposure to  both hypoxia as well as chemical hypoxia mimetics such as DMOG in glioblastoma cell line A172.

overall_design: Hypoxia: expression profile of A172 cells under hypoxic (1% oxygen) and normoxic (18.6% oxygen) conditions after 5 days (n = 5). DMOG: expression profile of A172 cells treated with 3mM dimethyloxalylglycine (DMOG) for 24 hours compared to EtOH control (n=3).

first: Soumya

last: Mohapatra

first: Christiane

middle: A

last: Opitz


title: Assessing Genetic Diversity of Asian Salamanders (Hynobiidae) lived in Far East Asia using Transcriptome data

status: Public on Dec 24 2019

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

institute: Ulsan National Institute of Science and Technology

summary: Asian salamander Hynobiidae is commonly observed in the Far East Asia regions, including Korea, Japan, China, and the eastern region of Russia. In Korea, there are four Hynobiidae species known to be lived: Hynobius leechii, Hynobius quelpaertensis, Hynobius yangi, and recently reported Hynobius unisacculus. However, even H. leechii which is broadly colonized in Korea peninsula seems to have a new species candidate, which has distinctive genetic and phenotypic characteristics. Genomic resources are essential to understand the current status of these species, but due to the large size of their genomes (about 16 to 20 Gb), it is not easy to analyze. To reveal the genomic characteristics of these species, we constructed more than ten thousands of protein-coding gene sequences from multiple samples of each species, using the de novo transcriptome assembly approach from RNA-Seq data, confirming their taxonomic relationship which was reported based on mitochondrial DNA and marker genes. Also, by comparing previously reported transcriptome of Hynobius chinensis and Hynobius retardatus, lived in China and Japan, respectively, we found that Korean species have unique genetic signatures. By comparing vertebrate model organism genes, we reported Hynobidaii specific proteins. These data would be a useful resource to study other Caudata species in the future.   This research was supported by the National Institute of Biological Resources, Republic of Korea, under the project "Genetic diversity of animal resources” (NIBR201703203 and NIBR201803101).

sample_organism:
Hynobius leechii
Hynobius quelpaertensis
Hynobius yangi
Hynobius unisacculus

overall_design: We collect adult salamanders lived in Korea

first: Sinhyeok

last: Chae

first: Mi

last: Min


title: RNA-sequencing of murine WT and MAZR-cKO FOXP3+ regulatory T cells (Treg cells)

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

summary: The analysis of WT and MAZR-cKO mice indicates that the transcription factor MAZR plays an important role in Treg cell development and function. The aim of this NGS experiment was to determine the MAZR-dependent transcriptome in regulatory T cells to elucidate how MAZR controls Treg cell biology. The results of this genome-wide analysis indicate that MAZR-cKO Treg cells display only minor transcriptional differences, suggesting that MAZR has a minor role in establishing the transcriptional program in ex vivo analyzed Treg cells once the Treg cell fate has been acquired.

overall_design: mRNA expression profiles of 6-8 week old splenic WT,DEREG and MAZR-cKO,DEREG (CD4-cre) mice were generated by deep sequencing.

first: Liisa

last: Andersen


title: ChIP-seq analysis of HIF-1b binding in hypoxic cancer cell lines

city: Oxford

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

institute: University of Oxford

summary: Pan-genomic analysis of hypoxic HIF-1b binding by ChIP-seq in cancer cell lines

overall_design: ChIP_seq analysi of HIF-1b binding in 4 cancer cell lines incubated in 0.5% hypoxia for 16 hours

middle: R

first: Olivia

last: Lombardi


title: Polymorphisms in mitochondrial DNA genes coding for subunits in complex I differentially control lifespan and ageing-related pathways in mice.

status: Public on Dec 23 2019

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Mitochondrial complex I, the largest enzyme complex of the mitochondrial oxidative phosphorylation machinery, has been proposed to contribute to variety of age-related pathological alterations as well as longevity. The enzyme complex-consisting proteins are encoded by both nuclear- (nDNA) and mitochondrial DNA (mtDNA). While some association studies of mtDNA-encoded complex I genes and lifespan in humans have been reported, experimental evidence and functional consequence of such variants are limited to studies using invertebrate models. Here, we present experimental evidence that a homoplasmic mutation in mitochondrially encoded complex I gene, mt-Nd2, modulates lifespan by altering cellular tryptophan levels and consequently ageing-related pathways in mice. A conplastic mouse strain carrying a mutation at m.4738C>A in mt-Nd2 lived significantly shorter than the controls. The same mutation led to higher susceptibility to glucose intolerance induced by high fat diet feeding. These phenotypes were not observed in mice carrying a mutation in another mtDNA-encoded complex I gene, mt-Nd5, suggesting functional relevance of particular mutations in complex I to ageing and age-related diseases.

overall_design: The transcriptomes of liver obtained from C57BL/6J-mtALR (mutation in mt-Nd2 gene) was compared with those from C57BL/6J-mtBPL  (mutation in mt-Nd5 gene)  by RNAseq.

