title: Endothelial OTUD1 promotes Ang II-induced vascular remodeling by deubiquitinating SMAD3

address: Chashan Street

summary: Understanding the molecular mechanisms of pathological vascular remodeling is important for treating cardiovascular diseases and complications. Recent studies have highlighted a role of deubiquitinases in vascular pathophysiology. In this study, we investigated the role of a deubiquitinase, OTUD1, in angiotensin II (Ang II)-induced vascular remodeling. We identified upregulated OTUD1 in the vascular endothelium of Ang II-challenged mice and showed OTUD1 deletion attenuated vascular remodeling, collagen deposition, and EndMT. Conversely, OTUD1 overexpression aggravated these pathological changes both in vivo and in vitro. Mechanistically, SMAD3 was identified as a substrate of OTUD1 using co-immunoprecipitation followed with LC-MS/MS. We found OTUD1 stabilizes SMAD3 and facilitates SMAD3/SMAD4 complex formation and subsequent nuclear translocation through both K48- and K63-linked deubiquitination. OTUD1-mediated SMAD3 activation regulate the transcription of genes involved in vascular EndMT and remodeling in HUVECs. Finally, SMAD3 inhibition reversed OTUD1-promoted vascular remodeling. Our findings demonstrate endothelial OTUD1 promoted Ang II-induced vascular remodeling by deubiquitinating SMAD3. This study identified SMAD3 as a target of OTUD1 and indicates OTUD1 as a potential therapeutic target for the diseases related to vascular remodeling.

overall_design: we performed RNA sequencing analysis on the aortas of three WT+Ang II group mice and three KO+Ang II mice.


title: Identification of a minimum number of genes to predict triple negative breast cancer subgroups from gene expression profiles

status: Public on Dec 24 2022

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary: Background: Triple-negative breast cancer (TNBC) is a very heterogeneous disease. Several gene expression and mutation profiling approaches were used to classify it and all converged to the identification of distinct molecular subtypes, with some overlapping across different approaches. However, a standardised tool to routinely classify TNBC in the clinics and guide personalised treatment is lacking. We aimed at defining a specific gene signature for each of the six TNBC subtypes proposed by Lehman et al. in 2011 (Basal-like 1 (BL1); Basal-like 2 (BL2); Mesenchymal (M); Immunomodulatory (IM); Mesenchymal Stem like (MSL) and Luminal androgen receptor (LAR)), to be able to accurately predict them.  Methods: Lehman’s TNBCtype subtyping tool was applied to RNA-sequencing data from 482 TNBC (GSE164458) and a minimal subtype-specific gene signature was defined by combining two class comparison techniques with seven attribute selection methods. Several machine learning algorithms for subtype prediction were used and the best classifier was applied on microarray data from 72 Italian TNBC and on the TNBC subset of the BRCA-TCGA dataset.   Results: we defined two signatures with the 120 and 81 top up- and down-regulated genes that define the six TNBC subtypes, with prediction accuracy ranging from 88,6% to 89,4%, and even improving after removal of the least important genes. Network analysis was used to identify highly interconnected genes within each subgroup. Two druggable matrix metalloproteinases were found in the BL1 and BL2 subsets, and several druggable targets complementary to androgen receptor or aromatase in the LAR subset. Several secondary drug-target interactions were found among the up-regulated genes in the M, IM and MSL subsets.  Conclusions: Our study took full advantage of available TNBC datasets to stratify samples and genes into distinct subtypes, according to gene expression profiles. The development of a data mining approach to acquire a large amount of information from several datasets, has allowed us to identify a well-determined minimal number of genes that may help in the recognition of TNBC subtypes. These genes, most of which have been previously found to be associated with breast cancer, have the potential to become novel diagnostic markers and/or therapeutic targets for specific TNBC subsets.

overall_design: Prediction of triple negative breast cancer (TNBC) subgroups from gene expression profiles of 72 TNBC samples.

first: Laila

last: Akhouayri

first: Maurizia

last: Mello-Grnad

first: Ilaria

last: Gregnanin

first: Francesca

last: Crivelli

first: Sara

last: Laurora

first: Daniele

last: Liscia

first: Francesco

last: Leone

first: Angela

last: Santoro

first: Donatella

last: Guarino

first: Stefano

last: Magno

first: Giovanna

last: Chiorino


city: Bethlehem

first: Vassie

last: Ware

state: PA

address: 111 research drive

department: Biological Sciences

country: USA

institute: Lehigh University

type: Expression profiling by high throughput sequencing

summary: RNA-seq of Mycobacteriophage Island3 infection of Mycolicibacterium smegmatis mc2155, Mycolicibacterium smegmatis mc2155(Butters), and Mycolicibacterium smegmatis mc2155(Buttersgp57r) to assess the impact of Butters lysogen and specifically Buttersgp57r on transcript levels of island3 during infection.

sample_organism:
Mycolicibacterium smegmatis MC2 155
Mycobacterium phage Island3
Mycobacterium phage Butters

overall_design: Comparing Mycobacterium phage Island3 transcripts during infections of  Mycolicibacterium smegmatis mc2155, Mycolicibacterium smegmatis mc2155(Butters), and Mycolicibacterium smegmatis mc2155(Buttersgp57r)

first: Hamidu

middle: T

last: Mohammed

middle: C


title: Evidence that c-JUN stabilizes chromatin architecture of EpiSCs

city: Guangzhou

first: gibh

last: hpc

state: Guangdong

address: No. 190, Kaiyuan Avenue, Huangpu District,

department: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

country: China

institute: Biomedical Data & HPC

summary: c-JUN is a transcription factor and the founding member of AP1 family. Here we present evidence that c-JUN stabilizes chromatin architecture. We first show that c-JUN is expressed and occupies chromatin loci both open and closed in primed mEpiSCs, but not naive mESCs. Interestingly, naive open loci undergo closing during naive to primed transition independent of c-JUN, but ~2500 of them become occupied by c-JUN immediately. These loci then open more readily during the reverse primed to naive transition (PNT) in the presence of c-JUN N-terminal Kinase inhibitor or by ectopically expressed Esrrb and Klf4 as both bind to them. Finally, we show that these loci become more open in c-Jun-/- EpiSCs which undergo PNT more efficiently than wild type cells. These results suggest that c-Jun is activated during naive to primed transition to stabilize chromatin architecture.

overall_design: Gene expression profile of naïve-primed transition cells were generated by RNA-seq, in two replicates, using illumina nextseq 500

first: Dongwei

last: Li


title: Cancer-associated Fibroblast-derived SPP1 is a Potential Target for Overcoming Sorafenib and Lenvatinib Resistance in Hepatocellular Carcinoma

city: Suwon, Korea

first: Jung Woo

last: Eun

state: Korea

address: Department of Gastroenterology

country: South Korea

institute: Ajou University of Korea

summary:
Abstract: Cancer-associated fibroblasts (CAFs) play an important role in the induction of chemo-resistance. The objectives of this study were to clarify the mechanism underlying CAF-mediated sorafenib/lenvatinib resistance and identify a novel therapeutic target to overcome resistance to sorafenib/lenvatinib in hepatocellular carcinoma (HCC).
Methods: Whole transcriptome sequencing (WTS) data of nine pairs of CAFs and para-cancer-associated fibroblasts (PAFs) were analyzed to identify key molecules that induce resistance to tyrosine kinase inhibitors (TKIs). In vitro and in vivo experiments were performed to validate selected targets and related mechanisms. Plasma secreted phosphoprotein 1 (SPP1) expression levels prior to sorafenib/lenvatinib treatment as well as progression-free survival (PFS) and overall survival (OS) of an advanced HCC cohort (n=42) were evaluated using Kaplan–Meier analysis.
Results: Co-culturing CAFs and HCC cells significantly reduced the responsiveness of HCC cells to sorafenib/lenvatinib, in vitro and in vivo. Systematic integrative analysis of the WTS data of CAFs/PAFs and publicly available gene expression data indicated that CAF-derived SPP1 (CAF-SPP1) was suitable for use as a candidate molecule to induce sorafenib/lenvatinib resistance. An evaluation of the mechanisms involved indicated that CAF-SPP1 increased phosphorylation of PKCɑ, which then activated rapidly accelerated fibrosarcoma (RAF)-extracellular signal-related kinase 1/2-signal transducer and activator of transcription 3 (STAT3) and phosophoinositide 3-kinase (PI3K)-AKT-mechanistic target of rapamycin kinase (mTOR) in HCC cells. SPP1 inhibitors reversed CAF-induced sorafenib/lenvatinib resistance in vitro and in vivo. Patients showing high plasma SPP1 prior to sorafenib/lenvatinib treatment exhibited significantly poor PFS (P=0.005) and OS (P=0.041).
Conclusions: CAF-SPP1 enhances sorafenib/lenvatinib resistance in HCC by alternatively activating oncogenic pathways via PKCɑ phosphorylation. Inhibition of CAF-SPP1 may be utilized as a therapeutic strategy against TKI resistance in HCC. Plasma SPP1 level prior to TKI treatment shows potential as a promising biomarker for predicting sorafenib/lenvatinib response in advanced HCC patients.

overall_design: 1 Normal fibroblasts (NF), 9 Cancer-associated fibroblasts (CAF) and 9 para-cancer fibroblasts (PAF) samples of 19 patients who underwent NGS RNA-Seq.

first: Jae

middle: Y

last: Cheong

first: Jung

middle: W


title: microRNA172 targets APETALA2 to regulate anthocyanin biosynthesis

city: Zhengzhou

first: Tiyu

last: Ding

state: Henan

address: Hanghai East Road

institute: Chinese Academy of Agricultural Sciences

summary: MicroRNA172 (miR172) plays a role in regulating a diverse range of plant developmental processes. However, its role in regulating anthocyanin biosynthesis is unclear. In this study, we show that transgenic apple plants over-expressing miR172 show a reduction in red colouration and anthocyanin accumulation in multiple tissue types. This reduction was consistent with decreased expression of APETALA2 homolog MdAP2_1a (a miR172 target gene), MdMYB10, and targets of MdMYB10, as demonstrated by both RNA-seq and RT-PCR analyses. During the onset of anthocyanin biosynthesis in apple fruit skin, miR172 transcript abundance was negatively correlated and MdAP2_1a mRNA concentration was positively correlated with fruit skin red-colouration. The positive role of MdAP2_1a in regulating anthocyanin biosynthesis was supported by the enhanced petal anthocyanin accumulation in transgenic tobacco plants overexpressing MdAP2_1a, and by the reduction in anthocyanin accumulation in apple and cherry fruits transfected with an MdAP2_1a virus-induced-gene-silencing construct. We demonstrated that MdAP2_1a could bind directly to the promoter and protein sequences of MdMYB10 in yeast and tobacco, and enhance MdMYB10 promotor activity. In Arabidopsis, over-expression of miR172 reduced anthocyanin concentration and RNA transcript abundance of anthocyanin genes in plantlets cultured on medium containing 7% sucrose. The anthocyanin content and RNA abundance of anthocyanin genes could be partially restored by using a synonymous mutant of MdAP2_1a, which had lost the miR172 target sequences at mRNA level, but not restored by using a WT MdAP2_1a. These results indicate that miR172 inhibits anthocyanin biosynthesis through suppressing the expression of an AP2 transcription factor that positively regulates MdMYB10.

