title: RGCC balances self-renewal and neuronal differentiation of neural stem cells in the developing mammalian neocortex [2D NSCs]

first: Guang

last: He

state: China

address: 1954 Huashan Rd, Shanghai Jiao Tong University

institute: Bio-X Center

summary: Use cerebral organoid and mouse and mouse models to study the function of RGCC in neocortical development.

overall_design: Comparison of transcriptomes from WT groups and RGCC knockout cerebral organoid groups

first: Zhenming

last: Guo

first: Yiming

last: Chao

first: Liangjie

last: Liu

first: Weibo

last: Niu

first: Lei

last: Shi

first: Yan

last: Bi

first: Dengcheng

last: Ren

first: Fan

last: Yuan

first: Ke

last: Han

first: Yi

first: Shan

last: Bian


title: Deletion of the mitochondria-shaping protein Opa1 during early thymocyte maturation impacts mature memory T cell metabolism

status: Public on Jul 27 2021

city: Cologne

first: Mauro

last: Corrado

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: University of Cologne

type: Expression profiling by high throughput sequencing

summary: OPA1, a mitochondria-shaping protein controlling cristae biogenesis and respiration, is required for memory T cell function, but whether it affects intrathymic T cell development is unknown. Here we show that OPA1 is necessary for thymocyte maturation at the double negative (DN)3 stage when rearrangement of the T-cell receptor β (Tcrβ) locus occurs. By profiling mitochondrial function at different stages of thymocyte maturation, we find that DN3 cells rely on oxidative phosphorylation (OXPHOS). Consistently, Opa1 deletion during early T cell development impairs respiration of DN3 cells and reduces their number. Opa1-deficient DN3 cells indeed display stronger TCR signaling and are more prone to cell death. The surviving Opa1-/- thymocytes that reach the periphery as mature T cells display an Effector Memory phenotype even in the absence of antigenic stimulation but are unable to generate metabolically fit long-term memory T cells. Thus, mitochondrial defects early during T cell development affect mature T cell function.

overall_design: RNA-seq was performed on DN3 and DN4 thymocytes freshly sorted form 6 weeks old Wt;Lck-Cre+ and Opa1fl/fl;Lck-Cre+ mice

first: Dijana

last: Samardžić

first: Marta

last: Giacomello

first: Nisha

last: Rana

first: Erika

middle: L

last: Pearce

first: Luca

last: Scorrano


title: CLOCKWORK ORANGE promotes CLOCK-CYCLE activation via the Drosophila ortholog of CLOCK INTERACING PROTEIN, CIRCADIAN (RNA-Seq)

status: Public on Jul 23 2021

city: College Station

first: Paul

last: Hardin

state: Texas

address: 3258 TAMU Dept of Biology Buttler Hall room 100H

country: USA

institute: Texas A&M University

summary: The Drosophila circadian clock is driven by a transcriptional feedback loop in which the bHLH transcription factor CLOCK-CYCLE (CLK-CYC) binds E-boxes to transcribe genes encoding the PERIOD-TIMELESS (PER-TIM) repressor, which releases CLK-CYC from E-boxes to inhibit transcription. The bHLH-Orange transcription factor CLOCKWORK ORANGE (CWO) reinforces repression by binding E-boxes to displace CLK-CYC, but also acts through an unknown mechanism to promote CLK-CYC transcription. To determine how CWO activates CLK-CYC transcription, we identified CWO DNA binding targets that are upregulated in the absence of CWO repression, conserved in mammals and preferentially expressed in brain pacemaker neurons. Among the genes identified was the Drosophila ortholog of mammalian Clock Interacting Protein Circadian (Cipc) that acts to repress CLOCK-BMAL1 transcription. Reducing or eliminating Drosophila Cipc expression shortens circadian period while overexpressing Cipc lengthens circadian period in flies, consistent with previous analysis showing that Drosophila Cipc represses CLK-CYC transcription in S2 cell culture. Long period rhythms of cwo mutant flies are largely rescued when Cipc expression is reduced or eliminated, indicating that increased Cipc expression mediates period lengthening of cwo mutants. These results suggest a mechanism for CWO-dependent CLK-CYC activation: CWO inhibition of CIPC repression promotes CLK-CYC transcription. Such a mechanism may be conserved given that orthologs of cwo and Cipc carry out analogous roles in the mammalian circadian clock.

overall_design: RNA-seq: mRNA profiles of heads from Drosophila wild type (WT) and cwo5073 mutant at six different timepoints, ZT 02, ZT 06, ZT 10, ZT 14, ZT 18, ZT 22

first: Gustavo

middle: S

last: Rivas

first: Jian

last: Zhou

first: Christine

last: Merlin

middle: E


title: CLOCKWORK ORANGE promotes CLOCK-CYCLE activation via the putative Drosophila ortholog of CLOCK INTERACTING PROTEIN CIRCADIAN

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Persistent DNA damage rewires lipid metabolism and promotes histone hyperacetylation via MYS-1/Tip60

city: PITTSBURGH

first: Aditi

last: Gurkar

state: PA

address: 100 Technology Drive, Room # 414, Bridge side point

department: Department of Medicine

institute: UNIVERSITY OF PITTSBURGH

summary: The goal of the study was to gain a comprehensive understanding of the cellular and metabolic responses to chronic genotoxic stress. We analyzed global changes in the transcriptome of xpf-1 worms in mid-life (day 7 of adulthood), when they start displaying increased stress sensitivity but prior to any evidence of increased mortality. We compared the transcriptome changes with the wildtype N2. Enrichment analysis of differentially expressed genes, showed an upregulation of genes particularly involved in metabolism, stress response, signaling, and mRNA functions

overall_design: Comparitive analysis of mRNA profiles of day-7 adult N2 and xpf-1 DNA repair mutants

first: Shruthi

last: Hamsanathan

middle: U


title: Investigating the role of SMCHD1 in regulating the chromatin states of select autosomal gene clusters

city: Boston

first: Chen-Yu

last: Wang

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: To investigate the effect of Smchd1 ablation on the chromatin states of select autosomal gene clusters, we derived clonal neural progenitor cells (NPCs) from Smchd1+/+ (wild-type, WT) and Smchd1-/- mouse embryonic stem cells (ES cells; ESC). We generated allele-specific EZH2 ChIP-seq datasets from WT and Smchd1-/- NPCs to examine the effect of Smchd1 ablation on the distribution of Polycomb repressive complex 2 (PRC2).

overall_design: ChIP-seq for EZH2 in neural progenitor cell clones derived from WT and Smchd1-/- female mouse embryonic stem cells (ES cells).

first: Jeannie

middle: T

last: Lee


title: Effect of cell passage number on gene expression in NR8383 macrophages

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

country: France

institute: Université de lorraine

summary:
Continuous cell lines are important research tools in biology and medicine. However, literature demonstrates that over-subculturing changes cell lines properties over time. In addition, cultured cells adapt to stress and confusion by evolution - both genotypic and phenotypic. The aim of this study is to identify differentially expressed genes and key biological pathways at high-passage cells compared to lower-passage cells. To do that, we performed microarray analyses on NR8383 macrophages at 20 and 200 passages numbers.
This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 686098

overall_design: Changes in gene expression in NR8383 cells over times were measured. Cells at low (passage 20) and high (passage 200) passage numbers are used. For each condition, four biological replicates were performed: P 20-1; P 20-2; P 20-3; P 20-4 and P 200-1; P 200-2; P 200-3, P 200-4.

first: Ramia

last: Safar

first: Sara

last: Nahlé

first: Timeh

last: Saidou


title: RGCC balances self-renewal and neuronal differentiation of neural stem cells in the developing mammalian neocortex

city: Shanghai

first: Guang

last: He

country: China


title: Intercellular coupling between peripheral circadian oscillators by TGF-beta signaling [RNA-seq]

city: Berlin

first: Anna-Marie

last: Finger

address: Virchowweg 6

institute: Charité Universitätsmedizin Berlin

summary: Intercellular coupling is crucial to prevent desynchronization of cell-autonomous oscillator networks and thus, the disruption of circadian tissue functions. While, neuronal oscillators within the mammalian central clock, the suprachiasmatic nucleus (SCN), couple intercellularly via the exchange of secreted neurotransmitters, intercellular coupling among peripheral oscillators is highly debated and molecular mechanisms are unknown. In our study, we show that peripheral circadian oscillators couple intercellularly via the exchange of secreted signaling molecules and identify TGF-beta as peripheral coupling factor. TGF-beta signaling induces the cAMP response element dependent, immediate-early expression of the clock gene PER2, thereby phase-adjusting the molecular circadian oscillator. Genetic or pharmacologic disruption of TGF-beta signaling causes desynchronization of cellular oscillators resulting in amplitude reduction and increased sensitivity towards Zeitgeber cues. Our findings reveal a previously unknown mechanism of peripheral coupling and open a new perspective on the importance of peripheral clock synchrony for rhythmic organ functions and circadian health.

overall_design: Examination of transcriptome changes in densely and sparsely cultured U-2 OS cells following a 2 hs stimulation pulse with U-2 OS conditioned and control medium 16-18 hs after dexamethasone synchronization.

first: Sebastian

last: Jäschke

first: Marta

last: del Olmo

first: Robert

last: Hurwitz

first: Adrian

last: Granada

first: Hanspeter

last: Herzel

first: Achim

last: Kramer


title: Network Landscape of Photothermal Flowering in Soybean.

status: Public on Jul 25 2021

city: Northridge

first: Yoshie

last: Hanzawa

state: California

address: 18111 Nordhoff Street, CR 5217

department: Biology

institute: California State University, Northridge

summary: The project aims at elucidation of global gene expression patterns underlying photothermal flowering of soybean to clarify the molecular mechanisms of photothermal flowering in soybean.

sample_organism:
Glycine max
Glycine soja

platform_organism:
Glycine max
Glycine soja

overall_design: RNA-sequencing was conducted using five soybean varieties under different photoperiod and ambient temperature conditions.

first: Faqiang

last: Wu

first: Xiaohan

last: Kang

first: Bruce

last: Hajak


title: The critical and diverse roles of CD4-CD8- double negative T cells in non-alcoholic fatty liver disease

status: Public on Jul 22 2021

city: Beijing

first: Changying

last: Li

address: Panjiayuan Street 17, Chaoyang District

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Methods: RNA transcription profiling of intrahepatic CD4-CD8- double negative T cells were compared between C57BL/6 mice fed with control diet and methionine-choline deficient diet (MCD) for 5 weeks. Results: RNA sequencing data showed that intrahepatic DNT in NAFLD mice exhibited markedly decreased Prf1, Gzmb but increased Il17a expression.

overall_design: Examination of  different genes in intrahepatic double negative T cells of normal diet and methionine-choline deficient diet

first: Guangyong

last: Sun

first: Dong

last: Zhang


title: RGCC balances self-renewal and neuronal differentiation of neural stem cells in the developing mammalian neocortex [3D cerebral organoid]

first: Zhenming

last: Guo

first: Yiming

last: Chao

first: Liangjie

last: Liu

first: Weibo

last: Niu

first: Lei

last: Shi

first: Yan

last: Bi

first: Dengcheng

last: Ren

first: Fan

last: Yuan

first: Ke

last: Han

first: Yi

first: Shan

last: Bian


title: circRNA-sequencing analysis of Ishikawa human endometrial carcinoma cells treated with MPA or not

city: shanghai

first: shuang

last: yuan

email: frosty52@163.com, frosty52@126.com

address: No.910, Hengshan Road

institute: The international peace maternity and child health hospital

summary:
Progestins are commonly used as the conservative endocrine treatment of young early endometrial cancer (EC) patients.
Circular RNAs (circRNAs) are new group players in multiple cellular functions.
This study aims to identify the differentially expressed circular RNAs (DE-circRNAs) in endometrial cancer (EC) cells upon the progesterone treatment. aiding in the understanding of the impact of circRNAs in pregestin therapy.

