title: Perturbed liver gene zonation in a mouse model of non-alcoholic steatohepatitis

city: Tarrytown

first: Yuanqi

last: Zhao

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

summary: Liver zonation characterizes the separation of metabolic pathways along the lobules and is required for optimal hepatic function. Wnt signaling is a master regulator of spatial liver zonation. A perivenous-periportal Wnt activity gradient orchestrates metabolic zonation by activating genes in perivenous hepatocytes, while suppressing genes in their periportal counterparts. The understanding of liver gene zonation and zonation regulators in disease was limited. Non-alcoholic steatohepatitis (NASH) is a chronic liver disease characterized by fat accumulation, inflammation, and fibrosis. Here, we investigated the perturbation of liver gene zonation in a mouse NASH model by combination of spatial transcriptomics, bulk RNAseq and in situ hybridization. Wnt target genes represented a major subset of genes showing altered spatial expression in the NASH liver. The altered Wnt target gene expression level and zonation spatial pattern were in line with the upregulation of Wnt regulators and the augmentation of Wnt signaling. Particularly, we found that the Wnt activator Rspo3 expression was restricted to the perivenous zone in control livers, whereas expanded to the periportal zone in NASH livers. AAV8-mediated RSPO3 overexpression in controls resulted in a zonation change, and further amplified the disturbed zonation of Wnt target genes in NASH, but had no impacts on steatosis, inflammation and fibrosis. In summary, our study demonstrated the alteration of Wnt signaling in a mouse NASH model, leading to perturbed liver zonation.

overall_design: Age matched adult (7-10 months old) male C57BL/6 mice (The Jackson Laboratory) were housed in a controlled environment (12-hour light/dark cycle, 22±1 °C, 60-70% humidity). 3 Mice were fed ad libitum with standard chow (Purina Laboratory, Rodent diet 5001, LabDiet) and 4 mice are fed on  CDAA-HFD diets (Diet A16092201i containing 45% fat and 28% fructose in calorie, and 1% cholesterol, 0.1% methionine with no choline, Research Diets) inducing NASH for 8-12 weeks. Two sections from each mouse were used for 10X Visium platform library preparation and sequencing.

first: Ye

last: Zhou

first: Mary

last: Germino

first: Christina

last: Adler

first: Xiping

last: Cheng


title: Hepatic ACLY deficiency and bempedoic acid drive divergent responses to dietary lipid

status: Public on Aug 01 2024

city: Philadelphia

first: Kathryn

middle: E

last: Wellen

state: PA

address: 421 Curie Blvd

country: USA

institute: University of Pennsylvania

type: Expression profiling by high throughput sequencing

summary: ATP citrate lyase (ACLY) synthesizes acetyl-CoA for de novo lipogenesis (DNL), which is elevated in non-alcoholic fatty liver disease. Hepatic ACLY is inhibited by the LDL-cholesterol lowering drug bempedoic acid (BPA), which has been shown to improve steatosis in mice. However, the acetyl-CoA synthetase ACSS2 can compensate for ACLY deficiency to support DNL, potentially complicating the targeting of ACLY. We show that hepatic loss of both ACLY and ACSS2 reduces DNL. Nevertheless, even when ACSS2 is suppressed by dietary or genetic means, we find that steatosis is counterintuitively exacerbated with hepatic ACLY deficiency in mice fed a Western diet (WD), linked to reduced expression of PPARa target genes controlling fatty acid oxidation. Conversely, BPA treatment increased fat catabolism and ameliorated WD-mediated lipid accumulation in both WT and liver ACLY knockout mice. Thus, hepatic ACLY plays an unexpected role in restraining diet-dependent lipid accumulation, and BPA improves steatosis independent of ACLY.

overall_design: To investigate the roles of ACLY and ACSS2 in hepatic lipid accumulation on Western diet, we generated mice with simultaneous liver-specific deletion of Acly and Acss2 (double knckout, DKO) by injecting Acly f/f; Acss2 f/f mice with adeno-associated virus 8 expressing Cre under a hepatocyte-speific promoter (AAV8-TBG-Cre) or GFP (AAV8-TBG-GFP) to generate wild-type (WT) controls. We then performed gene expression profiling analysis using data obtained from RNA-seq of livers from DKO and WT mice.

first: Joyce

middle: Y

last: Liu

first: Prateek

middle: V

last: Sharma


title: Circulating Extracellular Vesicular MicroRNA Signatures in Early Gestation Show an Association with Subsequent Clinical Features of Pre-Eclampsia

city: los angeles

first: Shubhamoy

last: Ghosh

state: CA

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the differential abundance of cell free miRNAs extracted from extracellular vesicles (EV) in the peripheral blood of pregnant women with or without preeclampsia by Next Generation Sequencing. Maternal blood samples were collected form pregnant women enrolled in the study during first to very early second trimester (11–14 weeks ), mid- to late second trimester (19–22 weeks), third trimester (36 weeks) and at delivery. Extracellular vesicles were isolated from peripheral blood and total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Valencia, CA) following manufacturer’s instruction.  miRNA libraries were prepared utilizing  NEB Next Multiplex small RNA Library prep kit (NEB E7300S; New England Biolabs, Inc, Ipswich, MA, USA) and libraries were subsequently sequenced using the HiSeq-2500 platform with single-end 50bp reads (Illumina Inc.; San Diego, CA, USA).