first: Misa

last: Hirose

first: Saleh

last: Ibrahim


title: The effect of intermittent versus continuous low dose aspirin on nasal epithelium gene expression in current smokers: a randomized, double-blinded clinical study

city: Boston

first: Adam

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary:
A chemopreventive effect of aspirin (ASA) on lung cancer risk is supported by epidemiologic and preclinical studies. We conducted a randomized, double-blind, placebo controlled study in current heavy smokers to compare modulating effects of intermittent versus continuous low dose ASA on gene signatures of smoking and lung cancer from nasal brushings. Fifty-four participants were randomized to intermittent ASA (ASA 81 mg daily for one week alternating with placebo daily for one week) or continuous ASA (81 mg daily) for 12 weeks. The primary endpoint was modulation of a smoking gene signature in nasal brushings. Other [JB1] endpoints included modulation of nasal and bronchial gene signatures for smoking, lung cancer and chronic obstructive pulmonary disease (COPD) and changes in cyclooxygenase (COX)- and 5-lipoxygenase (LOX)-mediated arachidonic acid (ARA) metabolism.
Low dose ASA intervention caused minimal changes in smoking and lung cancer gene signature scores in nasal epithelium of current heavy smokers. The small sample size of the intervention groups may have limited the ability to detect modulation of the gene signatures. Low dose ASA lowered urinary prostaglandin E metabolite, a marker of COX-mediated ARA metabolic pathway with no change in urinary leukotriene E4, a marker of 5-LOX-mediated pathway. Exploratory genomic analysis showed that ASA intervention induced wide-ranging genomic changes in the nasal epithelium, including modulation of the arachidonic acid pathway and wound healing.  A companion study is underway using ASA plus zileuton to test dual suppression of COX- and  5-LOX-mediated pathways on these gene signature scores in current heavy smokers.

overall_design: The study was a single center randomized, double-blinded trial to determine the modulatory effects of intermittent ASA dosing (ASA 81 mg daily for one week alternating with placebo daily for one week) versus continuous ASA dosing (ASA 81 mg daily) for 12 weeks on nasal epithelium gene expression and arachidonic acid metabolism in current smokers.  Nasal brushings were collected at baseline, at end of intervention and 7-10 days post intervention.

first: Julian

last: Lel

first: Jennifer

last: Beane

first: Avrum

last: Spira

first: Marc

last: Lenburg


title: IMP1 and IMP2 have different RNA clients and functional programs in mouse embryo fibroblasts

status: Public on Dec 22 2019

first: Ning

last: Dai

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: Different from most publication to date, in this study we find IMP1 and IMP2, two closely related RNA binding proteins, have different clients in MEF cells

overall_design: Using IMP1 and IMP2 KO MEF cells to discover RNA clients.

first: Fei

last: Ji

first: Laura

last: Regué

first: Liping

last: Zhao

first: Ruslan

last: Sadreyev

first: Joseph

last: Avruch


title: Hepatic transcriptional responses of zebrafish to chronic, low dose pharmaceutical exposures

city: Hamilton

first: Andrew

middle: G.

last: McArthur

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

institute: McMaster University

summary: Our study makes use of zebrafish and has determined hepatic transcriptional changes after exposure to four single pharmaceuticals, a pharmaceutical mixture (MIX), and wastewater effluent (WWE) exposures.  The pharmaceuticals chosen include acetaminophen, carbamazepine, gemfibrozil, and venlafaxine. We have performed chronic (6 week), low concentration (0.5 and 10 μgL-1 or 5 and 25% effluent) exposure of male and female fish and previously determined a range of effects (reproductive, histological, hormonal) after exposure to single compounds, a mixture of these compounds or wastewater effluent.  Herein we determine by microarray the hepatic transcriptional responses of male and female zebrafish from the same exposures.

overall_design: Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (acetaminophen, carbamazepine, gemfibrozil, venlafaxine), a mixture of equal concentrations of the four pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration, including water or DMSO controls. Adult wild-type zebrafish were housed in aquaria at a density of 4 fish per liter in 1:1 sex ratio, with triplicate tanks for each treatment group housing 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  After 6 weeks of exposure, zebrafish were sacrificed, weighed and tissues (GI tract with livers) were fixed in RNA Later and stored at -80°C. For RNA extraction, livers were stripped from the GI tract, livers from 10-20 fish per gender were pooled to a maximum 100 mg of tissue, and total RNA extracted. RNA was bioanalyzed and then labeled with Cy3 and 1.65 ug Cy3 labeled cDNA hybridized to a customized Agilent zebrafish single-channel 4 x 44K V2 microarray by the University Health Network Microarray Centre (Toronto, Canada). Raw array data obtained from the University Health Network Microarray Centre were extracted using Agilent's feature extraction software using background detrending (spatial and multiplicative). Prior to normalization, Cy3 values below 5 were set to 5. The data were then normalized using the non-linear scaling method based on rank invariant probes. After normalization but before statistical analyses, probes not significantly above background in all microarrays were removed. None of the probes were saturated for Cy3 signal on any microarray, so no further filtering was applied. Statistical tests were performed using MeV. All data was log transformed and median centered for each probe.  For each experiment, a two-factor ANOVA was run for sex, treatment, and their interaction with p-value based on 1000 permutations of the data and alpha of 0.01.  For exposures with two treatments (i.e. VEN-ACE or GEM-MIX), there were five treatment groups (Control, Low 1, High 1, Low 2, High 2); for exposures with single compounds or effluent (i.e. CBZ or WWE), there were three treatment groups (Control, Low, High).  Probes found significant for treatment and/or interaction from the two-factor ANOVA, were secondarily examined using Rank Product (RP) analysis to provide lists of probes up- and down-regulated between control, low dose, and high dose for each treatment separately for males and females (VEN, ACE, CBZ, GEM, MIX, WWE).  For this, a two-class unpaired RP analysis was performed using 1000 permutation of the data and alpha of 0.01 with a false discovery rate not exceeding 10%.

