title: miRNA-Seq analysis of parental human leukemia K562 and clonal etoposide resistant K562 (designated K/VP.5) cell lines.

status: Public on Jan 31 2020

city: Columbus

first: Hatice Gulcin

last: Ozer

state: OH

address: 1800 Cannon Dr

department: Biomedical Informatics

country: USA

institute: The Ohio State University

type: Non-coding RNA profiling by high throughput sequencing

summary: We report that ~300 mature miRNAs were detected in these cells. 73 miRNAs were overexpressed (fold change > 2; adjusted P-value < 0.05) and 14 were underexpressed (fold change > 2; adjusted P-value < 0.05) in K/VP.5 compared to K562 cells.

overall_design: A mirVana miRNA Isolation Kit with phenol was used to isolate total RNA from K562 and K/VP.5 cells. The total RNA was subsequently DNase I treated and concentrated on a spin-column. NEB Next Small RNA libraries were prepared form the purified K562 and K/VP.5 total RNA samples and the libraries were size selected using Sage Pippin (130-200 bp range, adapters are ~128 bp) with an average final library size of 180 bp and sequenced on MiniSeq as 2 x 75 bp reads. 3′ adaptor sequences and low quality bases were trimmed from 75 base pair paired-end sequence reads using Cutadapt v2.4 (Martin, 2011). Trimmed reads with a sequence length between 15 and 50 base pairs were aligned to potential contaminant sequences of human genome (ribosomal RNAs and tRNAs) using Bowtie v1.1.2 (Langmead et al., 2009) with a seed length of 18 and allowing zero mismatches in the seed. Then, remaining reads were aligned to miRbase (Griffiths-Jones, 2004) v21 mature sequences using Bowtie v1.1.2 with a seed length of 18, allowing 1 mismatch in seed and reporting maximum 5 alignments per read. Finally, remaining reads were aligned to human reference genome, GRCh38, using Bowtie v1.1.2 with a seed length of 18, allowing 1 mismatch in seed and reporting only unique alignments for each read. Using Samtools (Li et al., 2009) and in-house R scripts, total number of reads for each mature miRNA was counted.

first: Evan

middle: E

last: Kania

first: Jessika

last: Carvajal-Moreno

first: Victor

middle: A

last: Hernandez

first: Anthony

last: English

first: Jonathan

middle: L

last: Papa

first: Nicholas

last: Shkolnikov

first: Hatice

middle: G

first: Ayse

middle: S

last: Yilmaz

first: Jack

middle: C

last: Yalowich

first: Terry

last: Elton


title: The metabolite receptor SUCNR1 in oxidative stress-induced age-related macular degeneration

city: Nijmegen

first: Elja

last: Louer

state: Select State

address: Geert Grootplein 26, M850 route 286

department: Physiology

country: Netherlands

institute: RadboudUMC

type: Expression profiling by high throughput sequencing

summary: Murine RPE transcriptomes were generated from SUCNR1 WT and KO mice from both the treated and untreated groups (n=4). When comparing all groups to each other, no significant difference in gene expression was observed.

overall_design:
Murine RPE transcriptomes were generated from SUCNR1 WT and KO mice from both the treated and untreated groups (n=4). Treated groups were exposed to hydroquinone to induce oxidative stress.
Each sample title represents "Animal number_eye(R=right eye, L=left eye)_genotype_treatment(-/+))"

middle: M

first: Anneke

middle: I

last: den Hollander

first: Peter

last: Deen


title: Cohesin removal reprograms mitotic gene expression upon mitotic entry [ChIP-seq]

status: Public on Jan 30 2020

city: Boston

first: Michael

middle: Demian

last: Blower

state: MA

address: 185 Cambridge St CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: During mitosis, the genome is restructured to facilitate chromosome segregation, accompanied by dramatic changes in gene expression. However, the mechanisms that underlie mitotic transcriptional regulation are unclear. In contrast to transcribed genes, centromere regions retain transcriptionally active RNA Polymerase II (RNAPII) in mitosis. Here, we demonstrate that chromosome-localized cohesin is necessary and sufficient to retain active RNAPII on mitotic centromeres. Failure to remove cohesin from mitotic chromosome arms dramatically alters mitotic gene expression, and results in a failure to release elongating RNAPII and nascent transcripts from mitotic chromosomes. We propose that prophase cohesin removal is the key step in reprogramming gene expression as cells transition from G2 to mitosis, and is temporally coupled with chromosome condensation to coordinate chromosome segregation with changes in gene expression.

overall_design: Control or WAPL-AID cells were arrested in G2 or mitosis. Cells were fixed and chromatin was fragmented. Input chromatin or immunoprecipitations from elongating RNAPII (pS2) were sequenced.

first: Carlos

last: Perea-Resa


title: Loss of KDM6A enhances human pancreatic cancer progression and potentiates HDAC inhibitor lethality via restoring CDKN1A

city: Bunkyo-ku

first: Shu

last: Shimada

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

country: Japan

institute: Tokyo Medical and Dental University

summary:
BACKGROUND & AIMS: Although genomic analysis have recently discovered the malignant subtype of human pancreatic ductal adenocarcinoma (PDAC) characterized by frequent mutations of a histone modifier KDM6A, the biological and molecular roles still remain obscure. We herein elucidated the clinical and biological impacts of KDM6A deficiency on human PDAC and identified the therapeutic potential by pathological and molecular evaluation.
METHODS: Immunohistochemical analysis of KDM6A was performed in 103 tumor specimens surgically resected from patients with PDAC. Cells knocked out for KDM6A by using the CRISPR/Cas9 system and expressing doxycycline-inducible KDM6A were established from each two human PDAC cell lines, respectively.
RESULTS: Loss of KDM6A in cancerous tissues was an independent prognostic factor for both recurrence-free and overall survival in the clinical samples. KDM6A knockout enhanced aggressive traits of human PDAC cell lines, whereas KDM6A overexpression suppressed them. Microarray analysis revealed reduced expression of 25 genes including five well-known tumor suppressors, such as CDKN1A, and ChIP-PCR analysis displayed depleted enrichment of histone H3 lysine 27 acetylation (H3K27ac) at the promoter regions of the five candidates. The epigenetic alterations were induced by the impaired recruitment of a histone acetyltransferase p300, which cooperatively interacted with KDM6A. Consistent with these results, the KDM6A knockout cells demonstrated higher vulnerability to histone deacetylase (HDAC) inhibitors through the reactivation of CDKN1A in vitro and in vivo than the KDM6A wild-type.
CONCLUSIONS: KDM6A exhibited essential roles in human PDAC as a tumor suppressor. KDM6A deficiency could be a promising biomarker for unfavorable outcome in PDAC patients and a potential surrogate marker for response to HDAC inhibitors.

overall_design: KDM6A-knockout pancreatic ductal adenocarcinoma cells (Panc1, BxPC3) were established by using a lentiviral CRISPR/Cas9 system.

first: Shuichi

last: Watanabe

first: Yoshimitsu

last: Akiyama

first: Yoshiya

last: Ishikawa

first: Kosuke

last: Ogawa

first: Hiroaki

last: Ono

first: Yusuke

last: Mitsunori

first: Daisuke

last: Ban

first: Atsushi

last: Kudo

first: Shoji

last: Yamaoka

first: Minoru

last: Tanabe

first: Shinji

last: Tanaka


title: MaHo001A: Identification of Novel Target Genes of Epstein-Barr Virus microRNAs

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: The human herpesvirus Epstein-Barr virus establishes persistent infections in the majority of the human population. Its main target cells are B lymphocytes and epithelial cells lining the oropharynx. Although primary infection usually occurs asymptomatically, EBV can cause mononucleosis. Moreover, EBV is strongly associated with multiple malignancies, including nasopharyngeal carcinoma, Burkitt Lymphoma, Hodgkin’s Lymphoma and post-transplant lymphoproliferative disease. In these EBV+ tumour tissues, the virus is latent and expresses only few proteins, yet up to ~40 miRNAs. Past research has indicated a possible causative link between these miRNAs and tumour development. However, the functions of these miRNAs remain poorly characterized. We aimed to explore the targetome of the EBV BART miRNAs by expressing these in a nasopharyngeal carcinoma cell line and performing whole genome gene expression profiling. Indeed, we identified numerous differentially expressed genes between miRNA-positive and -negative cells. By applying 3'UTR reporter assays, we validated eight genes as direct BART miRNA targets and identified the responsible miRNA(s). We found evidence for co-regulation of certain target genes by multiple miRNAs. Amongst these newly identified target genes was ATG16L1, a gene essential for autophagy. ATG16L1 protein levels were repressed by miR-BART18 in EBV+ Burkitt Lymphoma cells.

overall_design: HK-1 cells were lentivirally transduced to express the empty control vector (MH870) or a vector expressing the BART cluster 1 miRNAs (MH870-clus1). Sample versus common reference (cell line HK-1) hybridizations were performed on human whole genome gene expression microarrays V2 (Agilent, Belgium), in balanced dye-swap on 2 biological replicates per group.

first: Marjolein

middle: J

last: Hooykaas

first: Lione

last: Willems

first: Mario

last: Mauthe

first: Fulvio

last: Reggiori

first: Frank

last: Holstege

first: Maaike

last: Ressing

first: Emmanuel

last: Wiertz

first: Robert

last: Lebbink


title: ChIP-seq with the mouse bipotential  gonad

city: Dunedin

first: Megan

last: Wilson

address: 270 Great King St

country: New Zealand

institute: University of Otago

summary: ChIP-seq for H3K4me3 and H3K27me3 with E11.5 gonads.

overall_design: The Urogenital ridge from embryos (aged E11.5) were isolated and pooled for each litter.  A total of 5 litters per biological replicate was used per ChIP assay.


title: Cohesin removal reprograms mitotic gene expression upon mitotic entry [RNA-seq I]

first: Michael

last: Blower

overall_design: Control or WAPL-AID cells were arrested in G2 or mitosis. 2 replicates of each condition were analyzed. Nascent transcripts were labeled using EU, purified, and sequenced.

first: Carlos

last: Perea-Resa


title: RNA sequencing analysis of the whole genome expression profile in non-thermal atmospheric pressure plasma (NTAPP)-exposed and -unexposed human adipose tissue-derived stem cells (ASCs)

city: Seoul

first: Kiwon

last: Song

address: Yonsei-ro 50

country: South Korea

institute: Yonsei University

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

overall_design: Refer to individual Series


title: Expression data from p53 knocked-down human neuroepithelial stem (NES) cells

status: Public on Jan 28 2020

city: Stockholm

first: Margareta

middle: T

last: Wilhelm

address: Solnavägen 9

department: MTC

country: Sweden

institute: Karolinska Institutet

summary:
In this study, we take advantage of human induced pluripotent stem (iPS) cell-derived neural stem cells to study the role of p53 during human brain development. We knocked down (KD) p53 in human neuroepithelial stem (NES) cells derived from iPS cells. Upon p53KD, NES cells rapidly show centrosome amplification and genomic instability. Gene  expression analysis  show downregulation of genes involved in oxidative phosphorylation (OXPHOS) upon loss of p53. In addition, p53KD neural stem cells upregulate genes involved in neuronal differentiation and display an increased pace of differentiating into neurons and exhibit a phenotype corresponding to more mature neurons compared to control neurons. Taken together, this demonstrates an important role for p53 in controlling genomic stability of neural stem cells and regulation of neuronal differentiation.
We used microarrays to identify gene expression changes in human NES cells upon p53 knockdown

overall_design: NES cells were either transduced with lentivirus containing either Control or p53 shRNA construct. Transduced cells were selected by puromycin treatment to obtain NES cells with stable knock down of p53. Gene expression analysis was performed on RNA isolated from Control and p53 shRNA NES cells generated from three seperate lentiviral transductions.