overall_design: Differential abundance of EV specific miRNAs were examined at different trimesters. Their association with miRNA targets and pathways were reviewed in the context of preeclampsia. Furthermore, an attempt was made to establish an early predictive model of preeclampsia based on the differential abundance of miRNAs in EVs.

first: Jeanette

last: Fong

first: Shanthie

last: Thamotharan

first: Sherin

last: Devaskar


title: RNA-seq analysis of mouse NSCLC tissues in the PBS, Taraxasterol (Tara), DC tumor vaccine and Taraxasterol combined with DC tumor vaccine group

city: ZunYi

first: meng meng

last: Guo

state: GuiZhou

address: Zunyi Medical University

department: Immunology

country: China

institute: Zunyi Medical University

summary: Purpose:gene discrepancy analysis and signaling pathway of tumor tissues in the PBS, Taraxasterol, DC tumor vaccine and Taraxasterol combined with DC tumor vaccine group

overall_design: Methods: C57BL/6 wild-type (6-8 weeks old) was used to prepare a mouse NSCLC model use LLC cells injected into the dorsal side of the mouse. 7 days after tumor cell inoculation with confirmation of successful maturation of tumors, mice were randomly divided into 4 groups: PBS control group; Tara group (Tara); DCs-vac group (DCs); Tara combined with DCs-vac group (D+T). PBS group: intraperitoneal injection of PBS, 0.2ml per mouse, once every 3 days, a total of 6 injections. Tara group: intraperitoneal injection of tara, 10mg/kg, once every 3 days, a total of 6 injections. DCs group: tail vein injection of DCs-vac,inject once every 7 days, with a total of 3 interventions. D+T group:12 hours after the first intraperitoneal injection of Tara (10mg/kg) , DCs-vac was injected into the tail vein. Tara is injected every 3 days, with a total of 6 interventions. DCs-vac is injected once every 7 days, with a total of 3 interventions. A total amount of 1-3μg RNA per sample was used as input material for the RNA sample preparations. The purity of the sample was determined by NanoPhotometer ®（IMPLEN, CA, USA；The concentration and integrity of RNA samples were detected by Agilent 2100 RNA nano 6000 assay kit （Agilent Technologies, CA, USA）.

first: DongMei

last: Li

first: Lin

last: Xu

first: Mengmeng

first: JuanJuan


title: Muscle Inflammation is Regulated by NF-kB From Multiple Cells to  Muscle Inflammation is Regulated by NF-kB From Multiple Cells to Control Distinct States of Wasting in Cancer Cachexia

city: Charleston

first: Benjamin

last: Pryce

address: 173 Ashley Ave

institute: Medical University of South Carolina

summary: Although cancer cachexia is classically characterized as a systemic inflammatory disorder, emerging evidence indicates that weight loss also associates with local tissue inflammation. We queried the regulation of this inflammation and its causality to cachexia by exploring skeletal muscle, whose atrophy strongly associates with poor outcomes. Using multiple mouse models and patient samples, we show that cachectic muscle is marked by enhanced innate immunity. NF-B activity in multiple cells, including satellite cells, myofibers, and fibro-adipogenic progenitors, promotes macrophage expansion derived equally from infiltrating monocytes and resident tissue. Moreover, NF-B activated cells and macrophages undergo crosstalk: whereas NF-B+ cells recruit macrophages to inhibit regeneration and promote atrophy, while interestingly also protecting myofibers, macrophages stimulate NF-B+ cells to sustain inflammation in a feed-forward loop. Together, we propose that NF-B functions in multiple cells in the muscle microenvironment to stimulate macrophage inflammation that both promotes and protects against muscle wasting in cancer.

overall_design: Mononuclear cells were isolated from skeletal muscle of IKKb flox or Pax7-Cre ErT IKKb flox mice. Total RNA was extracted from mononuclear population

middle: R

first: Erin

last: Talbert

first: Denis

middle: C

last: Guttridge


title: TSA attenuates the progression of c-Myc-driven hepatocarcinogenesis by pAKT-ADH4 pathway

city: Shiyan

first: Shan

address: Renming Road 30th

institute: Hubei University of Medicine

summary: Histone deacetylase inhibitors (HDACi), such as Trichostatin A (TSA), hold enormous promise for the treatment of HCC. In this study, we investigated the effects of TSA treatment on a c-Myc-induced HCC model in mice. TSA treatment delayed the development of HCC, and liver function indicators such as ALT, AST, liver weight ratio, and spleen weight ratio indicated the effectiveness of TSA treatment. Oil red staining further demonstrated that TSA attenuated lipid accumulation in the HCC tissues of mice. Through mRNA sequencing, we identified that TSA mainly affected cell cycle and fatty acid degradation genes, with alcohol dehydrogenase 4 (ADH4) potentially being the core molecular downstream target. QPCR, immunohistochemistry, and western blot analysis revealed that ADH4 expression was repressed by c-Myc and recovered after TSA treatment both in vitro and in vivo. Furthermore, we observed that the levels of total NAD+ and NADH, NAD+, NAD+/NADH, and ATP concentration increased after c-Myc transfection in liver cells but decreased after TSA intervention. The levels of phosphorylated protein kinase B (p-AKT) and p-mTOR were identified as targets regulated by TSA, and they governed the ADH4 expression and the downstream regulation of total NAD+ and NADH, NAD+, NAD+/NADH, and ATP concentration. Overall, our study suggests that TSA has a therapeutic effect on c-Myc-induced HCC through the AKT-mTOR-ADH4 pathway.

