title: Deciphering the gene expression network regulated by ETV7

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

institute: University of Padova

summary: Cancer stem cells (CSCs) represent a population of cells within the tumor able to drive tumorigenesis and known to be highly resistant to conventional chemotherapy and radiotherapy. In this work, we show a new role for ETV7, a transcriptional repressor member of the ETS family, in promoting breast cancer stem-like cells plasticity and resistance to chemo- and radiotherapy in breast cancer (BC) cells. We observed that MCF7 and T47D BC-derived cells stably over-expressing ETV7 showed reduced sensitivity to the chemotherapeutic drug 5-Flouororuacil and to radiotherapy, accompanied by an adaptive proliferative behavior observed in different culture conditions. We further noticed that alteration of ETV7 expression could significantly affect the population of breast CSCs, measured by CD44+/CD24low cell population and mammosphere formation efficiency. By transcriptome profiling, we identified a signature of Interferon-responsive genes significantly repressed in cells over-expressing ETV7, which could be responsible for the increase in the breast CSCs population, as this could be partially reverted by the treatment with IFN-b. Lastly, we show that the expression of the IFN-responsive genes repressed by ETV7 could have prognostic value in breast cancer, as low expression of these genes was associated with a worse prognosis. Therefore, we propose a novel role for ETV7 in breast cancer stem cells’ plasticity and associated resistance to conventional chemotherapy and radiotherapy, which involves the repression of a group of IFN-responsive genes, potentially reversible upon IFN-b treatment. We, therefore, suggest that an in-depth investigation of this mechanism could lead to novel breast CSCs targeted therapies and to the improvement of combinatorial regimens, possibly involving the therapeutic use of IFN-b, with the aim of avoiding resistance development and relapse in breast cancer.

overall_design: We analyzed gene expression from 2 breast cancer-derived cell lines (MCF7 and T47D) stably transfected with ETV7 or an empty vector (pAIP backbone) as a control. Three biological replicates for each condition (4 Samples) have been prepared and processed.

first: Yari

last: Ciribilli

first: Laura

last: Pezzè

first: Silvio

last: Bicciato


title: mRNA expression profiling of untreated J82 and MDXC1 cultured cell lines using the Nanostring PanCancer Progression 770 gene panel

status: Public on Jul 28 2021

city: Bethesda

first: Donald

middle: P

last: Bottaro

state: MD

address: Bldg 10 CRC Rm 2-3952, 10 Center Drive

department: Center for Cancer Research

country: USA

institute: National Cancer Institute

type: Expression profiling by high throughput sequencing

summary:
J82 is a urothelial carcinoma (bladder cancer) derived cultured cell line (see COSMIC https://cancer.sanger.ac.uk/cosmic/sample/overview?id=753566). The cultured cell line MDXC1 was derived from J82 xenograft tumors grown in SCID/BEIGE mice for 50 days using conventional methods of tumor excision, cell dissociation and growth in culture for 15 passages. MDXC1 was confirmed to be solely of human origin and pathogen-free.
J82 and MDXC1 cells were compared for phenotypic changes in cancer-related genes associated with xenograft tumor growth. Experiments were included in the following larger study:  Title: Autocrine signaling by receptor tyrosine kinases in urothelial carcinoma of the bladder.    Authors: Young H. Lee, Molly M. Lee, Dinuka M. De Silva, Arpita Roy, Cara Wright, Tiffany Wong,   Rene Costello, Oluwole Olaku, Robert L. Grubb III#, Piyush K. Agarwal, Andrea B. Apolo*+   Donald P. Bottaro*    Affiliations: Urologic Oncology Branch and +Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 USA and #Department of Urology, Medical University of South Carolina, Charleston, South Carolina 29425 USA    Abstract: Comprehensive characterizations of bladder cancer (BCa) have established molecular phenotype classes with distinct alterations and survival trends. Extending these studies within the tyrosine kinase (TK) family to identify disease drivers could improve our use of TK inhibitors to treat specific patient groups or individuals. We examined the expression distribution of TKs as a class (n = 89) in The Cancer Genome Atlas (TCGA) muscle invasive BCa data set (n >400). Patient profiles of potentially oncogenic alterations (overexpression and/or amplification) clustered TKs into 3 groups; alterations of group 1 and 3 TKs were associated with significantly worse patient survival relative to those without alterations. Many TK pathways induce epithelial-to-mesenchymal transition (EMT), which promotes tumor invasiveness and metastasis. Overexpression and/or amplification among 9 EMT transcriptional activators occurred in 43% of TCGA cases. Co-occurring alterations of TKs and EMT transcriptional activators involved most group 1 TKs; 24% of these events were associated with significantly worse patient survival. Co-occurring alterations of receptor TKs and their cognate ligands occurred in 16% of TCGA cases and several BCa-derived cell lines. Suppression of GAS6, MST1 or CSF1, or their respective receptors (AXL, MST1R and CSF1R), in BCa cell lines was associated with decreased receptor activation, cell migration, cell proliferation and anchorage independent cell growth. These studies reveal the patterns and prevalence of potentially oncogenic TK pathway-related alterations in BCa and identify specific alterations associated with reduced BCa patient survival. Detection of these features in BCa patients could better inform TK inhibitor use and improve clinical outcomes.

overall_design: Cell lines were grown under identical plating and culture conditions prior to harvest and RNA extraction and hybridization.

first: Rene

last: Costello

first: Dinuka

last: De Silva

first: Arpita

last: Roy

first: Molly

last: Lee


title: Non-coding RNAs in the interaction between rice and Meloidogyne graminicola

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study we generated small RNA libraries from tissues rice plants infected with Meloidogyne graminicola (Mg)3 days postinoculation as well as from uninfected rice plants. The goal was to study the behaviour of small RNA (miRNA and siRNAs) in response to Mg infection. We combine the expression data gathered from this experiment together with degradome sequencing to predict the targets of differentially expressed miRNAs. Expression was validated using RT-qPCR. The small RNA sequencing datasets were also used with literature annotated siRNA loci for differential expression analysis. DNA methylation data and total RNA sequencing data were used to find siRNAs that were candidates to regulate gene expression through DNA methylation of promoter regions.

overall_design: Small RNA sequencing was done on RNA extracted from rice roots under two experimental conditions: infection with Meloidogyne graminicola and mock infection (three replicates per condition).

first: Mohammad

last: Reza Atighi

first: Tim

last: De Meyer

first: Tina

last: Kyndt


title: Specific targeting of KRAS using a novel antisense oligonucleotide exerts anti-tumor activity in multiple myeloma

city: Milan

first: Antonino

last: Neri

state: Milan

address: Via Francesco Sforza, 35

country: Italy

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

summary:
The multiple myeloma (MM) mutational landscape has identified alterations in KRAS as the most recurring somatic variant. Combining DNA and RNA sequencing, 756 patients were studied, and KRAS was observed as the most frequently mutated gene in patients at diagnosis; in addition, we demonstrated the persistence or de novo occurrence or the KRAS aberration at disease relapse. After several decades of effort, small molecule inhibitors targeting KRAS have emerged and are showing promising activity in clinical trials. However, these inhibitors are selective for tumors carrying that KRASG12C mutation and will only treat a subset of patients, predominantly with lung or colon tumors where this mutation is most prevalent. Therefore, there is still a need to develop novel therapeutic approachesto target the KRAS mutational events found in other tumor types, including MM.
AZD4785, is a potent and selectivetherapeutic antisense oligonucleotide (ASO), tested in phase I clinical trials, which selectively targets and down-regulates all KRAS isoforms. Therefore, we explored the activity of AZD4785 in MM models, demonstrating its ability to strongly down-regulate KRAS andto inhibit the growth of MM cells, both in vitro and in vivo, confirming KRAS as a driver and a therapeutic target in MM.

overall_design: Human MM Cell Lines (HMCLs), MM.1S, KMS20 (KRAS mutated), OPM2 (KRAS WT) and U266 (BRAF mutated), were analyzed after 3 µM AZD4785 exposure for 48 hours in comparison to untreated HMCL samples. Each cell line was considered in triplicates for each condition.

first: Antonio

last: Sacco

first: Cinzia

last: Federico

first: Katia

last: Todoerti

first: Bachisio

last: Ziccheddu

first: Palermo

last: Valentina

first: Arianna

last: Giacomini

first: Cosetta

last: Ravelli

first: Federica

last: Maccarinelli

first: Giada

last: Bianchi

first: Angelo

last: Belotti

first: Rossella

last: Ribolla

first: Vanessa

last: Favasuli

first: Alexey

middle: S

last: Revenko

first: Robert

last: Macleod

first: Brandon

last: Willis

first: Hongbo

last: Cai

first: Joana

last: Hauser

first: Claire

last: Rooney

first: Sophie

first: Philip

last: Lloyd Martin

first: Anna

last: Staniszewska

first: Helen

last: Ambrose

first: Lyndsey

last: Hanson

first: Chiara

last: Cattaneo

first: Alessandra

last: Tucci

first: Giuseppe

last: Rossi

first: Roberto

last: Ronca

first: Stefania

last: Mitola

first: Niccolò

last: Bolli

first: Marco

last: Presta

first: Michele

last: Moschetta

first: Sarah

last: Ross

first: Aldo

middle: M

last: Roccaro


city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: We wanted to correlate the protein cargo of secreted exosomes with gene expression pattern in B16-F1 and B16-F1R2. For that purpose, we performed RNA sequencing analysis of B16-F1, B16-F1R2 and B16-F1R2L (Fig.1E). We identified >3000 genes significantly up-regulated and >1000 significantly down-regulated in B16-F1R2 model compared to B16-F1, using a false discovery rate (FDR) of 0.05.

overall_design: Gene expression pattern in B16-F1 and B16-F1R2 cell lines

first: Ana

last: Amor

last: Graña-Castro

first: Hector

last: Peinado


title: HPV genome expression at invasive cervical carcinomas infected by multiple HPV genotypes

city: Rio de Janeiro

first: Ayslan

middle: Castro

last: Brant

state: Rio de Janeiro

address: Andre Cavalvanti 37

department: Genetics

country: Brazil

institute: National Institute of Cancer

summary: Multiple HPV genotypes infection is frequently detected in HPV+ cervical lesions, however it is not well stablished how is the different viral interaction during the carcinogenic process. Here we carried out a comprehensive study to characterize the multiple HPV genome expression and integration by RNA-Seq analysis in 19 invasive cervical carcinomas with HPV coinfections. Analysis of tumoral DNA by a hybridization kit indicated multi-infection ranging from 2 to 6 different HPV genotypes, without a preferential species coinfection. The expression analysis showed that a single HPV genotype preferentially expressed its genome, might indicating a competition between the infecting virus. Finally, the search for HPV/human chimeric transcripts indicated integration from just one HPV in almost all samples, corroborating the expression findings.

overall_design:
RNA-Seq analysis of 19 uterine cervix tumor with multiple HPV genotype infection.