overall_design: Three biological replicates were collected from whole flowers at two stages of flower development (BL, balloon flower; OF, open flower) and from mature fruit skin (FS) of wide type (WT) and miR172 transgenic ‘Royal Gala’.

first: Sumathi

last: Tomes

first: Andrew

middle: P

last: Gleave

first: Ruiping

last: Zhang

last: Dare

first: Blue

last: Plunkett

first: Richard

middle: V

last: Espley

first: Zhiwei

last: Luo

first: Zhenli

last: Yan

last: Allan

first: Zhe

last: Zhou

first: Huan

last: Wang

first: Mengmeng

last: Wu

first: Haiqing

last: Dong

first: Chonghuai

last: Liu

first: Jihong

first: Hengtao

first: Jia-Long

last: Yao


title: Characterization of three CpG ODN classes in plasmacytoid dendritic cells (pDCs)

city: Changchun

first: Tete

last: Li

state: Jilin

address: Dongminzhu Street No.519

institute: Jilin University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare distinct immunostimulatory activities of three classes of CpG ODNs in pDCs using RNA-seq. mRNA profiles of murine pDCs induced by three classes of CpG ODNs were generated by RNA-Seq studies.
Methods:  mRNA profiles of murine pDCs induced by three classes of CpG ODNs were generated by deep sequencing, in triplicate, using Illumina Hiseq Xten. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: HISAT based on Burrows-Wheeler transform and Ferragina-Manzini and Bowtie2 followed by RSEM.
Results: Using an optimized data analysis workflow, we mapped > 60 million total clean reads per sample to the mouse genome (build mm10), with a clean reads Q20 score > 98.58% and a mapping rate to the reference genome of each sample varying from 92.3% to 96.56%. The Pearson correlation coefficient between each sample revealed that CpG-A and CpG-C have the highest correlation. A total of 21,573 genes were detected as being expressed. More than 5,000 genes were downregulated and 2,000 genes were upregulated in CpG ODNs stimulated groups relative to control group, with a fold change ≥ 2 and Q value <0.001. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes uncovered several genes that may contribute to characterize the features of three classes of CpG ODNs in pDCs.
Conclusions: Our study represents the first detailed analysis of pDC transcriptomes stimulated with three classes of CpG ODNs, with biological replicates, generated by RNA-seq technology.

overall_design: mRNA profiles of murine pDCs stimulated with or without CpG-A, CpG-B or CpG-C were generated by RNA-Seq studies, in triplicate, using  Illumina Hiseq Xten.

first: Jingtao

last: Chen


title: Characterization of three CpG ODN classes in B cells

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare distinct immunostimulatory activities of three classes of CpG ODNs in B cells using RNA-seq. mRNA profiles of murine B cells induced by three classes of CpG ODNs were generated by RNA-Seq studies.
Methods:  mRNA profiles of murine B cells induced by three classes of CpG ODNs were generated by deep sequencing, in triplicate, using BGISEQ. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: HISAT based on Burrows-Wheeler transform and Ferragina-Manzini and Bowtie2 followed by RSEM.
Results: Using an optimized data analysis workflow, we mapped > 60 million total clean reads per sample to the mouse genome (build mm10), with a clean reads Q20 score >97% and a mapping rate to the reference genome of each sample varying from 89.33% to 93.29%. The Pearson correlation coefficient between each sample revealed that the all samples had a high correlation. In particular, CpG-B and CpG-C have the highest correlation. A total of 28,020 genes were detected as being expressed. More than 10,000 genes were downregulated and 1,000 genes were upregulated in CpG ODNs stimulated groups relative to control group, with a fold change ≥ 2 and Q value <0.001. In addition, only 91 genes were upregulated and 99 genes were downregulated in CpG-C group relative to CpG-B group. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes uncovered several genes that may contribute to characterize the features of three classes of CpG ODNs in B cells.
Conclusions: Our study represents the first detailed analysis of B-cell transcriptomes stimulated with three classes of CpG ODNs, with biological replicates, generated by RNA-seq technology.

overall_design: mRNA profiles of murine B cells stimulated with or without CpG-A, CpG-B or CpG-C were generated by RNA-Seq studies, in triplicate, using BGISEQ.


title: Time series transcriptional profiling of Ustilago maydis SG200 infecting Zea mays.

city: Cambridge

first: Clement

last: Pellegrin

address: Downing Site

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

summary:
Goals: Comparing the infection between Ustilago maydis SG200 with the wild-type strain FB1xFB2 previously published
Methods: Comparative RNASeq analysis between U. maydis SG200 and U. maydis FB1xFB2 at three timepoints (axenic, 2dpi, 12dpi)
Results:  The RNASeq analysis in SG200 identifies differences in gene expression with FB1xFB2. These differences could be the result of a unequal contribution of each nuclei to transcription. Further analysis identified a set of differentially transcribed genes.

first: Fumi

last: Fukuda

first: Jer-Sheng

last: Lin

first: Joachim

last: Jungmann

first: Andre

last: Müller

first: Marek

last: Franetza

first: Janine

last: Altmueller

first: Regine

last: Kahmann


title: Silencing miR-31 in naive CD4+ T cells by antagomiRNA

city: Shanghai

first: Lingyan

last: Zhu

address: 2901 Caolang Road, Jin Shan District

institute: Shanghai Public Health Clinical Center, Fudan University

summary: To describe the global profile of genes regulated by miR-31, we compared the transcriptomics between miR-31 silenced and antagomir control treated naive CD4+ T cells. Interestingly, the cells could be separated into two subsets according FCS and SSC by flow cytometer after the silence of miR-31, one (~65%) was small sized cells with low granularity, the other (~30%) was large cells with high granularity, whereas the antagoNC treated naïve CD4+ T cells only contain a marginal fraction of large cells. We pooled “antagoNC”, “antagomiR31S” and “antagomiR31L” naïve CD4+ T cells from 5 healthy donors, respectively, and analyzed the differential genes among those three subsets.

overall_design: naive CD4+ T cells were transfected with antagomiR31 and antagoNC and cultured for 48 hours. Cells were sorted by flow cytometer according to small size and granularity. Sample “antagoNC”, “antagomiR31S” and “antagomiR31L” naïve CD4+ T cells were pooled from 5 healthy donors, respectively.

first: Jianqing

last: Xu

first: Chenli

last: Qiu


title: Characterization of three CpG ODN classes in plasmacytoid dendritic cells and B cells

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

overall_design: Refer to individual Series


title: N-Glycosylated Intestinal Protein BCF-1 Shapes Microbial Colonization by Binding Bacteria via its Fimbrial Protein

status: Public on Dec 23 2022

city: kunming

first: Bin

last: Qi

state: 云南

address: Yunnan University, Kunming, China

department: School of Life Sciences

institute: yunnan university

summary: We wondered if the innate immune response was not activated in the bcf-1(ylf1) mutant. We prpared  wild(N2) and bcf-1(ylf1) mutant (adults) for RNA-seq.

overall_design: RNA-seq was done with three biological replicates that were independently generated, collected, and processed. Adult animals [wild-type N2 and bcf-1(ylf1) mutant] growing on E. coli-OP50 were collected.

first: Yong

middle: J

last: He


title: Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [HiC]

city: Wuhan

first: Baibai

last: Gao

address: 1 Shizishan Street, Hongshan District

institute: National Key Laboratory of Crop Genetic Improvement

summary: Genome-wide rhythmic occupancy of RNA polymerase II (RNAPII) is highly coordinated with rhythmic genes expression. Rhythmic RNAPII binding dynamically modulates diurnal 3D genome architecture remodeling with 91% of the chromatin interactions were altered. The rhythmic genes cluster at the 8:00 (AM) circadian phase form spatial interacting clusters in turn assist coordinated rhythmic gene expression, while non-rhythmic genes tend to tether together and contribute to expression at 20:00 (PM) circadian window. Target genes and associated cis-binding motifs of transcription factors enrichment points to the existence of subnuclear organization hub enriched around the TFs. RNAPII-associated chromatin interaction domains (CIDs) are under circadian control, and static CIDs with common node genes but changed connecting genes along the circadian cycle, reveal they may function as distinct clock components in the interconnected circuits between morning and evening. Core circadian clock genes related chromatin connectivity networks reveal a compact and highly connected chromatin architecture serving to coordinate gene expression in the morning, whereas a scattered, loose chromatin architecture coordinates PM gene expression. Our findings uncover novel diurnal fundamental genome folding principles in plants, and reveal the distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation.

overall_design: Here, we generated genome-wide occupancy of RNA polymerase II (RNAPII) by ChIP-seq, whole-transcriptome by RNA-seq, and chromatin accessibility by FAIRE-seq throughout the six-time course. We also performed RNAPII long-read ChIA-PET from the same tissues used for ChIP-seq, RNA-seq, and FAIRE-seq at 8:00 and 20:00. Together, we constructed comprehensive high-resolution dynamic chromatin architecture, and dissected its effects on diurnal gene expression.

first: Li

last: Deng


title: Transcriptome analysis of control and OTUD1 knockout T24 Cells

first: Guanlan

last: Fan

address: Donghu Road, No. 115, Wuchang District

institute: Wuhan University

summary: We have confirmed that OTUD1 interacted directly with Akt and inhibited Akt phosphorylation. To investigate the exact mechanism of OTUD1 in the regulation of Akt signaling pathway, we established T24 cells with stable OTUD1 depletion by using sgRNA.

overall_design: RNA-seq was performed in T24-sgNC and T24-sgOTUD1 cells with 3 replicates. Gene expression profiling was analyzed according to the sequencing results.

first: Fan

last: Wang

first: Wei

last: Zhang

first: Feng

last: Li


title: Evaluation of expression profiles due to garlic intake in young men and women.

city: Copenhagen N

first: Atul

last: Anand

address: Ole Maaløes Vej 5, building 2, 3 floor

department: Department of Pathology

country: Denmark

institute: Rigshospitalet

summary: Allium sativum (garlic) is considered the source of the diverse beneficial effects on thrombosis, heart disease, diabetes, nerve disorders and cancer, as well as being circulatory strengthening. We describe the global changes in transcriptomic activity from a short period of using a moderate amount of fresh garlic and its potential link to some of the beneficial effects.

overall_design: 10 blood samples taken before and after garlic ingestion from healthy young men and woman. RNA detections from RNA extracts of the whole blood samples were obtained with RNA Clariom D Pico Assays using an Affymetrix GeneChip Fluidics Station and a GeneChipTM Scanner.

first: Klaus

last: Brusgaard

first: Mark

last: Burton


title: Impact of Hb contamination in obtaining reference profiles of exRNAs in healthy individuals

city: Boston

first: Ionita

middle: Calin

last: Ghiran

state: MA

address: 3 Blackfan Circle

department: Medicine

institute: Beth Israel Deaconess Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: The effect of increasing concentrations of haemoglobin in the starting material on the results of RNA-seq using plasma isolated from healthy donors.