overall_design: In this study, we investigated the effects of TSA treatment on a c-Myc-induced HCC model in FVB/N mice.


title: Maternal sterol 27-hydroxylase is crucial for securing fetal development

city: Lund

first: Mattias

last: Magnusson

address: BMC A12

department: Molecular Medicine and Gene Therapy

country: Sweden

institute: Lund university

summary: Sterol 27-hydroxylase (Cyp27a1) is a primary enzyme that is involved in the Alternative pathway of bile acid synthesis, which is particularly enhanced during pregnancy. However, the role of this enzyme during fetal organ formation was unclear. Here, we demonstrate that 27-hydroxylase activity in the mother is essential for the progression of pregnancy and organ formation in the fetuses. Maternal depletion of Cyp27a1 reduced success pregnancy rate and litter size. In addition, all of the delivered newborn mice died due to respiratory distress syndrome resulting from the absence of mature alveolar epithelial cells. These phenotypes were caused by 7α-hydroxycholesterol (7α-HC) accumulating in Cyp27a1 deficient mice. Mechanistically, 7α-HC bound to and destabilized a protein Fau, mediating the assembly of ribosomes, the down-regulation of which led to lower protein synthesis and polysome formation. Our study discovered the essential metabolic pathway protecting the developing fetuses from a toxic metabolite.

overall_design: Comparing gene expression profiles of lungs from E14.5 and E18.5 Cyp27a1-/- fetuses grown in either Cyp27a1+/- mother or Cyp27a1-/- mother, at single cell levels

first: Kenichi

last: Miharada

first: Mitsuyoshi

last: Suzuki

first: Satoshi

last: Nakano

first: Mark

last: van der Garde

first: Pavan

last: Prabhala


title: nCounter Mouse Inflammation (V2) Panel on Muscle from Cancer Cachexia Models

summary: Mice were eithier injected with LLC or C26 cells, or injected with tamoxifen to indcue pancratic cancer in the KPP model. Matched controls were injected with PBS to mimic cell injections and control mice were injected with tamoxifen as controls for KPP.

overall_design: RNA was extracted from three independent cancer cachexia models as well as respective controls. Expression profiles were of each tumor bearing model were compared to matched controls


title: CCL11/CCR3-dependent eosinophilia alleviates malignant pleural effusions and improves prognosis

city: hangzhou

first: min

last: zhang

state: Zhejiang

address: hangzhou,xihu

institute: zhejiang university

summary: The role of eosinophils in the development and progression of malignant pleural effusion (MPE) remains unclear. However, MPE is a frequently occurring manifestation of advanced cancer and is often associated with a poor prognosis. While current treatment options for MPE can provide palliative care, alternative therapies are urgently needed. To investigate this role, eosinophil counts were determined using flow cytometry and immunofluorescence. Eosinophil-deficient mice (Eos-null) and Cd3δ -promoter Il5 transgenic (Il5 Tg) mice were subjected to a mouse model of MPE. Eosinophils were isolated by magnetic-activated cell sorting (MACS) and fluorescence-activated cell sorting (FACS), and their transcriptional profile was obtained by RNA sequencing. Finally, we evaluated the effects of the C-C motif chemokine ligand 11 (CCL11) and a C-C motif chemokine receptor 3 (CCR3) axis on MPE pathology using recombinant mouse CCL11 and a CCR3 inhibitor. In humans, eosinophil counts were increased in MPE and negatively correlated with the LENT score. In animal models, eosinophils were rapidly recruited to the pleural cavity when challenged with tumor cells. Interestingly, eosinophil deficiency worsened MPE, while an increase in eosinophils through various methods improved MPE. Furthermore, the recruitment of eosinophils may be influenced by the CCL11-CCR3 axis. Taken together, the study highlights the protective role of eosinophils against MPE formation, indicating their potential as a therapeutic strategy. Moreover, the CCL11-CCR3 axis may be a viable target for MPE treatment.

overall_design: We sorted total eosinophils from the pleural lavage fluid and bone marrow of wildtype mice after the injection of LLC cells. The cells were then subjected to bulk RNA-seq indicated. Libraries were pair-end (100 bp) sequenced on a MGISEQ-500 (DNBSEQ).

first: Min

last: Zhang

first: Lixia

last: Xia

first: Wenbei

last: Peng

first: Guogang

last: Xie

first: Fei

first: Chao

first: Madiha

middle: Z

last: Syeda

first: Yue

last: Hu

first: Fen

last: Lan

first: Fugui

last: Yan

first: Zhangchu

last: Jin

first: Xufei

last: Du

first: Yinling

last: Han

first: Baihui

last: Lv

first: Yuejue

last: Wang

first: Miao

first: Xia

last: Fei

first: Yun

last: Zhao

first: Kaijun

last: Chen

first: Yan

first: Wen

first: Zhihua

first: Qiong

last: Zhou

first: Songmin

last: Ying

first: Huahao

last: Shen


title: Transcriptomic Plasticity of the Circadian Clock in Response to Photoperiod: A Study in Male Melatonin-Competent Mice