title: RNA-seq Analysis in 4T07 Control (4T07-CTL) and Six2 Overexpression (4T07-Six2) cells

city: Aurora

last: Oliphant

state: CO

department: Pharamacology

institute: University of Colorado Anschutz Medical Campus

summary: To determine the molecular mechanisms by which Six2 regulates metastatic colonization, we performed RNA-seq analysis on murine triple-negative 4T07 Control (4T07-CTL) and Six2 overexpressing (4T07-Six2) cells. Using both targeted and unbiased gene signature analyses, we found that Six2 differentially regulates gene signatures associated with stemness. Additionally, we confirmed that in several triple-negative breast cancer (TNBC) models, Six2 enhanced the expression of genes (identified as among the highest upregulated genes in response to Six2 overexpression) associated with embryonic stem cell programs. When combined with our in vitro and in vivo stemness-associated phenotypic assays, these data suggest that Six2 may play a similar role in mediating stemness characteristics during tumor progression as it does during development, and that this role may allow it to mediate late-stage metastasis by enhancing the ability of cells to self-renew and survive at secondary sites.

overall_design: 4T07 CTL and Six2-OE cells were harvested 48h after plating for total RNA extraction (4 samples total) and RNA-seq analysis.

first: Matthew

middle: D

last: Galbraith

first: Ahwan

last: Pandey


title: Effects of bacterial haemorrhagic septicemia on the immune response of Leiocassis longirostris (microRNA-Seq)

city: chengdu

first: Han

last: Zhao

address: Xiyuan avenue,

country: China

institute: Fisheries Institute, Sichuan Academy of Agricultural Sciences

summary: Leiocassis longirostris is a common fish variety widely cultivated in China, however, bacterial haemorrhagic septicemia, which occurs easily during the breeding process, can cause great economic loss for farmers. To understand the immune response of L. longirostris to Aeromonas hydrophila infection, Illumina sequencing was employed to identify changes in the mRNA and miRNA in spleen tissue. In this study, a total of 92.16 and 95.61 million (M) high-quality transcriptome reads were generated from the control group (CG) and experimental group (EG) spleen samples, respectively, and 207 up-regulated and 185 down-regulated genes were identified. These genes were enriched in 29 GO terms and 30 KEGG pathways (P ≤ 0.05), including cytokine-cytokine receptor interaction and complement and coagulation cascades, with 17 up-regulated genes and 12 down-regulated genes in the EG relative to the CG. Based on the zebrafish genome, miRNA-seq identified a total of 343 miRNAs, of which 15 were up-regulated and 10 were down-regulated (fold-change ≥ 2 or ≤ 0.5 and P ≤ 0.05). Target gene prediction and KEGG enrichment analysis revealed that all of the target genes were concentrated in 13 pathways associated with immune response, including the mTOR signaling pathway and the TGF-beta signaling pathway. The expression patterns of 8 differentially expressed genes and 4 miRNAs involved in immune response were validated by quantitative real-time RT-PCR. These results provide insights into the molecular mechanisms underlying the effects of bacterial haemorrhagic septicemia on the immune response of Leiocassis longirostris.

first: Song

last: Yang

first: Jian

last: Zhou


title: RNA sequencing data of NR-S1, mouse squamous cell carcinoma, and ME-180, human cervical carcinoma for controls and radioresistant cells

city: Suita-shi, Osaka

first: Masayasu

last: Toratani

address: (D10), 2-2, Yamadaoka

department: Radiation Oncology

institute: Osaka University Graduate School of Medicine

summary: We got transcriptome data from NR-S1, mouse squamous cell carcinoma, controls, X-ray resistant cells, C-ion resistant cells. We also performed RNA sequencing on ME-180, human cervical carcinoma, controls and X-ray resistant cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: total RNA profiles in 5 cell types.

first: Kazuhiko

last: Ogawa

first: Hideshi

last: Ishii


title: tRNA-derived fragments and microRNAs in the maternal-fetal interface of a mouse maternal-immune-activation autism model

city: Charlottesville

first: Anindya

last: Dutta

state: VA

address: 1340 Jefferson Park Ave

department: Department of Biochemistry and Molecular Genetics

institute: University of Virginia

summary: We analyzed the small RNA composition of mouse placenta/decidua to determine whether there are specific differences in small RNAs during fetal development and in response to maternal immune activation.

overall_design: Pregnant C57BL/6 mice were i.p injected saline (control samples) or Poly(I:C) (MIA samples) at E11.5 and E12.5. Placenta/decidua samples were collected 3/6/12/24/48/144 hours post second injection and subjected to small RNA sequencing.

first: Zhangli

last: Su

first: Elizabeth

last: Frost

first: John

middle: R

last: Lukens


title: The methylome of invasive melanoma cell lines

city: Debrecen

first: Viktoria

last: Koroknai

address: 26/B Kassai str.

department: Department of Public Health and Epidemiology

country: Hungary

institute: University of Debrecen

type: Methylation profiling by genome tiling array

summary: Melanoma cell lines were established and used for methylome profiling with Illumina HM450 beadchip. The molecular alterations in selected invasive melanoma cell populations were compared to those in the original cell lines by performing DNA methylation (Illumina HM450K) assays

overall_design: Selected invasive melanoma cell populations were compared to those in the original cell lines by performing DNA methylation (Illumina HM450K) to identified several novel hypermethylated candidate genes with altered gene expression patterns in invasive melanoma cells that may have significant implications for understanding the invasion process in melanoma cells

first: Margit

last: Balázs


title: Effects of bacterial haemorrhagic septicemia on the immune response of Leiocassis longirostris (RNA-Seq)

overall_design: L. longirostris to Aeromonas hydrophila infection, Illumina sequencing was employed to identify changes in the mRNA and miRNA in spleen tissue


title: RNA sequencing analysis of gene expression in non-thermal atmospheric pressure plasma (NTAPP)-exposed and -unexposed human adipose tissue-derived stem cells (ASC) [Ex.1]

last: Song

summary: We analyzed the whole genome expression profile of NTAPP-exposed ASCs to understand the molecular mechanism of the activated proliferation of adult stem cells by NTAPP exposure.

overall_design: Total RNA was extracted from NTAPP-exposed and unexposed ASCs at 9 h and 24 h after NTAPP exposure for 50 sec every hour in 10 times.

first: Jeongyeon

last: Park

first: Donghwa

last: Suh

first: Hyunyoung

last: Lee

first: Hae

first: Gyoo

last: Kim

first: Jae-Seok

last: Roe

first: Sungbum

last: Han


title: Removing a Double Bond from Ceramides Ameliorates Insulin Resistance and Hepatic Steatosis

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

summary: Ceramides contribute to the lipotoxicity that underlies diabetes, hepatic steatosis, and heart disease. By genetically engineering mice, we deleted the enzyme dihydroceramide desaturase-1 (DES1) which inserts a conserved double bond into the backbone of ceramides and other predominant sphingolipids. Ablation of DES1 from whole animals, or tissue-specific deletion in the liver, and/or adipose tissue resolved hepatic steatosis and insulin resistance in mice caused by leptin deficiency or obesogenic diets. Mechanistic studies revealed new ceramide actions that promoted lipid uptake and storage and impaired glucose utilization, none of which could be recapitulated by (dihydro)ceramides that lacked the critical double bond. These studies suggest that inhibition of DES1 may provide a means of treating hepatic steatosis and cardiometabolic disorders.

overall_design: Livers isolated from Control and Liver specific Degs1 knockout mice following either normal chow or high fat diet feeding

first: Scott

last: Summers

first: Bhagirath

last: Chaurasia


title: Effects of bacterial haemorrhagic septicemia on the immune response of Leiocassis longirostris

status: Public on Jan 29 2020

first: Han

last: Zhao


title: Patient-Derived Xenografts of Upper Tract Urothelial Cell Carcinoma: a tool for precision medicine

city: NEW YORK

first: WENHUO

last: HU

email: huwenhuo@gmail.com, huw@mskcc.org

state: NEW YORK

address: 1275 YORK AVENUE

department: HOPP

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

summary: Treatment paradigms for patients with upper tract urothelial carcinoma (UTUC) are typically extrapolated from studies of bladder cancer despite their distinct clinical and molecular characteristics. A major hurdle to the advancement of UTUC research is the lack of disease-specific models. Here, we report the establishment of patient derived xenograft (PDX) and cell lines models that reflect the heterogeneity of the human disease. Models demonstrated high genomic concordance with the tumors from which they were derived with muscle-invasive tumors more likely to successfully engraft. Treatment of PDX with chemotherapy recapitulated responses observed in the patients. Analysis of a S310F HER2 mutant PDX suggested that an antibody drug conjugate targeting HER2 would have superior efficacy to HER2-selective kinase inhibitors. In sum, the biologic and phenotypic concordance between patient and PDXs suggests that these models could facilitate studies of intrinsic and acquired resistance and the development of personalized medicine strategies for UTUC patients.

overall_design: 80 samples of RNA-Seq

first: Kwanghee

first: Wenhuo

last: Hu

first: François

last: Audenet

first: Nima

last: Almassi

first: Aphrothiti

last: Hanrahan

first: Katie

last: Murray

first: Aditya

last: Bagrodia

first: Nathan

last: Wong

first: David

middle: B

last: Solit

first: Jonathan

last: Coleman


title: RF003-V3: Glucocorticoid-responsiveness correlates with an Interferon signature in Rheumatoid Arthritis Patients

first: Marian

last: Groot Koerkamp

summary:
Background: Pathogenesis of Rheumatoid arthritis (RA) is driven by monocytes and T-cells, which are heavily influenced by Glucocorticoids (GC). Although a cornerstone of RA-therapy, one third of RA-patients do not respond adequately to GC and the mechanisms of resistance have not yet been clarified.
Objective: To find differences in GC-working mechanism in RA-patients responding versus GC-resistant patients by gene expression profiling.
Methods: Patients were treated with 3x 1000mg Methylprednisolone. Before start (T0) and 24 hours (T24) after first treatment, CD14+ and CD4+cells were MACS-isolated At day 5, response was determined using the DAS28. Labeled cRNA from 5 GC-Responders and 5 Non-Responders was hybridized to Agilent 4x44K microarray chips. Differentially expressed genes between T0 and T24 were identified using MAANOVA, FWER (family wise error rate) correction and a >1.5 ratio cut-off. Gene Ontology was used for pathway analysis; Transcription-factors were identified via TRANSFAC. Selected genes were validated by qPCR.
Results: After 24 hours, 48 genes were exclusively changed in GC-Responders’ monocytes (CD4+cells: 19), 253 exclusively in Non-Responders (CD4+cells: 104) and 104 genes in both (CD4+: 18). In both cell-types a more pronounced down-regulation of interferon related genes was seen in Non-Responders, which was validated by qPCR in CD4+cells. At T24 higher expression of ERAP2 and FAM26F was seen in GC-Responders compared to Non-Responders. Several relevant transcription-factors were identified, among which LEF1in both cell types.
Conclusion: GC treatment resulted in stronger suppression of the interferon signature in Non-Responders. This might be disease-specific, but should prompt further investigation of GC-mechanism in several auto-immune diseases known for an interferon signature.