overall_design: Examing 2 conditions, each with 3 replicates

first: Shuang

first: Panchan

last: Zheng

first: Yudong

last: Wang

first: Lihua


title: Lin28a and Lin28b are required for lung branching morphogenesis and epithelial cell differentiation via coordination of signaling pathway feedback loops in a let7-independent manner

first: Areum

address: Karp Family Building, 7th Floor. 300 Longwood Ave.

institute: Boston Children's Hospital

summary: We examined the role of Lin28a and b during lung development and found dual loss led to defects in branching.

overall_design: Double knockout of Lin28a and b using the epithelial specific cre,  NKX2.1creERT

first: George

middle: Q

last: Daley

first: Jihan

last: Osborne


title: The transcriptome-wide N6-methyladenosine (m6A) map profiling reveals the regulatory role of m6A in the yak ovary

city: Lanzhou

first: Xingdong

state: 未选择

address: No.335 Jiangouyan, Qilihe District

institute: CAAS: Chinese Academy of Agricultural Sciences

summary: The yak estrus is a seasonal phenomenon, probably involving the epigenetic regulation of the synthesis and secretion of sex hormones as well as the growth and development of follicles. In this study, we collected the yak ovarian tissues at the three different states of anestrus, estrus, and pregnancy, and obtained the full transcriptome m6A map in yak by MeRIP-seq. The RT-qPCR showed that the expression of METTL3, METTL14, FTO, YTHDC1 were significantly different across different periods in the ovaries. Next, we identified 20174, 19747 and 13523 m6A peaks in the three ovarian samples of YO-A, YO-F and YO-P using the methylated RNA immunoprecipitation sequencing (MeRIP-seq). The m6A peaks are highly enriched in the coding sequence (CDS) region and 3′untranslated region (3′UTR) as well as the conserved sequence of “RRACH.” Functional analysis revealed the involvement of m6A in many physiological activities of the yak’s ovary during estrus and pregnancy. The association analysis found that some genes such as BNC1, HOMER1, BMP15, BMP6, GPX3, and WNT11 were related to ovarian functions. The comparison of the distribution patterns of methylation peaks in the ovarian tissues across different periods further explored the m6A markers related to the regulation of ovarian ovulation and follicular development in the yak ovary. This comprehensive map provides a solid foundation for revealing the potential function of the mRNA m6A modification in the yak ovary.

overall_design: Detection of m6A in Yak ovaries during anestrus, estrus and pregnancy

first: Shaoke

first: Jie

last: Pei

first: Xian


title: Basal-epithelial stem cells cross an alarmin checkpoint for post-viral lung disease

city: St. Louis

first: Michael

middle: J

last: Holtzman

state: MO

address: 4939 Childrens Pl

department: Pulmonary & Critical Care

institute: Washington University in St. Louis School of Medicine

summary: Epithelial cells are charged with protection at barrier sites, but whether this normally beneficial response might sometimes become dysfunctional still needs definition. Here we identify a pattern of imbalance marked by basal epithelial cell growth and differentiation that replaces normal airspaces in a mouse model of progressive post-viral lung disease due to Sendai virus. Single-cell and lineage-tracing technologies identify a distinct subset of basal epithelial stem cells (basal_x0002_ESCs) that extend into gas-exchange tissue to form long-term bronchiolar-alveolar remodeling regions. Moreover, this cell subset is selectively expanded by crossing a cell growth and survival checkpoint linked to the nuclear-localized alarmin IL-33 that is independent of IL-33-receptor signaling and instead connected to autocrine chromatin accessibility. This mechanism creates an activated stem-progenitor cell lineage with potential for physiological or pathological function. Thus, conditional loss of Il33 gene function in basal epithelial cells disrupts homeostasis of the epithelial barrier at skin and gut sites but also markedly attenuates post-viral disease in the lung based on down-regulation of remodeling and inflammation. We thereby identify a basal-ESC strategy to deploy innate-immune machinery that appears to overshoot the primordial goal of self_x0002_defense. The findings reveal new targets to stratify and correct chronic and often deadly post-viral disease.

overall_design: Lung tissue RNA was purified from three mice per sample condition (12 or 21 d after SeV infection or PBS control challenge).

first: Kangyun

last: Wu

first: Kenji

last: Kamimoto

first: Yong

last: Zhang

first: Kuangying

last: Yang

first: Shamus

middle: P

last: Keeler

first: Benjamin

last: Gerovac

first: Eugene

last: Agapov

first: Stephen

last: Austin

first: Jennifer

last: Yantis

first: Kelly

middle: A

last: Gissy

first: Derek

last: Byers

last: Alexander-Brett

first: Christy

middle: M

last: Hoffmann

first: Matthew

last: Wallace

last: Hughes

first: Erika

last: Crouch

first: Samantha

last: Morris


title: The transcriptome and m6A-epitranscriptome during skeletal muscle differentiation

city: Guangzhou City

first: Shujuan

last: Xie

institute: The Third Affiliated Hospital,Sun Yat-Sen University

type: Methylation profiling by high throughput sequencing

summary: Mouse C2C12 myoblasts were used to mimic skeletal muscle differentiation in vitro.Using RNA-seq and MeRIP-seq, we generated the tascriptome and epitranscriptome data of undifferentited C2C12 myoblasts in growth medium (GM) and differentiated myotubes in differentitation medium for 4 days (D4).

overall_design: Differentially expression and m6A modification of RNA in myoblast and myotube

first: Zhendong

last: Xiao

first: Qi

first: Liting

last: Diao


title: AICAR regulate IEGs expression in ALL cells

city: MIAMI

first: Julio

middle: C

last: Barredo

state: Florida

address: 1580 NW 10th ave room

institute: University of Miami

summary: To identify genes transcriptionally regulated by AICAR under cellular stress, We treated NALM6 cells for 45 min with vehicle (DMSO) or AICAR (15 mM), and examined their RNA profile using RNA-Seq. The immediate early genes (IEGs) were identified as a subset of genes downregulated by AICAR.

overall_design: RNA-seq in NALM6 cells treated with vehicle or AICAR

first: Guangyan

last: Sun

first: Ana

last: Shvab

first: Guy

last: Leclerc

first: Bin

last: Li

first: Felipe

last: Beckedorff

first: Ramin

last: Shiekhattar


title: RNA-seq of parental MC38 and anti-PD-1 resistant MC38 subcutaneous tumors

city: Cambridge

first: Joon Sang

last: Lee

address: 270 Albany Street

department: Oncology

institute: Sanofi

summary: MC38 tumors resistant to anti-PD-1 treatment (MC38-resistant) were generated through serial in vivo passaging, and global gene expression analysis was used to compare resistant and parental tumors. MC38 and MC38-resistant tumors exhibited widespread changes in global gene expression.

overall_design: RNA-seq of parental MC38 (n=13) and anti-PD-1 resistant MC38 (n=12) subcutaneous tumors implanted in C57BL6 mice.

first: Marie

last: Bernardo

first: Timothy

middle: R

last: Wagenaar

first: Hui

last: Cao

first: Jack

last: Pollard

first: Joon


title: RNA-Sequencing of heart tissue obtained from cardiac specific-Dsg2-/- and wild-type (Dsg2+/+) mice at 2-weeks and 10-weeks of age

city: London

first: Keat-Eng

last: Ng

state: England

address: William Harvey Heart Centre

country: United Kingdom

institute: Queen Mary University of London

summary: We studied how loss of the desmosome associated protein, desmoglein-2 (Dsg2), in the heart leads to Arrhythmogenic Cardiomyopathy with particular interest in the early stages of disease progression. Mice expressing the cardiac αMHC-Cre promoter were crossed with Dsg2 floxed mice in which exon 4-5 of the Dsg2 gene was flanked by loxP sites, resulting in Cre-mediated excision of Dsg2 in cardiac myocytes. Wild type Dsg2+/+ (Cre-, Dsg2flx/flx) and knockout Dsg2-/- (Cre+, Dsg2flx/flx) mice were generated. RNA-seq was performed on heart tissue obtained from wild-type and Dsg2-/- mice at 2-weeks and 10-weeks of age.

first: Stephen

last: Murtough


title: CLOCKWORK ORANGE promotes CLOCK-CYCLE activation via the Drosophila ortholog of CLOCK INTERACING PROTEIN, CIRCADIAN (ChIP-Seq)

first: Paul

last: Hardin

summary: CWO reinforces PER-TIM repression of core clock gene transcription by antagonizing CLK-CYC binding to E-boxes, but also functions to promote CLK-CYC transcription of core clock genes. To determine the relationship between CWO and CLK-CYC binding across the genome, we identified CWO and CLK binding sites via ChIP-seq.

overall_design: ChIP-seq: to identify CWO target genes, HA antibody was used to IP CWO-HA from heads of cwo-HA; cwo5073 flies collected during transcriptional repression at Zeitgeber Time 2 (ZT2, where ZT0 is lights-on and ZT12 is lights-off during an LD cycle) and transcription activation at ZT14 for ChIP-seq analysis. CLK was IPed with anti-CLK antibody in parallel

first: Gustavo

last: Rivas

first: Jian

last: Zhou

first: Christine

last: Merlin


title: Maternally inherited piRNAs direct transient heterochromatin formation at active transposons during early Drosophila embryogenesis

first: Martin

middle: Heinrich

last: Fabry

state: Cambridgeshire

address: Li Ka Shing Centre, Robinson Way

department: Cancer Research UK, Cambridge Institute

institute: University of Cambridge

type: Non-coding RNA profiling by high throughput sequencing

summary: The piRNA pathway controls transposon expression in animal germ cells, thereby ensuring genome stability over generations. piRNAs are maternally deposited and required for proper transposon silencing in adult offspring. However, a long-standing question in the field is the precise function of maternally deposited piRNAs and its associated factors during embryogenesis. Here, we probe the spatio-temporal expression patterns of several piRNA pathway components during early stages of development. Amongst those, factors required for transcriptional gene silencing (TGS) showed ubiquitous abundance in somatic and pole cells throughout the first half of embryogenesis. We further analyzed the transcriptomes of various embryo stages and correlated these with the presence of selected chromatin marks. We found that a number of transposon families show bursts of transcription during early embryonic stages. Transposons heavily targeted by maternally deposited piRNAs accumulated repressive chromatin marks following their spike in expression. Furthermore, depletion of maternally deposited Piwi protein in early embryos resulted in increased expression of transposons targeted by inherited piRNAs and was accompanied by a strong loss of repressive chromatin marks at coding sequences. Overall, our data suggests a pivotal role for the piRNA pathway in transposon defence during Drosophila embryogenesis in somatic cells.

overall_design: RNA-Seq, ChIP-Seq, smallRNA-Seq and whole genome sequencing (WGS) experiments from Drosophila melanogaster embryo and adult tissues performed to study the impact of the piRNA pathway on genome integrity and transposon silencing during embryogenesis

first: Fabry

last: Martin H.

first: Falconio

last: Federica A.