city: Nashville

first: Douglas

last: McMahon

state: Tennessee

address: Department of Biological Sciences/MRB III, Vanderbilt University

department: Department of Biological Sciences

institute: Vanderbilt University

summary: Seasonal daylength, or circadian photoperiod, is a pervasive environmental signal that profoundly influences physiology and behavior. In mammals, the central circadian clock resides in the suprachiasmatic nuclei (SCN) of the hypothalamus where it receives retinal input and synchronizes, or entrains, organismal physiology and behavior to the prevailing light cycle. The process of entrainment induces sustained plasticity in the SCN, but the molecular mechanisms underlying SCN plasticity are incompletely understood. Entrainment to different photoperiods persistently alters the timing, waveform, period, and light resetting properties of the SCN clock and its driven rhythms. To elucidate novel molecular mechanisms of photoperiod plasticity, we performed RNAseq on whole SCN dissected from mice raised in Long (LD 16:8) and Short (LD 8:16) photoperiods. Fewer rhythmic genes were detected in Long photoperiod and in general the timing of gene expression rhythms was advanced 4-6 hours. However, a few genes showed significant delays, including Gem. There were significant changes in the expression clock-associated gene Timeless and in SCN genes related to light responses, neuropeptides, GABA, ion channels, and serotonin. Particularly striking were differences in the expression of the neuropeptide signaling genes Prokr2 and Cck, as well as convergent regulation of the expression of three SCN light response genes, Dusp4, Rasd1, and Gem. Transcriptional modulation of Dusp4 and Rasd1, and phase regulation of Gem, are compelling candidate molecular mechanisms for plasticity in the SCN light response through their modulation of the critical NMDAR-MAPK/ERK-CREB/CRE light signaling pathway in SCN neurons. Modulation of Prokr2 and Cck may critically support SCN neural network reconfiguration during photoperiodic entrainment. Our findings identify the SCN light response and neuropeptide signaling gene sets as rich substrates for elucidating novel mechanisms of photoperiod plasticity. Data is also available on our corresponding website, where users can search and view the expression and rhythmic properties of genes across these photoperiod conditions.

overall_design: RNAseq was conducted on whole SCNs dissected from mice with intact melatonin signalling (C3A.BLiA-Pde6b+/J strain; JAX stock #001912) raised in Long-day (hours Light: hours Dark 16:8) and Short-day (LD 8:16) photoperiods from embryonic day zero (E0). To accomplish this, breeder pairs were placed under Short or Long photoperiods (ca. 100 lux) and litters were born and maintained under these conditions. As rodent circadian rhythms develop in utero, the first litters born under the experimental photoperiods were not used in this experiment in order to avoid any potential after-effects of parental entrainment to previous photoperiod (standard institutional housing (LD 12:12)). Male mice from second and subsequent litters were used at age postnatal day 50 (P50; early adolescence). At postnatal day 50, the lighting regime was switched to constant darkness (DD) at the respective time of lights off (ZT 12) for each photoperiod. Mice spent a minimum of 36h in DD before sample collection began, such that gene expression in the samples likely represents the state of the endogenous clock rather than acute responses to the previously light cycle (Hughes et al., 2017). After this interval, SCN dissections took place at intervals of 4h over 2 circadian cycles (Hughes et al., 2017), until a minimum n of 4 was achieved per timepoint per cycle. Short and Long photoperiod samples were collected at 36, 40, 44, 48, 52, 56, 60, 64, 68, 72, 76, and 80 hours after lights off. A dim red headlamp was worn by the experimenter during the first steps of dissection. Mice were euthanized by cervical dislocation and the eyes removed to prevent potential light signaling to the SCN. The subsequent steps took place under light: the optic nerve was cut and the brain was removed such that it was situated ventral side up in a petri dish. The SCN was dissected from the brain under a microscope. Each SCN sample was put in a 1.5mL sterile DNase- RNase-free tube, and tubes were immediately placed in powered dry ice. RNA and DNA were extracted from each SCN sample using the AllPrep DNA/RNA Micro Kit (Qiagen) according to the instructions. (DNA was stored for later use and is not used in this study).

first: Olivia

middle: H

last: Cox

first: Manuel

middle: A

last: Giannoni-Guzman

first: Matthew

last: Cottam

first: Jean-Philippe

last: Cartailler

middle: G


city: MEXICO CITY

first: LORENA

last: AGUILAR ARNAL

address: TERCER CIRCUITO EXTERIOR, CU

department: BIOLOGIA CELULAR Y FISIOLOGIA

country: Mexico

institute: INSTITUTO DE INVESTIGACIONES BIOMEDICAS- UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO

summary: The circadian clock system coordinates metabolic, physiological, and behavioral functions across a 24-hour cycle, crucial for adapting to environmental changes. Disruptions in circadian rhythms contribute to major metabolic pathologies like obesity and Type 2 diabetes. Understanding the regulatory mechanisms governing circadian control is vital for identifying therapeutic targets. It is well characterized that chromatin remodeling at distal enhancer elements shapes the genome topology, supporting rhythmic transcriptional cycles; yet the impact of rhythmic chromatin topology and circadian enhancers in disease states is largely unexplored. In his study, we use 4C-seq techniques in mouse liver to explore how the spatial configuration of the genome adapts to diet, rewiring circadian transcription and contributing to dysfunctional metabolism. We describe daily fluctuations in chromatin contacts between distal regulatory elements of metabolic control genes in livers from lean and obese mice and identify specific lipid-responsive regions recruiting the clock molecular machinery. Our findings highlight the intricate coupling of circadian gene expression to a dynamic nuclear environment under high-fat feeding, supporting a temporally regulated program of gene expression and transcriptional adaptation to diet.