overall_design: 12 samples from 3 healthy subjects, 4 (0%, 0.05%, 0.50%, 5%) concentrations of lysed RBC were used in plasma from each subject.


title: scRNA-seq of pancreatic islets from adult male mice with Fltp-reporter sorting and pancreatic head-tail separation

city: Munich

first: Karin

last: Hrovatin

address: Ingolstädter Landstraße 1

department: Institute of Computational Biology

country: Germany

institute: Helmholtz Munich

summary: Single-cell RNA sequencing of pancreatic islets from adult male mice. To disect islet heterogeneity we sorted cells based on anatomical location and maturity marker (Fltp).

overall_design: We used the Fltp reporter mouse line FltpZV (Gegg, et al., 2014; https://doi.org/10.7554/elife.03842) in male mice with the age of 4 months. Pancreas head and tail were anatomically separated prior islet isolation. Islets from six FltpZV/+  mice were pooled. Fltp Venus reporter positive and negative cells were sorted. Four libraries were generated based on anatomical region and cell sorting.

first: Aimée

last: Bastidas-Ponce

first: Luke

last: Zappia

first: Mostafa

last: Bakhti

first: Maren

last: Büttner

first: Ciro

last: Sallino

first: Michael

last: Sterr

first: Anika

last: Böttcher

first: Adriana

last: Migliorini

first: Heiko

last: Lickert

first: Fabian

last: Theis


title: scRNA-seq of pancreatic islets from male and female aged mice with Fltp-reporter sorting

summary: Single-cell RNA sequencing of pancreatic islets from aged male and female mice. To disect islet heterogeneity we included both sexes and sorted cells based on maturity marker (Fltp).

overall_design: Islets of Langerhans isolated from the Fltp lineage tracing mouse model Fltp iCre mTmG (Lange, et al. 2012; https://doi.org/10.1016/j.diff.2011.11.003) in male and female mice older than 2 years. We sorted Fltp negative (tomato positive), Fltp lineage positive (GFP positive), and Fltp transient (double positive) populations and generated separate libraries for each population. Male and female mice were pulled together after sorting.


title: The target antigen determines the mechanism of acquired resistance to T cell based therapies

city: Barcelona

first: Lara

last: Nonell

address: C/ NATZARET, 115-117

department: VHIOinformatics

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

summary:
Immunotherapy is a revolution in cancer treatment. Despite its success, cancer patients eventually progress due to the emergence of resistance. In this scenario, the selection of the tumor antigen is important and can be decisive in the success of the clinical response, particularly when resistance emerge. T cell bispecific antibodies (TCBs) are engineered molecules that include, within a single entity, binding sites to the T cell receptor and to a tumor-specific or a tumor-associated antigen. It is assumed that, as all TCBs have the same mechanism of action, mechanisms of resistance are independent of the tumor antigen. Using gastric CEA+/HER2+ MKN45 cells as a model and TCBs directed against CEA or HER2, here we show that the mechanism of resistance to a T cell-based therapy is dependent on the tumor antigen.
Acquired resistant models to a high-affinity CEA-targeted TCB exhibit a reduction of CEA antigen levels due to transcriptional silencing, which is reversible upon 5-AZA treatment in vitro and in vivo. In contrast, a HER2-TCB resistant model maintains HER2 levels as HER2 downregulation led to an impairment of proliferation. Furthermore, using this latter model, we identify the disruption of the interferon-gamma signaling as the cause of resistance to killing by active T lymphocytes. Our results unveil different mechanisms of acquired resistance to TCBs depending on the selected antigen, which will help in the design of combinatorial strategies to increase the efficacy of cancer immunotherapies and to anticipate and overcome resistances.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for gastric cell line MKN45 and its immunotherapy resistant derivatives MKN-HER2R (resistant to a HER2-TCB) and MKN-CEAR (resistant to a CEACAM5-TCB)

first: Alex

last: Martínez-Sabadell

first: Beatriz

last: Morancho

first: Irene

last: Rius Ruiz

first: Macarena

last: Román Alonso

first: Pablo

last: Ovejero Romero

first: Marta

last: Escorihuela

last: Chicote

first: Hector

middle: G

last: Palmer

first: Mercè

last: Alemany-Chavarria

first: Christian

last: Klein

first: Marina

last: Bacac

first: Joaquín

last: Arribas

first: Enrique

last: Arenas


title: Genomic profiles of asbestos-induced mesothelioma developed in wild-type and BRCA1+/- SD rats

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

type: Genome variation profiling by genome tiling array

summary: Intraperitoneal administration of crocidolite or chrysotile is an established method to induce peritoneal malignant mesothelioma(MM), which shares common genetic alterations to those in humans.  We conducted high-resolution microarray comparative genomic hybridization mesothelioma tissues obtained from both wild-type and BRCA1+/- rats to evaluate the involvement of BRCA1 haploinsufficiency in carcinogenesis.

overall_design: The carcinogenesis protocol was started with 37 BRCA1+/- and 37 wild-type Jcl: SD rats. 26/37 (70.2%) of BRCA1+/- rats and 27/37 (72.9%) wild-type rats developed MMs in total. Genomes of 8 samples from MMs for each genotype (16 in total) were profiled on Agilent 180K rat genome CGH microarrays.

first: Yaguang

last: Luo

last: Akatsuka


title: RNA-Seq Analyses of TGAC8 and WT mouse Left Ventricles

city: BALTIMORE

first: Kirill

last: Tarasov

state: Maryland

address: 251 Bayview Boulevard, Room 9B133, Room 9B133

department: NIA

institute: NIH

summary:
8  LV samples from WT and TGAC8 mouse hearts were analyzed. Mice were 3 m.o.
Human ADCY8 gene was overexpressed in mouse heart under cardiac-specific MYH7 promoter

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for TGAC8 and WT mice

Please note that the 'TGLV*' and 'WTLV*' data columns (in the LV_transcriptome_cuffdiff.xlsx) correspond to the 'MLV*' and 'WLV*' samples.

The mouse strain (background) is C57BL/6. Detailed description of this strain is in the PMID 10764414 (https://pubmed.ncbi.nlm.nih.gov/10764414/)

first: Khalid

last: Chakir

first: Yelena

middle: S

last: Tarasova

first: Edward

last: Lakatta


title: Effect of hBD-2 treatment on gene expression in the colon of acute graft-versus-host disease (GVHD) mice

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Wildtype (WT) BALB/c mice were treated with allogeneic hematopoietic cell transplantation (allo-HCT) in order to induce acute GVHD. C57BL/6 mice were used bone marrow (BM) and T cell donor mice. We studied the effect of oral hBD-2 treatment versus vehicle (PBS) control treatment on the gene expression in the colon, as main GVHD target organ.

overall_design: 4 GVHD mice were orally treated with PBS and 4 GVHD mice were orally treated with hBD-2 (1.2 mg/kg) from day 0-7 after allo-HCT. Colon was isolated for RNA isolation on day 7 post allo-HCT

first: Natalie

last: Koehler

first: Robert

last: Zeiser

first: Melanie

last: Boerries


title: Spontaneous NLRP3 inflammasome-driven IL-1-β secretion is induced in severe COVID-19 patients and responds to anakinra treatment

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

institute: IRCCS Istituto Giannina Gaslini

summary: SARS-CoV-2 infection may result in a severe pneumonia associated to elevation of blood inflammatory parameters, reminiscent of cytokine storm syndrome. Steroidal anti-inflammatory therapies have shown efficacy in reducing mortality in critically ill patients, however the mechanisms by which SARS-CoV2 virus trigger such an extensive inflammation remain unexplained. A pivotal cytokine driving inflammatory phenotypes  is IL-1β, whose  maturation and secretion is regulated by NLRP3 inflammasome. In the present report we provide a mechanistic explanation for the strong inflammatory manifestations associated to COVID-19 and further evidence that NLRP3 and IL-1β targeting could be an effective strategy in this disease.

overall_design: Whole blood samples were collected upon informed consent from 4 SARS-CoV2 infected patients with a positive nasopharyngeal swab and a clinical presentation including dyspnea associated with fever, systemic inflammation, rapidly worsening respiratory distress and marked lung abnormalities on chest computed tomography. Patients were treated with anakinra compound. Blood samples for RNA-seq analysis were collected before and 7 days after treatment.

first: Stefano

last: Volpi

first: Davide

last: Cangelosi


title: Effect of human beta defensin-2 (hBD-2) on T cells

summary:
In this experiment, we studied how human beta defensin-2 (hBD-2) affects gene expression of T cells.
Murine splenic C57BL/6 CD4/CD8 T cells were stimulated with anti-CD3/anti-CD28 beads and hBD-2 or vehicle (PBS) control for 48h before RNA isolation

overall_design: Murine splenic CD4/CD8 T cells were treated with hBD-2 or vehicle (PBS) control for 48h (n=4 per group). T cells from 4 individual C57BL/6 mice were used.


title: Studying the effect of hBD-2 on allogeneic immune responses


title: Microarray analysis of lung cancer cell lines

city: kashiwa

first: Eri

last: Sugiyama

address: 6-5-1 kashiwanoha

department: Division of Cancer Immunology

institute: National Cancer Center

summary: We performed microarray analysis using PC-9, HCC827 and NCI-H322 with/without erlotinib or EGF to investigate of relationship between EGFR-signal and other molecule expression.

overall_design: Microarray analysis was performed using the Clarion S array according to the manufacturer's instructions (Thermo Fisher Sciencetific).

first: Hiroyoshi

last: Nishikawa


title: Single-nucleus transcriptomic profiling of multiple organs from rhesus macaque model with SARS-CoV-2 infection

status: Public on Dec 22 2022

city: Beijing

first: Qiang

last: Ma

address: Datun Road, #15

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Here we profiled about 77000 single-nucleus transcriptomes of lung, liver, kidney, and cerebral cortex from rhesus macaques infected with SARS-CoV-2. Our work of multi-organ single-nucleus transcriptomic survey of SARS-CoV-2 infected animal model expanded our understanding of disease features and antiviral immune defects caused by the novel coronavirus at cellular and molecular level, which may facilitate the development of potential therapeutic intervention for COVID-19.

overall_design: Single-nucleus RNA-seq with lung, liver, kidney, cerebral cortex from two infected macaques as well as one or two healthy control. 10X Genomics platform was applied.

first: Tianzhang

last: Song

first: Zeyuan

last: Liu

first: Wenji

first: Qian

last: Wu

first: Yonggang

last: Yao

first: Yongtang

last: Zheng

first: Xiaoqun

last: Wang


title: DNA methylation in AZA+/AZA- mesenchymal stromal cells (MSCs) from patients with chronic myelomonocytic leukemia or healthy individuals

city: Guangzhou

first: Ruohao

last: Xu

address: Zhongshan Second Road, Guangzhou, China

department: Hematology

institute: Guangdong Provincial People's Hospital

type: Methylation profiling by genome tiling array

summary: DNA methylation is a fundamental epigenetic modification regulating gene expression. Aberrant DNA methylation may be involved in the transcriptionally/functionally altered CMML-MSCs. However, understanding the overall DNA methylation profile in MSCs and its changes after the intervention of demethylating drugs such as AZA is still lacking. In this present study, In vitro expanded MSCs from CMML patients (n=10) and healthy individuals (n=5) were treated with AZA or DMSO, and then used for DNA methylation profiling (EPIC) respectively. A total of 30 MSC samples were included. MSCs. Our study reveals that MSCs from different individual cohorts (healthy vs. CMML) exhibit significantly different sensitivity and reactivity to AZA. AZA treatment in vitro modulates aberrant DNA methylation profiles in CMML-MSCs and restores their impaired support for healthy hematopoiesis. Our study shows that the therapeutic effect of AZA on CMML patients is not limited to its inhibitory effect on malignant clones, but also manifested in its regulatory effect on the damaged bone marrow stromal microenvironment. Targeted improvement of bone marrow microenvironment may be a potential way to improve and restore normal hematopoiesis in patients with CMML.