first: Joanna

last: Wilson

first: Emily

last: Smith

first: Michal

last: Galus

first: Sarah

last: Higgins

first: Nina

last: Kirischian

first: Judith

last: Jeyaranjaan


title: Genome-wide DNA methylation assessment in mouse oocytes: effects of in vitro growth, superovulation and sexual immaturity

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: There is legitimate concern over epigenetic abnormalities that could be induced by procedures applied during assisted reproduction, necessitating epigenetic assessment of new methodologies. The effect of in vitro follicle culture (IFC) and superovulation on DNA methylation in the oocyte is not fully known. Here, we present the first genome-wide analysis of oocyte DNA methylation in IFC, superovulated mouse oocytes and, uniquely, we compare these data with naturally ovulated counterparts. Globally, the distinctive methylation landscape of oocytes, comprising alternating hyper- and hypomethylated domains, is preserved irrespective of the procedure. The conservation of methylation extends to the germline differential methylated regions (DMRs) of imprinted genes, necessary for their monoallelic expression in the embryo after fertilisation. However, we do detect specific, consistent and coherent differences in DNA methylation between IFC and oocytes from other groups, and between oocytes obtained after superovulation from pre-pubertal compared with sexually mature females. Several methylation differences span entire transcription units, consistent with effects on methylation downstream of transcriptional differences. Amongst these, we found alterations in Sox5, Zfp521 and Tcf4, genes for transcripton factors related to nervous system development. These observations also suggest transcriptional and epigenetic differences between oocytes from the initial and later phases of follicle recruitment. Our results provide an important reference for the use of in vitro growth and maturation, particularly from prepubertal females, in assisted reproductive technologies or fertility preservation.

overall_design: 16 samples, 4 experimental groups: In vitro follicle culture (IFC, 4 samples); Superovulation prepubertal (SO, 5 samples), Superovulation Adult (SOA, 4 samples); In vivo (IV, 3 samples).

first: Mara

last: Saenz-deJuano


title: Mediator MED23 induces premature senescence by interacting with BCLAF1 via blocking autophagy flux in lung cancer cells

city: Tianjin

first: Zhenyi

last: Ma

address: 22 Qixiangtai Road

department: Biochemistry and Molecular Biology

institute: Tianjin Medical University

summary: macroautophagy/autophagy plays a key role in regulating the balance between cell survival and senescence during the progression of lung cancer. Med23 (also known as Sur2), a protein belonging to an evolutionarily conserved high-molecularmass complex composed of more than 20 distinct subunits, promotes the growth, metastasis , and migration of lung cancer cells and is overexpressed in multiple cancers. However, the function of MED23 in autophagy regulation remains unknown. Here, we observes that MED23 expression is significantly upregulated in a subset of cancer cells and reversely correlated with overall survival rates and clinical stage for lung cancer patients. Mechanistically, MED23 is found to interact with BCLAF1 (BCL-2-associated transcription factor 1, BTF) ,a nuclear protein that can induce apoptosis and autophagy. Moreover, BCLAF1 interacts with the promoter of NUPR1 and downregulates its expression. We further show that BCLAF1 and MED23 depletion inhibits autophagy and induces premature senescence in vitro. Remarkably, the expression of BCLAF1 and MED23 are negatively correlated with NUPR1 in the human lung cancer tissues and adjacent normal tissues. Collectively, our data reveal a physical and genetic interaction between BCLAF1 and MED23, suggesting that MED23 constitutes a molecular node in the regulatory network of autophagy and this pathway may be an important therapeutic target in lung cancer.

overall_design: mRNA profiles of BCLAF1-depleted A549 and control cells were generated by RNA-sequencing, using HiSeq X Ten.

first: Ma

middle: Z

last: Yi

first: Liu

last: Zhe

first: Li

first: Wang

last: Bin

first: Sun

last: Shen

first: Yin

last: Yuan


title: Next Generation Sequencing Facilitates Quantitative Analysis of MicroRNA-148a Inhibited Transcriptomes

city: Shanghai

first: Haibo

last: Zhou

address: No.160, Pujian Road

department: Department of Rheumatology

institute: Renji Hospital

summary:
Purpose: MicroRNA-148a regulates the differentiation of dendritic cells. The goals of this study are to identify genes and pathways invovled in the regulation.
Methods: Monocytes isolated from wild type or microRNA-148a-/- BM were cultured with GM-CSF and IL-4, or not. Cells were collected at day 0 and day 3. Then, the next-generation libraries of mRNA were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA). Then the mRNA-seq libraries were sequenced in HiSeq ⅹ10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run. The differentially expressed genes were selected as having more than 0.5 fold difference in their geometrical mean expression between the compared groups and a statistically significant p-value (<0.05) by analysis of DEseq2. The GO analysis on differentially expressed genes was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories. Pathway analysis was used to determine the significant pathway of the differential genes according to Kyoto Encyclopedia of Genes and Genomes Database (http://www.genome.jp/kegg/) and DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/).
Results: Gene ontology analysis showed that obviously changed genes enriched in autoimmune disease related pathways, suggesting miR-148a is important in autoimmune responses.  990 protein-coding genes upregulated in their mRNA abundance in miR-148a-/- monocytes on day 0, and 1036 genes in miR-148a-/- monocytes on day 3. Among them, 136 genes were found upregulation on both day 0 and 3 in miR-148a-/- monocytes.