overall_design: Chromatin conformation capture (4C-seq) from mouse liver was used to asses genomic contacts engaged by regulatory elements from the Dbp, Srepbp1c, Ppara and Pparg2 genes. Mice were fed either a control or a high fat diets and livers were harvested at two circadian time points: ZT6 and ZT18. Two biological replicates were used per condition.

first: Lorena

last: Aguilar Arnal

first: Ignacio

last: Pacheco Bernal

first: Fernando

last: Becerril Pérez

first: Marcia

last: Bustamante Zepeda

first: Ricardo

last: Orozco Solis

first: Inti

last: de la Rosa Velázquez


title: Leo1 and Set1-mediated H3K4me3 contribute to sterol homeostasis in yeast [RNA-seq]

city: Chuncheon-si

first: Shinae

last: Park

address: Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

summary: Project Abstract : Trimethylation of histone H3 lysine 4 (H3K4me3) is predominantly associated with transcriptional start sites (TSSs) and is believed to facilitate transcription initiation. Furthermore, H3K4me3 plays a role in defining cell fate and specific cellular functions. Nevertheless, the precise function of H3K4me3 in transcription activation remains a topic of ongoing debate. The Polymerase-associated factor 1 complex (Paf1C), which is integral to various transcription-related cellular processes, consists of five highly conserved subunits: Paf1, Ctr9, Rtf1, Cdc73, and Leo1. While all subunits of Paf1C are indispensable for the maintenance of H3K4 methylation levels, it is noteworthy that strains lacking Leo1 exhibited unaltered levels of H3K4me3. To elucidate the role of H3K4me3, we conducted a transcriptome analysis coupled with ChIP-sequencing of H3K4me3 in cells lacking Leo1. Our research uncovers a distinctive role of Leo1 in yeast, whereby it plays a pivotal role in maintaining sterol homeostasis through the suppression of Upc2 expression. Importantly, this role stands apart from the functions of other Paf1C subunits. H3K4me3 is essential for promoting the expression of sterol uptake genes that are Upc2-dependent when Leo1 is absent. Additionally, Set1 contributes to sterol homeostasis by regulating iron metabolism and mitochondrial functions rather than directly suppressing Upc2 expression. Therefore, our findings reveal a novel role for Leo1 in sterol homeostasis and highlight the importance of H3K4me3 in promoting transcription of response genes required for sterol uptake.

overall_design: Sample number (1-6): We performed RNA-seq with WT(1,2), Δleo1(3,4), and Δset1(5.6) strains. Experiments were performed in duplicates.

first: Jung-Shin

last: Lee


title: Leo1 and Set1-mediated H3K4me3 contribute to sterol homeostasis in yeast [ChIPseq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Sample number (1-5): We performed anti-H3K4me3 ChIPseq with WT(1,2), Δleo1(3,4), and Δset1(5) strains. Experiments in WT and Δleo1 strains were performed in duplicates, and anti-H3K4me3 ChIPseq with Δset1 strain(5) was performed to reveal the background signal of the experiment.


title: WNK2 regulates the response to hyperosmotic stress in chondrocytes

city: Saltlake city

first: Michael

last: Jurynec

state: UT

institute: University of Utah

summary: How chondrocytes of the synovial joint sense and respond to hyperosmotic stress to maintain joint homeostasis over time is undetermined. The With-No-Lysine (K) (WNK) protein kinases are major intracellular sensors of hyperosmotic stress that respond by regulating ion channel activity and signaling pathways. To determine if WNK2 is a hyperosmotic sensor in chondrocytes and to identify the genes and pathways regulated by WNK2, we examined the molecular response of chondrocytes to WNK2 overexpression and hyperosmotic stress.

overall_design:
To determine WNK2 function in osteoarthritis, we used CRISPR/Cas9 to delete exon 2 of WNK2 in the T/C-28a2 human chondrocyte cell line by designing two gRNA around exon 2.
We then perfomed gene expression profiling analysis using data obtained from RNA-seq of wildtype and WNK2 deleted T/C-28a2 cells at 4 different conditions (Control, Sorbitol, WNK2 overexpression, Sorbitol+WNK2 overexpression)

first: Veerabhadraiah

last: Shivakumar

first: Matheson

middle: J

last: Derek

first: Honeggar

last: Matthew

first: Aslor

last: Collin

first: Jurynec

last: Michael


title: Effect of medication with Belinostat and Dasatinib on gene expression during MGG8, Glioblastoma Stem cell

city: Okayama-shi

first: Shuichiro

last: Hirano

address: kita-ku, shikata-cho, 2-5-1

country: Japan

institute: Okayama University

summary: To evaluate the effects of selected therapeutic drugs focusing on gene expression, we administered drugs to MGG8 GSCs, extracted RNA, and compared them.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MGG8 treated with Belinostat, Dasatinib, Combination of both drugs and 0.1%DMSO(Control)

first: Atsuhito

last: Uneda

first: Yoshihiro

last: Otani


title: RNA-seq  analysis of knockdown of ANXA2 in uterine carcinosarcoma cell line FU-MMT-1 cells.

