title: Epithelial memory of resolved inflammation limits tissue damage while promoting pancreatic tumorigenesis [ATAC-seq]

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

institute: IRCCS San Raffaele Scientific Institute

summary: Inflammation is a major risk factor for pancreatic ductal adenocarcinoma (PDAC). When occurring in the context of pancreatitis, mutations of KRAS accelerate tumor development. We discovered that long after its complete resolution, a transient inflammatory event primes pancreatic epithelial cells to subsequent transformation by oncogenic KRAS. Upon recovery from acute inflammation, epithelial cells of the pancreas display an enduring adaptive response associated with sustained transcriptional and epigenetic reprogramming. Such adaptation enables the prompt reactivation of acinar-to-ductal metaplasia (ADM) upon subsequent inflammatory events, thus efficiently limiting tissue damage via rapid decrease of zymogen production. We propose that since activating mutations of KRAS maintain an irreversible ADM, they may be beneficial and under strong positive selection in the context of recurrent pancreatitis.

overall_design: For pancreatic cells ATAC-seq (sample 1-4), pancreata were harvested from C57BL/6J wild-type mice at different time points before and after caerulein-induced acute inflammation and digested to obtain single cell suspension. Epithelial cells were then purified followed by ATAC-seq library preparation. For pancreatic DCLK1-positve cell ATAC-seq (sample 5-7), pancreata were harvested from Dclk1-DTR-ZsGreen mice at different time points before and after caerulein-induced acute inflammation and digested to obtain single cell suspension. DCLK1-positive epithelial cells were then purified followed by ATAC-seq library preparation.

first: E

last: Del Poggetto

first: I

last: Ho

first: C

first: G

last: Natoli

first: A

last: Viale


title: Integrated methylomic and transcriptomic characterisation of postoperative systemic inflammatory dysregulation

status: Public on Sep 17 2021

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

type: Expression profiling by high throughput sequencing

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Small RNA sequencing of small extracellular vesicles derived from senescent vs. nonsenescent human dermal fibroblasts (HDFs)

status: Public on Sep 16 2021

city: Seoul

first: Ok Sarah

last: Shin

address: 148, Gurodongro, Gurogu

country: South Korea

institute: Korea Univ.

type: Non-coding RNA profiling by high throughput sequencing

summary: We report small RNA sequencing technology for high-throughput profiling of microRNA content within small extracellular vesicles isolated from nonsenescent and senescent human dermal fibroblasts.

overall_design: Comparison of microRNA profiles of small extracellular vesicles isolated from senescent vs. nonsenescent human dermal fibroblasts

first: Ok

middle: S

first: Jae

middle: K

last: Lee


title: An inhibitor-mediated beta cell dedifferentiation model reveals distinct roles for FoxO1 in glucagon repression and insulin maturation

city: Vienna

first: Stefan

last: Kubicek

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: We have determined that chemical FoxO1 inhibition can effectively mimic many aspects of beta cell dedifferentiation in vitro and that this can be countered by loperamide treatment.

overall_design: RNAseq results of murine beta cell line, Min6, treated for 48h with DMSO, AS1842856 (FoxO1 inhibitor), loperamide and in combination.

first: Tamara

last: Casteels

first: Michael

last: Schuster


title: Brd4 regulates the homeostasis of CD8+ T-lymphocytes and their proliferation in response to antigen stimulation [RNA-seq]

status: Public on Sep 15 2021

city: 广州

first: Peng

middle: zhi

last: lin

address: 74 Zhongshan 2 Rd

department: zhongshan school of medicine

country: China

institute: Sun-Yat sen university

summary:
Purpose: The goals of this study are to compare the differentially expressed genes between in wild type and Brd4-/- CD8+T cells.
Methods:  RNA extracted from wild type and Brd4-/- CD8+T cells was used to generate RNA-seq library，followed by sequencing.
Results: In naïve CD8+T cells, Brd4 deletion casued 956 downregulated genes and 841 upregulated genes. In in vitro-activated CD8+T cells（18hr），Brd4 deletion resulted in 1182 downregulated genes and 789 upregulated genes. Importantly，we noticed that Brd4 is required for the migration- and glucose-related genes. expression
Conclusions: Our study represents the first detailed analysis of transcriptomes in wild type and Brd4-/- CD8+T cells. Our results show that Brd4 deletion resulted in more downregulated genes exceeding the upregulated genes and the downregulation of many migration- and glucose-ralated genes. We conclude that Brd4-mediated gene expresssion program promotes  glucose metabolism and cell migartion.

overall_design: mRNA profiles of  wild type (WT) and Brd4-/-  CD8+T cells

first: Zhilin

last: Peng

first: Hui

last: Zhang


title: SNX18 inhibits melanoma migration by modulating the activation ratio of Cdc42 & RhoA

city: Ramat Gan,

first: Maya

middle: Ramot

last: Goshen

address: Derech Sheba 2,

department: Clinical Microbiology and Immunology

country: Israel

institute: Tel Aviv University

summary:
To identify novel proteins that control melanoma development and progression, we integrated high-throughput proteomics, mRNA and miRNAs datasets from isogenic primary (WM115) and metastatic (WM266-4) melanoma cell-lines. We focused on differentially expressed proteins that had non-differential mRNA levels and were putatively targeted by a high number of miRNAs. SNX18, a sub-family member of sorting-nexins that participates in endocytosis and autophagy was down-regulated by 6-fold in WM266-4, and predicted to be targeted by 17 miRNAs. Over-expression of SNX18 in several melanoma cell-lines significantly reduced migration rate, while silencing of SNX18 resulted in the opposite effect. Notably, progression tissue microarrays demonstrated a trend for SNX18 downregulation in early metastasis. Luciferase assays confirmed the direct regulation of SNX18 by multiple miRNAs. Indeed, over-expression of these miRNAs repressed endogenous SNX18 expression at the protein but not mRNA level. Further, protein but not mRNA expression levels correlated with better overall survival as determined in a cohort of 48 metastatic melanoma patients and in the TCGA database. Mechanistically, SNX18-mediated reduced migration coincided with RhoA activation and Cdc42 inactivation. Both play a role, as RhoA inhibitor and constitutively activated Cdc42 mutants abrogated this effect. Moreover, phosphorylation-defective SNX18 mutants (S233A,S233D) migrated faster, with S233A inactivating RhoA and activating Cdc42, while S233D activated both. The downstream phosphorylation of the p38>MAPKAPK2>HSP27 signaling pathway was concordant. Both mutants were more abundant in the plasma membrane. Taken together, phosphorylation of S233 is crucial for SNX18 activation, but de-phosphorylation dynamics, which may occur at the membrane, is required for functional effect.
miRNA expression profile of primary (WM115) and metastatic (WM266-4) melanoma cell lines.

overall_design: Three biological replicates of WM266-4 and WM115 isogenic melanoma cell lines were compared

middle: R

first: Michal

last: Harel

first: Ettai

last: Markovits

first: Keren

last: Shapira

first: Erez

last: Baruch

first: Iris

last: Barshack

middle: J

last: Besser

first: Jacob

last: Schachter

first: Rona

last: Ortenberg

first: Metsada

last: Pasmanik-Chor

first: Jasmine

last: Hirsch

first: Yoav

last: Henis

first: Tamar

last: Geiger

first: Gal

last: Markel


title: METTL3 mediated m6A mRNA modification promotes esophageal cancer initiation and progression via Notch signaling pathway

city: guangzhou

first: hui

last: han

state: guangdong

address: yuexiu

institute: the first affiliated hospital，sun yat-sen university

summary: Esophageal cancer is a lethal malignancy with high mortality rate, while the molecular mechanisms underlying esophageal cancer pathogenesis are stillis poorly understood. Here we found that the N6-methyladenosine (m6A) methyltransferase METTL3 is significantly up-regulated in esophageal squamous cell carcinoma (ESCC) and associated with poor patient prognosis. Depletion of METTL3 results in decreased ESCC growth and progression in vitro and in vivo. We further established ESCC initiation and progression models using Mettl3 conditional knockout mouse and revealed that Mettl3 mediated m6A modification is essential for promotes ESCC initiation and progression in vivo. Moreover, using METTL3 overexpression ESCC cell model and Mettl3 conditional knockin mouse model, we demonstrated the critical function of Mettl3 in promoting in vivo ESCC tumorigenesis in vitro and in vivo. Mechanistically, Mettl3 catalyzed m6A modification promotes NOTCH1 expression and the activation of Notch signaling pathway. Forced activation of Notch signaling pathway successfully rescues the growth, migration and invasion capacities of METTL3 depleted ESCC cells. Our data uncovered important mechanistical insights underlying ESCC tumorigenesis and provided molecular basis for the development of novel strategies for ESCC diagnosis and treatment.

overall_design: RNA-seq was used to study the differenially expressed genes upon METTL3 knockdown or ctrl cells.

last: Han

first: Shuibin

last: Lin


title: Brd4 regulates the homeostasis of CD8+ T-lymphocytes and their proliferation in response to antigen stimulation [Cut&Tag]

first: Peng

last: lin

summary: CD8+ T cells are major components of adaptive immunity and confer robust protective cellular immunity, which requires adequate T-cell numbers, targeted migration, and efficient T-cell proliferation. Altered CD8+ T-cell homeostasis and impaired proliferation result in dysfunctional immune response to infection or tumorigenesis. However, intrinsic factors controlling CD8+ T-cell homeostasis and immunity remain largely elusive. Here, we demonstrate the prominent role of Brd4 on CD8+ T cell homeostasis and immune response. By upregulating Myc and GLUT1 expression, Brd4 facilitates glucose uptake and energy production in mitochondria, subsequently supporting naïve CD8+ T-cell survival. Besides, Brd4 promotes the trafficking of naïve CD8+ T cells partially through maintaining the expression of homing receptors (CD62L and LFA-1). Furthermore, Brd4 is required for CD8+ T cell response to antigen stimulation, as Brd4 deficiency leads to a severe defect in clonal expansion by decreasing glycolysis. Importantly, as JQ1, the specific inhibitor of Brd4, severely dampens CD8+ T-cell immune response, its usage as an anti-tumor agent or latency-reversing agent for human immunodeficiency virus type I (HIV-1) should be more cautious. Collectively, our study identifies a previously-unexpected role of Brd4 in the metabolic regulation of CD8+ T cell-mediated immune surveillance and also provides a potential immunomodulation target.

overall_design: Examination of Brd4' binding sites throughout the genome in mouse naïve CD8+T cells.

first: Zhilin

last: Peng

last: Zhang


title: Epithelial memory of resolved inflammation limits tissue damage while promoting pancreatic tumorigenesis [ChIP-seq]

first: Chiara

last: Balestrieri

department: Center for Omics Sciences

country: Italy

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Pancreatic spheroids were derived from untreated as well as post caerulein-treated C57BL/6J wild-type mice. Chromatin from spheroid was immunoprecipitated with histone modification targeting antibodies and subjected to multiparallel sequencing.