overall_design: PBMC from patients were obtained 24 hours after start of pulse therapy (T24) by density centrifugation of heparinized blood over Ficoll-Hypaque (Amersham Biosciences). CD14+ monocytes and CD4+ T-cells were isolated by positive (CD14-cells) or negative (CD4-cells) selection by AutoMACS (Miltenyi Biotec, Auburn, CA) and the respective isolation kits for CD14- or CD4- isolation (Miltenyi Biotec). Purity of the viable population assessed by flow cytometry was generally >90%.  RNA was isolated using the RNeasy Mini Kit from Qiagen (Venlo, The Netherlands).    All patient sample cRNAs were labeled with cy5,  and co-hybridized with reference cRNA, labeled with cy3 on Human Whole Genome Gene Expression Microarrays v1. Differences between responders (RF-iv-r-) and non-responders (RF-iv-nr-) were analyzed.

first: Ruth

last: Fritsch-Stork

first: Sandra

last: Cardoso

last: Koerkamp

first: Jasper

last: Broen

first: Kim

last: Wurff-Jacobs

first: Floris

middle: P

last: Lafeber

first: Johannes

middle: W

last: Bijlsma


title: Genome-wide DNA methylation profiling identifies two novel genes in cervical neoplasia

city: Montreal

last: Cheishvili

state: Quebec

address: 3655 Sir William Osler

country: Canada

institute: McGill

summary: Using a genome-wide DNA methylation profiling of 186 cervical samples from women with different CIN grades and well-characterized HPV genotyping, we identified novel methylation markers of epigenetic changes that discriminate accurately between clinically significant and transient cervical disease. In particular, a 2-gene DNA methylation classifier (ATP10A and HAS1) showed a promising ability to discriminate among pre-invasive cervical lesion grades. The identified markers are excellent candidates for future diagnostic or prognostic assays in cervical cancer screening.

overall_design: Examination of genome-wide DNA methylation profiling in 186 cervical samples from women with different CIN grades and well-characterized HPV genotyping

first: Mariam

last: El-Zein


title: RNA sequencing analysis of gene expression in non-thermal atmospheric pressure plasma (NTAPP)-exposed and -unexposed human adipose tissue-derived stem cells (ASC) [Ex.2]

first: Kiwon

last: Song

summary: We analyzed the whole genome expression profile of NTAPP-exposed ASCs to understand the molecular mechanism of the activation of adult stem cells proliferation by NTAPP exposure through nitirc oxide  response.

overall_design: ASCs were pretreated with culture medium alone, 30 uM carboxy-PTIO (CP) or 30 uM DETA-NONOate (NONOate) prior to NTAPP exposure. CP-treated and untreated cells were exposed to NTAPP for 50 s per h for 10 times, and collected at 9 h after NTAPP exposure to extract total RNA.

first: Jeongyeon

last: Park

first: Donghwa

last: Suh

first: Hyunyoung

last: Lee

first: Hae

first: Gyoo

last: Kim

first: Jae-Seok

last: Roe

first: Sungbum

last: Han


title: Cohesin removal reprograms mitotic gene expression upon mitotic entry [RNA-seq II]

first: Michael

last: Blower

summary: During mitosis, the genome is restructured to facilitate chromosome segregation, accompanied by dramatic changes in gene expression. However, the mechanisms that underlie mitotic transcriptional regulation are unclear. In contrast to transcribed genes, centromere regions retain transcriptionally active RNA Polymerase II (RNAPII) in mitosis. Here, we demonstrate that chromosome-localized cohesin is necessary and sufficient to retain active RNAPII on mitotic centromeres. Failure to remove cohesin from mitotic chromosome arms dramatically alters mitotic gene expression, and results in a failure to release elongating RNAPII and nascent transcripts from mitotic chromosomes. We propose that prophase cohesin removal is the key step in reprogramming gene expression as cells transition from G2 to mitosis, and is temporally coupled with chromosome condensation to coordinate chromosome segregation with changes in gene expression.

overall_design:
Control or WAPL-AID cells were arrested in mitosis and released into G1 for 2 hours. 3 replicates of each condition were analyzed. Nascent transcripts were labeled using EU, purified, and sequenced.

The file G2MG1EnsemblGenesCuffdiff.txt.gz includes re-analyzed data from GSE130558 in order to compare all values between two set of samples.

first: Carlos

last: Perea-Resa


title: Functional RNAi Screens Define Distinct Protein Kinase Vulnerabilities in EGFR-Dependent HNSCC Cell Lines

city: Cleveland

first: Jihye

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

summary: Cetuximab, an epidermal growth factor receptor (EGFR) inhibitory antibody, is an approved therapy for head and neck squamous cell carcinoma (HNSCC). Despite the EGFR dependency of HNSCC, cetuximab alone or combined with radio- or chemotherapy fails to yield long-term control or cures. Herein, we submitted EGFR-dependent HNSCC cell lines to RNAi-based functional genomics screens to identify, in an unbiased fashion, essential protein kinases for growth and survival as well as synthetic lethal targets for combined inhibition with EGFR inhibitors. MTOR and ERBB3 were identified as the highest ranking essential kinase hits. MTOR dependency was confirmed by distinct shRNAs and high sensitivity of the cell lines to AZD8055 while ERBB3 dependency was validated by shRNA-mediated silencing. Further, a synthetic lethal kinome shRNA screen with a pan-ERBB inhibitor, AZD8931, identified multiple components of the ERK MAPK pathway, consistent with ERK reactivation and/or incomplete ERK pathway inhibition in response to EGFR inhibitor monotherapy. As validation, distinct MEK inhibitors yielded synergistic growth inhibition when combined with the EGFR inhibitors, gefitinib and AZD8931. The findings identify ERBB3 and MTOR as important pharmacological vulnerabilities in HNSCC and support combining MEK and EGFR inhibitors to enhance efficacy of agents such as cetuximab.

overall_design: Five EGFR-dependent HNSCC cell lines treated 72 hours with DMSO or a pan-ERBB inhibitor, AZD8931 to identify synthetic lethal targets (a kinome-targeting shRNA library). Also, genomic DNA (gDNA) in the five cell lines and HN6 cell line was isolated from replicate plates (n=4, exception in JHU011 and UMSCC25) after 48 hrs and 14 days of culture post lentiviral transduction.

first: Trista

middle: K

last: Hinz

first: Emily

last: Kleczko

first: Aik-Choon

last: Tan

first: Lindsay

last: Marek

first: Katherine

last: Singleton

first: Jacob

last: Calhoun

first: Lynn

last: Heasley


title: Induction of the Germ-Cell Fate from Pluripotent Stem Cells in Cynomolgus Monkeys [bulk RNA-Seq]

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: In vitro reconstitution of germ-cell development from pluripotent stem cells (PSCs) has created key opportunities to explore the fundamental mechanisms underlying germ-cell development, particularly in mice and humans. Importantly, such investigations have clarified critical species differences in the mechanisms regulating mouse and human germ-cell development, highlighting the necessity of establishing an in vitro germ-cell development system in other mammals, such as non-human primates. Here, we show that multiple lines of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) in cynomolgus monkeys (Macaca fascicularis; cy) can be maintained stably in an undifferentiated state under a defined condition with an inhibitor for WNT signaling, and such PSCs are induced efficiently into primordial germ cell-like cells (PGCLCs) bearing a transcriptome similar to early cyPGCs. Interestingly, the induction kinetics of cyPGCLCs from cyPSCs is faster than that of human (h) PGCLCs from hPSCs, and while the transcriptome dynamics during cyPGCLC induction is relatively similar to that during hPGCLC induction, it is substantially divergent from that during mouse (m) PGCLC induction. Our findings delineate common as well as species-specific traits for PGC specification, creating a foundation for parallel investigations into the mechanism for germ-cell development in mice, monkeys and humans.

sample_organism:
Macaca fascicularis
Mus musculus

platform_organism:
Macaca fascicularis
Mus musculus

overall_design: RNAseq analysis during cynomolgus monkey PGCLC induction.

first: Yoshitake

last: Sakai

first: Tomonori

last: Nakamura

first: Ikuhiro

last: Okamoto

first: Sayuri

last: Gyobu-Motani

first: Hiroshi

last: Ohta

first: Tomoyuki

last: Tsukiyama

first: Chiduru

last: Iwatani

first: Hideaki

last: Tsuchiya

first: Masatsugu

last: Ema

first: Asuka

last: Morizane

first: Jun

last: Takahashi

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: Omics analysis with modeling  reveals global adaptation of Aspergillus niger to hypoxic condition

city: Shanghai

first: Weiqiang

last: Cao

state: Shanghai

address: 130 Meilong Road

institute: East China University of  Science and Technology

summary: Oxygen limitation is regarded as a useful strategy to improve enzyme production by mycelial fungus like Aspergillus niger. However, the intracellular metabolic response of A. niger to oxygen limitation is still obscure. To address this, the metabolism of A. niger was studied using multi-omics integrated analysis based on the latest GEMs (genome-scale metabolic model), including metabolomics, fluxomics and transcriptomics. Upon sharp reduction of the oxygen supply, A. niger metabolism shifted to higher redox level status, as well as lower energy supply, characterized by the accumulation of intermediates from the TCA cycle, down-regulation of genes for fatty acid synthesis and a rapid decrease of the specific growth rate. The gene expression of the glyoxylate bypass was activated, consistent with the increasing flux, which was assumed to reduce the NADH formation from TCA cycle and benefit maintenance of the cellular redox balance under hypoxic conditions. In addition, the relative fluxes of the EMP pathway were increased, which possibly relieved the energy demand for cell metabolism.

overall_design: Gene expression of 4 sampling times in triplicate during A.niger fermentation was examined.

first: Hongzhong

last: Lu


title: Microarray analysis of Med23 mutation in E9.5 mouse embryos relative to control littermates

city: Kansas City

first: Chris

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: Development of the vertebrate head is a complex and dynamic process, which requires integration of all three germ layers and their derivatives. Of special importance are ectoderm-derived cells that form the cranial placodes, which then differentiate into the cranial ganglia and sensory organs. Critical to a fully functioning head, defects in cranial placode and sensory organ development can result in congenital craniofacial anomalies. In a forward genetic screen aimed at identifying novel regulators of craniofacial development, we discovered an embryonically lethal mouse mutant, snouty, which exhibits malformation of the facial prominences, cranial nerves and vasculature. The snouty mutation was mapped to a single nucleotide change in a ubiquitously expressed gene, Med23, which encodes a subunit of the global transcription co-factor complex, Mediator. This experiment examines transcriptional differences between Med23 mutant mice and their wt littermates at embryonic day 9.5.

overall_design: Two wt and three Med23 mutant embryos are compared across 6 microarrays using a dye swap strategy. The third mutant is compared to a mixture of the 1st and 2nd wt replicates.

first: Soma

last: Dash

first: Shachi

last: Bhatt

first: Lisa

last: Sandell

first: Youngwook

last: Ahn

first: Robb

last: Krumlauf

first: Paul

last: Trainor


title: Gene expression in a mouse model of Pantothenate Kinase-Associated Neurodegeneration

city: Memphis

first: Jackowski

last: Suzanne

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: A mouse model lacking systemic expression of Pank1 together with neuronal deletion of Pank2 was generated and revealed a developmental requirement for CoA that, when deficient, resulted in abnormal motor behavior preceding early death.  Neuronal Pank2 expression in Pank1-/-Syn-Pank2-/- double knockout mice (dKO) decreased starting at P9-11 and brain CoA levels did not increase subsequently, in contrast to wild-type matched control animals.  The Pank1-/-Syn-Pank2-/- dKO mice developed a forelimb deformity and abnormal gait behavior, similar to PKAN patients, and lost weight when brain CoA became depressed relative to wild-type levels.  Comparative gene expression analysis revealed significant alteration of a relatively small selection of genes, including reduction of gene transcripts affecting heme and hemoglobin synthesis together with upregulation of gene transcripts related to the response to oxygen/glucose deprivation.