overall_design: MRNA profiles of WT and microRNA-148a monocyte derived dendritic cells were generated by deep sequencing, in triplicate, using illumina HiSeq ⅹ10 system


title: The stress response of Bradyrhizobium japonicum

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

country: Switzerland

institute: ETH Zürich

summary:
Expression data from B. japonicum stress response; aerobic treatment of B. japoncium culture under different stress conditons; pH stress (8 and 4; 4 h); salt stress (80 mM NaCl; 4 h); heat shock (43 °C; 15 min) and temperature stress (35.2 °C; 48 h); as reference wildtype without treatment (AG media; pH 6.9; without NaCl; 28 °C) was used
heat shock data were verified by using rpoH-mutant strains B. japonicum 5009; B. japonicum 5032 and B. japonicum 09-32 as described in Narberhaus et al. 1997

overall_design: B. japonicum transcriptome was determined under different stress conditons

first: K

last: Lang

first: G

last: Pessi

first: M

last: Göttfert


title: Next Generation Sequencing Facilitates Quantitative Analysis of Changed MicroRNAs in Psoriasis Patients.

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: MicroRNAs are small noncoding RNAs involved in autoimmune diseases. The goals of this study are to identify changed miRNAs in the peripheral blood mononuclear cell (PBMC) of psoriasis patients.
Results: Gene ontology analysis showed that obviously changed genes enriched in autoimmune disease related pathways, suggesting miR-148a is important in autoimmune responses.  990 protein-coding genes upregulated in their mRNA abundance in miR-148a-/- monocytes on day 0, and 1036 genes in miR-148a-/- monocytes on day 3. Among them, 136 genes were found upregulation on both day 0 and 3 in miR-148a-/- monocytes.

overall_design: Peripheral blood mononuclear cells (PBMC) were isolated from healthy control (HC) and psoriasis patients (P) by using Ficoll . Then, miRNA libraries were prepared by using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) and then purified by QIAquick® PCR Purification Kit (Qiagen, Hilden, Germany), and put to size selection by using gel Prep. The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).The GO analysis on differentially expressed genes was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories.


title: MicroRNA-148a regulated the development of inflammatory dendritic cells.

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Disease-specific alteration of karyopherin-alpha 4 subtype establishes feed-forward oncogenic signaling in squamous cell carcinoma

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

summary: Nuclear import, mediated in part by karyopherin-alpha 4 (KPNA) subtypes, regulates transcription factor access to the genome and determines cell fate. However, the cancer-specific changes of KPNA subtypes and the relevancy in cancer biology remain largely unknown. Here, we report that KPNA4, encoding karyopherin-alpha 44 (KPNA4), is exclusively amplified and overexpressed in various forms of squamous cell carcinomas (SCCs). Depletion of KPNA4 suppressed malignant phenotypes and induced epidermal differentiation. Mechanistically, KPNA4 mediated nuclear transport of Ras-responsive element-binding protein (RREB1), which sustains Ras/ERK pathway signaling through repressing miR-143/145 expression. Notably, MAPK signaling enhanced trafficking activity of KPNA4 via phosphorylation of KPNA4 at Ser60. These data reveal that KPNA4 establishes a feed-forward cascade that potentiates Ras/ERK signaling in SCCs.

overall_design: Comaprison between negative control cells and KPNA4 knocked down cells. There are two biological replicates for each conditions.

first: Masaharu

last: Hazawa

first: Kie

last: Sakai

first: Akiko

last: Kobayashi

first: Hironori

last: Yoshino

first: Yan-Yi

last: Jiang

first: De-Chen

last: Lin

first: Richard

middle: W

last: Wong


title: A novel urinary microRNA biomarker panel for detecting gastric cancer

summary: Purpose: Gastric cancer (GC) is one of the most common causes of cancer deaths worldwide; however, reliable and non-invasive screening methods for GC are not established. Therefore, we conducted this study to develop a biomarker for GC detection, consisting of urinary microRNAs (miRNAs). Experimental Design: We matched 306 participants by age and sex (153 pairs consisting of patients with GC and healthy controls [HCs]), then randomly divided them across three groups: (1) the discovery cohort (4 pairs); (2) the training cohort (95 pairs); (3) the validation cohort (54 pairs). Moreover, 64 participants (32 pairs) with serum samples were also enrolled in the serum cohort. Result: There were 22 urinary miRNAs with significantly aberrant expressions between the two groups in the discovery cohort. Upon multivariate analysis of the training cohort, urinary expression levels of miR-6807-5p and miR-6856-5p were significantly independent biomarkers for diagnosis of GC, in addition to Helicobacter pylori (H. pylori) status. A diagnostic panel that combined the aberrant miRNAs and H. pylori status distinguished between HC and GC samples with an area under the curve (AUC) = 0.736. In the validation cohort, urinary miR-6807-5p and miR-6856-5p showed significantly higher expression levels in the GC group, and the combination biomarker panel of miR-6807-5p, miR-6856-5p, and H. pylori status also showed excellent performance (AUC = 0.885). In addition, serum levels of miR-6807-5p and miR-6856-5p were significantly higher in the GC group. Conclusion: This novel biomarker panel enables early and non-invasive detection of GC.

overall_design: Comaprison between patients with gastric cancer and healthy controls. There are three or four biological replicates for each conditions, respectively.

first: Hiroyasu

last: Iwasaki

first: Takaya

last: Shimura

first: Tamaki

last: Yamada

first: Yusuke

last: Okuda

first: Makoto

last: Natsume

first: Mika

last: Kitagawa

first: Hiromi

last: Kataoka


title: Expression of a dominant‐negative AtNEET‐H89C protein disrupts iron–sulfur metabolism and iron homeostasis in Arabidopsis