first: E

last: Del Poggetto

first: I

last: Ho

first: C

first: G

last: Diaferia

last: Natoli

first: A

last: Viale


title: Sturgeon chondroitin sulfates inhibit the proliferation of colorectal cancer cells by inducing cell cycle arrest and apoptosis

city: Beijing

first: Wu

last: Ruiyun

address: 17 Qinghua East Road, Haidian District, Beijing

institute: China Agricultural University

summary: Cell proliferation assay and flow cytometric analysis were used to examine the effects of SCS treatment on viability and apoptosis of colon cancer cell HT-29 cells and normal colonic epithelial cell NCM460 cells. Transcriptomic and proteomic studies were used to identify the main targets of SCS. SCS showed little effect on the gene expression profile of NCM460 cells whereas188 genes and 10 proteins were differentially regulated in HT-29 cells after SCS treatment. Enrichment analysis of those genes / proteins showed that majority of them are involved in DNA replication, cell cycle progression, and apoptosis.

overall_design: Construction of RNA-seq in HT-29 and NCM460 cells treated with chondroitin sulfate(SCS)

first: Shen

last: Qian

first: Li

last: Guangyue

last: Pinglan


title: Dynamic patterns of DNA methylation in the normal prostate epithelial differentiation program are targets of aberrant methylation in prostate cancer [Methyl Capture]

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

country: USA

institute: Roswell Park Cancer Institute

type: Methylation profiling by high throughput sequencing

summary: Understanding the epigenetic control of normal differentiation programs might yield principal information about critical regulatory states that are disturbed in cancer. We utilized the established non-malignant HPr1-AR prostate epithelial cell model that upon androgen exposure commits to a luminal cell differentiation trajectory from that of a basal-like state. We profile the dynamic transcriptome associated with this transition at multiple time points (0hr, 1hr, 24hr, 96hr), and confirm that expression patterns are strongly indicative of a progressive basal to luminal cell differentiation program based on human expression signatures. Furthermore, we establish dynamic patterns of DNA methylation associated with this program by use of whole genome bisulfite sequencing (WGBS).

overall_design: HPr1-AR cells exposed to DHT (10nM) for 0, 1, 24 and 96 hours were analyzed by TruSeq Methyl Capture sequencing. Raw sequencing reads were aligned to the human genome (hg19) and methylation levels called using bismark.

first: Dominic

last: Smiraglia

first: Mark

last: Long


title: Follicular dendritic cells restrict IL4 availability in germinal centers and foster memory B cell generation

city: San Francisco

first: Lihui

last: Duan

state: CA

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: UCSF

summary: Germinal centers (GCs) are sites of antibody affinity maturation and memory B cell generation. Follicular dendritic cells (FDCs) form a dense stromal network within GCs, but the full extent of their supportive activity is not understood. Here we showed that FDCs expressed IL4Ra and they reduced IL4 availability in GCs. We used scRNA-seq to examine IL4 actions within the GC and identified a subset of light zone cells marked by high IL4Ra and CD23 and lack of a Myc gene-expression signature. Trajectory inference analysis suggested this population could differentiate into pre-memory and pre-plasma cells. Genetic experiments showed that IL4Ra and STAT6 acted intrinsically to restrain pre-memory B cell generation. By reducing IL4 availability, FDCs enhanced GC B cell selection and fostered memory cell generation. This work suggests that GC FDCs provide a niche that limits bystander IL4 activity, focusing IL4 action on B cells undergoing selection and enhancing memory cell differentiation

overall_design: Adult mice were immunized intraperitoneally with NP-haptenated antigen in alum adjuvant. GC B cell were sorted at different days after immunization for scRNA-seq.

first: Dan

last: Liu

first: Hsin

last: Chen

first: Michelle

middle: A

last: Mintz

first: Marissa

middle: Y

last: Chou

first: Dmitri

middle: I

last: Kotov

first: Ying

last: Xu

first: Jinping

last: An

first: Brian

last: Laidlaw

first: Jason

middle: G

last: Cyster


title: Dynamic patterns of DNA methylation in the normal prostate epithelial differentiation program are targets of aberrant methylation in prostate cancer

overall_design: HPr1-AR cells exposed to DHT (10nM) for 1, 24 and 96 hours were analyzed by RNA-seq. Sequenced samples were aligned to the human genome (hg19) using tophat2, and aligned reads translated to expression counts via featurecounts, followed by a standard DESeq2 pipeline for data normalization and differential expression analysis.


title: Gene expression profiles of splenic pDCs in C57Bl6/J and Siglec-H deficient mice

city: Erlangen

first: Lars

last: Nitschke

state: Bavaria

address: Staudtstr. 5

department: Biology

country: Germany

summary: The steady-state gene expression of pDCs of two different mouse strains was analyzed. Splenic plasmacytoid dendritic cells (pDCs) of Siglec-H knock-out mice on C57Bl& background and the Siglec-H expression littermates (+/+) were enriched and sorted by FACS before generating RNA, followed by cDNA generation and sequencing.

overall_design: There are 11 samples in total. Five replicate for the Siglec-H +/+ and six for the Siglec-H -/- condition.


title: Dynamic patterns of DNA methylation in the normal prostate epithelial differentiation program are targets of aberrant methylation in prostate cancer [BiSulfite-seq]

overall_design: HPr1-AR cells exposed to DHT (10nM) for 0, 1, 24 and 96 hours were analyzed by whole genome bisulfite sequencing. Raw sequencing reads were aligned to the human genome (hg19) and methylation levels called using bismark.


title: Single-cell cloning of cancer cells secreting specific subsets of extracellular vesicles

city: Houston

first: Navin

last: Varadarajan

state: TX

address: 4722 Calhoun Rd

department: Chemical and Biomolecular Engineering

institute: University of Houston

summary: Expression profiling of mouse mammary cell lines, 67NR and 4T1, and glioblastoma cell lines, U87 and GSC20 stem cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single cell RNA sequencing profile of 67NR, 4T1, U87, and GSC20 cell lines cultured in vitro

first: Mohsen

last: Fathi

first: Robiya

last: Joseph

first: Jay

last: Adolacian

first: Melisa

last: Martinez-Paniagua

first: Xingyue

first: Konrad

last: Gabrusiewicz

first: Sendurai

last: Mani


title: Splenic immune response to Plasmodium infection initiated by two different routes

city: London

first: Jean

last: Langhorne

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: Plasmodium chabaudi parasite obtained from recently mosquito transmitted infections give rise to an attenuated blood-stage infection when compared to serially blood passaged parasites. We compared the immune response in the spleens induced by these two types of parasites in order to determine what may cause this attenuation. Spleens were taken at several timepoints during the blood-stage infection and RNA-seq analysis was performed.

overall_design: 5 Time points - (Days 1, 2, 3, 4, 6) and 2 infection conditions (RMT and SBP). Each group contains 4 replicates, using age/sex matched C57BL/6 mice. Controls/Naïve mouse with no infection were age/sex matched.

first: Chris

last: Alder

first: Katrien

last: Deroost

first: Caroline

last: Hosking

first: Sarah

last: Manni


title: Identification of a novel FUS/ETV4 fusion and comparative analysis with other Ewing sarcoma fusion proteins [RNA-seq]

city: Columbus

first: Megann

middle: A.

last: Boone

state: OH

address: 700 Children's Drive, WA5011

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

summary: The purpose of this study was to determine the transcriptional regulatory similarities and differences in the FET/ETS translocations that have been identified as drivers of Ewing sarcoma.

overall_design:
Endogenous EWS/FLI was knocked-down in the Ewing sarcoma A673 cell line and FET/ETS cDNA constructs were expressed in these cells via viral transduction. Cells were collected after 8 days and total RNA was extracted to study the transcriptomic profiles of each FET/ETS fusion protein. 2 biological replicates of each sample were performed for this experiment.
Please note that each processed data was generated from both replicates and is linked to the corresponding *R1 sample records

first: Cenny

last: Taslim

first: Stephen

middle: L

last: Lessnick


title: Spen regulates X chromosome inactivation (SPEN SPOC domain rescue)

city: heidelberg

first: samuel

last: collombet

address: Meyerholfstrasse

institute: EMBL

summary: RNAseq of SPOC-tethering mESCs.

overall_design:
RNAseq on BglG-GFP and BglG-GFP-SPOC Spen-degron TX1072 mESCs. RNAseq in 4 biological replicates at 3 different times of dox induction or auxin-depletion: untreated, Dox24h and Dox+Auxin24h (note that in the last one, cells are treated with auxin for 12h to pre-deplete SPEN, and then treated with Dox+Auxin for 24h).
The TX1072 is a mESC cell line, derived from hybrid F1 embryo obtained by crossing mouse from 2 different backgrounds (BL/6J x CAST-EiJ) therefore allowing allele specific analysis. The count table (processed data) contains the raw and normalize count without allele specific analysis, as well as the allele-specific count for the BL6 and CAST alleles, for each sample.

first: Francois

last: Dossin

first: Samuel

last: Collombet

first: Edith

last: Heard


title: AR-negative prostate cancer is vulnerable to loss of JMJD1C demethylase

first: Chang-Jiun

last: Wu

address: 1515 Holcombe Blvd

department: Genomic Medicine

institute: University of Texas, MD Anderson Cancer Center

summary: To explore the cooperative interactions of AR and JMJD1C, we performed comparative transcriptomics of JMJD1C-expressing versus JMD1C-depleted AR-positive or AR-negative prostate cancer cells.

overall_design: Total RNA obtained from human prostate cancer cell lines

first: Ronald

last: DePinho

first: Yohei

last: Yoshihama


title: Identification of a new ADAR1-dependent RNA editing event in the cyclin dependent kinase CDK13 that promotes thyroid cancer cell hallmarks

city: Madrid

first: Julia

last: Ramirez-Moya

address: Arturo Duperier, 4

country: Spain

institute: Instituto de Investigaciones Biomédicas Alberto Sols

summary: Adenosine deaminases acting on RNA (ADAR) catalyze the conversion of adenosines into inosines (A-to-I), modifying a large proportion of cellular RNAs and associated with diverse cancers. We reported previously that ADAR1 is functionally important for thyroid cancer progression and A-to-I editing events are elevated in these tumors. However, the downstream effectors regulated or edited by ADAR1 and the significance of ADAR1 dysregulation in thyroid cancer remain unclear. Here we provide insight, by whole transcriptome sequencing, into the consequences of ADAR1 dysregulation on global gene expression, RNA splicing and RNA editing. Furthermore, we describe for the first time an oncogenic function for CDK13 in thyroid cancer and identified a new ADAR1-dependent RNA editing event that occurs in the coding region of its transcript. Moreover, CDK13 was significantly over-edited in tumor samples and our functional analysis revealed the importance of this specific editing event in promoting cancer cell hallmarks. Finally, we showed that the editing of CDK13 modifies its subcellular localization and that this event could explain, at least in part, the global change in splicing produced by ADAR1 dysregulation. In summary, our data reinforces A-to-I editing as an important pathway in cancer progression, identifying novel mechanisms that open new insights into future treatments in thyroid and other cancer types.

overall_design: mRNA from Cal62 Thyroid cancer cells silenced for ADAR1 (#1 and #2) and siControl cells

last: Ramírez-Moya

first: Chistos

last: Miliotis

first: Allison

last: Baker

first: Frank

last: Slack

first: P

last: Santisteban


title: Dynamic changes in tRNA modifications and abundance during T-cell activation [ncRNA-seq]