Please note that chimeric transcripts were not identified in HPVco_2, HPVco_6, HPVco_10, HPVco_13, and  HPVco_15-17 samples and thus no fasta data file is provided.

middle: C

first: Miguel

last: Moreira


title: Transcriptomics analysis of proliferation and differentiation of buffalo muscle stem cells

city: Nanning

first: Ruimen

last: Zhang

address: NO.100 University Road,Xi xiang tang

country: China

institute: Guangxi University

summary: Buffalo breeding has become an important branch of beef cattle industry. It is of great significance to study buffalo meat production and meat quality. However, the important role of mRNA and lncRNA molecules in muscle stem cells (MuSCs) development in buffalo has not been explored. Then, we performed mRNA and lncRNA expression profiling analysis on the proliferation and differentiation of MuSCs in buffalo. The results showed that there were 4,820 differentially genes, 12,227 mRNAs, and 1,352 lncRNAs. These differentially expressed mRNAs are enriched in biological processes such as cell cycle, p53 signaling pathway, RNA transport, and Calcium signaling pathway and others. We also identified a number of genes, such as MCMC4, SERDINE1, ISLR, LOC102394806, and LOC102403551, and found that interference with MYLPF expression significantly inhibited the differentiation of MuSCs. In conclusion, our research revealed the role of mRNA and lncRNA expression in the differentiation of buffalo MuSCs. This study can be used as an important reference for the study of RNA regulation during muscle development in buffalo.

overall_design: Profiles of mRNAs and non-coding RNAs during the proliferation（GM) and differentiation(DM) of buffalo muscle stem cells

first: Sufang

last: Yang

first: Yanfei

last: Dend

first: Yingming

last: Wei


title: m6A RNA methylation regulates promoter proximal pausing of RNA Pol II

city: Mainz

first: Junaid

last: Akhtar

state: Rheinland-Pflaz

address: Johannes-Joachim-Becherweg, 32

department: Institute of Neurobiology and Developmental Biology

country: Germany

institute: University of Mainz

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Three-axis classification of mouse lung mesenchymal cells reveals two populations of myofibroblasts

status: Public on Jul 27 2021

city: Houston

first: Odemaris

middle: Narvaez

last: del Pilar

state: Texas

address: 6565 MD Anderson Blvd

department: Pulmonary

institute: MD Anderson Cancer Center

summary: The mesenchyme consists of heterogeneous cell populations that support neighboring structures and are integral to intercellular signaling. Despite such importance, mesenchymal cell types are poorly defined morphologically and molecularly, lagging behind their counterparts in the epithelial, endothelial, and immune lineages. Leveraging single-cell RNA-seq, three-dimensional imaging, and lineage tracing, we classify the mouse lung mesenchyme into three proximal-distal axes that are associated with the endothelium, epithelium, and interstitium, respectively. From proximal to distal, (1) the vascular axis includes vascular smooth muscle cells and pericytes that transition as arterioles and venules ramify into capillaries; (2) the epithelial axis includes airway smooth muscle cells and two populations of myofibroblasts: ductal myofibroblasts, surrounding alveolar ducts and marked by CDH4, HHIP, and LGR6, which persist post-alveologenesis, and alveolar myofibroblasts, surrounding alveoli and marked by high expression of PDGFRA, which undergo developmental apoptosis; (3) the interstitial axis, residing between the epithelial and vascular trees and sharing a newly-identified marker MEOX2, includes fibroblasts in the bronchovascular bundle and the alveolar interstitium that are marked by IL33 and Wnt2, respectively. Single-cell imaging reveals distinct morphology of each mesenchymal cell population. This classification provides a conceptual and experimental framework applicable to other organs.

overall_design: FACS-purified lung cells were processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics)

last: Narvaez del Pilar

first: Jichao

last: Chen


title: Single-Cell RNA Sequencing of Mouse Left Ventricle Reveals Cellular Diversity and Intercommunication

city: Shanghai

first: Lan

last: Wu

address: No.279 Zhouzhu Road

institute: 1Shanghai University of Medicine & Health Sciences

summary: Previous studies have revealed the diversity of the whole cardiac cellulome but not refined the left ventricle, which is essential for finding therapeutic targets. Here, we characterized single-cell transcriptional profiles of the mouse left ventricular cellular landscape using single-cell RNA sequencing (10×Genomics). Detailed t-Distributed Stochastic Neighbor Embedding (tSNE) analysis revealed the cell types of left ventricle with gene markers. Left ventricular cellulome contained cardiomyocytes highly expressed Trdn, endothelial cells highly expressed Pcdh17, fibroblast highly expressed Lama2 and macrophages highly expressed Hpgds, also proved by in situ hybridization. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analysis (ListHits>2, p<0.05) were employed with the DAVID database to investigate subtypes of each cell type with the underlying functions of differentially expressed genes (DEGs). Endothelial cells included five subtypes, fibroblasts comprised of seven subtypes and macrophages contained eleven subtypes. The key representative DEGs (p<0.001) are Gja4 and Gja5 in cluster 3 of endothelial cells, Aqp2 and Thbs4 in cluster 2 of fibroblasts, as well as Clec4e and Trem-1 in in cluster 3 of marcophages perhaps involved in the occur of atherosclerosis, heart failure and acute myocardial infarction proved by literature review. We also revealed extensive networks of intercellular communication in left ventricle. We suggested possible therapeutic targets for cardiovascular disease and autocrine and paracrine signaling underpins left ventricular homeostasis. This study provides new insights into the structure and function of the mammalian left ventricular cellulome and offers an important resource that will stimulate studies in cardiovascular research.

first: Yan-fei

last: Li

first: Jun-wei

last: Shen

first: Xin-ming


title: Identification and characterization analysis of the different  genes in primary neurons response to circSCMH1 using RNA-seq.

city: Nanjing

first: Li

state: Jiangsu

address: Dingjiaqiao 87

department: Pharmacology

institute: Southeast University

summary: Whole RNA-sequencing analysis was performed by LC-Bio. Day-10 neurons from the Vector or circSCMH1 overexpression groups were collected in Trizol. Total RNAs were extracted from Trizol. UMI technology was used to label each sequence fragment with sequence tags, which minimizes the interference of duplication generated by PCR amplification on the quantitative accuracy of transcriptome. RNA-seq reads were aligned to the mouse genome (GRCh37/hg19) using the software Hisat2 (2.0.4). Transcript abundance was quantified as fragments per kilo base of exon per million fragments mapped (FPKM). Differentially expressed genes were determined by DESeq2 (DOI: 10.1186/s13059-014-0550-8).

overall_design: Examination of different genens in circSCMH1-treated primary neurons by RNA-seq.

first: Honghong

last: Yao


title: m6A RNA methylation regulates promoter proximal pausing of RNA Pol II (DRB-4sU-seq)

summary: RNA modification has emerged as an important layer in the control of gene expression. The N6-methyladenosine (m6A) RNA modification is the most prevalent and influences several processes including pre-mRNA splicing, alternative polyadenylation, mRNA decay and translation. Here, we show that m6A regulates transcription by controlling promoter proximal pause release of RNA Pol II. Our results show that the m6A methyltransferase complex together with the nuclear reader Ythdc1 are recruited to gene promoters. Loss of m6A methyltransferase complex leads to increased levels of promoter proximal pausing of RNA Pol II, decrease in Ser2P occupancy on gene body, and affects nascent RNA transcription. Furthermore, we show that the binding of the complex is Spt6-dependent and can be predicted by collective features, with Pol II and pause factors (GAF and M1BP) binding being the most important. We also demonstrate that tethering Mettl3 to a heterologous gene promoter was sufficient to increase the release of RNAP II from the promoter, and this effect was dependent on its m6A catalytic domain. Collectively our data indicate that m6A RNA feeds back to the transcription machinery via its recruitment to the chromatin, and thus uncovering an important link between epigenetic modification of RNA and transcription.

overall_design: DRB-4sU seq in control, Mettl3 (ime4) and Ythdc1 (YT521) depleted S2R+ cells


title: Factor Xa and factor IIa inhibitors differentially regulate inflammation in myocardial ischemia reperfusion injury

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research


title: RNA-seq analysis of mouse hippocampal gene expression changes after Gulf War toxicant exposure

city: East Orange

first: Bruce

middle: A.

last: Citron

state: NJ

address: 385 Tremont Ave.

department: Pharmacology, Physiology, & Neuroscience, Rutgers- NJMS

institute: VA New Jersey Health Care System

summary: Differentially expressed genes may provide insight into the underlying mechanisms of Gulf War Illness involved in neurodegeneration.

overall_design: Six different control and six different Gulf War model mice were examined. C57Bl/6 male mice at 12 weeks of age received two weeks (M-F) of daily subcutaneous injections of a mixture resulting in 2.5 mg/kg pyridostigmine bromide, 12.5 mg/kg chlorpyrifos, and 7.5 mg/kg DEET. Hippocampi were collected at the end of the exposure, RNA was extracted and examined by RNA-Seq.

middle: A

first: Kathleen

middle: E

last: Murray


title: m6A RNA methylation regulates promoter proximal pausing of RNA Pol II (ChIP-Seq)

summary: The transcriptional regulation is often controlled by the epigenetic modifications or by chromatin associated proteins. To understand this regulation, chromatin immunoprecipitation (ChIP) followed by next generation sequencing is an invaluable and powerful technique. However, the major limitation of this approach is often the requirement of large amount of starting material for generating high-quality datasets, and often the workflow is laborious. This limitation also results in application of this approach to study of rare cell populations even more challenging, if not impossible. Here, we present a tagmentation-assisted fragmentation ChIP (TAF-ChIP) and sequencing method to generate high quality dataset from as few as 100 human and 1000 Drosophila cells. The method itself is straightforward and is by far less labor-intensive than conventional library preparation, and other contemporary low amount ChIP-Seq methods. Furthermore, this approach can be applied directly on 100 cells rather than relying on de-multiplexing strategies to generate the profile from limited number of cells. This can be extremely useful when the access to the starting material is very restricted, for example clinically isolated cells from patients. Using this approach we generated the H3K4Me3 and H3K9Me3 profiles from 100 K562 cells and 1000 sorted neural stem cells (NSC) from Drosophila. We benchmarked our TAF-ChIP datasets from K562 cells against the Encode datasets. For validating the TAF-ChIP datasets obtained from Drosophila NSCs we took advantage of Notch induced over proliferation specifically in type II NSCs. The epigenetic profile obtained from conventional ChIP-Seq approach and TAF-ChIP approach shows high degree of agreement, thereby underlining the utility of this approach for generating ChIP-Seq profiles from very low cell numbers.

overall_design: HA ChIP-seq  with S2R+ cell extracts transfected with HA tagged Mettl3, Mettl14, fl2d, Ythdc1 and Control. Pol II ChIP-seq in  cells depleted for either Mettl3, Mettl14, fl2d, Ythdc1 and Control. Ser2P ChIP-seq with S2R+ cell extract where Mettl3, Mettl14, fl2d were depleted along with control knockdwon condition.


title: RNA-Seq analysis of WT and Ron1 disruption strain in Beauveria bassiana

city: jinan

first: Jizheng

last: song

address: guyunhu

department: school of bioengineering

institute: qilu university of technology

summary: Ron1 is a protein with the function of regulating chitin metabolism in Beauveria bassiana.