overall_design: Bisulphite converted DNA from the 30 samples were hybridised to the Illumina Infinium MethylationEPIC (850K) Beadchip

first: Suxia

last: Geng

first: Peilong

last: Lai

first: Jianyu

last: Weng

first: Xin

last: Du


title: Comprehensive analysis of mRNA N6-methyladenosine modification in Eimeria tenella unsporulated oocysts and sporulated oocysts

city: Jinzhong

first: Qing

address: Taigu, Shanxi Province, PR China

institute: Shanxi Agricultural university

summary: N6-methyladenosine (m6A) modification, one of the most abundant RNA modification forms, is associated with almost all the aspects of RNA metabolism. In the present study, we surveyed the transcriptome-wide prevalence of m6A in sporulated oocysts and unsporulated oocysts of E. tenella. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) analysis showed that m6A modifications were most abundant in the coding sequence, followed by stop codon. There were 3903 hypermethylated and 3178 hypomethylated mRNAs in sporulated oocysts compared with unsporulated oocysts. Further joint analysis suggested that m6A modifications of the majority of genes were positively correlated with mRNA expression. The mRNA relative expression and m6A level of the selected genes were confirmed by quantitative reverse transcription PCR (RT-qPCR) and MeRIP-qPCR. GO and KEGG analysis indicated that differentially m6A methylated genes with significant differences in expression were closely related to processes such as regulation of gene expression, epigenetic, microtubule, autophagy-other and TOR signaling. Moreover, a total of 96 differentially expressed m6A genes without significant differences in expression showed significant differences at protein level. GO and pathway enrichment analysis of the 96 genes showed that RNA methylation may be involved in cell biosynthesis and metabolism of E. tenella.

overall_design: MeRIP-seq and RNA-seq of sporulated oocysts and unsporulated oocysts of E. tenella.

first: Bing-Jin

last: Mu

first: Yi-Jing

last: Meng

first: Lin-Mei

last: Yu

first: Zi-Rui

first: Tao

last: Jia

first: Wen-Bin

first: Wen-Wei

last: Gao

first: Shi-Chen

last: Xie

first: Xing-Quan

last: Zhu


title: Compendium of functional regulatory variants in human neuropsychiatric disease (MPRA-seq)

city: Stanford

first: Margaret

last: Guo

state: CA

address: 269 Campus Dr. CCSR Room 2150

institute: Stanford University

summary:
Abstract: Noncoding variants of presumed regulatory function contribute to neuropsychiatric disease heritability. 4442 noncoding variants connected to risk for 10 neuropsychiatric disorders, including autism spectrum disorder, attention deficit hyperactivity disorder, bipolar disorder, borderline personality disorder, major depression, generalized anxiety disorder, panic disorder, post-traumatic stress disorder, obsessive-compulsive disorder, and schizophrenia, were studied within developing human neural cells. Integrating epigenomic and transcriptomic data with massively parallel reporter assays identified 637 disease-associated single-nucleotide variants (daSNVs) with altered transcription-regulating activity. Expression-gene mapping, network analyses, and chromatin looping identified 619 candidate disease-relevant target genes modulated by these daSNVs. Specific daSNV-associated molecular pathways mapped to prevalent mental health symptoms. These data provide a framework resource to study inherited pathogenic risk for human neuropsychiatric disorders.
Purpose: To place disease-associated single nucleotide variants (daSNVs) in genomic context within human neural cells, matched RNA-seq, chromatin accessibility profiling via ATAC-seq, and enhancer-promoter looping via H3K27ac HiChIP was performed in ES cells and at day 2 (N-D2), 10 (N-D10), and 28 (N-D28) of neuronal differentiation. Additionally, anterior (A-NPC) and posterior (P-NPC) neuronal stem cells were generated and studied. Matched sequencing was also performed on primary human astrocytes from adult brains. Processed data for all cell types can be found in this repository. Raw data D10 and D28 RNA seq samples can be found here. Raw data for D0, D2, A-NSC, A-D2, P-NSC, and P-D2 data can be found here: https://www.biorxiv.org/content/10.1101/2020.12.02.398677v1.abstract. Raw data for Astrocytes can be found with the Donohue, et al. "The combinatorial cis-regulatory vocabulary of cell type-specific gene regulation in homeostasis and disease".

overall_design: MPRA sequence data


title: Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression [E/L Repli-seq (BrdUIP), scRepli-seq]

city: Tsu

first: Takuya

last: Hayakawa

state: Mie

address: 1577 Kuriyamachiya

department: Bioresources

institute: Mie University

summary: The temporal order of DNA replication along chromosomes is reorganized in the context of cell differentiation and disease states and is thought to reflect transcriptional competence of the genome. During differentiation of mouse 3T3-L1 cells into adipocytes, cells undergo one or two rounds of cell division called mitotic clonal expansion (MCE). MCE is an essential step for adipogenesis; however, little is known about the regulation of DNA replication during this period. Here, we performed genome-wide mapping of replication timing (RT) in mouse 3T3-L1 cells before and during MCE and identified a number of chromosomal regions shifting toward either earlier or later replication through two rounds of replication. These RT changes were confirmed in individual cells by single-cell DNA replication sequencing. Coordinate changes between a shift toward earlier replication and transcriptional activation of adipogenesis-associated genes were observed. RT changes occur before full expression of these genes, indicating that RT reorganization may contribute to the mature adipocyte phenotype. To support this, cells undergoing two rounds of DNA replication during MCE have higher potential to differentiate into lipid droplet-accumulating adipocytes, compared with cells undergoing a single round of DNA replication and non-replicating cells.

overall_design: E/L Repli-seq and single-cell Repli-seq analyses in 3T3-L1 cells before and during adipogenesis.


title: Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression [RNA-seq]

overall_design: RNA-seq analysis in mouse 3T3-L1 cells before and during adipogenesis.


title: H9c2 cell response after retinoic acid stimuli

city: Monterrey

first: Victor

last: Trevino

state: Nuevo León

address: Ave. Eugenio Garza Sada 2501 Sur

department: Investigación e Innovación

country: Mexico

institute: Tecnológico de Monterrey

summary: During culture, H9c2 cells acquire a myotubule phenotype where a critical component is the inclusion of retinoic acid (RA). The results from some authors on H9c2 suggested that thousands of genes respond to RA stimuli, while other authors report hundreds of genes responding to RA over different cell types. We investigated the response to RA in H9c2 cells controlling for culture time.

overall_design: Transcriptomic comparison of H9c2 cells with and without RA stimuli during 14 days using RNA-Seq

first: Carlos

last: Campero-Basaldua

first: Jessica

last: Herrera-Gamboa

first: Gerardo-de-Jesus

last: Garcia-Rivas

first: Victor-Manuel

last: Trevino-Alvarado


title: Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression

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

overall_design: Refer to individual Series


title: DNA methyltransferase inhibition induces dynamic gene expression changes in lung CD4+ T cells of neonatal mice with E. coli pneumonia [RNA-Seq]

city: Philadelphia

first: Sylvia

middle: N

last: Michki

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

summary: Bacterial pulmonary infections are a major cause of morbidity and mortality in neonates, with less severity in older children (juveniles). Previous studies demonstrated that CD4+ T cells in the mouse lung, whose primary responsibility is coordinating the immune response foreign pathogens, are differentially methylated in neonates compared with juveniles. Nevertheless, the effect of this differential methylation on CD4+ T cell gene expression and response to infection remains unclear. We treated E. coli-infected neonatal (4-day-old) and juvenile (13-day-old) mice with decitabine (DAC), a DNA methyltransferase inhibitor with broad-spectrum DNA demethylating activity, and performed simultaneous genome-wide DNA methylation and transcriptional profiling on lung CD4+ T cells. Juvenile and neonatal mice experienced differential demethylation in response to DAC treatment, with larger methylation differences observed in neonates. By cross-filtering differentially expressed genes between juveniles and neonates with those sites that were demethylated in neonates, we found that interferon-responsive genes such as Ifit1 are the most down-regulated methylation-sensitive genes in neonatal mice. DAC treatment shifted neonatal lung CD4+ T cells toward a gene expression program similar to that of juveniles. Following lung infection with E. coli, lung CD4+ T cells in neonatal mice exhibit epigenetic repression of important host defense pathways, which are activated by inhibition of DNA methyltransferase activity to resemble a more mature profile.

overall_design: 4 bulk mRNA-seq replicates were generated from CD4 T cells isolated from mouse lungs for each of the following experimental cohorts: neonatal (P4) DMSO-treatment (control), neonatal DAC-treatment, juvenile (P13) DMSO-treatment (control), and juvenile DAC-treatment. All mice were infected with E. coli prior to DAC/DMSO treatment.

first: Nigel

first: Roland

last: Ndeh

first: Kathryn

middle: A

last: Helmin

first: Benjamin

middle: D

last: Singer

first: Sharon

last: McGrath-Morrow


title: DNA methyltransferase inhibition induces dynamic gene expression changes in lung CD4+ T cells of neonatal mice with E. coli pneumonia [RRBS]

type: Methylation profiling by high throughput sequencing

overall_design: 4 mRRBS replicates were generated from CD4 T cells isolated from mouse lungs for each of the following experimental cohorts: neonatal (P4) DMSO-treatment (control), neonatal DAC-treatment, juvenile (P13) DMSO-treatment (control), and juvenile DAC-treatment. All mice were infected with E. coli prior to DAC/DMSO treatment.


