title: Epi-genomewide study identifies epigenetic outliers in normal mucosa of colorectal cancer patients

first: Carmen

last: Sapienza

address: 3307 N Broad Street, Room 300 PAHB

department: Fels Cancer Institute for Personalized Medicine

institute: Temple University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of normal healthy patients and tumor and non-tumor samples of patients with colorectal cancer (CRC). The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation across ~850,000 CpG sites. Samples include 78 normal sample from CRC patients, 76 tumor samples from CRC patients, and 68 samples from non-CRC patients

overall_design: Bisulphite converted DNA from 222 samples were hybridised to the Illuminia Methylation EPIC BeadChip v1.0

first: Jayashri

last: Ghosh

first: Bryant

last: Schultz

first: Joe

last: Chan


title: Transcriptomic analysis of human regulatory T cells treated with chronic myeloid leukemia-derived extracellular vesicles

status: Public on Mar 30 2022

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

type: Expression profiling by high throughput sequencing

summary: The aim of our study was to evaluate if and how leukemic extracellular vesicles (EVs) modulate human regulatory T cells (Treg). Treg in myeloid leukemias have a pro-leukemic function, but mechanisms driving these cells are unknown. We hypothesised that leukemia-derived extracellular vesicles (EVs) may be a factor that polarizes Treg into pro-leukemic cells. Using bulk RNA sequencing we study transcriptomic differences in human regulatory T cells (3 biological replicates = Treg from 3 different donors) treated with leukemic EVs released by chronic myeloid leukemia K562 cells. We observed significant transcriptomic differences, e.g. in genes responsible for RNA processing and alternative splicing, as well as genes engaged in T cell maturation, origin and activity. Using obtained datasets we also identified transcription factors engaged in this regulation. RNA sequencing data is part of a bigger study, where we study leukemic EVs-Treg interaction using human regulatory T cells, analysis by multicolor flow cytometry, functional studies, in vivo models.

overall_design: 3 biological replicates (Treg from 3 donors), either CTRL (untreated) or treated with leukemic extracellular vesicles. Overall 6 samples.

first: Julian

last: Swatler

first: Katarzyna

last: Piwocka

first: Wioleta

last: Dudka

first: Elyas

last: Mohammadi


title: Analysis of long noncoding RNAs expression profiles explores mechanisms of hyperbaric oxygen treatment promoting spinal cord injury recovery

status: Public on Mar 24 2022

city: Beijing

first: Xuehua

last: Liu

address: 8 Gongti South Road, Chaoyang District Beijing

department: Department of Hyperbaric Oxygen

country: China

institute: Beijing Chaoyang Hospital, Capital Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Aims: To better understand the potential mechanisms of hyperbaric oxygen (HBO) treatment alleviating spinal cord injury (SCI).
Materials and methods: The SCI model was firstly built in mice, which were randomly divided into three groups: Sham (SH), SCI and HBO groups, followed by hind limb motor function evaluation. Then the spinal cord tissue samples were harvested for  genome-wide transcriptional analysis at 1 week after injury. Finally, some highly expressed lnc-rna were selected for functional analysis.
Results: the present study uncovered the lncRNAs expression profile of spinal cord following HBO treatment, and identified 577 DE lncRNAs in spinal cord sample among the SH, SCI and HBO groups. The key biological process and pathways were also identified and may be important mechanisms by which HBO treatment alleviating SCI
Conclusions: Moreover, this study indicated that lncRNAs NONMMUT 092674.1 and NONMMUT042986.2 may be involved in the process of HBO treatment promoting the recovery of neurological function after SCI.

overall_design: Spinal cord lncRNAs profiles of sham, spinal cord injury and HBO treatment groups on the 7th day after SCI

first: Zhencheng

last: Sun

first: Fang

last: Liang

first: Jing

last: Yang

first: Qingjun

last: Su


title: Profile analysis of circRNAs in human THP-1 derived macrophages infected with intracellular Staphylococcus aureus

city: Suzhou

first: xiaolu

last: xie

address: No. 1055, Sanxiang Road, Gusu District,

institute: Second Affiliated Hospital of Soochow University

summary: Background: Intracellular Staphylococcus aureus (S. aureus) infection is generally persistent, recurrent and difficult to treat due to the poor availability of antibiotics within macrophages cells and the lack of ideal diagnostic markers. Circular RNA (circRNA), with covalently closed circular structures, exists in the serum stably and is not easily degraded by nucleases. CircRNAs play important roles in the eukaryotic regulation of genes expression and served as biomarkers in variety disease including infections. However, the function of host circRNAs in intracellular S. aureus infection remains largely unclear.  Methods: In this study, an intracellular survival THP-1 derived macrophages model of S. aureus infection was established. Then, the circRNA expression profile was investigated by RNA sequencing technology in both S. aureus -infected THP-1 cells and mock control cells. The differentially expressed (DE) circRNAs with a fold-change ≥2.0 (p<0.05) are analyzed using functional pathway clustering prediction. RT-qPCR was performed to verify the top 9 DE circRNAs.   Results: A total of 5,299 circRNAs were detected during the intracellular S. aureus infection. 61 DE circRNAs with a fold-change ≥1.5 (p<0.05) after S. aureus infection were identified. 22 circRNAs were up-regulated while 39 circRNAs were down-regulated. Functional annotation analysis demonstrated that Lysine degradation, RNA degradation and Neurotrophin signaling pathway are most important in intracellular S. aureus infection.   Conclusion: Our study provides the first profile analysis of circRNAs involved in intracellular S. aureus infection, which may contribute to the understanding of its host evasion mechanisms.

overall_design: circRNAs profile of  in human THP-1 derived macrophages infected with intracellular Staphylococcus aureus and mock control cells

first: Haifang

last: Zhang

first: Xiaolu

last: Xie


title: Differential expression of bone marrow derived mesenchymal stem cells in patients with multiple myeloma

status: Public on Mar 23 2022

city: Nantong

first: Jianmei

last: Gu

address: 30 Tongyang North Road

department: Clinical Laboratory Medicine

institute: Affiliated Cancer Hospital of Nantong University

summary: Bone marrow-derived mesenchymal stem cell (BMSC) is one crucial component of the multiple myeloma (MM) microenvironment and supports the malignant progression of MM. Whether BMSCs act on MM cells via exosomes has not been well characterized. Herein, we used microarrays to screen out differentially expressed miRNAs in BMSCs from patients with MM (MM-MSCs) or benign diseases (BD-MSCs).

overall_design: 2 pairs of bone marrow derived MSCs from MM patients and bone marrow derived MSCs from benign disease patients

first: Maoye

last: Wang

first: Xu

first: Hong


title: BRD4 inhibitor GNE987 exerts anti-cancer effects in Neuroblastoma (ChIP-Seq)

first: Zimu

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Neuroblastoma (NB) is the most common extracranial solid tumor of childhood, which is derived from primordial neural crest cells. GNE987 is a newly developed von Hippel-Lindau tumor suppressor (VHL)-based pan-BET-targeting PROTAC, which can bind to the target proteins (BET proteins, including BRD2, BRD3, and BRD4) and recruit them to the ubiquitin/ proteasome system for selective degradation. However, the function of GNE987 has not been assessed in NB models so far. In the present study, ChIP-Seq analysis was performed to explore the effect of GNE987 on NB cells.

overall_design: Genome binding/occupancy profiling of SK-N-BE(2) cells treated with 10 nM for 24 h were generated by ChIP-Seq using BGISEQ 2000.

first: Yanling

last: Chen

first: Jian

last: Pan


title: Simultaneous Single-cell Genome and Transcriptome Sequencing with Digital Microfluidics Identifying Essential Driving Genes

city: Xiamen

first: Xing

last: Xu

state: Fujian

address: 422 Road, Siming District, Xiamen, China

institute: Xiamen University

summary: Single-cell genome and transcriptome sequencing investigates how genotype influences the phenotype of single cells, so as to comprehensively interpret biological inheritance and explain functional heterogeneity at the single-cell level. Current sample preparation technologies for simultaneous DNA and RNA sequencing of the same cell are cumbersome, expensive, and suffer from cross-contamination and limited sensitivity. Herein we describe DMF-DR-seq, a single-cell multi-omics sample preparation platform based on digital microfluidics. DMF-DR-seq integrates the major steps of single-cell isolation, DNA/RNA separation, and nucleic acid amplification in situ. The results confirm the enhanced ability of DMF-DR-seq relative to current state-of-the-art technology, with lower amplification bias, higher genome-wide coverage in DNA sequencing and better gene detection ability in RNA sequencing results. By using DMF-DR-seq, we identified the genome variation-induced abnormal transcriptome expression of single circulating tumor cells (CTCs) and cancer cells from multiple myeloma patients. The results identified essential genes, known as transporters associated with antigen presentation (TAP1 and TAP2), that participate in the pathologic progress. The unique flexibility, sensitivity, and accuracy of DMF-DR-seq suggest its potential utility in deeper multi-omics analysis for inheritance mechanism study in single-cell biology.

overall_design: DNA and mRNA profiles of different cancer cell lines

first: Lin

last: Li

first: Song

last: Jia

first: Chaoyong


title: Diosmin inhibits glioma growth through inhibition of autophagic flux

city: Taipei

first: Yung Lung

last: Chang

address: Rm. 7309, 7F., No.161, Sec. 6, Minquan E. Rd., Neihu Dist.

department: Biochemistry

country: Taiwan

institute: National Defense Medical Center

summary: RNA microarray was performed from glioma cell LN229 and GBM8401 that were treated with Diosmin (160 nM) for 48hr in comparison to DMSO vehicle control.

overall_design: To study the growth inhibition of glioma cells in response to diosmin treatment, total 8 samples were prepared from glioma cells LN229 and GBM8401 for RNA extraction and hybridization on OneArray® Gene Microarrays. Glioma cells treated with diosmin or DMSO, which is taken as vehicle control samples (control).

first: Yung

middle: L

first: Chia

middle: K

last: Tsai


title: Expression data from MDSC treated with STAT3 inhibitor Napabucasin

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: MDSC (myeloid-derived suppressor cells) were generated in vitro using IL-6 and GM-CSF. To identify the role of STAT3 in MDSC, we treated the generated cells for 24 hours with DMSO (control) or 1 µM STAT3 inhibitor Napabucasin (also known as BBI608) and compared their expression profile by microarray. We found genes and pathways that are up- or downregulated upon STAT3 inhibition in MDSC.

overall_design: Total RNA was isolated from in vitro generated MDSC after 24 hours of DMSO (control) or 1 µM Napabucasin treatment and hybridized to Affymetrix microarrays. To generate biological replicates, MDSC generated from the bone marrow of three different mice were used.

first: Annina

last: Kurzay

first: Rebekka

last: Bitsch

first: Carolina

last: De La Torre


title: Transcriptome profiling of Arabidopsis roots upon lateral root induction in WT and TOR knock down [dataset1]

city: Heidelberg

first: Alexis

last: Maizel

address: Im Neuenheimer Feld 230

department: Center for Organismal Studies

institute: Heidelberg University

summary: To get a genome wide picture of the effects of TOR knockdown during the early phase of lateral root formation, we compared by RNA-seq the transcriptomes of roots 6h after the synchronous induction of lateral formation by auxin treatment (Himanen et al, 2002 - http://dx.doi.org/10.1105/tpc.004960) in the inducible UB10pro>>amiR-TOR background.