overall_design: Transcriptome comparison of wild type (WT) and  Ron1 disruption type in Beauveria bassiana

first: Lei

last: Qiu

first: Ji-Zheng

last: Song

first: Tong-Sheng

first: Shun-Juan

last: Hu

first: Jia-Hua

last: Liu

first: Juan-Juan

last: Wang


title: B cells acquire a unique and differential transcriptomic profile during pregnancy in mice

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: Pregnancy significantly alters B cells development and function. B cell activation is initiated by antigens specific binding to the BCR, leading to an intricate signaling pathway responsible for B cell survival, proliferation, antigen processing/presentation and antibody production.  We performed a genome-wide transcriptome profiling in splenic B cells from pregnant (P) and non-pregnant (NP) mice. We identified 1136 genes with differential expression in B cells from P mice (625 up- and 511 down-regulated) compared to NP animals. In silico analysis showed that B cell activation through BCR-signaling pathway as well as antigen processing/presentation and TLR cascades seems to be lowered during pregnancy. Further RT-qPCR analysis confirmed these data. In addition, B cells from pregnant women stimulated in vitro through BCR in combination with CpG, produced significantly lower levels of cytokines compared to non-pregnant women. Our results suggest that B cells acquire a state of hypo-responsiveness during gestation, probably as part of the maternal immune strategy for fetal tolerance. However, our results also open new avenues to understand why pregnant women are at highest risk for some infections.

overall_design: We performed a genome-wide transcriptome profiling in splenic B cells from 4 pregnant (P) and 4 non-pregnant (NP) mice.

first: Federico

last: Jensen

first: Marek

last: Zygmunt


title: AKT signaling contributes to neural crest cells migration in patients affected with Bosma Arhinia and Microphtalmia syndrome.

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

country: France

institute: Aix-Marseille Université - Marseille Medical Genetics

summary: To gain further insights into the specificity of SMCHD1 mutations and identify pathways associated with the disease phenotypes, we have derived induced pluripotent stem cells from patients affected with BAMS or FSHD. We then differentiated these cells into neural crest stem cells, corresponding to the cell type that is mainly affected in BAMS and analyzed their transcriptome by RNA Seq.

overall_design: Patients affected with Bosma Arhinia and Microphtalmia syndrome

first: Frédérique

first: Camille

last: Laberthonnière

first: Raphael

last: Chevalier


title: Subcellular and regional localization of mRNA translation in midbrain dopamine neurons

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: Local translation within excitatory and inhibitory neurons is known to be involved in neuronal development and synaptic plasticity. Despite the extensive dendritic and axonal arborizations of monoaminergic neurons, the subcellular localization of protein synthesis has not been well-characterized in these populations. Here, we investigated mRNA localization in midbrain dopaminergic (mDA) neurons, cells with enormous axonal and dendritic projections, both of which can release dopamine (DA). Using highly-sensitive sequencing and imaging approaches in mDA axons, we found no evidence for axonal mRNA localization or translation. In contrast, we found that mDA neuronal dendritic projections into the substantia nigra reticulata (SNr) contain ribosomes and mRNAs encoding the DA synthesis, release, and reuptake machinery. Surprisingly, we found dendritic localization of mRNAs encoding synaptic vesicular release proteins in mDA neurons. Our results are consistent with a role for local translation in the regulation of DA transmission from dendrites, but not striatal axons. Finally, we defined a molecular signature of sparse mDA neurons in the SNr, including enrichment of an ER calcium pump previously undescribed in mDA neurons.

overall_design: RNA-sequencing of brain tissue, RiboTagged dopamine neurons, and synaptosomes using PLATE-seq 3'-tag sequencing or Clontech SMARTer full-length RNA library preparation

first: Benjamin

middle: D

last: Hobson

first: Etienne

last: Herzog

first: David

last: Sulzer


title: Two groups of control and RANBP1-knockdown HCT116 cells

city: 南京

first: Dandan

last: Zheng

state: 江苏

address: 南京医科大学江宁校区

institute: 南京医科大学

summary: Colorectal cancer (CRC) is among the top five most common malignant tumors worldwide and has a high mortality rate. Identification of the mechanism of CRC and potential therapeutic targets is critical for improving survival. In the present study, we observed high expression of RAN binding protein 1 (RANBP1) in CRC tissues. Upregulated RANBP1 expression was strongly associated with TNM stages and was an independent risk factor for poor prognosis. In vitro and in vivo functional experiments demonstrated that RANBP1 promoted the proliferation and invasion of CRC cells, affected the cell cycle, and inhibited the apoptosis of CRC cells. Low RANBP1 expression reduced the expression levels of hsa-miR-18a, hsa-miR-183, and hsa-miR-106 microRNAs (miRNAs) by inhibiting the nucleoplasmic transport of precursor miRNAs (pre-miRNAs), thereby promoting the accumulation of the latter in the nucleus and reducing the expression of mature miRNAs. Further experiments and bioinformatic analyses demonstrated that RANBP1 promoted the expression of YAP by regulating miRNAs and the Hippo pathway. We also found that YAP acted as a transcriptional cofactor to activate RANBP1 transcription in combination with TEAD4 transcription factor. Thus, RANBP1 further promoted the progression of CRC by forming a positive feedback loop with YAP. Our results revealed the biological role and mechanism of RANBP1 in CRC for the first time, suggesting that RANBP1 can be used as a diagnostic molecule and a potential therapeutic target in CRC.

overall_design: Total RNA, including small RNAs from two groups of control and RANBP1-knockdown HCT116 cells, were extracted using the Total RNA Purification Kit from Norgen Biotek Corp (Thorold, Canada). Approximately 1 μg total RNA was used to prepare a small RNA library according to the protocol of the TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA). Then, single-end sequencing (36 bp or 50 bp) was performed on the Illumina HiSeq 2500 System (LC Sciences, Houston, TX) according to the manufacturer’s recommended protocol. Raw reads were processed with ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity reads, common RNA families (rRNA, tRNA, snRNA, and snoRNA) and repeats. Subsequently, unique sequences containing 18–26 bases were mapped to specific species precursors in miRBase 22.0 using a BLAST search to identify known miRNAs and novel miRNA-3p- and miRNA-5p-derived miRNAs. The mapped sequences were identified as known miRNAs. The remaining sequences were mapped to other selected species precursors in miRBase 22.0 by BLAST search.  Differential expression of miRNAs as a function of normalized deep sequence counting was analyzed through the selective use of Student’s t-test. The significance threshold was set at <0.05.

first: Meng

last: Cao

first: Siyu

last: Zuo

first: Xiaoqin

last: Yuan


title: Treatment of TRAMP-C2-Ras tumors with IL-27 and IL-18 therapies

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

institute: Purdue University

summary: Interleukin-27 (IL-27) can partially reduce tumor growth in several animal models, including pros-tate cancer. We describe our findings on the effects of IL-27 gene delivery on prostate cancer cells and how sequential therapy with IL-18 enhances the efficacy of IL-27. We applied IL-27 and IL-18 deliv-ery with the goal of reducing prostate tumor growth, first in cell culture and then in an immunocom-petent mouse model. The combination of IL-27 followed by IL-18 (2718) successfully reduced can-cer cell viability, with significant effects found for a particular combination sequence. Interestingly, when we compared the 2718 combination with a single cytokine targeted to IL-6R via an oligo-peptide (27pepL) recently developed by our group, we observed similar efficacy. This efficacy was further enhanced when 27pepL was sequenced with IL-18 (27pepL18)

overall_design: We examined total RNA sequencing from tumors on day 26

first: Marxa

last: Figueiredo

first: Todd

last: Emrick


title: Epigenome analysis of low-grade neuroepithelial tumors with FGFR2 fusions

city: Stanford

last: Solomon

state: CA

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of 8 low-grade neuroepithelial tumors (LGNET) with FGFR2 fusions with various histologic diagnoses including ganglioglioma, multinodular and vacuolating neuronal tumor (MVNT), low-grade glioneuronal tumor NOS, and polymorphous low-grade neuroepithelial tumor of the young (PLNTY). The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of 8 low-grade neuroepithelial tumors with FGFR2 fusions.

overall_design: Bisulfite converted genomic DNA extracted from the 8 tumor samples was hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchip


title: Transcript expression analysis of Drosophila melanogaster reveals sex-specific alternative splicing of qtc gene

city: Orenburg

first: Alexander

last: Balkin

address: 11 Pionerskaya st.

country: Russia

institute: Institute for Cellular and Intracellular Symbiosis

summary: Here, we report transcriptome analysis in different tissues of Drosophila melanogaster, enriched with qtc transcripts.

overall_design: Here we examined transcript expression in different tissues of male and female Drosophila melanogaster flies using Nanopore long-read RNA-seq.


title: Effector differentiation downstream of lineage commitment in ILC1 is driven by Hobit across tissues.

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Innate lymphoid cells (ILCs) mediate early immunity against infection and participate in tissue inflammation and homeostasis. It is unclear how ILCs acquire effector function, and whether these mechanisms differ between organs. Through multiplexed single-cell mRNA-sequencing we identified cKit+CD127hiTCF-1hi early differentiation stages of T-bet+ ILC1. These cells were present across different organs and had the potential to mature towards CD127intTCF-1int and CD127-TCF-1- ILC1. Paralleling a gradual loss of TCF-1, differentiating ILC1 forfeited their expansion potential while increasing expression of effector molecules, reminiscent of T cell differentiation in secondary lymphoid organs. The transcription factor Hobit was induced in TCF-1hi ILC1s and was required for their effector differentiation. These findings reveal sequential mechanisms of ILC1 lineage commitment and ILC1 effector differentiation that are conserved across tissues. Our analyses suggest that ILC1 emerge as TCF-1hi cells in the periphery and acquire a spectrum of organ-specific effector phenotypes through a uniform Hobit-dependent differentiation pathway driven by local cues.

overall_design: Single cell mRNA sequencing of liver ILC1 and NK cells from WT and Hobit-deficient mice.

