title: Comparison of human skin- and nerve-derived Schwann cells reveals many similarities and subtle genomic and functional differences

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

institute: University of Calgary

summary: Skin is an easily accessible tissue and a rich source of Schwann cells (SCs). Toward potential clinical application of autologous SC therapies, we aim to improve the reliability and specificity of our protocol to obtain SCs from small skin samples. As well, to explore potential functional distinctions between skin-derived SCs (Sk-SCs) and nerve-derived SCs (N-SCs), we used single-cell RNA-sequencing and a series of in vitro and in vivo assays. Our results showed that Sk-SCs expressed typical SC markers. Single-cell sequencing of Sk- and N-SCs revealed an overwhelming overlap in gene expression with the exception of HLA genes which were preferentially up-regulated in Sk-SCs. In vitro, both cell types exhibited similar levels of proliferation, migration, uptake of myelin debris and readily associated with neurites when co-cultured with human iPSC-induced motor neurons. Both exhibited ensheathment of multiple neurites and early phase of myelination, especially in N-SCs. Interestingly, dorsal root ganglion (DRG) neurite outgrowth assay showed substantially more complexed neurite outgrowth in DRGs exposed to Sk-SC conditioned media compared to those from N-SCs. Multiplex ELISA array revealed shared growth factor profiles, but Sk-SCs expressed a higher level of VEGF. Transplantation of Sk- and N-SCs into injured peripheral nerve in nude rats and NOD-SCID mice showed close association of both SCs to regenerating axons. Myelination of rodent axons was observed infrequently by N-SCs, but absent in Sk-SC xenografts. Overall, our results showed that Sk-SCs share near-identical properties to N-SCs but with subtle differences that could potentially enhance their therapeutic utility.

overall_design: Human skin and nerve samples were dissected and minced to liberate single cells. Schwann cells were selected by immunopanning based on p75 expression. Schwann cells enriched for p75 were subsequently expanded in vitro for 1 month. All Schwann cell cultures were fed every fourth day and treated identically. Human skin-derived fibroblasts were selected by immnopanning based on Thy-1 expression. Fibroblast cultures were fed every fourth day. Approximately 10,000 single cells from each culture were loaded onto the micro-fluidic platform for barcoding. All samples were processed according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry as per the manufacturer’s protocol. In brief, cultured Schwann cells and fibroblasts were partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. D11 primers, D12 and C12  primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using DTape station 1000. Sequencing was performed first using Illumina MiSeq SR50 to approximate the number of recovered cells in each sample. We recovered 7123 skin-derived Schwann cells , 7137 nerve-derived Schwann cells and 9585 skin-derived fibroblasts. Based on this, we determined lane distributions for sequencing using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of ~40,000 reads/cell.

first: Tak-Ho

last: Chu

first: Kabita

last: Baral

first: Elodie

last: Labit

first: Nicole

last: Rosin

first: Sarthak

last: Sinha

first: Daniel

last: Umansky

first: Saud

last: Alzahrani

first: Derrick

last: Rancourt

first: Rajiv

last: Midha


title: RNA-seq of HEK293-TRDMT1-KD and HEK293 control

status: Public on Jul 07 2022

city: Yanghzou

first: Songlei

last: Xue

state: Jiangsu

address: Wenhui Road 48#

country: China

institute: Yangzhou University

type: Expression profiling by high throughput sequencing

summary: RNA-seq of 6 samples, 3 of them are TRDMT1 knockdown in HEK293 cells named HEK293-TRDMT1-KD and 3 of them are HEK293 control.

overall_design: Examination 2 conditions, each with 3 replicates and the function of  TRDMT1 in HEK293 cells.

first: Hengmi

last: Cui

first: Sonlei


title: Distinct transcriptional programs of ascitic and solid cancer cells induce a different response to chemotherapy in high-grade serous ovarian cancer

status: Public on Jul 06 2022

city: Zwijnaarde

first: Jordy

last: De Coninck

address: Technologiepark 71

department: Department of Biomedical Molecular Biology

country: Belgium

institute: University Gent

summary: High-grade serous ovarian cancer (HGSOC) is responsible for the largest number of ovarian cancer deaths. The frequent therapy-resistant relapses necessitate a better understanding of mechanisms driving therapy-resistance. Therefore, we mapped more than hundred thousand cells of HGSOC patients in different phases of the disease, using single-cell RNA sequencing. Within patients, we compared chemonaive with chemotreated samples. As such, we were able to create a single cell atlas  of different HGSOCs lesions  and their treatment.

overall_design: We sampled the ovarian tumor, ascites and different metastases for three patients in both chemonaive and chemotreated status.

first: Nele

last: Loret

first: Niels

last: Vandamme

first: Joachim

last: Taminau

first: Kato

last: Declercq

first: Gillian

last: Blancke

first: Sven

last: Jonckheere

first: Steven

last: Goossens

first: Kelly

last: Lemeire

first: Sofie

last: De Prijck

first: Kevin

last: Verstaen

first: Ruth

last: Seurinck

first: Jo

last: Van Dorpe

last: Weyers

first: Hannelore

last: Denys

first: Koen

last: Van de Vijver

first: Bart

middle: N

last: Lambrecht

first: Philippe

last: Tummers

first: Yvan

last: Saeys

first: Geert

last: Berx


title: Effects of methamphetamine on gene expression in Jurkat, NK-92, THP-1 cells

city: Kunming

first: Deshenyue

last: Kong

address: 1168 West Chunrong Road

institute: Kunming Medical University

summary: To investigate the effects of methamphetamine on immune cells, we established three methamphetamine abuse immune cell models. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different immune cell models.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for immune cells and their methamphetamine-treated (250 μM, 24 h) derivatives.

first: Junhong

last: Mao

first: Hong

last: Li

first: Jianyu

last: Wang

first: Yuyang

first: Xiaocong

last: Wu

first: Guofen

last: Re

first: Huayou

last: Luo

first: Yiqun

last: Kuang

first: Kunhua


title: Single-cell RNA-seq analysis of a soft-tissue sarcoma model reveals the critical role of tumor expressed MIF in shaping macrophage heterogeneity. [CITE-Seq]

city: Houston

first: Jlenia

last: Guarnerio

state: TX

address: 6767 Bertner Ave

department: Genetics

country: USA

institute: MD Anderson Cancer Center

summary: The standard of care is unsuccessful to treat recurrent and aggressive soft-tissue sarcomas. Interventions aimed at targeting components of the tumor microenvironment have shown promise for many solid tumors, yet have been only marginally tested for sarcoma, partly because knowledge of the sarcoma microenvironment composition is limited. We employed single-cell RNA-sequencing to characterize the immune composition of an undifferentiated pleiomorphic sarcoma mouse model, showing that macrophages in the sarcoma mass exhibit distinct activation states. Sarcoma cells used the pleiotropic cytokine Macrophage Migration Inhibitory Factor (MIF) to interact with macrophages expressing the CD74 receptor to switch macrophages’ activation state and pro-tumorigenic potential. Blocking the expression of MIF in sarcoma cells favored the accumulation of macrophages with inflammatory and antigen-presenting profiles, hence reducing tumor growth. These data may pave the way for testing new therapies aimed at re-shaping the sarcoma microenvironment, in combination with the standard of care.

overall_design: We performed scRNA sequencing to profile the major cell types present in the microenvironment of a murine sarcoma model, with or without the silencing of tumor-expressed MIF. To see how tumor Mif expression affected the composition of the immune microenvironment, p53-/- Ccne1+ mouse sarcoma cells were first transduced with Cas9 and either a control sgRNA (sgCTR), or a guide targeting Mif (sgMif). The MIF-KO and MIF-WT sarcoma cells were transplanted subcutaneously on polyurethane scaffolds into recipient mice, and allowed to grow until reaching ~1cm3 in size. The tumors were extracted, digested to single-cell suspensions, and partially enriched for CD45+ immune cells. The samples were hashtagged using sequenceable oligonucleotides in order to later identify cells as coming from either MIF-KO tumors or MIF-WT tumors, pooled together, and captured on the 10X Genomics Chromium platform for single-cell 3’ RNA sequencing, using two reactions to target ~20,000 cells total.

first: Emily

middle: Y

last: Ko


title: Melanoma Brain Metastasis Atlas [TCR-Seq]

city: New York

first: Jana

last: Biermann

state: New York

address: 622 W168th Street

institute: Columbia University

summary: We performed matched TCR-seq and single-cell RNA-sequencing of 5 treatment-naïve melanoma brain metastases (MBM) from 5 individual patients.

overall_design:
Single-cell/nuclei RNA sequencing of 145,555 cells from 22 treatment-naïve melanoma brain metastses (MBM) and 10 treatment-naïve peripheral (extracranial) metastases (ECM) with additional TCR-seq in 5 scRNA-seq samples.
>>>Submitter states: Due to patient privacy concerns the raw data will be submitted to dbGAP.<<<

first: Benjamin

last: Izar

first: Johannes

middle: C

last: Melms


title: Functional definition of thyroid hormone response elements based on a synthetic Starr-seq screen

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

country: France

institute: ENSL

summary:
We performed an original protocol called synthetic STARR-seq (PMID: 30427832) in which a library of putative response elements are tested for their capacity to bind thyroid hormone (T3) nuclear receptors and convey T3 transactivation
More than 10 000 putative T3 response elements (T3RE) were cloned in the hSTARR-seq-ORI vector with a minimal promoter, in the 3' end of the transcribed sequence.  These are variant of the consensus T3RE (5'NGGTCANNNNRGGNNA3')
Therefore the most active T3RE are over-represented in the RNA of cells transfected with the plasmid library and treated with T3.

overall_design:
After transfection of  the  STARR-seq plasmid library (600 g or 1200 ng, +/-T3) RNA was extracted, and the 3'end of the transcript containing T3RE was amplified by RT-PCR. Deep sequencing was used to address the influence  of T3 treatment on the representation of individual T3RE.
Counts table can be used to compair the frequency of a given T3RE is the input library, transfected cells without T3, and transfected cells with T3.

first: Romain

last: Guyot


title: Bulk RNAseq analysis of hypertrophic cardiomyopathy (HCM) hiPSC-derived cardiomyocytes (hiPSC-CMs) and the isogenic control

city: Minneapolis

first: Brenda

last: Ogle

state: MN

address: 7-130 Hasselmo Hall 312 Church St. SE

department: Biomedical Engineering

institute: University of Minnesota

summary: To investigate HCM mutation-associated molecular details at the early stage of disease development, we performed bulk RNA-seq analysis at Day 15 of differentiation using RNA isolated from the isogenic control and mutant hiPSC-CMs. We performed pair-end sequencing with >30 million reads per sample with clean read counts of more than 96% for each sample.

overall_design: mRNA profiles of Day15 MYH7 R723C with MYH6 R725C mutant hiPSC-CMs and isogenic control

middle: M

first: Jeanne

last: Hsieh

first: Bhairab

last: Singh


title: Melanoma Brain Metastasis Atlas [patient_cell_lines_RNA-seq]

summary: Bulk RNA-seq on 24 patient-derived cell lines corresponding to 4 melanoma brain metastases (MBM) and 4 peripheral/extracranial melanoma metastses (ECM).