city: Zhengzhou

first: Xuexiang

last: Cha

state: Henan

address: Kexue Avenue 100

department: Basic Medical Science

institute: Zhengzhou University

summary: Uterine carcinosarcomas (UCS) are rare highly aggressive gynecological malignancy. ANXA2 is a calcium-dependent phospholipid binding protein that is over-expressed in various cancers, and plays a pivotal role in tumor migration, metastasis. However, the exact function and mechanism of ANXA2 in UCS have not been elucidated. Herein, we aim to elucidate the role of ANXA2 in UCS and the molecular mechanism involved in it.

overall_design: To investigate knockdown of ANXA2 on changes in gene expression profiles in uterine carcinosarcoma, we performed gene expression profiling analysis and compare RNA-seq data between FU-MMT-1 cells transfected with si-ANXA2 and control non-silencing siRNA 48 hours

first: Huanfei

last: Ding

first: Yufeng

last: Guo

first: Ruixia


title: Electro-assisted cell printing directs in vitro gastrulation and epiblast-like morphogenesis from human pluripotent stem cells

city: 北京

first: yixue

last: Luo

state: 北京市

address: Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, China

institute: 清华大学

summary: This study develop a versatile techonology to largely generate biomimetic epiblast-like tissues based on human induced pluripotent stem cells (hiPSCs) and well-defined biomatrix.  Single hiPSCs are wrapped in laminin-alginate (L-A) hydrogel with optimized concentration and stably fabricated a large number of uniform hiPSCs-contained microspheres via electro-assisted bioprinting technology. It was observed that hiPSCs self-organized into disc-like cell clusters in L-A microspheres. Transition of microenvironment to L-A microspheres triggers the fate specification of disc-shaped tissues towards gastrulation with the identity resemble posterior epiblast population of human embryos around gastrulating stage, which is supported by transcriptome analysis.

overall_design: To investigate the time-dependent change of the cell fate of hiPSC clusters within bioprinted microspherese.

first: Yixue

first: Rui

last: Yao


title: Leo1 and Set1-mediated H3K4me3 contribute to sterol homeostasis in yeast

first: Shinae

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

overall_design: Refer to individual Series


title: Single-cell transcriptomics reveals ferrimagnetic vortex nanoring-mediated mild magnetic hyperthermia exerts antitumor effects by alleviating tumor-associated macrophages suppression

city: Xi’an

first: Penggao

last: Dai

state: Shaanxi Province

address: No.229, North Taibai Road

department: National Engineering Research Center for Miniaturized Detection Systems

institute: Northwest University

summary: In the present study, single-cell transcriptome sequencing was employed to investigate the antitumor mechanism of FVIO-MHT in breast cancer . Cell–cell communication was performed to predict the interaction between tumor cells and macrophages.

overall_design: Breast cancer tumors of the Balb/c treated with FVIO-MHT or PBS after 24 hours were analyzed using Drop-seq-based single-cell RNA sequencing.

first: Pei

last: Xi

first: Hailong

last: Shi


title: The role of human endogenous retrovirus (HERV)-K env in THP-1 monocytic cell differentiation

city: Busan

first: Eun-Ji

last: Ko

address: 2, Busandaehak-ro

institute: Pusan National University

summary: We generated HERV-K env gene KO in THP-1, a monocytic cell can be differentiated into macrophage, to investigate the role of HERV-K env in immune regulation. As the results, cell migration and invasion were significantly increased in HERV-K env KO THP-1 cells compared to MOCK, and these results were completely opposite to those of cancer cells

first: Hee-Jae

first: Do-Ye

last: Kim

first: Min-Hye

first: Hyojin

last: An

first: Sun-hee

last: Leem

first: YungHyun

last: Choi

first: Heui-Soo


title: Germline inheritance of H3K9me3 and its function in constitutive heterochromatin establishment.  [GRO-seq]

city: Milano

first: Yinxiu

last: Zhan

address: Via Adamello 16

country: Italy

institute: European Institute for Oncology

summary: To investigate the function of H3K9me3 in constitutive heterochromatin formation in early embryo we have created embryos that are devoid of H3K9me3

overall_design: cycle 14 embryos of control (3 replicates) and H3K9me3 devoid embryos (4 replicates) were collected and subjected for Gro-seq

first: Nazerke

last: Atinbayeva

first: Nicola

last: Iovino


title: Functional analysis of membrane-associated scaffolding tight junction (TJ) proteins in tumorigenic characteristics of B16-F10 mouse melanoma cells.

summary: Tight junction (TJ) proteins (Tjps), Tjp1 and Tjp2, are tight junction-associated scaffold proteins that bind to the transmembrane proteins of tight junctions and the underlying cytoskeleton. In this study, we first analyzed the tumorigenic characteristics of B16-F10 melanoma cells, including cell proliferation, migration, invasion, metastatic potential, and the expression patterns of related proteins, after the CRISPR-Cas9-mediated knockout (KO) of Tjp genes. The proliferation of Tjp1 and Tjp2 KO cells significantly increased in vitro. Other tumorigenic characteristics, including migration and invasion, were significantly enhanced in Tjp1 and Tjp2 KO cells.