first: Christin

last: Friedrich

first: Renske

last: Taggenbrock

first: Rèmi

last: Doucet-Ladevèze

first: Gosia

last: Golda

first: Rebekka

last: Moenius

first: Panagiota

last: Arampatzi

first: Natasja

last: Kragten

first: Nina

last: Kreymborg

first: Wolfgang

last: Kastenmueller

first: Antoine

first: Dominic

last: Grün

first: Klaas

last: van Gisbergen

first: Georg

last: Gasteiger


title: RNA-sequencing of CD4+ T cells in Relapsing-Remitting Multiple Sclerosis patients at relapse; deciphering the involvement of novel genes and pathways

city: Tehran

first: zahra

last: salehi

state: Iran (the Islamic Republic of)

address: 16 Azar

department: Immunology

country: Iran

institute: Tehran University of Medical Sciences

summary: Objective: CD4+ T cells known as a noteworthy potential modulator of inflammation in multiple sclerosis (MS). In the current study, we proposed a systems biology approach to investigate the transcriptome profile of CD4+ T cells in patients at relapse phase.   Materials and Methods: We performed RNA sequencing of CD4+ T cells isolated from four relapsing-remitting MS (RRMS) patients at relapse phase and four age- and sex-matched healthy controls. The edgeR statistical method was employed to determine differential expression genes (DEGs). The gene set enrichment analysis was subsequently performed. Applying physical interaction network, genes with higher degrees were selected as hub genes.    Results: A total of 1278 genes and 1034 gens were defined at significantly higher or lower levels, respectively, in CD4+ T cells of RRMS patients as compared with healthy controls. The top up- and down-regulated gene were JAML and KDM3A. The detected DEGs were remarkably on chromosomes 1 and 2, respectively. The DEGs were mainly enriched in pathways such as ‘regulation of transcription, DNA-templated’, ‘regulation of B cell receptor signaling pathway’, ‘protein phosphorylation’, ‘epidermal growth factor receptor signaling pathway’, and ‘positive regulation of neurogenesis’. Moreover, 16 KEGG pathways mostly associated with the immune system and viral infections were enriched. In the constructed physical interaction networks, UBA52 and TP53 were illustrated as the most highly ranked hub genes among up- and down-regulated genes, correspondingly.   Conclusions: By applying global transcriptome profiling of CD4+ T cells, we deciphers the involvement of several novel genes and pathways in MS pathogenesis. The present results need to be affirmed by in vivo and in vitro studies.

overall_design: Investigating transcriptome profile of CD4+ T cells in RRMS patients at relapse phase compared to healthy controls

first: Salehi

last: Zahra

first: Talebi

last: Saeed

first: Maleknia

last: Samaneh

first: Palizban

last: Fahimeh

first: Naser

last: Abdorreza

first: Kavousi

last: Kaveh

first: Sahraian

last: Mohammad Ali

first: Izad

last: Maryam


title: Epigenetic mapping of the somatotropic axis reveals differential DNA hydroxymethylation marks with potential implication in growth

city: Bodø

first: Ioannis

last: Konstantinidis

state: Nordland

address: Universitetsalléen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

summary: We report an association of DNA hydroxymethylation profiling at single nucleotide resolution with gene expression in the fast muscle of Nile tilapia.

overall_design: Fast muscle RNA-Seq from rRNA depleted libraries of 5-month old full-sib males in five replicates.

first: Pål

last: Sætrom

first: Artem

middle: V

last: Nedoluzhko

first: Dafni

last: Anastasiadi

first: Robin

last: Mjelle

first: Tomasz

last: Podgorniak

first: Francesc

last: Piferrer

first: Jorge

last: Fernandes


title: Regional specialization and fate specification of mesenchymal stromal cells in skeletal development [bulk RNA-seq]

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

summary: To gain insight into the molecular signatures and heterogenity of bone mesenchymal stromal cells population between metaphysis (mpMSC) and diaphysis (dpMSC).  mpMSCs and dpMSCs were sorted from three weeks old Hey1-GFP metaphysis and Pdgfra-EGFP BM using a flow cytometer for bulk-RNA sequencing analysis.

overall_design: Bulk-RNA sequencing -mpMSC and dpMSC bulk-RNA seq. libraries prepared by using SMARTer Ultra Low input RNA kit-V3 and NexteraXT DNA library prep kit.

first: Kishor

middle: K

last: Sivaraj

first: Ralf

middle: H

last: Adams


title: Regional specialization and fate specification of mesenchymal stromal cells in skeletal development

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

overall_design: Refer to individual Series


title: FGFR1 associates with gene promoters and regulates gene transcription: Implications for endocrine resistance in ER+/FGFR1-amplified breast cancer [CAMA1 RNA-Seq]

city: Dallas

last: Kittler

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Using ChIP-Seq analysis of ER+/FGFR1-amplified breast cancer cells and PDXs, we found FGFR1 occupancy at transcription start sites with high overlap with histone modifications associated with active gene transcription. Mass spectrometry analysis of the nuclear and chromatin-bound FGFR1 interactome identified RNA-Polymerase II (Pol II) and FOXA1, with FOXA1 silencing impairing FGFR1 recruitment to chromatin. Transduction of FGFR1(SP-)(NLS) into MCF7 cells resulted in overexpression of nuclear FGFR1 and resistance to antiestrogens. Finally, an expression signature associated with nuclear FGFR1 correlated with endocrine resistance in patients treated with antiestrogens

overall_design: Examination of transcription profile in ER+/FGFR1-amplified CAMA1 breast cancer cells, treated with Vehicle or FGF2 5 ng/ml for 6 h. Three biological replicates for each cell line.

first: Alberto

last: Servetto

first: Rahul

last: Kollipara

first: Carlos

last: Arteaga


title: FGFR1 associates with gene promoters and regulates gene transcription: Implications for endocrine resistance in ER+/FGFR1-amplified breast cancer [CAMA1_ChIP-Seq]

overall_design: Examination of FGFR1 genomic distribution in CAMA1 stimulated with FGF2 5 ng/ml ± Erdafitinib 250 nM for 3 h breast cancer cells.  Two replicates were used


title: Analyzing The Effects of ProL1 Upregulation On PC3 Global Gene Expression

city: Bronx

first: Kelvin

middle: Paul

last: Davies

state: New York

address: 1300 Morris Park Avenue, Forchheimer 742

department: Urology

institute: Albert Einstein College of Medicine

summary:
Purpose: To examine the effects of proL1 upregulation on global gene expression in PC3 cells using RNA sequencing (RNA-Seq)
Methods: PC3 cells were transformed to overexpress proL1 using lentiviral vectors. The proL1 overexpressing variant (PC3 proL1+) and their parental cell line were plated in 6-well plates in triplicate (3 wells for each cell line). After 3 days, their RNA was isolated using the Qiagen RNeasy Mini kit and their global gene expression patterns were analyzed using RNA-Seq
Results: We identified 1698 differentially expressed genes between PC3 proL1+ and its parental cell line. Of these differentially expressed genes (DEGs), 209 were in common with LNCaP when proL1 was overexpressed. To identify biological functions that may be regulated through overexpression of proL1 in LNCaP cells, the list of DEGs was submitted to the DAVID, GOC, and KEGG databases, which identified 1250, 1366, and 480 unique genes within each database, respectively, which were then used for ontological analysis. According to these databases, proL1 overexpression regulated gene expression in ontological groups involved "anatomical structure development/morphogenesis" (more specifically "prostate gland morphogenesis"), extracellular matrix organization," "signaling," and "signal transduction. DEGs were also overrepresented in ontological groups potentially involved in vascularization and blood flow regulation. Analysis of the list of DEGs using the KEGG database identified the ontologic group "pathways in cancer" as having the greatest number of DEGs. DEGs were also identified with significant overrepresentation in specific biochemical pathways, such as the P13K-Akt, VEGF, and MAPK signaling pathways as well as steroid metabolic pathways. However, there were differences in the regulation of specific genes related to the androgen response between LNCaP and PC3. Unlike PC3, where overexpression of ProL1 caused a significant increase in expression of the androgen receptor gene (AR) and a decrease in expression of the estrogen receptor (ESR1), in LNCaP neither of these genes were changed in expression. In contrast, proL1 overexpression in LNCaP reduced expression of the progesterone receptor gene (PGR) but not in PC3 cells.
Conclusion: Global analysis of the changes in gene expression caused by proL1 overexpression in PC3 and LNCaP cells supports that it has a role both in the modulation of genetic pathways involved in both overcoming hypoxia and the development of androgen-insensitivity. Opiorphins have previously been shown to be directly involved in regulation of blood-flow to tissues through their modulation of smooth muscle tone, and therefore their upregulation in tumors may directly contribute to overcoming the hypoxic barrier that develops in the growing tumor. In addition, overexpression of ProL1 in both PC3 and LNCaP cells modulated expression of genes involved in angiogenesis and morphogensis; the activation of these pathways would likely be involved in vascularization of the tumor and thereby also contribute to overcoming hypoxia. Overexpression of proL1 also affected genes involved in steroid metabolism and response pathways in both LNCaP and PC3, which could potentially contribute to the modulation of androgen sensitivity. In PC3 proL1+ cells we observed a significant upregulation of the Androgen Receptor (AR). Increased activity of the AR could subsequently lead to the activation of secondary messengers involved in modulating the activity of other signaling pathways such as the PI3K-Akt signaling and MAPK pathways, which had significant over-representation of DEGs in PC3 proL1+ cells. The PI3K-Akt signaling pathway is considered one of the most commonly dysregulated pathways in prostate cancer with approximately 40% of early stage, and 70-100% of advanced staged cancer exhibiting dysregulation of this pathway.

overall_design: Total RNA of PC3 cells overexpressing proL1 and their parental cell line

first: Amarnath

last: Mukherjee

first: Augene

last: Park

first: Li

last: Wang


title: FGFR1 associates with gene promoters and regulates gene transcription: Implications for endocrine resistance in ER+/FGFR1-amplified breast cancer [ChIP-Seq]

overall_design: Examination of FGFR1 genomic distribution in breast cancer cells.  Three replicates were used


title: FGFR1 associates with gene promoters and regulates gene transcription: Implications for endocrine resistance in ER+/FGFR1-amplified breast cancer [RNA-Seq]

overall_design: Examination of transcription profile in MCF7EV and MCF7(FGFR1)(SP-)(NLS) ER+ breast cancer cells. Three biological replicates for each cell line.


title: Regional specialization and fate specification of mesenchymal stromal cells in skeletal development [scRNA-seq]

summary: To identify cellular heterogeneity and molecular signatures of bone marrow stromal (BMSCs) cells, we performed scRNA-seq of non-hematopoietic stromal cells from 3-week-old mice. In addition, to gain further insight into MSC differentiation in vivo, Pdgfrb-CreERT2 Rosa26-mTmG (Pdgfrb-Cre R26-mT/mG) double transgenic mice were treated with tamoxifen at P1-3 and sacrificed at P21 for the isolation of GFP+ cells from long bone followed by scRNA-seq analysis.

overall_design: Single cell -RNA sequencing of non-hematopoietic  bone stromal cells (BSC) postnatal day 21 old bone and PdgfrbCre-R26 mTmG GFP+ sorted cells using  10X genomics.


title: Alveolar macrophage gene expression in a mouse model of MAS

city: Cincinnati

first: Denny

middle: Kan

last: Gao

state: OH

address: 3333 Burnet Avenue

department: Rheumatology

institute: Cincinnati Children's Hospital Medical Center

summary:
Macrophage activation syndrome (MAS) is a life-threatening complication of systemic juvenile idiopathic arthritis (SJIA), and increasingly reported in association with severe lung disease (SJIA-LD) of unknown etiology. This study mechanistically defines the novel observation of pulmonary inflammation in the TLR9 mouse model of MAS that recapitulate key features of SJIA-LD, including IFNg activation. In acute MAS, lungs exhibit a mild but diffuse lymphocyte-predominant perivascular, interstitial inflammation with elevated IFNg, IFN-induced chemokines, and alveolar macrophage (AMf) expression of IFNg-induced genes. However, MAS resolution demonstrated AMf expansion and increased interstitial inflammation. AMf microarrays confirmed IFNg-induced proinflammatory polarization during acute MAS, which switches towards anti-inflammatory phenotype during MAS resolution. Interestingly, recurrent MAS increased alveolar inflammation, and reset polarization towards a pro-inflammatory state. Furthermore, in mice bearing macrophages insensitive to IFNg, both systemic feature of MAS and pulmonary inflammation were markedly attenuated. These findings demonstrate experimental MAS induces IFNg-driven pulmonary inflammation, and define this system for further study of and treatment validation in SJIA-LD.
We used microarrays to study whole transcriptome analysis of alveolar macrophages in the TLR9 mouse model of MAS during both acute MAS and MAS resolution.