overall_design:
We performed bulk RNA-seq on 24 patient-derived cell lines (in triplicates) corresponding to 4 melanoma brain metastases (MBM) and 4 peripheral/extracranial melanoma metastses (ECM).
>>>Submitter states: Due to patient privacy concerns the raw data will be submitted to dbGAP.<<<


title: Melanoma Brain Metastasis Atlas [patient_cell_lines_ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Bulk ATAC-seq on 24 patient-derived cell lines corresponding to 4 melanoma brain metastases (MBM) and 4 peripheral/extracranial melanoma metastses (ECM).

overall_design:
We performed bulk ATAC-seq on 24 patient-derived cell lines (in triplicates) corresponding to 4 melanoma brain metastases (MBM) and 4 peripheral/extracranial melanoma metastses (ECM).
Due to patient privacy concerns the raw data will be submitted to dbGAP.


title: Novel players in renal fibrosis uncovered by gene expression analyses of TGF-β1 treated renal tubular epithelial cells and diseased kidneys

city: Chicago

first: Vidhi

last: Dalal

state: Illinois

address: 225 East Chicago Ave, Box 37

institute: Lurie Children's Hospital

summary:
Tubular epithelial cells (TECs) play a major role in potentiating renal fibrosis. While TGF-β1 is a key inducer of the pro-fibrotic phenotype in TECs, inhibition of TGF-β1 also blocks its protective effects, making this an unsuccessful strategy for treating renal fibrosis. Molecules induced by TGF-β1 to regulate TEC phenotype would serve as more specific and effective targets.
To uncover such molecules, we performed high throughput analyses on TGF-β1 treated renal tubular epithelial cells (HKC). RNA sequencing identified 3565 genes and proteomics identified 74 proteins differentially regulated by TGF-β1 in HKC. We then selected 47 genes that were most upregulated in our in vitro datasets and that do not have well-characterized roles in renal fibrosis based on our review of the literature.
We searched 8 publicly available datasets containing transcriptomic data from diseased human kidneys for gene expression patterns of the selected genes and found that MARCKS and DOCK2 were amongst the most consistently upregulated in the human datasets.
In HKC, MARCKS knockdown decreased TGF-β1 mediated upregulation of pro-fibrotic markers, while DOCK2 knockdown had the opposite effect. Our data suggests novel roles for these proteins in renal TECs as potential promoters the pro-fibrotic phenotype.

overall_design: Gene expression analysis of RNA sequencing data from HKC treated with vehicle vs. TGF-β1.

first: Pan

last: Liu

first: Jing

last: Jin

first: Katia

last: Scheri

first: Tomoko

last: Hayashida


title: p53-dependent mitochondrial compensation in heart failure with preserved ejection fraction

city: Shanghai

first: Xiaonan

last: Chen

state: Shanghai

address: 639 Zhizaoju Road

department: Department of Cardiology

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary:
BACKGROUND: Heart failure with preserved ejection fraction (HFpEF) accounts for 50% of heart failure patients. Clinically, HFpEF prevalence show age and gender biases. Although the majority of HFpEF patients are elderly, there is an emergence of young HFpEF patients. A better understanding of the underlying pathogenic mechanism is urgently needed. Here, we aimed to determine the role of aging in the pathogenesis of HFpEF.
METHODS AND RESULTS: HFpEF dietary regimen (HFD + L-NAME) was used to induce HFpEF in wildtype and telomerase RNA knockout mice (mTRG2 and mTRG3), an aging murine model. First, both male and female animals develop HFpEF equally. Second, cardiac wall thickening preceded diastolic dysfunction in all HFpEF animals. Third, accelerated HFpEF onset was observed in mTRG2 (at 6-weeks) and mTRG3 (at 4-weeks) compared to wildtype (8-weeks). Fourth, we demonstrate that mitochondrial respiration transitioned from compensatory state (normal basal yet loss of maximal respiratory capacity) to dysfunction (loss of both basal and maximal respiratory capacity) in a p53 dosage dependent manner. Last, using myocardial-specific p53 knockout animals, we demonstrate that p53 is necessary for the development of HFpEF.
CONCLUSIONS: Here we demonstrate that p53 activation is critical for the pathogenesis of HFpEF. We show that short telomere animals exhibit a basal level of p53 activation, mitochondria upregulate mtDNA encoded genes as a mean to compensate for blocked mitochondrial biogenesis, and loss of myocardial p53 prevents HFpEF upon HFD + L-NAME challenge.

overall_design: Cardiomyocyte mRNA profiles of 16weeks old wild type (WT) and second generation TERC-/- (mTRG2) mice,which had fed 8 weeks L-NAME and high fat diet.

first: Hao

last: Lin

first: Alex

last: Chang

first: Huili

last: Zhang


title: Transcriptomic analysis reveals genes releated to pistil abortion in Prunus sibirica

city: Shenyang

first: Jianhua

state: Liaoning

address: No.120 Dongling Road, Shenhe District

institute: Shenyang Agricultural University

summary: Pistil development is an important developmental process that directly affects the yield of Prunus sibirica. Through transcriptome sequencing analysis of clones with abortive pistil (No. 595) and normal pistil (No. 28) of Prunus sibirica, a total of 1950 significantly differentially expressed genes were obtained, among which 1000 genes were up-regulated and 950 genes were down-regulated. The results provide a theoretical basis for further investigation of the formation mechanism of pistil abortion.

overall_design: Transcriptome sequencing was performed on two Prunus sibirica clones No. 595 (treatment group, with abortive pistil) and No. 28 (control group, with normal pistil).There were 3 biological replicates in each clone. Transcriptome sequencing was completed by Biomarker Technologies Co，LTD.

first: Sheng

middle: J

last: Dong

first: Jian

middle: H

first: Quan

middle: G


title: High-throughput muscle fiber typing from RNA sequencing data

city: Lund

first: Nikolay

last: Oskolkov

address: Sölvegatan 35

country: Sweden

institute: Lund University

summary: Skeletal muscle fiber type distribution has implications for human health, muscle function and performance. This knowledge has been gathered using labor intensive and costly methodology that limited these studies. Here we present a method based on muscle tissue RNA sequencing data (totRNAseq) to estimate the distribution of skeletal muscle fiber types from frozen human samples, allowing for larger number of individuals to be tested. By using single-nuclei snRNA sequencing (snRNAseq) data as a reference, cluster expression signatures were produced by averaging gene expression of cluster gene markers and then applying these to totRNAseq data and inferring muscle fiber nuclei type via linear matrix decomposition. This estimate was then compared with fiber type distribution measured by ATPas staining or myosin heavy chain protein isoform distribution of 62 muscle samples in two independent cohorts (n = 39 and 22). The correlation between the sequencing-based method and the other two were rATPas = 0.65 [0.46 – 0.84], [95% CI] and rmyosin = 0.80 [0.71 – 0.89], with p = 7.96 x 10-6 and 8.06 x 10-6 respectively. The deconvolution inference of fiber type composition was accurate even for very low totRNAseq sequencing depths, i.e., down to an average of ~5.000 paired end reads. This new method consequently allows for measurement of fiber type distribution of a larger number of samples using totRNAseq in a cost and labor efficient way. For the first time it is now feasible to study the association between fiber type distribution and health outcomes in large well-powered studies.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: snRNAseq data from 1 human and 1 chimpanzee skeletal muscle sample

first: Ola

last: Hansson

first: Svante

last: Pääbo

first: Gray

last: Camp

first: Kristoffer

last: Ström


title: Transcriptomic characteristics and impaired immune function of patients with sepsis

city: Hefei

first: Dongyao

last: Wang

state: Anhui

address: Department of Hematology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.

summary: Sepsis is a life-threatening condition caused by a dysregulated host response to infection.Although our understanding in the pathophysiological features of sepsis has increased  significantly during the past decades, there is still lack of mechanism of sepis.Neutrophils are important regulators against invading pathogens, and their role during  sepsis has been studied extensively. However, whether neutrophils could inhibit the immune response of CD8+T cells and the mechanism is unkown in sepsis.

overall_design: Here, 3 sepsis patients and 3 healthy controls were enrolled for analysis of the immunological characteristics of their neutrophils. We sought to comprehensively characterize the transcriptional changes in the two groups by transcriptome sequencing.

first: Xiaokang

last: Dai


title: PLK1 inhibition selectively induces apoptosis in ARID1A deficient cells through uncoupling of oxygen consumption from ATP production

city: Singapore

first: Anand

middle: D

last: Jeyasekharan

state: Outside US/Canada

address: 14 Medical Drive,  Centre for Translational Medicine, 13-02 Bench 13

country: Singapore

institute: Cancer Science Institute of Singapore

summary: We have identified a synthetically lethal relationship between the loss of chromatin modulator, ARID1A, and the inhibition of PLK1 kinase through a mechanism that involves mitochondrial dysfunction.  Using normal gastric epithelium cell line, GES1, we performed a comparative gene expression analysis comparing the various permutations of wild type (WT) and ARID1A knockout (KO) genotypes and untreated cells or those treated with PLK1 inhibitor,Volasertib. Consistent with ARID1A's role as a chromatin modulator, there was widespread gene expression modulation observed when comparing the WT cells with the ARID1A KO cells. In particular, we noted that oxidative phosphorylation and ROS pathway genes were enriched in ARID1A KO cells compared to wild type cells. Volasertib treatment appeared to exacerbate the effects on gene expression induced by ARID1A KO. We also investigated how ARID1A KO and Volasertib treatment specifically modulated the expression of mitochondrial encoded genes using a more recent human genome build, hg38 (as opposed to hg19), that enabled the correct alignment of these mitochondrial genes. For this analysis, in addition to GES1s, we used the ovarian cancer cell line, OVCAR3. To answer the question of which genes facilitate preferential cell killing of Volasertib-treated ARID1A KO cells, using normal breast epithelial cells, MCF10A, we performed a genome-wide CRISPR screen using the Brunello library.  We identified many genes whose knockout made ARID1A KO cells resistant to Volasertib, many of which were involved in mitochondrial process.

overall_design:
RNAseq: GES1s: WT, ARID1A KO, WT+Volasertib treatment, ARID1A KO+Volasertib treatment; 2 indpendent biological replicates each.
OVCAR3: WT, ARID1A KO; 2 indpendent biological replicates each.
CRISPR screen: MCF10A: WT, ARID1A KO, WT+Volasertib treatment, ARID1A KO+Volasertib treatment.

first: Upadhyayula

middle: S

last: Srinivas


title: The activation of protamine 1 using epigenome editing decreases the proliferation of tumorigenic cells

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Dr.