overall_design: Compare gene expression of knockout mice vs control at days 10 and 20, segregated for sex.

first: Jiangwei

last: Yao

first: Suzanne

last: Jackowski


title: Cohesin removal reprograms mitotic gene expression upon mitotic entry

city: Boston

first: Michael

last: Blower

address: 185 Cambridge St CPZN-7250

institute: Massachusetts General Hospital

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

overall_design: Refer to individual Series


title: Immunological fingerprints of controllers developing neutralizing HIV-1 antibodies

city: Cambridge

first: Ce

last: Gao

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

summary: Induction of broadly neutralizing antibodies (bnAbs) is highly desired for an effective vaccine against HIV-1. Typically, bnAbs develop in patients with high viremia, but can also evolve in some untreated HIV-1 controllers with low viral loads. Here, we identify a subgroup of neutralizer-controllers characterized by myeloid DC (mDCs) with a distinct inflammatory signature and a superior ability to prime T follicular helper (Tfh)-like cells in an STAT4-dependent fashion. This distinct immune profile is associated with a higher frequency of Tfh-like cells in peripheral blood (pTfh) and an enrichment for Tfh-defining genes in circulating CD4+ T cells. Correspondingly, Monocytes from this neutralizer controller subgroup upregulate genes encoding for chemotaxis and inflammation, and secrete high levels of IL-12 in response to TLR stimulation. Together, our results suggest multi-compartment immune networks between mDCs, Tfh and Monocytes that might facilitate development of bnAbs in a subgroup of HIV-1 controllers.

overall_design: RNAseq study from 4 different immune populations: Dendritic cells, CD4 T cells, Monocytes and B cells from two groups of HIV-1 controllers classified by the presence or the absence of  a broader breadth of neutralizing antibodies against HIV-1 on plasma.

first: Enrique

last: Martin-Gayo

first: Hsiao-Rong

last: Chen

first: Zhengyu

last: Ouyang

first: Dhohyung

last: Kim

first: Kellie

middle: E

last: Kolb

first: Alex

last: Shalek

first: Brue

last: Walker

first: Mathias

last: Lichterfeld

first: Xu

last: Yu


title: Next Generation Sequencing Facilitates Quantitative Analysis of human breast cancer cell T47D and T47D-TR Transcriptomes

city: chongqing, China

first: qianni

last: jin

address: 1# Yixueyuan Road, Yuzhong District, Chongqing 400016, P.R. China

institute: chongqing medical university

summary: To gain new insight into the resistance to hormonal therapy in breast cancer, we generated a tamoxifen-resistant human breast cancer cell line T47D-TR by exposing estrogen-sensitive cell line T47D to increasing concentrations of 4-hydroxy tamoxifen (4-OHT) and identified its resistance with different ways. What we interested is the underlying mechanisms of breast cancer tamoxifen resistance which was not reported yet.Here, we detect the RNA sequence of both the two cell lines hoping to find some evidence.

overall_design: The mRNA profiles of T47D and T47D-TR cells were generated by deep sequencing, in triplicate.

first: Mengjia

last: He

first: Tingmei


title: RNA-Seq analysis of genes and pathways involved in the TGF-β-driven transformation of fibroblasts to myofibroblasts

city: Bruce

first: Reena

last: Ghildyal

state: ACT

address: Kirinari St

country: Australia

institute: University of Canberra

summary:
Background: Asthma is the most common chronic lung disease in children and young adults worldwide. Airway remodelling (including increased fibroblasts and myofibroblasts in airway walls due to chronic inflammation) differentiates asthmatic from non-asthmatic airways. The increase in airway fibroblasts and myofibroblasts occurs via epithelial to mesenchymal transition (EMT) where epithelial cells lose their tight junctions and are transdifferentiated to mesenchymal cells, with further increases in myofibroblasts occurring via fibroblast-myofibroblast transition (FMT). Transforming growth factor (TGF)-β is the central EMT- and FMT-inducing cytokine. In this study, we have used next generation sequencing to delineate the changes in the fibroblast transcriptome induced by TGF-β treatment in both the short term and after differentiation into myofibroblasts, to gain an understanding of the contribution of TGF-b induced transdifferentiation to the asthmatic phenotype. The data obtained from RNAseq analysis was confirmed by quantitative PCR (qPCR).
Results: As expected, we found that genes coding for intermediates in the TGF-β signalling pathways (SMADs) were differentially expressed after treatment, and genes involved in cytoskeletal pathways (FN1, LAMA, ITGB1) were differentially expressed in myofibroblasts compared to fibroblasts. Importantly, genes that were previously shown to be changed in asthmatic lungs (ADAMTS1, DSP, TIMPs, MMPs) were differentially expressed in myofibroblasts, strongly suggesting that TGF-β mediated differentiation of fibroblasts to myofibroblasts may underlie important changes in the asthmatic airway. We also identified new signalling pathways (AKT, PTEN) that are changed in myofibroblasts compared to fibroblasts.
Conclusion: We have found a significant number of genes that are altered after differentiation of fibroblasts into myofibroblasts by TGF-β treatment, many of which were expected or predicted. However, we also identified novel genes and pathways that were affected after treatment of fibroblasts with TGF-β, which suggests additional pathways that that are activated during the transition between fibroblasts and myofibroblasts, and may contribute to the asthma phenotype.

overall_design: cDNA profiles from WI-38 fibroblasts treated with or without TGFb and collected on day 1 and day 20 after treatment. Triplicate samples were analysed for each timepoint and treatment (12 samples in total).

first: Erin


title: FAMIN is a multifunctional purine enzyme enabling the purine nucleotide cycle (Macrophage RNA Seq dataset)

first: Gavin

last: Sewell

state: Cambridgeshire

address: Puddicombe Way

department: Jeffrey Cheah Biomedical Centre, University of Cambridge

country: United Kingdom

institute: Cambridge Institute of Therapeutic Immunology and Infectious Disease

summary: FAMIN (LACC1, C13orf31) loss-of-function causes systemic juvenile idiopathic arthritis and very early-onset inflammatory bowel disease, while a common I254V substitution results in hypomorphic function and increases susceptibility to Crohn’s disease and leprosy. In this study, we compare the mRNA transcriptional profiles of M0, M1 and M2-polarised bone marrow-derived macrophages from mice engineered at their endogenous locus to express human non-risk (Faminp.254I), risk (Faminp.254V) and monogenic (Faminp.284R) disease variants.

overall_design: Bone marrow-derived macrophages were cultured from Faminp.254I (n=5), Faminp.254V (n=5) and Faminp.284R (n=5) mice, polarised to M0, M1 or M2 phenotype, and transcriptional profiles compared. Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, 74104) in accordance with the manufacturer's instructions. Strand-specific single-end sequencing libraries were prepared using TruSeq Stranded mRNA kit (Illumina Inc.). Eleven libraries were sequenced at a time in one lane on an Illumina HiSeq4000. FastQ files were quality-checked (FastQC) and any residual adaptor sequences were removed (Cutadapt). Reads were then aligned to the reference genome (mm10, UCSC) using STAR.

first: Lea

last: Haag

first: M. Zaeem

last: Cader

first: Jana-Fabienne

last: Ebel

first: Philip

last: Rosenstiel

first: Arthur

last: Kaser


title: Myc and loss of p53 cooperate to drive formation of choroid plexus carcinoma

first: Yong-Dong

last: Wang

address: 262 Danny Thomas Pl, MS1135

summary: Choroid plexus carcinoma (CPC) is a rare brain tumor that occurs most commonly in very young children, and has a dismal prognosis despite intensive therapy. Improved outcomes for CPC patients depend on a deeper understanding of the mechanisms underlying the disease. We developed transgenic models of CPCs by activating the Myc oncogene and deleting the Trp53 tumor suppressor gene in murine neural stem cells or progenitors. Murine CPCs resemble their human counterparts at a histological level, and like the hypodiploid subset of human CPCs, exhibit multiple whole-chromosome losses, particularly of chromosomes 8, 12 and 19. Analysis of murine and human CPC gene expression profiles and copy number changes reveals altered expression of genes involved in cell cycle, DNA damage response and cilium function. Finally, high throughput drug screening identifies small molecule inhibitors that decrease the viability of CPCs. These models will be valuable tools for understanding the biology of choroid plexus tumors and for testing novel approaches to therapy.

overall_design: Profiling the copy number changes in mouse normal choroid plexus, choroid plexus papilloma, choroid plexus carcinoma.

first: Jun

first: Brian

last: Murphy

first: Martine

middle: F

last: Roussel

first: Richard

last: Gilbertson

first: Robert

last: Wechsler-Reya


title: Expression data from MM231 and MM231-FGD5-cas9 breast cancer cells

status: Public on Jan 27 2020

city: Beijing

first: Tingting

last: Zhang

address: Nanwei street

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

summary:
To identify the differiational genes and pathways in MM231 and MM231-FGD5-cas9, we examined the microarray gene expression profile of MM231 breast cancer cells vs FGD5-cas9 cells.
Ectopic expression or activation of EGFR is found in most TNBCs, and EGFR inhibitors can suppress TNBC growth in vitro. However, these agents exhibit limited efficacy in TNBC patients, possibly due to the nonkinase oncogenic functions of EGFR and the compensatory effects of other oncogenic activities following anti-EGFR therapy. Here, we identified a positive correlation between EGFR and FGD5 expression in TNBC samples. FGD5 deletion attenuated TNBC initiation and progression by decreasing EGFR stability and expression. Moreover, the proteins involved in mutual compensation of EGFR signaling were significantly downregulated in FGD5-deleted TNBC cells. Mechanistically, FGD5 interacted with EGFR to maintain EGFR stability by impeding EGFR ubiquitylation and degradation mediated by the E3 ligase ITCH; disrupting the FGD5-EGFR interaction accelerated EGFR degradation and produced robust anti-TNBC activity. Our study shows that targeted degradation of EGFR through disrupting the FGD5-EGFR interaction is a promising therapeutic strategy for the TNBC subtype of breast cancer.

overall_design: Total RNA of MM231 and MM231-FGD5-cas9 breast cancer cells were obtained, and RNA quantity and quality were measured by NanoDrop ND-1000. RNA microarrays were performed.

first: Ke

last: Li


title: Transcriptomic and barrier responses of human airway epithelial cells exposed to cannabis smoke with and without LABA/GC intervention

city: Waterloo

first: Jennifer

middle: A.

last: Aguiar

state: ON

address: 200 University Avenue East

department: Biology

institute: University of Waterloo

summary:
Purpose: Globally, many jurisdictions are legalizing or decriminalizing cannabis, creating a potential public health issue that would benefit from experimental evidence to inform policy, government regulations, and user practices. Tobacco smoke exposure science has created a body of knowledge that demonstrates the conclusive negative impacts on respiratory health; similar knowledge remains to be established for cannabis. To address this unmet need, we performed in vitro functional and transcriptomic experiments with a human airway epithelial cell line (Calu-3) exposed to cannabis smoke, with tobacco smoke as a positive control.