overall_design: 11 mice were given 5 injections over 10 days with vehicle (PBS) or CpG. BAL fluid was obtained on day 10 (acute MAS) or day 30 (MAS resolution). Alveolar macrophages were purified by adherence, and RNA extraction for hybridization on Affymetrix microarrays.

first: Nathan

last: Salomonis

first: Maggie

last: Henderlight

first: Christopher

last: Woods

first: Kairavee

last: Thakkar

first: Alexei

last: Grom

first: Sherry

last: Thornton

first: Michael

middle: B

last: Jordan

first: Kathryn

last: Wikenheiser-Brokamp

first: Grant

last: Schulert


title: FGFR1 associates with gene promoters and regulates gene transcription: Implications for endocrine resistance in ER+/FGFR1-amplified breast cancer (RNA-seq)

first: Ralf

last: Kittler

overall_design: Examination of transcriptome of ER+/FGFR1-amplified human breast cancer CAMA1 cells. Three biological replicates

first: Alberto

last: Servetto


title: Regulation of VEGF-induced genes by Rab5A and Rab5C

city: Amsterdam

first: Aldo

last: Jongejan

address: Meibergdreef 9

department: Epidemiology & Data Science

country: Netherlands

institute: Amsterdam University Medical Centers

summary: The goal was to investigate whether the induction of gene expression by vascular endothelial growth factor (VEGF) in endothelial cells depends on endosomal GTPases Rab5A or Rab5C.

overall_design: Human umbilical vein endothelial cells (HUVECs) were lentivirally transduced with short hairpins against Rab5A or Rab5C or control short hairpins. Cells were then starved overnight and subsequently stimulated with VEGF for 1 or 4 hours. The cells were then lysed and RNA was isolated.

first: Coert

last: Margadant


title: Transcriptomic analysis of ON4T cells growing with and without molinate

city: Porto

first: Ana

middle: Rita Rego

last: Lopes

state: Porto

address: Rua Dr. Roberto Frias s/n

country: Portugal

institute: Faculdade de Engenharia Universidade do Porto

summary: Identify the genes coding for the potential enzymes involved in molinate degradation

overall_design: Two samples were analysed, one treatment and one control, data was further validated by RT-qPCR with triplicates

middle: R

first: Olga

last: Nunes


title: FGFR1 associates with gene promoters and regulates gene transcription: Implications for endocrine resistance in ER+/FGFR1-amplified breast cancer (ChIP-seq)

overall_design: Examination of FGFR1, H3K27ac, H3K4me3, Pol II S5P, FOXA1 genomic distribution in breast cancer cells. Examination of FGFR1 genomic distribution upon siRNA mediated FOXA1 knockdown in breast cancer cells.  For each ChIP-Seq experiment, two replicates for each antibody were used

first: Rahul

last: Kollipara

first: Carlos

last: Arteaga


title: FGFR1 associates with gene promoters and regulates gene transcription: Implications for endocrine resistance in ER+/FGFR1-amplified breast cancer


title: LYAR promotes colorectal cancer progression by up-regulating FSCN1 expression and is closely related to fatty acid metabolism

status: Public on Jul 26 2021

city: Hefei

first: xiaoyuan

last: song

address: Huangshan Road

institute: University of Science & Technology of China

summary: Colorectal cancer (CRC) is a highly malignant tumor associated with a poor prognosis, yet the molecular mechanisms are not fully understood. In this study, we showed that LYAR expresses at a higher level in CRC than normal tissue and LYAR expression is closely associated with distant CRC metastasis. LYAR significantly promotes the migration and invasion of CRC cells in vitro, and reduction of LYAR expression in CRC cells inhibites xenograft tumor metastasis in vivo. Microarray analysis of LYAR knockdown (KD) cells combined with ChIP assay, gene reporter assay and rescue experiment indicate that FSCN1 (fascin actin-bundling protein 1, Fascin-1) serves as a new and key regulator of the LYAR-promoted migration and invasion of CRC cells. In addition, knockdown of FSCN1 significantly inhibites subcutaneous tumorigenesis of CRC cells. Moreover, we found that FSCN1 affects some key enzymes in lipid fatty acid metabolism such as FASN and SCD. In summary, this study reveals a novel mechanism by which LYAR promotes tumor cell migration and invasion by up-regulating FSCN1 expression and further promoting fatty acid synthesis  in CRC.

overall_design: RNA-sequencing of NC cells and FSCN1 siRNA cells

first: Wu

last: Yupeng

first: Ma

last: Sai


title: Transcriptomic analysis of locoweed fungal endophyte mutant after supplement with L- lysine

city: Lanzhou

first: wei

middle: shang

last: Li

address: No. 335, Qilihe District

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Science

summary: This study provides the molecular bases to understand the impacts of L-lysine on swainsonine production in Alternaria oxytropis.

overall_design: A. oxytropis mRNA profiles of supplement with L- lysine and non-supplement with L- lysine were generated by deep sequencing.

first: Liang

last: Yan

first: Li

last: Shangwei

first: Zhou

last: Deshun


title: Dissecting transcriptional and chromatin accessibility heterogeneity of proliferating cone precursors in human retinoblastoma tumours by single cell sequencing [scATAC-seq]

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

country: United Kingdom

institute: Newcastle University

summary:
Background: Retinoblastoma (Rb) is a malignant neoplasm arising during retinal development from mutations in the RB1 gene. Loss or inactivation of both copies of RB1 results in initiation of retinoblastoma tumours, however additional genetic changes are needed for the continued growth and spread of the tumour. Ex vivo research has shown that in humans, retinoblastoma may initiate from Rb depleted cone precursors. Notwithstanding, it has not been possible to assess the full spectrum of clonal types within the tumour itself in vivo and the molecular changes occurring at the cells of origin, enabling their malignant conversion. To overcome these challenges, we have performed the first single cell (sc) RNA- and ATAC-Seq analyses of primary tumour tissues, enabling us to dissect the transcriptional and chromatin accessibility heterogeneity of proliferating cone precursors in human Rb tumours.
Methods: Two Rb tumours each characterised by two pathogenic RB1 mutations were dissociated to single cells and subjected to scRNA-Seq & scATAC-Seq using the 10x Genomics platform. In addition, nine embryonic and fetal retina samples were dissociated to single cells and subjected to scRNA- and ATAC-Seq analyses. The scRNA- and ATAC-Seq data were embedded using Uniform Manifold Approximation and Projection (UMAP) and clustered using Seurat graph based-clustering. Integrated scATAC-Seq analysis of Rb tumours and human embryonic/fetal retina samples was performed to identify Rb cone enriched subsets. Pseudotime analysis of proliferating cones in the Rb samples was performed with Monocle. Ingenuity Pathway Analysis (IPA) was used to identify the signalling pathway and upstream regulators in the Rb cone enriched subclusters.
Results: Our single cell analyses revealed the predominant presence of cone precursors at different stages of the cell cycle in the Rb tumours and amongst those identified the G2/M subset as the cell type of origin. scATAC-Seq analysis identified two Rb enriched cone subsets, each characterised by activation of different upstream regulators and signalling pathways, leading proliferating cone precursors to escape cell cycle arrest and/or apoptosis.
Conclusions: Our study provides evidence of Rb tumor heterogeneity and defines molecular pathways that can be targeted to define new treatment strategies

overall_design: Two Rb tumours each characterised by two pathogenic RB1 mutations were dissociated to single cells and subjected to scRNA-Seq & scATAC-Seq using the 10x Genomics platform. In addition, nine embryonic and fetal retina samples were dissociated to single cells and subjected to scATAC-Seq analyses.

first: Joseph

last: Collin

first: Rachel

last: Queen

first: Darin

last: Zerti

first: David

last: Steel

first: Claire

last: Bowen

first: Manoj

last: Parulekar


title: Single cell analysis of tumor infiltrating immune cells in wild-type (WT) and Ifnar1-SA (SA) mice

city: New York

first: Jinyang

address: 1230 York Ave

institute: The Rockefeller University

summary: Single cell analysis of tumor infiltrating CD8 T cells in wild-type (WT) and Ifnar1-SA (SA) mice identifies differentially expressed genes and signaling pathways.

overall_design: MC38 tumor cells were inoculated into WT and SA mice. Immune cells were isolated on day 14 post-inoculation for single cell RNA-seq analysis.

first: Hongru

last: Zhang

first: Serge

middle: Y

last: Fuchs


title: Hepatic lncRNA profile of offspring from maternal inulin early treatment

city: Beijing

first: Qian

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

summary: Male offspring mice affected by maternal inulin treatment

overall_design: We performed microarray analyses of male mice from maternal inulin early treatment

first: Xinhua

last: Xiao

first: Jia

last: Zheng

first: Ming

first: Miao

last: Yu

first: Fan

last: Ping

first: Tong

last: Wang

first: Xiaojing


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of Osteochondroma Explants Nontreated or Treated with Selective Agonist of Retionic acid Nuclear Receptor  Gamma (RARg) I

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St

department: Institute for Genome Sciences

institute: Institute of Genome

summary:
Purpose: Next-generation sequencing (NGS) has used to detect alterations in cellular pathways by various drugs. The goal of this study is to identify alteration of gene expression in human osteochondromas in response to identify nontreated or RARg agonist-treated osteochondorma transcriptome profiling (RNA-seq)  and to evaluate the actions of RARg agonists on osteochondromas.
Methods: Osteochondroma mRNA profiles of untreated or RARg agonist treated (4 days) osteochondroma explants were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results and Conclusions: Our study represents the  detailed analysis of human osteochondromas, with biologic replicates, generated by RNA-seq technology.   We conclude that RNA-seq based transcriptome revealed that RARg agonists acts on human osteochondromas and altered various types of  biological functions.

overall_design: Osteochondroma explant mRNA profiles without or with RARg agonist treatment

first: Enmoto-Iwamoto

last: Motomi

first: Iwamoto

last: Masahiro

first: Yuka

last: Imamura


title: Global gene expression in Brachypodium during embryo development

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

summary: We present an atlas of global gene expression of embryo, endosperm and seed coat in Branypodium, providing insights into the evolution of gene expression in embryogenesis.

overall_design: We investigate the dynamics and evolution of gene expression throughout seven stages of embryonic development from embryo, endosperm and seed coat in Brachypodium.

first: Daoquan

last: Xiang

first: Raju

last: Datla

first: Dolf

last: Weijers


title: Different gene expression in the tomato trichome and leaf

city: East Lansing

first: koichi

last: Sugimoto

state: MI

address: 612 Wilson Rd

institute: Michigan State University

summary: We report the transcriptome difference between glandular cells of type VI trichome and leaf cells of trichome shaved leaf.