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: DNA methyltransferases (DNMT) and histone deacetylases (HDAC) inhibitors are used as cancer epigenome drugs. However, these epigenetic drugs lack targeting specificity and could risk inducing genome instability and the expression of oncogenes. Therefore, there is a need to develop new therapeutic strategies where specific cancer genes can be targeted for silencing or activation. The CRISPR-dCas9 system represents a promising powerful therapeutic tool because of its simplicity and specificity. Protamine 1  (PRM1) is exclusively expressed in sperm and has a vital role in the tight packaging of DNA, thus inducing transcriptional silencing in sperm cells. We hypothesized that the activation of the PRM1 gene in tumorigenic cells would lead to DNA condensation and reduce the proliferation of these cells. We transfected human embryonic kidney cells 293T with a dCas9-P300 plasmid that adds acetyl groups to the promoter region of PRM1. RNA-Seq analysis of transfected cells revealed high specificity of targeted gene activation. PRM1 expression resulted in a significant decrease in cell proliferation as measured by the BrdU ELISA assay.  To confirm that the activation of PRM1 was due to acetyl groups deposited to H3K27,  a ChIP-qPCR was performed. The acetylation of the PRM1 promoter region targetted by dCa9-p300 in transfected cells was higher than that of the control cells. Interestingly,  the targeted promoter region for acetylation showed reduced DNA methylation.  These findings demonstrate the efficacy of epigenome editing in activating PRM1 in non-expressing tumorigenic cells, which can be used as a promising therapeutic strategy in cancer treatment.

overall_design: HEK293T cells were transfected with dCas9-p300 and two PRM1 gRNAs targeting the promoter region. Non-transfected cells were assigned as control group. RNA-Seq was carried out for both groups

first: Hadjer

last: Namous

first: Camila

last: Urbano Braz

first: Yiding


title: SPATULA and ALCATRAZ confer fruit cavity and female sterility via mediating transmitting tract development in cucumber

city: Beijing

first: zhongyi

last: wang

state: Beijing

address: No.2 Yuanmingyuan Xi Lu

institute: CAU(China Agricultural University)

summary: The successful fusion of sperms and eggs need firstly the reception of pollens by stigmatic papillae, and then the unobstructed transmitting tract (TT) providing an extension channel for pollen tubes carrying with sperm cells.  However, the genes involved in transmitting tract specification and cavity formation in cucumber remained largely unknown. Here, we characterized the bHLH gene, Cucumis sativus SPATULA (CsSPT) and its redundant function with Cucumis sativus ALCATRAZ (CsALC) in TT development and stigma convergence in cucumber.

overall_design: Stigmas of wild type and Csspt, Csalc, Csspt Csalc mutants at athesis were collected for RNA-seq analysis. Three biological replicates were performed.

first: Zhihua

last: Cheng

first: Xiaofeng

last: Liu

first: Shuangshuang

last: Yan

first: Zhongyi

first: Weiyuan

last: Song

first: Lijie

last: Han

first: Jianyu

last: Zhao

first: Zhaoyang

last: Zhou

first: Xiaolan


title: Systematic variation of RhoA activity reveals an inhibitory impact of active RhoA on the homeostasis and angiogenic capacity of human endothelial cells

city: Halle

first: Robert

last: Eckenstaler

address: Kurt-Mothes-Str. 3

department: Institute of Pharmazie

country: Germany

institute: Martin-Luther-University

summary: The small GTPase RhoA regulates a variety of cellular processes, including cell motility, proliferation, survival and permeability. In addition, there are reports suggesting that the RhoA-ROCK axis plays a role in VEGF-mediated angiogenesis, whereas other work has shown opposite effects. To elucidate this conflicting data, we examined HUVEC and HCAEC after stable overexpression (lentiviral transduction) of constitutively active (G14V/Q63L), dominant-negative (T19N), or wild-type RhoA using a variety of in vitro angiogenesis assays (proliferation, migration, tube formation, angiogenic sprouting, endothelial cell viability) and a HUVEC xenograft assay in immune incompetent NSGTM mice in vivo. We observed that expression of active as well as wild-type RhoA but not expression of dominant-negative RhoA significantly increased endothelial cell death as well as inhibited endothelial cell proliferation, migration, tube formation and angiogenic sprouting of endothelial cells in vitro and reduced HUVEC-related angiogenesis in vivo. Inhibition of RhoA by C3 transferase antagonized inhibitory RhoA effects and strongly enhanced VEGF-induced angiogenic sprouting in control-treated cells. In contrast, inhibition of RhoA effectors ROCK1/2 and LIMK1/2 had no significant effect  on RhoA-related effects, but again increased angiogenic sprouting and migration of control-treated cells. In line with these data, VEGF did not activate RhoA in HUVEC as measured by a FRET-based biosensor. Furthermore, global transcriptome and subsequent bioinformatic gene ontology (GO) enrichment analyses revealed that constitutively active RhoA induces a differentially expressed gene pattern that is enriched for GO biological process terms such as mitotic nuclear division, cell proliferation, cell motility and cell adhesion and includes a significant decrease in VEGFR-2 and NOS3 expression. Thus, our data demonstrate that increased RhoA activity has the potential to trigger endothelial dysfunction and anti-angiogenic effects independently of its well-characterized downstream effectors ROCK and LIMK.

overall_design: Three biological replicates were analyzed for each of three different conditions (overexpression of constitutively active RhoA (Q63L) and dominant negative RhoA (T19N) compared to control without overexpression of RhoA).

first: Michael

last: Hauke

first: Anne

last: Ripperger

first: Heike

last: Braun

first: Ralf

middle: A

last: Benndorf


title: Circulating miRNA associated with hepatocellular carcinoma in mice

city: Dallas

first: Lianghao

last: Ding

address: 2201 Inwood Rd

department: Radiation Oncology

institute: University of Texas Southwestern Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Biomarker studies for early stage or preclinical hepatocellular carcinomas (HCC) are hindered by the difficulties of obtaining samples from asymptomatic individuals. We established animal models using irradiated mice to investigate circulating miRNA as non-invasive markers for detection of early stage HCC. We hypothesized that certain miRNAs that play pivotal roles in molecular pathways are conserved across species and identification of these miRNAs will facilitate studying human markers in mice. To test the hypothesis, we performed weighted gene co-expression analysis by integrating circulating miRNA and tumor gene expression profiles from individual mice and discovered hub miRNAs in highly correlated expression modules. We validated the hub miRNAs using F2 hybrid mice derived from radiogenic HCC susceptible and resistant founders and identified 38 circulating miRNA markers associated with radiation-induced HCC.  Through literacy search, we selected 10 human HCC-associated circulating miRNAs that had been validated in multiple independent patient cohorts. Nine of the 10 human markers overlapped with the mouse hub miRNAs, indicating the feasibility of using mouse model to study human circulating HCC markers. Using serially collected plasma samples from irradiated mice, we studied the kinetics of circulating miRNAs. We found that the mouse plasma levels of 4 human circulating markers, miR-122-5p, miR-100-5p, miR-34a-5p and miR-365-3p increased linearly as the time approaching towards HCC detection, indicating the correlations of the 4 miRNAs with oncogenic progression. Estimation of change points in the kinetics of the 4 circulating miRNAs suggested the changes started months before HCC detection, ranging from 17.5 to 6.8 months. Our data demonstrated that the 4 circulating miRNAs were sensitive biomarkers potentially valuable for the screening of early stage HCC.

overall_design: In the study presented here, C3H mice and the second generation progeny of C3HxBalb/c hybid (F2) were used as discovery cohort and validation cohort respectively. In total 13 male C3H, 53 time-series samples from F2 mice, including 7 females and 8 males were inculded in the study.

first: Liang-Hao


title: Stress Keratin 17 mediates immune evasion in head and neck cancer [scRNA-seq]

first: Huy

last: Dinh

state: WI

address: 1111 Highland Avenue

summary: We previously identified stress keratin 17 (K17) as a host factor that contributes to immune evasion in the context of mouse papillomavirus-induced disease. Analyses of head and neck squamous cell carcinoma (HNSCC) patient TCGA and tissue microarray data revealed that K17 can be overexpressed in both HPV+ and HPV- human cancer samples, with a more profound upregulation in HPV- HNSCC samples. In this report, we investigated the role of K17 in regulating immune response in HPV- head and neck cancer. To test whether K17 mediates immune evasion and resistance to immune checkpoint blockade (ICB) therapy in HPV- HNC, we used MOC2, a K17-expressing murine HNC cell line, and knocked out the K17 gene from it using CRISPR/Cas9 (K17KO MOC2 cells). Then we injected K17KO MOC2 cells or parental MOC2 cells into NSG and C57BL/6 mice and monitored tumor growth, immune cell infiltration, and response to ICB treatment in vivo. In NSG mice, the K17KO MOC2 cell lines grew as fast as parental MOC2 tumors. In C57BL/6 mice, K17KO MOC2 tumors grew significantly slower than parental MOC2 tumors, with 50% tumor rejection rate, in a T-cell dependent manner. Flow cytometry of tumor infiltrating T cells and bulk tumor RNA seq analyses show an active anti-tumor microenvironment in the K17KO MOC2 tumors, compared to parental MOC2 tumors. In addition, we observed that 5 out of 5 anti-PD1 + anti-CTLA4 treated K17KO MOC2 tumors completely regressed, while only 1 out of 5 parental MOC2 tumors similarly treated at the same size completely regressed (p<0.05). In exploring the role of chemokine CXCL9 in increased T cell infiltration, we blocked the receptor CXCR3, a receptor often upregulated on activated T cells, and saw a delay in the immune-mediated rejection K17KO MOC2 tumors. Single cell RNA seq analyses revealed a completely different immune landscape including both lymphoid and myeloid populations in K17KO MOC2 tumors. Overall, we demonstrated that K17 expression in HNSCC contributes to immune evasion and resistance to immune checkpoint blockade treatment through modulating the immune landscape in the tumor microenvironment.

overall_design: Expression profiling by high throughput sequencing for head and neck cancer mouse models

first: Wei

last: Wang

middle: Q

first: Paul

middle: F

last: Lambert


title: Stress Keratin 17 mediates immune evasion in head and neck cancer

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

overall_design: Refer to individual Series


title: Pathways and patient-specific gene targets associated with anti-tumor activity of HSP90 inhibitor, SNX2112 in papillary renal cancer

city: BETHESDA

first: Ramaprasad

last: Srinivasan

state: MD

address: 1-W-5888, 10 center drive

department: Urologic Oncology Branch

institute: National Cancer Institute – NIH

summary: We aimed to use next-generation sequencing that may provide intriguing insights into the molecular pathways mediating anti-tumor activity for HSP90 inhibitor, SNX2112 in papillary renal cancer. Our findings uncovered unique set of target genes and pathways of significance in papillary renal cancer that have potential to be translated into clinically effective therapeutic strategies for patients.

overall_design: Examination of treatment of drug SNX2112 in Papillary renal cell cancer (PRCC).

first: Roma

last: Pahwa

first: Alexei

last: Lobanov


title: Stress Keratin 17 mediates immune evasion in head and neck cancer [RNA-seq]


title: Mismatch repair protein coordinate with SETD2 to activate DNA oxidative damage response and repair in human cells

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

summary: There is mounting evidence that mismatch repair (MMR) proteins are involved in oxidative DNA damage response. SETD2, the histone H3K36 tri-methyltransferase, is a newly found factor participate in MMR pathway in human cells. In this study, we show that SETD2 can directly interact with MMR protein MutSα, and they are enriched and colocalized in chromatin in response to oxidative damage, which maybe the reason for the amplification of H3K36me3. Moreover, MutSα and SETD2 are essential for ATM and CHK2 activation upon H2O2 treatment, loss of SETD2 and MutSα will display impaired DNA damage response and oxidative DNA repair, which will accumulate oxidative damage and lead to more cell apoptosis and cell death. Our finding provided a novel SETD2 dependent mechanism for the oxidative DNA damage response together with MMR protein.