first: Lythgoe

last: Emily

first: Joud

last: Fadwa

first: Czech

last: Benjamin

first: Hannon

last: Gregory J.


title: Fatty acid binding proteins shape the cellular response to activation of the glucocorticoid receptor

city: Parkville

first: Michelle

last: Halls

state: VIC

address: 399 Royal Parade

department: Drug Discovery Biology

country: Australia

institute: Monash Institute of Pharmaceutical Sciences, Monash University

summary: Glucocorticoids are steroid hormones that are essential for life in mammals. Therapeutically, they are some of the most cost-effective drugs for the treatment of inflammatory diseases ranging from skin rashes to COVID-19, but their use is limited by adverse effects. Glucocorticoids exert their effects via the glucocorticoid receptor, a type I nuclear hormone receptor which modulates gene expression. The transcriptional activity of some related, but nuclear restricted, type II nuclear hormone receptors can be enhanced by a family of intracellular transport proteins, the fatty acid binding proteins (FABPs). We find that the transcriptional activity of the GR can be altered by a sub-set of FABP family members dependent on the GR-ligand. The ability of some FABPs to selectively promote or limit the transcriptional activity of the GR in a ligand-dependent manner could facilitate the discovery of drugs that narrow GR activity to only the desired subset of therapeutically relevant genes.

overall_design: Effect of vehicle (DMSO) vs dexamethasone treatment on COS-7 cells transfected with the glucocorticoid receptor and vector control, glucocorticoid receptor and FABP1 or glucocorticoid receptor and FABP4. Samples are from four biological repeats of each condition (n=4).

last: Scanlon

first: Christopher

last: Porter


title: Exploiting volatile organic compounds as eco-friendly alternatives against the phytopathogenic fungus Thielaviopsis ethacetica

city: Campinas

first: Juliana

last: Oliveira

state: São Paulo

address: Giuseppe Máximo Scolfaro, 10.000

department: Brazilian Biorenewables National Laboratory (LNBR)

country: Brazil

institute: National Center for Research in Energy and Materials (CNPEM)

summary: In this study, we showed that three bacteria were able to inhibit the mycelial growth of the phytopathogenic fungus Thielaviopsis ethacetica, by the emission of microbial volatile organic compounds (mVOCs). Aiming to understand the molecular mechanisms of these interactions, we evaluated the transcriptomic response of T. ethacetica to the mVOCs produced by one of these bacterial isolates.

overall_design: Evaluation of the effect of bacterial volatiles on the transcriptome of the phytopathogenic fungus T. ethacetica. The RNA-seq experiment was carried out using 4 replicates in the treated condition (fungus + volatiles) and 4 replicates in the control condition (fungus only), totaling 8 samples.

first: Carla

last: Freitas

first: Aline

last: Mulato

last: Aricetti

first: Renato

last: Santos

first: Lucas

middle: F

last: Maciel

first: Gabriela

last: Persinoti

first: Henrique

last: Franco

middle: V


title: DNA methylation-based prediction of response to immune checkpoint inhibition in metastatic melanoma

city: Frankfurt am Main

first: Patrick

middle: Nikolaus

last: Harter

address: Heinrich-Hoffmann Strasse 7

department: Edinger Institute

institute: Goethe University

summary: A novel approach of reference-free deconvolution of large-scale DNA methylation data enabled to develop a machine learning classifier based on CpG sites, specific for Latent Methylation Components (LMC), that allowed for patient allocation to prognostic clusters. DNA methylation data was processed using reference-free analyses (MeDeCom) and reference-based computational tumor deconvolution (MethylCIBERSORT, LUMP).   These results demonstrate that LMC-based segregation of large-scale DNA methylation data is a promising tool for classifier development and treatment response estimation in cancer patients under targeted immunotherapy.

overall_design: 65 specimens of melanoma skin metastasis were analyzed using the Illumina Infinium MethylationEPIC BeadChip all patients belong to AJCC Stage IV

first: Katharina

last: Filipski

middle: N


title: RNA-seq of H1299 overexpressing GFP(control) and SALL4

status: Public on Jul 21 2021

city: Singapore

first: Daniel

middle: G

last: Tenen

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

summary: Gene expression profile was determined in H1299 cells after SALL4 overexpression compared with GFP overexpression to identify potential gene targets and biology pathways that responsible for engineered SALL4 dependency of its negative cells

overall_design: H1299 cells stable over-expressing GFP and SALL4 were used.  Subsequently, paired-end RNA-seq was performed for the samples. RNA-seq reads of each sample were mapped to hg19 using the STAR aligner.

first: Chong

last: Gao

first: Junyu

last: Yang

first: Kalpana

last: Kumari

first: Xi

last: Tian


title: Dissecting transcriptional and chromatin accessibility heterogeneity of proliferating cone precursors in human retinoblastoma tumours by single cell sequencing

status: Public on Jul 26 2021

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

institute: Newcastle University

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

overall_design: Refer to individual Series


title: Long noncoding RNA lnc-LEMGC combines with DNA-PKcs to suppress gastric cancer metastasis

city: Jinan

first: Peng

address: Wen Hua Xi Road 44

institute: Shandong University

summary: Long non-coding RNAs (lncRNAs) play important roles in cancer development and progression; however, their contributions to gastric cancer metastasis remain largely unknown. By lncRNA microarray screening, our study showed that 10 lncRNAs are dysregulated in gastric cancer tissues with or without lymph node metastasis, of which lnc-LEMGC ranks as one of the most significantly downregulated lncRNAs. Lnc-LEMGC inhibited cell migration and invasion both in vitro and in vivo, by combining with protein DNA-PKcs. Importantly, nucleotides 1,300–1,800 of lnc-LEMGC prevented DNA-PKcs phosphorylation of serine 2056 and partially abrogated the effects of downstream effectors, transforming growth factor alpha, EGFR, Src kinase, paxillin, and focal adhesion kinase, in the epidermal growth factor receptor (EGFR) pathway. The results of this study extend our knowledge of lncRNA’s molecular mechanisms, in which lnc-LEMGC functions by directly suppressing the phosphorylation of its combined protein DNA-PKcs and inactivating the DNA-PKcs downstream EGFR signaling.

overall_design: We transfected GC SGC7901 cells with lnc-LEMGC vector or NC for 48h. We then used the Whole Human Genome Oligo Microarray Assay (KangChen Bio-Tech, Shanghai, China) to analyze differential gene expression between the lnc-LEMGC-overexpression SGC7901 cells and negative control cells.


title: Cohesin regulates homology search during recombinational DNA repair

city: PARIS

first: Helene

last: Bordelet

address: 25-28 Rue du Dr Roux

institute: Institut Pasteur


title: Gene expression analysis of HP1C mutants in D. melanogaster

city: Birmingham

first: Nicole

last: Riddle

state: AL

address: 506 10th St S

institute: University of Alabama at Birmingham

summary: We profile gene expression changes in a mutant strain lacking the D. melanogaster HP1 homolog HP1C at the third instar larval stage. Compared to the yw control strain (previously published) several hundred genes are deregulated.

overall_design: Examination of gene expression in two genotypes

first: N


title: AMPK activation reverts mouse epiblast stem cells to naïve state

city: KYOTO

first: LIU

last: YAJING

address: 53 KAWAHARA-CHO,SHOGOIN,SAKYO-KU

department: STEM CELL DIFFERENTIATION

country: Japan

institute: CIRA

summary: Reversion from primed to naïve pluripotent status has been achieved by various signaling manipulation, but it is still unclear what signaling is the actual driving force to get over the hurdle from primed to naïve pluripotency. We previously reported that activation of AMP kinase (AMPK) contributed to maintenance of naïve pluripotency. Here, we further show that AMPK activators, AICAR, A769662 or metformin, can induce the reversion of primed mouse epiblast stem cells (mEpiSCs) to naïve pluripotent state. Primed mEpiSCs in our naïve cell culture condition with leukemia inhibitory factor (LIF) and 2 kinase inhibitors (2i) (2iL) never gave rise to naïve state cells. Addition of AICAR alone even in the absence of 2iL or either of AMPK inhibitors with LIF induced appearance of naïve-like cells from primed mEpiSCs. Through maintenance and passages of these cells in 2iL condition, clear naïve-like morphology colonies were purely obtained. They showed core naïve protein expression, and global naïve gene expression profiles. These cells contributed to chimeric mice including germline transmission. Inhibition of p38 signaling abolished the AMPK-elicited reversion and forced activation of p38 in primed mEpiSCs partially reproduced the naïve cell induction, suggesting that p38 is one of the critical downstream in AMPK activation. Single cell RNA-seq analysis under AICAR stimulation successfully demonstrated the reversion process with appearance of intermediate naïve-like population. AMPK pathway should be a novel critical driving force in reversion of primed to naïve pluripotency.

overall_design:
We analyzed single cell RNA-seq profiles of naïve mESCs (500 cells), primed mEpiSCs (500 cells), AICRA+LIF d8 (9000 cells), AICAR+LIF d16 (9000 cells) and AICAR+LIF reverted d16+10p (1000 cells)，we used combination of Biotin-CD9 and Biotin-CD63 (Biolegend) conjunction with TotalSeq™-A095(1-5) PE Streptavidin, respectively. naïve mESCs tagged with A951,primed mEpiSCs tagged with A952,AICRA+LIF d8 tagged with A953, AICAR+LIF d16 tagged with A954, AICAR+LIF reverted d16+10p tagged with A955.
5 samples:
A951: Naïve mESCs (Rex1-GFP)
A952: Primed mEpiSCs (Oct4GIP)
A953: AICAR+LIF d8
A954: AICAR+LIF d16
A955: AICAR+LIF reverted d16+10p

first: YaJing

last: Liu

first: Junko

last: Yamane

first: Wataru

last: Fujibuchi

first: Abe

last: Sugimoto


title: Cohesin regulates homology search during recombinational DNA repair [ChIP-Seq]

summary: Homologous recombination (HR) is an ubiquitous DNA double-strand break (DSB) repair mechanism. It entails a homology search step, carried out along a conserved RecA/Rad51-ssDNA nucleoprotein filament (NPF) assembled on each DSB ends. In contrast to the extensive knowledge of DNA damage checkpoint (DDC)-induced changes in chromatin composition and mobility,  the questions of if, how, and to what extent a DSB impacts the spatial organization of chromatin, and whether this organization in turn influences the homology search process, remain ill-defined. Here we characterize two layers of spatial chromatin reorganization following DSB formation in S. cerevisiae. While cohesin folds chromosomes into cohesive arrays of ~20 kb-long chromatin loops as cells arrest in G2/M, the DSB-flanking regions interact locally in a resection- and 9-1-1 clamp-dependent manner, independently of cohesin, Mec1ATR, Rad52 and Rad51. This local structure blocks cohesin progression, constraining the DSB region at the base of a loop. Functionally, cohesin promotes DSB-dsDNA interactions and donor identification in cis, while inhibiting them in trans. This study identifies multiple direct and indirect ways by which cohesin regulates homology search during HR repair.

overall_design: Scc1-Pk/HA ChIP-seq analysis were performed on yeast pellets collected 4 hours after DSB induced by galactose addition on several samples WT and mutants. Scc1-Pk ChIP-seq IP and input in WT (no DSB + nocodazole), WT (DSB 4hrs), WT and rad17 (DSB 4 hrs + nocodazole) were performed once. Scc1-HA ChIP-seq IP and input in WT, rad17, pds5 and pds5 rad17 (DSB 4 hrs + nocodazole) were performed twice and only once for WT (no DSB + nocodazole) and untagged control. In order to compare quantitatively the samples, the ChIP-seq experiments are calibrated with Candida glabrata as described in Hu et al. 2015.