overall_design: Four independent sample collections from isolated type VI trichome glands and trichome shaved leaf.

first: Koichi

first: Gregg

last: Howe


title: Transcriptomic profiles of type I/III interferon-responsive keratinocyte subsets from WT with or without Poly:IC injection

city: Bethesda

first: Keisuke

middle: Chris

last: Nagao

state: Maryland

address: 9000 Rockville Pike, Bldg 10, Rm12N240B

institute: National Institute of Arthritis and Musculoskeletal and Skin Diseases

summary: Inflammation triggered by viral infections can obscure tissue function. We utilized a model of systemic anti-viral immunity and found distinct type I IFN responses within the epidermal compartments.

overall_design: Transcriptomic changes in sorted interfollicular epidermis (IFE) and bulge cells from WT mice without Poly:IC and WT mice 1 day after intraperitoneal poly(I:C) injection.

first: Keiko

last: Sakamoto


title: Dissecting transcriptional and chromatin accessibility heterogeneity of proliferating cone precursors in human retinoblastoma tumours by single cell sequencing [scRNA-seq]

first: Majlinda

last: Lako

overall_design: Two Rb tumours each characterised by two pathogenic RB1 mutations were dissociated to single cells and subjected to scRNA-Seq & scATAC-Seq using the 10x Genomics platform. In addition, nine embryonic and fetal retina samples were dissociated to single cells and subjected to scRNA-seq.

first: Joseph

last: Collin

first: Rachel

last: Queen

first: Darin

last: Zerti

first: David

last: Steel

first: Claire

last: Bowen

first: Manoj

last: Parulekar


title: CHIP-Seq analysis of CREB1 binding after ALVAC vaccination in NHP

status: Public on Jul 25 2021

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

institute: RPM Bioinfo Solutions

summary: The RV144 HIV vaccine trial remains the only study to demonstrate significant protection from future HIV-1 acquisition. One of the key components of the RV144 vaccine was the use of the canarypox vector ALVAC as the priming component. Since AIDSVAX, the booster component, alone failed to provide protection we hypothesized that the ALVAC prime contributed significantly to the generation of protection. To test this, we designed a NHP immunogenicity trial to mechanistically link ALVAC vaccination with the magnitude of V1V2 titers, the most significant immune correlate of reduced HIV-1 acquisition in RV144. Our objective was to use a systems biology approach to identify the transcription factors, target genes and immune pathways which were being induced by ALVAC vaccination and associated with higher V1V2 titers. We identified the transcription factor CREB1 and its target genes as rapidly induced by ALVAC in multiple immune subsets and that CREB1 drives the expression and activation of a network of other TFs which are critical for modulating immune responses. Pathways induced by this ALVAC-CREB1 axis include lymphocyte/leukocyte migration, lymphocyte differentiation, antigen processing and presentation, T cell co-stimulation and cytokine signaling.

overall_design: PBMCs were infected in vitro with an MOI 10:1 of ALVAC-HIV or empty ALVAC, with media cultured cells as a control.  ALVAC-infected PBMCs were compared with media condition at 24 and 48 hours after CREB1 chromatin immunoprecipitation.

first: Jeffrey

last: Tomalka

first: Slim

last: Fourati

first: Muhammad

last: Latif

first: Ashish

last: Sharma

first: Kathryn

last: Furr

first: Kevin

last: Carlson

first: Michelle

last: Lifton

first: Ana

last: Gonzalez

first: Peter

last: Wilkinson

first: Genoveffa

last: Franchini

first: Robert

last: Parks

first: Norman

last: Letvin

first: L

last: Nicole

first: E

middle: S

last: Kelly

first: Georgia

last: Tomaras

first: Jim

last: Tartaglia

first: Merlin

last: Robb

first: Nelson

last: Michael

first: Richard

last: Koup

first: Barton

last: Haynes

first: Sampa

last: Santra

first: Rafick-Pierre

last: Sékaly


title: A novel role for the conserved, orphan deaminase APOBEC2 [ChIP-seq]

city: Heidelberg

first: Nina

last: Papavasiliou

address: Im Neuenheimer Feld 280

department: Division of Immune Diversity (D150) Deutsches Krebsforschungszentrum

institute: German Cancer Research Center (DKFZ)

summary: The AID (activation induced deaminase)/APOBEC (apolipoprotein B mRNA editing catalytic polypeptide-like) family of proteins are zinc-dependent cytidine deaminases active on polynucleotides and involved in RNA editing, DNA demethylation or DNA editing. The enzymatic activity, substrate or physiological target(s) of APOBEC2, a member of the AID/APOBEC, remain elusive. Here, we combined next generation sequencing (NGS) techniques with state-of-the-art molecular biology to comprehensively examine the physiological effects of APOBEC2 on the transcriptome and methylome using C2C12 myoblasts differentiating in culture. We also examined APOBEC2’s genome wide-binding specificity. Using RNA sequencing (RNA-seq) by polyA capture, we detected no evidence that APOBEC2 is an RNA editor. In the same system, enhanced reduced representation bisulfite sequencing (eRRBS) data did not support the proposed role of APOBEC2 as a 5-methyl-C (5mC) deaminase. However, chromatin immunoprecipitation sequencing (ChIP-Seq) did reveal specific locations of genomic occupancy of APOBEC2 with a specific motif preference. Combining biochemical, ChIP-Seq and RNA-Seq gene expression analyses we demonstrate that APOBEC2 acts as a negative regulator of gene expression in muscle cells. Our data support a model of APOBEC2 acting as a chromatin-binding factor that leads to inhibition of transcription of genes involved in cell cycle regulation during C2C12 differentiation.

overall_design: Here we have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. We use a cell culture muscle differentiation system (C2C12), a system where APOBEC2 protein expression progressively increases. Control (GFP shRNA) and APOBEC2 deficient (A2shRNA, where Apobec2 is knocked down) C2C12 cells were evaluated at different time points following induction of differentiation. We profiled these cells for: gene expression changes and RNA editing changes between control and APOBEC2 deficient groups (n=3) using RNA sequencing (RNA-Seq) by polyA capture; 5-methylCytosine changes between control and APOBEC2 deficient group (n=5) in DNA using enhanced Reduced Representation Bisulfite Sequencing (eRRBS). Lastly, we identify specific APOBEC2 binding regions in the DNA using Chromatin Immunoprecipitation Sequencing (ChIP-Seq) (n=3).

first: Linda

last: Molla

first: F

middle: N

first: Dewi

last: Harjanto

first: S

middle: T

last: Carroll


title: A novel role for the conserved, orphan deaminase APOBEC2 [methylation]

type: Methylation profiling by high throughput sequencing

overall_design: Here we have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. We use a cell culture muscle differentiation system (C2C12), a system where APOBEC2 protein expression progressively increases. Control (GFP shRNA) and APOBEC2 deficient (A2shRNA, where Apobec2 is knocked down) C2C12 cells were evaluated at different time points following induction of differentiation. We profiled these cells for: gene expression changes and RNA editing changes between control and APOBEC2 deficient groups (n=3) using RNA sequencing (RNA-Seq) by polyA capture; 5-methylCytosine changes between control and APOBEC2 deficient group (n=5) in DNA using enhanced Reduced Representation Bisulfite Sequencing (ERRBS). Lastly, we identify specific APOBEC2 binding regions in the DNA using Chromatin Immunoprecipitation Sequencing (ChIP-Seq) (n=3).


title: A novel role for the conserved, orphan deaminase APOBEC2

summary:
The AID (activation induced deaminase)/APOBEC (apolipoprotein B mRNA editing catalytic polypeptide-like) family of proteins are zinc-dependent cytidine deaminases active on polynucleotides and involved in RNA editing, DNA demethylation or DNA editing. The enzymatic activity, substrate or physiological target(s) of APOBEC2, a member of the AID/APOBEC, remain elusive. Here, we combined next generation sequencing (NGS) techniques with state-of-the-art molecular biology to comprehensively examine the physiological effects of APOBEC2 on the transcriptome and methylome using C2C12 myoblasts differentiating in culture. We also examined APOBEC2’s genome wide-binding specificity. Using RNA sequencing (RNA-seq) by polyA capture, we detected no evidence that APOBEC2 is an RNA editor. In the same system, enhanced reduced representation bisulfite sequencing (eRRBS) data did not support the proposed role of APOBEC2 as a 5-methyl-C (5mC) deaminase. However, chromatin immunoprecipitation sequencing (ChIP-Seq) did reveal specific locations of genomic occupancy of APOBEC2 with a specific motif preference. Combining biochemical, ChIP-Seq and RNA-Seq gene expression analyses we demonstrate that APOBEC2 acts as a negative regulator of gene expression in muscle cells. Our data support a model of APOBEC2 acting as a chromatin-binding factor that leads to inhibition of transcription of genes involved in cell cycle regulation during C2C12 differentiation.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Here we have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. We use a cell culture muscle differentiation system (C2C12), a system where APOBEC2 protein expression progressively increases. Control (GFP shRNA) and APOBEC2 deficient (A2shRNA, where Apobec2 is knocked down) C2C12 cells were evaluated at different time points following induction of differentiation. We profiled these cells for: gene expression changes and RNA editing changes between control and APOBEC2 deficient groups (n=3) using RNA sequencing (RNA-Seq) by polyA capture; 5-methylCytosine changes between control and APOBEC2 deficient group (n=5) in DNA using enhanced Reduced Representation Bisulfite Sequencing (ERRBS). Lastly, we identify specific APOBEC2 binding regions in the DNA using Chromatin Immunoprecipitation Sequencing (ChIP-Seq) (n=3).