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

institute: Agriculture Research Organization

summary: The tRNA pool determines the efficiency, throughput, and accuracy of translation. Previous studies have identified dynamic changes in the tRNA supply and mRNA demand during cancerous proliferation. Yet, dynamic changes may occur also during physiologically normal proliferation, and these are less characterized. We examined the tRNA and mRNA pools of T-cells during their vigorous proliferation and differentiation upon triggering of the T cell antigen receptor. We observe a global signature of switch in demand for codon at the early proliferation phase of the response, accompanied by corresponding changes in tRNA expression levels. In the later phase, upon differentiation of the T cells, the response of the tRNA pool is relaxed back to basal level, potentially restraining excessive proliferation. Sequencing of tRNAs allowed us to also evaluate their diverse base-modifications. We found that two types of tRNA modifications, Wybutosine and ms2t6A, are reduced dramatically during T-cell activation. These modifications occur in the anti-codon loops of two tRNAs that decode “slippery codons”, that are prone to ribosomal frameshifting. Attenuation of these frameshift-protective modifications is expected to increase proteome-wide frameshifting during T-cell proliferation. Indeed, human cell lines deleted of a Wybutosine writer showed increased ribosomal frameshifting, as detected with a reporter that consists of a critical frameshifting site taken from the HIV gag-pol slippery codon motif. These results may explain HIV’s specificity to proliferating T-Cells since it requires ribosomal frameshift exactly on this codon for infection. The changes in tRNA expression and modifications uncover a new layer of translation regulation during T-cell proliferation and exposes a potential trade-off between cellular growth and translation fidelity.

overall_design: tRNA-sequencing of naïve and in-vitro activated T-cells

first: Michal

last: Polonskey

first: Inbal

last: Eizenberg

first: Orna

last: Dahan

first: Nir

last: Friedman

first: Yitzhak

last: Pilpel


title: Transcriptional profiling of canine acanthomatous ameloblastoma

city: Ithaca

first: Jennifer

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: Ameloblastomas are odontogenic tumors that are rare in people but have a relatively high prevalence in dogs. Because canine acanthomatous ameloblastomas (CAA) have clinicopathologic and molecular features in common with human ameloblastomas (AM), spontaneous CAA can serve as a useful translational model of disease. However, the molecular basis of CAA and how it compares to AM are incompletely understood. In this study, we compared the global genomic expression profile of CAA with AM and evaluated their dental origin by using a bulk RNA-seq approach. For these studies, healthy gingiva (HGIN) and canine oral squamous cell carcinoma (COSCC) served as controls. We found that aberrant RAS signaling, and activation of the epithelial-to-mesenchymal transition cellular program are involved in the pathogenesis of CAA, and that CAA is enriched with genes known to be upregulated in AM including those expressed during the early stages of tooth development, suggesting a high level of molecular homology. These results support the model that domestic dogs with spontaneous CAA have potential for pre-clinical assessment of targeted therapeutic modalities against AM.

overall_design: A total of 25 canine tissue samples, representing 12 CAA, 8 COSCC and 5 HGIN samples, were profiled with RNA-seq. The 12 CAA samples are represented by SRA BioProject accession #PRJNA533473.

first: Santiago

last: Peralta


title: Identification of a novel FUS/ETV4 fusion and comparative analysis with other Ewing sarcoma fusion proteins

first: Megann

last: Boone

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

overall_design: Refer to individual Series


title: Transcriptomic analsyis of Epithelial and Mesenchymal carcinoma cells using the nCounter PanCancer Immune Profiling panel (Nanostring Technologies) [mouse]

city: Cambridge

first: Anushka

last: Dongre

address: 455 Main St

institute: Whitehead Institute

summary: We undertook to determine whether carcinoma cells residing in the epithelial or quasi-mesenchymal phenotypic states differ in their expression of immunomodulatory markers. To do so, we used the nCounter PanCancer Immune Profiling Panel (Nanostring Technologies)to perform transcriptomic analyses of the E and qM mammary carcinoma cells; these cells were either cultured in vitro or prepared by FACS sorting of GFP-labelled carcinoma cells from their corresponding tumors

overall_design: RNA was extracted from the indicated cell lines cultured in vitro or from sorted GFP+ tumor cells using the RNeasy Mini Kit (Qiagen) and transcriptomic analysis was performed using the nCounter PanCancer Immune Profiling Panel (Nanostring Technologies) Normalization of Nanostring nCounter gene expression values and differential expression were assayed by DESeq2. SnailLO cells express low levels of endogenous Snail and high levels of Epcam. SnailHI cells express high levels of Snail and low levels of Epcam.

first: Robert

last: Weinberg


title: Urocortin-3 Neurons in the Mouse Perifornical Area Promote Infant-directed Neglect and Aggression

first: Catherine

last: Dulac

state: MA

address: 16 Divinity Avenue, BL4000

department: Molecular and Cellular Biology

institute: Harvard University

summary: PeFA Ucn3 neurons were identified as a dedicated circuit component for the expression of infant-directed neglect and aggression, providing a new framework to understand the positive and negative regulation of parenting in health and disease.

overall_design: Neuronal activity induced Phosphorylated S6 protein bound mRNAs were immunoprecipitated and sequenced to reveal transcript specifically enriched in infanticide activated neurons of the perifornical area of the mouse hypothalamus.

first: Anita

last: Autry

first: Dhananjay

last: Bambah-Mukku

first: Johannes

last: Kohl

first: Nimrod

last: Rubunstein


title: Plant DNA methylation sensitive to parent seed N content and mediated the influence of external nitrogen on OsNAR2.1 overexpression rice growth

city: Nanjing, Jiangshu Province

first: Xiaorong

last: Fan

state: Jiangshu

address: Tongwei Road 1

institute: Nanjing Agricultural University

summary: DNA methylation is an important mechanism of  plant epigenomes regulated environment stress. Nitrogen (N) resource is a significant limiting factor for plant growth and productivity in both natural and agricultural systems. Here, we use Whole Genome Bisulfite Sequencing  (WGBS)  study genome-wide methylation influence by seed N content

overall_design: Comparison of WYG7 and overexpression of OsNAR2.1 line (Ox1) rice with HN and LN seed N content in HN and NN field

first: Xiaoru

first: Jingguang

last: Chen

first: Yuyue

last: Zhang

first: Kaiyun

last: Qian

first: Peng

last: Xie

first: Man

last: Xu

first: Zhi

last: Hu

first: Kaiwen

last: Yan

first: Guohua


title: Expression data of iPS microglia treated with TREM2 agonist antibody

city: FUJISAWA

first: Yuumi

last: Okuzono

state: KANAGAWA

address: 26-Muraoka-higashi 2-chome

country: Japan

institute: Takeda Pharmaceutical Company Limited

summary: Loss-of-function variants of triggering receptor expressed on myeloid cells 2 (TREM2) increase the risk of developing Alzheimer's disease (AD). The mechanism through which TREM2 contributes to the disease (TREM2 activation vs inactivation) is largely unknown. Here, we analyzed changes in a gene set downstream of TREM2 to determine whether TREM2 signaling is modified by AD progression. We generated an anti-human TREM2 agonistic antibody and defined TREM2 activation in terms of the downstream expression changes induced by this antibody in microglia developed from human induced pluripotent stem cells (iPSC). Differentially expressed genes (DEGs) following TREM2 activation were compared with the gene set extracted from microglial single nuclear RNA sequencing data of patients with AD, using gene set enrichment analysis. We isolated an anti-TREM2-specific agonistic antibody, Hyb87, from anti-human TREM2 antibodies generated using binding and agonism assays, which helped us identify 300 upregulated and 251 downregulated DEGs. Pathway enrichment analysis suggested that TREM2 activation may be associated with Th2-related pathways. TREM2 activation was lower in AD microglia than in microglia from healthy subjects or patients with mild cognitive impairment. TREM2 activation also showed a significant negative correlation with disease progression. Pathway enrichment analysis of DEGs controlled by TREM2 activity indicated that TREM2 activation in AD may lead to anti-apoptotic signaling, immune response, and cytoskeletal changes in the microglia. We showed that TREM2 activation decreases with AD progression, in support of a protective role of TREM2 activation in AD. In addition, the agonistic anti-TREM2 antibody can be used to identify TREM2 activation state in AD microglia.

overall_design: iPS microglia was treated with PBS/control IgG/TREM2 agonist antibody (Hyb87), and amplicon sequencing was performed with the Ion Torrent platform.

first: Masataka

last: Ifuku

first: Shuji

last: Sato


title: Expression profiling of contralateral dorsal root ganglia of a rat model of complex regional pain syndrome type-I uncovers potential mechanisms involved in mirror-image pain

city: Hangzhou

first: Chengyu

last: Yin

state: Zhejiang

address: 548 Binwen Road, Binjiang District, Hangzhou

department: The Third Clinical Medical College

institute: Zhejiang Chinese Medical University

summary:
Background: Mirror-image pain (MIP), which develops from the healthy body region contralateral to the actual injured site, is a mysterious pain phenomenon accompanying many chronic pain conditions, including complex regional pain syndrome (CRPS). However, the pathogenesis of MIP still remained largely unknown. The purpose of this study is to perform an expression profiling to identify genes related with MIP in an animal model of CRPS-I.
Methods: We established a rat chronic post-ischemic pain (CPIP) model to mimic human CRPS-I. RNA-sequencing (RNA-Seq), bioinformatics, qPCR, immunostaining and animal behavioral assays were used to screen potential genes in contralateral dorsal root ganglia (DRG) that may be involved in MIP.
Results: The CPIP model rats developed robust and persistent MIP in contralateral hind paws. Bilateral DRG neurons did not exhibit obvious neuronal damage. RNA-Seq of contralateral DRG from CPIP model rats identified a total 527 differentially expressed genes (DEGs) vs. control rats. The expression changes of several representative DEGs were verified by qPCR. Bioinformatics analysis indicated that immune system process, innate immune response and cell adhesion were among the mostly enriched biological processes, which are all important processes involved in pain sensitization, neuroinflammation and chronic pain. We further identified DEGs potentially involved in pain mechanisms or enriched in small- to medium-sized sensory neurons or TRPV1-lineage nociceptors. By comparing with published datasets summarizing genes enriched in pain mechanisms, we sorted out a core set of genes which might contribute to nociception and pain mechanism in MIP.
Conclusions: We provided by far the first study to profile gene expression changes and pathway analysis of contralateral DRG for investigating MIP mechanisms.    This work may provide novel insights into understanding the mysterious mechanisms underlying MIP.