overall_design: Samples (Col-0 or inducible UB10pro>>amiR-TOR line) were prepared for harvesting using the synchronous induction of lateral root procedure. All samples were pre-treated with 10 µM NPA for 24 h then shifted to plates containing 10 µM NPA and 10 µM Estradiol or DMSO control for additional 24 h before being shifted to either 10 µM IAA + 10 µM Estradiol or DMSO for LR induction or maintained on the same plates. Root tissue was harvested after 6 h. All sampling points were performed in triplicate. For each sample, about 200 segments of the lower two-thirds of the seedling roots were pooled.


title: Profiling of bulk and ribosome associated mRNA  of Arabidopsis roots upon lateral root induction upon TOR activity inhibition with AZD8055 [dataset2]

summary: We performed targeted purification of polysomal mRNA (TRAP-Seq, Vragović et al, 2015 - http://dx.doi.org/10.1073/pnas.1417947112) using a transgenic line ubiquitously expressing a GFP-tagged RPL18 (Mustroph et al, 2009 - https://doi.org/10.1073/pnas.0906131106) 6h after the synchronous induction of lateral root formation by auxin treatment (IAA) upon inhibition of TOR activity (AZD8055 treatment, AZD). To correct for abundance of mRNA, bulk RNA-Seq was performed on the same samples and used to normalise the reads purified with the ribosomes.

overall_design: Samples were prepared as described in  (Thellmann et al, 2020 - https://dx.doi.org/10.3791/60919). Samples ubiquitously expressing a GFP-tagged RPL18 ribosomal protein (p35S:HF-GFP-RPL18, N69096, (Mustroph et al, 2009 - https://www.pnas.org/doi/full/10.1073/pnas.0906131106)) were pretreated at 7 DAG for 16h either with 10 µM AZD8055 or DMSO control media before being transferred to DMSO, 10 µM IAA, 10 µM AZD8055 or 10 µM AZD8055 + 10 µM IAA. Root tissues were then dissected after 6h. All sampling were performed in triplicate.


title: Effect of enhanced melanin synthesis on the production of extracellular vesicles in melanocytes and communication with keratinocytes

city: Taigu

first: Lijun

last: Zhao

state: Shanxi

address: No. 1 Mingxian South Road,Taigu,  Shanxi Province, China

department: College of Veterinary Medicine

institute: Shanxi Agricultural University

summary: Extracellular vesicle(EV) secretion and capture is an important method of communication between cells. Melanocytes and their surrounding keratinocytes form epidermal melanin units in the thin, outermost layer of the skin to protect the skin from ultraviolet radiation damage. It is important to understand the mechanisms by which changes in melanocyte EV signal transduction influence pigmentation. Mouse melanocytes (melan-α cell) overexpressing MITF and CD63-GFP were used to to investigate the effect on vesicle formation by WB and SEM. Coculturing of melanocyte with keratinocyte(PAM212) was used to explore the polarization of vesicles and transfer between cells by immunofluorescence, flow cytometry. EVs from melanocytes were extracted and used to investigate changes in the miRNA profile of EVs, and the effect of exosomal miR-28 on keratinocyte growth and transcriptomics was analyzed by flow cytometry, TEM, particle size analysis, WB, the iCELLigence system and RNA-seq analysis.Our results indicate that melanocytes in the skin affected vesicle synthesis under the condition of enhanced melanin synthesis function: the expression of CD81, VPS37, VPS36B and Rab27b (melanosome and vesicle transport protein during ESCRT machinery) increased. Keratinocytes can cause the polarization of vesicles in melanocytes and capture EVs from melanocytes via plasmalemma fusion. Analysis of the miRNA profile derived from melanocyte EVs showed that the expression levels of miR-125, miR-130, miR-211, miR-127, miR-692 and miR-709 were increased, while the expression levels of miR-28, miR-744, let-7g and miR-6240 were decreased. The content of miR-28 in EVs may be reduced to induce keratinocytes to prevent carcinogenesis, resist infection and prevent premature apoptosis.

overall_design: Extracellular vesicle(EV) -miRNA profiles of MITF overexpression and Control in mice melanocytes

first: Quanhai

last: Pang

first: Hongyu

last: Han

first: Yang


title: Transcriptional effects of LXR nuclear receptors on M-CSF-derived macrophages

city: Madrid

first: Miguel

middle: A

last: Vega

address: Ramiro de Maeztu 9

country: Spain

institute: CIB (CSIC)

summary:
Analysis of the role of LXR transcriptions factors on the transcriptional signature of human M-CSF-dependent monocyte-derived macrophages.
Methods: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes from three independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were treated with LXR agonist GW3965 (1 uM, Tocris), LXR antagonist GSK2033 (1 uM, Tocris), GW3965 and GSK2033, or dimethyl sulfoxide (DMSO) as vehicle. In the dual condition, the antagonist was added 1-hour prior to agonist treatment.
Then, monocytes were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO2 and 21% O2 for 7 days in the presence of 1000 U/ml M-CSF, with cytokine addition every two days.

overall_design: mRNA profiles of human M-CSF-derived macrophages treated modulators of LXR nuclear receptors

first: Arturo

last: González de la Aleja

first: Angel

last: Corbí


title: Corticosterone induces discrete epigenetic signatures in the dorsal and ventral hippocampus that depend upon sex and genotype: focus on methylated Nr3c1 gene

city: New York

first: Jordan

last: Marrocco

state: NY

address: 1230 York Ave

country: USA

institute: The Rockefeller University

summary: It was our goal to discern the genomic signatures of the dorsal and ventral hippocampus, in both mle and female mice after exposure to exogenous corticosterone, an animal model that induces a blunted response to stress. In addition to wildtype mice, we used mice heterozygous for the single nucleotide polymorphism of the gene encoding for brain-derived neurotrophic factor, BDNF Val66Met, a mouse model that shows susceptibility to stress.

overall_design: Wild-type mice or BDNF Val66Met male mice were maintained on chronic oral corticosterone or vehicle for two weeks prior dissection of the ventral hippocampus and extraction of RNA for sequencing. VV/WT = Wildtyple, VM/BDNF = Heterozygous BDNF Val66Met, VEH = vehicle, CORT = corticosterone.

first: Salvatore

middle: G

last: Caradonna

first: Marrocco

last: Jordan

first: Nathan

middle: R

last: Einhorn


title: Hematopoietic progenitor cell liabilities and alarmins S100A8/A9 – related inflammaging associate with frailty and predict poor cardiovascular outcomes in older adults

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

summary: Frailty affects the physical, cognitive, and social domains exposing older adults to an increased risk of cardiovascular disease (CVD) and death. The mechanisms linking frailty and cardiovascular outcomes are mostly unknown. Here, we studied the association of abundance (flow cytometry) and gene expression profile (RNAseq) of stem/progenitor cells (HSPCs) and molecular markers of inflammaging (ELISA) with the cardiorespiratory phenotype and prospective adverse events of individuals classified according to levels of frailty. Two cohorts of older adults were enrolled in the study. In a cohort of pre-frail 35 individuals (average age: 75 years), a physical frailty score above the median identified subjects with initial alterations in cardiorespiratory function. RNA sequencing revealed S100A8/A9 upregulation in HSPCs from the bone marrow (>10-fold) and peripheral blood (>200-fold) of individuals with greater physical frailty. Moreover higher frailty was associated with increased alarmins S100A8/A9 and inflammatory cytokines in peripheral blood. We then studied a cohort of 104 more frail individuals (average age: 81 years) with multi-domain health deficits. Reduced levels of circulating HSPCs and increased S100A8/A9 concentrations were independently associated with the frailty index. Remarkably, low HSPCs and high S100A8/A9 simultaneously predicted major adverse cardiovascular events at 1-year follow-up after adjustment for age and frailty index. In conclusion, inflammaging characterized by alarmin and pro-inflammatory cytokines in pre-frail individuals is mirrored by the pauperization of HSPCs in frail older people with comorbidities. S100A8/A9 is upregulated within HSPCs, identifying a phenotype that associates with poor cardiovascular outcomes.

overall_design: mRNA profiles of cd34+ cell from bone marrow and peripherical blood in patients with different fragility index

first: Benedetta

middle: M

last: Bonora

first: Maria

middle: T

last: Palano

first: Gianluca

last: Testa

first: Gian

middle: P

last: Fadini

first: Elena

last: Sangalli

first: Fabiana

last: Madotto

first: Giuseppe

last: Persico

first: Francesca

last: Casciaro

first: Rosa

last: Vono

first: Ornelia

last: Colpano

first: Francesco

last: Scavello

first: Roberta

last: Cappellari

first: Pasquale

last: Abete

first: Patrizia

last: Orlando

first: Franco

last: Carnelli

first: Andrea

last: Berardi

first: Stefano

last: De Servi

first: Angela

last: Raucci

first: Marco

last: Giorgio

first: Paolo

last: Madeddu

first: Gaia

last: Spinetti


title: The H.pylori CagA oncoprotein induces replication fork collapse and DNA double strand breaks through Fanconi Anemia pathway downregulation

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: Although H.pylori infection is known to induce host genomic double strand breaks, (DSBs), the role of CagA, a central virulence factor with oncogenic properties  in DSB generation remains unclear. Here, using transcriptomic and proteomic analyses, we show that CagA downregulates the expression of major DNA repair factors such as FANCD2, BRCA1 and BRCA2 of the Fanconi Anemia (FA) pathway of DNA repair and leads to compromised host replication fork speed, stability and toxic DSB induction. Our results highlight the mechanism of CagA-mediated genome instability at the level of replication forks and can be used to devise strategies that  mitigate the genotoxic effects of H.pylori-infection.

overall_design: WTA10 cells are modified MKN-28 cells where CagA is induced in the absence of Doxycycline in the culture medium. Cells were cultured either in the presence of Doxycycline (WTA10-Pos1 and WTA10-Pos2 are biological replicates) or in the absence of Doxycycline (WTA10-Neg1 and WTA10-Neg2 are biological replicates)

first: Vaidehi

last: Krishnan


title: RNA-sequencing of wild-type and IRF4-deficient splenic cDC2s

city: San Francisco

first: Lihui

last: Duan

state: CA

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: UCSF

summary: We analyzed the transcriptome differences of wild-type and IRF4-deficient (CD11c-cre x Irf4fl/fl) type-2 conventional dendritic cells (cDC2s) in spleen. Wild-type or IRF4-deficient (CD11c-cre x Irf4fl/fl) bone marrow cells were transferred into lethal irradiated CD45.1 mice. 8 weeks later, splenic cDC2s were purified and prepared for RNA-seq analysis. Three technical repeats of ~10^5 cells per sample from each of one mouse were included. CD97 was downregulated in IRF4-deficient cDC2s. GSEA showed that upregulated and downregulated genes in CD97-deficient cells were strongly enriched in IRF4-regulated genes. These data are in accord with CD97 acting within the IRF4 gene-expression network.