title: Transmissible ER stress between macrophage and tumor cells configures tumor microenvironment

city: Lanzhou

first: Wei

last: Wei

state: Gansu Province

address: No. 222 South Tianshui Road

institute: Lanzhou University

summary:
Purpose: To investigate the critical role ER stress exhibit in cellular crosstalk between tumor cells and macrophages in the tumor microenvironment. We performed the two different polarized macrophages under ER stress and harvested the ER-stressed conditioned media. To figure out how two macrophage polarities generated conditioned media impact LLC tumor cells diversely, we use RNA-sequencing (RNA-seq) strategies to profile the deep-sequencing research and find the potential molecular mechanisms during the ER stress transmission from macrophages to tumor cells. The major differential influences the two macrophages proceeded were attribute to macrophages polarization characteristics, which instruct us to study the two polarized macrophages. Hence, we also performed RNA-sequencing during in vitro stimulation of ER stress inducer Tm in two polarized bone marrow derived macrophages.
Methods: After different treatment, LLC tumor cells mRNA was extracted and LLC tumor cells transcriptome profiles were generated by deep sequencing, using Illumina. Under ER stress, the different polarized macrophages transcriptome profiles were also generated by deep sequencing, using Illumina.
Results: Macrophages displayed different polarization characteristics could respond to ER stress differentially. Notably, GM-BMDMs were more susceptible to ER stress and facilitated the induction of proinflammatory signals, and M-BMDMs facilitate tumor growth, process, and metastasis. LLC cells exhibit different gene expression profiles in response to transferred ER stress from two polarized macrophage populations. Tumor cells that received transmissible ER stress from M2 macrophages has potential to facilitate the tumor survival, while transmissible ER stress from M1 macrophages could lead to more acute cell death and inflammation.
Conclusion: Our study revealed that tumor cells could receive the transmissible ER stress from distinct macrophage populations with different extents of ER stress activation in the tumor microenvironment. The proinflammatory M1-like macrophages respond to ER stress more potently and transmit stronger ER stress to tumor cells. By analyzing the secreted components of two ER stressed macrophage populations, we identified that S100A8 and S100A9, which are dominantly secreted by M1-like macrophages, could lead to significant recipient tumor cell death in synergy with transferred ER stress.

overall_design: GM-BMDMs and M-BMDMs were treated with or without Tunicamycin for 12 hrs. After washing with 3 × Dulbecco’s PBS, fresh serum-containing media were added. Sixteen hours later, ER stressed-conditioned media (CM_GM and CM_M) were collected and used to culture LLC cells for 24 h. Then the RNA of unstim and treated LLC cells were obtained. The samples from LLC cells were named as NT, CM_G0, CM_G12, CM_M0, CM_M12. Another RNA-seq for macrophages is different. mRNA preparations from GM-BMDMs and M-BMDMs treated with Tunicamycin for 0, 4 h were analyzed.

first: Chenyang

last: Zhao

first: Jinbo

last: Yang


title: Fibroblast-expressed LRRC15 is a receptor for SARS-CoV-2 spike and controls antiviral and antifibrotic transcriptional programs

city: Camperdown

first: Matthew

last: Waller

state: NSW

address: D17 - Charles Perkins Centre, Johns Hopkins Drive, The University of Sydney

department: School of Life and Environmental Sciences

country: Australia

institute: University of Sydney

summary: In order to identify novel SARS-CoV-2 Spike binding proteins, we carried out a whole genome CRISPR activation screen using the Calabrese Library Set A (Human CRISPR Activation Pooled Library, Addgene #92379).

overall_design: HEK293T cells stably expressing CRISPRa-SAM were transduced with Calabrese Set A library (Human CRISPR Activation Pooled Library, Addgene #92379). Cells were selected on puromycin and then incubated with SARS-CoV-2 Spike protein conjugated with Alexa Fluor 488. FACS was performed to identify Spike488-binding cells. Genomic DNA was isolated from sorted and unsorted cell populations and PCR performed to prepare samples for next generation sequencing. NGS fast files were processed using MAGeCK (v0.5.9) to produce read count tables. Three screens were carried out. Screen 1 used SARS-CoV-2 Hexapro Spike (Gift from Jason McLellan; Addgene, #154754) protein and 72 h puromycin selection. Screen 2 used SARS-CoV-2 (residues 1-1208, complete ectodomain) Spike (gift from Dr Florian Krammer) and 72h puromycin selection. Screen 3 used SARS-CoV-2 Hexapro Spike protein and 8 days puromycin selection.

first: Greg

last: Neely

first: Lipin

last: Loo


title: Effect of ZBTB18 on gene expression and chromatin organization

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing


title: CRISPR-mediated synergistic epigenetic and transcriptional control

first: Michael

middle: Gregory

last: Chavez

address: 443 Via Ortega, Rm 062

department: Bioengineering

summary: Targeted activation of endogenous genes is an important approach for genome engineering. Here we report that the nuclease-deactivated dCas9 fused to a transcriptional activator (VPR) and an epigenetic effector (the catalytic domain of histone acetyltransferase p300core) simultaneously, sequentially, or as a quadripartite effector, can lead to synergistic activation of target genes. The composite activator, VPRP, behaves more efficiently than individual activators across a set of genes in various cell types. We report unintended off-target changes to chromatin acetylation and transcription from expression of p300core. Our work demonstrates that transcriptional and epigenetic effectors can synergize with enhanced gene activation and highlights the need for optimization of epigenetic effectors to reduce off-targets for further applications.

overall_design: For RNA-seq, 12 samples were sequenced with paired-end sequencing. The set contains 6 groups, each containing two biological replicates. For H3k27Ac ChIP-seq, 10 samples were sequenced. The set contains 5 groups, each containing two biological replicates.

first: Lei

last: Qi

first: Antonia

last: Dominguez


title: MicroRNA-592 inhibits the progression of breast cancer through targeting CYP20A1

city: Hefei

first: Kan

last: He

address: 111 Jiulong Road

department: School of life sciences

institute: Anhui University

summary: Previous studies have shown that miR-592 may play an important role in the development of various cancer types. However, the mechanism of miR-592 in breast cancer progression remains unclear. Functional analysis showed that overexpression of miR-592 significantly inhibited the cell proliferation, clonal formation, and migration and invasion of MCF-7 cells in vitro. RNA sequencing (RNA-seq) was then used to identify the significantly dysregulated genes and enriched pathways in response to miR-592 overexpression in MCF-7 cells.

overall_design: MCF-7 cells transfected with miR-592 mimics were the treatment group, and MCF-7 cells transfected with mimics NC were used as controls. Experiments were performed in duplicate. Gene expression profiling analyses by high throughput sequencing were performed on mRNA samples isolated from the MCF-7 cells transfected with miR-592 mimics (592mic) and MCF-7 cells transfected with mimics NC(592micNC).

first: K

first: R

last: Pan

first: J

last: Su

first: X

last: Meng


title: Effect of ZBTB18 on gene expression and chromatin organization [RNA-seq]

summary: This study set out to delineate gene expression programs that are differentially modulated in metastatic breast cancer cells with high versus low ability to further metastasize. To this end, the gene expression profiles of E0771GFP cells, M11GFP and M12GFP cells were determined. Analysis of these data sets identified ZBTB18 as a transcriptional repressor with lower activity in tumor cells that retain a high metastatic potential. To determine how ZBTB18 affects gene expression and chromatin organization, ZBTB18 was overexpressed in E0771GFP breast cancer cells. Gene expression profiles and differentially accessible DNA regions analyses were performed and identified Tgfbr2 as one of the genes most significantly repressed by ZBTB18. To determine the contribution of the TGFb1 -TGFBR2 signaling axis towards ZBTB18-mediated effects, E0771GFP cells overexpressing ZBTB18 were transduced with a doxycycline-inducible Tgfbr2 construct. These cells were then treated with doxycycline and recombinant TGFb1 or vehicle control and gene expression profiles were determined. These studies revealed that inhibition of ZBTB18 activity in tumor cells promotes metastasis by increasing chromatin accessibility and by enabling pro-metastatic TGFb1-TGFBR2-driven changes.

overall_design: This project aims at identifying the global changes in gene expression and open chromatin regions between ZBTB18-overexpressing and control mouse cancer cell lines.

first: Ruishan

last: Wang

first: Beisi

last: Xu

first: Myriam

last: Labelle


title: Transcriptome analysis of V336Y mutant and G313R mutant mitochondrial ribosomal protein in human HEK293 cell line

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

summary: Analysis of HEK293 cells lines expressing V336Y mutant and G313R mutant mitochondrial ribosomal protein

overall_design: mRNA profiles of wild-type, V336Y mutant and G313R mutant HEK293 cell culture samples generated by deep sequencing

first: Dimitri

last: Scherbakov

first: Erik

last: Böttger


title: ZIKV prevents host mRNA export from the nucleus by disrupting UPF1 function

city: San Francisco

first: Kristoffer

middle: Edgar

last: Leon

address: 1650 Owens Street

institute: University of California, San Francisco

summary: Zika virus (ZIKV) is a mosquito-borne virus that can have dramatic neurodevelopmental consequences when infection occurs in utero. Previous studies demonstrated that ZIKV downregulates the master regulator of nonsense mediated decay, UPF1. To examine whether this process contributes to disruption of neural development, we investigated the effect of ZIKV infection on UPF1 interaction with host RNA in neural progenitor cells.  Here, we show that ZIKV-mediated disruption of UPF1 function in neural progenitor cells causes retention of mRNA in the nucleus, resulting in decreased protein levels of specific transcripts involved in neural differentiation.

overall_design: UPF1-CLIP Sequencing, RNA Sequencing and Fractionated RNA sequencing comparing Mock and ZIKV-infected Neural progenitor cells

first: Ryan

last: Flynn

first: Melanie

last: Ott


title: The transcription factor IRF4 represses pro-apoptotic BMF and BIM to licence Multiple Myeloma survival

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

summary: The transcription factor Interferon Regulatory Factor 4 (IRF4) is essential for the survival of the plasma cell malignancy multiple myeloma (MM), although the mechanism by which this is achieved remains unknown. Here we have explored the genetic basis for IRF4 addiction through CRISPR-Cas9 genetic ablation of IRF4 across several MM cells lines. We report that IRF4 loss uniformly resulted in the upregulation of two related pro-apoptotic proteins belonging to the BH3-only subgroup of the BCL2 family: BCL2 modifying factor (BMF) and BCL2 interacting mediator of cell death (BIM). Direct IRF4 binding was identified in the proximal promoter region of both genes. Remarkably, genetic ablation of BMF alone or in combination with BIM largely prevented the cell death that follows IRF4 inactivation, establishing that IRF4 maintains MM survival through the direct transcriptional repression of BMF and BIM.

overall_design: Transcriptional profiling of MM cell lines following CRISPR mediated IRF4 inactivation

first: Simon

last: Willis

first: Yang

last: Liao

first: Pasquale

middle: L

last: Fedele

first: Jianan

last: Gong

first: Yuan

last: Yao

first: Mark

middle: F

last: van Delft

first: Michael

last: Low

first: Lin

last: Tai

first: Marco

last: Herold

first: Julie

last: Tellier

first: George

last: Grigoriadis

first: David

last: Huang

first: Stephen

last: Nutt


title: Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer’s disease

status: Public on Dec 21 2022

city: Columbus

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

institute: The Ohio State University Wexner Medical Center

summary: Human middle temporal gyrus (MTG) is a vulnerable brain region in early Alzheimer’s disease (AD), but little is known about the molecular mechanisms underlying this regional vulnerability. Here we utilize the 10x Visium platform to define the spatial transcriptomic profile in both AD and control (CT) MTG. We identify unique marker genes for cortical layers and the white matter, and layer-specific differentially expressed genes (DEGs) in human AD compared to CT. Deconvolution of the Visium spots showcases the significant difference in particular cell types among cortical layers and the white matter. Gene co-expression analyses reveal eight gene modules, four of which have significantly altered co-expression patterns in the presence of AD pathology. The co-expression patterns of hub genes and enriched pathways in the presence of AD pathology indicate an important role of cell-cell-communications among microglia, oligodendrocytes, astrocytes, and neurons, which may contribute to the cellular and regional vulnerability in early AD. Using single-molecule fluorescent in situ hybridization, we validated the cell-type-specific expression of three novel DEGs (e.g., KIF5A, PAQR6, and SLC1A3) and eleven previously reported DEGs associated with AD pathology (i.e., amyloid beta plaques and intraneuronal neurofibrillary tangles or neuropil threads) at the single cell level. Our results may contribute to the understanding of the complex architecture and neuronal and glial response to AD pathology of this vulnerable brain region.