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: Iron–sulfur (Fe–S) clusters play an essential role in plants as protein cofactors mediating diverse electron transfer reactions. Because they can react with oxygen to form reactive oxygen species (ROS) and inflict cellular damage, the biogenesis of Fe–S clusters is highly regulated. A recently discovered group of 2Fe–2S proteins, termed NEET proteins, was proposed to coordinate Fe–S, Fe and ROS homeostasis in mammalian cells. Here we report that disrupting the function of AtNEET, the sole member of the NEET protein family in Arabidopsis thaliana, triggers leaf‐associated Fe–S‐ and Fe‐deficiency responses, elevated Fe content in chloroplasts (1.2–1.5‐fold), chlorosis, structural damage to chloroplasts and a high seedling mortality rate. Our findings suggest that disrupting AtNEET function disrupts the transfer of 2Fe–2S clusters from the chloroplastic 2Fe–2S biogenesis pathway to different cytosolic and chloroplastic Fe–S proteins, as well as to the cytosolic Fe–S biogenesis system, and that uncoupling this process triggers leaf‐associated Fe–S‐ and Fe‐deficiency responses that result in Fe over‐accumulation in chloroplasts and enhanced ROS accumulation. We further show that AtNEET transfers its 2Fe–2S clusters to DRE2, a key protein of the cytosolic Fe–S biogenesis system, and propose that the availability of 2Fe–2S clusters in the chloroplast and cytosol is linked to Fe homeostasis in plants.

overall_design: Col (as WT), 3 NEET lines and 3 H89C lines were analyzed for RNAseq in 3 replicates

first: Sara

middle: I

last: Zandalinas

first: Luhua

last: Song

first: Sam

last: McInturf

first: DeAna

last: Grant

first: Norma

last: Castro-Guerrero

first: Rajeev

last: Azad

first: David

last: Mendoza Cozatl

first: Rachel

last: Nechushtai

first: Ron

last: Mittler


title: FOXD3 suppresses tumor-initiating features in lung cancer via transcriptional repression of WDR5 and SET

first: Ji

middle: Xiang

last: jun

state: Shanghai

address: 500 Dongchuan Rd

department: the Institute of Biomedical Sciences and School of Life Sciences

institute: East China Normal University

summary: In this study, we demonstrated that FOXD3, acting as a repressor in the expansion of lung cancer TICs, was negatively correlated with histological grades and metastasis in lung cancer, and provided evidence that FOXD3 repressed the TIC expansion, cell invasion and drug resistance in vivo and in vitro. Global genomic RNA-Seq and Chip-seq analyses identified WDR5 and SET as the direct targets of FOXD3 in lung cancer. Inhibition of WDR5 and SET could partially rescue TIC abundance, cell invasion, osteogenesis, and gene expression signature upon depletion of FOXD3. Clinically, we revealed that FOXD3 was negatively correlated with WDR5 and SET expression, CSC abundance, and prognosis of lung cancer.

overall_design: mRNA profiles of  wild type (WT) and siFOXD3 of A549 cells were generated by deep sequencing, using Illumina Genome Analyzer.

first: Wei

last: Xu


title: Analysis of transcriptome of mouse melanoma cells co-cultured with HEK293T cells expressing mouse Siglec1.

city: Goyang-si

first: Rohit

last: Singh

state: Gyeonggi-do

address: 323 Ilsan-ro, Ilsandong-gu

department: Division of Tumor Immunology

institute: National Cancer Center

summary: To evaluate the effect of mouse Siglec1 on B16F10 melanoma we used co-culture methos where HEK293T cells were transiently transfected with plasmid containg mouse Siglec1 or empty plasmid (mock). These HEK293T cells were cultured with B16F10-GFP mouse melanoma cells for 18 hours in low binding plates. After 18 hours of incubation on 37°C, 5% CO2, melanoma cells were FACS sorted based on GFP expression and total RNA was isolated and used for TruSeq RNA library construction for transcriptome analysis. Samples were from 3 independent experiments. The library preparation and NGS data aquisition were performed by Macrogen (Macrogen, Inc., Korea)

overall_design: Transcriptome profile of mouse melanoma cells cocultured with mouse Siglec1 expressing cells generated by NGS, in triplicate using Illumina HiSeq4000.

first: Beom K

last: Choi


title: RNA-seq analysis of gene regulation by miR-34a and expression changes induced by DNA damage in zebrafish