overall_design: Examination of 2 proteins and 1 histone modification H3K36me3 in Hela cell line before and after H2O2 treatment.

first: Jun

last: Fang

first: Sida

last: Guo


title: Dihydroorotate dehydrogenase inhibition reveals metabolic vulnerability in chronic myeloid leukemia

city: Torino

first: Ivan

last: Molineris

state: TO

address: Via Nizza 52

department: Life Science and System Biology

country: Italy

institute: University of Turin

summary: The development of different generations of BCR-ABL1 tyrosine kinases inhibitors (TKIs) has led the overall survival (OS) of the chronic myeloid leukemia (CML) patients to become almost similar to that of a control population without leukemia, but the TKI therapy can be successfully discontinued only in half of those who are achieving a deep molecular response, that  eans in approximately 15-20% of the entire population. In addition, although few, there are CML patients who show resistance to TKI therapy, are prone to progress to more advanced phases of the disease and die of CML related causes. Therefore, implementing an alternative approach for targeting TKI resistant leukemic cells would be of the essence in trying to solve these problems. Dihydroorotate dehydrogenase (DHODH) is a druggable enzyme in the de novo pyrimidine biosynthesis pathway that is located in the inner membrane of mitochondria. Here, we found that CML CD34+ cells and CML cell lines are vulnerable to DHODH inhibition mediated by Meds433, a new and potent DHODH inhibitor recently developed by our group. Meds433 significantly activated the apoptotic pathway and suppressed cell growth of CML cells in vitro and in vivo in a xenograft mice model. Moreover, inhibition of DHODH led to the reduction of amino acids and induction of huge metabolic stress in CML CD34+. Altogether, our study shows that targeting pyrimidine synthesis is a promising approach for targeting CML stem/progenitor cells, helping more patients to achieve good molecular response and possibly successful treatment discontinuation.

overall_design: Gene expression profiling was performed on CD34+ cells from five CML patients, untreated, and after three days of treatment with Meds433 100nM, for a total of 10 matched samples.

first: Mohammad

last: Houshmand

first: Nicoletta

last: Vitale

first: Francesca

last: Orso

first: Alessandro

last: Cignetti

first: Valentina

last: Gaidano

first: Stefano

last: Sainas

first: Marta

last: Giorgis

first: Donatella

last: Boschi

first: Carmen

last: Fava

last: Gai

first: Massimo

last: Geuna

first: Federica

last: Sora

first: Alessandra

last: Iuro

first: Elisabetta

last: Abruzzese

last: Breccia

first: Giovanni

last: Caocci

first: Fausto

last: Castagnetti

first: Daniela

last: Taverna

first: Salvatore

last: Oliviero

first: Fabrizio

last: Pane

first: Marco

middle: L

last: Lolli

first: Paola

last: Circosta

first: Giuseppe

last: Saglio


title: FXR protects cisplatin-induced AKI via transcriptional regulation of ferroptosis.

city: Hwasun-gun, Jeollanam-do

first: Dong-Hyun

last: Kim

state: Not Applicable

address: 264, Seoyang-ro, Hwasun-eup,

country: South Korea

institute: Medispan

summary: Farnesoid X receptor (FXR, also known as NR1H4) is crucial to nephroprotective in several kinds of kidney diseases, including obesity, diabetes, aging, acute kidney injury and chronic kidney disease. FXR plays a key role in maintaining cholesterol and bile acid levels and is highly expressed in the liver, intestine and kidneys. In kidney diseases, it is reported that FXR has anti-lipogenic, anti‐inflammatory, antifibrotic, and antioxidant functions. Here, using genomics analysis, we investigated whether FXR attenuates cisplatin-induced AKI through the regulation of ferroptosis. The increased blood urea nitrogen, serum creatinine and ferroptotic responses in cisplatin-induced AKI mice were attenuated by treatment with FXR agonist, GW4064, while those were exacerbated in FXR knockout mice. Using RNA-sequencing analysis, we found novel target genes for FXR associated with ferroptosis. FXR agonist treatment increases lipid and glutathione metabolic gene expression and decreases cell death genes expression. This study identifies transcriptional regulation of ferroptosis by FXR as a potential therapeutic target for cisplatin-induced AKI.

overall_design: Kidney mRNA profiles were generated by deep sequencing, were profiled in the kidney of wild-type (WT) and FXR knockout (FXR KO) mice treatment with GW4064 for 6h after fasting overnight.

first: Soo

middle: W


title: Expression analysis using microarray of overexpression and mutant lines of ERF60 plants as compared to Wt-Col plants

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Microarray analysis to study the expression of up and down regulated genes in the ERF60-OX and mutant Arabidopsis plants.

overall_design: Agilent Arabidopsis thaliana 8x60k Microarray Gene Expression: AMADID: 32721

first: Rakesh

middle: K

last: Shukla

first: Ujjal

last: Phukan

first: Gajendra

last: Jeena


title: SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells

city: Illkirch CEDEX

first: Veronique

last: Fischer

address: 1 Rue Laurent Fries

institute: IGBMC

summary: To analyse the genome-wide impact of inactivation of the Supt3h subunit of the SAGA complex on RNA polymerase II (Pol II) transcription in human U2OS cells and mouse embryonic stem cells (mESCs), we analysed newly synthesized RNA using 4sU-labelling in mutant and wildtype conditions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Newly synthesized RNA from wildtype (WT) and mutant conditions of human U2OS cells and mESCs. mESCs were cultured in FCS+2i conditions. Samples were sequenced in two independent sequencing projects and RNA from two independent clones per cell line were sequenced.

first: Vincent

last: Hisler

first: Elisabeth

last: Scheer

last: Lata

first: Bastian

last: Morlet

first: Damien

last: Plassard

first: Dominique

last: Helmlinger

first: Didier

last: Devys

first: László

last: Tora

first: Stéphane

last: Vincent


title: Circular RNA expression analysis of orbital venous malformation [RNA-Seq]

first: Jie

last: Yu

address: No. 639, Zhizaoju road, Huangpu district

department: Department of Ophthalmology

institute: Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology

summary: This research aimed to investigate the aberrant expression of circRNA, messenger RNA, and microRNA in orbital venous malformation. A competitive endogenous RNA network was constructed to elucidate their potential roles in orbital venous malformation.

overall_design: Investigation of mRNA expression profile in orbital venous malformation

first: P

last: Chai

first: R

last: Jia


title: Pseudomonas phaseolicola preferentially modulates genes encoding leucine rich repeat and malectin domains in the bean landrace G2333

city: Davis

first: Cristian

last: Jacob

state: CA

address: 3800 Solano Park CR., Apt. 4022

department: Plant Sciences

institute: University of California, Davis

summary: Common bean (Phaseolus vulgaris L.) is an important crop both as a source of protein and other nutrients for human nutrition and as a nitrogen fixer that benefits sustainable agriculture. This crop is affected by halo blight disease, caused by the bacterium Pseudomonas syringae pv. phaseolicola (Pph), which can lead to 45% yield losses. The resistance of common bean to Pph is conferred by six loci (Pse-1 to Pse-6) and minor-effect quantitative trait loci (QTLs); however, information is lacking on the molecular mechanisms implicated in this pathosystem. Here, we describe an in-depth RNA-sequencing analysis of the tolerant G2333 bean line in response to the Pph strain NPS3121. We identified 275 upregulated and 357 downregulated genes in common bean in response to Pph infection. These differentially expressed genes were mapped to all 11 chromosomes of P. vulgaris. The upregulated genes were primarily components of plant immune responses and negative regulation of photosynthesis, with enrichment for leucine-rich repeat (LRRs) and/or malectin-like carbohydrate-binding. Interestingly, LRRs and malectin genes mapped to same location as previously identified Pph resistance loci or QTLs. For instance, the major loci Pse-6/HB4.2 involved in broad-resistance to many Pph races, co-located with induced LRR-encoding genes on Pv04. These findings indicate a coordinated modulation of genes involved in pathogen perception and signal transduction. In addition, the results further support these LRR/malectin loci as resistance genes in response to halo blight. Thus, these genes are potential targets for future genetic manipulation, enabling the introduction of resistance to Pph into elite cultivars of common bean.

overall_design: Fully expanded primary leaves of the bean genotype G2333 were syringe-infiltrated with bacterial inoculum or water as a mock control. After inoculation, plants were grown under the same conditions as described below until the time of sampling. Leaflets from the same plant were collected at each time point, 6 and 12 hours post inoculation (hpi), flash frozen in liquid nitrogen, and stored at -80°C until processing. Leaves collected at 6 and 12 hpi were pooled for total RNA extraction, and RNA from two different plants were pooled for RNA sequencing. The experiment was repeated twice, resulting in four biological replicates.

first: Maeli

last: Melotto

first: Paula

middle: R

last: Oblessuc


title: RNA-seq analysis lncRNA and mRNA between crushed sciatic nerves and intact contralateral nerves

first: Haodong

last: Lin

address: Haining Road100, Shanghai, People’s Republic of China

department: Orthopedic Surgery

institute: Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200080, China

summary: To investigate the potential function of lncRNAs in Schwann cell (SCs) response to sciatic nerve damage and repair, we extracted the total RNA of crushed sciatic nerves and intact contralateral nerves for RNA-sequencing (RNA-seq). A total of 98 differentially expressed lncRNAs (including 46 up-regulated and 52 down-regulated lncRNAs) and 77 differentially expressed mRNAs (including 55 up-regulated and 22 down-regulated mRNAs) were identified between crushed sciatic nerves and normal control (log 2 FC > 1 and p < 0.001).

overall_design: Nerve lesions were produced on the right side and the intact contralateral nerve served as the uninjured control. At the appropriate time points, total RNA of crushed sciatic nerves and intact contralateral nerves were extracted. RNA-seq data from 3 biological replicates was collected.

first: Gang

last: Yin


title: Gene expression changes associated with knockdown of lncRNA PVT1 in ovarian cancer cell line SK-OV3

city: Birmingham

first: Ryan

last: Miller

state: AL

address: 1824 Sixth Ave S

department: Pathology

institute: UAB

summary: lncRNA PVT1 is an emerging lncRNA of significance in cancer due to alterations in both the RNA and genomic locus in multiple cancers and its established relationship to the oncogene MYC. Several recent studies have documented potential important roles for the lncRNA in ovarian cancer. Herein RNA sequencing was performed to determine the impact of PVT1 on global gene expression by performing RNA sequencing in SK-OV3 cells after silencing PVT1 (siPVT1) of cells grown upon transient knockdown of the lncRNA PVT1. SK-OV3 cells were cultured to 50% confluence in 6 well plates. Pooled siRNA’s to human PVT1 or non targeting control siRNA’s from Dharmacon were used to transfect SK-OV3 cells for 48 hrs in full serum media carefully maintaining cell confluence to not exceed approximately 80%. This was followed by RNA extraction and verification of knockdown using primers to PVT1 followed by sequencing. We find that 450 protein coding genes were differentially expressed between control (siControl) and siPVT1 cells with 50 additional found to be non-protein coding. The top 50 differentially expressed genes include 12 that were downregulated by siPVT1 and 32 that were upregulated. Several pathways associated with metabolic and stress processes, ribosome biogenesis and ncRNA processing were altered based on GO pathway analysis. Additional pathways included pathways associated with cell motility and differentiation.