overall_design: Examination of 2 different groups mRNA profiles in DRG: control group and CPIP group

first: Huimin

last: Nie

first: Danyi

last: Zeng

first: Boyu

last: Liu

first: Boyi


title: Transcriptomic analsyis of Epithelial and Mesenchymal carcinoma cells using the nCounter PanCancer Immune Profiling panel (Nanostring Technologies) [human]

first: Anushka

last: Dongre

summary: We undertook to determine whether carcinoma cells residing in the epithelial or quasi-mesenchymal phenotypic states differ in their expression of immunomodulatory markers.To demonstrate a direct association between activation of the EMT program and immunosuppression, we induced EMT programs in vitro in an array of cultured BrCa cell lines via the doxycycline-induced expression of various EMT-inducing transcription factors (EMT-TFs) and proceeded to determine whether activation of the EMT program also alters cell-intrinisc immuno-modulatory markers To do so, we used the nCounter PanCancer Immune Profiling Panel (Nanostring Technologies)to perform transcriptomic analyses of control E cells or those induced to undergo an EMT

overall_design: RNA was extracted from the indicated cell lines cultured in vitro or from sorted GFP+ tumor cells using the RNeasy Mini Kit (Qiagen) and transcriptomic analysis was performed using the nCounter PanCancer Immune Profiling Panel (Nanostring Technologies) Normalization of Nanostring nCounter gene expression values and differential expression were assayed by DESeq2

first: Robert

last: Weinberg


title: Identification of direct transcriptional targets of Nfatc2 that promote β-cell proliferation in human islets (ChIP-seq)

city: Madison

first: Shane

middle: P

last: Simonett

state: Wisconsin

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

summary: The transcription factor Nfatc2 is a potent β-cell mitogen in mouse and human islets, however, the direct genomic targets that mediate the mitogenic effects have not been identified. We expressed a constitutively active form of Nfatc2, and the closely related Nfatc1, in human islets and identified ~5,600 differentially expressed genes. Nfatc2 binding sites in human islets were identified via ChIP-seq, yielding ~8,600 high-confidence peaks. By integrating gene expression changes induced by Nfatc2 with genomic binding sites for Nfatc2, we identified ~2,200 direct transcriptional targets of Nfatc2 in human islets. Direct targets that were induced by Nfatc2 were enriched for transcripts that regulate the cell cycle, and for motifs associated with the transcription factor FoxP1. We showed that islets from an endocrine-specific FoxP1, FoxP2 and FoxP4 triple-knockout mouse are less responsive to Nfatc2-induced β-cell proliferation, suggesting the FoxP family may work in concert with Nfatc2 to regulate β-cell proliferation. Nfatc2 induced β-cell proliferation in both mouse and human islets, whereas Nfatc1 does so only in human islets. Exploiting this species difference in Nfatc1-responsiveness, we identified ~250 direct transcriptional targets with similar transcriptional profiles. This gene set strongly enriches for cell cycle-associated transcripts, and includes the nuclear hormone receptor, Nr4a1. We show that deletion of Nr4a1 greatly reduces the capacity of Nfatc2 to induce β-cell proliferation, suggesting that much of the effect on Nfatc2 occurs through its induction of Nr4a1. Integration of ncRNA profiling, chromatin accessibility and Nfatc2 binding sites enabled us to identify key Nfatc2-dependent enhancer loci that mediate enhanced β-cell proliferation.

overall_design: Nfatc2 binding sites were identified in human islets using ChIP-seq after adenoviral transduction of a constitutively active Nfatc2 protein. Six human islets samples were used as biological replicates.

first: Mark

last: Keller

first: Alan

last: Attie


title: Identification of direct transcriptional targets of Nfatc2 that promote β-cell proliferation in human islets (ATAC-seq)

overall_design: 50 average sized human islets were collected for ATAC-seq 48 hours after GFP or ca-Nfatc2 adenoviral transduction. Three independent human islet donors were used in the ATAC-seq analysis.


title: Transcriptomal profiling of liver microphysiological system (MPS) co-culture NASH model under varying culture conditions

first: Tomasz

last: Kostrzewski

address: 332 Cambridge Science Park

institute: CN Bio Innovations

summary: Purpose: Liver MPS NASH model was cultured in the presence or absence of six independent cues to identify the culture conditions that produce a model of NAFLD/NASH that most closely represents the human disease state.

overall_design:
Methods: Liver MPS microtissues were cultured for 14 days in the PhysioMimix MPS platform (CN Bio Innovations) under varying culture conditions. Liver tissue mRNA profiles were generated and compared by deep sequencing, in triplicate, using Illumina NexstSeq500. The sequencing data was demultiplexed using Illumina bcl2fastq2-v2.16. The quality of the reads was assessed using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc). The reads were processed and mapped to the human genome using the Bcbio-nextgen framework version 1.1.2 (https://github.com/chapmanb/bcbio-nextgen). The aligner used was Hisat2 v.2.1.0 (www.ncbi.nlm.nih.gov/pmc/articles/PMC4655817). The alignment quality was assessed with QualiMap v.2.2.2 (http://qualimap.bioinfo.cipf.es). Transcript-level abundances were imported and utilized for counts estimation using the TxImport package. Identification of differentially expressed genes at False Discovery Rate < 5% per comparison was performed using DESeq2 in R.

>>>Submitter states that raw data are not available due to patient privacy concerns.<<<

first: Sophie

last: Snow

first: Aurelie

last: Bornot

first: Julia

last: Lindgren

first: Maria

last: Ryaboshapkina

first: Marya

last: Clausen

first: Manasa

last: Surakala

first: Lorna

last: Ewart

first: David

last: Hughes


title: Gene signature profiles in lung tisses of wild type mice or PD-1 or PD-L1 deficient mice  infected with Mycobacterium avium

city: TSUKUBA

first: Masashi

last: Matsuyama

state: IBARAKI

address: 1-1-1 AMAKUBO

department: respiratory medicine

institute: Tsukuba university

summary: Rationale: T cell activation is a key antimicrobial component against mycobacterial disease. Programmed cell death-1 (PD-1) and programmed cell death-ligand 1 (PD-L1) pathway could affect the antimicrobial immune responses by suppressing T cell activity. Several recent studies demonstrated that blocking of PD-1/PD-L1 pathway exacerbated Mycobacterium tuberculosis infection. However, the influence of blocking this pathway in pulmonary Mycobacterium avium-intracellulare complex (MAC) infection was not fully understood.   Objective: We aimed to determine the influence of genetic depletion of PD-1/PD-L1 pathway on the disease activity of MAC infection.  Methods: Wild-type, PD-1-deficient mice and PD-L1-deficient mice were intranasally infected with Mycobacterium avium bacteria.   Measurements and Main Results: The depletion of PD-1 or PD-L1 did not affect mortality and bacterial burden in mice infected with MAC. However, remarkable infiltration of CD8 T lymphocytes was observed in the lungs of PD-1 and PD-L1 deficient mice compared to wild-type mice. Comprehensive transcriptome analysis showed that levels of gene expressions related to Th1 immunity did not differ according to the genotypes. However, genes related to the activity of CD8 T cells and related chemokine activity were up-regulated in the infected lungs of PD-1 and PD-L1 deficient mice.   Conclusions: Depletion of PD-1/PD-L1 pathway did not affect the activation of Th1 immunity in response to MAC infection, which may explain why MAC infection was controlled in these mice. In addition, CD8-positive T cell pulmonary inflammation in knockout mice might have some clinical implication in the treatment of cancer patients with immune checkpoint inhibitors when the patients are infected with MAC.

overall_design: 18 strand-specific RNA libraries for high-throughput sequencing were prepared (3 from the lungs of the wild type mice treated with saline, 3 from the lungs of the PD-1-/- mice treated with saline, 3 from the lungs of the PD-L1-/- mice treated with saline,3 from the lungs of the wild type mice infected with M. avium for 2 months,  3 from the lungs of the PD-1-/- mice infected with M. avium for 2 months, and 3 from the lungs of the PD-L1-/- mice infected with M. avium for 2 months) using the Illumina Stranded mRNA Sample Preparation Kit with 500ng of total RNA according to manufacturer’s instructions.

first: Masayuki

last: Nakajima

first: Masafumi

last: Muratani

first: Nobuyuki

last: Hizawa


title: NCOR1 sustains CRC growth and protects from cellular senescence

city: Sherbrooke

first: Francois

last: Boudreau

state: QC

address: 3201 Jean-Mignault

department: Immunology and Cell Biology

country: Canada

institute: Université de Sherbrooke

summary: The nuclear corepressor NCOR1 is a transcriptional repressor that regulates gene expression by associating with nuclear receptors or transcription factors such as AP-1 and NF-KB. The objective of this work was to determine how NCOR1 regulates proliferation and inflammatory response in human colorectal cancer cell lines. We observed that upon targeting NCOR1 expression from the use of shRNAs, Caco-2/15 and HT-29 colorectal cancer cells stopped proliferating with characteristics of being senescent. In addition, we noticed an induction of inflammatory molecules associated with SASP in these cells. We analyzed the transcriptome of shNCOR1_655 cells and identified the SOX2 pluripotency factor as being induced when the expression of NCOR1 is decreased. This transcriptome was also enriched in molecules normally associated with migration and invasion biological processes.

overall_design: mRNA profiles of shNonTarget (Control) and shNCOR1 (NCOR1 knockdown) HT-29 and Caco-2/15 CRC cells after 7 days of lentiviral infection (3 replicates/condition)

first: Stéphanie

last: St-Jean


title: Identification of a novel FUS/ETV4 fusion and comparative analysis with other Ewing sarcoma fusion proteins [CUT&Tag]

first: Megann

last: Boone

summary: The purpose of this study was to determine the genomic localization similarities and differences in the FET/ETS translocations that have been identified as drivers of Ewing sarcoma.

overall_design:
Endogenous EWS/FLI was knocked-down in the Ewing sarcoma A673 cell line and FET/ETS cDNA constructs were expressed in these cells via viral transduction. Cells were collected after 8 days in antibiotic selection and CUT&Tag was performed, using an antibody directed-Tn5 enzyme, to show specific binding regions for each of the FET/ETS fusions. 2 biological replicates of each sample were performed for this experiment.
Please note that each processed data was generated from both replicates and is linked to the corresponding *rep1 sample records

first: Cenny

last: Taslim

first: Stephen

last: Lessnick


title: Whole genome RNA-Sequencing analysis to identify targets of miR-642a-5p in 22Rv1 prostate cancer cells.

city: Nedlands

first: Peter

middle: J.

last: Leedman

state: Western Australia

address: 6 Verdun Street

department: Cancer and Cell Biology

institute: Harry Perkins Institute of Medical Research

summary: We overexpressed miR-642a-5p or a negative control miR-NC in 22Rv1 prostate cancer cells and subjected subsequent total RNA extracted from these samples to RNA-Sequencing to generate lists of differentially regulated genes between the two treatments.

overall_design: Determining the genes which are up or down regulated following miR-642a-5p overexpression in 22Rv1 prostate cancer cells.


title: Cell state diversity promotes metastasis through heterotypic cluster formation in melanoma [RNA-Seq]

city: New York

first: Nathaniel

last: Campbell

institute: Memorial Sloan Kettering Cancer Center

summary: We report single-cell gene expression profiling of the zebrafish melanoma cell lines ZMEL1-PRO and ZMEL1-INV under multiple in vitro and in vivo (zebrafish transplant) conditions

overall_design: Single-cell RNA-seq of ZMEL1-PRO and ZMEL1-INV cells in one of four conditions: 1) in vitro individual culture; 2) in vitro co-culture; 3) in vivo primary tumors; and 4) in vivo metastases

first: Anjali

last: Rao

first: Joao

middle: B

last: Xavier

first: Richard

middle: M

last: White

first: Itai

last: Yanai


title: Effect of Clostridia strains on EAE clinical outcome as a therapeutic treatment

city: Barcelona

first: Carmen

last: Espejo

address: Passeig de la Vall d'Hebron, 119-129, Edifici Collserola, Laboratory 149-151

institute: Vall d'Hebron Institute of Research - Centre d'Esclerosi Múltiple de Catalunya

summary: Researchers have induced an experimental model of multiple sclerosis [experimental autoimmune encephalomyelitis (EAE)] in mice to investigate the therapeutic effect of the oral treatment with selected Clostridia strains on the clinical outcome of EAE and its mechanisms of action

overall_design: The experimental conditions to be considered in this study are: 1. Tissue: (a) Spleen (SPL): 12 samples (b) Spinal Cord (SC): 12 samples - 2. Treatment: (a) Vehicle (VE): 12 samples (b) Clostridia strains (CL): 12 samples

first: Laura

last: Calvo-Barreiro


title: Multiplex genome-editing in Arabidopsis thaliana using Mb3Cas12a

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: The use of CRISPR/Cas proteins for the creation of multiplex genome-engineering represents an important avenue for crop improvement, and further improvements for creation of knock-in plant lines via CRISPR-based technologies may enable the high-throughput creation of designer alleles. To circumvent limitations of the commonly used CRISPR/Cas9 system for multiplex genome-engineering, we explored the use of Moraxella bovoculi 3 Cas12a (Mb3Cas12a) for multiplex genome-editing in Arabidopsis thaliana. We identified optimized promoter sequences for driving expression of single transcript multiplex crRNA arrays in A. thaliana, resulting in stable germline transmission of Mb3Cas12a-edited alleles at multiple target sites. By utilizing this system, we demonstrate single-transcript multiplexed genome-engineering using of up to 13 crRNA targets. We further show high target specificity of Mb3Cas12a-based genome-editing via whole-genome sequencing. Taken together, our method provides a simplified platform for efficient multiplex-genome-engineering in plant-based systems.