first: Piazza

last: Aurele

first: Bordelet

last: Helene

first: Dumont

last: Agnes

first: Thierry

first: Savocco

last: Jerome

first: Girard

last: Fabien

first: Koszul

last: Romain


title: Transfer of small RNA from extracellular vesicles secreted by primary human airway epithelial cells to Pseudomonas aeruginosa

city: Hanover

first: Katja

last: Koeppen

state: NH

address: 504 Remsen

institute: Geisel School of Medicine at Dartmouth

summary: P. aeruginosa were exposed to extracellular vesicles (EVs) secreted by primary human airway epithelial cells from 3 donors or PBS vehicle control for 6 h. Total RNA was isolated, small RNA libraries were prepared with the QIAseq smRNA kit (Qiagen) and 75-bp single-end reads were generated using Illumina MiniSeq. To assess transfer of human EV small RNAs to P. aeruginosa, sequences that did not map to the PA14 reference genome were aligned to the human genome.

overall_design: P. aeruginosa (1.5*E+07 CFU) were exposed to PBS vehicle control or EVs (5E+09 EV/ml) for 6 h. To avoid possible carry-over of EVs (and miRNA) attached to the outside of the bacteria, the bacteria were washed with PBS and the bacterial outer membrane was lysed with EDTA to release periplasmic contents and factors associated with the bacterial outer membrane and periplasm (77-79). The cells were then washed again in PBS, and cytoplasmic RNA was harvested after lysis of bacterial cell wall and inner membrane. Total RNA was isolated with the miRNeasy Mini Kit (Qiagen, Germantown, MD, Cat. # 217004), including the on-column DNA digestion. Sequencing libraries were prepared with the QIAseq smRNA kit (Qiagen) and 75-bp single-end reads were generated using an Illumina MiniSeq. Sequences that did not map to the PA14 reference genome were aligned to the human genome using CLC Genomics Workbench software (Qiagen).

first: Fred

middle: W

last: Kolling


title: Insulin and IGF-1 Receptors Regulate Complex-I Dependent Mitochondrial Bioenergetics and Supercomplexes via FoxOs in Muscle

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Decreased skeletal muscle strength and mitochondrial dysfunction are characteristic of diabetes. Action of insulin through insulin receptor (IR) and IGF-1 receptor (IGF1R) maintain muscle mass via suppression of FoxOs, but whether FoxO activation coordinates atrophy in concert with mitochondrial dysfunction is unknown. In the absence of systemic glucose or lipid abnormalities, muscle-specific IR knockout (MIRKO) or combined IR/IGF1R knockout (MIGIRKO) impaired mitochondrial respiration, decreased ATP production, and increased ROS. These mitochondrial abnormalities were not present in muscle-specific IR/IGF1R and FoxO1/3/4 quintuple knockout mice (QKO). Although autophagy was increased when IR/IGF1R were deleted in muscle, mitophagy was not increased. Mechanistically, RNA-seq revealed that complex-I core subunits were decreased in MIGIRKO muscle, and these were reversed with FoxO knockout. Thus, insulin-deficient diabetes or loss of insulin/IGF-1 action in muscle decreases complex-I driven mitochondrial respiration and supercomplex assembly, in part by FoxO-mediated repression of Complex-I subunit expression.

overall_design: Male mice were used in all animal studies unless stated otherwise. Muscle-specific IR knock-out (MIRKO), IGF1R knock-out (MIGF1RKO) combined IR/IGF1R knock-out (MIGIRKO), and combined IR/IGF1R with FoxO1/3/4 quintuple knock-out (QKO) mice were generated as previously described (PMID: 25981038, 27525440). Briefly, MIRKO, MIGIRKO, and QKO mice were generated using Acta1-Cre (stock 006149; Jackson Laboratory).  Each mouse line was maintained in a separate colony and floxed littermates were used as controls in each experiment. All animals were on a mixed background containing C57Blk6, C57Blk6J, and 129 strains and as such may contain random mutations in the Nnt (Nicotinamide nucleotide transhydrogenase) gene.  A post-hoc determination of Nnt genotype revealed that MIGIRKO and IRIGFRlox were heterozygous, whereas other strains (MIRKO, IRlox, QKO, and Qlox were mixed homozygous and heterozygous for Nnt gene (data not shown), but did not correlate with the mitochondrial differences demonstrated in our study.

first: Gourav

last: Bhardwaj

first: Brian

last: O’Neill


title: small RNAseq of extracellular vesicles secreted by primary human airway epithelial cells

summary: Characterization of the small RNA content of extracellular vesicles isolated from cell culture supernatants of primary human airway epithelial cells from 3 donors.

overall_design: The sequencing of EV small RNA content was performed by System Biosciences. EVs were harvested from 15 ml cell culture supernatants using the ExoQuick-TC EV isolation kit. Total EV RNA was isolated with the SeraMir Exosome RNA Purification Column kit (System Biosciences, Cat. #RA808A-1) according to the manufacturer’s instructions. For each sample, 1 µl of the final RNA eluate was used for measurement of small RNA concentration by Agilent Bioanalyzer Small RNA Assay using the Bioanalyzer 2100 Expert instrument (Agilent Technologies, Santa Clara, CA, Cat. # 5067-1548). Small RNA libraries were constructed with the CleanTag Small RNA Library Preparation Kit (TriLink Biotechnologies, San Diego, CA, Cat. # L-3206) according to the manufacturer's protocol. The final purified library was quantified with High Sensitivity DNA Reagents (Agilent Technologies, PO # G2933-85004) and High Sensitivity DNA Chips (Agilent Technologies, PO # 5067-4626). The libraries were pooled, and the 140 bp to 300 bp region was size selected on an 8% TBE gel (Thermo Fisher Scientific, Ref. # EC6215). The size selected library was quantified with High Sensitivity DNA 1000 Screen Tape (Agilent Technologies, PO # 5067-5584), High Sensitivity D1000 reagents (Agilent Technologies, PO # 5067-5585), and the TailorMix HT1 qPCR assay (SeqMatic, Fremont, CA, Cat. # TM-505), followed by a NextSeq High Output single-end sequencing run at SR75 using NextSeq 500/550 High Output v2 kit (Illumina, San Diego, CA, Cat. # FC-404-2005) according to the manufacturer's instructions.


title: Single-cell RNA-seq in pancreatic islets of Tg7 mice

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: Objective: beta-cell dedifferentiation has been revealed as a pathological mechanism underlying pancreatic dysfunction in diabetes. However, exactly how such dedifferentiation process affects beta-cell gene expression and islet microenvironment remains incompletely understood Method: We performed single-cell RNA-Sequencing (RNA-seq) in islets obtained from beta-cell-specific miR-7a2 overexpressing mice (Tg7), a murine model of beta-cell dedifferentiation and diabetes. Results: Single-cell RNA-seq revealed that beta-cell dedifferentiation is associated with the induction of genes associated with epithelial to mesenchymal transition (EMT) specifically in beta-cells of diabetic (12-week-old) Tg7 mice. These molecular changes are associated with a weakening of beta-cell:beta-cell contacts, increased extracellular matrix (ECM) deposition and TGFb-dependent islet fibrosis. We find that the mesenchymal reprogramming of beta-cells is explained in part by the downregulation of Pdx1 and its inability to regulate a myriad of target genes preserving the epithelial cell phenotype. Notable among epithelial genes transactivated by Pdx1 is Ovol2, a transcriptional repressor of the EMT transcription factor ZEB2. Following compromised beta-cell identity, the reduction of Pdx1 mRNA levels decreases  Ovol2 gene expression, which triggers mesenchymal reprogramming of beta-cells through the induction of Zeb2. Finally, we provided evidence that EMT signalling associated with the upregulation of Zeb2 expression is a molecular feature of islet of T2D subjects. Conclusions: Our study indicates that beta-cell dedifferentiation triggers a chronic response to tissue injury, which alters the pancreatic islet microenvironment and contribute to islet fibrosis. It suggests that regulators of EMT signalling may represent novel therapeutic targets for the treatment of beta-cell dysfunction and fibrosis in T2D.

overall_design: We performed single-cell RNA-Sequencing (RNA-seq) in islets obtained from beta-cell-specific miR-7a2 overexpressing mice (Tg7), a murine model of beta-cell dedifferentiation and diabetes. These analyses were performed with islets isolated from 12-week-old male Tg7 mice and littermate controls.

first: Daniel

middle: S

last: de Jesus

first: Yi-Fang

last: Wang

first: Catherine

last: Chahrour

first: Mathieu

last: Latreille


title: Loss of FOXC1 contributes to the corneal epithelial fate switch and pathogenesis

city: Bengbu

first: Mingsen

last: Li

state: Anhui

address: No. 2600, Donghai Avenue, Bengbu City, Anhui Province

department: Interdisciplinary Eye Research Institute (EYE-X Institute)

institute: Bengbu Medical University

summary: Forkhead box C1 (FOXC1) is required for neural crest and ocular development, and mutations in FOXC1 lead to inherited Axenfeld–Rieger syndrome. Here, we find that FOXC1 and paired box 6 (PAX6) are co-expressed in the human limbus and central corneal epithelium. Deficiency of FOXC1 and alternation in epithelial features occur in patients with corneal ulcers. FOXC1 governs the fate of the corneal epithelium by directly binding to lineage-specific open promoters or enhancers marked by H3K4me2. FOXC1 depletion not only activates the keratinization pathway and reprograms corneal epithelial cells into skin-like epithelial cells but also disrupts the collagen metabolic process and interferon signaling pathways. Loss of interferon regulatory factor 1 (IRF1) and PAX6 induced by FOXC1 dysfunction is linked to the corneal ulcer. Collectively, our results reveal a FOXC1-mediated regulatory network responsible for corneal epithelial homeostasis and provide a potential therapeutic target for corneal ulcer.

overall_design: ATAC-seq and ChIP-seq for H3K4me2 and FOXC1 in wildtype limbal stem cells (LSCs). RNA-seq for wildtype LSCs and 3D-differentiated corneal epithelial cells (dCECs). RNA-seq for scrambled shRNA- and shFOXC1-treated LSCs. RNA-seq for scrambled shRNA- and shFOXC1-treated dCESs.


title: STL427944 suppresses FOXM1 via nuclear export and subsequent autophagic degradation

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

institute: University of Illinois at Chicago

summary: FOXM1 transcription factor is an oncogene and a crucial regulator of cancer chemoresistance. Existing pharmacological FOXM1 inhibitors attenuate resistance of cancer cells to treatment but exhibit insufficient specificity. We performed in silico screening of small molecules from NIH LINCS database to identify STL427944 compound that suppresses FOXM1 through a novel two-step mechanism. STL427944 treatment induces relocalization of nuclear FOXM1 protein to cytoplasm, where it is subsequently degraded in an autophagosome-dependent manner. Human cancer cells treated with STL427944 exhibit increased sensitivity to cytotoxic effects of conventional chemotherapeutic agents. Transcriptome-based analysis of STL427944-induced gene expression changes revealed prominent suppression of gene signatures characteristic for FOXM1 and its downstream targets but no significant changes in other important regulatory pathways, thereby suggesting high selectivity of STL427944 towards FOXM1. We expect that STL427944 or its derivatives may be used in combination with different chemotherapeutical drugs to overcome tumor chemoresistance and improve anti-cancer treatment efficacy.