overall_design: Transcriptome analysis of WT and CD11c-Cre Irf4fl/fl splenic cDC2s

first: Dan

last: Liu

first: Ying

last: Xu

first: Jason

last: Cyster


title: RNA-sequencing of wild-type, CD97- and Gα13-deficient splenic cDC2s

summary: We analyzed the transcriptome differences of wild-type, CD97- and Gα13-deficient (Adgre5-/- and CD11c-cre x Gna13fl/fl) type-2 conventional dendritic cells (cDC2s) in spleen. Three technical repeats of ~10^5 cells per sample from each of one mouse were included. Compared to wild-type cDC2s, CD97- and Gα13-deficient cDC2s differentially expressed many genes, but CD97- and Gα13-deficient cDC2s were almost the same. GSEA showed that Mrtf-a dependent genes were upregulated in CD97- and Gα13-deficient cDC2s, which code for cytoskeleton proteins. These data support that CD97-Gα13 signaling regulates splenic cDC2 motility by the actin cytoskeleton.

overall_design: Transcriptome analysis of WT, Adgre5-/- and CD11c-Cre Gna13fl/fl splenic cDC2s


title: Adhesion GPCR CD97 promotes spleen dendritic cell retention and function through sensing of CD55-expressing red blood cells

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

overall_design: Refer to individual Series


title: RNA-seq data for parental and  lenvatinib-resistant HCC cells

city: Maywood

first: Wei

last: Qiu

state: Illinois

address: 2160 S 1st Ave

department: Cancer Biology

institute: Loyola University Chicago

summary: RNA-seq data for parental and  lenvatinib-resistant HCC (Hep3B, Huh7) cells

overall_design: We compared transcriptional profiling of parental and lenvatinib-resistant HCC (Hep3B, Huh7) cells by RNA-Seq. 3 replicates for each group.

last: Hou


title: Single cell RNA sequencing profiles on whole tumors from a Kras/Rnf43 genetically engineered mouse model of pancreatic adenocarcinoma

first: Anirban

last: Maitra

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

summary: We report single cell RNA sequencing of pancreatic enzymatically digested whole, fresh tumors from a genetically engineered mouse model (GEMM) of pancreatic adenocarcinoma.  This GEMM consists of pancreas specific expression of oncogenic Kras (Kras-G12D) in addition of homozygous deletion of the ring finger domain (catalytic domain) of Rnf43.  This GEMM is termed 'KRC'.

overall_design: KRC mice were sacraficed at prespecified time points: 2 months (early, n=2 mice), 4 months (intermediate, n=2 mice), moribund (n=3 mice)

first: Abdel

middle: N

last: Hosein

first: Kimal

middle: I

last: Rajapakshe


title: Siglec receptors modulate dendritic cell activation and antigen presentation to T cells in cancer

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Sialoglycan - Siglec axis has been reported to modulate the functions of multiple immune cell types. We found that inhibitory molecules human Siglec-9 and mouse Siglec-E both expressed at high level in tumor-infiltrating dendritic cells(DCs). Therefore, we generated mouse DC cell line lacking the expression of Siglec-E, and used bulk RNA sequencying to analyse how Siglec-E affects DC functions.

overall_design: Examination of the functions of Siglec-E on mouse dendritic cells

first: Jinyu

last: Wang

first: Robert

last: Ivanek

first: Heinz

last: Läubli


title: Antigen presenting cell response to Polysaccharide A is characterized by the generation of anti-inflammatory macrophages

city: Cleveland

first: Brian

last: Cobb

state: OH

address: 10900 Euclid Avenue, WRB 5132

department: Pathology

institute: Case Western Reserve University School of Medicine

summary: MHC class II positive antigen presenting cells stimulated by polysaccharide A from the capsule of Bacteroides fragilis elicits an innate immune response characterized by the induction of antigen presentation and regulatory (anti-inflammatory) pathways.

overall_design: Murine splenic MHCII+ cells were purified by magnetic bead isolation and then stimulated for 24 hours with 50ug/ml purified polysaccharide A (PSA) from the capsule of Bacteroides fragilis. mRNA was purified from the 24 hour stimulated samples as well as freshly purified MHCII+ cells (unstimulated) and subjected to deep RNA sequencing from each sample at LC Sciences. One control (day zero) and three experimental samples (day 1) are provided.

first: Julie

middle: Y

last: Zhou

first: David

first: Kevin

last: Telfer

first: Mark

middle: B

last: Jones

first: John

last: Hambor


title: 24-nt phasiRNAs move from tapetal to meiotic cells in maize anthers

city: Stanford

first: Xue

address: 371 Serra Mall

department: Biology

institute: Stanford University

summary: In maize, 24-nt phased, secondary small interfering RNAs (phasiRNAs) are abundant in meiotic stage anthers, but their distribution and functions are not precisely known. Using laser capture microdissection we analyzed tapetal cells, meiocytes, and other somatic cells at several stages of anther development to establish the timing of 24-PHAS precursor transcripts and the 24-nt phasiRNA products. By integrating RNA and small RNA (sRNA) profiling plus single-molecule and sRNA FISH (smFISH or sRNA-FISH) spatial detection, we demonstrate that the tapetum is the primary site of 24-PHAS precursor and Dcl5 transcripts and the resulting 24-nt phasiRNAs. Interestingly, 24-nt phasiRNAs accumulate in all cell types, with the highest levels in meiocytes, followed by tapetum. Our data support the conclusion that 24-nt phasiRNAs are mobile from tapetum to meiocytes and to other somatic cells. We discuss possible roles for 24-nt phasiRNAs in anther cell types.

overall_design: RNA profiling of three different cell types (meiocytes, tapetum and other somatic cells) plus fixed anthers at two stages in maize anthers

first: Virginia

last: Walbot

first: Blake

middle: C

last: Meyers


title: Modulation of miR-181 influences dopaminergic neuronal degeneration in a mouse model of Parkinson’s disease

city: Iowa City

first: Ethan

middle: J.

last: Anderson

state: Iowa

address: 180 South Grand Ave, CPB 548

department: Pharmaceutical Sciences and Experimental Therapeutics

institute: University of Iowa - College of Pharmacy

summary: Parkinson’s disease (PD) is caused by loss of dopaminergic (DA) neurons in the substantia nigra (SN). Although PD pathogenesis is not fully understood, studies implicate perturbations in gene regulation, mitochondrial function, and neuronal activity. MicroRNAs (miRs) are small gene regulatory RNAs that inhibit diverse subsets of target mRNAs, and several studies have noted miR expression alterations in PD brains. For example, miR-181a is abundant in brain and is increased in PD patient brain samples; however, the disease relevance of this remains unclear. Herein, we show that miR-181 target mRNAs are broadly down-regulated in aging and PD brains. To address if the miR‑181 family plays a role in PD pathogenesis, we generated adeno-associated viruses (AAV) to overexpress and inhibit miR-181 isoforms. After co-injection with AAV overexpressing alpha-synuclein (aSyn) into mouse SN (PD model), we found that moderate miR-181a/b overexpression exacerbated aSyn-induced DA neuronal loss, whereas miR‑181 inhibition was neuroprotective, relative to controls (GFP-alone and/or scrambled RNA). Also, prolonged miR-181 overexpression in SN alone elicited measurable neurotoxicity coincident with an increased immune response. RNA-seq analyses revealed that miR-181a/b inhibits genes involved in synaptic transmission, neurite outgrowth, and mitochondrial respiration, along with several genes having known protective roles and genetic links in PD.

overall_design: AAV-virus overexpressing either microRNA-181 or GFP (green fluorescent protein) were injected into the substantia nigra of naive mice. The contralateral side was uninjected and used as control. Total RNA was extracted from sumstantia nigra tissue and prepared for standard polyA mRNA sequencing using the Illumina TruSeq® Stranded mRNA Library Prep kits, multiplexed, and sequenced across two lanes on the HiSeq 4000 or NovaSeq 6000. Reads were aligned and quantified using the kallisto/sleuth pipeline. Supplementary files includes  features for all genes with statistics for differential expression and normalized abundance measurements for each gene in each sample.

first: Ryan

last: Boudreau

first: Jared

last: McLendon


title: BRD4 inhibitor GNE987 exerts anti-cancer effects in Neuroblastoma

city: Suzhou

first: Zimu

last: Zhang

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: Neuroblastoma (NB) is the most common extracranial solid tumor of childhood, which is derived from primordial neural crest cells. GNE987 is a newly developed von Hippel-Lindau tumor suppressor (VHL)-based pan-BET-targeting PROTAC, which can bind to the target proteins (BET proteins, including BRD2, BRD3, and BRD4) and recruit them to the ubiquitin/ proteasome system for selective degradation. However, the function of GNE987 has not been assessed in NB models so far. In the present study, RNA-seq analysis was performed to explore the effect of GNE987 on NB cells.

overall_design: mRNA profiles of SK-N-BE(2) cells treated with 10 nM or same volume DMSO for 24 h were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Yanling

last: Chen

first: Jian

last: Pan


title: Single-cell transcriptomic landscapes of the otic neuronal lineage at multiple early embryonic ages

city: Shanghai

first: Luyue

state: 徐汇区

address: Yue yang road

institute: Shanghai institute of nutrition and health

summary: Inner ear vestibular and spiral ganglion neurons (VGNs and SGNs) are known to play pivotal roles in balance control and sound detection. However, the molecular mechanisms underlying otic neurogenesis at early embryonic ages have remained unclear. Here, we use single-cell RNA-sequencing to reveal the transcriptomes of mouse otic tissues at three embryonic ages, embryonic day 9.5 (E9.5), E11.5, and E13.5, covering proliferating and undifferentiated otic neuroblasts and differentiating VGNs and SGNs. We validate the high quality of our studies by using multiple assays, including genetic fate-mapping analysis, and we uncover several previously unknown genes upregulated in neuroblasts or differentiating VGNs and SGNs, such as Shox2, Myt1, Casz1, and Sall3. Notably, our findings suggest a general cascaded differentiation trajectory during early otic neurogenesis. The comprehensive understanding of early otic neurogenesis provided by our study holds critical implications for both basic and translational research.

overall_design: Foxg1-ires-Cre/+; Ai9/+ mouse strain is used. Otic vesicle cells are Tdtomato+. At E9.5 and E11.5, otic and periotic cells are dissected together under fluorescent dissecting microscope. In contrast, at E13.5, we are able to dissect out inner ear with minimal cells from tissues nearby. After dissection, tissues are subject to single cell suspension and 10x library construction. One replicate (sample 1) is performed at E9.5, 3 replicates (samples 2-3-4) at E11.5 and 4 replicates (samples 5-6-7-8) at E13.5.

first: Yuwei

last: Sun

first: Chao

last: Li

first: Tong

last: Zhu

first: Guangqin

first: Bailin

last: Wu

first: Zhengnan

last: Luo

first: Wu

last: Wei

first: Zhiyong

last: Liu


title: CRISPR screens uncover protective effect of PSTK to targeted therapy induced ferroptosis in hepatocellular carcinoma

city: Beijing

first: Jun

last: Liang

state: Beijing

address: 1 Life Park Road, Life Science Park of Zhongguancun, Changping

department: Department of Oncology

institute: Peking University International Hospital

summary: Hepatocellular carcinoma (HCC) is one of the most frequent malignancies with extremely poor prognosis. Clinical efficacies of existing targeted therapy strategies were not satisfied due to targeted therapy resistance. In this study, we performed a series of CRISPR/Cas9 screens to identify synthetic lethality genes to improve the clinical response of HCC.  CRISPR loss-of-function genetic screens were performed to identify synthetic lethality genes of targeted therapies (Abemaciclib, Palbociclib, Sorafenib, Lenvatinib, Regorafenib and Erastin) in HCC cell lines. RNA-seq analysis were performed to clarify potential mechanism. We identified that inhibition of phosphoseryl-tRNA kinase (PSTK) sensitized HCC cells to targeted therapies. PSTK contributes to resistance of targeted therapy induced ferroptosis.