Results: We demonstrate that cannabis smoke induced functional and transcriptional responses that overlapped with tobacco smoke. Ontology and pathway analysis revealed that cannabis smoke induced DNA replication and oxidative stress responses. Functionally, cannabis smoke impaired epithelial cell barrier function, antiviral responses, and increased inflammatory mediator production. Our study reveals striking similarities between cannabis and tobacco smoke exposure on impairing barrier function, suppressing antiviral pathways, potentiating of pro-inflammatory mediators, and inducing oncogenic and oxidative stress gene expression signatures. LABA/GC intervention in airway epithelial cells exposed to cannabis smoke reduces levels of pro-inflammatory (CXCL8) and antiviral (CXCL10) mediators, while transcriptomic signatures of neutrophil mediated immunity and oxidative stress remain elevated.

Conclusions: Collectively our data suggest that cannabis smoke exposure is not innocuous and may possess many of the deleterious properties of tobacco smoke, warranting additional studies to support public policy, government regulations, and user practices.

overall_design: mRNA profiles of Calu-3 cells exposed to 10% cannabis smoke extract (CSE) with and without formoterol/budesonide intervention compared to 10% tobacco smoke extract (TSE) and control (both also with and without formoterol/budesonide intervention) were generated by deep sequencing, with 4 biological replicates per exposure, using Illumina 2500.

middle: A

first: Ryan

last: Huff

first: Wayne

last: Tse

first: Martin

last: Stampfli

first: Brendan

last: McConkey

first: Andrew

last: Doxey

first: Jeremy

last: Hirota


title: Combined proteomics and miRNomics of a glioblastoma immunotherapy cohort reveal resistance factor candidates and potential counterstrategies

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

summary: Glioblastoma is the most prevalent and aggressive brain cancer. With a median overall survival of ~15-20 months under standard therapy, novel treatment approaches are desperately needed. A recent phase II clinical trial with a personalized immunotherapy based on tumor lysate-charged dendritic cells (DCs), however, failed to prolong survival. Here, we investigated tumor tissue from patients from this trial to explore glioblastoma (immuno)resistancesurvival-related factors.  and strategies to overcome them. We followed an innovative approach of combining mass spectrometry-based quantitative proteomics (n=36) with microRNA sequencing plus RT-qPCR (n=38). Protein quantification identified e.g. huntingtin interacting protein 1 (HIP1), retinol binding protein 1 (RBPP1), ferritin heavy chain (FTH1) and focal adhesion kinase 2 (FAK2) as resistance factor candidates. MicroRNA analysis identified miR-216b, miR-216a, miR-708 and let-7i as molecules potentially associated with overcoming resistancefavourable tissue characteristics as they were enriched in patients with a comparably longer survival. In silico target prediction and subsequent analyses indicated focal adhesion as a pathway of interest.  Taken together, we here mapped possible drivers of glioblastoma outcome under immunotherapy’s (immuno)resistance in one of the largest DC vaccination tissue analysis cohorts so far – demonstrating usefulness and feasibility of combined proteomics/miRNomics approaches. Future research should investigate agents that sensitize glioblastoma to (immuno)therapy – potentially building on insights generated here.

overall_design: Examination of microRNA profiles in glioblastomas of long-term and short-term surviors under immuno- and conventional therapy

first: Friedrich

last: Erhart

first: Hannes

last: Hahne

first: Johanna

last: Buchroithner

first: Cheng

last: Meng

first: Simone

last: Klingenbrunner

first: Rene

last: Reitermaier

first: Katrin

last: Fischhuber

first: Susanna

last: Skalicky

first: Walter

last: Berger

first: Sabine

last: Spiegl-Kreinecker

first: Daniela

last: Lötsch

first: Gerda

last: Ricken

first: Bernhard

last: Kuster

first: Adelheid

last: Wöhrer

first: Georg

last: Widhalm

first: Johannes

last: Hainfellner

first: Thomas

last: Felzmann

first: Alexander

last: Dohnal

first: Christine

last: Marosi

first: Carmen

last: Visus


title: RNA-seq control (sgNT) and TLE3KO (sgTLE3) cells treated with 10 uM enzalutamide or vehicle

city: Amsterdam

first: Sander

last: Palit

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

summary: To investigate the transcriptional consequences of TLE3 loss in the presence/absence of AR inhibitor enzalutamide in prostate cancer cells, the transcriptomes of WT and TLE3KO cells treated with vehicle or enzalutamide (10 uM) were compared. .

overall_design: WT and TLE3KO LNCaP cells treated with 10 uM enzalutamide or vehicle for 5 days (3 replicates)

first: S

first: D

last: Vis

first: C

last: Lieftink


title: Transcriptional profile of recurrent breast cancer cells with RIPK3 silencing

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Dr., 2133 CIEMAS Box 3382 DUMC

department: Center for Genomic and Computational Biology

institute: Duke University

summary: To understand to role of RIPK3 during tumor recurrence, we performed RNAseq to study the transcriptional response of mouse recurrent breast cancer cells to RIPK3 knockdown.

overall_design: Recurrent tumor cells isolated and expanded from Her2 driven murine model of MTB/TAN tumor were silenced by two RIPK3 shRNA for RNAseq.

first: Chao-Chieh

last: Lin


title: Importance of superoxide dismutases A and M for protection of Staphylococcus aureus in the oxidative stressful environment of the cystic fibrosis airways

city: Braunschweig

first: Diego

last: Chaves-Moreno

address: inhoffenstrasse 7

department: Department of Medical Microbiology (MMIK)

country: Germany

institute: Helmholtz Centrum for Infection Research

summary: Staphylococcus aureus is one of the earliest pathogens that persists the airways of cystic fibrosis (CF) patients and contributes to increased inflammation and decreased lung function. In contrast to other staphylococci, S. aureus possesses two superoxide dismutases (SODs), SodA and SodM, with SodM being unique to S. aureus. Both SODs arm S. aureus for its fight against oxidative stress, a byproduct of inflammatory reactions. Despite complex investigations it is still unclear, if both enzymes are crucial for the special pathogenicity of S. aureus. To investigate the role of both SODs during staphylococcal persistence in CF airways, we analyzed survival and gene expression of S. aureus CF isolates and laboratory strains in different CF-related in vitro and ex vivo settings. Bacteria located in inflammatory and oxidized CF sputum transcribed high levels of sodA and sodM. Especially expression values of sodM were remarkably higher in CF sputum than in bacterial in vitro cultures. Interestingly, also S. aureus located in airway epithelial cells expressed elevated transcript numbers of both SODs, indicating that S. aureus is exposed to oxidative stress at various sites within CF airways. Both enzymes promoted survival of S. aureus during PMN killing and seem to act compensatory, thereby giving evidence that the interwoven interaction of SodA and SodM contributes to S. aureus virulence and facilitates S. aureus persistence within CF airways

overall_design: RNAseq from sputum samples of CF patients collected during their clinical visits

first: Janina

last: Treffon

first: Silke

last: Niemann

first: Dietmar

middle: H

last: Pieper

last: Vogl

last: Roth

first: Barbara

last: Kahl


title: MYCN Drives Disparate Medulloblastoma from Human Embryonic and iPSC-Derived Stem Cells [array]

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

institute: Uppsala University

summary: How tumors develop or respond to therapies vary significantly among species. Here we report that medulloblastoma (MB) the most frequent malignant childhood brain tumor can develop from human hindbrain neuro-epithelial stem (hbNES) cells or induced pluripotent stem cell (iPSC)-derived NES (NES) cells via MYCN overexpression in mice. NES tumors developed fast with leptomeningeal dissemination, while hbNES tumors formed significantly later with no dissemination. By using large cohorts of MB patients we show that tumors resemble a common subgroup of Sonic Hedgehog (SHH) MBs and that pluripotency and mTOR signaling correlate with poor prognosis. To conclude, both iPSC-derived and embryonic NES cells can be transformed into distinct humanized MB models valuable for identifying better diagnostic markers and drug targets.

overall_design: Total of 18 snap frozen tumor model biopsies were profiled for DNA methylation.

first: Matko

last: Čančer

first: Sonja

last: Hutter

first: Gabriela

last: Rosén

first: Anders

last: Sundström

first: Jignesh

last: Tailor

first: Alexandra

last: Garancher

first: Magnus

last: Essand

first: Robert

last: Wechsler-Reya

first: Anna

last: Falk

first: Holger

last: Weishaupt


title: Adipose tissue mediate insulin resistance in obesity mice through the exosomal transfer of miR-141-3p into hepatocytes

city: Guangzhou

first: Shiying

last: Dang

address: Institute of Biomedicine, Department of cellular Biology, Jinan University, 601 Huangpu Ave West, Guangzhou 510632, Guangdong, People’s Republic of china

institute: Institute of Biomedicine & Dept. Cellular Biology, Guangdong Province Key Lab of Bioengineering Medicine, Jinan University

summary: Exosomes which are nano-vesicles and released from living cells, have attracted more attention as an important mediator for cell-to-cell communication. Given that obesity often causes insulin resistance, it is significant to test whether exosomes derived from obesity adipose tissue possess any capacity in regulating insulin sensitivity. In this study we purified exosomes from the adipose tissue. Exosomes derived from ob/ob mice (Ob-exosomes) and B6 mice fed a high-fat diet (HFD-exosomes) displayed similar size and molecular maker to those originated from the normal B6 mice (WT-exosomes), but their regulatory role in insulin sensitivity was opposite. Abundant exosomal miRNAs were detected by the Next Generation Sequencing. Ob-exosomes encapsulated the lower levels of miR-141-3p compared to WT-exosomes, furthermore, miR-141-3p can be effectively delivered into AML12 cells accompanied by the absorption of Ob-exosomes and WT-exosomes. But the absorption of miR-141-3p from adipose tissues to AML12 cells could be blocked by GW4869, an inhibitor of exosome biogenesis and release. Importantly, the exosomal miR-141-3p functionally down-regulated its target gene Pten expression in AML12 cells, and the knockdown of miR-141-3p inhibited the insulin response and glucose uptake in AML12 cells, however Ob-exosomes-mediated inhibitory effects on insulin function disappeared after overexpression of miR-141-3p. These data indicate that the absorption of exosomes released from obesity adipose tissue including lower level of miR-141-3p than healthy adipose tissue into hepatocytes can significantly inhibit the insulin sensitivity and glucose uptake. Thus, our study may certify a novel mechanism that the secretion of “harmful” exosomes from obesity adipose tissues cause insulin resistance.

overall_design: exosomal miRNA profiles of 4 month wild type (WT), ob/ob, HFD mice adipose tissue were generated by high throughout sequencing, using illumina HiSeqTM2500.

first: Yi

last: Ma


title: miRNA profiling of CLL

city: New Delhi

first: Ritu

last: Gupta

state: Delhi

address: Dr. B.R.A.IRCH, Ansari Nagar

department: Laboratory Oncology

country: India

institute: All India Institute of Medical Sciences, New Delhi

summary: The miRNA profiles of CLL patients were compared with normal controls.

overall_design: A total of 28 cases of CLL and 2 pooled male and female controls were recruited as experiment cohort.