overall_design:
Examination of off-target edtiing via WGS.
7 and 14 are two independent transgenic lines.  Samples 7.1 and 7.2 are siblings as are 7.2 and 7.3, etc (from the same parents) and likewise for 14.1 through 14.3.

first: William

last: Jordan

first: Seth

last: Currie


title: Fractalkine Antibody Attenuates Venous Neointimal Hyperplasia of Arteriovenous Fistula in Mice model

city: Rochester

first: Sanjay

last: Misra

state: MN

address: 200 First Street SW

department: Radiology

institute: Mayo Clinic

overall_design: Fractalkine Antibody  vs. vehcle

first: Sreenivasulu

last: Kilari

first: Binxia

last: Yang

first: Amit

last: Sharma

first: Steven

last: Kerr

first: Mary

last: McFarland


title: Identification of direct transcriptional targets of Nfatc2 that promote β-cell proliferation in human islets

first: Shane

last: Simonett

overall_design: Refer to individual Series


title: Transcriptional adaptation to chronic exposure to Cytolethal Distending Toxin in HeLa cells

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

country: France

institute: INRAE

summary: The Cytolethal Distending Toxin (CDT) is a bacterial genotoxin that promotes persistent bacterial colonization during infection and is associated with many inflamatory disorders and cancer. At the cellular level, CDT induces DNA damage and inflammatory signatures in host cells. The aim of this study was to better understand the links betwen CDT-mediated genotoxic activity and immunomodulatory effects. HeLa cells were exposed to a chronic (8 weeks) treatment to 0.25 ng/ml of wild-type (WT) or the catalytic mutant H153A (HA) of CDT from Escherichia coli and transcription analysis was performed using  Agilent Sureprint G3 Human GE v2 8x60k microarray.

overall_design: Human HeLa cells were exposed to 0.25 ng/ml of WT or HA CDT for 8 weeks,then RNAs were extracted.

first: Julien

last: Vignard

first: Saleha

last: Hashim

first: Claire

last: Naylies


title: Hepatic transcriptional profiles reveals the role of diet and genetic variation on cardiometabolic traits in progenitor strains of the Collaborative Cross mouse

city: Davis

first: Brian

last: Bennett

address: 430 West Health Sciences Drive

department: Obesity and Metabolism

institute: Western Human Nutrition Research Center, ARS

summary:
Purpose: To investigate the diet- or strain-dependence of liver transcriptome in eight Diversity Outbred (DO) founder strains [A/J, C57BL/6J (B6), 129S1/SvImJ (129), NOD/ShiLtJ (NOD), NZO/HILtJ (NZO), and three wild-derived strains CAST/EiJ (CAST), PWK/PhJ (PWK), and WSB/EiJ (WSB)]
Methods: Total RNA from eight DO founder strains was extracted from snap frozen liver using Maxwell® 16 LEV simplyRNA Tissue Kit (Promega) according to the manufacturer’s protocol. The quality and amount of liver RNA was evaluated using a qubit RNA assay (Invitrogen R11490) and run on an Biorad Bioanalyzer Chip to verify RNA integrity. RNASeq library was prepared by using Illumina TruSeq RNA library construction protocol. RNA samples from 24 mice-fed AIN-93 M diet and 24 mice-fed HFCA diet were submitted to the David H. Murdock Research Institute (DHMRI) for sequencing. The RNA-seq libraries were constructed from 1 µg total RNA after poly-A library preparation. The pooled libraries were sequenced on two lanes of the Illumina HiSeq2500 Instrument.
Results: Our liver transcriptomic analysis of eight mouse strains shows that diet and genetic background have a strong effect on the liver transcriptome, which may be related to differences in cardo-metabolic traits. We calculated a gene module consisting of highly correlated transcripts that enriched the biological pathway and provided a searchable database of liver transcript profiles. To further investigate the association of hepatic gene modules with cardio-metabolic traits, Fmo3, a key enzyme in the production of trimethylamine N-oxide (TMAO), and Nox4, which showed strong association with plasma TMAO and liver triglyceride, were identified as the highest expressed in the laboratory-like inbred strains (B6, 129 and NZO) and the lowest expressed transcripts in the CAST strain. We found differences in the production of TMAO and liver triglyceride, which contributes to metabolic syndrome, depending on genetic backgrounds.
Conclusions: Our study provide a valuable data resource to the research community and show that liver transcriptomic analysis identified diet- or strain-specific pathways to pathogenesis of metabolic syndrome.

overall_design: Liver mRNA profiles of 24-week old eight Diversity Outbred founder strains.

first: Blythe

last: Durbin-Johnson


title: Gene expression profiling in myeloid cells of chronic myeloid leukemia patients

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

institute: Yokohama City University

summary: To clarify whether myeloid cells in chroninc myeloid leukemia (CML) harbor any signs of altered characteristics, we performed transcriptome analyses of type 1 conventional dendritic cells (cDC1s), basophils, monocytes, and neutrophils isolated from peripheral blood of CML patients and healthy donors. Taken together with the flow cytometric analyses of these cells and bone marrow progenitors, our results indicated that anti-tumor immunity is impaired in CML patients by BCR-ABL via both disrupting cDC1 development and promoting myeloid cell-mediated immune suppression.

overall_design: RNA from human neutrophils (Neu), monocytes (Mo), basophils (Baso), type 1 conventional dendritic cells (cDC1), and neutrophils (Neu) were isolated from CML patients and healthy donors.

first: Akira

last: Nishiyama

first: Haruka

last: Sasaki

first: Koichi

last: Murakami

first: Ibuki

last: Harada


title: The RNA helicase DHX30 coordinates cytoplasmic translation and mitochondrial function contributing to cancer cell survival

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

institute: University of Trento

summary: Total RNA profiling of control and DHX30-silenced HCT116 cells, either with no treatment and after Nutlin-3 treatment.

overall_design: 4 biological samples per condition are used. A total of 16 samples were used: 8 total DMSO (scramble, DHX30 silencing), 8 total Nutlin (scramble, DHX30 silencing)

first: Alberto

last: Inga


title: Cell state diversity promotes metastasis through heterotypic cluster formation in melanoma [2D culture]

first: Nathaniel

last: Campbell

summary: We report the gene expression differences between the zebrafish melanoma cell lines ZMEL1-PRO and ZMEL1-INV

overall_design: RNA-seq of ZMEL1-PRO and ZMEL1-INV cells grown in standard adherent (2D) culture

first: Joao

last: Xavier

first: Richard

last: White


title: Cell state diversity promotes metastasis through heterotypic cluster formation in melanoma [tfap2a/e]

summary: We report how the ZMEL1-PRO cell line changes following CRISPR-Cas9 inactivation of tfap2a and tfap2e

overall_design: RNA-seq of ZMEL1-PRO zebrafish melanoma cells following CRISPR-Cas9 with either tfap2a and tfap2e sgRNA or non-targeting control sgRNA (N=3 replicate samples each)


title: Cell state diversity promotes metastasis through heterotypic cluster formation in melanoma [3D culture]

overall_design: RNA-seq of ZMEL1-PRO and ZMEL1-INV cells grown as clusters (3D) in Corning ultra-low attachment plates


title: Transcriptomic analsyis of Epithelial and Mesenchymal carcinoma cells using the nCounter PanCancer Immune Profiling panel

first: Anushka

last: Dongre

address: 455 Main St

institute: Whitehead Institute

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


title: Intracellular accumulation of IFN-λ4 contributes to protection from liver cirrhosis by inducing ER stress and enhancing IRF1 signaling

city: Bethesda

first: Ludmila

last: Prokunina-Olsson

state: MD

address: 9615 Medical Center Dr

department: Division of Cancer Epidemiology and Genetics

institute: National Cancer Institute

summary: Chronic hepatitis C virus (HCV) infection and cirrhosis are major risk factors for developing hepatocellular carcinoma (HCC). Genetic polymorphisms in the IFNL3/IFNL4 locus have been associated both with poor clearance of HCV and protection from liver fibrosis, an early stage of cirrhosis. Here, we aimed to address the genetic and functional relationships between IFNL3/IFNL4 polymorphisms, cirrhosis, and HCC risk. We evaluated associations between IFNL4 genotype (presence of rs368234815-dG or rs12979860-T alleles) with cirrhosis and HCC risk in patients with chronic HCV - 2,931 from Taiwan and 3,566 from Japan, and with gene expression and somatic mutations in 370 HCC tumors in The Cancer Genome Atlas (TCGA). Functional analyses were performed in primary human hepatocytes and hepatic stellate cells and a panel of hepatoma HepG2 cell lines with gene-edited IFNLR1 and inducible expression of IFN-λ3 or IFN-λ4. We detected associations between IFNL4 genotype and decreased risk of cirrhosis (OR=0.66, 95%CI=0.46-0.93, P=0.018, in Taiwan), but increased risk of HCC in patients without HCV clearance (OR=1.28, 95%CI=1.07-1.52, P=0.0058, in Japan). IFNL4 genotype was also associated with reduced cell proliferation and enrichment of CTNNB1 mutations in HCC tumors in TCGA. Reduced proliferation in hepatic cells was contributed by intracellular accumulation of IFN-λ4 leading to induction of ER stress and enhanced IRF1 signaling. The strong anti-proliferative effects of IFN-λ4 in hepatic cells could explain the association of IFNL3/IFNL4 polymorphisms with decreased cirrhosis. However, by sustaining persistent HCV infection, IFN-λ4 may contribute to the development of CTNNB1 mutations and increased risk of HCC in patients without viral clearance.

overall_design: Differentially expressed genes (DEGs, P-FDR < 0.05) were identified by RNA-seq analysis in IFN-λ3-GFP, IFN-λ4-GFP and IFN-λ4-GFP-IFNLR1KO HepG2 cells after 8, 24, and 72 hrs of induction by dox, comparing to controls (dox- conditions).