Refer to individual Series


title: Expression data for heat tolerant and susceptible cultivars of indica rice

city: New Delhi

first: Jitendra

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

summary: Heat stress along with other abiotic stresses is one of the major factors affecting crop health and overall yield in a tropical country like India. Thus, there is an urgent need to understand the dynamics of heat responsiveness at the molecular as well as physiological level. Fortunately, India has a number of indigenous varieties that show tolerance to extremes in temperature during the scorching summer months. The cultivar Annapurna is a fast growing dwarf variety of rice that is heat tolerant while the most widely grown indica rice in South and Southeast Asia, IR64, is susceptible to high temperatures. These two cultivars present an excellent opportunity to study the differences in response to heat stress, and, thereby help in elucidating the genes involved in conferring tolerance to high temperature. The present study involves transcript profiling of the two cultivars, Annapurna (tolerant) and IR64 (susceptible) under both control and heat stressed conditions.

overall_design: Seven-day-old seedlings of Annapurna and IR64, grown hydroponically, were subjected to heat stress by giving them pre-treatment at 37 oC for 1 h followed by exposure to a higher temperature of 42 oC for 2 h at 40% relative humidity in light conditions. For control samples, seedlings were kept in RGM (root growth medium) for 3 h at 28±1oC. RNA extracted from each sample was hybridized on rice Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. Overall, eighteen samples were analyzed representing control, 37 oC and 42 oC of heat stress for each cultivar (Annapurna and IR64).

first: Pratikshya

last: Borah

first: Sanjay

last: Kapoor

middle: P


title: A novel role for the conserved, orphan deaminase APOBEC2 [RNA-seq]


title: Transcriptome analysis ofLu134A cells following ASCL1 knockdown and SBC5 cells transfected by miR455-3p mimic

city: Bunkyo-ku

first: NAOYA

last: MIYASHITA

state: Tokyo

department: Respiratory Medicine

country: Japan

institute: The University of Tokyo

summary: Molecular subtypes of SCLC have been defined by the expression status of ASCL1, NEUROD1, YAP1, and POU2F3 transcription regulators. ASCL1 knockdown resulted in decreased and increased expression of miR-375 and miR-455-3p, respectively. Analyses of publicly available transcriptome datasets suggested that miR-375 induced by ASCL1 is involved in YAP1 suppression whereas miR-455-3p is higher in non-neuroendocrine SCLC cells lacking ASCL1 expression.

overall_design: Lu134A cells were trasfected with siRNAs for ASCL1, and RNA-sequencing was performed using Illumina HiSeq. SBC5 cells were tranfected with miR455-3p mimic, and RNA-sequencing was performed ugsing Illumina HiSeq.

first: Kazuko

last: Miyakawa

first: Naoya

last: Miyashita

first: Masafumi

last: Horie

first: Akira

last: Saito

first: Takahide

last: Nagase


title: MicroRNA analysis of Lu134A cells following ASCL1 knockdown

overall_design: Lu134A cells were trasfected with siRNAs for ASCL1, and microRNA array was performed using Affymetrix GeneChip® miRNA 4.0 Array.


title: Human Cardiac Fibroblasts in Producing Cell-Derived Matrices

city: San Francisco

first: Todd

last: McDevitt

address: 1650 Owens St

department: GICD

country: USA

institute: Gladstone Institutes

summary: We reported a specialized protocol to produce human cardiac cell-derived matrices without the introduction of exogenous matrix proteins. Human cardiac fibroblasts cultured under conditions to produced cell-derived matrices were harvested at the beginning, middle and completion of the experiment - corresponding to days 0, 5 and 10. Fetal and adult human cardiac fibroblasts were cultured densely in the presence of ficoll as a macromolecular crowder on the adhesive biopolymer l-polydopamine, and sampled throughout matrix deposition to determine the age-specific responses of primary human cardiac fibroblasts to macromolecular crowders and enhanced matrix deposition.

overall_design: Analysis of sequential timpoints during culture of fetal and adult human cardiac fibroblasts with ficoll.

middle: C

first: M

middle: A

last: Kauss

first: David

last: Joy


title: Gene expression data from lung tissues of C57BL/6J mice

status: Public on Jul 24 2021

city: Daegu

first: Eok-Cheon

last: Kim

address: hyunchung-ro 170

department: Biochemistry and Molecular Biology

country: South Korea

institute: College of Medicine, Yeungnam University

summary:
Homoharringtonine could be a novel therapeutic agent for the treatment and the prevention of aging and age-related diseases (ARDs).
Cellular senescence contributes to aging and ARDs. Removal and modulation of senescent cells (SCs) improve physical functions and extend healthspan in animal models. Thus, the development of therapeutics that target SCs (i.e., senotherapeutics) has been proposed as a promising strategy for the treatment and the prevention of aging itself and ARDs. We used drug repositioning to discover new senotherapeutics from 2,150 clinically applied compounds and found that homoharringtonine (HHT) has a senolytic activity in human dermal fibroblasts (HDFs) in vitro and in vivo models. HHT improved physical status and rescued aging phenotypes in progeroid mice and aged mice. In addition, HHT administration ameliorates bleomycin-induced lung fibrosis in mice.

overall_design: Lung tissues were selected at successive stages of fibrosis for RNA extraction and hybridization on Affymetrix microarrays. Total 9 Samples, 3 Sample Groups, 3 Comparisons. (test vs. control)     B_vs_C   H_vs_C   H_vs_B

first: Jae-Ryong


title: Lentiviral-based mutagenesis to identify mutations that confer resistance to anti-cancer drugs

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Dietary restriction regulates microRNAs in longevity regulons

city: Shanghai

first: Yizhen

last: Yan

address: 320 Yue Yang Road

institute: Shanghai Institutes for Biological Sciences

summary: Aging is a complex process involving multiple pathways, each of which takes place and dominates at various stages of aging. It is largely unclear how these pathways coordinate with each other and take turns to function. Here we focus on microRNAs (miRNAs), for their multi-targeting, fine-tuning nature, and thus a potential to act as systems–level anti-aging regulator. We used C. elegans treated with dietary restriction as an anti-aging model to reveal how miRNAs link the regulatory modules of different stages to convert starvation signal into longevity benefits. miRNAs show a delayed response pattern upon DR, repress early response genes and fine-tune late response genes.

overall_design: miRNA profile in C. elegans treated with CR, IF, and ad libitum (AL) in time series during aging


title: Efficient Dicer processing of virus-derived double-stranded RNAs and its modulation by RIG-I-like receptor LGP2

first: Yang

last: Li

address: 2005 Songhu Road

institute: Fudan University

summary: The function and mechanism of the interferon-regulated antiviral responses have been extensively characterized. Recent studies have demonstrated induction of antiviral RNA interference (RNAi) in somatic cells against several mammalian RNA viruses rendered incapable of RNAi suppression. However, little is known about Dicer-mediated production of virus-derived small-interfering RNAs (vsiRNAs) in these cells active in the type I interferon response. Here we show that the dsRNA precursors of influenza vsiRNAs were processed more efficiently than cellular precursor microRNA hairpins by wild-type human Dicer expressed de novo in Dicer-knockout somatic cells. We found that infection of two strains of suckling mice with wild-type Nodamura virus (NoV) was associated with production of silencing-active vsiRNAs and direct sequestration of duplex vsiRNAs by its RNAi suppressor protein B2. Our findings from in vivo infection with Sindbis virus recombinants expressing NoV B2 or carrying a vsiRNA-targeted insert provide evidence for an antiviral function of the induced RNAi response. Interestingly, NoV infection induces expression of RIG-I-like receptor LGP2 to inhibit vsiRNA biogenesis and promote virulent infection in suckling mice. Our findings together reveal efficient Dicer processing of vsiRNA precursors in interferon-competent somatic cells and suckling mice in contrast to synthetic long dsRNA examined previously by in vitro dicing.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 19 virus-derived small RNA from mice muscle or 293T cells infected with different viruses was detected by small RNA-seq.

first: Yuqiang

last: Zhang

first: Yan

last: Xu

first: Yunpeng

last: Dai

first: Zhe

first: Jiaxing

last: Wang

first: Zhi

last: Ye

first: Yanxin

last: Ren

first: Hua

first: Wan-xiang

first: Jinfeng

last: Lu

first: Shou-Wei

last: Ding


title: Transcriptome of Melampsora larici-populina sexual stages [JGI version 2 genome]

city: Champenoux

first: Sebastien

last: Duplessis

address: INRA Centre Grand Est - Nancy

department: UMR 1136 IAM

institute: INRA

summary: Illumina HiSeq2500 technology was used to generate mRNA-sequencing expression profiles of sexual stages of the poplar rust fungus M. larici-populina: - Basidia (BSD) were collected from rust-infected dead poplar leaves; - Pycnia (PYC) -also called spermogonia- were collected from rust-infected larch needles one week after inoculation with basidiospores and corresponded to different haploid fungal cell types such as in planta infection hyphae, receptive hyphae and pycniospores; - Aecia (AEC) were collected from rust-infected larch needles two weeks after inoculation, and corresponded to freshly produced aecia and dikaryotic aeciospores and remaining pycnia. Paired-end reads of 100bp were generated for three sets of biological replicates corresponding to each of the targeted stage and aligned to the genome of M. larici-populina isolate 98AG31 (version 2.0; US Department of Energy Joint Genome Institute; http://genome.jgi.doe.gov/Mellp2_3/Mellp2_3.home.html) using CLC Genomics Workbench 12.0

overall_design: In total, nine mRNA profiles of M. larici-populina sexual stages were generated by Illumina HiSeq2500 (2x100bp). Three biological replicates were sequenced for each stage BSD, PYC and AEC.

last: Dupessis


title: Long noncoding RNA TCONS_00027385 acts as a miR-874-5p sponge to suppress the progression of prostate cancer through regulating ASCC2 expression

city: Hangzhou

first: Jianxin

last: Han

address: Yuhangtang RD 866#

department: Department of Food Science and Nutrition, School of Biosystems Engineering and Food Science

institute: Zhejiang University

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

summary:
Coal tar pitch (CTP) is a byproduct of cooking process which is used in making coatings, corrosion protection materials, and electrode. and it has been verified that Coal tar pitch extract (CTPE) constitutes polycyclic aromatic hydrocarbons (PAHs) (87.91%) and monocyclic aromatic hydrocarbons, heterocyclic compounds and alkenes (the remaining total is 12.09%) using gas chromatography/mass spectrometry (GC/MS). In this study, we determine the lncRNA expression profile in CTPE group and control group. The key lncRNAs were screen out by using microarray analysis in defferent group.
The experiment is divided into two groups: 22RV1 cells as control group, 22RV1 cells induced with Robustanoids A. then perform lncRNAs chips by Arraystar Human lncRNAs chip (Arraystar).

overall_design: Jianxin,Han

first: Fanghuan

last: Zhu

first: Zhenlei

last: Zhao


title: Global mapping of PfCDP occupany on the genome of P. falciparum

city: Chennai

first: Arumugam

last: Rajavelu

state: Tamil Nadu

address: Adayar

institute: IITM

summary: We identified wew chromodomain containing protein that binds to H3K9me3 mark in P. falciparum. To identify its global positioning on the genome of P. falciparum, we perfromed ChIP sequencing using inhouse generated anti-PfCDP antibody. The sheared chromatin was prepared from the P. falciparum culture and subjected for ChIP followed by library preparation from the ChIP DNA and were subjected to sequencing using the HiSeqIllumina platform. The PfCDP binding sites were determined after sequence alignment and normalization with input sequence. We have found selective enrichment of PfCDP protein on the virulence genes of P. falciparum. Collectively, this study reports chromodomain binds to epigenetic mark H3K9me3 and regulats the subsets of virulence genes expression in human malaria parasite P.falciparum.

first: V

last: Devadathan


title: Identification and Transcriptome Analysis of C1 Nullisomic in Allotetraploid Brassica napus L

city: Gui'yang

first: hu

middle: li

last: juan

address: 116 Baoshan North Road, Guiyang City, Guizhou Province, China

institute: Guizhou Normal University

summary:
The purposes of this study are to compare euploid B. napus cv. “Oro” and the C1 nullisomics transcriptome profiling (RNA-seq) and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis.
Methods: Leaves mRNA profiles of 30-day-old euploid B. napus cv. “Oro” and the C1 nullisomics were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods. qRT–PCR validation was performed.
Results: After the high-throughput sequencing, each sample generated 7.2G Clean data on average and the 44.6-53.8 million clean reads were generated.
Our study represents detailed analysis of leaves transcriptomes in euploid B. napus and nullisomic, with biologic replicates, generated by RNA-seq technology for comparative investigations of expression profiles. Our results show that Dose complementary effect exists between highly homologous genes, and partial loss of C subgenomic chromosome will lead to increased expression of A genome.

