title: Exploring the phenomenon of ferroptosis in liver disease associated with intestinal failure in children with SBS

first: Siyang

last: Cheng

summary:
Background: Intestinal failure-associated liver disease (IFALD) is a common complication of long-term parenteral nutrition (PN) that is associated with significant morbidity and mortality. Ferroptosis, as an iron-dependent regulated cell death, has been shown to play an important role in the development of several liver diseases. This study focuses on investigating whether the ferroptosis phenomenon is present in TPN-induced IFALD and further exploring the potential regulatory mechanisms.
Methods: Ferroptosis hallmarkers were measured in children with short bowel syndrome (SBS) who had long-term PN use and caused IFALD. Sprague-Dawley (SD) rats were used to establish a rat model of IFALD with a concomitant ferroptosis inhibition intervention using liproxstain-1. The mir-431 lineage was identified as a potential upstream regulatory mir-RNA by mir-RNA sequencing. HepG2 and 293T cell line was used to demonstrate that mir-431 regulates ferroptosis through the GPX4 pathway at the cellular level in vitro.
Results: Ferroptosis is upregulated in liver of children with IFALD. Liproxstain-1 downregulates ferroptosis in a rat model of IFALD and attenuates hepatic steatosis through the lipid metabolism pathway. In vitro HepG2 and 293T cell experiments reveal that mir-431 affects ferroptosis by regulating GPX4 protein.
Conclusions: Ferroptosis plays an important role in the development of IFALD. Liproxstain-1 inhibits ferroptosis and attenuates hepatic steatosis in a rat model of IFALD through the lipid metabolism pathway. Mir-431 negatively regulates GPX4 protein-induced ferroptosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for short bowel syndrome children with or without  intestinal failure-associated liver disease

first: Ying

last: Wang

first: Lu

last: Jiang

first: Wei

last: Cai


title: A G-protein coupled receptor supports methionine response in Trichoderma reesei

status: Public on Jan 01 2024

city: Tulln

first: Miriam

last: Schalamun

address: Konrad Lorenz Strasse 24

country: Austria

institute: Austrian Institute of Technology

type: Expression profiling by high throughput sequencing

summary: We investigated the function of the G-protein coupled receptor 72004 in Trichoderma reesei and found that it is involved in methionine response and gene expression in light and darkness

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Trichoderma reesei QM6a (WT) and deletion mutant QM6aΔ72004

first: Monika

last: Schmoll


title: Function of histone deacetylases on fission yeast heterochromatin assembly

city: Charlestown

first: Richard

last: Joh

state: MA

department: Center for Cancer Research

country: USA

institute: Mass General Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate the role of histone deacetylases on heterochromatin assembly, we collected H3K9me2 samples on various HDAC deletion backgrounds.

overall_design: H3K9me2 ChIPseq on S pombe.  H3K9me2 antibody (ab1220) was used.

first: Jasbeer

last: Khanduja

first: Mo

last: Motamedi


title: Transcriptomic analysis of mouse ovary post-PMSG induction 40h

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

summary: Ovaries were collected post-PMSG induction 40h for 3 genotypes : wild-type (WT), DKO for LXRalpha and LXRbeta (DKO) and DKO for LXRalpha and LXRbeta rescued for LXRbeta in granulosa cells (TG-AMHb).

overall_design: RNA were extracted for analysis by deep sequencing, in triplicate, using Illumina NextSeq sequencing platform.

first: Silvère

last: Baron

first: Yoan

last: Renaud


title: Transcriptional analysis of the thalamus and rostral ventral medulla in rats with chronic orofacial pain

city: Chongqing

first: Cong

last: Yu

address: No. 426 Songshi North Road, Yubei District

department: Anesthesiology

country: China

institute: The stomatology hospital affiliated chongqing medical university

summary: We used RNA sequencing to screen differentially expressed genes (DEGs) in the rostral ventral medulla (RVM) and thalamus of rats during persistent orofacial pain to explore the mechanism of chronic orofacial pain.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for chronic orofacial pain.

first: Wenwen

last: Zheng

first: Jie

last: Zeng


title: Sir2 recruitment after synchronization

summary: To investigate the role of cell-cycle-dependent Sir2 recruitment, we collected Sir2-ChIP samples after HU treatment.

overall_design: Sir2-Flag ChIPseq on S pombe.  HU was used to arrest the cell cycle.  Number after HUR means minutes after cell cycle arrest (e.g. HUR20 is 20min after release).


title: CONSTANS alters the circadian clock in Arabidopsis thaliana

city: Sevilla

first: Pedro

last: de los Reyes

address: c/Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

country: Spain

institute: CSIC

summary: Plants are sessile organisms that have acquired highly plastic developmental strategies to adapt to the environment. Among these processes, the floral transition is essential to ensure reproductive success and is finely regulated by several internal and external genetic networks. The photoperiodic pathway, which controls the plant response to day length, is one of the most important pathways controlling flowering. In Arabidopsis photoperiodic flowering, CONSTANS (CO) is the central gene activating the expression of the florigen FLOWERING LOCUS T (FT) in the leaves at the end of a long day. CO expression is strongly regulated by the circadian clock. However, to date, no evidence has been reported regarding a feedback loop from the photoperiod pathway back to the circadian clock. Using transcriptional networks, we have identified relevant network motifs regulating the interplay between the circadian clock and the photoperiod pathway. Gene expression, chromatin immunoprecipitation experiments and phenotypic analysis allowed us to elucidate the role of CO over the circadian clock. Plants with altered CO expression showed a different internal clock period, measured by daily rhythmic movements in the leaves. We show that CO is able to activate key genes related to the circadian clock, such as CCA1, LHY, PRR5 and GI, at the end of a long day by binding to specific sites on their promoters. Moreover, a significant number of PRR5 repressed target genes are upregulated by CO, and this could explain the phase transition promoted by CO. The CO-PRR5 complex interacts with the bZIP transcription factor HY5 and helps to localize the complex in the promoters of clock genes. Our results indicate that there may be a feedback loop in which CO communicates back to the circadian clock, feeding seasonal information to the circadian system.

overall_design: Chromatin immunoprecipitation (ChIP-seq) for CONSTANS in Arabidopsis. Seedlings were grown in LD and harvested at 7DAG. CO ovexpressing lines were used to get high protein amount. CO mutants (co-10) were employed as control. The immunoprecipitation was carried out using specific anti-CO antibodies

first: Francisco

middle: J

last: Romero-Campero

first: He

last: Gao.

first: Gloria

last: Serrano-Bueno

first: Jose

middle: M

last: Romero

first: George

last: Coupland

first: Federico

last: Valverde


title: Effect of Heat Stress on Gene Expression of ZH11 and grp3/grp162 Double Mutants

city: 杭州市

first: 闯

last: 杨

state: 浙江省

address: 浙江省杭州市西湖区余杭塘路866号浙大紫金港校区生科院511

institute: 浙江大学

summary: In order to study the effects of GRP3 and GRP162 on rice resistance to high temperature stress, we knocked out these two genes.

overall_design: Then, we used the data obtained from RNA seq of two materials in two treatments for gene expression profile analysis.

first: Chuang

last: Yang


title: Transcriptomic analysis of corona radiata cells after hormonal stimulation (PMSG/hCG)

summary: Cumulus-oocyte complexes were collected post-PMSG/hCG induction at J4 for 3 genotypes : wild-type (WT), DKO for LXRalpha and LXRbeta (DKO) and DKO for LXRalpha and LXRbeta rescued for LXRbeta in granulosa cells (TG-AMHb). Corona radiata cells were isolated from oocytes using hyaluronidase treatment and collected for transcriptomic analysis.


title: MKL1 ChIP-seq in sham and hepatectomy mouse liver.

city: NANJING

first: ZILONG

last: LI

state: JIANGSU

address: 639 Longmian Avenue

institute: China Pharmaceutical University

summary: To investigate the function of MKL1 in liver regeneration. Wild-type C57/B6 mouse were performed sham operation or two-thirds hepatectomy. 24 hours later, ChIP-seq was did with MKL1 antibody.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for MKL1 in sham or two-thirds hepatectomy mouse liver tissues.

first: Li

last: Zilong

first: Xu

last: Yong


title: Recruitment of Clr4 to heterochromatin

first: Richard

last: Joh

summary: To investigate the role of Clr4 recruitment, we performed FLAG-Clr4 ChIP-seq in various genetic background

overall_design: Flag-Clr4 ChIPseq on S pombe.

first: Jasbeer

last: Khanduja

first: Mo

last: Motamedi


title: Stage-specific dual function: EZH2 regulates human erythropoiesis by eliciting histone and non-histone methylation [D15-EZH2-RNAseq]

city: zhengzhou

first: li

last: mengjia

address: Science Road 100, Zhengzhou, Henan, 450001, P.R.

institute: zhengzhou university

summary: To demonstrated that EZH2 regulates human erythropoiesis in a stage-specific, dual-function manner by catalyzing histone and non-histone methylation,We performed RNA-seq and ChIP-seq.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at two time points.  Comparative gene expression profiling analysis of RNA-seq data for early (day 7) and late (day 15) erythroid cells and its KD derivatives (Scramble-shRNA, EZH2-shRNA).

first: Mengjia

last: Li

first: Lixiang

last: Chen


title: Stage-specific dual function: EZH2 regulates human erythropoiesis by eliciting histone and non-histone methylation [ChIP-Seq]

summary: To demonstrate that EZH2 regulates human erythropoiesis in a stage-specific, dual-function manner by catalyzing histone and non-histone methylation, we performed RNA-seq and ChIP-seq.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27me3


title: Effect of knockdown APE1 on gene expression  in NCI-H460 cells

city: Nanjing

first: Fan

state: China

address: Wenyuan road 1

institute: Nanjing Normal University

summary: To investigate the  function APE1, we established NCI-H460 cell lines in which target gene has been knocked down by shRNA.We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at the same time.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NCI-H460 cells and its KD derivatives (shAPE1).

first: Zhigang

last: Guo

last: Hu


title: Stage-specific dual function: EZH2 regulates human erythropoiesis by eliciting histone and non-histone methylation

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

overall_design: Refer to individual Series


title: Stage-specific dual function: EZH2 regulates human erythropoiesis by eliciting histone and non-histone methylation [D7-EZH2-RNAseq]


title: Effect of LPS, sHVF18 and the combination therof on gene expression in murine lungs

city: Lund

first: Petter

last: Storm

state: Select...