first: Olusegun

middle: O

last: Onabajo

first: Fang

last: Wang

first: Mei-Hsuan

last: Lee

first: Oscar

last: Florez-Vargas

first: Adeola

last: Obajemu

first: Mauro

last: Castro

first: Chizu

last: Tanikawa

first: Joselin

last: Vargas

first: Shu-Fen

last: Liao

first: Ci

last: Song

first: Yu-Han

last: Huang

first: Chen-Yang

last: Shen

first: A

last: Rouf Banday

first: Thomas

last: O’Brien

first: Zhibin

last: Hu

last: Matsuda

last: Robertson


title: Lipin 1 regulates mRNA splicing in fasting and feeding in mouse liver

city: Los Angeles

first: Huan

state: California

address: 695 Charles E Young Dr RM6309

department: Human Genetics

institute: UCLA

summary: The lipin phosphatidate phosphatase (PAP) enzymes (lipin 1, lipin 2, and lipin 3) catalyze a step in triglyceride and phospholipid biosynthesis, and genetic lipin deficiencies cause human disease that is triggered by metabolic stress, such as fasting. We assessed the protein interactome of lipins 1, 2, and 3 in hepatocytes, and identified unique protein associations between lipin 1 and U2 mRNA spliceosome components. Lpin1–/– mouse liver exhibited aberrant mRNA splicing in the fasted state, including mRNAs involved in mRNA processing and liver maturation. Aberrant splicing could be induced in cultured hepatocytes by lipin 1 knockdown or elevated phosphatidic acid levels, suggesting a role for lipin 1 PAP activity in splicing fidelity. Refeeding Lpin1–/– animals after fasting largely restored mRNA splicing fidelity. Reduced levels of ESRP2 splicing factor exclusively in the fasted state of Lpin1–/– liver was associated with widespread aberrant exon inclusion.  These findings connect lipid homeostasis with mRNA splicing, and identify aberrant mRNA splicing in lipin 1 deficiency as a potential contributor to disease symptoms triggered by fasting.

overall_design: Mouse liver RNA was isolated from fasting and feeding conditions for RNA sequencing

first: Karen

last: Reue


title: Metformin Ingestion Rejuvenates Myoblasts from Older Adult Donors

city: Salt Lake City

first: Micah

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

summary: We tested the hypothesis that 2-weeks of metformin ingestion in healthy older adults would improve intrinsic age-related deficits in myoblast (activated satellite cell) function as tested by a series of in vitro functional assays to determine proliferation, fusion index, and myoblast-endothelial cell homing.

overall_design: Myoblasts were isolated from muscle biopsied from healthy community dwelling older (4m/4f, 69y) adult participants before (pre) and after (post) the metformin ingestion period. Myoblasts were harvested from young participants (4m/4f, 27y) to serve as a “youthful” comparator.

first: Ziad

middle: S

last: Mahmassani

first: Paul

middle: T

last: Reidy

first: Alec

last: McKenzie

first: Jonathan

last: Petrocelli

first: Dennis

last: Fix

first: Naomi

last: de Hart

first: Patrick

last: Ferrara

first: Katsuhiko

last: Funai


title: CD49f defines a subset of dysfunctional regulatory T cells circulating in the human peripheral blood

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

institute: QIMR Berghofer

summary: Integrin CD49f has been reported to modulate various aspects of T cell biology including cell differentiation, migration and functionality.  Here we define CD49f as a marker for a subset of dysfunctional human effector Tregs expressing a Th17-like profile in the blood of patients with active inflammatory bowl disease.

overall_design: RNA profiles of CD49f high and low Tregs extracted from healthy donor peripheral blood mononuclear cells (PBMC).

first: Ailin

last: Lepletier

first: Michelle

last: Hill


title: Identification of direct transcriptional targets of Nfatc2 that promote β-cell proliferation in human islets (ncRNA-seq)

first: Shane

last: Simonett

address: 433 Babcock Drive

institute: University of Wisconsin-Madison

summary: The transcription factor Nfatc2 is a potent β-cell mitogen in mouse and human islets, however, the direct genomic targets that mediate the mitogenic effects have not been identified. We expressed a constitutively active form of Nfatc2, and the closely related Nfatc1, in human islets and identified ~5,600 differentially expressed genes. Nfatc2 binding sites in human islets were identified via ChIP-seq, yielding ~8,600 high-confidence peaks. By integrating gene expression changes induced by Nfatc2 with genomic binding sites for Nfatc2, we identified ~2,200 direct transcriptional targets of Nfatc2 in human islets. Direct targets that were induced by Nfatc2 were enriched for transcripts that regulate the cell cycle, and for motifs associated with the transcription factor FoxP1. We showed that islets from an endocrine-specific FoxP1, FoxP2 and FoxP4 triple-knockout mouse are less responsive to Nfatc2-induced β-cell proliferation, suggesting the FoxP family may work in concert with Nfatc2 to regulate β-cell proliferation. Nfatc2 induced β-cell proliferation in both mouse and human islets, whereas Nfatc1 does so only in human islets. Exploiting this species difference in Nfatc1-responsiveness, we identified ~250 direct transcriptional targets with similar transcriptional profiles. This gene set strongly enriches for cell cycle-associated transcripts, and includes the nuclear hormone receptor, Nr4a1. We show that deletion of Nr4a1 greatly reduces the capacity of Nfatc2 to induce β-cell proliferation, suggesting that much of the effect on Nfatc2 occurs through its induction of Nr4a1. Integration of ncRNA profiling, chromatin accessibility and Nfatc2 binding sites enabled us to identify key Nfatc2-dependent enhancer loci that mediate enhanced β-cell proliferation.

overall_design: Whole-islet RNA was collected from 5 separate human donors 48 hours after adenovirus (Ad)-mediated expression of constitutively active (ca) Nfatc2 or Ad-GFP. ncRNAs were enriched using RiboZero purification and oligo-dT depletion.

first: Mark

last: Keller

first: Alan

middle: D

last: Attie


title: RNA Immunoprecipitation-sequencing from mouse liver using HuR antibody

city: ATHENS

first: Gargani

last: Sofia

state: Please Select

address: 34, Alexander Fleming Street

country: Greece

institute: BSRC Fleming

summary: We report the HuR-RNA interactions in the liver by performing RNA-immunoprecipitation sequencing (RIP-seq). RIP-seq was performed in healthy livers of wildtype (WT) mice using a HuR antibody. We found that 1380 cytoplasmic-target mRNAs bound to HuR, as assessed by the comparison between the HuR-specific antibody and the IgG control

overall_design: Examination of RNAs that are targets of HuR in the mouse liver

first: D

last: Kontoyiannis

first: S

last: Gargani


title: Genomic instability in the naturally and prematurely aged myocardium [variants: data set 2]

city: Münster

first: Monika

last: Stoll

institute: Institute for Human Genetics, Genetic Epidemiology, University of Muenster

summary: Our data demonstrate that genomic instability does not evidently contribute to naturally aging of the mouse heart and support the contention that the endogenous DNA repair machinery is remarkably active to maintain genomic integrity in cardiac cells throughout life.

overall_design: Investigation of variants in samples from small intestine, liver and spleen tissues of naturally aged mice of 12 and 104 weeks of age.

first: Federica

last: De Majo

first: Leonie

last: Martens

first: Frank

last: Rühle

first: Magda

last: Hamczyk

first: Rosa

last: Nevado

first: Vicente

last: Andrés

first: Christian

last: Bär

first: Thomas

last: Thum

first: Martine

last: de Boer

first: Dirk

last: Duncker

first: Blanche

last: Schroen

first: Anne-Sophie

last: Armand

first: Leon

last: De Windt


title: Sequencing of liver RNA from HuR WT and HuR KO mice

city: Dresden

first: Triantafyllos

last: Chavakis

address: Fiedlerstraße 42

department: Klinische Pathobiochemie

institute: Medizinische Fakultät der TU Dresden

summary: We aimed to identify genes that are altered upon deletion of HuR in hepatocytes under steady state conditions.

overall_design: RNA-seq of liver samples from 4 HuR WT mice and 4 HuR KO mice.

first: Pallavi

last: Subramanian


title: Identification of direct transcriptional targets of Nfatc2 that promote β-cell proliferation in human islets (RNA-seq)

city: Madison

first: Shane

last: Simonett

overall_design: Whole-islet RNA was sequenced from 8 separate human donors (1 – 8) 48 hours after adenovirus (Ad)-mediated expression of constitutively active (ca) Nfatc1 or Nfatc2; Ad-GFP was used as the negative control.

first: Mark

last: Keller

first: Alan

last: Attie


title: Bone metastatic variant of MCF7 cells

city: Nashville

first: Rachelle

last: Johnson

address: 2215B Garland Ave

institute: Vanderbilt University Medical Center

summary: A bone-metastatic variant of MCF7 cells was created from a spontaneous metastasis from the mammary fat pad to the bone marrow in the absence of exogenous estrogen. The goal of the study was to determine differences in gene expression between the parental MCF7 cells and the bone metastatic variant.

overall_design: There are three biological replicates of the control MCF7 cells containing a non-silencing shRNA construct, which was used in the initial experiment to create the bone-metastatic variant, and three biological replicates of the MCF7 bone metastatic cells (MCF7b). Each biological replicate was collected from independent experiments.

middle: W


title: Deoxyhypusine Synthase Promotes a Pro-Inflammatory Macrophage Phenotype

city: Chicago

first: Raghavendra

last: Mirmira

state: IL

address: 900 E. 57th Street

department: Medicine

institute: University of Chicago

summary: Obesity is characterized by adipose tissue expansion, macrophage infiltration, and the development of chronic low-grade meta-inflammation that drives insulin resistance and metabolic dysfunction.  Eukaryotic translation initiation factor 5A (eIF5A) is the only protein known to be uniquely post-translationally modified and activated by deoxyhypusine synthase (DHPS) to generate a hypusine (Hyp) residue. Activated eIF5A controls the translation of a subset of mRNAs that play a role in inflammation, but a role for the DHPS/eIF5AHyp axis in obesity-associated adipose tissue inflammation has not been tested. We found DHPS/eIF5AHyp levels to be increased in the stromal vascular fraction of adipose tissue from mice fed a high fat diet and in murine macrophages activated to a proinflammatory M1 phenotype. DHPS deficiency in M1 macrophages decreased global mRNA translation and protein synthesis of key inflammatory mediators, IL-1β and MIP-1α.  Transcriptomes of LPS+IFN-γ-stimulated DHPS-deficient macrophages revealed reduced characteristics of an M1 signature and a phenotypic switch consistent with characteristics of an anti-inflammatory M2 signature. In support of these observations, macrophage migration in a zebrafish tailfin injury model was reduced with chemical inhibition of DHPS, and DHPS deficiency in myeloid cells of HFD-fed mice inhibited M1 macrophage accumulation in adipose tissue and improved glucose tolerance. Together, these findings indicate that DHPS is required for the translation of a subset of mRNAs required for inflammation and chemotaxis in macrophages and may contribute to a proinflammatory M1-like phenotype.

overall_design: Purified total RNA was first evaluated for its quantity, and quality, using Agilent Bioanalyzer 2100. All RNA samples had a RIN (RNA Integrity Number) of eight or higher. Each library was quantified, and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled in equal molarity. Average size of library insert was approximately 110b. Pooled libraries were applied to Ion Sphere Particles (ISP) with template preparation and amplification using Ion OneTouch 2, followed by ISP loading onto a PI chip and sequencing on Ion Proton semiconductor (Life Technologies). A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).