overall_design: Human MTG was cryosectioned at 10 µm and mounted on the Visium GE slide for Visium profiling. Spatial resovled transcriptomic (SRT) was performed using the 10x Genomics Visium Spatial Gene Expression Kit (Slide Kit, Part# 1000188. Reagent Kit, Par# 1000189) by following 10x Visium user guide (CG000239 Rev A).

first: Shuo

last: Chen

first: Yuzhou

last: Chang

first: Liangping

last: Li

first: Diana

last: Acosta

first: Qi

last: Guo

first: Emir

last: Turkes

first: Cody

last: Morrison

first: Dominic

last: Julian

middle: E

last: Hester

first: Douglas

last: Scharre

first: Chintda

last: Santiskulvong

first: Xue

last: Song

first: Jasmine

middle: T

last: Plummer

first: Geidy

last: Serrano

first: Thomas

last: Beach

first: Karen

last: Duff

first: Qin

last: Ma

first: Hongjun

last: Fu


title: Expression data from Knockdown of BAF53A in DLD1 cell line

first: Ziqing

last: Yang

address: 26th Yuancun Erheng Road, Tianhe District

department: Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease

institute: Sun Yat-sen University

summary: BAF53A, an important subunit of the SWI/SNF epigenetic chromatin regulatory complex, has been implicated as the driver of diverse cancers. However, the role of BAF53A in colorectal cancer (CRC) remains poorly understood.

overall_design: Colorectal cancer cell line DLD1 with BAF53A high expression was selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain gene expression profiles regulated by BAF53A in CRC cells. To that end, we transfected DLD1 cells with scramble RNA (scramble-1 and scramble-2) and sh-BAF53A (shRNA-1 and shRNA-2).

first: Shaomin

last: Zou


title: Dietary methionine starvation impairs acute myeloid leukemia progression

city: Groningen

first: JJ

last: Schuringa

address: Hanzeplein 1

department: Experimental Hematology

country: Netherlands

institute: UMCG

summary: Targeting altered tumor cell metabolism might provide an attractive opportunity for patients with acute myeloid leukemia (AML). An amino acid dropout screen on primary leukemic stem cells and progenitor populations revealed a number of amino acid dependencies, of which methionine was one of the strongest. By using various metabolite rescue experiments, NMR-based metabolite quantifications and 13C-tracing, polysomal profiling, and ChIP-seq, we identified that methionine is used predominantly for protein translation and to provide methyl groups to histones via S-adenosylmethionine for epigenetic marking. H3K36me3 was consistently the most heavily impacted mark following loss of methionine. Methionine depletion also reduced total RNA levels, enhanced apoptosis and induced a cell cycle block. ROS levels were not increased following methionine depletion and replacement of methionine with glutathione or N-acetylcysteine could not rescue phenotypes, excluding a role for methionine in controlling redox balance control in AML. Although considered to be an essential amino acid, methionine can be recycled from homocysteine. We uncovered that this is primarily performed by the enzyme methionine synthase and only when methionine availability becomes limiting. In vivo, dietary methionine starvation was not only tolerated by mice, but also significantly delayed both cell line and patient-derived AML progression. Finally, we show that inhibition of the H3K36-specific methyltransferase SETD2 phenocopies much of the cytotoxic effects of methionine depletion, providing a more targeted therapeutic approach. In conclusion, we show that methionine depletion is a vulnerability in AML that can be exploited therapeutically, and we provide mechanistic insight into how cells metabolize and recycle methionine.

overall_design: 24hrs of growth in the absence and presence of methionine followed by crosslinking and performance of ChIP and sequencing

first: Alan

last: Cunningham

first: Vincent

last: van den Boom

first: Shanna

middle: M

last: Hogeling

first: Jan


title: Endothelial deletion of the cytochrome P450 reductase leads to cardiac remodelling

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe Universität Frankfurt am Main

summary: The cytochrome P450 reductase (POR) transfers electrons to all microsomal cytochrome P450 enzymes (CYP450) thereby driving their activity. In the vascular system, the POR/CYP450 system has been linked to the production of epoxyeicosatrienoic acids (EETs) but also to the generation of reactive oxygen species. In cardiac myocytes (CMs), EETs have been shown to modulate the cardiac function and have cardioprotective effects. The functional importance of the endothelial POR/CYP450 system in the heart is unclear and was studied here using endothelial cell-specific, inducible knockout mice of POR (ecPOR-/-). RNA sequencing of murine cardiac cells revealed a cell type-specific expression of different CYP450 homologues. Cardiac endothelial cells mainly expressed members of the CYP2 family which produces EETs, and of the CYP4 family that generates omega fatty acids. Tamoxifen-induced endothelial deletion of POR in mice led to cardiac remodelling under basal conditions, as shown by an increase in heart weight to body weight ratio and an increased CM area as compared to control animals. Endothelial deletion of POR was associated with a significant increase in endothelial genes linked to protein synthesis with no changes in genes of the oxidative stress response. CM of ecPOR-/- mice exhibited attenuated expression of genes linked to mitochondrial function and an increase in genes related to cardiac myocyte contractility. In a model of pressure overload (transverse aortic constriction, TAC with O-rings), ecPOR-/- mice exhibited an accelerated reduction in cardiac output (CO) and stroke volume (SV) as compared to control mice. These results suggest that loss of endothelial POR along with a reduction in EETs leads to an increase in vascular stiffness and loss in cardioprotection, resulting in cardiac remodelling.

overall_design: RNA-sequencing of heart tissue and cardiac endothelial cells isolated from either control or POR-knockout mice.

first: Melina

last: Lopez

first: Pedro

last: Malacarne

first: Deepak

last: Ramanujam

first: Niklas

last: Müller

first: Jiong

last: Hu

first: Matthias

last: Dewenter

first: Andreas

last: Weigert

first: Stefan

last: Günther

first: Ralf

last: Gilsbach

last: Engelhardt

last: Brandes

first: Flávia

last: Rezende


title: Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis

first: Katherine

last: Miller

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

summary: Rasmussen encephalitis (RE) is a rare childhood neurological disease characterized by progressive unilateral loss of function, hemispheric atrophy and drug-resistant epilepsy. Affected brain tissue shows signs of infiltrating cytotoxic T-cells, microglial activation, and neuronal  death, implicating an inflammatory disease process. Recent studies have identified molecular correlates of inflammation in RE, but cell-type-specific mechanisms remain unclear. We used single-nucleus RNA-sequencing (snRNA-seq) to assess gene expression across multiple cell types in brain tissue resected from two children with RE. We found transcriptionally distinct microglial populations enriched in RE compared to two age-matched individuals with unaffected brain tissue and two individuals with Type I focal cortical dysplasia (FCD). Specifically, microglia in RE tissues demonstrated upregulation of genes associated with cytokine signaling, interferon-mediated pathways, and T-cell activation. We extended these findings using spatial proteomic analysis of tissue from four surgical resections to examine expression profiles of microglia within their pathological context. Microglia that were spatially aggregated into nodules had increased expression of dynamic immune regulatory markers (PD-L1, CD14, CD11c), T-cell activation markers (CD40, CD80) and were physically located near distinct CD4+ and CD8+ lymphocyte populations. These findings help elucidate the complex immune microenvironment of RE.

overall_design: We performed a comparitive analysis of single cell gene expression (10X Genomics 3' v3.1) between cortical tissue from patients with Rasmussen Encephalitis and from both non-diseased controls and a non-inflammatory epilepsy (Focal cortical dysplasia type I) samples. After QC and normalization, single cell gene expression datasets were integrated and cell types were determined using a combination of canonical markers and reference from Allen Barin Map [6] (Figure 1). We perfomed diffferential expression (DE) analysis via DESeq2 [28] and Gene Ontology (GO) Anotation enrichment analysis [13] of microglia across disease contitions (Figure 2). Louvain clustering was performed on the microglia and subsequent DE and GO annotation enrichment analysis were perfomed between the clusters (Figure 3).

first: Jesse

last: Westfall

first: Tracy

last: Bedrosian


title: Autonomous and non-autonomous functions of IL10RA in intestinal macrophages

city: Boston

first: Izabel

last: Patik

state: Massachusetts

address: 300 Longwood Ave

department: Division of Gastroenterology, Hepatology, and Nutrition

institute: Boston Children's Hospital

summary: To investigate the effects of cell-intrinsic loss of IL10RA on inflammatory macrophage function we performed gene expression profiling analysis using data from sorted lamina propria macrophages from bone marrow chimeric mice.

overall_design: Colonic mRNA profile comparisons of sorted macrophages from 14 week-old Cdcs1 C57BL/6 (WT) bone marrow chimeric mice reconstituted with bone marrow from only WT, only Cdcs1 Il10ra -/- or a 1:1 mixture of both.

first: Naresh

last: Redhu

first: Alal

last: Eran

first: Bruce

last: Horwitz


title: Skeletal muscle fiber-derived small extracellular vesicle miR-690 inhibits satellite cell differentiation and muscle atrophy during aging

city: Nanjing

first: Xiaoyan

last: Shao

address: No. 22, Hankou Road

institute: Nanjing University

summary: Background: Sarcopenia is a common and progressive skeletal muscle disorder characterized by atrophic muscle fibers and contractile dysfunction. Accumulating evidence shows that the number and function of satellite cells (SCs) decline and become impaired during aging, which may contribute to impaired regenerative capacity. A series of myokines/ small extracellular vesicles (sEVs) released from muscle fibers regulate metabolism in muscle and extramuscular tissues in an autocrine/paracrine/endocrine manner during muscle atrophy. It is still unclear whether myokines/sEVs derived from muscle fibers can affect satellite cell function during aging.                                                                                Methods: Aged mice were used to investigate changes in the myogenic capacity of SCs during aging-induced muscle atrophy. The effects of atrophic myotube-derived sEVs on satellite cell differentiation were investigated by biochemical methods and immunofluorescence staining. Small RNA sequencing was performed to identify differentially expressed sEV microRNAs (miRNAs) between the control myotubes and atrophic myotubes. The target genes of the miRNA were predicted by bioinformatics analysis and verified by luciferase activity assays. The effects of identified miRNA on the myogenic capacity of SCs in vivo were investigated by intramuscular injection of adeno-associated virus (AAV) to overexpress or silence miRNA in skeletal muscle.   Results: Our study showed that the myogenic capacity of SCs was significantly decreased (50%, n = 6, P < 0.001) in the tibialis anterior muscle of aged mice. We showed that atrophic myotube-derived sEVs inhibited satellite cell differentiation in vitro (n = 3, P < 0.001) and in vivo (35%, n = 6, P < 0.05). We also found that miR-690 was the most highly enriched miRNA among all the screened sEV miRNAs in atrophic myotubes [Log2 (Fold Change) = 7, P<0.001], which was verified in the atrophic muscle of aged mice (3-fold, n = 6, P < 0.001) and aged humans (2.8-fold, n = 10, P < 0.001). miR-690 can inhibit myogenic capacity of SCs by targeting myocyte enhancer factor 2, including Mef2a, Mef2c, and Mef2d, in vitro (n=3, P < 0.05) and in vivo (n=6, P < 0.05). Specific silencing of miR-690 in the muscle can promote satellite cell differentiation (n = 6, P < 0.001) and alleviate muscle atrophy in aged mice (n = 6, P < 0.001).   Conclusions: Our study demonstrated that atrophic muscle fiber-derived sEV miR-690 may inhibit satellite cell differentiation by targeting myocyte enhancer factor 2 during aging.