status: Public on Dec 21 2019

city: Ottawa

first: Sergey

last: Prykhozhij

state: ON

address: Room 318/319 | CAREG, 20 Marie-Curie Private

institute: CHEO Research Institute/University of Ottawa

summary: Li-Fraumeni syndrome (LFS) is a disorder due to inherited mutations in the TP53 gene resulting in an increased risk of developing several types of cancer. MicroRNA miR-34a has been implicated downstream of p53 on the basis of being a direct transcriptional target and, when over-expressed, having pro-apoptotic phenotypes in cell lines. Moreover, miR-34a has been shown to be a modifier gene in the context of LFS, since its epigenetic silencing increases the likelihood of tumour development in patients with mutant TP53.  However, the in vivo consequences of miR-34 loss are still unclear. For example, mice lacking all three (a,b,c) miR-34 homologs show no detectable abnormalities in p53 responses. The relative expression of different miR-34 genes in zebrafish was studied using qRT-PCR with specific assays. The miR-34a, miR-34b and miR-34c display unique onset of developmental expression and expression levels, with miR-34a being the most abundant and constant in expression. All of the miR-34 genes also showed clear induction by p53 when DNA-damaging treatments are performed. Using CRISPR-Cas9 technology, we generated a zebrafish miR-34a deletion mutant to further investigate the roles of miR-34a on its own and its association with the p53 pathway. Predictably, a miR-34a deletion mutant demonstrated absence of miR-34a, though without miR-34b and miR-34c compensation beyond baseline expression levels. Mutants survive to adulthood, show no overt phenotypes and have normal apoptotic responses to DNA-damaging irradiation or camptothecin treatments. To further explore the effects of miR-34a, we performed gene expression profiling using RNA-seq of wild-type and miR-34a deletion mutant zebrafish embryos at 28 hpf with or without treatment with a DNA-damaging drug camptothecin. The results of this RNA-seq experiments showed that the loss of miR-34a does not strongly affect induction of genes by DNA-damage. However, the overall pattern of gene expression is significantly different as shown by Principal Component Analysis and there is a group of about 100 genes which are differentially expressed due to loss of miR-34a. The dataset we present in this submission was used to reach these conclusions.

overall_design: Zebrafish embryos at 24 hpf of wild-type and miR-34a-/- genotypes were dechorionated and the control (DMSO) or 1 uM camptothecin treatment for 4 hours was performed followed by RNA extraction from all samples.

middle: V

first: Gabriel

last: Wajnberg

first: Nicolas

last: Crapoulet

first: Jason

middle: N

last: Berman


title: Gene expression analysis of in vitro activated B cells from C57BL/6 and Ackr4-deficient mice

city: Hannover

first: Nadine

last: Eckert

state: Lower Saxony

address: Carl-Neuberg-Straße 1

department: Immunology

country: Germany

institute: Hannover Medical School

summary: To further understand differential phenotypes between C57BL/6 and Ackr4-deficient B cells, we have employed whole genome microarray expression profiling as a discovery platform to identify genes which are differentially expressed in the two genotypes.   Murine B cells from spleens of C57BL/6 and Ackr4-deficient mice were purified by negative magnetic activated cell sorting (MACS) and activated in vitro with 10 µg/mL polyclonal anti-IgM and10 µg/mL anti-CD40 (clone FGK4.5) antibodies for three days in culture (96well plate, 37°C, 5%CO2). On day three, living B cells were sorted and RNA was extracted.

overall_design: Differential gene expression of murine in vitro activated B cells from spleens of C57BL/6 and Ackr4-deficient mice was measured at day 3 of activation.  Two independent experiments were performed with different donors for each experiment.

first: Reinhold

last: Förster


title: Auxin regulates endosperm cellularization in Arabidopsis

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

institute: SLU

summary: The endosperm is an ephemeral tissue that nourishes the developing embryo, similar to the placenta in mammals. In most angiosperms, endosperm development starts as a syncytium, in which nuclear divisions are not followed by cytokinesis. The timing of endosperm cellularization largely varies between species, and the event triggering this transition remains unknown. Here we show that increased auxin biosynthesis in the endosperm prevents its cellularization, leading to seed arrest. Auxin-overproducing seeds phenocopy paternal-excess triploid seeds derived from hybridizations of diploid maternal plants with tetraploid fathers. Concurrently, auxin-related genes are strongly overexpressed in triploid seeds, correlating with increased auxin activity. Reducing auxin biosynthesis and signaling reestablishes endosperm cellularization in triploid seeds and restores their viability, highlighting a causal role of increased auxin in preventing endosperm cellularization. We propose that auxin determines the time of endosperm cellularization, and thereby uncovered a central role of auxin in establishing hybridization barriers in plants.

overall_design: We extracted total RNA from 6 DAP WT and DD25::IaaH seeds, using the MagJET Plant RNA Purification Kit (Thermo Fisher Scientific). We then purified messenger RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module and used this RNA to prepare sequencing libraries with the NEBNext Ultra II Library Prep Kit for Illumina. Three biological replicates for each sample were submitted for sequencing at the National Genomic Infrastructure (NGI) from SciLife Laboratory (Uppsala, Sweden) on an Illumina HiSeq2500 in paired-end 125bp read length.

first: Rita

last: Batista

first: Duarte

last: Figueiredo

first: Santos-Gonzalez

last: Juan

first: Claudia

last: Köhler


title: Exome Sequencing of Ackr4-deficient mice in generation 12 (backcrossing to C57BL/6)

summary:
Purpose: The goal of this study was to compare exome sequences of Ackr4-deficient mice with C57BL/6 wildtype sequences to understand phenotypic differences which can not be explained by Ackr4-deficiency.
Methods: Tail DNA of one wild-type (WT, C57BL/6) and atypical chemokine receptor 4 knockout (Ackr4−/−) mice was sequenced by exome sequencing using an Illumina NovaSeq 6000 sequencing system (2x 100bp). After demultiplexing (Illumina bcl2fastq 2.19) and adapter trimming (Skewer, 0.2.2), the trimmed reads were aligned with to the murine genome (mm10) with Burrows-Wheeler Aligner (BWA-mem 0.7.2-cegat). Reads aligned to multiple sides with the same mapping score were discarded. Further, duplicated reads were removed with SAMtool 0.1.18. Genetic variants were identified with Verscan 2.4.2-cegat and variants with a frequency of ≥ 2% were annotated with SnpEff (version 4.2 with GRCm38.75).
Results: 100,000 to 140,000  million sequence reads per mouse were mapped to the mouse genome (build mm10). Each mouse had approx. 20,000 variants (insertions, deletions, SNPs) compared to the reference genome. In Ackr4-/- mice, 3,367 variants were present in both mice analysed, yet not detected in the C57BL/6 mouse used as control.  1781 of these 'shared' variants were present on the chromosome with the targeted Ackr4 allele (Chr9) and predominantly in close proximity to the Ackr4 locus, indicating that these variants originate from the 129-genetic background which was used for targeted mutagenesis during the generation of these mice.
Conclusions: Our study shows that Ackr4-/- mice in generation F12 after backcrossing to the C57BL/6 background are still congenic for 129-derived DNA around the targeted Ackr4 locus, indicating that passenger mutations can influence the phenotype of these mice.