overall_design: The mRNA profiles of 30-day-old wild euploid Brassica napus cv. “Oro” and aneuploidy Brassica napus cv. "null".

first: Hu

middle: L

last: Juan


title: KDSR is required for 3-ketodihydrosphingosine metabolism and ER unfolded protein response in leukemia

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: Sphingolipids and their metabolic pathways have been implicated in disease development and therapeutic response; however, the detailed mechanisms remain unclear. Using a sphingolipid network focused CRISPR/Cas9 library screen, we identified an endoplasmic reticulum (ER) enzyme, 3-Ketodihydrosphingosine reductase (KDSR), to be essential for leukemia cell maintenance. Loss of KDSR led to apoptosis, cell cycle arrest, and aberrant ER structure. Transcriptomic analysis revealed the indispensable role of KDSR in maintaining the unfolded protein response (UPR) in ER. High-density CRISPR tiling scan and sphingolipid mass spectrometry pinpointed the critical role of KDSR’s catalytic function in leukemia. Meanwhile, depletion of KDSR resulted in accumulated 3-ketodihydrosphingosine (KDS) and dysregulated UPR checkpoint proteins PERK, ATF6, and ATF4. Finally, our study revealed the synergism between KDSR suppression and pharmacologically induced ER-stress, underscoring a therapeutic potential of combinatorial targeting sphingolipid metabolism and ER homeostasis in leukemia treatment.

overall_design: mRNA profiling in CRISPR KDSR-KO vs. control leukemia cells

first: Chun-Wei

middle: D

last: Chen

first: Qiao

last: Liu

first: Lu

last: Yang


title: Construction of Nanobody Library in Mammalian Cells by Linear-double-stranded DNA Based AND Gate Genetic Circuit

city: Tianjin

first: Shuai

last: Li

state: Tianjin

address: Huanhuxi Road

institute: Tianjin Tumor Hospital

summary: Nanobody is one special type of single-domain antibody fragment with multiple advantages over traditional antibody. Our previous work established linear-double-stranded DNA (ldsDNA, or PCR amplicon) as novel biological parts for building AND gate genetic circuits in mammalian cells. During this AND-gate circuit formation process, the co-transfected up- and down-stream ldsDNAs could be linked together to form intact gene expression cassette. Here, we employed this ldsDNA-based AND-gate (LBAG) strategy to construct nanobody library in mammalian cells. The sequence complexity of complementary determining regions (CDRs) was introduced into ldsDNA by PCR amplification. After being co-transfected into mammalian cells, the up- and down- stream ldsDNAs undergo AND gate linkage and form full nanobody coding regions, containing CDR1-3. High throughput sequencing identified 22,173 unique oligonucleotide sequences in total generated by this strategy. Thus, we developed a novel method to construct nanobody library, which is a start point for building high content nanobody library in mammalian cells.

overall_design: We apply ldsDNA-based AND gate (LBAG) calculation to generate nanobody library in mammalian cells.

first: Yanjie


title: Changes in adipose tissue microRNA expression across the menstrual cycle in regularly menstruating women: a pilot study.

status: Public on Jul 23 2021

city: Stirling

first: Colin

last: Moran

address: Univeristy of Stirling

institute: University of Stirling

summary:
Cyclical changes in hormone profiles across the menstrual cycle are associated with alterations in metabolic control. MicroRNAs (miRNA) contribute to the regulation of metabolic control, including adipose tissue metabolism. However, the effect of fluctuations in hormonal profile across the menstrual cycle on adipose tissue miRNA expression remain unknown.
We used Affymetrux microarray expression analysis to characterise adipose tissue miRNA expression in healthy, regularly menstruating females across the menstrual cycle.

overall_design: Female participants attended the laboratory at 4 timepoints across their menstrual cycle, as follows: early-follicular phase (cycle day 3 ± 1); late-follicular phase (11 ± 1), post-ovulatory phase (16 ± 2), late-luteal phase (24 ± 3). During each laboratory visit resting adipose tissue biopsies were obtained via the mini-liposuction technique in a repeat measures experimental design.

first: Kirstin

last: MacGregor

first: Nidia

last: Rodriguez-Sanchez

first: Thomas

middle: G

last: Di Virgilio

first: Iain

middle: J

last: Gallagher


title: Transcriptional response to seawater acidification and hyperthermal stress in the azooxanthellate octocoral, Scleronephthya gracillimum

city: Busan

first: Seonock

last: Woo

address: Haeyangro 385

institute: Korea Institute of Ocean Science and Technology

summary:
The soft coral Scleronephthya gracillimum is an azooxanthellate octocoral order Alcyonacea. In this study, stress responses to increased seawater temperature and marine acidification were investigated using a microarray. The S. gracillimum microarray was constructed.
The S. gracillimum microarray was constructed after RNA-seq. Oligonucleotides were picked from UniGene of S. gracillimum and the clones were annotated using Blast.

overall_design: For hyperthermal stress experiment consists of 24C vs. 26C, 24C vs. 28C. Each group has 3 individual corals. The experiment were duplicate. For acidification experiment consists of pH6.5, pH7.0, pH 7.5 groups and each group has 3 individual corals. For hyperthermal and acidification dual stress experiments consist of 8.0 vs. 7.0, 8.0 vs. 7.5 and 8.0 vs. 7.8 groups and each group has 3 individual corals and the experiments were duplicated.

first: Seungshic

last: Yum


title: Sperm methylome alterations following yoga-based lifestyle intervention in patients of primary male infertility: A pilot study

city: Hyderabad

first: Divya Tej

last: Sowpati

state: Telangana

address: Habsiguda

institute: CSIR Centre for Cellular and Molecular biology

summary: A majority of the cases of primary male infertility are idiopathic with the underlying molecular mechanisms contributing to the pathophysiology as yet unknown. Effects of the environment can alter the sperm epigenome thereby impacting male reproduc-tive health. Epigenetic mechanisms are crucial to understanding health and disease, and methylome alterations are now known to have far-reaching clinical implications. Here, we report the results from our pilot study, a first of its kind analysis of the ef-fect of the traditional practice of yoga on human sperm quality. We find marked im-provement in sperm characteristics in patients of idiopathic male infertility following asupervised21-dayyogaregimen.Furthermore,next-generationsequencing-basedmethylome  analysis  reveals  alterations  in  the  sperm  epigenome  of  these  patients.  We  find  that  the  practice  of  yoga  is  associated  with  DNA  methylation  changes  at  nearly 400 genes, 147 of which were hypermethylated while 229 were hypomethyl-ated.  These  included  promoters  of  several  genes  linked  to  maintenance  of  fertility  and genomic integrity. This novel piece of work draws a direct link between positive lifestyle practices and male reproductive health.

overall_design: Differentially methylation analysis between Pre-YBLI and Post-YBLI samples

first: Shilpa

last: Bisht

first: Sofia

last: Banu

first: Surabhi

last: Srivastava

first: Rashmi

middle: U

last: Pathak

first: Rajeev

last: Kumar

first: Rima

last: Dada

first: Rakesh

middle: K

last: Mishra


title: Expression data from human blastocyst stage embryo

city: London

first: Hui

last: Xiao

address: 237 Fulham Road

institute: The Institute of Cancer Research

summary:
Clinical data suggest that both undisturbed culture of embryos and selection algorithms based on TL morphometric parameters can in correlation and potentially improve embryo survival rates and live birth rates. However, there remains a need to validate and understand the mechanisms underlying the potential benefits of this technology remains.
We used microarray to obtain and analyse transcriptome data of individual human embryos grown for up to 6 days to blastocyst in a TL incubator to study associations between morphokinetic TL parameters and the human embryo gene expression.

overall_design: Human embryos surplus to treatment requirements were donated with informed consent from several Assisted Reproduction Technology (ART) centres. Embryos were cultured to blastocyst in an EmbryoScope TL incubator and analysed by Affymetrix microarray.

first: H

first: A

last: Stevens

last: Smith

first: K

last: Szczesna

first: M

last: Keramari

first: G

last: Horne

last: Dinnyes

first: S

last: Kimber

first: P

last: Lio

first: D

middle: R

last: Brison


title: Adipocyte-specific deletion of HuR induces spontaneous cardiac hypertrophy and fibrosis

city: Columbus

first: Michael

last: Tranter

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

institute: The Ohio State University

summary: The presence of functional brown adipose tissue in humans is known to be associated with cardiovascular health. Here, we show that adipocyte-specific deletion of the RNA binding protein HuR, which we have previously shown to reduce BAT-mediated thermogenesis, is sufficient to mediate a spontaneous development of cardiac hypertrophy and fibrosis, likely through increased inflammation and extracellular vesicle transport in subcutaneous white adipose tissue. These results may have implications on the mechanisms by which BAT function and adipose tissue homeostasis directly mediates CVD.

overall_design: RNA-seq to determine global gene expression profiles cardiac and subcutaneous white adipose samples from mice with adipocyte-specific HuR gene deletion.


title: Novel epigenetically dysregulated genes in Oral Submucous Fibrosis

city: Bangalore

first: Ruchi

last: Jain

state: Karnataka

address: C V Raman Road

department: Molecular Reproduction Development and Genetics

institute: Indian Institute of Science

summary: DNA methylation data of normal buccal mucosa and Oral Submucous Fibrosis (OSF) afflicted mucosa.

overall_design: We have compared global 5-methylCytosine methylation pattern in 5 normal samples and 7 OSF samples by utilizing Illumina's Infinium 450K  Bead Methylation Array technique.

first: Paramita

last: Kundu

first: Ila

last: Pant

first: Paturu

last: Kondaiah


title: IL-13 neutralization effect on COVID-19 severity

city: Charlottesville

first: Chelsea

last: Marie

state: VA

address: 345 Crispell Drive

department: Medicine

institute: University of Virginia School of Medicine

summary: We investigated the effect of IL-13 neutralization on COVID-19 disease progression in mice.

overall_design: We analyzed the bulk lung tissue transcriptomes in Covid19 infected mice treated with anti-IL-13 or isotype (IgG) control antibodies and uninfected mice as an additional control group. 8-16 week-old male Tg(K18-hACE2) 2Prlmn (Jackson Laboratories) mice were challenged with 5000 plaque forming units (PFUs) of SARS-CoV-2 Hong Kong/VM20001061/2020 (BEI 14 Resources) in 50 μL by an intranasal route under 100 μL ketamine/xylazine sedation. Mice were given 150 μg of anti-IL-13(Thermofisher, clone eBio1316H; cat # 16-7135-85) or an isotype matched control IgG (Thermofisher, clone eBRG1; cat # 16-4301-85) administered on day 0, 2, and 4 pi. Mice were euthanzied at 5 days post-infection and lung tissue was resected for RNA-sequencing analysis.

first: Ning-Jiun

last: Jan