overall_design: For the myogenic differentiation experiment, when confluence was reached to 80–90%, mouse C2C12 myoblasts  were induced with differentiation medium-DMEM containing 2% horse serum (Hyclone). Then we constructed a starvation-induced myotube atrophy model by starvating induction in Earle's balanced salt solution (EBSS) for 7 h. We isolated the small extracellular vesicle (sEVs) from control myotubes and atrophic myotubes.  MiRNA components in either control myotubes-EVs or atrophic myotubes-EVs were profiled by single-end sequencing (1x50bp) on an Illumina platform (NEB, USA) at Novogene (Beijing, China).

first: Wang

last: Gong

first: Qianjin

last: Wang

first: Pu


title: Constant production of FlhG ensures proper function of the flagellar counter in Shewanella putrefaciens

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

institute: Twincore

summary:
Purpose : Identification of the regulons directly and indirectly affected by the main regulators of flagellation in Shewanella putrefaciens CN-32
Methods : mRNA profiles were generated for Shewanella putrefaciens CN-32 samples by deep sequencing. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed using the tool ‘cutadapt’ (version 3.5) with default settings and mapped to the NC_009438.1 (Shewanella putrefaciens CN-32) reference genome from NCBI using ‘bowtie2’ (version 2.3.5.1) with default settings for single-end sequencing.

overall_design: mRNA profiles from Shewanella putrefaciens CN-32 strains derived from liquid LB cultures grown to an OD600 = 0.5 at 30C and deep sequenced using Illumina HiSeq2500

first: Meike

last: Schwan

first: Arian

last: Khaledi

first: Sven

last: Willger

first: Kai

last: Papenfort

first: Timo

last: Glatter

last: Thormann


title: NFAT5 induction by the tumor microenvironment enforces CD8 T cell exhaustion [overexpression]

city: Epalinges

first: Grégory

last: Verdeil

state: Vaud

address: Chemin des Boveresses 155

department: Department of Oncology

institute: University of Lausanne

summary: To decipher the molecular mechanism of NFAT5 or NFAT1 CA-RIT overexpressing CD8 T cells, we performed RNA sequencing on sorted P1A CD8 TILs seven days after CD8 T cell transfer.

overall_design: 24 hours activated P1A CD8 T cells were transduced with either empty-eGFP, NFAT5 or NFAT1 CA-RIT retroviral vectors and transferred 24h later into P511 mastocytoma bearing Rag1-/-B10D2 mice. Seven days post transfer CD8 TILs were sorted from the tumors and processed for RNAseq analysis.

first: Laure

last: Tillé

first: Joao

last: Lourenco

first: Sina

last: Nassiri


title: Effect of theta toxin secreted by live S. typhimurium inside spheroids of lung cancer cell lines H460 and H1819

city: New York

first: Dhruba

last: Deb

address: 550 W 120th Street

institute: Columbia University

summary: To investigate the effect of bacterially secreted Theta toxin on lung cancer cells, we established co-culture of live S. typhimurium and spheroids of H460 and H1819 cell lines. Once the bacteria colonized inside the spheroids, we induced the expression of Theta toxin by the bacteria. We extracted RNA after 1 week of treatment.

overall_design: We analyzed the transcriptional profiling from RNA-seq data comparing lung cancer spheroids with or without the expression of Theta toxin

first: Tal

last: Danino


title: NFAT5 induction by the tumor microenvironment enforces CD8 T cell exhaustion [NFAT5 KO]

summary: To decipher the molecular mechanism of NFAT5 KO CD8 T cells, we performed RNA sequencing on sorted P14 CD8 TILs seven days after CD8 T cell transfer.

overall_design: 48 hours activated NFAT5flox/flox CD4-Cre-/- (WT) or NFAT5flox/flox CD4-Cre+/- (NFAT5 KO) P14 CD8 T cells were transferred into mice bearing subcutaneous gp33-expressing B16 melanoma (B16-gp33). Seven days post transfer CD8 TILs were sorted from the tumors and processed for RNAseq analysis.


title: Liver sinusoidal endothelial cells induce BMP6 expression in response to non-transferrin bound iron

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine

summary: Homeostatic adaptation to systemic iron overload involves transcriptional induction of bone morphogenetic protein 6 (BMP6) in liver sinusoidal endothelial cells (LSECs). BMP6 is then secreted to activate signaling to the iron hormone hepcidin (Hamp) in neighboring hepatocytes. To explore the mechanism for iron sensing by LSECs, we generated TfrcTek-Cre mice with endothelial cell-specific ablation of transferrin receptor 1 (Tfr1). We also used wild type mice to characterize LSEC-specific molecular responses to iron by single cell transcriptomics. TfrcTek-Cre animals tend to have increased liver iron content compared to Tfrcfl/fl controls but do not exhibit blunted Bmp6 or Hamp mRNA expression. They respond to dietary iron challenges with Bmp6 and Hamp induction, yet sometimes to levels slightly lower relative to liver iron load. We noted that liver Bmp6 and Hamp mRNA levels significantly correlated with serum non-transferrin bound iron (NTBI) that emerged following dietary iron loading in both TfrcTek-Cre and Tfrcfl/fl mice. High dietary iron triggered more profound alterations in the LSEC transcriptome of Tfrcfl/fl mice compared to holo-transferrin injection. These culminated in robust induction of Bmp6 and other nuclear factor erythroid 2-related factor 2 (Nrf2) target genes, as well as Myc target genes involved in ribosomal biogenesis and protein synthesis. Taken together, our data suggest that during systemic iron overload, LSECs internalize NTBI, which promotes oxidative stress and thereby transcriptionally induces Bmp6 via Nrf2. The contribution of Tfr1 and transferrin-bound iron to Bmp6 induction is minimal.

overall_design: Three mice were fed iron deficient diet (IDD) for one week; one of them was used as control (IDD). The other 2 mice were either injected with holo-Tf (IDD + HTF) or switched to Hgh Iron Diet 2% for 18 h (IDD + HID).  At the endpoints, livers were dissociated, and single-cell suspensions were used for scRNA-Seq analysis.

first: Edouard

last: Charlebois

first: Carine

last: Fillebeen

first: Kostas

last: Pantopoulos


title: Transcriptomic landscape of TIMP3 oncosuppressor activity in thyroid carcinoma

city: Milan

first: Antonino

last: Neri

state: Milan

address: Via Francesco Sforza, 35

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

summary:
In thyroid tumors TIMP3 methylation, and hence its downregulation, has been reported (Hoque MO et al, J Clin Endocrinol Metabolism 2005) and also found significantly associated with several aggressive features of PTC, including extrathyroidal invasion, lymph node metastasis, multifocality, advanced tumor stages and BRAF mutation (Hu S et al, Int J Cancer 2006). In a previous work, in addition to confirming TIMP3 downregulation in a consistent fraction of PTC, we evaluated the functional consequences of TIMP3 downregulation in a PTC-derived cell line model. We found that TIMP3 restoration in NIM1 cell line, in which the expression of TIMP3 is silenced by promoter hypermethylation, reduced in vitro migration, invasion and anchorage-independent growth. Using a mouse xenograft model we demonstrated that restoration of TIMP3 activity reduces tumor growth, concomitantly with reduction of angiogenesis and macrophage recruitment at tumor site (Anania et al, Oncogene 2011).
Papillary thyroid cancer (PTC) is the most frequent thyroid tumor. The tissue inhibitor of metalloproteinase-3 (TIMP3) gene encodes a matrix metalloproteinases inhibitor that exerts a tumor suppressor role in several tumor types. TIMP3 is frequently downregulated in PTC by promoter methylation. We have previously functionally demonstrated that TIMP3 exerts an  oncosuppressor role in PTC: TIMP3 restoration in the PTC-derived NIM1 cell line affects in vitro migration, invasion and adhesive capability, while reduces tumor growth, angiogenesis and macrophage recruitment in vivo. To have a broader view on the mediators of TIMP3 oncosuppressor activity in thyroid tumors, here we focused on the TIMP3 related transcriptome.By interrogating the TCGA data set and performing a genome-wide expression analysis of NIM1 cell line TIMP3 in vitro model, we show that different expression levels of TIMP3 lead to transcriptional changes that modulate, among other, inflammatory functions.

overall_design: Genome wide expression analysis of clones NIM1-T23 (expressing a high level of TIMP3 protein) and NIM1-EV (control empty vector) was performed.  NIM1-T23 clone was produced by transfection of NIM1 cells with the TIMP3-myc expression plasmid carrying the TIMP3 cDNA into pcDNA3.1/mycHis(_)A vector. NIM1-EV clone was produced by transfection of NIM1 cells with the empty pcDNA3.1/mycHis(_)A vector. Both clones have been described in  http://dx.doi.org/10.1038/onc.2011.18 (M.C.Anania, M.Sensi, E.Radaelli, C.Miranda, M.G.Vizioli, S.Pagliardini, E.Favini, L.Cleris, R.Supino, F.Formelli, M.G.Borrello, M.A.Pierotti, and A.Greco, TIMP3 regulates migration, invasion and in vivo tumorigenicity of thyroid tumor cells. Oncogene 30 (2011) 3011-3023).

first: Mara

last: Mazzoni

first: Katia

last: Todoerti

first: Luca

last: Agnelli

first: Emanuela

last: Minna

first: Sonia

last: Pagliardini

first: Tiziana

last: Di Marco

first: Maria

last: Borrello

first: Angela

last: Greco


title: Lectin-like oxidized low-density receptor-1 attenuates pneumonia-induced lung injury

city: Worcester

first: Filiz

last: Korkmaz

address: 364 Plantation St.