address: Sölvegatan 19, BMC A11

country: Sweden

institute: Lund University

summary: Excessive Toll-like receptor (TLR) and NF-kB activation during infection causes the overactivation of inflammatory pathways seen in sepsis. Thrombin-derived C-terminal peptides (TCPs) target both bacteria and the resulting TLR-mediated inflammatory response during infection. The present study describes the design and development of a novel multifunctional stapled peptide mimicking the actions of such immunomodulatory TCPs, providing a new drug class based on nature’s own anti-infective strategies. Using a combination of structure-based design, nuclear magnetic resonance spectroscopy (NMR), biophysics, mass spectrometry, microbiology, cellular, and in vivo studies, we describe the development of a structurally locked active stapled form of the endogenous peptide HVFRLKKWIQKVIDQFGE, denoted sHVF18. The stapled peptide shows a higher affinity to CD14 than the linear peptide, retains a partly helical and stabilized structure, and is protease resistant. In vivo, it shows efficacy in experimental models of endotoxin shock in mice and pigs and increases survival in mouse models of polymicrobial sepsis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from murin lungs treated with LPS, Placebo and/or sHVF18

first: Manoj

last: Puthia

first: Ganna

last: Petruk


title: Single Cell RNA Sequencing of Young and Aged Murine Glioblastoma

city: Chicago

first: April

last: Bell

state: IL

address: 2053 N Mozart St Apt 3F

institute: Northwestern University

summary: To understand the effects of aging on glioblastoma (GBM) immune microenvironment, differential gene expression of extra-tumral brain tissues between young and old mice were investigated by sc-RNASeq in this study.

overall_design: C57BL/6 mice at the age of 8 weeks old and 93 weeks old were intracranially engrafted with either 1x10^3 CT2A-GFP-luc murine GBM cells or 1xPBS as sham control. Two weeks after tumor cell implantation, brain tissues from the non-tumor injection hemisphere (contralateral) were isolated and single cells were prepared using the Adult Brain Dissociation kit (Miltenyi Biotec) and subjected to sc-RNASeq.

first: Lijie

last: Zhai

first: Brandyn

last: Castro

first: Junfei

last: Zhao

first: Kristen

last: Lauing

first: Jason

last: Miska

first: Derek

last: Wainwright


title: Gene expression in glucose-grown L-pipecolic acid production strains C.glutamicum LPA-1A and LPA-5 compared to the non-L-pipecolic acid-producing strain C. glutamicum LPA-0

city: Saarbruecken

first: Michael

last: Kohlstedt

address: Campus A1.5

country: Germany

institute: Saarland University


title: Krüppel-like factor 2 in VCAM1+ endothelial cells is a critical regulator of vascular inflammation

city: Wuxi

first: Hao

last: Kan

address: The number of 1800 ,Li Hu Road

institute: jiangnan university

summary: Endothelial cells (ECs) act as an internal barrier to the vessel wall, hindering the development of inflammation, and only when activated will promote the development of vascular inflammation. However, the heterogeneity of the aortic ECs in the setting of vascular inflammation have not been fully assessed. Here, we defined 4 EC subpopulations, including Cd36+ EC, Notch3+ EC, Vcam1+ EC and Lyve1+ EC. Based on the enrichment analysis, Vcam1+ EC were considered to be a subpopulation of ECs susceptible to activation. After high-fat diet (HFD) intake, decreased expression of Krüppel-like factor 2 (Klf2) occurred only in Vcam1+ EC. Moreover, S1pr1 was validated as a downstream target protein of klf2. Upregulation of Klf2 expression ameliorated vascular ECs inflammation under HFD condition. Our study elucidates the Klf2 in Vcam1+ EC is a critical regulator of vascular inflammation and increases understanding of development and progression of aortic inflammatory disease.

overall_design: Single cell RNA-seq on aortic cells of normal diet or high-fat diet mice

first: Ka

last: Zhang

first: Aiqin

last: Mao


title: Gene expression in glucose-grown L-pipecolic acid production strains C.glutamicum LPA-1A and LPA-5 compared to the non-L-pipecolic acid-producing strain C. glutamicum LPA-0 [1]

summary:
mRNA was sampled during exponential growth (OD660 = 4)
strains: LPA-0 (L-lysine hyperproducing strain C. glutamicum LYS-12 (Becker et al. 2011) + pClik5a_MCS), C. glutamicum LPA-1A (C. glutamicum LPA-0 + pClik5a_peftu_lysDH_proC)

overall_design: 3 biological replicates of C. glutamicum LPA-0 (3 total samples) were compared to either 3 biological replicates of C. glutamicum LPA-1A

first: Sarah

last: Pauli

first: Christoph

last: Wittmann


title: Gene expression in glucose-grown L-pipecolic acid production strains C.glutamicum LPA-1A and LPA-5 compared to the non-L-pipecolic acid-producing strain C. glutamicum LPA-0 [2]

summary:
mRNA was sampled during exponential growth (OD660 = 4)
strains: LPA-0 (L-lysine hyperproducing strain C. glutamicum LYS-12 (Becker et al. 2011) + pClik5a_MCS), C. glutamicum LPA-5 (C. glutamicum LPA-0 + pClik5a_peftu_lat_proC)

overall_design: 3 biological replicates of C. glutamicum LPA-0 (3 total samples) were compared to either 3 biological replicates of C. glutamicum LPA-5


title: Deregulation of neuronal polarization promotes axonal growth after spinal cord injury

city: London

first: Franziska

last: Müller

address: Du Cane Road

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

summary: The developmental maturation of a neuron requires the completion of neuronal polarization preceding the formation of a synapse. Whether neuronal polarization marks the decline in growth competence in the injured mammalian adult nervous system remains elusive. Here we show that gene expression and epigenetic signatures associated with the regenerative growth ability of dorsal root ganglia (DRG) sensory neurons are lost during the transition from a non-polarized to a polarized state. The transcriptional co-factor Cited2 was found to be epigenetically upregulated in immature DRG and following a regenerative injury, but it remained unchanged by a non-regenerative spinal cord injury (SCI). Next, Cited2 was overexpressed in DRG neurons in a model of SCI in mice where it promoted sensory axon growth and reversed the gene expression signatures associated with neuronal maturation. Importantly, Cited2 expression stirred the maturation of DRG neurons towards a non-polarized state. Together, these data suggest that the transition from a non-polarized to a polarized state marks the reversible loss of the regenerative ability of a neuron, thus paving the way to targeted repair strategies relying on neuronal de-maturation.

overall_design: AAV-GFP or AAV-Cited2 was injected bilaterally into the sciatic nerve 4 weeks prior to a dorsal column axotomy. 24 hours post-injury, DRG were extracted and a neruonal enriched population processed for RNA-seq

first: Ilaria

last: Palmisano

first: Siimone

last: Di Giovanni


title: Genome-wide gene expression analysis to find ZDHHC11 targets

city: Groningen

first: Lotteke

last: Ziel-Swier

state: Groningen

address: Hanzeplein 1

department: Department of Pathology and Medical Biology

country: Netherlands

institute: University Medical Center Groningen

summary: In Burkitt lymphoma (BL), a network consisting of MYC, MYC-repressed miR-150 and miR-150 targets MYB and ZDHHC11 has been established. This network plays an important role on the growth of BL cells. Here, we performed gene expression analysis to identify targets of ZDHHC11.

overall_design: ST486 BL cell line was transduced with lentiviral miRZIP vector containing shRNAs against all ZDHHC11 transcripts or control shRNA, and a RFP reporter. Upon sorting of the RFP+ cells, RNA was isolated and gene expression analysis was performed to identify targets of ZDHHC11.

first: Yichen

last: Liu

first: Annika

last: Seitz

first: Jasper

last: Koerts

first: Joost

last: Kluiver

first: Anke

last: van den Berg


title: INDYCSB

city: Copenhagen N

first: Morten

last: Scheibye-Knudsen

state: Copenhagen N

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

summary: There is currently no established treatment for Cockayne syndrome, a disease characterized by progressive early onset neurodegeneration with features of premature aging and death in childhood. Here, we tested if acetyl-CoA precursors, citrate and beta-hydroxybutyrate, could reduce features of Cockayne syndrome. We identified the gene Helicase 89B (Hel89B) as a homologue of CSB in drosophila and found that the ketone beta-hydroxybutyrate rescued features of premature aging in Hel89B deficient flies. In mammals, loss of the citrate carrier Indy exacerbated the phenotype of Csbm/m mice, rescued by a ketogenic diet. The rescue effect appeared to be mediated through ketone stimulated histone acetylation and facilitation of transcriptional resolution of non-B DNA. Notably, this appears to be a common effect of a ketogenic diet.

overall_design: Examination of transcriptome in cerebella of WT, INDY, CSB and DKO mice, fed standard diet (SD) or ketogenic diet (KD).

middle: A

last: Petr

last: Ben Ezra

first: Jakob

last: Madsen


title: Molecular genomic studies of the obesogenic effects of tributyltin during adipogenic differentiation implicate a primary role for cytoskeletal damage.

city: Bronx

first: Taylor

last: Thompson

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine


title: CD34+ monocyte subset is highly susceptible to HIV-1 infection

city: Kumamoto

first: Naofumi

last: Takahashi

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

summary: HIV-1 persists in cellular reservoirs despite effective antiretroviral therapy (ART). CD4+ T cells are the well-known reservoir, but there is growing evidence that myeloid cells, including circulating monocytes, are also a clinically relevant reservoir. However, it is unclear what are preferentially infected monocyte subsets in vivo. Here, we show that a monocyte fraction expressing the stem cell marker CD34 is more susceptible to HIV-1 infection than the CD34-negative major subset. In ART-untreated viremic patients, CD34+ fraction increased in the percentage in total monocytes, and harbored more proviral DNA than the major subset. Consistent with this, when compared to the major subset, CD34+ fraction expressed HIV-1 receptors (CD4 and CCR5) at higher levels and HIV-1 restriction factors (MX2 and SAMHD1) at lower levels. Interestingly, proviral DNA was detected in CD34+ fraction of ART-treated virologically suppressed patients. CD34+ monocytes were also present in lymph nodes, and expressed CD4 and CCR5 at higher levels than the major subset, as observed for peripheral blood. Moreover, CD34+ monocytes present in peripheral blood and lymph nodes highly expressed CCR7 and sphingosine-1-phosphate receptor 1 (S1PR1), critical regulators of in vivo cellular trafficking. Our findings suggest that circulating CD34+ monocytes are infected with residual HIV-1 after migrating into tissues including lymph nodes and return to circulation, which explains the detection of proviral DNA in the cells even after long-term ART.

overall_design: In order to identifiy the feature of monocyte subsets, CD34+ and CD34- peripheral blood monocytes (CD14+) were isolated using cellsorter followed by RNA extraction and hybridization on Affymetrix microarrays.

first: Osamu

last: Noyori

first: Youssef

last: Eltalkhawy

first: Yoshihiro

last: Komohara

first: Hideki

last: Nakayama

first: Shinichi

last: Oka

first: Masafumi

last: Takiguchi

first: Shinya

last: Suzu


title: Molecular genomic studies of the obesogenic effects of tributyltin during adipogenic differentiation implicate a primary role for cytoskeletal damage [RNA-seq]

summary: Environmental obesogens are being studied for their potential role in the increasing prevalence of obesity globally.  A major area of focus in this field of research has been on the mechanism by which these agents act. In this study we focused on the organotin tributyltin (TBT), a water pollutant exposed to humans through diet.  The mechanism by which TBT is believed to act is by binding to the PPAR𝛾 nuclear receptor which heterodimerizes with RXR to alter gene regulation. To test whether this was the dominant mechanism for TBT activity, we performed time-course studies of transcription and chromatin accessibility in mesenchymal stem cells differentiating to adipocytes.  We found limited evidence for PPAR𝛾 effects by TBT, but a strong response by Ras-related GTPases and evidence for the loss of TEAD transcription factor activity during differentiation.  These observations combine to implicate a known property of organotins, to cause cytoskeletal depolymerization.  We propose a model for TBT activity involving a primary effect of cytoskeletal damage, leading to the loss of YAP co-regulator activity and the consequent failure of TEAD repression of adipogenesis.