overall_design: For each experimental model and condition, two biological replicates were analyzed. Control samples were treated with vehicle alone (DMSO), with vehicle percentage not exceeding 0.3%.

first: Mikhail

last: Chesnokov

first: Marianna

last: Halasi

first: Soheila

last: Borhani

first: Zarema

last: Arbieva

first: Carlos

last: Camacho

first: Rick

last: Oerlemans

first: Irum

last: Khan

first: Andrei

middle: L

last: Gartel


title: Effects of HIV protein Tat on  macrophage transcriptome

city: RIVERSIDE

first: ZHAOJIE

last: MENG

state: CA

address: 900 UNIVERSITY AVENUE

institute: UNIVERSITY OF CALIFORNIA, RIVERSIDE

summary:
Purpose: To investigate the impact of HIV protein Tat on macrophage transcriptome related to atherosclerosis development
Methods: Peritoneal macrophages were isolated from myeloid specific IKKβ deficient LDLR-/- (IKKβΔMyeLDLR-/-) mice and their littermates (IKKβF/FLDLR-/-). Then the macrophages were treated with HIV protein Tat  or control for 12 hr. Total RNA was extracted for RNAseq
Results: HIV protein Tat treatment induces 2640 differentially expressed genes (DEGs) with false discovery rate (FDR) < 1 % and fold change >  3 in control macrophages.  Those DEGs enriched in several biological processes that may contribute to atherogenesis. FAIME analysis demonstrated higher geneset scores of those GO terms in the Tat-treated macrophages from IKKβF/FLDLR-/- mice compared with the control ones. IKKβ deletion resulted in loss of geneset score in the macrophages of IKKβΔMyeLDLR-/- treated with HIV Tat.
Conclusions: These results indicate that HIV protein Tat may affect many genes in macrophages related atherosclerosis development through IKKβ signaling.

overall_design: Macrophagic mRNA profiles of control and IKKβ-deficient macrophages after 12-hour treatment of HIV protein Tat

first: Zhaojie

last: Meng

first: Tong

last: Zhou

first: Changcheng


title: Cohesin regulates homology search during recombinational DNA repair [Hi-C]

first: Helene

last: Bordelet

overall_design: Global and local genome organisation upon DSB damage was assessed by collecting cells for Hi-C 2, 4 and 6 hours after DSB induction. Some Hi-C were also performed before DSB induction. These experiments were performed in WT and mutants to determine the factors responsible for these global and local genome organisation upon DSB induction.

first: Piazza

last: Aurele

first: Bordelet

last: Helene

first: Dumont

last: Agnes

first: Thierry

first: Savocco

last: Jerome

first: Girard

last: Fabien

first: Koszul

last: Romain


title: Single-cell RNA-seq in mouse kidneys after IRI

city: Durham

first: Yoshihiko

last: Kobayashi

state: NC

address: 307 Research Dr

department: Cell Biology

institute: Duke University

summary: We performed Drop-seq using dissociated total kidney cells to identify cell types, gene expression patterns and signaling pathways in mouse kidneys after IRI.

overall_design: Single-cell RNA-seq (Drop-seq) in mouse kidneys after IRI

first: Shintaro

last: Ide

first: Purushothama Rao

last: Tata

first: Tomokazu

last: Souma


title: Bulk RNA-seq in pancreatic islets of Tg7 mice

first: LMS

last: Bioinformatics Core

summary: Objective: beta-cell dedifferentiation has been revealed as a pathological mechanism underlying pancreatic dysfunction in diabetes. However, exactly how such dedifferentiation process affects beta-cell gene expression and islet microenvironment remains incompletely understood Method: We performed bulk in islets obtained from beta-cell-specific miR-7a2 overexpressing mice (Tg7), a murine model of beta-cell dedifferentiation and diabetes.  Results: Bulk RNA-seq revealed that beta-cell dedifferentiation is associated with the induction of genes associated with epithelial to mesenchymal transition (EMT) in pre-diabetic (2-week-old) and diabetic (12-week-old) Tg7mice. These molecular changes are associated with a weakening of beta-cell:beta-cell contacts, increased extracellular matrix (ECM) deposition and TGFb-dependent islet fibrosis. We find that the mesenchymal reprogramming of beta-cells is explained in part by the downregulation of Pdx1 and its inability to regulate a myriad of target genes preserving the epithelial cell phenotype. Notable among epithelial genes transactivated by Pdx1 is Ovol2, a transcriptional repressor of the EMT transcription factor ZEB2. Following compromised beta-cell identity, the reduction of Pdx1 mRNA levels decreases  Ovol2 gene expression, which triggers mesenchymal reprogramming of beta-cells through the induction of Zeb2. Finally, we provided evidence that EMT signalling associated with the upregulation of Zeb2 expression is a molecular feature of islet of T2D subjects. Conclusions: Our study indicates that beta-cell dedifferentiation triggers a chronic response to tissue injury, which alters the pancreatic islet microenvironment and contribute to islet fibrosis. It suggests that regulators of EMT signalling may represent novel therapeutic targets for the treatment of beta-cell dysfunction and fibrosis in T2D.

overall_design: We performed bulk RNA-Sequencing (RNA-seq) in islets obtained from beta-cell-specific miR-7a2 overexpressing mice (Tg7), a murine model of beta-cell dedifferentiation and diabetes. These were done with islets isolated from 2w and 12-week-old male Tg7 mice and littermate controls.

first: Daniel

last: de Jesus

first: Yi-Fang

last: Wang

first: Catherine

last: Chahrour

first: Mathieu

last: Latreille


title: Generation of eosinophils with potent antitumor activity from human pluripotent stem cells

city: Beijing

first: Ligong

last: Chen

state: China

address: No.1, Qinghuayuan, Haidian District

department: School of Pharmaceutical Sciences

institute: Tsinghua University

summary: The efficient infiltration of immune cells into tumors is a prerequisite for effective cancer immunotherapy. Eosinophils have been demonstrated to be able to quickly infiltrate tumors and recruit other immune effector cells to enhance the effects of antitumor treatments, indicating that eosinophils might provide the key to more effective cancer immunotherapies. In this study, we established a stepwise differentiation approach for generating large numbers of functional EPX+ eosinophils from human pluripotent stem cells (hPSCs) at near-100% purity. These hPSC-derived cells not only displayed eosinophil-specific phenotypes and expressed cytotoxic granular proteins, but more importantly, could also kill tumor cells in vitro, quickly infiltrate solid tumors in vivo and significantly suppress tumor growth in colorectal carcinoma and ovarian cancer xenograft mouse models. Our study therefore opens new avenues for the development of eosinophil-based immunotherapies to treat cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
our goal was to compare and analysis the transcriptome of eosinophils from PSC with human naïve eosinophils from Cord blood.

This series includes tumor samples from cancer xenograft mice injected with CAR-T cells and tumor samples from cancer xenograft mice injected with the combination of CAR-T cells and PSC-derived eosinophils (E).

first: Weifeng

last: Lai

first: Huangfan

last: Xie

first: Yuting

last: Liu

first: Feng

last: Zheng

first: Jian

last: Song

first: Yingfeng

last: Zhang

first: Xue

last: Gao

first: Ming

last: Yin

first: Chengyan

first: Hongkui

last: Deng


first: YAJING

last: LIU

address: KAWARAMATI53, SHIOGOIN,SAKYOUKU

institute: Center for iPS Cell Research and Application (CiRA), Kyoto University

summary: Reversion from primed to naïve pluripotent status has been achieved by various signaling manipulation, but it is still unclear what signaling is the actual driving force to get over the hurdle from primed to naïve pluripotency. We previously reported that activation of AMP kinase (AMPK) contributed to maintenance of naïve pluripotency. Here, we further show that AMPK activators, AICAR, A769662 or metformin, can induce the reversion of primed mouse epiblast stem cells (mEpiSCs) to naïve pluripotent state. Primed mEpiSCs in our naïve cell culture condition with leukemia inhibitory factor (LIF) and 2 kinase inhibitors (2i) (2iL) never gave rise to naïve state cells. Addition of AICAR alone even in the absence of 2iL or either of AMPK inhibitors with LIF induced appearance of naïve-like cells from primed mEpiSCs. Through maintenance and passages of these cells in 2iL condition, clear naïve-like morphology colonies were purely obtained. They showed core naïve protein expression, and global naïve gene expression profiles. These cells contributed to chimeric mice including germline transmission. Inhibition of p38 signaling abolished the AMPK-elicited reversion and forced activation of p38 in primed mEpiSCs partially reproduced the naïve cell induction, suggesting that p38 is one of the critical downstream in AMPK activation. AMPK pathway should be a novel critical driving force in reversion of primed to naïve pluripotency.

overall_design: We analyzed gene expression profile of naive mESCs, primed mEpiSCs and reverted cells by different AMPK activator

first: Wataru

last: Fujibuchi

first: Junko

last: Yamane

first: Kentai

last: Kobayashi


title: Folding of cohesin's coiled coil is important for Scc2/4-induced association with chromosomes

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

institute: University of Oxford

summary: Cohesin’s association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being ‘clamped’ by Scc2 and ATP-dependent engagement of cohesin’s Smc1 and Smc3 head domains. Scc2’s replacement by Pds5 abrogates cohesin’s ATPase and has an important role in halting DNA loop extrusion. The ATPase domains of all SMC proteins are separated from their hinge dimerisation domains by 50 nm long coiled coils, which have been observed to zip up along their entire length and fold around an elbow, thereby greatly shortening the distance between hinges and ATPase heads. Whether folding exists in vivo or has any physiological importance is not known. We present here a cryo-EM structure of the apo form of cohesin that reveals the structure of folded and zipped up coils in unprecedented detail and shows that Scc2 can associate with Smc1’s ATPase head even when it is fully disengaged from that of Smc3. Using cysteine-specific cross-linking, we show that cohesin’s coiled coils are frequently folded in vivo, including when cohesin holds sister chromatids together. Moreover, we describe a mutation (SMC1D588Y) within Smc1’s hinge that alters how Scc2 and Pds5 interact with Smc1’s hinge and that enables Scc2 to support loading in the absence of its normal partner Scc4. The mutant phenotype of loading without Scc4 is only explicable if loading depends on an association between Scc2/4 and cohesin’s hinge, which in turn requires coiled coil folding.

overall_design: Characterisation of the effect of WT and mutant cohesin complexes and associated factors on loading onto chromosomes in S. cerevisiae, assessed by calibrated ChIP-seq on an Ion Torrent Proton (Life Technologies)

first: Naomi

last: Petela


title: Regnase-1 suppresses TCF-1+ precursor exhausted T cell formation to limit CAR T cell responses against ALL [WGBS]

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

summary: Defciency of Regnase-1 enhances CAR-T cell persistence and anti-tumor ability

overall_design: Regnase-1 deficient CAR T cells demonstrated an enhanced anti-tumor ability in an immune-competent murine model and xenograft model of B cell acute lymphoblastic leukemia. Characterization of the Regnase-1-deficient CAR T cells was consistent with TCF-1+ precursor exhausted cells and idenitfy Regnase-1 as a key player in CAR-T cell longevity.

first: Wenting

first: Jun

last: Wei

first: Caitlin

last: Zebley

first: Benjamin

last: Youngblood


title: Partial depletion of SRSF1 rescued the C9ORF72-repeat neurodegeneration-associated locomotor deficits in G4C2x36 Drosophila lines