first: Wenting

last: Wu


title: Dissecting the Transcriptomic Landscape of Circulating Mononuclear Phagocytes in Langerhans Cell Histiocytosis at Single-cell Level

city: Beijing

first: Han

last: He

address: No. 8 Dongdajie

institute: Fifth Medical Center of Chinese PLA General Hospital

summary: Langerhans cell histiocytosis (LCH) is a rarely clonal disorder caused by aberrant activation of MAPK pathway, which predominantly affects the mononuclear myeloid lineages. Many efforts have been devoted to tracking precursor cells in circulating blood and bone marrow by detection of BRAFV600E alleles and to exploring the differentiation potential of LCH-related myeloid cells in vitro. However, their cellular and molecular alterations remain unclear. Here, we constructed a single-cell transcriptional landscape of more than 3,000 monocytes and DCs from treatment-naïve pediatric LCH and targeted-therapy pediatric LCH cohorts, unraveling patient to patient heterogeneity and underlying molecular mechanisms of BRAF inhibitor, respectively. In parallel, we further investigated the precise relationship between circulating potential precursors and pathological LCH clusters based on unbiased joint analysis. In addition, we found that the proportion of pDC in Lin-HLA-DR+ population is closely linked with the severity of the disease, providing a novel promising indicator to optimize the stratification strategy. Taken together, our data update the molecular understanding of LCH biology, which might contribute to improvement of clinical therapeutics and promotion of the personalized medicine.

overall_design: We performed the STRT-seq of 3,271 cells to generate  transcriptomic landscapes of  circulating monocytes and DCs closely related to tissue pathological cells in LCH patients.

first: Hui

last: Shi

first: Zhilei

last: Bian

first: Tao

last: Huang

first: Lei

last: Cui

first: Rui

last: Zhang

first: Bing

last: Liu


title: Differentially expressed circRNAs in recurrent implantation failure

city: Jinan

first: Junhao

last: Yan

address: No.157 Jingliu Road

institute: Center for Reproductive Medicine

summary: Our study is designed to demonstrate altered profiles of circRNAs in the luteal-phase endometrium from patients with RIF. Functional studies will be further confirmed. This study will provide new viewpoint for understanding the roles of non-coding RNA for endometrial stromal cells and epithelial cells function, as well as potential etiologic mechanism for RIF.

overall_design: We have completed the human CircRNA microarray analysis of the 16 luteal-phase endometrial samples .

first: Tianxiang

last: Ni


title: Cell state diversity promotes metastasis through heterotypic cluster formation in melanoma

city: New York

first: Nathaniel

middle: R

last: Campbell

state: NY

institute: Memorial Sloan Kettering Cancer Center

overall_design: Refer to individual Series


title: Whole transcriptomes analyses of intestinal epithelial cells (IECs) isolated from Mst4F/F Villincre (Mst4 KO) mice and wildtype (WT) mice

city: Shanghai

first: hui

last: zhang

state: Shanghai

address: 2205 Songhu Road

institute: Fudan University

summary:
Purpose: To explore the molecular mechanisms of MST4 regulating intestinal stem cell homeostasis, RNA sequencing was performed to analyze the geome-wide change of MST4 KO IECs compared to those of WT mice.
Methods: Total mRNA was extracted from IECs which were isolated from small intestines of Mst4 KO mice and WT mice (8 weeks) in triplicate respectively. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina Hiseq 4000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: We mapped about 60 million sequence reads per sample to the mouse genome and identified about 50,000 transcripts in IECs of mice. Apprioximately 2,000 transcripts showed different expression between Mst4 KO and WT IECs, with a fold change ≥2 and p value <0.05. Gene set enrichment analysis (GSEA) showed a significantly negative enrichment of Wnt/b-catenin target genes and altered expression of 15 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method.
Conclusion: Our study present the datiled transcripts analysis of  IECs isolated from small intestines, with biologic replicates. Based on RNA-seq transcriptome characterization , we conclude a molecular mechanism of MST4 regulating intestinal stem cell homeostasis and provide a  framework to understand the crosstalk of MST4 and Wnt/b-catenin signaling.

overall_design: Total mRNA was extracted from IECs of Mst4 KO and WT mice (about 8 weeks) in triplicate. The quality was assessed using Agilent 2100, and the profiles were sequenced on the Illumina Hiseq X10.

first: Shi

last: Jiao


title: Genomic instability in the naturally and prematurely aged myocardium [RNA-Seq]

first: Monika

last: Stoll

overall_design: Investigation of variants in RNAseq for four different accelerated aging mouse models as well as natural aging at 3 different time points, each with 4 replicates.

first: Federica

last: De Majo

first: Leonie

last: Martens

first: Frank

last: Rühle

first: Magda

last: Hamczyk

first: Rosa

last: Nevado

first: Vicente

last: Andrés

first: Christian

last: Bär

first: Thomas

last: Thum

first: Martine

last: de Boer

first: Dirk

middle: J

last: Duncker

first: Blanche

last: Schroen

first: Anne-Sophie

last: Armand

first: Leon

last: De Windt


title: Genomic instability in the naturally and prematurely aged myocardium

type: Genome variation profiling by high throughput sequencing


title: Progesterone promotes immunomodulation and tumor development in the murine mammary gland

first: Howard

last: Yang

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

summary: Clinical studies have linked use of progestins (synthetic progesterone (P4)) to breast cancer risk. However, little is understood regarding the role native P4, signaling through the progesterone receptor (PR), plays in formation of breast tumors. Studies published by our lab highlighted a link between PR and immune signaling pathways, suggesting PR induces PR to repress the interferon signaling pathway. Given these findings, we sought to investigate whether P4/PR drive immunomodulation in the mammary gland and development of mammary gland tumors. We found that mice treated with P4 displayed changes in the mammary gland suggesting inhibited immune response compared to placebo-treated mice. Furthermore, transgenic mice with PR overexpression demonstrated decreased numbers of immune cell populations in their mammary gland, lymph nodes, and spleens. Upon long-term monitoring, we determined that multi-parous PR overexpressing mice developed significantly more mammary gland tumors than control mice. Additionally, tumors of PR overexpressing mice contained fewer infiltrating immune cells. Finally, RNA sequencing analysis of tumor samples revealed that immune-related gene signatures were enriched in tumors of control mice compared to tumors of PR overexpressing mice. Together, these findings provide a novel mechanism behind P4-mediated promotion of mammary gland tumor development and provide rationale to investigate anti-progestin treatment to promote immune-mediated elimination of mammary gland tumors.

overall_design: Total RNA isolated from mammary gland tumors developing in control GAL4 mice and PR/GAL4 mice

first: Christy

last: Hagan

middle: H


title: MicroRNA microarray of HBE cell exposed to Al2O3 NPs, PM2.5, DEP

first: Rui

last: Chen

address: No.10 Xitoutiao, You An Men

institute: Capital medical university

summary:
miRNAs have been implicated in the regulation of a broad range of biological processes including development, immunity and inflammation
We used miRNA microarray to explore the detailed biological processes and mechanisms underlying matter-induced pulmonary toxicity

overall_design: Microarray expression screening was performed using HBE cells exposed to PBS, Al2O3 NPs, PM2.5, DEP.

first: Xiaobo

last: Li


title: Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses

status: Public on Sep 14 2021

city: Chapel Hill

first: Paul

last: Grant

state: NC

address: 3105 Neuoscience Research Building

department: BARC

institute: UNC SOM

summary: RNAseq experiments of Enterovirus A71 wild type demonstrate that the pyrazine-carboxamide ribonucleotide stimulates catalyzed intra- and intermolecular template switching. These results suggest that pyrazine-2 carboxamide ribonucleotides do not induce lethal mutagenesis or chain termination, but function by promoting template switching and formation of defective viral genomes. We conclude that RdRp-catalyzed intra- and intermolecular template switching can be induced by pyrazine-carboxamide ribonucleotides, defining an additional mechanistic class of antiviral ribonucleotides with potential for broad-spectrum activity.

overall_design: mRNA profiles of Enterovirus A71-inefected RD cells, in presence of different T-1106 concentrations

first: Marco

last: Vignuzzi

first: Craig

middle: E

last: Cameron

first: Nynke

last: Dekker


title: The anti-inflammation effect of human alpha-1 antitrypsin (hAAT)

city: Gainesville

first: Lei

last: Zhou

address: 2033 Mowry Rd, CGRC 261

institute: University of Florida

summary: We tested the anti-inflammation effect of hAAT in transgenic Drosophila and human senescence in vitro model using RNA-seq. The results showed hAAT can extend the life-span and delay the aging-related motor activity decline in transgenic Drosophila via specifically suppressing the expression of inflammatory microbial peptides genes. Consistent with the findings observed in Drosophila, hAAT can specifically inhibit NF-kappaB mediated senescence-associated secretory phenotype genes expression.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Examination of 1) hAAT-expression and genetically matched control Drosophila; 2) hAAT treated and 1X PBS treated human senescent cells.

first: Sihong

last: Song


title: Genomic instability in the naturally and prematurely aged myocardium [variants: data set 1]

first: Monika

last: Stoll

overall_design: Investigation of genetic variants in natural aging and accelerated aging mouse model Ercc1.

first: Federica

last: De Majo

first: Leonie

last: Martens

first: Frank

last: Rühle

first: Magda

last: Hamczyk

first: Rosa

last: Nevado

first: Vicente

last: Andrés

first: Christian

last: Bär


title: A TALE homeodomain transcription factors-binding protein recruits Polycomb Repressive Complex 2 to a subset of loci in rice shoot apical meristem

city: Wuhan

first: Fengquan

last: Tan

address: Hongshan

institute: HZAU

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


title: 50 pairs of transcriptomes from 50 patients covering 9 types of cancer

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: We aimed to study the contribution of RNA binding proteins in shaping the highly divergent cancer spliceome

overall_design: 50 pairs of transcriptomes (normal and tumor) from 50 patients covering 9 types of cancer.

first: Yuxin

first: Yi

last: Zhang


title: Reactivation of Tumor Suppressor in Breast Cancer by Enhancer Switching through NamiRNA Network

first: Ying

last: Liang

address: Room 416, West Building 13, Dong'an Road 130, Xuhui District

summary: We reported that low expression of miRNA in cancer as a recognized signature leads to loss function of TSGs in breast cancer. In 157 paired breast cancer and adjacent normal samples, tumour suppressor gene GPER1 and miR-339 are both downregulated in Luminal A/B and Triple Negative Breast Cancer subtypes. Mechanistic investigations revealed that that miR-339 upregulates GPER1 expression in breast cancer cells by switching on the GPER1 enhancer, which can be blocked by enhancer deletion through the CRISPR/Cas9 system.

overall_design: 1). Examination of H3K27ac histone modification alterations in 293T cells after overexpressing miR-339; 2). mRNA profiles of  4175 cells after overexpressing miR-339

first: Shaoxuan

last: Wang

first: Wenxuan

last: Li

first: Wei

first: Wenqiang

last: Yu


title: SNX18 inhibits melanoma migration by modulating the activation ratio of Cdc42 & RhoA