overall_design: Genomic DNA from tail tissue of two Ackr4-deficient mice F12 and one C57BL/6 was compared by exome sequencing


title: ZNF599 and DNMT3A coordinately control nuclear envelope organization by repression of SUN4 expression

city: Martinsried

first: Martha

last: Smets

address: Großhaderner Str. 2

department: Department Biology II

institute: Ludwig-Maximilians University Munich

summary: Human-specific KRAB-ZF proteins are putative transcription factors and correlate with human cognitive and linguistic ability. The typical KRAB-ZF protein ZNF599 has been implicated in developmental delay. However, the underlying molecular mechanism is elusive. Here, we show a specific interaction of ZNF599 with DNMT3A, but not DNMT3B or DNMT1. Using CRISPR/Cas9, we generated a ZNF599-/- cell line that shows an irregular nuclear morphology with blebbings, dents and ridges. Interestingly, the irregular nuclear shape can be rescued by complement expression of wt ZNF599, but not with ZNF599 L178F, a mutant that has been described in patients with mental retardation. With transcriptome analysis by next-generation sequencing, we found several genes misregulated in ZNF599-/- cells, particularly an upregulation of SUN4, also known as SPAG4. Consistently, ectopic expression of GFP-SUN4 in wt cells shows a similar effect on nuclear morphology as observed in ZNF599-/- cells. Besides ZNF599, DNMT3A dependent DNA methylation is also required for repression of Sun4 expression as we observe an upregulation of Sun4 in murine Dnmt3a-/- cells. Thus, we conclude that ZNF599 and DNMT3A coordinately control SUN4 expression to regulate nuclear envelope organization providing a potential insight into the molecular mechanism of development delay pathology.

overall_design: HELA cells with wt genotype or ZNF599 -/- genotype were analysed in 4 independent replicates

first: Weihua

last: Qin


title: phytochrome A-mediated shade avoidance responses

city: Xiamen

first: Yi

last: Tao

address: South Xiangan Rd.

department: School of LIfe Sciences

country: China

institute: Xiamen University

summary: Arabidopsis is a shade avioding plant. Under simulated shade light with reduced red-to-far red (R:FR) ratio around 0.7, hypocotyls of Arabidopsis seedlings elongate, which is one of the typical shade avoidance responses.We discovered that when the R:FR ratio further decreases to around 0.1 (strong shade), the shade-induced elongation of hypocotyl is abolished and phytochrome A (phyA) mediates this response.In this study, we aim to examine the difference between shade and strong shade treatment and uncover the role of phyA in regulating the shade avoidance responses.

overall_design: In this study, there are a total of 16 samples. We used 5-day old arabidopsis seedlings, tested three light conditions: continuous light (wc), shade (s,R:FR=0.7) and strong shade (s_s, R:FR=0.1) and two genotypes Col-0 wild type (C) and phyA-211 (A, a null phyA mutant). For each conditions, three biological replicates were included, except for those of the continuous light treatment.

first: Kangmei

last: Dong


title: Compared the hepatic gene expression profile of two transgenic mouse lines

city: Milano

first: Cinzia

last: Parolini

address: via Balzaretti 9

institute: Università degli Studi di Milano

summary:
Homozygous gene targeting replacement mouse lines, one expressing the human apolipoproteinA-I (A-I k-in) and the other the natural variant apolipoproteinA-IMilano (A-IM k-in), have been used for the present study
We used microarray to investigate intrinsic differences in the hepatic gene expression of mice expressing human apoA-I or A-IM,

overall_design: The livers were harvested from the two mouse lines for RNA extraction and Hybridization on Affymetrix microarrays.

first: Elena

last: Rigamonti


title: Three-dimensional Oxabicycloheptene sulfonate targets the homologous recombination and repair programs through estrogen receptor α antagonism

status: Public on Dec 20 2019

city: Wuhan

first: Kaiwei

last: Liang

state: Hubei

address: # 185 Dong Hu Road

institute: Wuhan University

summary: Selective Estrogen Receptor Modulators (SERMs) are a class of structurally diverse compounds possessing unique partially agonistic and antagonistic properties and have been extensively used in treatments of hormone-responsive cancers and other diseases. Our previous studies have identified a three-dimensional SERM oxabicycloheptene sulfonate (OBHS) for estrogen receptor α (ERα), which is effective in vivo for the prevention and treatment of estrogen-dependent endometriosis. Here, using ChIP-seq and RNA-seq analysis, we found that OBHS rapidly induces genome-wide ERα occupancy behaves as a partial agonist and antagonist in ERα positive MCF-7 cells. Interestingly, OBHS downregulates the homologous recombination and repair (HRR) modules resulting in the increased DNA damage, apoptosis and cell cycle arrest, and leading to synthetic lethality with Poly (ADP-ribose) polymerase (PARP) inhibitor olaparib and genotoxic doxorubicin through blocking of ERα. Furthermore, we found that OBHS treatment results in defects of RNA polymerase II loading at the estrogen-responsive HRR genes, providing a mechanism for the regulation of HRR genes by OBHS. Together, our studies not only reveal a novel SERM OBHS which uniquely targets the homologous recombination and repair programs through ERα antagonism, but also propose a synthetic lethal strategy by combining OBHS with PARP inhibitor olaparib or genotoxic doxorubicin for ERα-responsive cancers.