overall_design: Mouse melanoma B16-F10 cells were transfected with CRISPR/Cas9+gRNA

first: Jeongtae

first: Jee-Yeong

last: Jeong

first: Kyoung

middle: S

last: Song


title: Diagnostic value of circulating miR-146b-5p and miR-222-5p in patients with acute myocardial infarction

city: Nanjing

first: Hejuan

last: Li

state: Nanjing

address: China Pharmaceutical University Xuanwumen Campus, No.24, Tongjiaxiang, Gulou Dis

institute: China Pharmaceutical University

summary:
In this study we aim to evaluate the diagnostic value of miRNAs for in the detection of acute myocardial infarction (AMI).
We used microRNA microarray to screen differentially expressed microRNAs (miRNAs) in rat myocardial infarcted tissues compared with healthy control tissues. Then the expression of these miRNAs was further verified by quantitative real-time polymerase chain reaction (RT-PCR) in rat myocardial infarcted tissues and plasma. Finally, the diagnostic value of these circulating miRNAs was explored in 44 patients with AMI, 53 with coronary heart disease (CHD) and 56 healthy controls.

overall_design: Firstly, the left ventricles of rats from 3 control groups and 3 myocardial infarction groups were collected and microarray analyzed to identify the differentially expressed miRNAs,then verified by RT-PCR at the animal level to screen out the differentially expressed miRNAs,and finally, the clinical patients with AMI were collected to further verify their diagnostic value in the clinic.

first: Jing

last: Liu

first: Zhenzhou

last: Jiang


title: Primitive macrophages promote a perivascular niche to enable vascular perfusion in human cardiac tissue

city: Toronto

first: Shira

last: Landau

state: ON

address: 170 College St.,, MB317

country: Canada

institute: University of Toronto

summary: The intricate anatomical structure and high cellular density of the myocardium significantly complicate the bioengineering of vascular networks within cardiac tissues, creating challenges in establishing a perfusable and stable vasculature within these tissues. Emerging evidence from murine in vivo studies underscores the significant role of resident cardiac macrophages in facilitating cardiac regeneration post-injury, specifically their role in enhancing angiogenesis processes. Here, for the first time, we integrate human pluripotent stem cell derived macrophages, resembling primitive yolk-sac derived macrophages, within human in vitro vascularized heart-on-chip platforms.  The incorporation of primitive macrophages had a profound impact on the long term functionality of microvascularized cardiac tissue, particularly in enabling formation of perusable vasculature with a stable barrier function. These effects were contingent on physical cell-cell interactions and significantly diminished in transwell culture. The inclusion of primitive macrophages mitigated tissue cytotoxicity and curtailed the release of cell-free mitochondrial-DNA, underscoring their indispensable role for bioengineered human cardiac tissues. Furthermore, their incorporation upregulated the secretion of pro-angiogenic, matrix remodeling and cardioprotective cytokines such as MMP-12, MMP-2, Angiopoietin-like 1, NRG-3, SIGIRR and Adiponectin. RNA sequencing disclosed upregulation of cardiac maturation (TTNI3, SCN5A, MYL2,  and RYR2), and endothelial cells genes (PDGF-B, PECAM-1 and CDH5) indicating a decrease in endothelial cells death. Collectively, our results offer valuable insights into the integral role of primitive macrophages in directing long-term functional vascularization of cardiac tissues, paving the way for novel therapeutic strategies and advancing heart-on-a-chip systems.

overall_design: RNA-seq was used to identify various effects in this study: 1. To investigate the effect of DPSCs, we performed RNA seq of fibrin tissues with only ECs vs. EC+DPSC 2. To investigate the effect of cardiomyocytes on vascularized tissues, we performed RNA seq of fibrin tissues with ECs+DPSC vs. EC+DPSC+CMs 2. To investigate the effect of macrophages on vascularized cardiac tissues, we performed RNA seq of fibrin tissues with ECs+DPSC+CMs vs. EC+DPSC+CMs+macrophages

first: Yimu

last: Zhao

first: Gregory

last: Kent

first: Sargol

last: Okhovatian

first: Rick

last: Lu

first: Chuan

first: Sarah

last: Shawky

first: Karl

middle: T

last: Wagner

first: Krisco

last: Cheung

first: Homaira

last: Hamidzada

first: Daniel

last: Vosoughi

first: Erika

last: Beroncal

first: Ian

last: Fernandes

first: Carolyn

middle: L

last: Cummins

first: Ana

last: Andreazza

first: Gordon

middle: M

last: Keller

first: Slava

last: Epelman

first: Milica

last: Radisic


title: Micronanoparticled risedronate exhibits potent vaccine adjuvant effects [RNA-Seq]

city: Xiamen

first: yee

last: chen

state: Fujian

address: Xiangannanlu

department: School of Public Health

institute: Xiamen University

summary: Nanoparticles and microparticles are widely used as vaccine adjuvants to enhance the immune response and improve the stability of antigens. While aluminum salt is one of the most common adjuvants approved for human use, its immunostimulatory capacity is suboptimal. In this study, we modified risedronate, an immunostimulant and anti‐osteoporotic drug, to create the zinc salt particle-based risedronate (Zn-RS), also termed particulate risedronate. Compared to soluble risedronate, the Zn-RS adjuvant demonstrated increased recruitment of innate cells, enhanced antigen uptake locally, and a similar antigen depot effect as aluminum salt. Furthermore, the Zn-RS adjuvant directly and quickly stimulated immune cells, accelerated the formulation of germinal centers in the lymph nodes, and facilitated the rapid production of antibodies. Importantly, the Zn-RS adjuvant exhibited superior performance in both young and aged mice, effectively protecting against respiratory diseases such as SARS-CoV-2 infection. Consequently, particulate risedronate showed great potential as a universal vaccine adjuvant, particularly beneficial for vaccines targeting the susceptible elderly.