overall_design: CRISPR screen: Toronto human knockout pooled library (TKOv3) was a gift from Jason Moffat (Addgene #125517). TKOv3 contains 70948 sgRNAs targeted to 18053 protein-coding genes. Library amplification and virus preparation were performed according to the protocol of Moffat Lab. Firstly, we established stable Cas9-expressing HCC cell lines by lentiviral transduction of Cas9 coding sequence together with mCherry coding sequence. Cas9 expressing cells were sorted by flow cytometry. Hep3B-Cas9 cells or SNU-398-Cas9 cells were transduced with TKOv3 library at low MOI (0.2-0.3) for 24 hours and cultured with fresh DMEM with 3μg/mL puromycin for 72 hours. Then cells were divided into eight groups (around 1000-fold coverage of the sgRNA library at each group). One group of transfected cells was harvested as baseline of screening (T0) and other groups were treated with inhibitors (IC20) or DMSO for 14 days respectively. After screening, cells were harvested and extracted for genomic DNA. Genomic DNA were further amplified and labeled with barcodes using NEBNext® High-Fidelity 2X PCR Master. Illumina deep sequencing were carried out by Annoroad (Beijing, China). The abundance of sgRNAs was counted by Bowtie2 and the synergistic/suppressor chemical genetic interactions were analyzed by DrugZ algorithm.  RNA-seq: For RNA sequencing, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Differential expression analysis of two groups (Hep3B_PSTK_KO vs. Hep3B_control, three biological replicates) was performed using the DESeq2 R package (1.20.0).

first: Yiran

first: Li

first: Jie

last: Lan


title: RNA-sequencing of wild-type and ArhGEF1-deficient splenic cDC2s

first: Lihui

last: Duan

summary: We analyzed the transcriptome differences of wild-type and ArhGEF1-deficient (Arhgef1-/-) type-2 conventional dendritic cells (cDC2s) in spleen. Wild-type or ArhGEF1-deficient (Arhgef1-/-) bone marrow cells were transferred into lethal irradiated CD45.1 mice. 8 weeks later, splenic cDC2s were purified and prepared for RNA-seq analysis. The gene expression profiles of CD97-, Gα13- and ArhGEF1-deficient cDC2s were highly similar, providing evidence that these molecules function in the same pathway.

overall_design: Transcriptome analysis of WT and Arhgef1-/- splenic cDC2s

first: Dan

first: Erick

last: Lu

first: Ying

last: Xu

first: Jason

last: Cyster


title: LncCCAT1 interaction protein PKM2 up-regulates SREBP2 phosphorylation to promote osteosarcoma tumorigenesis by enhancing the Warburg effect and lipogenesis

city: Wuhan

first: Dong

state: Hubei

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

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Pyruvate kinase M2 (PKM2) plays an important role in the consumption of glucose and the production of lactic acid, the striking feature of cancer metabolism. The association of PKM2 with osteosarcoma (OS) has been reported but its role in OS has not. To study this, we obtained PKM2-bound RNAs in HeLa cells. Peak calling analysis revealed that PKM2 binds to long noncoding RNAs (lncRNAs), which are associated with cancer pathogenesis and development. Validation of the PKM2-lncRNA interaction in the human OS cell line showed that lncRNA colon cancer associated transcript-1 (lncRNACCAT1) interacts with PKM2, which upregulates the phosphorylation of sterol regulatory element-binding protein 2. These factors promote the Warburg effect, lipogenesis, and OS cell growth. PKM2 seems to be a key regulator in OS by binding to lncCCAT1. This further extends the biological functions of PKM2 in tumorigenesis and makes it a novel potential therapeutic for OS.

overall_design: RIP-seq analysis of PKM2 IP versus input in Hela cells.

first: Feifei

last: Pu

first: Zhicai

first: Zengwu

last: Shao


title: Transcriptomic Profile of OCI-AML-20 Cell Line in response to PRMT5 inhibition

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

summary: We investigated the role of protein arginine methyltransferase 5 (PRMT5) in leukemia patient cells with inversion of chromosome 3. This rearrangement leads to overexpression of the proto-oncogene EVI1 (ecotropic virus integration site 1). To further investigate the mechanism of PRMT5 dependency in these cells, we performed transcriptome and splicing analyses.

overall_design:
RNA-Seq transcriptome analysis of OCI-AML-20 cell line, DMSO control and PRMT5 inhibitor treated with three biological replicates.
Note from submitter: This is a human-derived cell line as such we will need to upload the raw data to the EGA.

first: Alex

first: Victoria

last: Vu

first: Dalia

last: Barsyte-Lovejoy


title: Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei

city: Tucson

first: Hao

last: Zhang

state: AZ

address: 1230 N Cherry Ave

department: CMM

institute: The University of Arizona

summary: The "Assay for Transposase Accessible Chromatin sequencing" (ATAC-seq) is an efficient and easy to implement protocol to measure chromatin accessibility that has been widely used in multiple applications studying gene regulation. While several modifications or variants of the protocol have been published since it was first described, there has not yet been an extensive evaluation of the effects of specific protocol choices head-to-head in a consistent experimental setting. In this study, we tested multiple protocol options for major ATAC-seq components (including three reaction buffers, two reaction temperatures, two enzyme sources, and the use of either native or fixed nuclei) in a well-characterized cell line. In addition, the native conditions were tested in a primary sample type (mouse lung tissue) with two different input amounts. In general, native samples yielded more peaks (particularly at loci not overlapping transcription start sites) than fixed samples, and the temperature at which the enzymatic reaction was carried out had a major impact on data quality metrics for both fixed and native nuclei. However, the effect of various conditions tested was not always consistent between the native and fixed samples. For example, the Nextera and Omni buffers were largely interchangeable across all other conditions, while the THS buffer resulted in markedly different profiles in native samples. In-house and commercial enzymes performed similarly. We found that the relationship between commonly used measures of library quality differed across temperature and fixation, and so evaluating multiple metrics in assessing the quality of a sample is recommended. Notably, we also found that these choices can bias the functional class of elements profiled and so we recommend evaluating several formulations in any new experiments. Finally, we hope the ATAC-seq workflow formulated in this study on crosslinked samples will help to profile archival clinical specimens.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We created 24 experimental conditions with all possible combinations of three ATAC-seq buffers, two reaction temperatures, two Tn5 enzyme sources, and the use of either native or fixed cells in GM12878 cell line. A total of 96 samples were generated with four replicates for each condition. All experimental conditions were also repeated in native nuclei isolated from lungs from three different mice, and performed using two different input amounts. Through this extensive comparison, we were able to observe the effect of different ATAC-seq conditions on data quality and to examine the utility and potential redundancy of various quality metrics.

first: Michael

middle: E

last: Rice

first: Joseph

middle: W

last: Alvin

first: Dominique

last: Farrera-Gaffney

first: James

middle: J

last: Galligan

last: Johnson

first: Darren

last: Cusanovich


title: Conservation and divergence of DNA methylation patterns and functions in vertebrates

city: Illkirch

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

country: France

institute: CNRS

type: Methylation profiling by high throughput sequencing

summary: Cytosine DNA methylation is a heritable epigenetic mark present in most eukaryotic groups. While the patterns and functions of DNA methylation have been extensively studied in mouse and human, their conservation in other vertebrates remain poorly explored. In this study, we interrogated the distribution and function of DNA methylation in primary cells of seven vertebrate species including bio-medical models and key livestock species.

sample_organism:
Gallus gallus
Homo sapiens
Canis lupus familiaris
Sus scrofa
Bos taurus
Oryctolagus cuniculus
Mus musculus

overall_design:
To study the conservation of DNA methylation patterns among vertebrates, we performed Whole Genome Bisulfite Sequencing (WGBS) in primary dermal fibroblasts from 7 vertebrate species (human, mouse, rabbit, dog, cow, pig, and chicken).
To study the functions of DNA methylation, we performed RNA-seq in triplicates in control and 5-Aza-2′-deoxycytidine (5-AzadC) treated primary dermal fibroblasts from 6 vertebrate species (human, mouse, rabbit, cow, pig, and chicken). The effect of 5-AzadC treatment was validated by performing Reduced Representation Bisulfite Sequencing (RRBS) in control and 5-AzadC treated fibroblasts.

first: Hala

last: Al Adhami

first: Anais

last: Bardet

last: Dumas


title: Cell-wall damage activates DOF transcription factors to promote wound healing and tissue regeneration in Arabidopsis thaliana

city: Uppsala

first: Ai

state: Uppsala

address: Biocenter, Almas allé 5

department: Plant Biology

country: Sweden

institute: SLU

summary: Wound healing is a fundamental property of plants and animals that requires recognition of cellular damage to initiate regeneration. In plants, wounding activates a defense response via the production of jasmonic acid and a regeneration response via the hormone auxin and several ethylene response factor (ERF) and NAC domain-containing protein (ANAC) transcription factors. To better understand how plants recognize damage and initiate healing, we searched for factors upregulated during the horticulturally relevant process of plant grafting and found four related DNA binding with one finger (DOF) transcription factors, HIGH CAMBIAL ACTIVITY2 (HCA2), TARGET OF MONOPTEROS6 (TMO6), DOF2.1, and DOF6, whose expression rapidly activated at the Arabidopsis graft junction. Grafting or wounding a quadruple hca2, tmo6, dof2.1, dof6 mutant inhibited vascular and cell-wall-related gene expression. Furthermore, the quadruple dof mutant reduced callus formation, tissue attachment, vascular regeneration, and pectin methylesterification in response to wounding. We also found that activation of DOF gene expression after wounding required auxin, but hormone treatment alone was insufficient for their induction. However, modifying cell walls by enzymatic digestion of cellulose or pectin greatly enhanced TMO6 and HCA2 expression, whereas genetic modifications to the pectin or cellulose matrix using the PECTIN METHYLESTERASE INHIBITOR5 overexpression line or korrigan1 mutant altered TMO6 and HCA2 expression. Changes to the cellulose or pectin matrix were also sufficient to activate the wound-associated ERF115 and ANAC096 transcription factors, suggesting that cell-wall damage represents a common mechanism for wound perception and the promotion of tissue regeneration.

overall_design: The grafting transcriptomic dataset is consists of 36 samples, including col-0, dof quadruple, erf114,115 and anac071,096. Each genotype contains intact, scion and rootstock tissues, whereas each tissue of genotype is represented by three biological replicates.

first: Charles

last: Melnyk


title: Circular RNA microarray expression profile in preeclampsia and natural pregnancy placenta tissues

city: shenyang

first: ziwei

last: li

address: nanjingstreet 155

department: obstetric

institute: China medical university

summary: To determine the circRNA expression profile in preeclampsia and natural pregnancy placenta tissues, we uesed circRNA microArray analysis form Arraystar to examine the expression of circRNAs in preeclampsia and natural pregnancy placenta tissues.