overall_design: Comparative gene expression profiling or RNA-seq from Tri-Butyltin(TBT), and Rosiglitazone(ROSI) exposed MSCs with control MSCs during adipogenesis

middle: V

first: John

last: Greally

first: Masako

last: Suzuki


title: Themis directs T cell exhaustion by promoting PD-1 signaling and key transcription factors TCF-1 and TOX expression

city: Xiamen

first: Guo

last: Fu

address: No. 422, Siming South Road, Xiamen, Fujian, China.

institute: Xiamen University

summary: We adopted scRNA-seq to examine whether Themis is required for Tex initiation. To strengthen the rigorousness of scRNA-seq analysis, we contransferred P14 WT and P14 Themis cKO cells, enabling them to experience the same viral burden and inflammatory environment. Then cells from all conditions (including naïve control cells) were combined and subjected to analysis.

overall_design: T cells were FACS-sorted from lungs, or spleen of recipient mice which were co-transferred Themisflox/flox-dLck-Cre  P14 and WT P14 Naive T cells 8 days after infection with Lymphocytic choriomeningitis virus Clone 13 strain, and subjected to single-cell RNA-seq by MARS-Seq protocol.

first: Jian

last: Tang

first: Xian

last: Jia

first: Yuzhou

last: Bao


title: Analysis of differentially expressed genes in the sea cucumber Apostichopus japonicus under heat stress

city: Qingdao

first: Dongxue

last: Xu

address: Changcheng road No.700

institute: Qingdao Agricultural University

summary: The high-throughput RNA-seq was applied under both 26°C and 30°C heat stress in Apostichopus japonicus, which revealed characterization of gene expression at sub-lethal and lethal limit temperature. The results will help to better understand the characteristics of heat shock response in A. japonicus.

overall_design: The sea cucumbers in control group were still kept at 18°C without any change, and the intestine tissue was sampled from the control group. For the heat stress experiment, sea cucumbers went through a temperature-rise process from 18°C to 26°C or to 30°C respectively, with a rate of 2°C per hour by using a heating rod. Then the water maintained at the treatment temperature, and the initial time was set with the moment when the temperature reached 26°C or 30°C. After 6 h and 48 h from initial time, the sea cucumbers 26°C treatment were sampled with intestine tissue, which was regarded as the group 26°C_6h and 26°C_48h respectively. After 6 h from initial time, the sea cucumbers 30°C treatment were sampled with intestine tissue, which was regarded as the group 30°C_6h. All the samples were quickly frozen in liquid nitrogen, and then stored at -80°C for further usage.

first: Bin

last: Xia


title: Molecular genomic studies of the obesogenic effects of tributyltin during adipogenic differentiation implicate a primary role for cytoskeletal damage [ATAC-seq]

first: Taylor

last: Thompson

first: Reanna

last: Doña


title: Transcriptome profiles of differentiated mouse embryonic stem cells cultured in normal condition and static magnetic field condition by RNA-seq analysisanalysis

first: ZHAOYUAN

last: GUO

address: XuanWuqu

institute: Nanjing Agricultural University

summary: Embryonic stem cells (ESCs) have the ability to differentiate into cells of the three germ layers, and leukemia inhibitory factor (LIF) maintains the pluripotency and promotes the proliferation of ESCs. In the absence of LIF, ESCs spontaneously differentiate and form three-dimensional aggregates known as embryoid bodies (EBs). The differentiation of EBs mimics the process of embryonic development, that is, the differentiation of cells into the three embryonic germ layers (endoderm, mesoderm, and ectoderm), some of which differentiate into beating cardiomyocytes. Static magnetic fields have diverse effects on organisms, studies on the regulation of the differentiation of ESCs to cardiomyocytes by static magnetic fields are not sufficient. To better understand transcriptional landscape and signal transductions, we performed RNA-seq analysis of EBs cultured in two different conditions: conventional incubator, static magnetic field incubator.

overall_design: We sought to investigate the differentiated expressed genes of J1 ESCs-derived differentiated cells cultured in two conditions: conventional incubator (short as NC), static magnetic field incubator (short as MF). EBs with biological triplicates were collected for RNA extraction and RNA-seq analysis simultaneously.

first: Zhaoyuan

last: Guo

first: Renpeng


title: Single-cell transcriptome analysis of stem cells from human exfoliated deciduous teeth investigating functional heterogeneity in immunomodulation

city: Beijing

first: Xueying

last: Wu

state: Beijing

address: No. 10, Tieyi Road, Yangfangdian, Haidian District

department: Beijing Shijitan Hospital

institute: Capital Medical University

summary: Background: Mesenchymal stem cells (MSCs) have been widely used in the treatment of various inflammatory diseases. The inadequate understanding of MSCs and its heterogeneity can impact the immune environment maybe the cause of the good outcomes of MSCs-based therapy cannot be always achieved. Recently, stem cells from human exfoliated deciduous teeth (SHED) showed a great potential in inflammatory and autoimmune diseases due to its unique immunomodulation properties. However, the cellular heterogeneity and the corresponding immunomodulation functions of SHED remains unclear. Methods: In this study, we applied single-cell RNA sequencing (scRNA-seq) to analyze and performed bioinformatic analysis to clarify the variations immunomodulation functions of SHED subpopulations in different differentiation state. After the integration of public available databases, we analyzed the transcriptome and compared the difference of immunomodulation functions of MSCs from different tissues. Results: SHED in low differentiation state (S7) exhibited the powerful ability to recruit multiple types of immune cells, whereas SHED in relatively high differentiation state (S1) may hold strong ability to secret many factors with paracrine signaling capacity. Compared with human bone marrow derived mesenchymal stem cells (hBMSCs) or human umbilical cord-derived mesenchymal stem cells (hUCMSCs), SHED is stronger in immunomodulatory property, especially in recruitment of Th17, Th22 and Treg cells. Conclusion: SHED was a heterogeneous MSCs population with different differentiation states and immunomodulatory functions. SHED may have some advantages in treatment of inflammatory and autoimmune diseases. Our works provides some theoretical foundation for the SHED-based therapy in clinical applications.

overall_design: single cell RNA sequencing onmesenchymal stem cell from naturally exfoliated deciduous incisors from an 8-year-old child.

first: Yin

last: Li


title: RNAseq  and scRNAseq analysis of UPFL mouse tumors

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

summary: Fibroblast growth factor receptor 3 (FGFR3) is altered in up to 50% of urothelial cancers (UC), yet its functional impact is not fully understood. We generated a Cre-inducible FGFR3 S249C allele (LSL-FGFR3 S249C) to understand the functional impact of FGFR3 activation on UC biology, the immune microenvironment, and how FGFR inhibition combines with PD1 immune checkpoint inhibition (ICI). Uroplakin3a (Upk3a) driven expression of Trp53 R270H and FGFR3 S249C (UPFL) promoted tumor formation.

overall_design:
bulk RNAseq from primary UPFL tumors (n=7) and scRNAseq from primary UPFL control (n=2) or Erdafitinib (n=2) treated tumors.
Pooled scraped urothelium from 10 wild-type female mice without treatment are anlyzed using scRNAseq

first: Atsushi

last: Okato

first: Takanobu

last: Utsumi

first: Michela

last: Ranieri

first: Xingnan

last: Zheng

first: Mi

last: Zhou

first: Luiza

middle: D

last: Pereira

first: Ting

last: Chen

first: Di

first: Ujjawal

last: Manocha

first: Sara

middle: E

last: Wobker

first: Jeffrey

middle: S

last: Damrauer

first: Kwok-Kin

last: Wong

middle: Y


title: Cardiac patch treatment alleviates ischemic cardiomyopathy correlated with unloading pathological stretch and reverting Piezo1/2 expression in left ventricular myocardium

city: hangzhou

first: sibo

last: jiang

address: zhejiang

institute: zju

summary: Pathologically elevated mechanical load promotes the adverse remodeling of left ventricle (LV) post myocardial infarction, which results in the progression from ischemic cardiomyopathy to heart failure. Cardiac patches could attenuate adverse LV remodeling by providing mechanical support to infarcted and border zone myocardium. However, the mechanism of the translation from mechanical effects to favorable therapeutic outcome is still not clear. This study aims to strengthen the foundation of the theory of cardiac patch treatment. By transcriptome analysis, we found that the myocardial transcription levels of mechanosensitive ion channel proteins Piezo1 and Piezo2 significantly increased in patients with ischemic cardiomyopathy. In vitro tensile tests with local tissue information and finite element modeling revealed a significant decrease in local strain and mechanical load in rat infarcts and sheep LV. Cardiac function and geometry were preserved compared to non-treated control. Further, in LV myocardium of the patch-treated group, MI induced expression levels of Piezo1/2 were significantly reverted to the similar levels of the control group, indicating that Piezo1/2 are key contributors as mechanosensor which initiated the signaling cascade and translated the beneficial mechanical support to therapeutic effects. These findings demonstrated the potential of cardiac patches in treating ICM patients with remodeling risks, and could provide guidance for improvement in next generation of patch devices.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for heart of sham, MI and patch rats

first: Yang

last: Zhu

first: Yuwen

last: Lu

first: Sibo

last: Jiang

first: Lenan

last: Zhuang


title: Neoadjuvant immune checkpoint blockade in retroperitoneal dedifferentiated liposarcoma and extremity/trunk undifferentiated pleomorphic sarcoma (NCT03307616)

city: Houston

first: Jennifer

last: Wang

state: TX

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: Recent evidence suggests that immune checkpoint blockade (ICB) has some activity in metastatic dedifferentiated liposarcoma (DDLPS) and undifferentiated pleomorphic sarcoma (UPS). We conducted a randomized, non-comparative phase 2 trial (NCT03307616) of nivolumab or nivolumab/ipilimumab in patients with resectable retroperitoneal DDLPS (n=17) and extremity/truncal UPS (n=10), with UPS patients receiving concurrent radiation therapy. The primary endpoint of pathologic response as assessed by percent hyalinization was observed to be a median of 8.8% in DDLPS patients and 89% in UPS patients and similar in nivolumab and ipilimumab/nivolumab arms in both cohorts . Higher intratumoral densities of T-regulatory cells were associated with absence of pathologic response (hyalinization<30%). Tumor infiltration by B-cells was associated with higher densities of T-regulatory cells before treatment;  this association was lost upon ICB treatment. Our data demonstrate that neoadjuvant ICB with concurrent radiation may have significant efficacy in UPS and is associated complex immune changes in the tumor microenvironment in DDLPS and UPS.

overall_design: Tumor samples were collected at baseline, on treatment and at surgery for all patients, and analyzed using bulk RNA sequencing.