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

institute: Tel Aviv University

summary:
To identify novel proteins that control melanoma development and progression, we integrated high-throughput proteomics, mRNA and miRNAs datasets from isogenic primary (WM115) and metastatic (WM266-4) melanoma cell-lines. We focused on differentially expressed proteins that had non-differential mRNA levels and were putatively targeted by a high number of miRNAs. SNX18, a sub-family member of sorting-nexins that participates in endocytosis and autophagy was down-regulated by 6-fold in WM266-4, and predicted to be targeted by 17 miRNAs. Over-expression of SNX18 in several melanoma cell-lines significantly reduced migration rate, while silencing of SNX18 resulted in the opposite effect. Notably, progression tissue microarrays demonstrated a trend for SNX18 downregulation in early metastasis. Luciferase assays confirmed the direct regulation of SNX18 by multiple miRNAs. Indeed, over-expression of these miRNAs repressed endogenous SNX18 expression at the protein but not mRNA level. Further, protein but not mRNA expression levels correlated with better overall survival as determined in a cohort of 48 metastatic melanoma patients and in the TCGA database. Mechanistically, SNX18-mediated reduced migration coincided with RhoA activation and Cdc42 inactivation. Both play a role, as RhoA inhibitor and constitutively activated Cdc42 mutants abrogated this effect. Moreover, phosphorylation-defective SNX18 mutants (S233A,S233D) migrated faster, with S233A inactivating RhoA and activating Cdc42, while S233D activated both. The downstream phosphorylation of the p38>MAPKAPK2>HSP27 signaling pathway was concordant. Both mutants were more abundant in the plasma membrane. Taken together, phosphorylation of S233 is crucial for SNX18 activation, but de-phosphorylation dynamics, which may occur at the membrane, is required for functional effect.
In this study we compared the proteome, transcriptome and miRnome of primary and metastatic melanoma isogenic cell-lines and identified SNX18 as a novel inhibitor of melanoma migration.

overall_design: 2 biological repeats (A & B, performed at different days) of mock vs. SNX18-V1 OX cells in 2 cell lines (WM-266-4 and 624mel).

first: Maya

last: Goshen

first: Michal

last: Harel

first: Ettai

last: Markovits

first: Keren

last: Shapira

first: Erez

last: Baruch

first: Iris

last: Barshack

last: Besser

first: Jacob

last: Schachter

first: Rona

last: Ortenberg

first: Jasmine

last: Hirsch

first: Yoav

last: Henis

first: Tamar

last: Geiger

first: Gal

last: Markel


title: A TALE homeodomain transcription factors-binding protein recruits Polycomb Repressive Complex 2 to a subset of loci in rice shoot apical meristem [ChIP-seq]

first: Fengquan

last: Tan

summary: In this work, we investigated the function of PAP1 (LOC_Os03g01840) in gene expression, H3K27 tri-methylation, and Polycomb Repressive Complex 2 (PRC2) binding by high-throughput approaches. The PAP1 loss-of-function results in defects of meristem development and gene expression similar to those of PRC2 and/or KNOX gene mutants and decreases of H3K27me3 and PRC2 binding at KNOX-binding genes in the meristem. PAP1-meidated PRC2 recruitment may contribute to H3K27me3 shifting from heterochromatin silencing to developmental gene repression during land plant evolution.

overall_design: Examination of H3K27me3 modifications and EMF2b binding in wild type and pap1 mutant in rice.

first: Feng

middle: Q

first: Dao

middle: X

last: Zhou


title: Comparative transcriptome analysis reveals different adaptation mechanisms for degradation of very-long chain and normal-long chain alkanes in Dietzia sp. DQ12-45-1b

first: Hongxiu

last: XU

state: Beijing

address: Zhongguancun road

institute: PekingUniversity

summary: In this study we compare the transcriptome of the strain Dietzia sp. DQ12-45-1b grown in octacosane , hexadecane and glucose  for the characterization distinct adaption mechanisms under different alkane substrates

overall_design: RNA-seq was used to compare Dietzia sp. DQ12-45-1b grown to mid log phase in the presence of either octacosane, hexadecane and glucose (control condition) as the carbon source. The genes differentially expressed in the pairwise comparisons were studied to reveal the distinct degradation mechanisms between octacosane and hexadecane .

last: Xu

first: Yong

last: Nie

first: Xiaolei

last: Wu


title: Complement factor C1q mediates sleep spindle disruption and epileptic spikes after mild brain injury

city: San Francisco

first: Fiorella

middle: Carla

last: Grandi

address: 1650 Owens Street

institute: Gladstone

summary: While traumatic brain injury (TBI) acutely disrupts the cortex, most TBI-related disabilities reflect secondary injuries that accrue over time. The thalamus is a likely site of secondary damage because of its reciprocal connections with the cortex. Using a mouse model of mild cortical injury that does not directly damage subcortical structures (mTBI), we found a chronic increase in C1q expression specifically in the corticothalamic circuit. Increased C1q expression co-localized with neuron loss and chronic inflammation, and correlated with disruption in sleep spindles and emergence of epileptic activities. Blocking C1q counteracted these outcomes, suggesting that C1q is a disease modifier in mTBI. Single-nucleus RNA sequencing demonstrated that microglia are the source of thalamic C1q. Since the corticothalamic circuit is important for cognition and sleep, which can be impaired by TBI, this circuit could thus be a new target for treating TBI-related disabilities.

overall_design: Mice were euthanized mice with 4% isoflurane, perfused with ice-cold 1X PBS, and decapitated and   300-µm thick coronal slices were prepared with a Leica VT1200 microtome (Leica Microsystems) and placed under a Zeiss SteREO Discovery.V8 stereoscopic microscope (Zeiss) for visually-guided micro-dissections of the nRT and the adjacent relay thalamic nuclei (as shown in Fig. 3A).   Two replicate sham and mTBI groups were collected for this study. Replicate 1 contained tissue from n = five sham mice and n = six mTBI mice. Replicate 2 contained tissue from n = four sham mice and n = four mTBI mice.

first: Stephanie

last: Holden

middle: C

first: Jeanne

last: Paz

first: Ryan

last: Corces


title: Transcriptome sequencing of genes related to glucose availability in Schizosaccharomyces pombe by RNA-seq analysis

city: Istanbul

first: Ozgur

last: Cakir

address: Vezneciler

country: Turkey

institute: Istanbul University

summary: Gene expression profiles in Schizosaccharomyces pombe mid-log-phase cells grown in three different Synthetic Dextrose medium with different glucose content were compared using the RNA sequencing method. Expression patterns of genes that function in carbohydrate metabolism were downregulated as expected, and these genes were downregulated in line with the increase in glucose content. Significant and consistent changes in the expression were observed such as genes that encoding retrotransposable elements, heat shock proteins, glutathione S-transferase, cell agglutination protein, and conserved fungal proteins.

overall_design: Examination and comparement of transcriptom data from S.pombe wild type cells grown in different Synhetic Medium with different glucose content.

first: Cagatay

last: TARHAN

first: Özgür

last: ÇAKIR


title: Characterization of  CD4 T cells isolated from Mtb-infected lungs

city: Saint Louis

first: Shabaana

middle: Abdul

last: Khader

state: Missouri

address: 660 South Euclid Avenue

department: Department of Molecular Microbiology

institute: Washington University in St. Louis

summary: CD4+ T cells were sorted from the lungs of differentially treated mice and subjected to RNA sequencing to determine global gene signature profile

overall_design: CD4+ T cells were sorted from the lungs of unvaccinated mice, vaccinated mice and vaccinated mice that received ZDC transfer following Mtb infection

first: Shibali

last: Das


title: Sex-dependent gene expression dynamics in primary mouse hepatocytes

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary:
Transcriptome of primary hepatocytes from female and male C57BL/6N wild type mice after 0 to 96 hours of culture.
This study aimed to deliver fundamental information on sex differences in primary mouse hepatocytes in vitro.

overall_design: DNA-microarrays were hybridized with individual hepatocyte samples from 5 male and 5 female mice after 0, 24, 48, 72 and 96 h of culture. In total 50 DNA-microarrays were hybridized.

first: Kaja

last: Blagotinšek Cokan

first: Luise

last: Spormann

first: Madlen

last: Matz-Soja

first: Damjana

last: Rozman


title: RNA-sequencing in mouse mastocytoma cell line P815

city: Hangzhou

first: Xinyue

last: Guo

state: Zhejiang

address: 1 Xueshi Road

department: Department of Gynecology

institute: Women's hospital, School of Medicine, Zhejiang University

summary: We report the transcriptome sequencing results of the mouse mastocytoma cell line P815. After ESR1-specific shRNA vectors (SH) or the negative control vectors (NC) were transfected, the transcriptome in P815 after estrogen stimulation.  We also detected the transcriptome of P815 cells after estrogen stimulation with the administration of estrogen receptor inhibitors Tamoxifen and ICI-182780.

overall_design: Examination of the transcriptome of mouse mastocytoma cell line P815 with or without estrogen treatment.

first: Xinmei

last: Zhang


title: Effect of 8-oxoguanine DNA glycosylase 1 (OGG1) inhibitor on pro-inflammatory gene expression.

city: GALVESTON

first: Xu

last: zheng

state: Texas

address: 301 University Boulevard Basic Science building, 3.142

department: Microbiology and Immunology

institute: University of Texas Medical

summary:
Balbc J mouse received vehicle (solvent) or OGG1 inhibitor 1, 4, 8, 12, 24, 28 , 32, 36, 40 and 44h after RSV infection via intraperitoneal route.
RSV (10^6 PFU) was installed into lungs via intranasal route in 60 microliters of solvent).
One, 2, 3, 6, 12, 24, 48 and 72 hour after RSV challenge mice were sacrificed, lungs were removed and RNAs were isolated from individual lungs (n=6)
After reverse transcription cDNAs were pooled and changes in gene expression was determined by using SABiosciences Mouse Inflammatory Cytokines & Receptors PCR Array (PAMM-011ZD)

overall_design: Total pooled (n=6) cDNAs generated  Superscript® III First Strand Synthesis System (Invitrogen), mixed with equal amounts of 2X SYBR Green Supermix (Qiagen) and 20 μl of reaction mixture was added to each well of the PAM-011ZD array. The reaction was evaluated using an ABI PRISM® 7000 Sequence Detection System using recommended settings by SABiosciences.

last: Zheng

first: Istvan

last: Boldogh


title: Transitions in lineage specification and gene regulatory networks in hematopoietic stem/progenitor cells over human development

city: Oxford

first: Supat

last: Thongjuea

department: The MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: We developed a novel scRNAseq analysis pipeline called SingCellaR. This tool provides a comprehensive set of the functionalities necessary for analysis of large-scale single cell datasets generated by different single-cell technologies. The utility of SingCellaR is illustrated by analysis of a unique dataset capturing hematopoietic stem/progenitor cells (HSPC) across different stages of human ontogeny, from early fetal liver to adult bone marrow, identifying developmental stage- and site-specific differences in the HSPC compartment.

overall_design: We used 10x genomics platform to profile single-cell transcriptome of hematopoietic stem/progenitor cells (HSPCs) sampled throughout the course of human ontogeny. This included early FL (eFL) from first trimester fetuses, paired fetal bone marrow (FBM) and FL from the same second trimester fetuses, paediatric BM (PBM), and adult BM (ABM).

first: Anindita

last: Roy

first: Bethan

last: Psaila


title: Sex chromosomes versus gonadal hormones in neonatal hyperoxic lung injury

city: Houston

first: Krithika

last: Lingappan

address: 6621 Fannin

institute: Baylor College of Medicine

summary: This study was conducted in neonatal FCG male and female neonatal mice.

overall_design: Male and female four core genotypes neonatal mice were exposed to hyperoxia (95% FiO2) from P1-P5 and euthanized on P7 and P21

first: Cristian

last: Coarfa