overall_design: Placenta tissues from caesarean surgery were distributed into two experimental groups: natural pregnancy placenta tissue group and preeclampsia placenta tissue group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar)

first: Ziwei

last: Li

first: Tao

last: Meng


title: RNA-Seq in pancreatic islets isolated from Arid1aFl/Fl control and Arid1aFl/Fl; UBC-CreERT2 mice (Arid1a KO) with/without pancreatectomy.

status: Public on Mar 22 2022

city: Dallas

last: Zhu

state: TX

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Cetern

summary: To determine how ARID1A loss might regulate gene expression, we performed RNA-sequencing (RNA-seq) on islets isolated from control and Arid1a knockout (KO) mice at baseline and 6 days after 50% pancreatectomy (PPx).

overall_design: In vivo RNA-Seq on islets isolated from 3 months old male control and Arid1a KO mice at baseline and 6 days after PPx (Pre-PPx: 2 Arid1aFl/Fl control and 5 Arid1aFl/Fl; UBC-CreERT2 mice, Post-PPx: 2 Arid1aFl/Fl control and 2 Arid1aFl/Fl; UBC-CreERT2 mice)

first: Jen-Chieh

last: Chuang

first: Cemre

last: Celen

first: Xin

last: Luo


title: LncRNA GACAT2 binding protein PKM1/2 reverses inflammation-compromised mitochondrial function and cementoblastic differentiation of periodontal ligament stem cells

city: Xi'an

first: Xuan

address: 145, Changlexi Road

institute: School of Stomatology, Fourth Military Medical University

summary: This study investigated the role of mitochondrial function and the downstream long noncoding RNAs (lncRNAs) in regulating inflammation-induced changes to the cementoblastic differentiation of PDLSCs. We found that inflammatory cytokine-caused impairment to cementoblastic differentiation of PDLSCs was closely correlated to their mitochondrial function, and in terms of lncRNA microarray analysis and gain/loss-of-function studies, gastric cancer associated transcript 2 (GACAT2) was identified as a regulator across the cellular events of both inflammation-mediated mitochondrial function and cementoblastic differentiation. Next, comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) and parallel reaction monitoring (PRM) assay revealed that GACAT2 was directly binded to protein pyruvate kinase M1/2 (PKM1/2). Further functional studies demonstrated that GACAT2 overexpression increased cellular protein expressions of PKM1/2, PKM2 tetramer and phosphorylated PKM2, led to an enhanced pyruvate kinase (PK) activity along with increased translocation of PKM2 into mitochondria. Finally, we found that GACAT2 overexpression could reverse inflammation-compromised mitochondrial function and cementoblastic differentiation of PDLSCs, and this function could be abolished by PKM1/2 knockdown. Our data suggest that lncRNA GACAT2 plays a critical role in inflammation-compromised mitochondrial function and cementoblastic differentiation by binding protein PKM1/2.

overall_design: PDLSCs were incubated in normal α-MEM medium (Nor), medium with the presence of inflammatory cytokines TNF-α plus IL-1β (Infla), medium with the presence of cementoblastic inducer EMD (EMD), or medium with the presence of both inflammatory cytokines and EMD (Infla-EMD)

first: Bei-Min

last: Tian

first: Dao-Kun

last: Deng

first: Xiao-Tao

last: He

first: Fa-Ming

last: Chen


title: CELF1 upregulates MMP gene expression to regulate cataract development

first: Dong

summary: As a multifunctional RBP, CELF1 is known to preferentially binds to GU-rich elements (GREs) predominantly located in 3’ untranslated regions(UTRs) of target mRNA  to regulate various post-transcriptional process. However, the targeted genes that regulated by CELF1 during cataractogenesis remains unknown. In present study,the function of CELF1 in SRA01/04 cells was investigated with CELF1 overexpression, the expression of MMPs was regulated by CELF1.

overall_design: transcrptional analysis of CELF1 overexpression and control in SRA01/04 cells

first: He

last: Zou

first: Zhigang


title: SOX11-deficiency causes schizophrenia through disturbing progenitor polarity and disrupting mossy fiber projections in the hippocampus

first: Mengzhu

last: Xue

address: No.100, Haike Road

institute: Shanghai Advanced Research Institute

summary: To address how SOX11-deficiency caused abnormal differentiation of the dentate epithelium, we performed transcriptional sequencing of E14.5 dentate neuroepithelium. RSEM is taken for consequent data analysis, mapping each sample to the mouse genome (mm10)  to determine expressions of 35274 transcripts.

overall_design: Dentate neuroepithelium cells were separated from E14 wild type, SOX11f/+ and SOX11f/f mice. Decapsulated dentate neuroepithelium was placed in a 15-ml tube, washed with 5ml cold DPBS for twice and then stored on dry ice. Oligo(dT)-selected RNA was converted into cDNA for RNA sequencing using the Illumina TruSeq RNA Sample Preparation Kit v2, following the manufacturer’s instructions. Samples were sequenced on an Illumina HiSeq 2500 platform in the 150-nt paired-end sequencing mode. RNA sequences were aligned to the mouse genome (mm10) using TopHat (v2.0.11) with default parameters. Differentially expressed genes were analyzed using Cufflinks (v.2.2.1) with the RefSeq transcript annotation10.

first: Xianmixinuer

last: Abulaiti


title: The XRN1-regulated RNA helicase activity of YTHDC2 ensures mouse fertility independently of m6A recognition

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

summary: The functional consequence of N6-methyladenosine (m6A) RNA modification is mediated by ‘reader’ proteins like those of the YTH family that recruit additional factors to alter splicing, RNA stability or translation. Germline-specific YTH domain-containing 2 (YTHDC2) is essential for mammalian fertility, but its molecular function is poorly understood. Here we use a tagged mouse line to identify U-rich motifs as binding sites of YTHDC2 on 3′ UTRs of testicular RNA targets. Although its YTH domain is an m6A-binder in vitro, the YTH point mutant mouse lacking this ability displays no obvious phenotypes. Its 3′→5′ RNA helicase activity is essential for fertility, with the catalytic-dead mutation being dominant-negative. Single-cell transcriptomics reveal that Ythdc2 mutant mitotic testicular germ cells transition into meiosis but accumulate a transcriptome with mixed mitotic/meiotic identity. We also reveal a conserved role for YTHDC2 in animal fertility.

overall_design: iCLIP experiment was used to identify the RNA targets of YTHDC2, as well as its binding sites and motifs. RNA sequencing was applied to study the gene expression differences between Ythdc2YTHmut/+ and Ythdc2YTHmut/YTHmut  of testicular 2n and 4n cells, Ythdc2+/+, Ythdc2+/cat-dead, and Ythdc2cat-dead/cat-dead.

first: Lingyun

first: Kyrylo

last: Krasnykov

first: David

last: Homolka

first: Pascal

last: Gos

first: Mateusz

last: Mendel

first: Richard

last: Fish

first: Radha

last: Raman Pandey

middle: S


title: Hepatic stellate cells mediates transcription of TNFSF14 in hepatocellular carcinoma cells via H2S/CSE-JNK/JunB signaling pathway

first: Yanan

last: Ma

address: No.8, Youanmen wai St

department: Department of Gastroenterology and Hepatology

institute: Beijing You’an Hospital affiliated with Capital Medical University

summary: Purpose: Hepatic stellate cell (HSC) and Hydrogen sulfide (H2S) both play important roles in Hepatocellar carcinoma (HCC). Whereas, in the microenvironment of HCC, whether HSC participates in regulating the biological process of HCC cells by releasing H2S remains elusive. In this study, we investigate how activated HSC influence HCC fate.   Methods: The effects of LX-2 and H2S on biological functions of HCC cells were analyzed with Flow cytometry and CCK-8. RNA-sequencing, Western blotting, Quantitative real-time reverse transcription PCR (RT-qPCR), siRNA, immunofluorescence and chromatin immunoprecipitation (ChIP) assays were carried out to examine the effect of H2S on JNK/JunB-TNFSF14 (tumor necrosis factor superfamily member 14) signaling pathway. Specimens from HCC patients were analyzed by using RT-qPCR and Western blotting assays for evaluating the expression of TNFSF14. Statistical analysis was used to analyze the correlation between TNFSF14 expression and clinical data of HCC patients.  Results: LX-2 cells is able to induce HepG2 and PLC/PRF/5 cells apoptosis by releasing H2S. RNA- sequencing results showed that TNFSF14 gene was changed in both LX-2 and NaHS group. NaHS dosage and time-dependently up-regulated TNFSF14 mRNA and protein expression in both HepG2 and PLC/PRF/5 cells. NaHS treated in HCC cells led to JNK/JunB signaling pathway activating and greater binding of JunB to its responsive elements on TNFSF14 promoter. Impairment of TNFSF14 induction alleviated LX-2 and NaHS induced apoptosis of HepG2 and PLC/PRF/5 cells. Furthermore, mRNA and protein expressions of TNFSF14 in HCC tissues was lower than in the adjacent tissue. HCC patients with low expression of TNFSF14 have higher malignant degree and poor prognosis.  Conclusions: Demonstration of the involvement of HSC-derived H2S in JNK/JunB mediated expression of TNFSF14 gene strongly indicates H2S palys an important role in the regulation of HCC apoptosis.

overall_design: RNA profiles of HepG2 cells and HepG2 cells treated with NaHS and HepG2 cells co-cultured with LX-2 cells.

first: Shanshan

last: Wang

first: Yongle

last: Wu

first: Huiguo

last: Ding


title: Aberrant translation regulation by METTL1/WDR4-mediated tRNA N7-methylguanosine modification drives HNSCC progression

city: Guangzhou

first: Jie

address: No. 58, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: The cancer cells selectively promote the translation of specific oncogenic transcripts to stimulate cancer progression. Although growing evidence has revealed that tRNA modifications and related genes participate in this process, their roles in head and neck squamous cell carcinoma (HNSCC) remain largely uncharacterized. Here we found that tRNA m7G methyltransferase complex components METTL1/WDR4 were both upregulated in HNSCC and associated with poor prognosis. Functionally, METTL1/WDR4 promoted HNSCC progression and metastasis in cell-based and transgenic mouse models. Mechanistically, ablation of METTL1 reduced m7G levels of 16 tRNAs, causing translational inhibition of a subset of oncogenic transcripts, including the genes related to PI3K/AKT/mTOR signaling pathway. In addition, chemical modulators of PI3K/AKT/mTOR signaling pathway can reverse the effects of Mettl1 in HNSCC. Furthermore, single-cell RNA sequencing results revealed that depletion of Mettl1 in tumor cells altered the immune landscape and cell-cell interaction between tumor and stromal compartment. In summary, this study uncovered the physiological function and mechanism of mis-translation regulation mediated by tRNA m7G modification in HNSCC, and suggested that targeting METTL1 could be a promising treatment strategy for HNSCC patients.

overall_design: TRAC-Seq were developed to identify the tRNA m7G methylome in HNSCC cell line.  Polyribosome-bound-RNA-seq  was used to study the differentially translated genes in the METTL1 knockout and control cells. Ribo-seq was performed to study the differentially translated genes and ribosome processivity in the METTL1 knockout and control cells. scRNA-seq of murine HNSCC from 4NQO-induced Mettl1cKO and wild type transgenic mice.

first: Demeng


title: ATAC-seq chromatin accessibility profiling in pancreatic islets isolated from Arid1aFl/Fl ; MIP-rtTA control and Arid1aFl/Fl; MIP-rtTA; TRE-Cre mice (Arid1a βKO) with/without pancreatectomy.