overall_design:
mRNA sequencing of human ovarian cancer (SKOV3) cells, control and PVT1 knockdown with siRNA
Pooled siRNA’s to human PVT1 or scrambled control siRNA’s from Dharmacon were used to transfect SK-OV3 cells for 48 hrs followed by RNA extraction.

first: Mythreye

last: Karthikeyan

first: C

first: Abigail

last: Shelton

first: Zainab

last: Shonibare

first: Mehri

last: Monavarian


title: Circular RNA expression analysis of orbital venous malformation [miRNA-Seq]

city: Shanghai

overall_design: Investigation of miRNA expression profile in orbital venous malformation


title: Circular RNA expression analysis of orbital venous malformation


title: Effect of chemerin in primary human hepatocytes (PHH) and hepatic stellate cells (HSC)

city: Regensburg

first: Christa

last: Buechler

address: Franz Josef Strauss Allee 11

institute: University Hospital Regensburg

summary:
Effect of chemerin in these cells is hardly known.
Cells of three donors were used to identify genes regulated by the active chemerin isoform.

overall_design: Cultivation of cells with increasing doses of recombinant chemerin


title: miRNA in HUVEC culture supernatant

status: Public on Jul 05 2022

first: Donglinag

last: Zhang

address: Xinjiekou East Street No.31, Xicheng District, Beijing, China

institute: Beijing Jishuitan hospital

summary:
Human umbilical vein endothelial cells (HUVEC) were cultured in serum-free medium with 50 μmol/L ADMA (ADMA group) or without ADMA (NA group ).
Asymmetric dimethylarginine is a typical uremic toxin which used to induce HUVEC injury.

overall_design: ADMA treated HUVEC may release different miRNAs campared to normal control cells. The cells culture supernatant were collected and detected.

first: Dongliang


title: Distinct leukemogenic mechanism of acute promyelocytic leukemia based on genomic structure of PML-RARα fusion gene

city: Fukuoka City

first: Mariko

last: Minami

address: 3-1-1, Maidashi

department: Medicine and Biosystemic Science

country: Japan

institute: Kyushu University Graduate School of Medical Science

summary: Leukemic stem cells (LSCs) of acute myeloid leukemia (AML) are enriched in CD34+CD38- fraction, and self-renewing LSCs hierarchically organize and maintain the AML populations. In acute promyelocytic leukemia (APL), which is driven by PML-RARα fusion genes, the presence of LSCs has long been unidentified, due to the difficulty of efficient reconstitution of human APL in the immunodeficient mice. Here, we show that LSCs of short type isoform APL, subtype of APL defined by different breakpoint of PML gene, concentrate in CD34+CD38- fraction and express T cell immunoglobulin mucin-3 (TIM-3) as in other non-APL AML. Short type APL cells exhibited distinct gene expression signatures including LSCs-related genes from other types of APL. Moreover, CD34+CD38-TIM-3+ short type APL cells efficiently reconstituted huma APL in xenograft models with high penetration, whereas CD34- more differentiated APL cells did not. Furthermore, CD34+CD38-TIM-3+ short type APL cells also reconstituted leukemia in the serial transplantation. Thus, short type APL is showing hierarchically organized by self-renewing APL-LSCs same as in other types of AML. The identification of LSCs in a subset of APL and establishment of efficient patient derived xenograft model would contribute to further understanding of APL leukemogenesis and devising individual treatment for eradication of APL LSCs.

overall_design: To evaluate the characteristics of short and long type APL cells, we compared the gene expression pattern of FACS-purified CD33+ APL cells from each type of APL patients.

first: Yoshikane

last: Kikushige

first: Koichi

last: Akashi


title: Age-dependent impact of two exercise training regimens on genomic and metabolic remodeling in skeletal muscle and liver of male mice

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: How skeletal muscle adapts to different types of exercise intensity with age is not known. Adult and old C57BL/6 male mice were assigned to one of three groups: sedentary, daily high-intensity intermittent training (HIIT), or moderate intensity continuous training (MICT) for 4 weeks, compatible with the older group’s exercise capacity. Improvements in body composition, fasting blood glucose, and muscle strength were mostly observed in the MICT old group, while effects of HIIT training in adult and old animals was less clear. Skeletal muscle exhibited structural and functional adaptations to exercise training, as revealed by electron microscopy, OXPHOS assays, respirometry, and muscle protein biomarkers. Transcriptomics analysis of gastrocnemius muscle combined with liver and serum metabolomics unveiled an age-dependent metabolic remodeling in response to exercise training. These results support a tailored exercise prescription approach aimed at improving health and ameliorating age-associated loss of muscle strength and function in the elderly.

overall_design: A comparison of the adaptive responses of male C57BL/6J mice at either 5 months (adult group) or 24 months (old group), using age-matched sedentary controls (CON, N = 4) and two types of daily exercise training for 4 weeks to determine the benefits that high-intensity intermittent training (HIIT/AC, N = 4) and moderate-intensity continuous training (MICT/XR, N = 4) could provide to combat muscle loss.

first: Michel

last: Bernier

first: Ignacio

last: Navas-Enamorado

first: Mari

last: Gómez-Cabrera

first: Miguel

last: Calvo-Rubio

first: Jose

last: González-Reyes

first: Nathan

last: Price

first: Ana

middle: B

last: Cortés-Rodríguez

first: Juan

last: Rodríguez-Aguilera

first: Sandra

last: Rodríguez-López

first: Sarah

last: Mitchell

first: Kelsey

last: Murt

first: Krystle

last: Kalafut

first: Katrina

last: Williams

first: Christopher

last: Ward

first: Joseph

middle: P

last: Stains

first: Gloria

last: Brea-Calvo

last: Villalba

first: Sonia

last: Cortassa

last: Aon

first: Rafael

last: de Cabo


title: Neurodevelopmental ATM deficiency affects glutamatergic transmission through KCC2-KARs expression in the hippocampus but not in the cortex

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

summary: Interest in the function of ataxia-telangiectasia mutated protein (ATM) is extensively growing as evidenced by preclinical studies which continuously associate ATM loss with new intracellular pathways. To further investigate ATM involvement in neurotransmission, we initially exploited ATM+/- and ATM-/- mice. ATM defective animals display cognitive defects rescued by the delivery of the antidepressant Fluoxetine (Fluox). Prenatal Fluox increases levels of the chloride intruder NKCC1, previously described lowered in ATM defective mice. Surprisingly, this result occurs exclusively at hippocampal level suggesting an ATM context-specificity. Indeed, a deeper investigation of excitatory synapses revealed increased Gluk1 and Gluk5 subunit-containing kainate receptors (KARs) levels in the hippocampus, but not cortex, of ATM+/- and ATM-/- mice. The comparable composition between wt and ATM+/- post-synapses (TIF purification) suggests a presynaptic KARs localization and in vitro and in ex vivo electrophysiology that KARs are fully active. Since KAR subunits functionally interact with the chloride cotransporter KCC2, which is highly expressed in ATM deficient mice, we blocked KCC2 activity during the development of ATM+/- cultures and found reduced KARs levels. Conversely, the transient and acute blockade of ATM kinase activity achieved by KU55933 in adults does not move similar changes as indicated by a completely different panel of deregulated genes identified in RNA-seq investigation performed on hippocampi explanted from KU mice. Our data, indicating that such alterations are developmental regulated and linked to ATM kinase activity through the KCC2 regulation, add new findings useful for a deeper understanding of ATM function in central neurons. Importantly, controlling the KCC2/NKCC1 levels, ATM affects both the GABAergic and glutamatergic system in the hippocampus.

overall_design: Hippocampal RNAs from mice intranasally treated with the ATM kinase blocker KU55933 (n=4) or vehicle (4% DMSO in saline; n = 4). Direct comparison was performed

first: Elisa

last: Focchi

first: Clara

last: Cambria

first: Giovanni

last: Provenzano

first: Flavia

last: Antonucci


title: Glycosylated clusterin species facilitate amyloid beta toxicity in human neurons.

city: Oxford

first: Marco

last: Fernandes

address: Department of Psychiatry, Warneford Ln, Headington

country: United Kingdom

institute: University of Oxford

summary:
Clusterin (CLU) is one of the most significant genetic risk factors for late onset Alzheimer’s disease. Numerous studies have now demonstrated that CLU-AD mutations and amyloid-β (Aβ) treatment alter the trafficking and localisation of glycosylated CLU.
iPSCs with altered CLU trafficking were generated following the removal of CLU exon 2 by CRISPR/Cas9 gene editing. Neurons were generated from control, unedited and exon 2 -/- iPSCs and were incubated with aggregated Aβ peptides. Changes in cell death and neurite length were quantified to determine if altered CLU protein trafficking influenced neuronal sensitivity to Aβ.

overall_design: RNA-Seq analysis was performed to identify key transcriptomic differences between exon 2 -/- and CTR neurons.

first: Fernandes

last: Marco

first: Buckley

last: Noel


title: Real-Time Quantitative PCR Analyis of Neonatal Rat Aortic Neurospheres (ANS)

city: Toronto

first: Sarah

middle: Katherina

last: Steinbach

state: Ontario

address: 200 Elizabeth Street

department: Experimental Therapeutics

country: Canada

institute: University Health Network

summary: Progenitor/stem cell populations of the aorta have been poorly characterized and their self-renewal factors unknown.  In this report, we demonstrate that sphere forming progenitor/stem cells, here within termed aortic neurospheres (ANS), can be cultivated from the aorta that are similar to skin-derived precursors (SKPs).  Extensive mRNA transcript profiling revealed that ANS abundantly expressed the Inhibin βA transcript, of which the secreted protein dominantly formed the Inhibin βA-βA complex, or Activin A, in the proliferation medium.  Co-localization of Activin A, Nestin and Sox2 was observed in the adventitial and peri-adventitial regions of the aorta, indicative of a progenitor/stem cell niche in vivo.  Blockade of Activin A signaling, through the neutralization of the Type II Activin receptors ActRIIA and ActRIIB, resulted in the asymmetric differentiation, and epithelial-to-mesenchymal transition of the ANS, respectively. When treated with the latter neutralizing antibody, translocation of the ActRIIB receptor to the nucleus was observed in cells on the periphery of the sphere.  Examination of the ActRIIB protein sequence showed the presence of a putative nuclear localization signal of the PY family that was conserved across species.  The results from this study demonstrate that Activin A is a self-renewal factor required for maintaining ANS progenitor/stem cell identity and multipotency.

overall_design:
ANS cultivated from neonatal rat aortas were cultured in defined proliferation medium containing EGF, bFGF and B27.
qPCR gene expression profiling.  RNA was isolated from 3 separate ANS cultures.