first: Christina

middle: L

last: Roland

first: Chia

middle: C

last: Wu

first: Elise

middle: F

last: Nassif

first: Emily

middle: Z

last: Keung


title: Dual RNA-sequencing of macrophages infected with Mycobacterium avium reveals host-pathogen interaction in the context of clarithromycin treatment

city: Nijmegen

first: Jodie

last: Schildkraut

address: Geert Grooteplein Zuid 10

institute: Radboudumc

summary:
Background: Mycobacterium avium is an opportunistic pathogen that requires complex multidrug treatment. Macrolides, like clarithromycin, are the cornerstone of treatment, but even macrolide-based treatment regimens have suboptimal outcomes. Combining transcriptomic profiling of macrophages and mycobacteria in an in vitro infection model may increase our understanding of the host-pathogen interaction and the effect of antibiotic treatment.
Methods: To investigate the molecular interplay between pathogen and host, we developed an optimized protocol for dual RNA-sequencing of human monocyte-derived macrophages infected with M. avium.
Results: Upon phagocytosis, host defense processes including immune activation and pathogen recognition were upregulated, while M. avium upregulated expression of PE/PPE genes, which are important for immune recognition. Clarithromycin did not affect gene regulation of the host; the effect of clarithromycin on M. avium gene expression was very different in RPMI compared to intracellular mycobacteria, likely due to the influence of the host environment on expression of the important regulatory WhiB genes.
Conclusions These data identify the distinct stress responses of M. avium upon infection and clarithromycin treatment and underline the importance of taking the intracellular localization and interaction with the host into account when studying antibiotics against intracellular pathogens.

overall_design: RNA-sequencing of M. avium within human monocyte-derived macrophages  in the presence and absence of clarithromycin

last: Schidkraut

first: Jordy

middle: P

last: Coolen

first: Jakko

last: van Ingen

first: Valerie

last: Koeken

first: Reinout

last: van Crevel


title: Proteomic characteristics of mesenchymal subtypes of hepatocellular carcinoma

first: Ju-Seog

last: Lee

state: Texas

address: 6565 MD Anderson Blvd

institute: UT MD Anderson Cancer Ctr.

summary: Clinical heterogeneity of hepatocellular carcinoma (HCC) reflected in unequal outcome of treatment is poorly defined in molecular level, and molecular subtypes and their associated biomarkers have not been established to improve prognostification and treatment of HCC. Using reverse phase protein arrays (RPPA) technologies, we analyzed protein expression profiling data from HCC patients, uncovered mesenchymal subtype, and identified gene expression signature associated with mesenchymal phenotype of HCC.

overall_design: We generated proteomic data from tumors of 113 HCC tumors and matched surrounding liver tissues  from patients who underwent surgical resection as primary treatment

first: Yun

last: Jeong

first: Soo

last: Kim

first: Sun

last: Yim


title: Transcriptome profiling of rice plants in response to 2-Nitroaniline

city: Shanghai

first: zhenjun

last: li

address: Beidi rd 2901

institute: Shanghai academy of agricultural sciences

summary: In order to investigate the roles of ScOYE3, an old yellow enzyme gene from Saccharomyces cerevisiae, in detoxification and phytoremediation of 2-Nitroaniline (2-NA) in rice, we employed the RNA-seq approach to identify differentially expressed genes in 2-NA-treated wild-type (ZH11) rice plants and transgenic (OE1) rice plants overexpressing ScOYE3. Processing of RNA samples on the Illumina HiSeq 4000 system yielded more than 50 million reads, each 100bp in length, encompassing 6.28Gb of sequence data for each sample which was then mapped to the reference genome. Quantitative analysis of RNA-seq data identified substantial variation in expression profiles among different genotypes, consistent with known functional differences. Transcript abundance obtained from RNA-seq data was indicated as TPMs and therefore, Up- and down-regulated genes were determined by a greater than 2-fold change of normalized TPMs (padjust<0.05) in comparison analysis.

overall_design: RNA-sequencing was carried out using ZH11 and transgenic (OE1) rice seedlings. Total RNA was isolated with Trizol reagent (Invitrogen, USA) from untreated and 2-NA treated two-week-old seedlings of ZH11 and OE1 grown in parallel. Materials from 20 plants of each sample were pooled for RNA isolation.

first: Zhenjun

last: Li


title: Comparison p4 CA1 pyramidal cell layer MGE derived interneuronal transcriptomes between male and female GPHNWT and GPHNS268/270A mutant mice acquired using patch sequencing techniques

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

summary: In order to understand why blocking gephyrin phosphorylation via mutating serines 268 and 270 to alanine disrupts PV interneuron development in the hippocampus, we recorded spontaneous and elicited activity in developing MGE derived interneurons within the dorsal hippocampal CA1 pyramidal cell layer, then aspirated the contents of the cells to detect differences in the transcriptomic state between sexes and genotypes.

overall_design: We collected acute slices from post-natal day 4 male and female GPHNWT and GPHNS268/270A mouse pups which were crossed to an Nkx2.1 Cre: Ai14 TdT  background, allowing us to record electrophysiologically from TdTomato postive MGE-derived interneurons within the CA1 pyramidal cell layer, representing an enrichment of putative parvalbumin (PV) type basket cells.

first: Benjamin

last: Campell

first: Natalia

last: Cruz Ochoa

first: David

last: Lukacsovich

first: Wenshu

last: Luo

first: Shiva

last: Tyagarajan


title: TFAM loss induces nuclear actin assembly upon mDia2 malonylation to promote liver cancer metastasis [RNA-Seq]

city: Xi’an

first: QICHAO

last: HUANG

address: Changle Western Road

institute: Fourth Military Medical University

summary: The mechanisms underlying cancer metastasis remain poorly understood. Here, we report that TFAM deficiency rapidly and stably induced spontaneous lung metastasis in mice with liver cancer. Interestingly, unexpected polymerization of nuclear actin was observed in TFAM-knockdown HCC cells when cytoskeleton was examined. Polymerization of nuclear actin is causally linked to the high-metastatic ability of HCC cells by modulating chromatin accessibility and coordinating the expression of genes associated with extracellular matrix remodeling, angiogenesis and cell migration. Mechanistically, TFAM deficiency blocked the TCA cycle and increased the intracellular malonyl-CoA levels. Malonylation of mDia2, which drives actin assembly, promotes its nuclear translocation. Importantly, inhibition of malonyl-CoA production or nuclear actin polymerization significantly impeded the spread of HCC cells in mice. Moreover, TFAM was significantly downregulated in metastatic HCC tissues and was associated with overall survival and time to tumor recurrence of HCC patients. Taken together, our study connects mitochondria to the metastasis of human cancer via uncovered mitochondria-to-nucleus retrograde signaling, indicating that TFAM may serve as an effective target to block HCC metastasis.

overall_design: RNA-seq was performed on 6 cell lines (3 shTFAM SNU-368 vs 3 shCtrl SNU-368 )

first: Qichao

last: Huang


title: Transcriptome analysis the iPSC-RPE cells, iRPE cells, hUCMSCs and ARPE19

first: Haibin

last: Tian

address: 1239 Siping Road

institute: Tongji University

summary: We aim to explore the types and expression of RNA in  iPSC-RPE cells, iRPE cells, hUCMSCs and ARPE19.

overall_design: Two iPSC-RPE cells, two induced RPE cells (iRPE) from hUCMSCs, two hUCMSCs, two ARPE19, were analyzed with RNA sequencing.

first: Xiaoman

last: Zhu

first: Zhiyang

last: Chen


title: Insm1 regulates the expression of thymic tissue-restricted antigens and the immune tolerance

city: Guangzhou

first: Shiqi

last: Jia

address: Huangpu Avenue West 613

institute: Jinan University

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

overall_design: Refer to individual Series


title: Insm1 regulates the expression of thymic tissue-restricted antigens and the immune tolerance [RNA-seq]

summary: Insm1, encoding a zinc finger protein, is expressed specifically in neuroendocrine cells. Recent study showed the first evidence of Insm1 expression in medullary thymic epithelial cells (mTEC). Here we investigated the expression and function of Insm1 in mTEC. Mutation of Insm1 resulted in decreased proportion of mTEChi although normal development of other types of thymic cells. We detected altered expression of a subset of tissue-restricted antigens (TRAs) and mild decreased expression of Aire and Fezf2 in Insm1 mutant mTEC. We further showed that Insm1 recognizes a DNA sequence which is similar to the CCCTC-Binding factor (CTCF) binding motif. Mutation of Insm1 altered CTCF binding genome widely and thus the expression of genes. In nude mice transplanted with Insm1 mutant thymus, autoimmune responses were observed in multiple peripheral tissues. In thymus specific Insm1 mutant mice, we detected decreased induction of regulatory T (Treg) cells in the thymus, obvious lymphocytes infiltration and autoimmune antibody reaction in several peripheral tissues. In thymic epithelial cells specific Insm1 overexpression mice, we detected enlarged mTEC proportion and increased expression of mTEC specific genes. Thus, we suggest that Insm1 is a novel regulator of mTEC function and autoimmunity.

overall_design: mRNA profiles of wt and Insm1-mutate mouse medullary thymic epithelial cells

first: Wehuai

last: Tao

first: Jieyi

last: Xiong

first: Yiqiu

last: Wei


title: RNAseq in human TALL cells expressing shRNA control or against SIRT1

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany Street

institute: Rutgers Cancer Institute of New Jersey

summary: The human T-ALL cell line DND41 was treated to induced the expression of the shRNA-Control or the shRNA-SIRT1. Here we report the gene expression profile of leukemic cells treated in vitro.

overall_design: RNAseq analysis of DND41 cells after expression shControl or shSIRT1, three samples per condition.

first: Olga

last: Lancho

first: Amartya

last: Singh

first: Hossein

last: Khiabanian


title: The interfering transcription activator-like effector DR16 and OsSOG1 attenuates OsTOPBP1C-activated rice bacterial blight resistance

first: Wenxue

last: Zhai

address: NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China

department: Molecular Agrobiology

institute: Institute of Genetics and Developmental Biology

summary: we monitored the responsive changes of rice genes at 0 and 6 hours across Xoo pathotype GIV infection in Nipponbare (NIP), ostopbp1c mutant and OsTOPBP1C-overexpressor by RNA sequencing. These findings provide new insights for directly identifying iTALEs-targeted resistance gene and the regulatory roles of OsTOPBP1C in rice-Xoo interactions.

overall_design: Examination of the  responsive changes of rice genes at 0 and 6 hours under Xoo pathotype GIV treatment in Nipponbare (NIP), ostopbp1c mutant and OsTOPBP1C-overexpressor by RNA sequencing

first: Quanlin

last: Li

first: Yongli

last: Zhou


title: Hepatic enhancer signature and regulatory network of non-alcoholic steatohepatitis (NASH) resistance in humans with obesity [leChRO-seq]

city: Ithaca

first: Praveen

last: Sethupathy

state: New York

address: 618 Tower Road, T7006

institute: Cornell University

summary: Assessment of chromatin transcription activity of liver biopsies from individuales who were stratified to either NASH prone (NP) or NASH resistance (NR)

overall_design: Length extension chromatin run-on sequencing (leChRO-seq) was performed to determine genomewide chromatin activity of 18 human livers (n = 6 NR, n = 8 NP, n = 4 did not satified NP or NR criteria based on clinical profiles).