first: Hao

last: Zhu

summary: To determine how ARID1A loss might regulate genes that were preferentially regulated on the gene expression level, we performed an assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) on islets isolated from control and Arid1a β-cell knockout (βKO) mice at baseline and 6 days after 50% pancreatectomy (PPx).

overall_design: In vivo ATAC-Seq on islets isolated from 3 months old male control and Arid1a βKO mice at baseline and 6 days after PPx (Pre-PPx: 4 Arid1aFl/Fl; MIP-rtTA control and 3 Arid1aFl/Fl; MIP-rtTA; TRE-Cre mice, Post-PPx: 4 Arid1aFl/Fl; MIP-rtTA control and 4 Arid1aFl/Fl; MIP-rtTA; TRE-Cre mice, all males)

first: Cemre

last: Celen

first: Yuemeng

last: Jia

first: Tianshi

last: Lu


title: Target-agnostic discovery of Rett Syndrome therapeutics by coupling computational network analysis and CRISPR-enabled in vivo disease modeling

city: Boston

last: Novak

state: MASSACHUSETTS

address: 3 Blackfan Cir

department: Wyss Institute

institute: Harvard University

summary: It is difficult to develop effective treatments for neurodevelopmental genetic disorders, such as Rett syndrome, which are caused by a single gene mutation but trigger changes in numerous other genes, and thereby also severely impair functions of organs beyond the central nervous system (CNS).  This challenge is further complicated by the lack of sufficiently broad and biologically relevant drug screens, and the inherent complexity in identifying clinically relevant targets responsible for diverse phenotypes. Here, we combined human gene regulatory network-based computational drug prediction with in vivo screening in a population-level diversity, CRISPR-edited, Xenopus laevis tadpole model of Rett syndrome to carry out target-agnostic drug discovery, which rapidly led to the identification of the FDA-approved drug vorinostat as a potential repurposing candidate. Vorinostat broadly improved both CNS and non-CNS (e.g., gastrointestinal, respiratory, inflammatory) abnormalities in a pre-clinical mouse model of Rett syndrome. This is the first Rett syndrome treatment to demonstrate pre-clinical efficacy across multiple organ systems when dosed after the onset of symptoms, and network analysis revealed a putative therapeutic mechanism for its cross-organ normalizing effects based on its impact on acetylation metabolism and post-translational modifications of microtubules.

overall_design: Xenopus embryos were genetically modified using CRISPR-Cas9 indel formation in the MeCP2 gene to generate a model of Rett syndrome to be used for drug screening.

first: Frederic

last: Vigneault

first: Michael

last: Levin

first: Donald

last: Ingber


title: Cleavage of histone H2A during embryonic stem cell differentiation destabilizes nucleosomes to counteract gene activation [ARID2 and PBRM1 ChIP-seq]

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Histone proteolysis is a poorly understood phenomena by which the N-terminal tail of histones are irreversible cleaved by intracellular proteases. During development histone PTMs are known orchestrate gene expression and ultimately cell fate decision, therefore it will be key to decipher underlying mechanisms that lead to proteolysis during cellular differentiation. Previous reports have found that histone H2A is cleaved at the C-terminus, and here we found that the N-terminal is also proteolytically clipped and removed by the lysosomal protease Cathepsin L. Using quantitative mass spectrometry (MS), we identified L23 to be the primary site for this protease, with this clipped H2A (cH2A) form representing ~1% of the total H2A reaching a maximum after 4 days of differentiation. Using Chip-seq, we found reduced proteolysis, lead to increase acetylated H2A at promoter regions in differentiated ES cells.  We also report novel readers of acetylated H2A during in pluripotency as we identified members of the pBAF complex to recognize different forms of H2A acetylation. Moreover, our data showed that this recognition is abolished upon proteolysis. All in, our data suggest that proteolysis serve as a quick mechanism to silence genes involve in pluripotency and destabilize the nucleosome core particle as indicated by protein degradation studies.

overall_design:
AID2 and PBRM1 ChIP-seq in mESCs differentiation with CTSL KD.

Please note that peaks were detected for each sample against the corresponding input control and is linked to the corresponding *rep1 ChIP sample records.

first: Mariel

last: Coradin

first: Benjamin

middle: A

last: Garcia


title: An analysis of the Neoantigen burden in Breast Carcinoma Patients

city: Singapore

first: XI

last: REN

state: Choose State

address: National University of Singapore, 14 Medical Drive, MD6, #12-01

institute: Cancer Science Institute of Singapore

summary: In this study we report the neoantigen landscape, tumor mutational burden and tumor microenvironment of seven breast cancer patients, consisting of three Estrogen receptor (ER) positive and four Triple negative breast cancer (TNBC) subtypes.

overall_design: RNA-Seq and Whole Exome Sequencing of seven braest cancer patients.

first: Sambhavi

last: Animesh

first: Ren

last: Xi

first: Omer

last: An

first: Kaijing

last: Chen

first: Lee

last: Chin

first: Henry

last: Yang

first: Melissa

last: Fullwood


title: Loss of TDP-43 in male germ cells causes meiotic failure and impairs fertility in mice

city: Urbana

first: Jenny

last: Drnevich

state: IL

address: 1206 W. Gregory Dr.

institute: University of Illinois

summary: TAR DNA binding protein of 43 kDa (TDP-43; gene name: Tardbp), a ubiquitously expressed evolutionarily conserved protein, is highly expressed in the preleptotene and pachytene spermatocytes. TDP-43 is linked to several human neurodegenerative disorders. Exploring its functional requirement for spermatogenesis for the first time, we show here that conditional knockout (cKO) of Tardbp in male germ cells of mice leads to failure of meiosis and arrest of spermatogenesis. Fertility trials indicated severe subfertility. Spermatocytes of cKO mice showed failure to complete prophase I of meiosis with arrest at mid-pachytene stage. Our work reveals a crucial role for TDP-43 in male meiosis and suggests that some forms of meiotic arrest seen in infertile men may result from loss of function of TDP-43. In order to identify putative direct genes of TDP-43, we performed RNA-seq using testes from postnatal day 12 (PND12) wild type (control) and cKO (experimental) mice.

overall_design: mRNA profiles of 12 day-old (PND12) Tardbp conditional knockout (cKO) and control (WT) mice

first: Prabhakara

last: Reddi


title: RNA-seq analysis of MDA-MB-231 and HCT-166 cells treated with 100 microM H2O2

city: Seoul

first: Jimin

last: Hwang

address: 52, Ewhayeodae-gil, Seodaemun-gu

country: South Korea

institute: Ewha Womans University

summary: We report a role of Heat shock protein 60 (Hsp60) in the oxidative stress-induced gene expression in cancer cells.

overall_design: mRNA profiles from MDA-MB-231, HCT116 cells before and after treatment of H2O2 as well as H2O2 plus Hsp60N antibody. For 3 conditions (control, H2O2, H2O2 plus Hsp60N), replicates were generated.

first: Sangwon

last: Kang

first: Chengchun

last: Min

first: Ji-Yeon

last: Kim

first: Hyo-Min

last: Cho

first: Sujin

last: Park

first: Ji-Min

first: HyeJin

last: You

first: Won-Jae

last: Lee

first: Woong

last: Sun

first: Dongmin

first: Sanghyuk


title: Repeat Detector: accurate, efficient, and flexible sizing of expanded CAG/CTG repeats from targeted DNA sequencing

city: Cardiff

first: Vincent

last: Dion

address: Hadyn Ellis Building

department: Dementia Research Institute

country: United Kingdom

institute: Cardiff University

summary: Targeted DNA sequencing approaches will improve how the size of short tandem repeats is measured for diagnostic tests and pre-clinical studies. The expansion of these sequences causes dozens of disorders, with longer tracts generally leading to a more severe disease. In addition, interruptions are sometimes present within repeats and can alter disease manifestation. Despite advances in methodologies, determining repeat size and identifying interruptions in targeted sequencing datasets remains a major challenge. This is because standard alignment tools are ill-suited for the repetitive nature of these sequences. To address this, we have developed Repeat Detector (RD), a deterministic profile weighting algorithm for counting repeats in targeted sequencing data. We tested RD using blood-derived DNA samples from Huntington’s disease (HD) and Fuchs endothelial corneal dystrophy patients sequenced using either Illumina MiSeq or Pacific Biosciences single-molecule, real-time sequencing platforms. RD was highly accurate in determining repeat sizes of 609 HD blood-derived samples and did not require prior knowledge of the flanking sequences or their polymorphisms within the patient population. We demonstrate that RD can be used to identify individuals with repeat interruptions and may provide a measure of repeat instability within an individual. RD is therefore highly versatile and may find applications in the diagnosis of expanded repeat disorders and the development of novel therapies.

overall_design: 22 DNA samples from Huntington's disease individuals obtained from Coriell.org. 4 Samples from HEK-derived GFP(CAG)x lines with different repeat sizes.

first: Alysha

last: Taylor


title: ChIP-seq of EYA2 in breast cancer cell lines

city: La Jolla

first: Zhixin

last: Qiu

address: 2880 Torrey Pines Scenic Dr

institute: UCSD

overall_design: ChIP-seq analysis of EYA2 binding in breast cancer cell line after FBXO7 knockdown. FLAG-EYA2 was overexpressed in MDA-MB-231 cell line

first: Shen

last: Jia


title: microRNA levels data from Melan-a cells expressing reduced level of Dicer and control Melan-a cells

city: ORSAY Cedex

first: Juliette

last: BERTRAND

address: Bat 110, Centre universitaire

department: CNRS UMR3347, INSERM  U1021

institute: Institut Curie

summary:
To investigate the molecular mechanism of the hypopigmentation observed in Dicer KO mice, Dicer knockdown was realised in vitro in normal C57BL/6 mouse melanocyte Melan-a cells.
Transient transfection of Melan-a cells with siRNA directed against Dicer reduced Dicer protein levels to approximately 40% of that of siScr Melan-a cells 24 hours after transfection. We analyzed the miRnome of Melan-a cells 24 and 48 hours after transfection with siDicer or siScr to understand the molecular mechanisms involved in Dicer-dependent melanocyte migration.

overall_design: We extracted total RNA from mouse melanocytes Melan-a cells 24 and 48 hours after transfection of siRNA against Dicer (siDicer) or a siRNA control (siScr) and performed microarray-based miRnome analysis. Three biological replicates were used for each condition.

last: Bertrand

first: Lionel

last: Larue


title: Melan-a cells expressing reduced level of Dicer and control Melan-a cells

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

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: Transcriptome analysis of collagen VI-related muscular dystrophy muscle biopsies

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH


title: Transcriptome analysis of collagen VI-related muscular dystrophy muscle biopsies [RNA-Seq].