title: Comparison of the Gr-1+ and Gr-1- monocyte gene expression in cell-type specific Fcgr2 deficiency on the Yaa backgound

city: Yokohama

first: Hidehiro

last: FUKUYAMA

state: Kanagawa

address: 1-7-22, Suehirocho, Tsurumi-ku

department: IMS

institute: RIKEN

summary: We generated 5 mouse lines:(1) Fcgr2 -/-.Yaa,(2)CD19Cre;Fcgr2 fl/fl.Yaa, (3)CEBPaCre;Fcgr2 fl/fl.Yaa, (4)CD11cCre;Fcgr2 fl/fl.Yaa, and (5)Fcgr2 fl/fl.Yaa. Peripheral blood mononuclear cells from each mouse at 8 months old were collected and sorted by CD11b and Gr-1 cell surface markers. Sorted cells were subjected to RNA extraction and RNA-seq analysis

overall_design: Either Gr-1+CD11b+ or Gr-1-CD11b+ cell mRNA profiles of various 8 month-old mice were generated by deep sequencing using HiSeq 1500 sequencer (Illumina)

last: Fukuyama

first: Ryota

last: Sato


title: Real-Time Quantitative PCR Analyis of Neonatal Rat Whisker Pad Skin-derived Precursors (SKPs)

overall_design:
SKPs cultivated from neonatal rat whisker pads were cultured in defined proliferation medium containing EGF, bFGF and B27.
qPCR gene expression profiling.  RNA was isolated from 3 separate SKP cultures.


title: Real-Time Quantitative PCR Analyis of Rat Aortic Neurospheres (ANS) treated with Activin A

overall_design:
ANS cultivated from neonatal rat aortas were cultured in defined proliferation medium containing EGF, bFGF and B27, treated with 50ng/mL and 100 ng/mL Activin A.
qPCR gene expression profiling.  RNA was isolated from 3 separate ANS cultures.


title: The Lung Microenvironment Instructs Gene Transcription in Neonatal and Adult Alveolar Macrophages

city: Palo Alto

first: Lawrence

middle: Stephen

last: Prince

address: 1701 Page Mill Rd

department: Pediatrics

institute: Stanford University

summary: Immaturity of alveolar macrophages (AMs) around birth contributes to the susceptibility of newborns to lung disease. However, the molecular features differentiating neonatal and mature, adult AMs are poorly understood. Here we identify the unique transcriptomes and enhancer landscapes of neonatal and adult AMs. While the core AM signature was similar, adult AMs expressed higher levels of genes involved in lipid metabolism, while neonatal AMs expressed a largely proinflammatory gene profile. Open enhancer regions identified by ATAC-seq contained motifs for nuclear receptors, MITF, and STAT in adult AMs and AP-1 and NF-kB in neonatal AMs. Intranasal LPS activated a similar innate immune response in both neonates and adults, with higher basal expression of inflammatory genes in neonates. The lung microenvironment drove many of the distinguishing gene expression and open chromatin characteristics of neonatal and adult AMs. Neonatal AMs retained high expression of some proinflammatory genes, suggesting the differences in neonatal AMs result from both inherent cell properties and environmental influences.

overall_design: RNA-seq and ATAC-seq for FACS sorted AMs from C57BL/6 mice at postnatal day 4 (P4) and 8 week of age following intranasal administration of LPS or PBS (control). RNA-seq and ATAC-seq for freshly isolated adult and neonatal AMs and after maintenance in culture for 20h.

first: Asami

last: Honda

first: Marten

last: Hoeksema

first: Mashito

last: Sakai

first: Sean

last: Lund

first: Omar

last: Lakhdari

first: Lindsay

last: Butcher

first: Tara

middle: C

last: Rambaldo

first: Neal

last: Sekiya

first: Chanond

last: Nasamran

first: Kathleen

last: Fisch

first: Eniko

last: Sajti

last: Glass


title: The central clock suffices to drive the majority of circulatory metabolic rhythms

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

summary: This dataset was generated to investigate the independence of the central clock in regulating hepatic transcriptional rhythms.

overall_design: The core clock gene Bmal1 was knocked out using a floxed STOP codon (KO mice). By crossing these mice with Syt10-Cre mice we were able to rescue the Bmal1 expression in the suprachiasmatic nucleus (RE mice). These mice were compared with mice expressing Bmal1 in all tissues (WT). Livers were collected at 6 time points over the circadian 24-hour period.

first: Paul

last: Petrus

first: Pierre

last: Baldi


title: CROPSeq of Putative AD- and PSP-associated cis-Regulatory Regions in iPSC-derived Neurons and Microglia

city: San Francisco

first: Martin

last: Kampmann

state: California

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

institute: University of California San Francisco

summary: We performed a pooled CRISPRi screen (CROP-seq) and genome editing to validate 19 genetic variants prioritized from massively parallel reporter assays to screen 5,706 polymorphisms from genome-wide association studies for both Alzheimer’s disease (AD) and Progressive Supranuclear Palsy (PSP) across 11 distinct loci. This allowed us to pinpoint regulatory targets in a cell-type specific manner.

overall_design: sgRNAs were created targeting putative cis-regulatory regions and were transfected into iPSC-derived iNeurons and iMicroglia containing CRISPRi machinery. These were then collected for 10X sequencing using the CROPseq method.

first: Noam

last: Teyssier

first: Nina

last: Dräger

first: Syd

last: Sattler


title: Dimethylmonothioarsenate (DMMTA) is highly toxic for plants and induce strong transcriptome changes.

city: Bayreuth

first: Fabrizio

last: Barozzi

address: Universitätsstraße 30

department: Lehrstuhl Pflanzenphysiologie

institute: Universität Bayreuth

summary: Arsenic is one of the most relevant environmental pollutants and human health threats. Several arsenic species occur in soil pore waters. Recently it was discovered that these include inorganic and organic thioarsenates. Dimethylmonothioarsenate (DMMTA) belong to organic thioarsenates and in mammalian cells its toxicity was found to exceed even that of arsenite. We investigated DMMTA toxicity in Arabidopsis thaliana (Col-0) and we found strong transcriptome changes dominated by stress-responsive genes.

overall_design: RNA-seq anlysis of Arabidopsis thaliana (ecotype Col-0) seedlings exposed (treated) or not exposed (control) for 6h to 15 µM DMMTA.

first: Erik

last: Pischke

first: Andrea

middle: E

last: Colina Blanco

first: Carolin

last: Kerl

first: Britta

last: Planer-Friedrich

first: Stephan

last: Clemens


title: Archetype tasks link intratumoral heterogeneity to plasticity in recalcitrant small cell lung cancer [cell lines]

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

summary: Intratumoral heterogeneity underlies cancer treatment resistance, but approaches to neutralize it remain elusive. Here, we recast heterogeneity in a systems perspective that considers cancer cell functional tasks inherited from cells of origin. We apply Archetype Analysis to bulk transcriptomics data from small cell lung cancer (SCLC), which forms tumors composed of neuroendocrine (NE) and non-neuroendocrine (non-NE) transcriptional subtypes. SCLC subtypes fit well in a 5-dimensional polytope whose vertices optimize tasks reminiscent of pulmonary NE cells, the SCLC normal counterpart, and include injury repair, slithering, and chemosensation. SCLC cells near a vertex are specialists for a task, while more distant cells are generalists, bearing gene signatures of multiple archetypes. Evolutionary theory and dynamical systems modeling suggest a division of labor strategy for adaptation to treatment, based on task trade-offs amongst specialists and generalists. Cell Transport Potential, a metric derived from single-cell RNA velocity, uncovers plasticity trends from specialists to generalists, and NE to non-NE subtypes. Transcription factor network simulations indicate that MYC overexpression increases plasticity by de-stabilizing NE subtypes. Framing heterogeneity in archetype space provides insights into transformative cancer treatments aimed at tumor cell plasticity.

overall_design: scRNA-seq on 8 independent samples of human SCLC cell lines

first: Sarah

last: Groves

first: Vito

last: Quaranta

first: Qi

last: Liu


title: lncRNAs expression in the liver of large yellow croaker fed with fish oil, soybean oil, olive oil, and palm oil diets

city: Qingdao

first: xiufei

last: cao

address: Wenhai Road

institute: ocean university of china

summary: To investigate the role of lncRNAs on lipid metabolism, we did RNAseq to find the difference among large yellow croaker fed with fish oil (FO), soybean oil (SO), olive oil (OO), and palm oil (PO) diets

overall_design: RNA sequencing was performed on 12 liver samples of fish fed with FO, SO, OO, and PO diet, respectively (three biological replicates for each group).

first: Xiufei

last: Cao

first: Qinghui

last: Ai


title: Combinatorial Gli activity directs immune infiltration and tumor growth in pancreatic cancer

city: Ann Arbor

first: Michael

middle: Kemper

last: Scales

state: MI

address: 109 Zina Pitcher Place

department: Cell and Developmental Biology

institute: University of Michigan

summary: Proper Hedgehog (HH) signaling is essential for normal embryonic and postnatal development, while de-regulated HH signaling drives numerous pediatric and adult cancers. In pancreatic cancer, paracrine HH signaling from tumor cells to fibroblasts contributes to tumor progression. However, the role of HH signaling in pancreatic cancer remains controversial, with both tumor-promoting and tumor-restraining functions reported. Notably, the GLI family of transcription factors (GLI1, GLI2, GLI3), key downstream effectors of HH signaling, remain poorly understood in pancreatic cancer. In this study we investigated the individual and combined roles of GLI1-3 in pancreatic cancer progression. Inducible, fibroblast-specific deletion of Gli2 and Gli3 in a mouse model of pancreatic cancer progression reduces collagen deposition and decreases immunosuppressive myeloid cell infiltration. Further, Gli2 and Gli3 deletion leads to an increase in T cells during PanIN stages and an increase in NK cells in implanted tumors, which in turn suppresses tumor growth. Surprisingly, combined loss of all three Glis leads to a widespread loss of acinar cells, an increase in macrophage infiltration, and an increase in tumor growth. Together, these data indicate that a baseline level of Gli is necessary to maintain proper balance of cell types in the pancreas, and the coordinated activity of GLI1-3 directs the fibroinflammatory response in pancreatic cancer.

overall_design: Three independent biological replicates of wildtype and Gli2/Gli3 knock-out pancreatic fibroblasts.

first: Ashley

last: Velez-Delgado

last: Steele

first: Hannah

last: Schrader

first: Anna

middle: M

last: Stabnick

first: Wei

last: Yan

first: Nayanna

last: Mercado Soto

first: Zeribe

last: Nwosu

first: Craig

last: Johnson

first: Yaqing

last: Zhang

first: Daniel

middle: J

last: Salas-Escabillas

first: Rosa

last: Menjivar

first: H

last: Maurer

first: Kenneth

last: Olive

first: Marina

last: Pasca di Magliano

first: Benjamin

last: Allen


title: Activin A is Required for the Self-Renewal of Aortic Sox2+ Neurospheres

first: Sarah

last: Steinbach

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

overall_design: Refer to individual Series


title: STAT1 is essential for hematopoietic stem cell function and maintains a MHC IIhi stem cell subset that resists myeloablation and neoplastic expansion [LK]

city: Cambridge

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

institute: Wellcome - MRC Cambridge Stem Cell Institute

summary: Adult hematopoietic stem cells (HSCs) are predominantly quiescent and can be activated in response to acute stress such as infection or cytotoxic insults.  STAT1 is a pivotal mediator of interferon (IFN) signaling and is required for IFN-induced HSC proliferation, but the downstream mechanisms remain unclear and in particular little is known about the role of STAT1 in regulating hematopoietic stem/progenitor cells during homeostasis. Here we show that loss of STAT1 alters the steady state hematopoietic stem and progenitor (HSPC) landscape, impairs HSC function in transplantation assays and delays blood cell regeneration following myeloablation.  Under steady state conditions STAT1 was essential for several HSC transcriptional programs including expression of genes involved in virus life cycle, a subset of interferon-stimulated genes, MHC class I genes and genes involved in cell cycle arrest.  In addition Stat-1 deficient mice lacked a previously unrecognized quiescent subset of homeostatic HSCs with high levels of MHC II expression (MHC IIhi HSCs). This subset was refractory to 5’-FU induced myeloablation and displayed reduced megakaryocytic potential. Mutant calreticulin, which causes increased megakaryopoiesis in human myeloproliferative neoplasms, gave rise to preferential expansion of MHC IIlo HSCs. These data reveal a STAT1 dependent MHC IIhi quiescent HSC subset and show that STAT1 protects HSCs from proliferative exhaustion.