institute: UMass Chan Medical School

summary: Identifying host factors that contribute to pneumonia incidence and severity are of utmost importance to guiding the development of more effective therapies. Lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) is a scavenger receptor known to promote vascular injury and inflammation, but it is unknown whether and how LOX-1 functions in the lung. Here, we provide evidence of substantial accumulation of LOX-1 in the lungs of ARDS patients and in mice with pneumonia. Unlike previously described injurious contributions of LOX-1, we found that LOX-1 is uniquely protective in the pulmonary airspaces, limiting proteinaceous edema and inflammation. We also identified alveolar macrophages and recruited neutrophils as two prominent sites of LOX-1 expression in the lungs, whereby macrophages are capable of further induction during pneumonia and neutrophils exhibit a rapid, but heterogenous elevation of LOX-1 in the infected lung. Blockade of LOX-1 led to dysregulated immune signaling in alveolar macrophages, marked by alterations in activation markers and a concomitant elevation of inflammatory gene networks. However, bone marrow chimeras also suggested a prominent role for neutrophils in LOX-1-mediated lung protection, further supported by LOX-1+ neutrophils exhibiting transcriptional changes consistent with reparative processes. Taken together, this work establishes LOX-1 as a tissue-protective factor in the lungs during pneumonia, possibly mediated by its influence on immune signaling in alveolar macrophages (AMs) and LOX-1+ airspace neutrophils.

overall_design: 1. An assessment of transcriptional differences in alveolar macrophages isolated from mice with pneumonia + anti-LOX-1  or control antibody treatment 2. An assessment of transcriptional differences in LOX-1+ v LOX-1- neutrophils isolated from mice with pneumonia

first: Lee

last: Quinton


title: Effects of deproteinized extract of calf blood on the energy metabolism of acute hypoxia model mice and its targets

city: jilin city

first: guangyu

last: xu

address: Binjiang Road 3999,jilin city,132013

institute: College of Pharmacy, Beihua University

summary: Deproteinized extract of calf blood (DECB) can improve the transport and utilization of blood oxygen and glucose in hypoxic tissue cells, and accelerate the oxidative phosphorylation process of mitochondria, to improve the energy metabolism of cells. Due to its complex composition, the mechanism of DECB on energy metabolism is not entirely clear yet. Effects of DECB on the energy metabolism of acute hypoxia model mice were observed by detecting glucose, lactic acid, and protein and ATP contents in the brain, heart and liver of the mice. Differentially expressed genes related to the effect of DECB on the energy metabolism of acute hypoxia model mice were screened with the mRNA chip and the correlation analysis was performed. Hmgcs2, Cpt1a, Angptl4, Cyp8b1 and Ehhadh genes were involved in the energy metabolism in mice, and mainly closely related to some biological processes, including ABC transporters, adipocytokine signaling pathway and PPAR signaling pathway. DECB can improve the body energy metabolism in mice, of which Angptl4, Cyp8b1 and Ehhadh are important factors in regulating pathways of glucose metabolism, Hmgcs2 gene can directly provide the energy in the lack of energy in the body, and Cpt1a may regulate the inflammatory reaction and promote the energy metabolism.

overall_design: Male ICR mice, weighing 18-22g, were randomly divided into two groups, namely control group (CON) and DECB group, and 12 mice in each group. All the mice were administered continuously for 5 weeks and their body weights were weighed once every three days. Mice in the control group and DECB group were placed in containers with the same volume, the container mouth was evenly coated with a layer of vaseline, and all the container covers were closed at the same time while the timing started to ensure the start time of closing was the same. The asthmatic breathing accompanied by a slight convulsion of mice was taken as the indicator to immediately open the closed container, and then the hypoxia tolerance time of mice was observed and recorded.

first: Guangyu

last: Xu


title: Direct and indirect effects of a social supergene

city: Griffin

first: Brendan

middle: G.

last: Hunt

state: GA

address: 125 Redding Building, Griffin Campus, 1109 Experiment Street

department: Entomology

institute: University of Georgia

summary: To investigate the effect of supergene status and social environment pre- and post-pupation, we used RNA-sequencing of fire ant ant workers to assess gene expression differences.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for monogynous and polygynous workers with SB/SB and SB/SB, SB/Sb genotypes respectively. Additionally we assayed gene expression in monogynous SB/SB workers who had been cross-fostered in polygyne colonies upon pupation.

first: Samuel

last: Arsenault

first: Oksana

last: Riba-Grognuz

first: Laurent

last: Keller


title: Skeletal muscle of aged mice, and aged treated with myriocin

city: Lausanne

first: Maroun

last: Bou Sleiman

address: Rue Cantonale

department: IBI

institute: EPFL

summary: To investigate the effect of intraperitoneal myriocin treament on skeletal muscle gene expression in aged mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data skeletal muscle of myriocin treatment for 10 weeks of aged C57L/6JRj mice, treatment started at age of 18 months

first: Pirkka-Pekka

last: Laurila

first: Johan

last: Auwerx


title: Effects of dopamine on HIV latently-infected U1 macrophage cell line

city: San Diego

middle: Cecilia

last: Marcondes

address: 3525 John Hopkins Ct. #200

institute: San Diego Biomedical Research Institute

summary:
U1 monocytic cell line was cloned from U937 cells that survived an infection with Human Immunodeficiency Virus HIV-1 and bear integration sites, serving as one of the most studied HIV latent models.
Under the hypothesis that the hyperdopaminergic environment of the brain of substance users affects HIV-infected cells and latency, we tested the effects of Dopamine and two dopamine receptors that were identified as able to signal changes ininnate immune cells, DRD1 and DRD4.

overall_design: U1 cells were exposed for 24 hrs to Dopamine 1uM, SKF 38393 (1uM DRD1 selective agonist), and PD 168077 (1uM DRD4 selective agonist). The concentrations were pre-determined in dose-response experiments, and

middle: C

first: Liana

middle: V

last: Basova


first: Pierre

last: Bady

address: Quartier UNIL-Sorge

department: Swiss Institute of Bioinformatics

institute: CHUV / BCF / SIB

summary: Two cell lines were used for methylation profiling to investigate how BET protein inhibition sensitizes glioblastoma cells to temozolomide treatment by attenuating MGMT expression

overall_design: Bisulphite converted genomic DNA from the 2 GBM cell lines were hybridized to the Illumina Infinium MethylationEPIC Beadchip

first: Alessandro

last: Tancredi

first: Olga

last: Gusyatiner

first: Michelle

last: Buri

first: Rémy

last: Lomazzi

first: Davide

last: Chiesi

first: Mahmoud

last: Messerer

first: Monika

last: Hegi


title: Methylation differences in Alzheimer’s disease neuropathologic change in the aged human brain

city: Berlin

first: Anna-Lena

last: Lang

address: Charitéplatz 1

department: Institute of Neuropathology

institute: Charité – Universitätsmedizin Berlin

summary: AD neuropathologic change (ADNC) is known to be associated with numerous DNA methylation changes in the human brain, but the oldest old (>90 years) have so far been underrepresented in epigenetic studies of ADNC. Our study participants were individuals aged over 90 years (n= 47) from The 90+Study. We analyzed DNA methylation from bulk samples in eight precisely dissected regions of the human brain: middle frontal gyrus, cingulate gyrus, entorhinal cortex, dentate gyrus, CA1, substantia nigra, locus coeruleus and cerebellar cortex. We deconvolved our bulk data into cell type specific (CTS) signals using computational methods (EpiSCORE, TCA). CTS methylation differences were analyzed across different levels of ADNC. The highest amount of ADNC related methylation differences was found in neurons of the dentate gyrus, a region that has so far been underrepresented in large scale multi-omic studies. Amongst others, higher amyloid plaque burden was associated with promoter hypomethylation of the Presenilin enhancer 2 (PEN-2) gene, one of the rate limiting genes in the formation of γ-secretase, a multicomponent complex that is responsible in part for the endoproteolytic cleavage of amyloid precursor protein into amyloid β peptides. In addition to novel ADNC related DNA methylation changes, we present the most detailed array-based methylation survey of the old aged human brain to date. Our open-sourced dataset can serve as a brain region reference panel for future studies and help advance research in aging and neurodegenerative diseases.

overall_design: DNA from 8 different brain regions from 47 individuals was extracted, bisulfite converted and hybridised to the Illumina Infinium 850k Human Methylation Beadchip. Replicates and low-quality samples were removed, leading to a total of 321 samples for which raw and processed data was uploaded to GEO. Processed data files include bulk and cell type specific data.

first: Tiffany

last: Eulalio

first: Eddie

middle: J

last: Fox

first: Koya

last: Yakabi

first: Syed

last: Bukhari

first: Claudia

middle: H

last: Kawas

first: Maria

last: Corrada

first: Stephen

middle: B

last: Montgomery

first: Frank

last: Heppner

first: David

last: Capper

first: Daniel

last: Nachun

first: Thomas

last: Montine


title: Expression data from colorectal cancer cell lines and CX-5461 treatment

city: Taipei

first: Michael

last: Hsiao

address: Academia Road, Section 2, Nankang, Taipei, 115, Ta

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary:
We demonstrate that CX-5461 treatment suppresses multiple canonical pathways and transcriptions factors
We used microarrays to analyze the potential mechanism by which CX-5461 regulates gene expression.

overall_design: DLD-1, HT-29 and SW480 cell lines with or without CX-5461 treatment for RNA extraction and hybridization on Affymetrix microarrays.

first: Yu-Chan

last: Chang


title: mTORC1-independent translation control in mammalian cells by methionine adenosyltransferase 2A and S-adenosylmethionine

city: Sendai

first: Mitsuyo

last: Matsumoto

address: 2-1 Seiryo-machi Aoba-ku

department: Biochemistry

institute: Tohoku university school of medicine

summary: Methionine adenosyltransferase (MAT) catalyzes the synthesis of S-adenosylmethionine (SAM). As the sole methyl-donor of methylation of DNA, RNA and proteins, SAM amount affects gene expression by changing their methylation. Expression of MAT2A, the catalytic subunit of isozyme MAT2, is positively correlated with proliferation of cancer cells. However, how MAT2A promotes cell proliferation is largely unknown. Given that the protein synthesis is induced in proliferating cells and that RNA and protein components of translation machinery are methylated, we tested whether MAT2 and SAM are coupled with protein synthesis. By measuring ongoing protein translation with puromycin labeling in HeLa and Hepa1 cells, we revealed that MAT2A depletion by siRNA or chemical inhibition by cycloleucine reduced protein synthesis in mammalian cells. Overexpression of MAT2A enhanced protein synthesis, indicating that SAM is limiting under normal culture conditions. MAT2 inhibition did not accompany a reduction in the mTORC1 activity but reduced polysome formation. Polysome-bound RNA sequencing revealed that MAT2 inhibition decreased translation efficiency of a fraction of mRNAs. MAT2A was also found to interact with the proteins involved in rRNA processing and ribosome biogenesis. Depletion or inhibition of MAT2 reduced 18S rRNA processing. In addition, by quantitative mass spectrometry, we observed that some translation factors were dynamically methylated in response to the activity of MAT2A or the availability of SAM. These observations suggest that cells possess an mTOR-independent regulatory mechanism that tunes translation in response to the amount of SAM. Such a system may acclimate cells for survival when SAM synthesis is reduced whereas it may support proliferation when SAM is sufficient.

overall_design: RNA sequencing of total 8 samples was performed. Each sample is biologically duplicated. There are four different conditions: CLEU-treated total RNA, CLEU-treated polysome-binding RNA, untreated total RNA, and untreated polysome-binding RNA.

first: Mahabub

last: Alam

first: Yoshitaka

last: Matsuo

first: Kazuhiko

last: Igarashi