first: Yu-Han

last: Hung


title: Difference expression genes analysis of wild type and csa mutant during rice seed germination

first: Linlin

last: Sun

address: Dong chuan Rd. 800 Ming hang

institute: SJTU

summary: Transcriptomic analyses (RNA-seq) on RNA isolated from rice embryo at 3 h, 6 h, and 12 h pot-imbibition was performed to identify changes in gene expression in response to CSA.

overall_design: Examination of 2 different gene expression in rice embryo after 3 h, 6 h and 12 h imbibition.

first: Dabing

last: Zhang


title: RNA-sequencing  of wild type and Piezo1-Cko mice under sham or TAC surgery

first: Yuhao

state: zhejiang

address: jiefang road 88

institute: Second Affiliated Hospital Zhejiang University School of Medicine

summary: Mechanotransduction has been lately recognized as a major regulator of organ homeostasis under a myriad of pathological conditions. The role of Piezo1 in cardiac hypertrophy has never been explored. Here we performed  RNA-Seq assay for  wild type and Piezo1-Cko mice under sham or TAC surgery.

first: Sheng'an

last: Su

first: Wudi

first: Hong

last: Ma


title: Transcriptomic profiling of HepaRG cells with or without fat-loading

city: Regensburg

first: James

middle: A.

last: Hutchinson

department: Surgery

institute: UKR

summary: We report whole genome gene expression in HepaRG cells, a human hepatocellular carcinoma cell line, that were either treated with palmitic and oleic acid or solvent only. These data capture transcriptional events related to the response of human hepatocyte-like cells to fat-loading.

overall_design: Four paired, independent replicates of fat-loaded (FL) and control unloaded (UL) HepaRG cells.

first: J

last: HUTCHINSON

first: N

last: STRIEDER

first: M

last: REHLI

first: P

last: BECKHOVE


title: Depletion of PEA15 expression in FOCUS cells

first: Ju-Seog

last: Lee

summary: To understand roles of PEA15 in HCC, expression of PEA15 was depleted in FOCUS cells.

overall_design: We generated gene expression data from FOCUS cells treated with shRNA spcecific to PEA15 and control shRNA

first: Yun

last: Jeong

first: Bo

middle: H

last: Sohn


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and β-cateninΔ(ex3)/+  liver tissues Transcriptomes

first: Fangming

last: Liu

address: No.5 Dongdan 3 Tiao

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

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: Liver tissues‘ mRNA profiles of 8-week-old wild-type (WT) and liver specific β-cateninΔ(ex3)/+ mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, Genes differential expression analysis between the WT and β-cateninΔ(ex3)/+ was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Conclusions: Our study represents the first detailed analysis of liver transcriptomes, with 3 biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Liver mRNA profiles of 8 weeks old wild type (WT) and  β-cateninΔ(ex3)/+ mice

first: Xiaochen

last: Gai


title: TFAM loss induces nuclear actin assembly upon mDia2 malonylation to promote liver cancer metastasis

first: QICHAO

last: HUANG


title: Legumain dependent gene signatures in stromal progenitors

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

institute: University of Southern Denmark and Odense University Hospital

summary: LGMN has been shown to regulate cell fate decission of stromal progenitors of the bone. To understabnd the underlying mechanisms and gene signatures that are responsive to elevated or diminished levels of LGMN we performed RNA-seq analysis on stable cell lines with diminished (LGMN knockdown) or elevated (LGMN overexpression) levels of LGMN at the progenitor level. Genes responsive to LGMN levels show invers dynamics during osteoblast and adipocyte differentiation.

overall_design: Stable cell lines were generated from human stromal progenitor cells of bone marrow origin (BM-hMSC-TERT4 cells) with overexpression or knockdown of the asparaginyl endopeptidase (AEP) legumain (LGMN). RNA-seq was performed on 3 replicates of cells with LGMN overexpression (T4_LGMN) and control (T4_pBabe) as well as LGMN knockdown (T4_shLGMN) and control (T4_shCtrl).

first: Abbas

last: Jafari


title: Human PDAC Cells: scramble Control vs. RINT shRNA downregulated

city: Ulm

first: Hans

last: Kestler

address: Albert-Einstein-Allee 11

department: Research Group Bioinformatics and Systems Biology

institute: University of Ulm

summary: Time resolved transcriptional profiling of scramble and RINT1 down-regulated MIA PaCa-2 PDAC cells

overall_design: Eight-condition experiment, MIA PaCa-2 cells with either doxycycline inducible scramble or RINT1 shRNA vector. Four different time points  (0h, 24h, 48h, 96h) Biological replicates: 2 control replicates per time point, 2 transfected replicates per time point.

first: Frank

last: Arnold

last: Kleger


title: Card9 protects zymosan-induced peritonitis through regulating autophagy in macrophage

city: nanjing

first: zhen

last: xu

address: hankou street 22

institute: nanjing university

summary: CARD9 is an adapter protein, which plays a critical role in anti-fungal immunity. However, the role of CARD9 in fungal-induced autophagy remains unknown. In this study, we demonstrated that Card9-/- mice displayed more severe phenotype of zymosan-induced peritonitis, presenting as multiple organs injury and increased systemic inflammation. Moreover, the number of macrophage in spleen was increased in Card9-/- mice. Further studies revealed that autophagy was impaired in peritoneal macrophages of Card9-/- -peritonitis mice. Notably, the autophagy agonist, rapamycin, ameliorated peritonitis in Card9-/- mice. Moreover, Card9 mediates the interaction of Malt1 and P62 upon zymosan stimulation. Together, our results confirmed the protective role of Card9 in the development of peritonitis via regulates autophagy in macrophage cells. The study indicates Card9 may be a potential therapeutic target for peritonitis.

overall_design: peritoneal macrophages from wt and card9-/- mice with zymosan treated for 4 hours.

first: Zhen

last: Xu


title: Swine jejunum  at single cell level

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: jejunum scRNA-seq

overall_design: scRNA-seq of pig intestine in different locations

first: X

last: Wen

first: Y

first: H

last: Zhang

first: L

last: Chen

first: Q

last: Meng


title: Gene expression dynamics reveal Sprouty mediated regulation of Wnt pathway genes

city: Evanston

first: Neda

last: Bagheri

address: 2145 Sheridan Road, Tech E154

department: Chemical and Biological Engineering

institute: Northwestern University

summary: Sprouty genes (Spry) are feedback regulators of receptor tyrosine kinase signaling, and are genes with known tumor suppressing activity. The impact of Spry induction is ligand specific, but it is well-understood to be a negative feedback regulator of the mitogen-activated protein kinase pathway in response to fibroblast growth factor (FGF). However, the precise impact Spry has on transcription resulting in tumor suppression remains unknown. We use DiffExPy to analyze time-series gene expression data in Spry124fl/fl and Spry124-/- murine embryonic fibroblasts (MEFs). We show that the expression dynamics of Spry in response to FGF encode transcriptional regulation that spans RNA production, metabolism, and apoptotic processes. We also present results that suggest Spry regulates the angio- and oncogenic gene connective tissue growth factor (Ctgf ) via the Wnt signaling pathway. Our results clarify the transcriptional role of Spry, and provide quantitative, testable models of gene expression that can be applied and validated in different experimental contexts.

overall_design: We assessed gene expression changes upon loss of feedback regulation through Sprouty (Spry) deletion. Spry124fl/fl (WT) and Spry124-/- (KO) MEFs were profiled at 0, 15, 60, 120, and 240min after FGF treatment. Microarray profiling was performed in biological triplicate, except at 0min which, was conducted in quadruplicate. The genetic condition, replicate, and time point is included in the sample name.

first: Justin

last: Finkle

first: Behnam

last: Nabet

first: Jonathan

last: Licht


title: Insm1 regulates the expression of thymic tissue-restricted antigens and the immune tolerance [CUT&Tag]

first: Shiqi

last: Jia

overall_design: CUT&Tag (Cleavage Under Targets and Tagmentation) sequencing of Insm1- and Ctcf-target in mouse medullary thymic epithelial cells

first: Wehuai

last: Tao

first: Jieyi

last: Xiong

first: Yiqiu

last: Wei


title: Gut IgA Enhances Systemic IgG Responses to Pneumococcal Vaccines Through the Commensal Microbiota

city: New York

first: Lewis

last: Tomain

address: 225 East 95th Street, Apt16E

department: Population Health Science and Policy

institute: Icahn School of Medicine at Mount Sinai

summary: We set up to characterize the global transcriptome of splenic follicular (FO) B cells from control wild type (Wt) and Igha-deficient (IgAKO) mice with the aim of gaining new insights into how translocated gut antigens may impair IgG production to vaccines in the absence of IgA. Splenic Marginal zone (MZ) B cells were also included in this study, as IgA deficiency impaired IgG responses to T-independent immunogens as well.

overall_design: RNA from sorted splenic MZ B cells and FO  B cells were obtained from 4-5 age- and sex-matched wild type and IgA-deficient (IgAKO) mice.

first: Cindy

last: Gutzeit

first: Emilie

middle: K

last: Grasset

first: Paul

last: Maglione

last: Tomalin

first: Mayte

last: Suarez-Farina

first: Andrea

last: Cerutti


title: PDGFRα+ not CD137+ progenitors control visceral obesity via glucocorticoid mediated TEAD1 methylation state

first: yifan

last: lv

state: jiangsu

address: 300 Guangzhou Road

department: Department of Geriatrics

institute: the First Affiliated Hospital to Nanjing Medical University

type: Methylation profiling by high throughput sequencing

summary: summary:Glucocorticoids have impact on visceral obese which crucial contributor to the burden of obesity complications. Subcutaneous and visceral adipose have the heterogeneity of cellular populations. However, the mechanism of glucocorticoids mediated depot-specific regulation remains unclear. Here, we report PDGFRα+ progenitors, dominated in visceral adipose which can convert to white-typical adipocytes, are glucocorticoid-sensitive progenitors. While CD137+ progenitors, mainly harbored in subcutaneous adipose, which are beige-typical adipocytes, are glucocorticoid-passivated progenitors. Mechanistically, we proved that Glucocorticoids elevate TEAD1, transcriptional coactivator of glucocorticoid receptor, by down-regulating the methylation states in PDGFRα+ progenitors. TEAD1 bonds the accessible binding sites in miR-27b promoter region and transcriptionally increases miR-27b expression which previously proved to be the browning ability inhibitor in human and rodent white adipose. These data provide insight into the mechanism of glucocorticoids mediation of visceral obesity and the pathophysiology of depot-specific variations of high fat diet induced obesity.