overall_design: Determination of the gene exression profiles by  estrogen or OBHS for 12 hours, examination of the  genome-wide ERα and Pol II occupancy after treatment of estrogen or OBHS for 1 hour.

first: Jian

last: Huang


title: Discrimination of dormant and active hematopoietic stem cells by G0 markers reveals dormancy regulation by cytoplasmic calcium

city: minato-ku

first: Tsuyoshi

last: Fukushima

state: tokyo

address: siroganedai 4-6-1

department: Cell therapy

institute: Institute of Medical Science

summary: High-throughput small molecule screening revealed that high  concentrations of cytoplasmic calcium ([Ca2+]c) were linked to dormancy of  HSCs.To clarify molecular difference between [Ca2+]chigh and [Ca2+]clow  cells, we performed RNA-Seq analysis using [Ca2+]chigh and [Ca2+]clow cells.

overall_design: Transcriptomes of [Ca2+]high HSCs and  [Ca2+]low HSCs were generated by deep sequencing, in 7 replicates, using Next-Seq system.

first: Yosuke

last: Tanaka

first: Terumasa

last: Umemoto

first: Hitoshi

last: Takizawa


title: Conditional expression of HGAL leads to the development of diffuse large B-cell lymphoma in mice

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary:
We used microarrays to investigate gene expression changes in splenic cells from HGAL transgenic mice (Rosa26HGAL/Sca1-Cre; Rosa26HGAL/Mb1-Cre and Rosa26HGAL/Aid-Cre).
Diffuse large B cell lymphomas (DLBCLs) are clinically and genetically heterogeneous tumors. Deregulation of diverse biological processes specific to B cells, such as B cell receptor (BCR) signaling and motility regulation contribute to lymphomagenesis. HGAL is a B cell specific adaptor protein controlling BCR signaling and B lymphocyte motility. In normal B cells it is expressed in Germinal Center (GC) B lymphocytes and promptly downregulated upon further differentiation. Majority of DLBCL tumors, mainly GC B cell but also activated types, express HGAL. To investigate the consequences of constitutive expression of HGAL in vivo, we generated mice that conditionally express the human HGAL at different stages of hematopoietic development using three different restricted Cre-mediated approaches to initiate expression of HGAL in hematopoietic stem cells (HSC), pro-B cells or GC B cells, respectively. Following immune stimulation, we observed larger GCs in mice where HGAL expression was initiated in GC B cells. All three mouse strains developed DLBCL at a frequency of 12-30% starting at age 13 months, leading to shorter survival. Immunohistochemical studies showed that all analyzed tumors were of the GC B cell type. Exon sequencing demonstrated mutations reported in human DLBCL. Our data demonstrate that constitutive enforced expression of HGAL leads to DLBCL development.

overall_design: Splenic cells from Rosa26HGAL/Sca1-Cre; Rosa26HGAL/Mb1-Cre and Rosa26HGAL/Aid-Cre mice compared with splenic cells from 3 WT-control mice.

first: Javier

last: Raboso-Gallego

first: Ana

last: Casado-García

first: Xiaoyu

last: Jiang

first: Marta

last: Isidro-Hernández

first: Andrew

middle: J

last: Gentels

first: Shuchun

last: Zhao

first: Yaso

last: Natkunam

first: Oscar

last: Blanco

first: Verónica

last: Domínguez

first: Belén

last: Pintado

first: Diego

last: Alonso-López

last: De Las Rivas

first: Carolina

last: Vicente-Dueñas

first: Izidore

middle: S

last: Lossos

last: Sanchez-Garcia


title: Transcriptome analysis of activated fibroblasts isolated from fibrotic livers

city: Tokyo

first: Michiko

last: Itoh

address: 1-5-45 Yushima, Bunkyo-ku

institute: Tokyo Medical and Dental University

summary: RNA-seq analysis of steady-state hepatic stllate cells and activated fibroblasts isolated from distinct liver fibrosis models; Western diet–induced NASH and carbon tetrachrolide–induced liver fibrosis. RNA was subjected to RNA-seq to identify differentially expressed gene profiles.

overall_design: RNA-seq was done to analyze transcriptome of activated fibroblasts from NASH livers, and understand how activated fibroblasts contribute to the progression from NASH to HCC.

first: K

last: Fujiu

first: I

last: Manabe

first: M

first: T

last: Suganami

first: Y

last: Ogawa


title: In Vivo, Computationally-inspired Approach Identifies Amygdalar Transcriptional Heterogeneity and Distinct Social Behavior in ‘Anxious’ Mice

city: Boston

first: Meeta

last: Mistry

address: 655 Huntington Ave

country: USA

institute: Harvard School of Public Health

summary: Ribonucleic acid sequencing was carried out on amygdalar tissue of C57/BL6 mice exposed to three behavior tests. Bioinformatics unbiasedly linked gene expression patterns to behavior styles. Gene ontology pathway analyses identified known features of anxiety, as well as non-obvious findings

overall_design: We integrated mouse behavior testing with transcriptional features of the amygdala (known as the “alarm center of the brain”) in order to stratify mice into "anxiety" groups  by mathematical inference.

first: Aaron

last: Goldman

first: Ilana

last: Braun