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

institute: University of Sheffield

summary:
In this study we investigated the role of SRSF1 in mitigating locomotor defect in C9ORF72-ALS/FTD Drosophila lines. We analysed the transcriptomes of Drosophila heads from the same lines: (i) control flies expressing 3 G4C2 repeats and a luciferase-RNAi control (G4C2x3 + C-RNAi); (ii) C9ORF72-ALS/FTD model expressing 36 G4C2 repeats and the RNAi control (G4C2x36 + C-RNAi); (iii) C9ORF72-ALS/FTD-neuroprotected flies expressing 36 G4C2 repeats and the disrupted SRSF1 allele (G4C2x36 + ΔSRSF1).
RNA samples were profiled using Drosophila 3' IVT gene expression Affymetrix microarrays prior to qRT-PCR validation of the SRSF1 depletion in neuroprotected flies. This study is part of a larger study that investigates the mitigating role of SRSF1 at whole-genome level to detect transcriptomal alterations and neuronal hyperexcitability in C9ORF72-linked amyotrophic lateral sclerosis.

overall_design: We used RNA from Drosophila heads belonging to the same lines. The over we analysed 9 Affymetrix GeneChip. The experimental design consisted in: (i) 3 samples from control flies expressing 3 G4C2 repeats and a luciferase-RNAi control (G4C2x3 + C-RNAi); (ii) 3 samples C9ORF72-ALS/FTD model expressing 36 G4C2 repeats and the RNAi control (G4C2x36 + C-RNAi); (iii) 3 samples C9ORF72-ALS/FTD-neuroprotected flies expressing 36 G4C2 repeats and the disrupted SRSF1 allele (G4C2x36 + ΔSRSF1).

first: Guillaume

last: Hautbergue


title: Reinforcement of DNA methylation in CHH context through RNA-directed DNA methylation ensures sexual reproduction in rice [RNA-seq]

city: Nanjing

first: Lili

last: Wang

address: Weigang No.1

institute: Nanjing Agricultural University

summary: DNA methylation is an important epigenetic mark that regulates the expression of genes and transposons. RNA-directed DNA methylation (RdDM) is the main molecular pathway responsible for de novo DNA methylation in plants. Although the mechanism of RdDM has been well understood in Arabidopsis, mutations in RdDM genes cause no visible developmental defects in Arabidopsis. Here, we isolated and cloned Five Elements Mountain 1 (FEM1), which encodes RNA-dependent RNA polymerase 2 in rice. Mutation in OsRDR2 abolished the accumulation of 24-nt small interfering RNAs, and consequently substantially decreased genome-wide CHH methylation levels. Moreover, male and female reproductive development was disturbed, which led to the sterility of osrdr2 mutants. We discovered that OsRDR2-dependent DNA methylation likely regulates the expression of multiple key genes involved in stamen development and meiosis. In wild-type (WT) plants but not in osrdr2 mutants, genome-wide CHH DNA methylation levels were greater in panicles, stamens, and pistils than in seedlings. The global increase of methylation in reproductive organs of the WT was mainly explained by the enhancement of RdDM activity including OsRDR2 activity. Our results, which revealed a global increase in DNA methylation through enhancement of RdDM activity in reproductive organs, demonstrate the crucial role of OsRDR2 in the sexual reproduction of rice.

overall_design: Transcriptome sequencing

first: Dong-Lei

last: Yang


title: Reinforcement of DNA methylation in CHH context through RNA-directed DNA methylation ensures sexual reproduction in rice [sRNA-seq]

sample_organism:
Oryza sativa
Oryza sativa Japonica Group

overall_design: small RNA sequencing data


title: Reinforcement of DNA methylation in CHH context through RNA-directed DNA methylation ensures sexual reproduction in rice [Bisulfite-seq]

overall_design: whole genome wide DNA methylation data by bisulfite sequencing


title: Reinforcement of DNA methylation in CHH context through  RNA-directed DNA methylation ensures sexual reproduction in rice

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

platform_organism:
Oryza sativa
Oryza sativa Japonica Group

overall_design: Refer to individual Series


title: ATAC-seq of the following human primary CD4 T cell subsets: GM-CSF producing, GM-CSF negative, bulk, memory and naive CD4 T cells.

city: Stockholm

first: Szabolcs

last: Éliás

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institute

summary: Above primary T cell subsets were isolated by magnetic isolation (including GM-CSF capture and secretion assay) from peripheral blood of 5 to 6 human healthy donors. Genomic DNA (and total RNA for an accompanying dataset) was extracted and processed for ATAC-seq to determine DNA accessibility. By integration of ATAC-seq data with corresponding RNA-seq data we generated a novel gene regulatory network of human GM-CSF producing and memory T helper cells.

overall_design: Single-end ATAC-seq analysis of 4-5 different CD4 T cell populations from 6 biological replicates (donors) and 2-3 technical replicates.

last: Elias

first: Jesper

last: Tegner


title: mRNA-seq of the following human primary CD4 T cell subsets: GM-CSF producing, GM-CSF negative, bulk, memory and naive CD4 T cells.

summary: Above primary T cell subsets were isolated by magnetic isolation (including GM-CSF capture and secretion assay) from peripheral blood of 5 to 6 human healthy donors. Total RNA (and genomic DNA for an accompanying dataset) was extracted for transcriptome analysis. By integration of RNA-seq data with corresponding ATAC-seq data we generated a novel gene regulatory network of human GM-CSF producing and memory T helper cells.

overall_design: Paired-end mRNA-seq analysis of 4-5 different CD4 T cell populations from 6 biological replicates (donors).


title: Mapping targets for small nucleolar RNAs in human cells

city: Edinburgh

first: Hywel

last: Dunn-Davies

address: Max Born Crescent

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh


title: Mapping targets for small nucleolar RNAs in human cells [CLASH/FLASH]

summary: We report the identification of potential novel RNA targets for box C/D snoRNAs in human HEK293 cells, using the approaches of UV crosslinking and sequencing of hybrids (CLASH), and formaldehyde crosslinking and sequencing of hybrids (FLASH).

overall_design: 18 different CLASH or FLASH experiments were carried out on human HEK293 cells, with Fibrillarin and NOP56 used as bait proteins.

first: Tatiana

last: Dudnakova

first: Jean-Louis

last: Langhendries

first: Nicholas

last: Watkins

first: Denis

last: Lafontaine

first: David

last: Tollervey


title: ATAC-seq and mRNA-seq  of the following human primary CD4 T cell subsets: GM-CSF producing, GM-CSF negative, bulk, memory and naive CD4 T cells.


title: Mapping targets for small nucleolar RNAs in human cells [RNA-seq]

summary: To study the functional role of U3 interactions we depleted U3 in HEK cells with morpholino oligo

overall_design: Samples subjected to U3 knockdown over 2 and 3 days were sequenced in triplicate, and differential expression analysis was performed in comparison to mock controls


title: A new understanding of the molecular pathway in human keloid fibroblasts and development of a novel treatment

city: Clayton

first: Seungmin

last: Ham

state: Victoria

address: 27-31, Wright Street

department: Obstetrics and Gynaecology

institute: Monash University

summary: The goals of this study are to compare differential gene expression of normal and keloid fibroblasts with/without treatment using RNA sequencing (Day 1 and 5)

overall_design:
RNA profiles of human normal and keloid fibroblasts were generated by deep sequencing, in triplicate, using Illumina
contributor: MHTP Medical Genomics Facility
contributor: Monash Bioinformatics Platform

first: Peter

last: Temple-Smith

first: Graeme

last: Southwick


title: Claudin-7 in keratinocytes is downregulated by the inhibition of HMG-CoA reductase and is highly expressed in the stratum granulosum of the psoriatic epidermis

status: Public on Jul 20 2021

city: Nagasaki

first: Sayaka

last: Kuwatsuka

department: Dermatology

institute: Nagasaki University Graduate School of Biomedical Sciences

summary:
Background: Cholesterol is de novo synthesized in the upper epidermis and plays an important role in maintaining the normality of skin. Studying the impact of the inhibition of cholesterol de novo synthesis in the epidermis may help understand how skin homeostasis is regulated.
Objective: In this study, we created a gene expression profile to investigate the effect of hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase inhibitors on epidermal homeostasis.
Methods: A microarray analysis was performed using normal keratinocytes with or without HMG-CoA reductase inhibitor (pitavastatin) treatment. Real-time PCR confirmed the reproducibility of genes with altered expression in keratinocytes treated with HMG-CoA reductase inhibitors. Among these genes, we focused on reduced expression of claudin 7 histologically confirmed by immunohistochemical staining, in situ hybridization, and immunoelectron microscopy.
Results: Claudin-7 was highly expressed in the stratum granulosum of psoriatic lesions but was not expressed in the normal epidermis. Immunoelectron microscopy revealed that claudin-7 was localized in the keratohyalin granules of psoriatic lesions.
Conclusion: These results indicate that claudin-7 expression was regulated by HMG-CoA reductase in the epidermis and might play a pathogenic role in the keratohyalin granules found in the epidermal granular layer of psoriasis.

overall_design: Adult human epidermal keratinocytes were used. According to the preliminary studies, the administration concentration was set to 0.1   M, at which level pitavastatin does not affect cell proliferation abilities. The cells (1.0    106) were seeded in a 10 cm   dish and cultured in 10 mL of EpiLife medium (Thermo Fisher Scientific, USA) for 3 days. Pitavastatin solution was then added to the culture medium to reach a final concentration of 0.1   M, and the solution was cultured for 6 hours. The same amount of DMSO alone was added as a control and cultured (culture conditions: 5% CO2, 37  C). The cells treated with pitavastatin and the cells treated with the vehicle had the same passage number (each n = 2). After culturing, the cells were collected, and total RNA was extracted using the SV Total RNA Isolation System (Promega, Tokyo, JAPAN). The resulting RNA was labeled with Cyanine-3 and was used for the microarray analysis. Three normalization procedures were performed on the samples. First, genes with signal intensities of 0.01 or less were corrected to 0.01. The normalized value of the corresponding pitavastatin-treated sample was then divided by the normalized value of the measured vehicle-treated sample on each chip. Genes with low expression levels with a signal intensity of less than 100 were filtered out in both the vehicle-treated samples and the pitavastatin-treated samples. A comparative analysis of the expression variability in genes that passed filtering was performed.