overall_design: Bone marrow cells were harvested from STAT1KO and WT control mice, lineage negative cKit positive LK cells (lin-cKit+) were sorted

first: Juan

last: Li

first: Matthew

last: Williams

first: Hyun

last: JPark

first: Xiaonan

last: Wang

first: Nicola

last: Wilson

first: Berthold

last: Göttgens

first: Anthony

last: Green


title: Next generation sequencing comparing RNA-seq data from Arabidopsis Col-0 wild type and splicing factor mutant prp8a-14

city: Houston

first: Bonnie

last: Bartel

state: TX

address: 6100 Main St

department: Biosciences

institute: Rice University

summary: Purpose: Identify alternative splicing events and changes to transcript expression levels

overall_design: RNA-seq of 8 day old continuous light grown whole seeding extract of Arabidopsis wild type Col-0 (3 biological replicates) as a control and prp8a-14 mututant (3 biological replicates). Six total samples analyzed

first: Roxanna

last: Llinas

first: Natalie

last: Clark


title: An Immune Gene Expression Signature Associated With Development of Human Hepatocellular Carcinoma Identifies Mice That Respond to Chemopreventive Agents II

city: Barcelona

first: Sara

last: Torrecilla

state: Catalonia

address: Rossello Street, 149

country: Spain

institute: IDIBAPS

summary:
Background & Aims: Cirrhosis and chronic inflammation precede development of hepatocellular carcinoma (HCC) in approximately 80% of cases. We investigated immune-related gene expression patterns in liver tissues surrounding early-stage HCCs and chemopreventive agents that might alter these patterns to prevent liver tumorigenesis.

Methods: We analyzed gene expression profiles of non-tumor liver tissues from 392 patients with early-stage HCC (training set, n=167 and validation set, n=225) and liver tissue from patients with cirrhosis without HCC (n=216, controls) to identify changes in expression of genes that regulate the immune response that could contribute to hepatocarcinogenesis. We defined 172 genes as markers for this deregulated immune response, which we called the immune-mediated cancer field (ICF). We analyzed the expression data of liver tissues from 216 patients with cirrhosis without HCC and investigated the association between this gene expression signature and development of HCC and outcomes of patients (median follow-up 10 years). Human liver tissues were also analyzed by histology. C57BL/6J mice were given a single injection of N-nitrosodiethylamine followed by weekly doses of carbon tetrachloride to induce liver fibrosis and tumorigenesis. Mice were then given orally the multiple tyrosine inhibitor nintedanib or vehicle (controls); liver tissues were collected and histology, transcriptome, and protein analyses were performed. We also analyzed transcriptomes of liver tissues collected from mice on a choline-deficient high-fat diet, which developed chronic liver inflammation and tumors, given orally aspirin and clopidogrel or the anti-inflammatory agent sulindac vs mice on a chow (control) diet.

Results: We found the ICF gene expression pattern in 50% of liver tissues from patients with cirrhosis without HCC and in 60% of non-tumor liver tissues from patients with early-stage HCC. The liver tissues with the ICF gene expression pattern had 3 different features: increased numbers of effector T cells; increased expression of genes that suppress the immune response and activation of transforming growth factor beta signaling; or expression of genes that promote inflammation and activation of interferon gamma signaling. Patients with cirrhosis and liver tissues with the immunosuppressive profile (10% of cases) had a higher risk of HCC (hazard ratio, 2.41; 95% 1.21–4.80). Mice with chemically-induced fibrosis or diet-induced steatohepatitis given nintedanib or aspirin and clopidogrel downregulated the ICF gene expression pattern in liver and developed fewer and smaller tumors than mice given vehicle.

Conclusions: We identified an immune-related gene expression pattern in liver tissues of patients with early-stage HCC, called the ICF, that associates with risk of HCC development in patients with cirrhosis. Administration of nintedanib or aspirin and clopidogrel to mice with chronic liver inflammation caused loss of this gene expression pattern and developed fewer and smaller liver tumors. Agents that alter immune regulatory gene expression patterns associated with carcinogenesis might be tested as chemopreventive agents in patients with cirrhosis.
To assess the impact of sulindac or aspirin/clopidogrel treatment on the immune-mediated cancer field, we collected samples from a choline-deficient high-fat diet fed mouse model developing NASH, HCC and fibrosis, previously published (Malehmir M et al, Nat Med, 2019) . We analyzed gene expression profiling of non-tumor liver samples from mice fed a CD-HFD for 12 weeks treated with vehicle that presented HCC and fibrosis (considered as high-risk group) (n=4); as well as mice fed a CD-HFD for 12 weeks treated with sulindac (n=10) or aspirin/clopidogrel (n=6). As controls, we analyzed samples from mice fed a chow-diet for 12 weeks (considered as healthy group) (n=5).

overall_design: Fresh-frozen liver tissues from 30 mice (5 control, 4 vehicle-treated, 10 sulindac-treated and 6 aspirin/clopidogrel treated), were collected and RNA was extracted. Whole-genome transcriptome analysis was obtained using ene Chip HT MG-430 (Affymetrix) according to manufacturer’s protocols. Raw expression data from microarrays were normalized using the ExpressionFileCreator [RMA with quantile normalization method].

first: Josep

last: Llovet

first: Daniela

last: Sia

first: Mathias

last: Heikenwälder


title: Extrathymic expression of Aire controls the induction of effective TH17 cell-mediated immune response to Candida albicans

city: Rehovot

first: Jakub

last: Abramson

address: 234 Herzl st.

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

summary: To investigate the effect of Candida albicans on ILC3 cells and dendritic cells these subytpes were isolated by flow cytometry, in similar fashion candida specific T-cells were obtained and subjected to bulk mRNA sequencing

overall_design: mRNA profiling of conventional ILC3, MHCII+ ILC3, Aire+ ILC3 and DCs in homeostasis or stimulated by heat-killed Candida albicans. mRNA profilling of T-cells stimulated by Candida albicans, mRNA profiling of Aire-suficient or deficient Aire-expressing ILC3 cells stimulated by Candida albicans


title: Expression data of bone marrow-derived osteoclasts expressing wild-type or mutant PSS1

status: Public on Jul 04 2022

city: Tokyo

first: Nozomu

last: Kono

address: Hongo 7-3-1, Bunkyo-ku

institute: Universtiy of Tokyo

summary:
Phosphatidylserine (PS) is an acidic phospholipid that is involved in various cellular events. Heterologous dominant mutations have been identified in the gene encoding PS synthase 1 (PSS1) in patients of a congenital disease called Lenz-Majewski syndrome (LMS). LMS patients show various symptoms, including craniofacial/distal-limb bone dysplasia and progressive hyperostosis. The LMS-causing gain-of-function mutants of PSS1 (PSS1-LMS) have been shown to synthesize PS without control, but why the uncontrolled synthesis would lead to LMS is unknown.
We investigated the effect of PSS1-LMS(Q353R) on osteoclasts to elucidate the causative mechanism of LMS and found that PSS1-LMS inhibited the formation, multinucleation, and activity of osteoclasts. We used microarrays to comprehensively examine the effects of PSS1-LMS on osteoclast gene expression.

overall_design: Bone marrow cells were treated with MCSF alone or MCSF and RANKL and infected one day later with a retroviral vector expressing wild-type or mutant PSS1. Cells were collected for microarray analysis on days 3 and 6 after MCSF/RANKL treatment.

first: Sugahara

last: Sari

first: Kono

last: Nozomu


title: Aberrant astrocyte protein secretion contributes to altered neuronal development in diverse disorders

city: San Diego

first: April

middle: Elizabeth

last: Williams

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Astrocytes negatively impact neuronal development in a range of neurodevelopmental disorders (NDs), however how they do this, and if mechanisms are shared across multiple disorders, is not known. We developed an in vitro system to ask how astrocyte protein secretion and gene expression change in 3 genetic NDs (Fragile X syndrome (FXS), Rett's syndrome (RTT), Down's syndrome (DS)). This identified disorder specific changes, as well as core proteins that are increased in release in all 3 NDs. We provide a resource of astrocyte secreted proteins and gene expression in health and NDs, as well as novel targets for intervention in diverse NDs.

overall_design: Astrocytes isolated from the P7 mouse cortex of WT, FXS, RTT, DS mice using immunopanning. Maintained in vitro in defined serum free media for 12 days before RNA collection. Biological replicates for NDs: WT=6, FXS=6, RTT=6, DS=4. For comparing gene expression in WT astrocytes treated with BMP6, WT astrocytes were treated for the last 5 days of the culture period with BMP6 or left untreated (Alone condition). Biological replicates for BMP6: Alone=6, BMP6=6.

first: Allison

last: Caldwell

first: Maxim

middle: N

last: Shokhirev

last: Allen


title: Cooperative engagement and subsequent selective displacement of SR proteins define the pre-mRNA 3D structural scaffold for early spliceosome assembly

city: La Jolla

first: Kaushik

last: Saha

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: University of California San Diego

summary: We recently reported that serine-arginine-rich (SR) protein-mediated pre-mRNA structural remodeling generates a pre-mRNA 3D structural scaffold that is stably recognized by the early spliceosomal components. However, the intermediate steps between the free pre-mRNA and the assembled early spliceosome are not yet characterized. By probing the early spliceosomal complexes in vitro and RNA-protein interactions in vivo, we show that the SR proteins bind the pre-mRNAs cooperatively generating a substrate that recruits U1 snRNP and U2AF65 in a splice signal-independent manner. Excess U1 snRNP selectively displaces some of the SR protein molecules from the pre-mRNA generating the substrate for splice signal-specific, sequential recognition by U1 snRNP, U2AF65, and U2AF35. Our work thus identifies a novel function of U1 snRNP in mammalian splicing substrate definition, explains the need for excess U1 snRNP compared to other U snRNPs in vivo, demonstrates how excess SR proteins could inhibit splicing, and provides a conceptual basis to examine if this mechanism of splicing substrate definition is employed by other splicing regulatory proteins.