overall_design: two samles

first: Yifan

last: Lv

first: Guoxian

last: Ding


title: TFAM loss induces nuclear actin assembly upon mDia2 malonylation to promote liver cancer metastasis [ATAC-seq]

first: QICHAO

last: HUANG

institute: Fourth Military Medical University

summary: The mechanisms underlying cancer metastasis remain poorly understood. Here, we report that TFAM deficiency rapidly and stably induced spontaneous lung metastasis in mice with liver cancer. Interestingly, unexpected polymerization of nuclear actin was observed in TFAM-knockdown HCC cells when cytoskeleton was examined. Polymerization of nuclear actin is causally linked to the high-metastatic ability of HCC cells by modulating chromatin accessibility and coordinating the expression of genes associated with extracellular matrix remodeling, angiogenesis and cell migration. Mechanistically, TFAM deficiency blocked the TCA cycle and increased the intracellular malonyl-CoA levels. Malonylation of mDia2, which drives actin assembly, promotes its nuclear translocation. Importantly, inhibition of malonyl-CoA production or nuclear actin polymerization significantly impeded the spread of HCC cells in mice. Moreover, TFAM was significantly downregulated in metastatic HCC tissues and was associated with overall survival and time to tumor recurrence of HCC patients. Taken together, our study connects mitochondria to the metastasis of human cancer via uncovered mitochondria-to-nucleus retrograde signaling, indicating that TFAM may serve as an effective target to block HCC metastasis.

overall_design: ATAC-seq  was performed on 6 cell lines (3 shTFAM SNU-368 vs 3 shCtrl SNU-368 )

first: Qichao

last: Huang


title: Dynamics of NRSF/REST motif evolution favor the canonical NRSE/RE1 form

city: IRVINE

first: Shan

last: Jiang

address: 2300E Biological Sciences III

institute: UNIVERSITY OF CALIFORNIA, IRVINE

summary: The transcription factor NRSF/REST represses many vertebrate neuronal genes in non-neuronal cells by binding to 3 distinct motif classes, which are the canonical 21bp NRSEs, longer non-canonical sites and solo half-sites. We used ChIP-seq in four mammalian species to determine the evolution of the NRSF binding repertoire. We show that while some NRSEs are deeply conserved, genes with several NRSEs show evidence of compensatory site turnover, suggesting that the association of the transcription factor to its target gene is more important than the specific binding site. We also found that many newborn sites in human are associated with primate specific indels and transposable elements. Our analysis of sites with conserved ChIP-binding in all 4 species demonstrates that both the non-canonical and solo half-sites convert preferentially to canonical motifs. These findings support a model of dynamic conversion between different motif types that account for the preferential accumulation of the canonical NRSE during evolution.

sample_organism:
Canis lupus familiaris
Equus caballus
Mus musculus

overall_design: Performed NRSF/REST ChIP-seq on mouse macrophages, dog myelomonocytic leukemia cells and horse skin fibroblasts. Each group with two IP replicates and one DNA input.

first: Nicole

last: El-Ali

first: Ricardo

last: Ramirez

first: Ali

last: Mortazavi


title: RNAseq in Sirt1 wild-type or deleted mouse T-ALLs

first: Daniel

last: Herranz

summary: C57BL6 mice harboring Sirt1 conditional knockout NOTCH1-HDDPEST-induced leukemias were treated with vehicle (control) or tamoxifen to induce isogenic deletion of Sirt1. Here we report the gene expression profile of leukemic blasts obtained from the spleen from control- or tamoxifen-treated leukemic mice.

overall_design: RNAseq analysis of leukemic spleens in two genotypes and five samples per genotype.

first: Olga

last: Lancho

first: Amartya

last: Singh

first: Hossein

last: Khiabanian


title: Differential activation states of direct pathway striatal output neurons associated with the development of L-DOPA-induced dyskinesia II

status: Public on Dec 31 2023

city: Birmingham

first: David

last: Figge

state: AL

address: 1719 6th Ave. S, CIRC 520

department: Neurology

institute: University of Alabama-Birmingham

summary: L-DOPA-induced dyskinesia (LID) is a debilitating motor side effect arising from chronic dopamine replacement therapy with L-DOPA for the treatment of Parkinson disease (PD). We found repeated L-DOPA exposure induces unique transcriptional behavior in striatal neurons that is associated with the development of dyskinetic behaviors. These results suggest the development of a long-term neuronal engram underlying the persistence of LID .

overall_design:
Nuclei from 3-4 dorsal striata pooled per sample, and sorted for Live Nuclei  on a BD FACsAria. Sorted nuclei were loaded onto the 10X Chromium 303 platform (10X genomics), and libraries were constructed using the Single Cell 3′ 304 Reagent Kit V2 according to the manufacturer’s instructions. Two biological replicates for each group were processed separately.
-------------------------------------
Authors state "due to data corruption the raw fastq files for the remaining 4 samples are no longer available".

first: Karen

last: Jaunarajs


title: NF-κB memory coordinates transcriptional responses to dynamic inflammatory stimuli

city: Chicago

first: Savas

last: Tay

address: 5640 South Ellis Avenue, Chicago, IL 60637

department: PME

institute: University of Chicago

summary: We stimulate cells with three different MyD88-dependent ligands in a microfluidic device and collect cells after 2 hours

overall_design: Comparison of triplicate RelA-/- RelA-DsRed NIH3T3 populations exposed to IL-1B, LPS, or PAM collected 2 hours after stimulus.

first: Minjun

last: Son

first: Andrew

middle: G

last: Wang


title: Effect of SRI-41315 on translation termination in rabbit reticulocyte lysate-based in vitro translation system

city: Boston

first: Sichen

last: Shao

state: MA

address: 240 Longwood Ave. Room C2-451

department: Cell Biology

institute: Harvard Medical School

summary: Translation termination is an essential cellular process that is also of therapeutic interest for diseases that manifest from premature stop codons. In eukaryotes, translation termination requires eRF1, which recognizes stop codons, catalyzes the release of nascent proteins fom ribosomes, and facilitates ribosome recycling. The small molecule SRI-41315 triggers eRF1 degradation and enhances translational readthrough of premature stop codons. SRI-41315 promotes retention of eRF1 on ribosomes and leads to a higher frequency of translation termination at near-cognate stop codons. In this study, the systematic effect of SRI-41315 on translation termination at cognate and near-cognate stop codons is evaluated using a rabbit reticulocyte lysate-based in vitro translation system with endogenous transcript as well as reporter transcripts containing defined near-cognate stop codon.

overall_design: In vitro translation (IVT) reactions in rabbit reticulocyte lysate (RRL) were subject to ribosome profiling to investigate termination level at cognate and near-cognate stop codons. All IVT reactions contained endogenous transcripts as well as reporter transcripts containing cognate (UGA) or near-cognate (UGG or UGG_QW) stop codon as internal control to establish a baseline level of translation termination in the absence of SRI-41315. In SRI-41315 treatment groups (UGA_SRI, UGG_SRI, or UGG_QW_SRI), SRI-41315 was added to the IVT reactions to investigate its effect on translation termination on endogenous and reporter transcripts. The eRF1-AAQ mutant is known to trap terminating ribosomes in place and therefore was used as positive control (UGG_AAQ). Each condition contains two biological replicates using independently assembled IVT reactions.

first: Yingshi

last: Peng


title: Differential activation states of direct pathway striatal output neurons associated with the development of L-DOPA-induced dyskinesia

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

overall_design: Refer to individual Series


title: Structural basis of the DEK-nucleosome complex and its functional implications

city: changsha

first: shen

last: yunfan

state: hunan

address: xiangya road

institute: central south university

summary: The nuclear factor Dek is notably enriched within chromatin; nevertheless, the precise binding mechanism of Dek to the nucleosome remains elusive. In this study, we employ cryo-electron microscopy (cryo-EM) to elucidate the high-resolution structure of the Dek-Nucleosome Core Particle (NCP) complex. We identify specific domains responsible for DEK interaction with the histone octamer and DNA within the nucleosome. The veracity of these binding domains is confirmed through a series of meticulous biochemical experiments. Subsequently, cellular experiments reveal that Dek lacking nucleosome-binding capacity exhibits a deficiency in chromatin interaction. Remarkably, this impairment induces a shift towards the primitive endoderm fate in mouse embryonic stem cells, underscoring the pivotal role of Dek in determining cell fate through its nucleosomal interactions.

overall_design: HA-labeled wild-type DEK and various key domain mutations were overexpressed in DEK-knockout cells. CUT&Tag for HA was employed to assess the impact of mutations on the distribution of Dek on chromatin, while RNA-seq was used to identify transcriptomic changes induced by these mutations in the cells.

first: Shen

last: Yunfan

first: Liu

last: Yanhong

first: Huang

last: Hongda

first: Yuan

last: Kai


title: PELOTA and HBS1 suppress co-translational messenger RNA decay in Arabidopsis [GMUCT]

city: Philadelphia

first: Rong

last: Guo

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

summary: Various messenger RNA (mRNA) decay mechanisms play major roles in controlling mRNA quality and quantity in eukaryotic organisms under different conditions. While it is known that the recently discovered co-translational mRNA decay (CTRD), the mechanism that allows mRNAs to be degraded while still being actively translated, is prevalent in yeast, human, and various angiosperms, the regulation of this decay mechanism is less well studied. Moreover, it is still unclear whether this decay mechanism plays any roles in regulation of specific physiological processes in eukaryotes. Here, by re-analyzing the publicly available polysome profiling or ribosome footprinting and degradome sequencing datasets, we discovered that highly translated mRNAs tend to have lower co-translational decay levels. Based on this finding, we then identified Pelota and Hbs1, the translation-related ribosome rescue factors, as suppressors of co-translational mRNA decay in Arabidopsis. Furthermore, we found that Pelota and Hbs1 null mutants have lower germination rates compared to the wild type plants, implying that proper regulation of co-translational mRNA decay is essential for normal developmental processes. In total, our study provides further insights into the regulation of CTRD in Arabidopsis and demonstrates that this decay mechanism does play important roles in Arabidopsis physiological processes.

overall_design: GMUCT and mRNA-Seq libraries were constructed using 12-day-old seedlings of wild type (WT), Pelota and HBS1 null mutants

first: Brian

last: Gregory


title: PELOTA and HBS1 suppress co-translational messenger RNA decay in Arabidopsis [mRNA-Seq]


title: PELOTA and HBS1 suppress co-translational messenger RNA decay in Arabidopsis


title: Transient Inhibition of 53BP1 Increases the Frequency of Targeted Integration in Human Hematopoietic Stem and Progenitor Cells

city: Freiburg

first: Kay

middle: Ole

last: Chmielewski

address: Breisacherstr. 115

department: Institute for transfusion medicine and gene therapy

institute: University clininics Freiburg

summary: Genome editing by homology directed repair (HDR) is leveraged to precisely modify the genome of therapeutically relevant hematopoietic stem and progenitor cells (HSPCs). Here, we present a new approach to increasing the frequency of HDR in human HSPCs by the delivery of an inhibitor of 53BP1 (named "i53") as a recombinant peptide. We show that the use of i53 peptide effectively increases the frequency of HDR-mediated genome editing at a variety of therapeutically relevant loci in HSPCs as well as other primary human cell types. We show that incorporating the use of i53 recombinant protein allows high frequencies of HDR while lowering the amounts of AAV6 needed by 8-fold. HDR edited HSPCs were capable of long-term and bi-lineage hematopoietic reconstitution in NSG mice, suggesting that i53 recombinant protein might be safely integrated into the standard CRISPR/AAV6-mediated genome editing protocol to gain greater numbers of edited cells for transplantation of clinically meaningful cell populations.