summary: Collagen VI-related muscular dystrophies (COL6RD) are a rare, inherited group of congenital muscular dystrophies. The phenotype spans from an early-onset, severe, and rapidly progressive clinical course in Ullrich congenital muscular dystrophy (UCMD), to a late-onset, mild and slowly progressive form in Bethlem muscular dystrophy (BM). COL6RD are caused by pathogenic variants in any of the three collagen type VI genes (COL6A1, COL6A2, COL6A3), which cause absence, reduction, mislocalization, or dysfunction of the collagen VI microfibrils in the skeletal muscle extracellular matrix (myomatrix), leading to yet incompletely understood downstream effects. Pathologic alterations in muscle biopsies of COL6RD varies, ranging from severely dystrophic changes, to mildly myopathic, represented by isolated myofiber atrophy. In this study, we aim to define the pathophysiologic events responsible for the histologic alterations of muscle and their progression in COL6RD. Aided by automated image analysis, we reviewed COL6RD patient muscle biopsies (n=22) and stratified them to three groups based on the degree of fibrosis and muscle fiber atrophy. Using microarray and RNA-Seq, we then performed global gene expression profiling on the same muscle biopsies and compared it with controls (n=14). Different histologic groups were characterized by similar transcriptional signatures predominantly featuring the upregulation of myomatrix component genes and downregulation of skeletal muscle and mitochondrion-specific genes. Our results also identified the TGFβ1 pathway in strong correlation with the development of COL6RD pathology at the histologic level, beginning early in the disease process, preceding fibrosis, and increasing in direct correlation with increased histologic severity. Overall, our study identifies COL6RD as a primary disorder of the myomatrix and posits dysregulation of TGFβ1-dependent pathways as a potential factor in pathogenesis of the disease.

overall_design: RNA profiles for 36 human muscle biopsies were generated via deep sequencing using the Illumina HiSeq 2000 with version 3 flow cells and reagents.  Included among the 36 biopsies sequenced were 14 from persons with no COL6RD mutation and 22 with a COL6RD mutation  For those biopsies sequenced having a COLD6RD mutation, three hisology-grades are represented; COL6RD-1, COL6RD-2, and COL6RD-3.

first: Eleonora

last: Guadagnin

first: Payam

last: Mohassel

first: Lin

last: Yan

first: Mariarita

last: Santi

first: Prech

last: Uapinyoying

first: Jahannaz

last: Dastgir

first: Ying

last: Hu

first: Allissa

last: Dillmann

first: Mark

last: Cookson

first: A Reghan

last: Foley

first: Carsten

middle: G

last: Bonnemann


title: RNA-seq of FBXO7 knockdown in breast cancer cell line

last: Qiu

state: CA

overall_design: RNA-seq analysis of FBXO7 knockdown in breast cancer cell line MDA-MB-231.


title: Transcriptome analysis of collagen VI-related muscular dystrophy muscle biopsies [Microarray].

middle: R

overall_design: RNA profiles for 36 human muscle biopsies were generated using the Illumina microarray.  Included among the 36 biopsies sequenced were 14 from persons with no COL6RD mutation and 22 with a COL6RD mutaiton.  For those biopsies sequenced having a COLD6RD mutation, three hisology-grades are represented; COL6RD-1, COL6RD-2, and COL6RD-3.


title: FBXO7-EYA2 axis in cancer stem cell maintenance


title: Functional expression of melanocortin 4 receptor in monocytes to suppress aortic aneurysm and atherosclerosis in mice

status: Public on Mar 21 2022

city: Chuo

first: Kentaro

last: Mori

address: 1110, Shimokato

country: Japan

institute: Yamanashi University

summary:
Melanocortin-4 receptor (MC4R) mediates most anorectic leptin response effects to an agonist, α-melanocyte-stimulating hormone (α-MSH). MC4R mutations are considered to be the main cause of monogenetic obesity in humans. It has been reported that the activity loss of MC4R gene increases body mass index and cardiovascular event risk in humans. This study aimed to investigate our hypothesis that MC4R signaling directly modulates vascular functions and that MC4R signaling loss leads to vascular diseases, such as vascular vulnerability and abdominal aortic aneurysm (AAA).
To understand the molecular mechanism by which myeloid MC4R inhibits atherosclerosis and Ang II-induced AAA in mice, we first conducted a microarray analysis of LysM (+);MC4RTB/TB and MC4RTB/TB mouse primary BM-derived macrophages.

first: Kyoichiro

last: Tsuchiya


title: Tissue Eosinophilia is Effective for Studying Differential Expression of Genes by RNA sequencing, and may offer Superior Insights into Chronic Rhinosinusitis than Study by Polyp Status

city: Rochester

first: Chantal

last: McCabe

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: RNA sequencing (RNAseq) is being used to study inflammatory pathways in chronic rhinosinusitis (CRS). Our goal was to probe validity of tissue eosinophilia as a metric to study RNAseq in CRS. The study was conducted on prospectively enrolled subjects undergoing sinonasal surgery. Subjects were categorized as control, CRS, CRS with nasal polyps (CRSwNP) and CRS without nasal polyps (CRSsNP). CRS was also categorized by tissue eosinophil levels per high power field (EOS/HPF) as <10 EOS/HPF or ≥10 EOS/HPF. Ethmoidal tissue samples were processed, differentially expressed (DE) genes were calculated and Ingenuity pathway analysis (IPA) performed.Controls separated clearly from CRS by both study criteria (polyp status, EOS/HPF). In both analyses, CRS differentiated into two distinct CRS subgroups. However, heatmaps showed greater homogeneity within each CRS subtype when studied by eosinophilia versus polyp status. Overall, high differential gene expression was found in CRS versus controls, with 736 statistically significant differentially expressed (DE) genes. On comparison between between CRSwNP and CRSsNP, 60 DE genes were found and on analyzing by tissue EOS/HPF, 110DE genes were statistically significant between CRS <10 EOS/HPF and CRS ≥10 EOS/HPF analyses.  Tissue eosinophilia as a metric was further validated by finding of IL 17 signalling pathway between <10EOS/HPF (increased) versus ≥10 EOS/HPF samples on pathway analysis.  As a metric, tissue eosinophilia is at least as effective as analysis by polyp status for RNA sequencing and may potentially offer superior insights into mechanistic pathways.

overall_design: 20 samples; 4 control, 16 CRS

first: Devyani

last: Lal

first: Tripti

last: Brar


title: Gene expression data from Melan-a cells expressing reduced level of Dicer and control Melan-a cells [24 hours]

first: Juliette

last: BERTRAND

summary:
To investigate the molecular mechanism of the hypopigmentation observed in Dicer KO mice, Dicer knockdown was realised in vitro in normal C57BL/6 mouse melanocyte Melan-a cells.
Transient transfection of Melan-a cells with siRNA directed against Dicer reduced Dicer protein levels to approximately 40% of that of siScr Melan-a cells 24 hours after transfection. We analyzed the transcriptome of Melan-a cells 24 hours after transfection with siDicer or siScr to understand the molecular mechanisms involved in Dicer-dependent melanocyte migration.

overall_design: We extracted total RNA from mouse melanocytes Melan-a cells 24 hours after transfection of siRNA against Dicer (siDicer) or a siRNA control (siScr) and performed microarray-based transcriptome analysis. Three biological replicates were used for each condition.

last: Bertrand

first: Lionel

last: Larue


title: Effect of IL-13 and Vitamin D treatment on gene expression and epigenetics in the esophageal epithelial cell line EPC2

city: Cincinnati

last: Rochman

address: 3333 Burnett Ave

department: Allergy and Immunology

institute: CCHMC

summary: We report RNA- and ChIP-sequencing profiling of the esophageal epithelial cell line EPC2 in response to IL-13 and Vitamin D either alone or in the combined treatment

overall_design: EPC2 cells were seeded at high confluency and treated with either IL-13, or Vitamin D, or both for 6 hours. STAT6, VDR, H3K9ac, H3K27ac and H3K4me3 were assessed by ChIP-sequencing. Transcriptome was analyzed by RNA-sequencing

first: Mike

last: Brusilovsky

first: Marc

last: Rothenberg


title: m6A-seq of human cell lines

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

summary: We performed m6A-seq on human cell lines to profile m6A and/or m6Am sites in transcriptome

overall_design: Each experiment result (biological replicate) consists of 1 immunoprecipitation and 1 input.

first: Tao

last: Huang

first: Jianheng

last: Liu


title: Gene expression data from Melan-a cells expressing reduced level of Dicer and control Melan-a cells [48 hours]

summary:
To investigate the molecular mechanism of the hypopigmentation observed in Dicer KO mice, Dicer knockdown was realised in vitro in normal C57BL/6 mouse melanocyte Melan-a cells.
Transient transfection of Melan-a cells with siRNA directed against Dicer reduced Dicer protein levels to approximately 40% of that of siScr Melan-a cells 48 hours after transfection. We analyzed the transcriptome of Melan-a cells 48 hours after transfection with siDicer or siScr to understand the molecular mechanisms involved in Dicer-dependent melanocyte migration.

overall_design: We extracted total RNA from mouse melanocytes Melan-a cells 48 hours after transfection of siRNA against Dicer (siDicer) or a siRNA control (siScr) and performed microarray-based transcriptome analysis. Three biological replicates were used for each condition.


title: RNA sequencing (RNA-seq) for identifing differentially expressed genes for mitochondrial unfolded protein response in Arabidopsis

city: Shijiazhuang

first: Yanmin

last: Zou

state: Hebei

address: 286 Huaizhong Road

department: Center for Agricultural Resources Research

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: The purpose of this study is to identify differentially expressed expressed genes for mitochondrial unfolded protein response in Arabidopsis. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. We using an optimized data analysis workflow,

overall_design: RNA isolated from seedlings of 7-day old wild type arabidopsis plants(Col-0) treated with H2O, Dox and EtBr,and with 3 repeats of each sample

first: Dongping

last: Lu


title: CDK9 inhibition with AZD4573 in DLBCL

city: Duarte

first: Alexey

last: Danilov

state: California

address: 1500 East Duarte Road

department: Toni Stephenson Lymphoma Center

institute: City of Hope

summary: We report the effects of CDK9 inhibition (AZD4573) on the epigenetic landscape in Diffuse Large B-cell Lymphoma (DLBCL). This study utilized the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to assess genome-wide chromatin accessibility in two DLBCL cell lines, OCI-LY3 and VAL, treated with AZD4573 (30 nM) at 0, 3, and 8 hours. We found that CDK9 inhibition led to gain and loss of accessible chromatin genome-wide, with enrichment of CTCF/BORIS motifs in decreased accesibility regions.

overall_design: Two DLBCL cell lines, OCI-LY3 (GC-DLBCL) and VAL (ABC-DLBCL), were treated with AZD4573 (30 nM) for 0, 3, and 8 hours then were subjected to ATAC-sequencing. Each condition had two replicates prepared with an input of 50,000 cells using the standard ATAC-seq methodology, and two samples prepared with 5,000 cells using the fast-ATAC-seq method. Samples with different input number from the same condition merged together well using PCA.

first: Elana

last: Thieme

first: Daniel

last: Coleman

first: Zheng

last: Xia


title: Therapeutic targeting of differentiation state-dependent metabolic vulnerabilities in DIPG pontine gliomas