title: STAT1 is essential for hematopoietic stem cell function and maintains a MHC IIhi stem cell subset that resists myeloablation and neoplastic expansion

first: Hugo

last: Bastos

overall_design: Bone marrow cells were harvested from STAT1KO and WT control mice, single ESLAM HSCs was FACS sorted

first: Juan

last: Li

first: Matthew

first: Hyun

last: Park

first: Xiaonan

last: Wang

first: Nicola

last: Wilson

first: Sarah

last: Kinston

first: Berthold

last: Göttgens

last: Green


title: Archetype tasks link intratumoral heterogeneity to plasticity in recalcitrant small cell lung cancer [Human tumor]

first: Marisol

last: Ramirez

overall_design: scRNA-seq on two human tumors

last: Groves

first: Vito

last: Quaranta

first: Qi

last: Liu


title: miRNA expression in Drosophila

city: STRASBOURG

first: Nicolas

last: MATT

address: 15 rue René Descarte

department: IBMC

institute: CNRS

summary: miRNA expression in adult flies infected with the Gram-positive bacteria Micrococcus luteus or the fungi Beauveria bassiana.

overall_design: 18-25nt RNAs were extracted from 6-day-old adult flies that were raised at 25°C. Aside of the control, M. luteus and B. bassiana infection were performed. A total of 3 samples were obtained. No independent biological replicates were included.

first: Alexandre

last: Cammarata-Mouchtouris

first: Aleksandra

last: Krupa

first: Vincent

last: Leclerc

last: Matt

first: Jean-Marc

last: Reichhart

first: Laurent

last: Troxler


title: Effect of IVIG on the activation of plasmacytoid dendritic cells

city: Shanghai

first: Haibo

last: Zhou

address: No.160, Pujian Road

department: Department of Rheumatology

institute: Renji Hospital

summary:
To investigate the effect of IVIG and desialylated IVIG on the activation of plasmacytoid dendritic cells (pDCs). Human primary plasmacytoid dendritic cells were treated with TLR stimulation together with or without IVIG or desialylated IVIG, and the change of genes were analyzed.
Primary  human  pDCs  were preincubated with or without 10mg/ml IVIG or desialylated IVIG followed by stimulation with CpG overnight. The different genes between IVIG+CpG and  desialylated IVIG+CpG were analyzed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pDCs with different treatment. Three biological replicates were made for each treatment. The reference samples are CpG stimulated pDCs.

first: Wen

last: Di

last: Shen

first: You


title: EZH2 and JARID2 change their binding profiles on RNA and DNA to promote hepatocellular carcinoma [ChIP-seq]

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary: The molecular mechanisms of carcinogenesis have been deeply studied benefit from the highly developing biotechnologies. Here we used high throughput sequencing method to capture the global binding profiles on RNA and DNA of EZH2 and JARID2 in liver normal (THLE-2) and carcinoma (HepG2) cells, respectively. We found that EZH2 and JARID2 showed distinct binding profile in HepG2 and THLE-2 cells. By binding to the primary RNAs, bound transcripts of EZH2 and JARID2 in HepG2 showed significantly increased transcriptional level in hepatocellular carcinoma (HCC) patients. They bound transcripts were also highly related to the HCC development by performing gene set enrichment analysis (GSEA). By exploring the DNA binding profile, we also detected similar phenomena that EZH2 could increase the transcriptional level of bound genes in HepG2 cells, showing PRC2-independent functions in liver cancer cells. Integrating analysis of the RNA and DNA binding profile showed EZH2 could independent function at the transcriptional and post-transcriptional stages. In summary, we proposed that the novel regulatory functions of EZH2 and JARID2 that may promote the cancer development in carcinoma liver cells.

overall_design: We performed ChIP-seq experiment for EZH2, JARID2 and H3K27me3 proteins in THLE-2 cell line, and JARID2 protein in HepG2 cell line. Two biological replicates were obtained for each protein in each cell line with corresponding Input controls.

first: Dong

last: Chen

first: Yi

last: Zhang


title: Effect of 660-nm diode laser in the treatment of human breast epithelium by RNA sequencing

city: Kaifeng

first: Haigang

last: wu

state: Henan province

address: dongjing Road

department: School of Life Sciences

institute: Henan University

summary: Red light radiation has been proven to provide clinical benefits to human health. Our investigation was conducted to characterize tissue morphology of mouse breast post 660 nm-laser radiation with low power and long-term exposure.

overall_design: Examination of transcriptome level in mouse breast  epithelial cells treated with LED 660 nm.

last: Wu

first: Beier

last: Jiang


title: RNA Sequencing of sorted CD31+ meningeal endothelial cells from naïve Lewis rats

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: The meninges, comprising the leptomeninges (pia and arachnoid layers) and the pachymeninx (dura layer), participate in CNS autoimmunity but their relative contributions remain unclear. Here, we report on findings in animal models of CNS autoimmunity and in multiple sclerosis patients, where, in chronic disease, the leptomeninges were highly inflamed and showed structural changes, while the dura mater was only marginally affected. Although dural vessels were leakier than leptomeningeal vessels, effector T cells adhered more weakly to the dural endothelium. Furthermore, local antigen presenting cells presented myelin and neuronal autoantigens less efficiently and the activation of autoreactive T cells was lower in dural than leptomeningeal layers, preventing local inflammatory processes. Direct antigen application was required to evoke a local inflammatory response in the dura. Together, our data  demonstrate an uneven involvement of the meningeal layers in CNS autoimmunity, in which effector T cell trafficking and activation are functionally confined to the leptomeninges, while the dura remains largely shielded from CNS autoimmune processes.

overall_design:
Bulk RNA-Seq of CD31+ endothelial cells extracted from different brain meningeal compartments
Brain meningeal tissues were harvested from naïve Lewis rats, endothelial cells extracted by digestion protocol and FACS sorted. Four animals were pooled for each tissue. The experiment was performed in 4 biological replicates.

first: Alexander

last: Flügel

first: Francesca

last: Odoardi

first: Arianna

last: Merlini

first: Michael

last: Haberl


title: EZH2 and JARID2 change their binding profiles on RNA and DNA to promote hepatocellular carcinoma


title: SMYD3 promotes aerobic glycolysis in diffuse large B-cell lymphoma via H3K4me3-mediated PKM2 transcription

status: Public on Jul 03 2022

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

summary: Genetic abnormalities in histone methyltransferases (HMTs) frequently occur in diffuse large B-cell lymphoma (DLBCL) and are related to its progression. SET and MYND domain containing 3 (SMYD3) is an HMT that is upregulated in various tumors and promotes their malignancy. To further explore the functional role of SMYD3 in DLBCL, RNA-Seq was carried out on total RNA isolated from SMYD3-knockdown or control OCI-LY8 cells.

overall_design: Total RNA isolated from stable SMYD3-knockdown OCI-LY8 cells (shSMYD3 #1 and shSMYD3 #2) and LY8-NC cells was used for RNA-Seq to profile differentially expressed mRNA transcripts.

first: Tian

last: Tian

first: Ping

last: Wei

first: Xiaoyan


title: Specific CBF transcription factors and cold‐responsive genes fine‐tune the early triggering response after acquisition of cold priming and memory

status: Public on Jul 02 2022

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

institute: MPI of Molecular Plant Physiology

summary: Plants need to adapt to fluctuating temperatures throughout their lifetime. Previous research has shown that A. thaliana retains memory of a first cold stress (priming) and improves its primed freezing tolerance even further when subjected to a second similar stress after a lag phase. This study investigates primary metabolomic (gas chromatography–mass spectrometry) and transcriptomic (RNA-Seq) changes during 24 h of cold priming or cold triggering at 4°C. During triggering higher expression of genes encoding Late Embryogenesis Abundant (LEA), antifreeze proteins or proteins function as detoxifiers of reactive oxygen species (ROS) was observed compared to cold priming. Examples of early responders to triggering were xyloglucan endotransglucosylase/hydrolase genes encoding proteins involved in cell wall remodeling while late responders were identified to act in fine-tuning of stress response and development regulation. Four transcription factors, CBF2/DREB1C, CBF4/DREB1D, DDF2/DREB1E and DDF1/DREB1F were strongly and uniquely significantly induced throughout the entire triggering response. The induction of unusual members of the DREB subfamily of ERF/AP2 transcription factors, the relatively small number of induced genes of the CBF regulon and slower accumulation of selected cold stress associated metabolites proposes that a cold triggering stimulus might be sensed as milder stress in plants compared to priming. Further, the strong induction of CBF4 throughout triggering suggests a unique function of this gene during cold stress memory.

overall_design: RNA-Sequencing of a priming and triggering time course. 28 d old Arabdiopsis thaliana plants were primed (C28P) (4°C) and then subjected to a 7 day lag phase and triggered (C28PLT) (4°C). A developmental control of 35 d old plants (C35P) were further primed at 4°C. For all conditions samples were taken at 0, 2, 4, 6, 12 and 24 h after priming or triggering.

first: Kora

last: Vyse

first: Stephanie

last: Schaarschmidt

last: Erban

first: Joachim

last: Kopka


title: Transcriptomics analysis of dsu and WT response to infection of U. maydis.

city: Taian

first: Ru Chang

last: Ren

address: Daizong

department: College of Life Sciences

institute: Shandong Agricultural University

summary: To investigate the different responses of WT and dsu to U. maydis, transcriptome analysis was perfromed and the results showed that reprogramming of maize transcription after infection U. maydis.

overall_design: The whorls leaves of WT and dsu seedlings were infected with SG200 strains at three leaves stage. Total RNA were isolated from the SG200- and mock-infected plant leaves at 4 day after infection.

first: Ru

first: Xiang

last: Zhao


title: Effects of B cell depletion on bulk RNAseq on colonic tissue repair after acute inflammation

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

institute: KTH

summary: Using an experimental model of intestinal epithelial damage and repair, we identified B cells as the dominant cell type in the healing colon. Single-cell RNA-sequencing (scRNAseq) revealed the expansion of an IFN-induced B cell subset during experimental mucosal healing which was predominantly located in damaged areas and associated with colitis severity. In line with this, B cell depletion during mucosal healing resulted in accelerated recovery upon injury, decreased epithelial ulceration and enhanced gene expression programs associated with tissue remodeling.

overall_design: CD19-cre x iDTR mice were kindly provided by Prof. Dr. Nadine Hövelmeyer (University of Mainz, Germany), imported from Germany and bred locally. Animals were maintained under specific pathogen-free conditions at Astrid Fagraeus Laboratory or AKM animal facility and handled according to protocols approved by the Institutional Animal Care and Use Committee at the Karolinska Institutet (Stockholm, Sweden). All experimental procedures were performed according to national and institutional regulations and guidelines. Mice of C57BL/6J background, aged 8–12 weeks at the beginning of experiments, were used for all experiments. Murine colitis was induced by administration of 2-3% of dextran sodium sulfate (DSS, company, Alfa Aesar) dissolved in drinking water ad libitum for 7 days, followed by 7 days of regular water, when samples were collected. For B cell-depletion experiments CD45.1 mice were irradiated with 2x 6Gy with a time interval of 3 hours in between. Within 24hours after the second irradiation mice received 3 x 106 bone marrow cells (CD45.2) intravenously. 6 weeks after bone marrow transfer reconstitution of cells was analysed by flow cytometric analysis of the blood. 8-10 weeks after BM transfer mice were subjected to DSS and were injected i.p. with 25ng/g BW diphtheria toxin (Sigma-Aldrich) or PBS on days 9, 10, 12 and 13 during DSS-induced colitis. Success of B cell depletion was analysed at the end of the experiment by flow cytometry of splenic B cells.

first: Edurado

last: Villablanca