overall_design: Hematopoietic stem and progenitor cells (HSPCs) of two different donors were edited with RNP or RNP + i53 peptide in the absence of AAV donor.

first: Ron

last: Baik

first: Kyle

last: Cromer

first: Steve

last: Glenn

first: Christopher

last: Vakulskas

last: Ole Chmielewski

first: Amanda

last: Dudek

first: William

middle: N

last: Feist

first: Julia

last: Klermund

first: Suzette

last: Shipp

first: Toni

last: Cathomen

first: Daniel

last: Dever

first: Matthew

last: Porteus

first: Geoffroy

last: Andrieux


title: Ribosome profiling of WT strain in Neurospora crass

city: Kunming

first: Yunkun

last: Dang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

department: School of Life Sciences

institute: Yunnan university

summary: Codon usage bias, which refers to uneven use of synonymous codons, was shown to associate with mRNA stability from yeast to human. However, the underlying molecular basis is largely unknown. With bioinformatic analyses we unexpectedly found that codon usage bias is inversely correlated to density of out-of-frame stop codons (hidden stop codon or HSC). To understand the physiological function of HSCs, we use the frequency gene of Neurospora crassa to examine the role of HSCs in circadian rhythm. We show that deleting HSCs in the upstream of frequency (frq) open reading frame without altering FRQ sequence resulted in loss of circadian rhythm. Further analyses revealed that HSC deletion of frq resulted in elevated stability of frq mRNA, which consequently causes higher FRQ protein level. Combined various methods, we showed that rare codons in the upstream frq region generates significant amount of aberrant translation at +1 frame, possibly via ribosomal frameshifting. Consistently, at genome wide we showed that both in N. crassa and S. cerevisiae, the codon usage bias combined with numbers of HSC are inversely correlated to mRNA stability. Together, these data indicate that HSCs might act as an intrinsic mechanism to terminate aberrant ribosomal frameshifting events triggered by non-optimal codons, thus fine-tune mRNA stability.

overall_design: Ribosome profiling of a Neurospora crassa wt strain was performed to get its translational landscape.

first: Zhanbiao

last: Li

first: Zeyu

last: Wang


title: Prognostic Significance of Immune Cell Infiltration in Muscle Invasive Bladder Cancer Treated with Definitive Chemoradiation: A Secondary Analysis of RTOG 0524 and 0712

city: baltimore

first: yang

last: song

state: MD

address: 670 W. Baltimore St.

institute: university of maryland in baltimore

summary: Chemoradiation therapy (CRT) is a treatment for muscle invasive bladder cancer (MIBC). Using a novel transcriptomic profiling panel, we validated prognostic immune biomarkers for response to CRT on 70 pre-treatment tumor samples from NRG/RTOG 0524 and 0712, two prospective trials of MIBC. Disease-free survival (DFS) and overall survival (OS) was estimated by Kaplan-Meier method and stratified by genes correlated with immune cell proportions and activation.  Cox proportional hazards models were used to assess group differences. Sample clustering based on gene expression profiles driven by immune cell proportions demonstrated cluster 2 with a high percentage of immune cell content with significantly longer DFS (Hazard Ratio (HR): 0.53 (95% CI: 0.26 – 1.10), p=0.071) and OS (HR: 0.48 (95% CI: 0.24 – 0.97), p=0.040) than cluster 1 with a low percentage of immune cell content.  Higher expression of T cell infiltration genes (CD8A and ICOS ) showed longer DFS (HR: 0.40 (95% CI: 0.21 – 0.75), p=0.005) and OS (HR: 0.49 (95% CI: 0.25 – 0.94), p=0.033). Higher expression of interferon gamma signaling (IDO1) also showed longer DFS (HR: 0.44 (95% CI: 0.24 – 0.88), p=0.021) and OS (HR: 0.49 (95% CI: 0.24 – 0.99), p=0.048). These findings have treatment implications that should be validated in CRT MIBC trials particularly those that integrate immunotherapy.

overall_design: To validate the prognostic value of T cell infiltration and IGS gene signatures in MIBC treated with CRT using a novel next-generation RNA-sequencing (NGS) profiling platform (Cofactor ImmunoPrism assay) that requires as little as 20 ng input RNA utilizing samples from two prospective trials of CRT in MIBC (NRG/RTOG 0524 (4) and 0712 (5)).Samples from the NRG biobank were profiled with the Cofactor Genomics ImmunoPrism assay, a CAP-CLIA certified NGS platform to quantify TME immune cell populations and activation using novel deconvolution algorithms from bulk tumor RNA .Using 64 differentially expressed genes associated with total immune cell proportions we identified high and low total immune cell proportions.

first: Zaker

last: Rana

first: Sophia

last: Kamran

first: Phuoc

middle: T

last: Tran

last: Deek

first: Amol

last: Shetty

first: Yang

last: Song


title: Vitamin D status associates with skeletal muscle loss after anterior cruciate ligament reconstruction.

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

summary:
BACKGROUND. Although 25-hydroxyvitamin D (25(OH)D) concentrations ≥30ng/mL are known to reduce injury risk and boost strength, the influence on anterior cruciate ligament reconstruction (ACLR) outcomes remains unexamined. This study aimed to define the vitamin D signaling response to ACLR, assess the relationship between vitamin D status and muscle fiber cross-sectional area (CSA) and bone density outcomes, and discover vitamin D receptor (VDR) targets post-ACLR.
METHODS. 21 young, healthy, physically active participants with recent ACL tears were enrolled (62% female; 17.8 ± 3.2 yr, BMI: 26.0 ± 3.5 kg/m2). Data were collected through blood samples, vastus lateralis biopsies, DXA bone density measurements, and isokinetic dynamometer measures at baseline, 1 week, 4 months, and 6 months post-ACLR. The biopsies facilitated CSA, western blot, RNA-seq, and VDR ChIP-seq analyses.
RESULTS. ACLR surgery led to decreased circulating bioactive vitamin D and increased VDR and activating enzyme expression in skeletal muscle one week post-operation. Participants with <30 ng/mL 25(OH)D levels (n=13) displayed more significant quadriceps fiber CSA loss one week and 4 months post-ACLR than those with ≥30 ng/mL (n=8; p<0.01 for post-hoc comparisons; p=0.041 for time x vitamin D status interaction). RNA-seq and ChIP-seq data integration revealed genes associated with energy metabolism and skeletal muscle recovery, potentially mediating the impact of vitamin D status on ACLR recovery. No difference in bone mineral density (BMD) losses between groups was observed.

overall_design: The purpose of this experiment was to identify potential target of the vitamin D receptor in human skeletal muscle (quadriceps) one week after anterior cruciate ligament recontruction (ACLR). Skeletal muscle samples from several participants were combined for 1 week post-ACLR quadriceps samples . This approach was necessary to provide the requisite 150m, and only data from this one combined sample is included here. Participants were 16-30 years of age, healthy, and included males anf females.

first: Jean

last: Fry

first: Christopher


title: Genome-wide maps of chromatin state in human adipose derived stem cells isolated from abdominal (abd) and gluteofemoral (glut) subcutaneous adipose tissue

status: Public on Jan 02 2024

city: St Petersburg

first: Edina

last: Erdős

address: 501 6th Ave S

institute: Johns Hopkins University

summary: Over the past two decades, studies have identified distinct transcriptional signatures between ABD and GF-adipose tissues and between both body shapes. Remarkably, a significant fraction of these depot specific gene expression patterns and more recently the differential chromatin structure profiles have been shown to be conserved during the culture and in vitro differentiation of the precursor cells into mature adipocytes. Our team and others have also shown distinct DNA methylation levels between ABD and GF-AT, that are preserved in isolated ADSCs cultured in vitro. Altogether, these data suggest that depot specific epigenomic profiles contribute significantly to the unique transcriptional profiles of ABD vs GF adipose tissues depots. To extend these earlier studies and to determine how the differential gene expression patterns in different adipose depots may be significantly influenced by chromatin landscape we performed H3K4me3, H3K4me2, H3K27me3, H3K9me3 and CTCF ChIP-seq and ATAC-seq on chromatin isolated from ABD and GF-ADSCs. We paired this with highly differentially expressed genes between ABD and GF-ADSCs. Then, to evaluate the potential role for long range chromatin interactions we utilized an H3K27Ac Hi-ChIP approach to capture putative regulatory loops with at least one anchor being marked by this enhancer associated histone mark. This in-depth analysis of the chromatin structure and organization of ABD and GF-ADSCs provides a better understanding of the intrinsic genomic regulatory features that help define the functionally distinct phenotypes of different subcutaneous adipose tissue depots and how they influence fat distribution in women.

overall_design: Human adipose derived stem cells (hASC) isolated from abdominal (abd) and gluteofemoral (glut) adipose tissue obtained from premenopausal women were used to perform assess accessible chromatin regions by ATAC-seq, chromatin marks, CTCF and RNAPII identification by ChIP-seq

first: T

last: Osborne

first: S

middle: R

last: Smith


title: Sex-based disparities in DNA methylation and gene expression in late-gestation mouse placentas

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

country: Canada

institute: CHU Ste-Justine Research Center/Université de Montréal

summary:
Background : The placenta is vital for fetal development and its contributions to various developmental issues, such as pregnancy complications, fetal growth restriction, and maternal exposure, have been extensively studied in mice. The placenta forms mainly from fetal tissue and therefore has the same biological sex as the fetus it supports. Extensive research has delved into the placenta’s involvement in pregnancy complications and future offspring development, with a notable emphasis on exploring sex-specific disparities. However, despite these investigations, sex-based disparities in epigenetic (e.g., DNA methylation) and transcriptomic features of the late-gestation mouse placenta remain largely unknown.

Methods : We collected male and female mouse placentas at late gestation (E18.5, n = 3/sex) and performed next-generation sequencing to identify genome-wide sex differences in transcription and DNA methylation.

Results
Our comparison between male and female revealed 358 differentially expressed genes (DEGs) on autosomes, which were associated with signaling pathways involved in transmembrane transport and the responses to viruses and external stimuli. X chromosome DEGs (n = 39) were associated with different pathways, including those regulating chromatin modification and small GTPase-mediated signal transduction. Differentially methylated regions (DMRs) were more common on the X chromosomes (n = 3756) than on autosomes (n = 1705). Interestingly, while most X chromosome DMRs had higher DNA methylation levels in female placentas and tended to be included in CpG dinucleotide-rich regions, 73% of autosomal DMRs had higher methylation levels in male placentas and were distant from CpG-rich regions. Several DEGs were correlated with DMRs. A subset of the DMRs present in late-stage placentas were already established in mid-gestation (E10.5) placentas (n = 348 DMRs on X chromosome and 19 DMRs on autosomes), while others were acquired later in placental development.