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

summary: H3K27M diffuse intrinsic pontine gliomas (DIPG) exhibit cellular heterogeneity comprising less-differentiated, stem-like glioma cells that resemble oligodendrocyte precursors (OPC) and more differentiated astrocyte (AC)-like cells. H3K27M DIPG stem-like cells exhibit tumor-seeding capabilities in vivo, a feature lost or greatly diminished in the more differentiated AC-like cells. In this study, we established isogenic in vitro models of DIPG that closely recapitulated the OPC-like and AC-like phenotypes of DIPG cells. Using these tools, we performed transcriptomics, metabolomics, and bioenergetic profiling to identify metabolic programs operative in the different cellular states. From this, we defined new strategies to selectively target metabolic vulnerabilities within the specific tumor populations. Namely, we showed that the AC-like cells exhibited a more mesenchymal phenotype and were thus sensitized to ferroptotic cell death. In contrast, OPC-like cells upregulated cholesterol metabolism and mitochondrial oxidative phosphorylation (OXPHOS) and were accordingly more sensitive to statins and OXPHOS inhibitors. Additionally, statins and OXPHOS inhibitors showed efficacy and extended survival in preclinical orthotopic models established with stem-like H3K27M DIPG cells. Together, this study demonstrates that cellular subtypes within DIPGs harbor distinct metabolic vulnerabilities that can be uniquely and selectively targeted for therapeutic gain.

overall_design: mRNA was extracted from three replicates each of DIPG-007, SF7761, and DIPG-13 (aka DIPG-XIII) gliomaspheres (GS) and differentiated glioma cells (DGC), for a total of 18 samples.

first: Nneka

last: Mbah

first: Amy

middle: L

last: Myers

first: Chan

last: Chung

first: Joyce

middle: K

last: Thompson

first: Hanna

last: Hong

first: Peter

last: Sajjakulnukit

first: Zeribe

last: Nwosu

first: Mengrou

last: Shan

first: Stefan

last: Sweha

first: Daniella

last: Maydan

first: Brandon

last: Chen

first: Li

first: Zirui

last: Zui

last: Wahl

first: Luigi

last: Franchi

first: Sameer

last: Agnihotri

first: Carl

last: Koschmann

first: Sriram

last: Venneti

first: Costas

last: Lyssiotis


title: The maternal microbiome promotes placental development in mice

city: Los Angeles

first: Geoffrey

last: Pronovost

address: 610 Charles E Young Drive South, Hsiao Lab MSB 3560

institute: UCLA

summary: We report that depletion of the maternal microbiota results in abberant placental development in mice - these data show gene expression changes in E14.5 placental labyrinth samples from microbiota-depleted dams and controls.

overall_design: Examination of gene expression in E14.5 placental labyrinth in mice.

first: Elaine

last: Hsiao


title: Impact of different anticoagulants in obtaining reference profiles of exRNAs in healthy individuals

first: Ionita

middle: Calin

last: Ghiran

state: MA

address: 3 Blackfan Circle

department: Medicine

institute: Beth Israel Deaconess Medical Center

overall_design: 24 samples from 3 male (M1-M3) and 3 female (F1-F3) subjects, 4 anticoagulants (E-EDTA, H-Heparin, C-Citrate, R-Hirudin) used for each subject


title: Distinct N6-methyladenosine (m6A) Regulation of Innate Immune Responses During Bacterial and Viral Infections

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio


title: Comparison of the effect of induction of AtGDU1 and the constitutive over-expression of the AtGDU genes on the transcriptome of Arabidopsis thaliana

city: Blacksburg

first: Guillaume

last: Pilot

state: VA

address: 220 Ag Quad Lane

department: School of Plant and Environmental Sciences

institute: Virginia Tech

summary: The over-expression of the AtGDU genes in Arabidopsis leads to strong phenotypes, which have in common glutamine secretion by the hydathodes, increased amino acid export from seedlings, early senescence and lesions on the leaves, and small sized-plants. The goal of the study was (1) to describe the primary effects of the AtGDU1 overexpression on the transcriptome using a dexamethasone-inducible construct, and (2) to compare the transcriptomes of plants overexpressing AtGDU1 to AtGDU6, in order to identify the differences in the function of each of the genes.

overall_design: The 6Op-LHGRn system was used for inducible expression of AtGDU1. The AtGDU1 to AtGDU6 genes were expressed under the control of the CaMV 35S promoter in wild type Col plants. All lines were brought to homozygosity. All plants were grown in parallel on soil for 4 weeks in a growth chamber. Dex-GDU1 and parental 4c-S7 lines were sprayed with 100 µM dexamethasone and leaf samples were collected 7 and 25 hours after. Leaves from the Col and the 35S-GDU lines were collected at the same time. Total RNA were extracted and analyzed by RNAseq. Each library was sequenced twice (L001 and L002, or L003 and L004), with 100 bp paired-end each time (R1 and R2). Information for each sample can be found in the GSE198853_CuffDiff_DIFF.xlsx file below. Each sequencing run is represented by a separate SRR.

first: Shi

last: Yu

first: Delasa

last: Aghamirzaie


title: Distinct N6-methyladenosine (m6A) Regulation of Innate Immune Responses During Bacterial Infections II

summary: N6-methyladenosine (m6A) is a dynamic post-transcriptional RNA modification influencing all aspects of mRNA biology. Here, we examined cellular m6A epitranscriptomes during P.aeruginosa infection to identify m6A-regulated innate immune response genes with or without ALKBH5 knockdown. We showed that a significant portion of cellular genes including many innate immune response genes underwent m6A modifications in 5’UTR and 3’UTR, from which we identified common and distinct m6A-modified genes under different stimulating conditions.

overall_design: RAW264.7 cells at 4×10^5 cells per mL were infected with P. aeruginosa at 107 per mL and harvested at 0, 2, 4, and 6 h post treatment. RAW264.7 cells with ALKBH5 knockdown were infected with P. aeruginosa 6 hr post infection. MeRIP was performed to enrich m6A methylated mRNA with m6A antibody, and sequenced with corresponding inut RNA.

first: Shou-jiang

last: Gao

first: Jian

last: Feng

first: Océane

last: Sorel

first: Zhao

last: Lai


title: Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis

city: bethesda

first: Xiang

last: Guo

address: 50 south drive, blg50

department: NIDDK

institute: NIH


title: SOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes [RNA-Seq]

city: Atlanta

first: Sergio

last: Ramirez-Perez

state: Georgia

address: 615 Michael St NE

department: Orthopaedics

institute: Emory University

summary:
Purpose: Our goal was to evaluate the transcriptional profiles of FLS. We used genome wide approaches to uncover the interactions between SOXC transcription factors and RELA/p65 transcription factor, downstream of TNF signaling.
Methods: We analyzed RNA-seq of TNF-treated FLS in control and SOXC gene knockout backgrounds. FLS isolated from Sox4fl/fl 11fl/fl 12fl/fl mice were transduced with Ade5CMV-eGFP virus for controls or transduced with Ade5CMV-Cre adenovirus for knockout of the three SOXC family genes, Sox4, Sox11 and Sox12
Results: paired-end reads were mapped to the mm10 genome assembly. RNA levels were normalized using DESeq.
Conclusion: SOXC family genes regulate TNF mediated gene expression.

overall_design: Identification of SOXC-dependent and independent aspects of the TNF-regulated transcriptome.

first: Pallavi

last: Bhattaram


title: Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis [ChIP-seq]

summary: To determine hemogen function in regulatory elements, ChIPmentation was performed in both WT and hemogen KO K562 cells and H3K27ac enrichment was significantly reduced at both promoters and enhancers in loss of hemogen. To identify direct targets and the regulatory role of hemogen in murine erythroid gene expression, hemogen and BRG1 ChIP-seq was performed in the WT and hemogen KO E14.5 fetal liver cells. Hemogen was found enriched in GATA1/TAL1 binding motifs and equally bind to the promoter and potential enhancer region. Notably, BRG1 occupancy (95%) was almost completely coincident with hemogen binding sites and loss of hemogen greatly impaired the BRG1 occupancy at both erythroid promoters and enhancers.

overall_design: ChIPmentation was performed using H3k27ac antibody to identify promoter and enhancer activity. ChIP-seq was performed in the E14.5 fetal liver cells to identify global occupancy of hemogen, BRG1 and H3K27ac at erythroid genes.

first: Ann

last: Dean


title: Distinct N6-methyladenosine (m6A) Regulation of Innate Immune Responses During Bacterial and Viral Infections I

last: Chen

summary: N6-methyladenosine (m6A) is a dynamic post-transcriptional RNA modification influencing all aspects of mRNA biology. Here, we examined cellular m6A epitranscriptomes during infections of herpes simplex virus type 1 (HSV-1) and lipopolysaccharide (LPS) stimulation to identify m6A-regulated innate immune response genes. We showed that a significant portion of cellular genes including many innate immune response genes underwent m6A modifications in 5’UTR and 3’UTR, from which we identified common and distinct m6A-modified genes under different stimulating conditions.

overall_design: HeLa cells were infected with HSV1 at 5 MOIs and harvested at 5 or 8 hr post-infection. RAW264.7 cells at 4×105 cells per mL were treated with LPS at 10 ng/mL and harvested at 6 hr post treatment. MeRIP was performed to enrich m6A methylated mRNA with m6A antibody, and sequenced with corresponding inut RNA.


title: Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis [ATAC-seq]

summary: To determine hemogen function in chromatin accessbility, ATAC Seq was performed in both WT and hemogen KO mouse liver.  Loss of hemogen caused generally decresed of chrmoatin accessbility on the hemogen/BRG1 binding promoter and enhancer .

overall_design: ATAC seq  was performed in both WT and KO E14.5 fetal liver cells to identify accessible DNA regions  .


title: Root cell layer specific AGO1-bound sRNA and total sRNA from Arabidopsis ktn1 mutant

city: Riverside

first: Xuemei

state: CALIFORNIA

address: 900 University AVe

institute: University of California

summary: We profiled total sRNA and root cell layer specific AGO1-bound sRNA in ktn1 mutant to study the role of KTN1 in miRNA non-cell autonomous activiy in Arabidopsis.

overall_design: Total sRNA and sRNA from GFP-AGO1 IP in plants expression GFP-AGO1 under EN7 (Endodermis) and ACL5 (Metaxylem and procambia) were examined.

first: Lusheng

last: Fan


title: Auxin and ABA responsiveness in the root or the shoot of dark-grown Arabidopsis thaliana 5 day old seedlings in the aba2-3 or wild-type (Col-O) background

city: Saint Louis

first: Ryan

middle: Joseph

last: Emenecker

state: MO

address: 660 S Euclid Ave

department: Biochemistry and Molecular Biophysics

institute: Washington University School of Medicine

summary: We report differences in the transcriptional responses of the root and the shoot to either auxin or ABA in comparison to mock treatment in dark-grown Arabidopsis thaliana seedlings. By examining the auxin responsiveness in the shoot or the root of a dark-growh ABA biosynthesis mutant, we found that auxin relies on intact ABA biosynthesis in order to regulate aspects of transriptional output.

overall_design: All seedlings were first stratified for 2 days at 4 degress celsius and then grown under continious light for 24 hours to initiate germination, which was followed by 4 days in complete darkeness at 22 degrees celsius. At this point, the seedlings were treated with either 10uM IAA, 10uM ABA, or equivalent ethanol for mock for 2 hours using a green safe light for seedling transfer. After 2 hours the seedlings were bisected at the root shoot junction and immediately frozen in liquid nitrogen, which was followed by RNA isolation. In total 10 different genotype/treatment/tissue combinations analyzed and each combination had 3 replicates bringing the total number of samples to 30. The mock treatments of either Col-O or aba2-3 were the controls used.

first: Irene

last: Yuan

first: Lucia

last: Strader