first: Anubha

first: Gurvinder

last: Kaur

first: Nilesh

last: Chaturvedi

first: Lata

last: Rani


title: Expression data from MCF7 cells treated with RITA or Nutlin

city: Solna

first: Gema

last: Sanz Santos

state: Stockholm

address: Nobels väg 16

institute: Karolinska Institutet

summary: We used microarrays to detail the global programme of gene expression underlying p53 activation

overall_design: MCF7 cells were treated either with RITA or Nutlin during 8 hr for RNA extraction and hybridization on Affymetrix microarrays.

first: G

last: Sanz


title: Disruption of the MBD2-NuRD complex but not MBD3-NuRD induces high level HbF expression in human adult erythroid cells

city: Richmond

first: Gordon

last: Ginder

address: 401  College St

department: Massey Cancer Center

institute: Virginia Commonwealth University

summary: As high fetal hemoglobin (HbF) levels ameliorate the underlying pathophysiologic defects in sickle cell anemia and β-thalassemia, understanding the mechanisms that enforce silencing of HbF postnatally offers the promise of effective molecular therapy.  Depletion of Methyl cytosine Binding Domain protein 2 (MBD2) causes a 10-20 fold increase in γ-globin gene expression in adult β-YAC transgenic mice. To determine the effect of MBD2 depletion in human erythroid cells, CRISPR-Cas9 mediated knockout (KO) was carried out in Human Umbilical cord Derived Erythroid Progenitor-2 (HUDEP-2) erythroid cells resulting in γ/γ+β mRNA levels of ~50% and ~40% HbF by HPLC. In contrast, MBD3 KO had no appreciable effect on γ-globin mRNA. Knockdown (Kd) of MBD2 in primary adult erythroid cells consistently increased γ/γ+β mRNA ratios by ~10-fold resulting in ~30-40% γ/γ+β mRNA levels and a corresponding increase in γ-globin protein.  MBD2 exerts its repressive effects through recruitment of the CHD4 chromatin remodeling component of NuRD through a coiled-coil (CC) domain, and the histone deacetylase (HDCC) component via an intrinsically disordered region (IDR). Enforced expression of wild-type MBD2 in MBD2KO HUDEP-2 cells caused a 5-fold decrease in γ-globin mRNA while neither the CC mutant nor the IDR mutant MBD2 proteins had an inhibitory effect.  Consistently, co-immunoprecipitation assays showed that the CC and IDR domain mutations disrupt NuRD complex formation by dissociating the CHD4 and HDCC domains respectively.  These results establish MBD2-NuRD as a major silencer of HbF in human erythroid cells and point to the CC and IDR domains of MBD2-NuRD as potential therapeutic targets.

overall_design: RNA-seq was performed on scrambled gRNA control and MBD2 knockout HUDEP-2 cells before and after erythroid differentiation in order to investigate the effects of MBD2 depletion on gene expression in a human erythroid cell model system.  3 replicates were performed for each of these 4 conditions, for a total of 12 samples.

first: Alexander

last: Azzo

first: Xiaofei

last: Yu

first: Mikhail

last: Dozmorov


title: Single cell analysis reveals human cytomegalovirus drives latently infected cells towards an anergic-like monocyte state

status: Public on Jan 26 2020

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: Human cytomegalovirus (HCMV) causes a lifelong infection through establishment of latency. Although reactivation from latency can cause life-threatening disease, our molecular understanding of HCMV latency is incomplete. Here we use single cell RNA-seq analysis to characterize latency in monocytes and hematopoietic stem and progenitor cells (HSPCs). In monocytes, we identify host cell surface markers that enable enrichment of latent cells harboring higher viral transcript levels, which can reactivate more efficiently, and are characterized by an intrinsic reduced immune response that is critical for viral gene expression. Significantly, in latent HSPCs, viral transcripts could be detected only in monocyte progenitors and were also associated with reduced immune-response. Overall, our work demonstrates that regardless of the developmental stage in which HCMV infects, HCMV drives hematopoietic cells towards a weaker immune-responsive monocyte state and that this anergic-like state is crucial for the virus ability to express its transcripts and to eventually reactivate.

overall_design: MARS-Seq bulk protocol was used for monocytes-derived macrophages, monocytes FACS-sorted according to the levels of DC74, and monocytes with and without treatment by ruxolitinib, all infected with HCMV.

first: Miri

last: Shnayder

first: Aharon

last: Nachshon

first: Biana

last: Bernstein

last: Fein

first: Batsheva

last: Rozman

first: Emma

last: Poole

first: Michael

last: Lavi

first: Selmir

last: Avdic

first: Emily

last: Blyth

first: David

last: Gottlieb

first: Allison

last: Abendroth

first: Barry

last: Slobedman

first: John

last: Sinclair

first: Michal

last: Schwartz


title: Signal-Transducing Adaptor Protein-2 Governs Recovery of B Lineage Lymphocytes during hematopoietic stress.

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Signal-transducing adaptor protein-2 (STAP-2) was discovered as a c-fms/M-CSFR interacting protein and subsequently found to function as an adaptor of signaling or transcription factors. These include STAT5, MyD88 and IB kinase (IKK) in macrophages, mast cells and T cells. There is additional information about roles in several types of malignant diseases including chronic myeloid leukemia, but none concerning B lineage lymphocytes. We have now exploited gene targeted and transgenic mice to address this issue and learned that it is not required under normal, steady-state conditions. However, recovery of B cells following transplantation was augmented in the absence of STAP-2. This appeared to be restricted to cells of this lineage and myeloid rebound was unremarkable. Furthermore, all hematological parameters were normal once recovery from transplantation was complete. Overexpression of STAP-2 specifically in lymphoid cells resulted in reduced numbers of late-stage B progenitors within bone marrow. While numbers of mature peripheral B and T cells were unaffected, recovery from sub-lethal irradiation or transplantation was dramatically reduced. LPS normally suppresses B precursor expansion in response to interleukin 7, but STAP-2 deficiency made them more resistant. Preliminary RNA-Seq analyses indicate many signaling pathways in B progenitors are STAP-2 dependent. These findings suggest STAP-2 modulates formation of B lymphocytes in demand conditions. Further study of this adapter protein could suggest ways to speed recovery of humoral immunity following chemotherapy or transplantation.

overall_design: To determine the molecular basis for the inefficient B lymphopoiesis in STAP-2 Tg BM, transcriptome analyses were used to identify the pathways regulated by STAP-2 under hematological stress. We evaluated the global gene expression profile of pre-B cells derived from WT and Tg BM under steady-state as well as WT and KO BM 1 month after transplantation by RNA-seq experiments.

first: Michiko

last: Ichii


title: Lineage-specific Transcription Factors suppress activation of Hepatic Stellate Cells during Liver Fibrosis

city: La Jolla

first: Tatiana

last: Kisseleva

address: 9500 Gilman Dr

department: School of Medicine

institute: UCSD

summary: Development of liver fibrosis is associated with activation of quiescent Hepatic Stellate Cells (qHSCs) into Collagen Type I-producing myofibroblasts (aHSCs). Cessation of liver injury often results in fibrosis resolution and inactivation of aHSCs/myofibroblasts into a quiescent-like state (iHSCs). To identify the molecular drivers of these HSC phenotypes, we investigated the global gene expression and epigenetic changes in H3K4me2 and H3K27ac marks of primary murine and human HSCs. Motif enrichment identified ETS1/2, GATA4/6, and IRF1/2 transcription factors (TFs) as putative regulators of the HSC lineage identity in murine and human HSCs. shRNA-knockdown of these TFs resulted in marked upregulation of fibrogenic and inflammatory genes and a loss of HSC-specific phenotype in targeted murine HSCs. In support, in vivo HSC-specific ablation of GATA4, GATA6, and ETS1, and ETS1 target genes NF1 (neurofibromin 1) and PPARγ exacerbated development of carbon tetrachloride (CCl4)-induced liver fibrosis in LratΔGATA6, LratETS1+/-, LratΔNF1, and LratΔPPARγ mice (vs wt littermates), but only LratΔGATA6, and LratΔPPARγ mice exhibited a defect in fibrosis resolution due to the lack of HSC inactivation. Therapeutic administration of a PPARγ agonist accelerated regression of liver fibrosis in CCl4-induced wt, but not in LratΔPPARγ mice, suggesting that PPARγ signaling in HSCs is critical for HSC inactivation and regression of liver fibrosis. Common transcription factors determine the phenotype of mouse and human HSCs. Similar to murine HSCs, human aHSCs can revert into a quiescent-like, inactivated phenotype. GATA4, GATA6, and PPARγwere identified as an important driver of human HSC inactivation.

overall_design: Expression/epigenetic profiling of hepatic stellate cells by RNA-seq and ChIP-seq for H3K27ac and H3K4me2

first: Xiao

last: Liu

first: Sara

last: Rosenthal

first: Christopher

last: Benner


title: RNA-seq analysis of WT and CARD11 point mutation mouse spleen B cells

city: Shanghai

first: Wei

last: Lv

address: 320 Yueyang Road

institute: Shang Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

summary: In order to investigate the molecular mechanism of CARD11 in immune cell system, we applied the RNA-seq analysis using RNA isolated from WT and CARD11 mutant (E134G and K215M) mouse spleen B cells. By comparing the transcriptome files, we found some different expressed gene involved in due to the CARD11 point mutation and in vitro RT-PCR had confirmed this result.

overall_design: Compare the transcriptome profiling of WT and CARD11 mutant spleen B cells to investigate the different among them.

first: Zheng

last: Wei


title: MYCN Drives Disparate Medulloblastoma from Human Embryonic and iPSC-Derived Stem Cells [seq]

first: Fredrik

last: Swartling

overall_design: In total 75 samples were profiled for RNA expression; 7 embryonic and iPS-derived stem cell lines, 1 pre-tumor cell line,  37 snap frozen tumor model biopsies, 10 tumor model derived cell lines, 20 PDX tumor biopsies. Total 16 samples were profiled for DNA methylation; 6 embryonic and iPS-derived stem cell lines,  3 snap frozen tumor model biopsies, 6 tumor model derived cell lines

first: Matko

last: Čančer

first: Sonja

last: Hutter

first: Gabriela

last: Rosén

first: Anders

last: Sundström

first: Jignesh

last: Tailor

first: Alexandra

last: Garancher

first: Magnus

last: Essand

first: Robert

last: Wechsler-Reya

first: Anna

last: Falk

first: Holger

last: Weishaupt


title: Interrogation of Enhancer Function by Enhanced CRISPR Epigenetic Editing

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

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

overall_design: Refer to individual Series


title: Establishment of novel atopic dermatitis model by Nestin-cre mediated Ikk2 deficiency

city: Saga

first: Satoshi

last: Nunomura

address: 5-1-1 Nabeshima

department: Department of Biomolecular Sciences

institute: Saga Medical School

summary: To generate novel atopic dermatitis model, we used Nestin-cre mediated Ikk2FL/FL mice. Nestincre-mediated conditional knockout mice of Ikk2 gene were generated by crossing female Ikk2FL/FL mice to male Nestin-cre;Ikk2FL/+mice. Nestin-cre;Ikk2FL/FL mice spontaneously develop chronic AD-like skin inflammation and severe pruritus. We further performed Cap analysis of gene expression (CAGE) to elucidate transcriptional profiles in lesional skin of Nestin-cre;Ikk2FL/FL mice.

overall_design: Four lesional and four non-lesional facial skins were prepared from 4 week-old Ikk2FL/FL;Nestin-cre and control mice, respectively.