title: T cell derived LTR signal regulates thymic egress via distinct thymic portal endothelial cells

first: Suijuan

last: Zhong

state: Haidian

address: No.19 Xinjiekouwai Street

institute: Beijing Normal University

summary: NOT PROVIDED; REQUESTED

overall_design: NOT PROVIDED; REQUESTED

first: Huan

last: Xia

first: Xiaoqun

first: Mingzhao

last: Zhu


title: Dysregulation of a Pdx1/Ovol2/Zeb2 axis in dedifferentiated beta-cells triggers the induction of genes associated with epithelial-mesenchymal transition in diabetes

city: London

first: LMS

last: Bioinformatics Core


title: ATF3 COORDINATES SERINE AND NUCLEOTIDE METABOLISM TO DRIVE CELL CYCLE PROGRESSION IN ACUTE MYELOID LEUKEMIA

city: St Louis

first: Stephen

last: Sykes

address: 660 South Euclid Avenue

department: McDonnell Pediatric Research Building, Room 5102

institute: Washington University in St Louis

summary: Murine cells with KMT2A-rearrangements, MLL-AF9; ATF3 initiates transcriptional programs associated with serine and nucleotide metabolism

overall_design: Cultured murine MLL-AF9 cells were infected with a shNT or shAtf3 lentivirus; and harvested for RNA-Seq


title: RNA sequencing profiles of control and PRPF19 knockdown TIG-3 cells

city: Hiroshima

first: Kimiyoshi

last: Yano

address: Kasumi 1-2-3, Minami-ku

institute: Hiroshima University

summary: Total RNA was purified from TIG-3 cells transfected with siControl or siPRPF19 using miRNeasy Mini Kit (QIAGEN) with RNase-free DNase (QIAGEN). Library preparation, sequencing, and data analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). Quality and quantity of extracted RNA was assessed by NanoDrop 8000 Microvolume UV-Vis spectrophotometer (Thermo Fisher Scientific) and Agilent RNA 6000 Nano kit of BioAnalyzer 2100 System (Agilent Technologies). RNA-seq library was prepared using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio) following the manufacturer’s instruction. In brief, ribosomal RNA was depleted employed RiboGone which included in the kit. After that, first strand cDNA synthesis was performed using N6 primer. The first-stranded cDNA was purified using equal volume of AMPure XP beads (Beckman Coulter). The purified cDNA was amplified into Illumina-specific RNA-seq libraries by PCR. The libraries were sequenced on a Hiseq sequencer (Illumina) to generate 150 nt paired-end reads. The quality of sequence data was first assessed using FastQC (ver. 0.11.7). Raw sequence reads were then trimmed and quality-filtered with Trim Galore! (ver. 0.4.4), Trimmomatic (ver. 0.36), and cutadapt (ver. 1.16) software. Trimmed reads were mapped to the human reference genome (GRCh38.p10) using STAR (ver. 2.6.1a).

overall_design: RNA sequencing profiles of TIG-3 cells 3 days after transfection with siControl or siPRPF19.

first: K

first: R

middle: U

last: Takahashi

first: B

last: Shiotani

first: J

last: Matsunaga

first: T

last: Shidooka

first: Y

last: Sudo

last: Yamamoto

first: S

last: Kan

first: H

last: Sakagami

last: Tahara


title: Intratumor Heterogeneity of MIF Expression Correlates with Extramedullary Involvement of Multiple Myeloma

city: Chengdu

first: Juan

last: Xu

address: Guo Xue Xiang #37

institute: West China Hospital, Sichuan University

summary: Macrophage migration inhibitory factor (MIF) has been shown to promote disease progression in many malignancies, including multiple myeloma (MM). We previously reported that MIF regulates MM bone marrow homing and knockdown of MIF favors the extramedullary myeloma formation in mice. Here, based on MIF immunostaining of myeloma cells in paired intramedullary and extramedullary biopsies from 17 patients, we found lower MIF intensity in extramedullary MM (EMM) versus intramedullary MM (IMM). Flow cytometry and histology analysis in ARD cell line-derived xenograft models showed a portion of inoculated human MM cells lost their MIF expression (MIFLow) in vivo. Of note, IMM had dominantly MIFHigh cells, while EMM showed a significantly increased ratio of MIFLow cells. We harvested the extramedullary human MM cells from a mouse and generated single-cell transcriptomic data. The developmental trajectories of MM cells from the MIFHigh to MIFLow state were indicated. The MIFHigh cells featured higher proliferation. The MIFLow ones were more quiescent and harbored abundant ribosomal protein genes. Our findings identified in vivo differential regulation of MIF expression in MM and suggested a potential pathogenic role of MIF in the extramedullary spread of disease.

overall_design: Total CD138+ cells sorted from splenic cells in an ARD myeloma-bearing mouse were subjected to single-cell RNA sequencing to reveal the molecular characteristics of MIFHigh versus MIFLow MM cells in EMM.

first: Nanhui

last: Yu

first: Wei

last: Lin

first: Yimin

first: Yuhuan

last: Zheng


title: Timecourse RNAseq for Drosophila TBI

city: Philadelphia

first: Nancy

last: Bonini

address: 433 South University Ave

institute: University of Pennsylvania

summary: Comparison of post-injury (sham versus severe TBI) gene expression changes using a Drosophila head-specific TBI model.

overall_design: 64 total libraries were prepared from 52 unique RNA samples, representing the molecular response to traumatic brain injury spanning 9 timepoints from 0 through 15 days post-injury. Samples consist of heads isolated from 3d old uninjured males (controls, 0 post injury timepoint) and paired sham vs TBI injured animals (3d old males) at 1h, 3h, 6h, 12h, 24h, 3d, 7d, 10d, and 15d post-injury. All times/conditions have 3 biological replicates, with the exception of 15d due to library prep failure. Library preparation took place on two separate days (noted as library 1 or library 2), hence libraries for control and sham/TBI 24 h timepoints were prepared twice and used for batch effect correct.

first: China

last: Byrns


title: Transcriptome changes associated with marbling fineness in the longissimus thoracis of Korean cattle steer

city: Seoul

first: Seok-Hyeon

last: Beak

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

summary: It has been proved that intramuscular fat (IMF) or marbling in beef improves palatability. Recently, consumers have considered not only the degree of marbling but also the size and distribution of marbling flecks for their health and appetizing looking of beef. Computer image analysis (CIA) systems have been developed to assess various characteristics of marbling particles (MPs) such as the number, size, and distribution (fineness or coarseness) objectively. Some CIA indexes about MPs indicating how MPs are distributed evenly had significant positive relationship with price which represents consumers’ interest. RNA-seq research about formation of fine MPs in the longissimus thoracis (LT) muscle tissue of cattle have not yet been tried in transcriptome level. This study was conducted to reveal the DEGs between groups which have high or low number of fine MPs in the Longissimus thoracis muscle of Korean beef cattle and to understand molecular events associated with marbling fineness.

overall_design: mRNA profiles of each three LT samples from high and low number of fine MP groups were generated, and DEGs were anayzed.

first: Myunggi

last: Baik


title: Immunoregulatory function of peripheral blood CD71+ erythroid cells in pediatric inflammatory diseases

city: Fukuoka

first: Hikaru

last: Kanemasa

state: Fukuoka

address: Maidashi, 3-1-1

department: Department of pediatric

institute: Kyushu university

summary: Human CD71+ erythroid cells (CECs) have been recognized to have an immunoregulatory function via direct cell-cell interaction and soluble mediators such as arginase-2 and reactive oxygen species. Circulating CECs increase in healthy newborns or patients with hemolytic, malignant and cardiopulmonary disorders. To assess the pathophysiological role of CECs in inflammatory diseases, we studied the gene expression and function focusing on systemic-onset juvenile idiopathic arthritis (SoJIA). Peripheral blood mononuclear cells obtained from patients with SoJIA expressed upregulated erythropoiesis-related genes, that determined the largest increase of circulating CECs during active phase SoJIA of all inflammatory diseases including polyarthritis, Kawasaki disease, bacteremia and systemic lupus erythematosus. Despite the opposite roles of erythropoietin and hepcidin in erythropoiesis, both serum levels positively correlated with the amounts of peripheral blood CECs in SoJIA patients. There were positive correlations between CECs and inflammatory markers of C-reactive protein, interleukin (IL)-6, IL-18, or soluble TNF receptor. Co-culture with active SoJIA-driven CECs significantly suppressed the secretion of IL-1β, IL-6, and IL-8 from healthy donor monocytes. The top of upregulated genes in SoJIA-driven CECs was ARG2 compared with those in CECs from cord blood controls. On the other hand, cytokine productions from monocytes were suppressed by co-culture even with an arginase inhibitor. CECs are mobilized to periphery in SoJIA for the control of excessive inflammation via the immuno-regulatory pathways partly involving arginase-2. Understanding the association between CECs and magnitude of systemic inflammation may clarify the unappreciated role of erythroid precursors in health and disease process of immune dysregulation.

overall_design: Gene expression in CD71+ erythroid cells obtained from human cord blood of healthy newborns (n=2) and human peripheral blood of patients with systemic-onset juvenile idiopathic arthritis (n=4) was measured.

first: Masataka

last: Ishimura

first: Katsuhide

last: Eguchi

first: Tamami

last: Tanaka

first: Etsuro

last: Nanishi

first: Akira

last: Shiraishi

first: Motohiro

last: Goto

first: Yoshitomo

last: Motomura

first: Shouichi

last: Ohga


title: Beauveria bassiana Swi6 (BbSwi6) regulating genes involved in asexual development

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

institute: Zhejiang University

summary: Gene BbSwi6 playes an essential role in asexual differentiation, a determinant to the biocontrol  potential of entomopathogenic fungi.  The genome-wide exprssion analysis involved in fungal development was analyzed by using high throughput sequencing (RNA-Seq).

overall_design: Total RNA obtained from ∆BbSwi6 disruption mutant were sequenced.

first: Sheng-Hua

first: Ming-Guang

last: Feng


title: Transcriptomic phenotyping of human labor myometrium.

city: Chicago

first: William

last: Ackerman

address: 820 South Wood Street, MC 808, Dept. of Obstetrics & Gynecology

department: Obstetrics and Gynecology

institute: University of Illinois Chicago College of Medicine

summary: Myometrial biopsies were collected from 31 women undergoing primary cesarean sections and were carefully phenotyped with respect to gestational age (GA), circumstances of labor onset, and clinical status at the start and end of the intervention. Cases were aggregated into groups as follows: Group 1: term birth following spontaneous onset of term labor (TL, n=5); Group 2: term birth by elective cesarean section not in labor (TNL, n=5); Group 3: PTB following spontaneous preterm labor with intact membranes (n=6); Group 4: preterm birth following PPROM (n=8); and Group 5: provider-initiated preterm birth in the absence of active labor contractions, cervical dilation or membrane rupture (n=7). Additional phenotyping of cases spontaneously committed to PTBs (Groups 3 and 4) involved presence or absence of Triple I based on cultures of amniotic fluid obtained via clinically-indicated amniocentesis. RNAs were profiled using second generation RNA sequencing.

overall_design: We applied RNA-sequencing of long RNA species to uncover molecular signals that could be responsible for the transition of the human myometrium from a quiescent to the contractile laboring state in term and preterm settings.

middle: E

first: Irina

last: Buhimschi

first: Catalin


title: Real-time quantitative PCR analysis of PMA differentiated THP-1 infected with H37Rv or M. marinum, or heat killed H37Ra (HKMT)

city: Lyon

first: Pauline

last: Bade

address: 40 avenue Tony Garnier

institute: Evotec LYON ID SAS

summary: THP-1 cells were differentiated into macrophages with 0,1 µM PMA overnight then infected for 2 days with either H37Rv, M. marinum or heat killed H37Ra. Then RNA was collected in order to quantify the inflammatory response transcription as compared with the relative uninfected controls.

overall_design: RNA quantity was normalized by using 500 ng Total RNA of each sample pror to RT-PCR. Each sample was treated equally.