Conclusion : Our study provides comprehensive lists of DEGs and DMRs between male and female that collectively cause profound differences in the DNA methylation and gene expression profiles of late-gestation mouse placentas. Our results demonstrate the importance of incorporating sex-specific analyses into epigenetic and transcription studies to enhance the accuracy and comprehensiveness of their conclusions and help address the significant knowledge gap regarding how sex differences influence placental function.

overall_design: To investigate the DNA methylation differences in the mouse placenta at E10.5 between males and females, we conducted Reduced Representation Bisulfite Sequencing (RRBS)

first: Lisa-Marie

last: Legault

first: Mélanie

last: Breton-Larrivée

first: Anthony

last: Lemieux

first: Alexandra

last: Langford-Avelar


title: A positive feedforward circuit shaped by DLGAP5 and E2F1 triggers bladder cancer progression

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

summary: Bladder cancer (BLCA) is a highly prevalent malignancy on a global scale, characterized by significant tumor heterogeneity. The investigation of molecular mechanisms that can be leveraged for the management of aggressive BLCA represents a particularly pertinent objective.DLGAP5 is mitosis-related protein widely existed in eukaryotic cells. The molecular mechanism of DLGAP5 in bladder cancer is still not clear, despite its role in tumorigenesis. Bladder cancer tissues exhibit a noteworthy increase in DLGAP5 expression, compared to normal bladder tissues. Furthermore, the expression of DLGAP5 shows a positive correlation with the clinical stage of the tumor and a negative impact on the prognosis. Cell proliferation and migration are significantly impacted by alterations in DLGAP5 expression, as demonstrated by in vitro and in vivo experiments. Further investigation reveals that DLGAP5 regulated E2F1 protein stability via USP11 deubiquitinase activity, and DLGAP5 is a direct target of E2F1. DLGAP5-E2F1 forms a positive feedback loop and influences the efficacy of BLCA progression. Collectively, DLGAP5 could potentially serve as a new therapeutic target for the treatment of bladder cancer.

overall_design: In our exploration of the role played by the DLGAP5 gene in bladder cancer development, we conducted gene expression profiling analysis utilizing RNA-seq data acquired from T24 cells.

first: Fenfang

last: Zhou

first: Zhao

last: Deng

first: Dexin

last: Shen


city: Shanghai

first: Jianhua

last: Luo

address: 800 Xiangyin Road

institute: National Key Laboratory of Immunology & Inflammation, Institute of Immunology

summary: Motif-enrichment analysis identified binding sites for XBP1s in Neo-2/15 stimulated BBζ NK cells following co-cultured with AsPC-1 cells, as determined using CUT&TAG-seq, were mainly at the gene encoding nuclear respiratory factor 1 (NRF1)

overall_design: The CUT&Tag assay was conducted using Hyperactive Universal CUT&Tag Assay Kit for Illumina. Briefly, 106 BBζ NK cells were collected after co-cultured with AsPC-1 cells and washed. BBζ NK cells were bound to ConA beads for 10 min at 25 °C. Then cells were incubated with H3K9me2 antibody at 4 °C overnight. Anti-mouse IgG was added and incubated for 1 hour at 25 °C. Then cells were washed and incubated with 0.04 μM pA/G–Tnp for 1 hour at 25 °C and washed three times with DIG 300 buffer, resuspended in tag mentation buffer and incubated at 37 °C for 1 hour. Tag mentation was stopped by adding proteinase K, buffer LB and DNA extract beads. After incubation at 55 °C for 10 min, cells were plated on a magnet and unbound liquid was removed. Beads were rinsed twice. Libraries were constructed using TD903 Hyperactive Universal CUT&Tag Assay Kit for Illumina, and TD202 TruePrep Index Kit V2 for Illumina (Vazyme Biotech).

first: Luo

last: Jianhua

first: Guo

last: Meng


title: Gene expression during CCK-induced damaged pancreatic acinar cells with or without the addition of OCA

city: Yangzhou

first: Guotao

last: Lu

address: 368 Hanjiang Middle Road, Yangzhou

institute: The Affiliated Hospital of Yangzhou University, Yangzhou University

summary: Obeticholic acid (OCA) has shown pharmacological protection activity in acinar cell injury and pancreatic necrosis in vitro. RNA sequencing was performed by extracting mRNA from CCK-induced damaged pancreatic acinar cells with or without the addition of OCA. Gene enrichment analysis by Kyoto Encyclopedia of Genes and Genomes (KEGG) identified oxidative phosphorylation in the top ten significantly changed pathways. Similarly, Gene Set Enrichment Analysis (GSEA) enrichment analysis revealed clear alterations in "mitochondrial ATP synthesis coupled electron transport", "mitochondrial respiratory chain complex assembly", "NADH dehydrogenase complex assembly", and "oxidative phosphorylation".

overall_design: Fresh primary pancreatic acinar cells (PACs) were quickly isolated from mice using IV collagenase. PACs injury was induced by adding 1 μM cholecystokinin octapeptide (CCK) for 6 h. Cells were incubated with increasing concentrations of OCA(2.5µM).

first: Weiqin

last: Li


title: Replacement of dietary vitamin E by an extract rich in hydrox-ytyrosol, from the olive oil by-product “alperujo”, in broiler chickens: part II - effects on liver traits, oxidation, lipid profile and transcriptome.

city: Madrid

first: David

last: Menoyo

state: Madrid

address: Avenida Puerta de Hierro, 2-4

department: Producción Agraria

institute: Universidad Politécnica de Madrid

summary: The present study aims to evaluate the impact of replacing vitamin E (VE) by a liquid obtained from alpeorujo, an olive oil by-product rich in hydroxytyrosol (HT), on broiler liver traits, oxi-dation, lipid profile and transcriptomic analysis. There were 5 diets that differed only in the substitution of supplemental VE (0 to 40 mg/kg with differences of 10 mg/kg) by HT (30 to 0 mg/kg with differences of 7.5 mg/kg). A linear decrease (p < 0.05) of α-tocopherol concentration in the liver was observed with the replacement of VE by HT with no significant changes in tri-glycerides, cholesterol, and TBARs concentrations. The hepatic transcriptome showed 378 dif-ferentially expressed genes between broilers fed HT15 (20 mg/kg VE and 15 mg/kg HT) and HT0 (40 mg/kg VE) diets (p < 0.05 and Fold-Change less or higher than 1.3). Significant changes in cell cycle, cell nucleus activity, neuroactivity and necroptosis pathways and functions were observed. It is concluded that the olive oil by-product, rich in HT, could be used to spare VE as antioxidant in broilers diets without affecting liver lipids and TBARs concentrations. The differentially gene expression analysis showed a potential role of olive polyphenols in enhancing the chicken im-mune response.

overall_design: The experiment included 560 1-day-old male Cobb 500 chickens were randomly distributed among 35 floor pens with controlled environmental conditions(0.96 x 1.50 m) with 16 birds each and fed their respective experimental diets. The experiment was conducted with 5 treatments (HT0, HT7.5, HT15, HT22.5, and HT30) that consisted in 5 levels of supplemented vitamin E (0 to 40 mg/kg) with a difference of 10 mg/kg between diets. The vitamin E was substituted in these diets by HT (30 to 0 mg/kg) with a difference of 7.5 mg/kg between diets. Animals were provided with feed and water ad libitum. For microarray analysis, six liver total RNA samples per group were randomly selected for array hybridization.

first: Javier

last: Herrero

first: Nereida

last: Luna

first: Fernando

last: Sevillano

first: Robert

last: Ringseis

first: Klaus

last: Eder


title: Spatial total RNA sequencing of formalin-fixed paraffin embedded tissue by Spatial Random-seq

city: Hangzhou

first: Yongcheng

last: Wang

state: Zhejiang

address: 1369 Wenyixi Rd.

institute: Liangzhu Laboratory

summary: Current spatial transcriptomic methods have been widely used to resolve gene expression; however, these methods are limited to fresh or fresh-frozen samples due to unsuccess of oligo(dT) primers in degraded RNA samples. Here we develop a spatial random-sequencing (spRandom-seq) technology for Formalin-fixed paraffin-embedded (FFPE) tissues by capturing full-length total RNAs with random primers. This approach provides a powerful spatial platform for clinical FFPE specimens and promises enormous applications in biomedicine.

overall_design: Spatial single cell RNA-sequencing of FFPE mouse tissues using spRandom-seq , benchmark analysis was performed.

first: Jiaye

last: Chen


title: Genome-wide chromatin accessibility and gene expression profiles of human DIPG cell lines

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center


title: Genome-wide chromatin accessibility profile of human DIPG cell lines

summary: To study the chromatin accessibility across the genome of DIPG-VII, DIPG-IV, and DIPG-XIII cell lines, we performed ATACseq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing).

overall_design: Chromatin accessibility profiles of human DIPG cell lines.

first: Jyothishmathi

last: Swaminathan

first: Shinji

last: Maegawa

first: Lin

last: Xu

first: Vidya

last: Gopalakrishnan


title: A comparison between GalT-/-;hCD39;hCD55 and GalT-/-;hCD39;hCD46;hCD55;TBM pig kidney transplanted in non-human primates

city: Jeongeup-si

first: Hanna

last: Suh

address: 30, Baekhak 1-gil, Jeongeup-si, Jeollabuk-do, Republic of Korea

country: South Korea

institute: Korea institute of toxicology

summary: Due to shortage of donor kidney, genetically modified kidney xenograft from pigs is considered. To select the optimal gene modification for xenotransplantation, knockout of carbohydrate genes or knockin of protective proteins have been applied. In this study, we utilized GalT- /-;hCD39;hCD55 and GalT-/-;hCD39;hCD46;hCD55;thrombomodulin (TBM) pigs for transplantation in non-human primates. NHPs survived for 4 weeks after kidney transplantation (4 WAT) from GalT-/-;hCD39;hCD55 pig and 6 WAT from GalT- /-;hCD39;hCD46;hCD55;TBM pig. However, mRNA sequencing and immunohistochemistry analysis revealed that 6 WAT kidney showed the severe apoptosis, inflammation, loss of renal function, and renal fibrosis than 4 WAT kidney. These results suggest that additional knockin of anti-complement (hCD26) and anti-coagulation (TBM) is not sufficient to inhibit the renal damage.

overall_design: To select genotype that effectively alleviates immune rejection reponse, we performed comparative transcriptome profiling using mRNA seq data obtained from kidneys of GalT-/-;hCD39;hCD55 and GalT-/-;hCD39;hCD46;hCD55;thrombomodulin (TBM) pigs.

first: Juyoung

last: Lee

first: Ikjin

last: Yun

first: Wanseop

last: Kim

first: Kimyung

last: Choi

first: JeongHo

last: Hwang


title: Transcriptional decay profiling of Neurospora crassa

first: Yunkun

last: Dang

summary: Codon optimality mediated decay(COMD) is a conserved phenomenon from yeast to human. Our data suggests that COMD alson exist in neurospora crass. We resort thiolutin(inhibitor for transcription) to treat cells in different time point and transcriptionally profiled them to get the landscape of transpcriptional decay profiling.

overall_design: 24h cultured cell under constant light were treat with thiolutin(12μg/ml), then cell were harvested from time point 0min, 20min, 40min, 60min.

first: Zhanbiao

last: Li

first: Zeyu