first: Kenji

last: Izuhara

first: Isao

last: Kitajima


title: Rimonabant suppresses RNA transcription of hepatitis B virus by inhibiting HNF4α

first: Daisuke

last: Okuzaki

summary: The emergence of drug-resistant viruses against nucleot(s)ide analogs (NAs), which are the main treatment for chronic hepatitis B virus (HBV) infection, has become a problem. To discover novel anti-HBV compounds with a low risk of emergence of drug-resistant viruses, we performed screening of a G protein-coupled receptor-associated compound library and identified Rimonabant as a candidate. Transcriptome analysis of Rimonabant-treated primary hepatocytes by RNA sequencing revealed that the transcriptional activity of HNF4α, which is known to stimulate viral RNA synthesis, was depressed.

overall_design: Transcriptome analysis of PHH treated with DMSO or Rimonabant (Rimo) upon infection with HBV.

first: Asuka

last: Sato

first: Takasuke

last: Fukuhara


title: TBX5-KO RNA-seq

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

summary: We Knocked out the TBX5 gene in iPSCs by TALEN-mediated NHEJ and report the gene expression in isogenic iPSC-CMs

overall_design: 3 isogenic cell lines; parent, TBX5-KO1 and TBX5-KO2

first: Ioannis

last: Karakikes

middle: C


title: MYCN Drives Disparate Medulloblastoma from Human Embryonic and iPSC-Derived Stem Cells

first: Fredrik

last: Swartling


title: Rat (Wistar) Liver CDAA Diet 4-8-12 Weeks Ensembl84 (BIBC)

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

institute: Boehringer Ingelheim Pharma GmbH & Co KG

summary: Nonalcoholic steatohepatitis (NASH) is a major cause of liver fibrosis with increasing prevalence worldwide. Currently there are no approved drugs available. The development of new therapies is difficult as diagnosis and staging requires biopsies. Consequently, predictive plasma biomarkers would be useful for drug development. Here we present a multi-omics approach to characterize the molecular pathophysiology and to identify new plasma biomarkers in a choline-deficient L-amino acid-defined diet rat NASH model. We analyzed liver samples by RNA-Seq and proteomics, revealing disease relevant signatures and a high correlation between mRNA and protein changes. Comparison to human data showed an overlap of inflammatory, metabolic, and developmental pathways.

overall_design: 48 samples: two conditions (CDAA vs. CSAA diet)  x three timepoints (4 weeks, 8 week, 12 weeks)  x eight animals per group

first: Daniel

last: Veyel

first: Andre

last: Broermann


title: Transcriptomic analysis of LSD1i-sensitive and resistant AML cells

city: milano

first: Saverio

last: Minucci

address: via Adamello 16

country: Italy

institute: European Institute of Oncology

summary: The goal of this study is to identify the molecular mechanisms underlying the resistance/sensitivity of AML cells to lysine specific demethylase 1 (LSD1) inhibitor.

overall_design: We performed the transcriptomic analysis at the earliest detected and last tested time points in which mTOR was regulated secondary to LSD1i (i.e. 6 and 72h in sensitive KASUMI-1 cells and 24 and 72h in resistant THP-1 cells)

first: Amal

last: Abdel-Aziz


title: 1H NMR metabolomic and transcriptomic analyses reveal urinary metabolites as biomarker candidates in response to protein undernutrition in adult rats

status: Public on Jan 25 2020

city: Zama

first: Yosuke

last: Komatsu

state: Kanagawa

address: 5-1-83 Higashihara

department: Wellness & Nutrition Science Institute

institute: Morinaga Milk Industry Co., Ltd.

summary: 1H NMR metabolomics was performed on urine samples weekly and on plasma and liver samples collected at week 4 from these animals, to identify metabolites that respond to protein undernutrition. To further investigate metabolites which were fluctuated in response to protein undernutrition in terms of metabolic enzymes, hepatic mRNA microarray and quantitative PCR analyses were also performed at week 4.

overall_design: Adult male Wistar rats were fed an 14% casein, control (CT) diet or an isocaloric [5% casein, low protein (LP)] diet for 4 weeks. 1H nuclear magnetic resonance metabolomic analysis was performed on urine samples weekly and on plasma and liver samples at week 4 to identify metabolites that respond to protein undernutrition. Liver samples were also subjected to mRNA microarray and quantitative PCR analyses at week 4 to further investigate metabolites responsive to protein undernutrition in terms of metabolic enzymes.


title: A Molecular signature for Delayed Graft Function (miRNA-Seq)

city: Glasgow

first: Paul

last: Shiels

address: Level 3, Wolfson Wohl Cancer Research Centre

department: Wolfson Wohl Translational Research Centre

institute: University of Glasgow

summary: Purpose: The aim of this study was to identify a molecular signature for extreme DGF in a retrospective analysis of paired renal allograft biopsies obtained at two time points: pre-implantation during preparatory phase (pre-perfusion biopsies, b) and after reperfusion when circulation was restored (post-perfusion biopsies , b1).

overall_design: smallRNA-seq in paired human renal allograft biopsies

first: P

middle: G

first: D

last: McGuinness

first: S

last: Mohammed

first: L

last: Monaghan


title: A Balance Between Intermediate Filaments and Microtubules Maintains Nuclear Architecture in the Cardiomyocyte

status: Public on Jan 24 2020

city: Philadelphia

first: Julie

last: Heffler

state: PA

address: 415 Curie Blvd

department: Physiology

institute: University of Pennsylvania

summary: In this manuscript we reported a unique role for desmin in the maintence of nuclear morphology. We performed this LaminB chip-seq to determine if there was a change in LAD organization with desmin KD.

overall_design: LaminB chip-seq was performed from n=3 biological replicates of scrambled (control) or shDesmin treated cells. Each ChIP was paired with an input, and after sequencing, all three replicates were unionized. After input normalization, BigWig files were generated from the control and shDesmin conditions. A bed file of LADs in the control sample is included; no LADs were defined in the shDesmin condition. Some libraries were re-run as noted below.

first: Parisha

last: Shah

first: Patrick

last: Robison

first: Sai

last: Phyo

first: Kimberly

last: Veliz

first: Keita

last: Uchida

first: Alexey

last: Bogush

first: Joshua

last: Rhoades

first: Rajan

last: Jain

first: Benjamin

middle: L

last: Prosser


title: Encapsulation boosts islet-cell signature in differentiating human induced pluripotent stem cells via integrin signalling

city: Bergen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

summary: Cell replacement therapies hold great therapeutic potential. Nevertheless, our knowledge of the mechanisms governing the developmental processes is limited, impeding the quality of differentiation protocols. Generating insulin-expressing cells in vitro is no exception, with the guided series of differentiation events producing heterogeneous cell populations that display mixed pancreatic islet phenotypes and immaturity. The achievement of terminal differentiation ultimately requires the in vivo transplantation of, usually, encapsulated cells. Here we show the impact of cell confinement on the pancreatic islet signature during the guided differentiation of alginate encapsulated human induced pluripotent stem cells (hiPSCs). Our results show that encapsulation improves differentiation by significantly reshaping the proteome  landscape of the cells towards an islet-like signature. Pathway analysis is suggestive of integrins transducing the encapsulation effect into intracellular signalling cascades promoting differentiation. These analyses provide a molecular framework for understanding the confinement effects on hiPSCs differentiation while confirming its importance for this process.

overall_design: human induced pluriopotent stem cells were differentiated towards S7 beta like cells either in 2D the entire protocol (CTRL), or in 3D by encapsulation in alginate (3D). We have 4 replicates.

first: Thomas

last: Legøy

first: Heidrun

last: Vethe

first: Shadab

last: Abadpour

first: Berit

last: Strand

first: Hanne

last: Scholz

first: Joao

last: Paulo

first: Helge

last: Ræder

first: Luiza

last: Ghila


title: Single-cell analysis reveals new evolutionary complexity in uveal melanoma

city: Miami

first: Michael

last: Durante

state: FL

department: Ophthalmology

country: USA

institute: University of Miami Miller School of Medicine

summary: Uveal melanoma (UM) is a highly metastatic cancer that, in contrast to cutaneous melanoma, is largely unresponsive to checkpoint immunotherapy. In this study we interrogate the tumour microenvironment at single-cell resolution using scRNA-seq of 59,915 tumour and non-neoplastic cells from 8 primary and 3 metastatic samples.  A subset analysis of tumour cells confirms the global genomic landscape established from bulk analysis and reveals newly described subclonal genomic complexity and transcriptional states consistent with phenotype plasticity.  The immune compartment comprises a previously unrecognized diversity of cell types, including CD8+ T cells expressing the checkpoint marker LAG3, as opposed to PD1 or CTLA4.  We identified clonally expanded plasma cells in a rare metastasis from an indolent slow-growing class 1B tumour indicating a role for of antibody-mediated immunity.  These findings reveal a dynamic ecosystem in which UM demonstrates new evolutionary complexity.  LAG3 is identified as a potential candidate for immune checkpoint blockade in high risk UM.

overall_design:
We performed single-cell RNAseq of primary and metastatic human uveal melanoma to profile the tumor microenvironment and indentify subclonal tumor architecture. Single cell 3' and 5' RNAseq data of primary and metastatic human uveal melanoma was performed using the 10X Genomics Chromium platform and sequenced on Illumina Nextseq500.

RNA-Seq raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns:
https://www.ncbi.nlm.nih.gov/gap/?term=phs001861.v1.p1

first: Daniel

last: Rodriguez

first: Stefan

last: Kurtenbach


title: In vivo hyperglycemia exposure elicits distinct period-dependent effects on human pancreatic progenitor differentiation, conveyed by oxidative stress

summary:
Aim: The loss of insulin-secreting β-cells, ultimately characterizing most diabetes forms, demands the development of cell replacement therapies. The common endpoint for all ex vivo strategies is transplantation into diabetic patients. However, the effects of hyperglycemia environment on the transplanted cells were not yet properly assessed. Thus, the main goal of this study was to characterize global effect of brief and prolonged in vivo hyperglycemia exposure on the cell fate acquisition and maintenance of transplanted human pancreatic progenitors.
Methods: To rigorously study the effect of hyperglycemia, in vitro differentiated human induced pluripotent stem cells (hiPSC)-derived pancreatic progenitors were xenotransplanted in normoglycemic and diabetic NSG RIP-DTR mice. The transplants were retrieved after one-week or one-month exposure to overt hyperglycemia and analyzed by large-scale microscopy or global proteomics. For this study we pioneer the use of the NSG RIP-DTR system in the transplantation of hiPSC, making use of its highly reproducible specific and absolute β-cell ablation property in the absence of inflammation or other organ toxicity.
Results: Here we show for the first time that besides the presence of an induced oxidative stress signature, the cell fate and proteome landscape response to hyperglycemia was different, involving largely different mechanisms, according to the period spent in the hyperglycemic environment. Surprisingly, brief hyperglycemia exposure increased the bihormonal cell number by impeding the activity of specific islet lineage determinants. Moreover it activated antioxidant and inflammation protection mechanisms signatures in the transplanted cells. In contrast, the prolonged exposure was characterized by decreased numbers of hormone+ cells, low/absent detoxification signature, augmented production of oxygen reactive species and increased apoptosis.
Conclusion: Hyperglycemia exposure induced distinct, period-dependent, negative effects on xenotransplanted human pancreatic progenitor, affecting their energy homeostasis, cell fate acquisition and survival.