first: Fabrizio

last: Simonetti

first: Stephanie

last: Sans

first: Patricia

last: Laboudie

first: Khadija

last: Kissane

first: Nicolas

last: Chappat

first: Sophie

last: Lagrange

first: Florence

last: Apparailly

first: Christine

last: Roubert

first: Isabelle

last: Duroux-Richard


title: DNA methylation analysis reveals epimutation hotspots in patients with dilated cardiomyopathy-associated laminopathies

city: Irvine

first: Timothy

middle: Lamont

last: Downing

address: 4151 Engineering Hall

department: Biomedical Engineering

institute: University of California Irvine

summary: Mutations in LMNA, encoding Lamin A/C, lead to a variety of diseases known as laminopathies that include dilated cardiomyopathy (DCM). The role of epigenetic mechanisms. such as DNA methylation, has not been thoroughly investigated. Furthermore, the impact of patient-specific LMNA mutations on DNA methylation is unknown. To explore the role of DNA methylation in the context of unique LMNA mutations, we performed reduced representation bisulfite sequencing (RRBS) on ten pairs of fibroblasts and their induced pluripotent stem cell (iPSC) derivatives from two families with DCM due to distinct LMNA mutations. Family-specific differentially methylated regions (DMRs) were identified by comparing the DNA methylation landscape of patient and control samples. Fibroblast DMRs were found to enrich for distal regulatory features and transcriptionally repressed chromatin and to associate with genes related to phenotypes found in laminopathies. These DMRs, in combination with transcriptome-wide expression data and Lamina-associated domain (LAD) organization, revealed the presence of inter-family epimutation hotspots near differentially expressed genes, most of which were located near redistributed LADs. Comparison of DMRs found in fibroblasts and iPSCs identified regions where epimutations were persistent across both cell types. Finally, a network of disease-associated genes dysregulated in LMNA mutated cells was uncovered, potentially due to aberrant methylation changes. In conclusion, the use of in vitro culture models of patient-derived cells and differential methylation analysis enabled the identification of epimutation hotspots and dysregulated genes, consistent with a Lamin A/C mutation-specific epigenetic disease mechanism that arose in somatic and early-developmental cell stages.

overall_design: RRBS on 5 control (4 unaffected siblings and 1 unrelated donor) and 5 patient lines of fibroblasts and their iPSC derivatives from two families with DCM due to distinct LMNA mutations.

first: Julien

last: Morival

first: Halida

last: Widyastuti

first: Cecilia

middle: H

last: Nguyen

first: Michael

last: Zaragoza


title: Sensitive and quantitative detection of MHC-I displayed neoepitopes using a semi-automated workflow and TOMAHAQ mass spectrometry

city: South San Francisco

first: Samuel

last: Pollock

address: 1 DNA way

department: MPL

institute: Genentech

summary: Advances in several key technologies, including MHC peptidomics, has helped fuel our understanding of basic immune regulatory mechanisms and identify T cell receptor targets for the development of immunotherapeutics. Isolating and accurately quantifying MHC-bound peptides from cells and tissues enables characterization of dynamic changes in the ligandome due to cellular perturbations. This multi-step analytical process remains challenging, and throughput and reproducibility are paramount for rapidly characterizing multiple conditions in parallel. Here, we describe a robust and quantitative method whereby peptides derived from MHC-I complexes from a variety of cell lines, including challenging adherent lines, can be enriched in a semi-automated fashion on reusable, dry-storage, customized antibody cartridges. TOMAHAQ, a targeted mass spectrometry technique that combines sample multiplexing and high sensitivity, was employed to characterize neoepitopes displayed on MHC-I by tumor cells and to quantitatively assess the influence of neoantigen expression and induced degradation on neoepitope presentation.

overall_design: Four treated samples were analyzed in technical triplicate (biological single replicate), from the same engineered cell line, MC38-idAdpgkG (which stands for inducible, degradable, Adpgk(R304M) neoantigen fused to turboGFP in the MC38 murine colon carcinoma cell line). The four treatments were as follows: mouse IFNg alone, mIFNg plus doxycycline, mIFNg plus doxycycline plus dTag13, and mIFNg plus dTag13 (see the treatment protocol section for full concentration and timing details).

middle: B

first: Christopher

last: Rose

first: Martine

last: Darwish

first: Romain

last: Bouziat

first: Lélia

last: Delamarre

first: Craig

last: Blanchette

first: Jennie

last: Lill


title: USP16 knockdown-induced gene expression in NCI-H23 cells

city: Shanghai

first: Guiqin

last: Xu

address: 800 Dongchuan Rd

institute: Shanghai cancer institute

summary: To determine the molecular signaling pathways responsible for USP16 regulation of cell growth, RNA sequencing was conducted on NCI-H23 cells with or without USP16 knockdown

first: Yongzhong

last: Liu


title: Gene expression levels of evolved thermotolerant yeast and its parent

city: Wuxi

first: Nai-Xin

last: Lin

address: lihu avenue

institute: Jiangnan University

summary: Samples for RNA-seq were collected from cell cultures in YPD medium under 30 °C or 37 °C at the logarithmic phase. The gene expression levels of thermotlerant yeast and the parent under these two temperatures were analyzed. We found the most upregualted genes of the parent under high temperature versus normal temperature were involved in autophay. the peroxisome pathway was significantly upregulated in G14 under high temperature versus the parent under normal temperature. The antixidant system of yeast was activated under thermal stress.

overall_design: the samples were classfied into different comparison groups. The expression level of thermotolerant yeast under 37℃ versus the parent under 30℃ were followed.

first: Yan

first: Xiao-Wei

last: Yu


title: Effect of serum amyloid A1 (SAA1) on gene expression in primary murine macrophages

city: Ulm

first: Ann-Kathrin

last: Gaiser

address: Helmholtzstr. 20

institute: Ulm University

summary: Macrophages are important regulators of the immune system and are critically involved in the pathophysiology of many diseases. Serum amlyoidosis is a protein misfolding disease which can follow chronic inflammatory conditions. Deposition of fibrils formed from serum amyloid A1 (SAA1) protein occurs systemically and can lead to severe or even fatal outcomes. Macrophages play a critical role in the misfolding and deposition of SAA1-derived fibrils and the role of macrophages in this context has been studied extensively. It is known that SAA1 can bind to some surface receptors on macrophages and it is taken up by the macrophages and metabolized in the lysosomes. On the other hand, the effect of SAA1 on macrophage physiology has been much less investigated so far. Therefore, we aim to investigate the effect of SAA1 on macrophage gene expression by gene microarray analysis. To this end, primary peritoneal macrophages from NMRI mice were treated with endotoxin-free recombinantly expressed full-length mSAA1 for 6 and 24 h and gene expression was analyzed.

overall_design: At each time point, 3 biological replicates were treated with either 50 µM (=0.58 mg/ml) mSAA1.1 or 5.8% water in medium, respectively. Cells were harvested after 6 or 24 h by scraping.

first: Stephanie

last: Claus

first: Karlheinz

last: Holzmann

first: Tatiana

last: Syrovets


title: Difference in mRNA between fast and slow type muscle fibers

city: Tsukuba

first: Mika

last: Oe

state: Ibaraki

address: Ikenodai 2

institute: Institute of Livestock and Grassland Science, NARO

summary: In order to invetigate the impact of CpG methylation on gene expression, transcriptomic profiling using microarray were conducted on the fast and slow type myofibers.

overall_design: The gene expressions of isolated and pooled fast and slow type myofibers were analysed. Fast and slow type muscle fibers were collected from extensor digitorum longus (EDL) and soleus muscles dissected from 8 male mouse.The total RNAs were isolated from the pooled 4,447 fast and 1,659 slow type fibers.

first: Koichi

last: Ojima

first: Susumu

last: Muroya


title: Global transcriptome of the fungal pathogen Sclerotinia sclerotiorum (strain 1980) during the colonization of six plant species - Global transcriptome of S. sclerotiorum and S. trifoliorum during growth on camalexin

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

institute: INRAE

summary: The host range of parasites is an important factor in assessing the dynamics of disease epidemics. The evolution of pathogens to accommodate new hosts may lead to host range expansion, a process the molecular bases of which are largely enigmatic. The fungus Sclerotinia sclerotiorum parasitizes more than 400 plant species from diverse eudicot families while its close relative, S. trifoliorum, is restricted to plants from the Fabaceae family. We analyzed S. sclerotiorum global transcriptome reprogramming on hosts from six botanical families and reveal a flexible, host-specific transcriptional program driven by core and host-response co-expression (SPREx) gene clusters. We generated a chromosome-level genome assembly for S. trifoliorum and found near-complete gene space conservation in broad and narrow host range Sclerotinia species. However, S. trifoliorum showed increased sensitivity to the Brassicaceae defense compound camalexin. Inter-specific transcriptome analyses revealed a lack of transcriptional response to camalexin in S. trifoliorum and provide evidence that cis-regulatory variation associates with the genetic accommodation of Brassicaceae in the Sclerotinia host range. Our work demonstrates adaptive plasticity of a broad host range pathogen with specific responses to different host plants and demonstrates the co-existence of signatures for generalist and polyspecialist life styles in the genome of a plant pathogen. We reason that this mechanism enables the emergence of new disease with no or limited gene flow between strains and species, and could underlie the emergence of new epidemics originating from wild plants in agricultural settings.

sample_organism:
Sclerotinia trifoliorum
Sclerotinia sclerotiorum 1980 UF-70

overall_design: Periphery and center of S. sclerotiorum disease lesions on A. thaliana (Ath), S. lycopersicum (Sly), H. annuus (Han), B. vulgaris (Bvu), R. communis (Rco), P. vulgaris (Pvu) Periphery and center of colony growth on Potato Dextrose Agar plates and in Potato Dextrose Broth serves as control samples collected in three independent replicates

first: Malick

last: Mbengue

first: Stefan

last: Kusch


title: Unresponsiveness to inhaled antigen is governed by conventional dendritic cells and overridden during infection by monocytes

city: Parkville

first: Alexandra

last: Garnham

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute of Medical Research

summary: The goal of this study was to compare the transcriptional profile (RNAseq) of dendritic cell (DC) subsets (XCR1+and CD11b+) with immunosuppressive activity recovered from the nasal associated lymphoid tissue (NALTs) to matched subsets with immunostimulatory activity recovered from the cervical lymph node.

overall_design: 12 samples were analyzed: 3 replicates of CD11b+ DCs isolated from the cervical lymph node of naïve C57BL/6 mice. 3 replicates of XCR1+ DCs isolated from the cervical lymph node of naïve C57BL/6 mice. 3 replicates of CD11b+ DCs isolated from the NALTs of naïve C57BL/6 mice. 3 replicates of XCR1+ DCs isolated from the NALTs of naïve C57BL/6 mice

first: Melanie

last: Heinlein

first: Daniel

middle: D

last: Gray

first: Linda

middle: M

last: Wakim


title: Chronic stress promotes EMT-mediated metastasis through activation of STAT3 signaling pathway by miR-337-3p in breast cancer

first: Peixin

last: Du

address: No.37, Guoxue Alley

institute: West china hospital

summary: The aim of this research is to explore the metastasis associated negative effect of chronic stress. The analysis of transcriptome sequencing implied that activation of STAT3 signaling pathway by miR-337-3p might be a potential mechanism to induce epithelial to mesenchymal transition (EMT) of cancer cell and promote metastasis under chronic stress. We also verified this biological process in further experiments. Downregulation of miR-337-3p could downregulate E-cadherin expression and upregulate vimentin expression in vitro and in vivo. STAT3, related signal pathways of which are involved in metastasis regulation, was directly targeted by miR-337-3p.

overall_design: Tumors removed from 4T1 tumor bearing mice suffered chronic restraint stress 2 hours a day for consecutive 28 days were labeled as stress group. Tumors removed from 4T1 tumor bearing mice with no treatment were used as control group. There were three samples in stress and control group respectively.

first: Hao

last: Zeng

first: Yinan

last: Xiao

first: Yunuo

last: Zhao

first: Bo

last: Zheng

first: Yu

last: Jiang

first: Xuelei

last: Ma