overall_design: hiPSCs were differantiated towards S5 pancreatic progenitor cells and S7 beta-like cells following the protocol by Rezania 2014

first: Andreas

last: Mathiesen


title: Mouse ESCs (ES-D3) with Ash2l depletion

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

address: Rm. 825, 7F., No.322, Sec. 2, Shipai Rd., Beitou D

country: Taiwan

institute: Taipei Veterans General Hospital

summary: We showed a novel mechanism in which Ash2l directly binds to super-enhancers of several stemness genes to regulate pluripotency and self-renewal in pluripotent stem cells. Ash2l recruits Oct4/Sox2/Nanog (OSN) to form Ash2l/OSN complex at the super-enhancers of Jarid2, Nanog, Sox2, and Oct4, and further drives enhancer activation, upregulation of stemness genes, and maintains the pluripotent circuitry. Ash2l knockdown abrogates the OSN recruitment to all super-enhancers and further hinders the enhancer activation.

overall_design: Mouse ESCs (ES-D3) were infected with lentivirus containing either control or shRNA targeting Ash2l sequence. DNA was then extracted from both samples and subjected to ChIP-seq analysis.

first: PingHsing

first: ShihHwa

last: Chiou


title: Peri-infarct region transcriptome of SCID mice trated with saline control, iPSC-derived cardiomyocytes (iCM), or iCM-derived exosomes (iCM-Ex)

first: Phillip

last: Yang

state: California

address: 269 Campus Drive, CCSR 3120

summary:
iPSC-derived iCMs represent a potential therapy for ischemic cardiomyopathy. Previous studies demonstrated enhanced cardiac function following injection of iCMs into the peri-infarct region in mice models. Cardioprotection despite poor engraftment suggests that iCMs may modulate their therapeutic activity by secreted molecules. Exosomes are discrete packages of secreted molecules that are readily taken up by target cells. iCM and iCM-Ex treatment of acute myocardial infarctions (Mis) significantly improved cardiac function in SCID mice.
We used microarrays to identify differentially-regulated genes in iCM- or iCM-Ex treated mice and control mice.

overall_design: Female 80-100 day SCID mice received acute MIs by LAD ligation and injections of iCMs, iCM-Ex, or saline. Four weeks post-MI, mice were sacrificed and the hearts were explanted. We focused our investigation on the peri-infarct region (PIR) and removed the core infarct and remote zones.

first: M

last: Santoso

first: P


title: Effect of cold atmospheric plasma (CAP) in MCF-7 breast cancer cell [dataset 3]

city: Goyang-si

first: sung bin

last: park

state: Gyeonggi-do

address: 32, Dongguk-ro, Ilsandong-gu

department: Department of Life Science

institute: Dongguk University-Seoul

summary: Paclitaxel is a widely used therapeutic chemical for breast cancer treatment, however, cancer recurrence remains obstacle for improved prognosis of cancer patients. In the current study, cold atmospheric plasma (CAP) was examined for its potential use to overcome the drug resistance, which mainly comprised of reactive oxygen and nitrogen species. After developing a paclitaxel (Tx)-resistant MCF-7 (MCF-7/TxR) breast cancer cell, CAP was applied to the cells and its effect on recovery of drug sensitivity was examined in cellular as well as molecular aspect. The MCF-7/TxR cells restored sensitivity against Tx up to 70% by CAP. Comparison of genome-wide expression profiles between the Tx resistance cell and its CAP-treated cell identified 86 genes that commonly appeared with significant change. Notably, 48 genes including DAGLA and CEACAM1, which are known to contribute to the acquisition of Tx resistance, showed opposite expression in the two cellular status. The protein expression level of selected genes, DAGLA and CEACAM1, was recovered to that of their parental cell by CAP. Furthermore, the dysregulation of DAGLA and CEACAM1 in MCF-7/TxR alleviated the drug sensitivity recovery effect of CAP. Taken together, CAP inhibited the growth of Tx-resistant MCF-7 cancer cells and recovered Tx sensitivity by resetting expression of multiple drug resistance–related genes. These findings may contribute to extending the application of CAP to the treatment of Tx-resistant cancer.

overall_design:
genom-wide expression profiling of MCF-7, MCF-7 and MCF-7/TxR cell. In result, Taxol resistant MCF-7 cell was change many genes.
Total RNA is obtained from MCF-7 and MCF-7/TxR

first: Sungbin

last: Park

first: Sunjung

last: Kim


title: Effect of cold atmospheric plasma (CAP) in MCF-7 breast cancer cells [dataset 1]

overall_design:
genom-wide expression profiling of MCF-7, MCF-7 and MCF-7/TxR and CAP MCF-7/TxR cell. In result, cold atmospheric plasma different effect the CAP-treated MCF-7 breast cancer cell.
Total RNA is obtained from MCF-7 and MCF-7/TxR and CAP treated MCF-7/TxR


title: Remodeling of Zn2+ Homeostasis Upon Differentiation of Mammary Epithelial Cells

city: Aurora

first: Yu

last: Han

address: 12700 E. 19th Ave Mail Stop-B139

institute: University of Colorado

summary: Using mouse mammary epithelial cells as a model system, we investigated the remodeling of zinc homeostasis during differentiation induced by treatment with the lactogenic hormones cortisol and prolactin. RNA-Seq at different stages of differentiation revealed changes in global gene expression, including genes encoding zinc-dependent proteins and regulators of zinc homeostasis. Increases in mRNA levels of three zinc homeostasis genes,.

overall_design: 3 replicates of each of 3 sample groups (R day1, D day1, D day6). R day1 was used as the reference condition for all comparisons.

first: Amy

last: Palmer


title: Contribution of mTOR and PTEN to Radioresistance in Sporadic and NF2-Associated Vestibular Schwannomas: A Microarray and Pathway Analysis.

city: Tuebingen

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

institute: Quantitative Biology Center (QBiC)

summary: The use of radiation treatment has increased for both sporadic and neurofibromatosis type 2 (NF2)-associated vestibular schwannoma (VS). However, there are a subset of radioresistant tumors and systemic treatments that are seldom used in these patients. We investigated molecular alterations after radiation in three NF2-associated and five sporadically operated recurrent VS after primary irradiation. We compared these findings with 49 non-irradiated (36 sporadic and 13 NF2-associated) VS through gene-expression profiling and pathway analysis. Furthermore, we stained the key molecules of the distinct pathway by immunohistochemistry. A total of 195 differentially expressed genes in sporadic and NF2-related comparisons showed significant differences based on the criteria of p value < 0.05 and a two-fold change. These genes were involved in pathways that are known to be altered upon irradiation (e.g., mammalian target of rapamycin (mTOR), phosphatase and tensin homolog (PTEN) and vascular endothelial growth factor (VEGF) signaling). We observed a combined downregulation of PTEN signaling and an upregulation of mTOR signaling in progressive NF2-associated VS after irradiation. Immunostainings with mTOR and PTEN antibodies confirmed the respective molecular alterations. Taken together, mTOR inhibition might be a promising therapeutic strategy in NF2-associated VS progress after irradiation.

overall_design: We used microdissected tumor samples of 9 recurrent irradiated VS (5 sporadic, 1 cystic and 3 NF2-associated VS), 36 sporadic, 13 NF2 associated and 9 cystic associated non-irradiated controls. There are also 7 controls of vestibular nerve tissue that were obtained post mortem.

first: Isabel

last: Gugel

first: Ghazaleh

last: Tabatabai


title: A unified strategy to clone modified/unmodified small RNAs and mRNAs for high throughput sequencing

city: Riverside

first: Weifeng

last: Gu

address: 900 University Ave

department: Molecular, Cell and Systems Biology

institute: University of California at Riverside

summary: The high-throughput sequencing has become a standard tool for analyzing gene expression. Usually a cDNA/DNA library is constructed with 5' and 3' linkers and then sequenced. Unlike mRNA, small RNA often contains modifications including 5' cap or triphosphate and 3' methylation, affecting the linker addition during cloning processes. Small RNA is expressed at much lower levels than mRNA, making it more difficult to clone small RNA using a small amount of total RNA. Here we have developed a new strategy to clone modified/unmodified small RNA in an all-liquid-based reaction in a single PCR tube using as little as 20 ng total RNA. The 7-hour cloning process only needs ~1 hour labor time. Moreover, this method can be used to clone mRNA, simplifying the need to prepare two cloning systems for small RNA and mRNA. Since the linkers used are derived from the Illumina Truseq linkers for DNA cloning, the PCR primers based on the linker sequences can be used to obtain amplicons derived from small RNA/mRNA/DNA. Not only is our method more convenient for cloning modified RNA than available methods, but it is also more sensitive, accurate and versatile. Moreover, the all-liquid-based reaction can be performed in an automated manner.

overall_design: Develop a novel protocol to clone small RNA and mRNA

first: Lichao

last: Li

first: An-phong

last: Nguyen

first: Hui

last: Dai


title: Gene expression pattern during MeJA treatment (WT, dof2.1-KO)

city: Bunkoy-ku

first: Shuichi

last: Yanagisawa

state: Tokyo

address: Yayoi 1-1-1

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

summary: To examine the effect of the mutation of Arabidopsis Dof2.1 on gene exoression, we performed microarray analysis using dof2.1-KO mutant.

overall_design: Rosette leaves from 3-week-old WT and dof2.1-KO were treated with 3 mM MES buffer (mock control) or 3 mM MES buffer containing 100 μM MEJA for 2 days.

first: Yasuhito

last: Sakuraba


title: Geographical temperature stress in the sea anemone Nematostella vectensis

city: Charlotte

first: Whitney

middle: at

last: Leach

address: 9201 University City Blvd.

department: Biological Sciences

institute: University of North Carolina at Charlotte

summary: Gene expression of Nematostella vectensis from 5 different locations under chronic (30 day) temperature stress

overall_design: Anemones were collected from 5 different locations (MA, ME, NC, SC, NS) and were chronically exposed to a range of temperature stresses (+/- 2C from that location temperature average)

last: Klock

first: Adam

middle: M

last: Reitzel


title: Comprehensive analysis of a mouse model of spontaneous uveoretinitis using single-cell RNA sequencing

city: Baltimore

first: Jacob

middle: S

last: Heng

state: MD

address: 725 North Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: Autoimmune uveoretinitis is a significant cause of visual loss, and mouse models offer unique opportunities to study its disease mechanisms.  Aire-/- mice fail to express self-antigens in the thymus, exhibit reduced central tolerance, and develop a spontaneous, chronic, and progressive uveoretinitis.  Using single-cell RNA sequencing (scRNA-seq), we characterized wild type and Aire-/- retinas to define, in a comprehensive and unbiased manner, the cell populations and gene expression patterns associated with disease.  Based on scRNA-seq, immunostaining, and in situ hybridization, we infer that (i) the dominant effector response in Aire-/- retinas is Th1-driven, (ii) a subset of monocytes convert to either a macrophage/microglia state or a dendritic cell state, (iii) the development of tertiary lymphoid structures constitutes part of the Aire-/- retinal phenotype, (iv) all major resident retinal cell types respond to Interferon gamma by changing their patterns of gene expression, and (v) Muller glia up-regulate specific genes in response to Interferon gamma and may act as antigen presenting cells.

overall_design: Single-cell RNAseq of AireKO and  age- and sex-matched WT retinas. For AireKO retinas, two replicates for Grade 2 disease and two replicates for Grade 3 disease were used.

first: Sean

last: Hackett

first: Genevieve

last: Stein-O'Brien

first: Briana

last: Winer

first: John

last: Williams

first: Peter

last: Campochiaro

first: Loyal

last: Goff

first: Jeremy

last: Nathans