overall_design: Comparative gene expression analysis and enrichment analysis of 6 weeks-8 weeks female mouse muscle RNA-seq data under S/AlPi condition and S/ZnRS condition at 6h,24h, and 72h

first: Meifeng

last: Nie

first: Shuyu

last: Wu

first: Yiyi

last: Chen

first: Yangtao


title: Micronanoparticled risedronate exhibits potent vaccine adjuvant effects [scRNA-Seq]

overall_design: Comparative gene expression analysis and enrichment analysis of 6 weeks - 8 weeks female mouse lymph node scRNA-seq data under STFK condition, S/AlPi condition and S/ZnRS condition

first: Ruitong


title: Micronanoparticled risedronate exhibits potent vaccine adjuvant effects


title: Transcriptome analysis of cardiac tissue from Wild-type (WT) andsalvianolate-treated  Zebrafish

city: shanghai

first: Jianxuan

last: Li

address: No. 180 Fenglin Road, Xuhui District, Shanghai

department: Department of Cardiology, Zhongshan Hospital

institute: Fudan University

summary: We analyzed the transcriptome of Wild-type (WT) and salvianolate-treated Zebrafish  by bulk RNA-seq

overall_design: To investigate the underlying mechanism by which salvianolate inhibits cardiotoxicity, we performed a comparative RNA-seq analysis of salvianolate-treated zebrafish embryos. Compared with the control group, RNA-seq analysis found that the salvianolate group had significant changes in the transcription, of which 109 genes were up-regulated and 565 genes were down-regulated. Interestingly, GO and KEGG pathway analysis showed that membrane part and lysosomal pathway was enriched in our study.

first: Yuxiang

last: Dai

first: Yang

last: Zhang

first: Zhi

last: Zuo


title: In vitro regulation of fibroblast growth factor 23 by 25(OH)D and 1,25(OH)2D3 synthesized by osteocyte-like MC3T3-E1 cells

city: Rotterdam

first: Bram

middle: CJ

last: van der Eerden

address: Wytemaweg 80

department: Internal medicine

country: Netherlands

institute: Erasmus University MC

summary: Fibroblast growth factor 23 (FGF23) is produced and secreted by osteocytes and is essential for maintaining phosphate homeostasis. One of the main regulators of FGF23, 1,25-dihydroxyvitamin D (1,25(OH)2D3), is primarily synthesized in the kidney from 25-hydroxyvitamin D (25(OH)D) by 1α-hydroxylase (encoded by CYP27B1). Hitherto, it is unclear whether osteocytes can convert 25(OH)D and thereby allow for 1,25(OH)2D3 to induce FGF23 production and secretion locally. Here, we differentiated MC3T3-E1 cells towards osteocyte-like cells expressing and secreting FGF23. Treatment with 10-6 M 25(OH)D resulted in conversion of 25(OH)D to 150 pmol/L 1,25(OH)2D3 and increased FGF23 expression and secretion but the converted amount of 1,25(OH)2D3 was insufficient to trigger an FGF23 response, so the effect on FGF23 was most likely directly caused by 25(OH)D. Interestingly, combining phosphate with 25(OH)D resulted in a synergistic increase in FGF23 expression and secretion, likely due to activation of additional signaling pathways by phosphate. Blockage of the vitamin D receptor (VDR) only partially abolished the effects of 25(OH)D or 25(OH)D combined with phosphate on Fgf23, while completely inhibiting the upregulation of cytochrome P450 family 24 subfamily A member 1 (Cyp24a1), encoding for 24-hydroxylase. RNA sequencing and in silico analyses showed that this could potentially be mediated by the nuclear receptors Retinoic Acid Receptor b (RARB) and Estrogen Receptor 2 (ESR2). Taken together, we demonstrate that osteocytes are able to convert 25(OH)D to 1,25(OH)2D3, but this is insufficient for FGF23 activation, implicating a direct effect of 25(OH)D in the regulation of FGF23, which occurs at least partially independent from its cognate vitamin D receptor Moreover, phosphate and 25(OH)D synergistically increase expression and secretion of FGF23, which warrants investigating consequences in patients receiving a combination of vitamin D analogues and phosphate supplements. These observations help us to further understand the complex relations between, phosphate, vitamin D and FGF23.

overall_design: RNA sequencing was performed on MC3T3-E1 (day 28) after 24 hour treament with 100 µM 25(OH)D, 100 µM 25(OH)D + 4 mM BGP, or 100 µM 25(OH)D + 100 µM ZK191784

first: Danielle

last: Ratsma

last: Van der Eerden


title: Division of labor among H3K4 Methyltransferases Define Distinct Facets of Homeostatic Plasticity

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

institute: University of Michigan

summary: Histone H3 lysine 4 methylaton (H3K4me), a hallmark of transcriptionally engaged chromatin, is installed by the lysine methyltransferases 2 (KMT2) family of six enzymes in mammals. The six enzymes appear to have arisen from gene duplication of the ancient three enzymes found in the fruit fly. Heterozygous mutations in any of the six enzymes result in monogenic neurodevelopmental disorders, indicating nonredundant yet poorly understood roles of KMT2 family enzymes in neurodevelopment. Recent evidence suggests that histone methyltransferase activity may not be central to KMT2 functions; however, the enzymatic activity is evolutionary conserved, implicating the presence of selective pressure to maintain the catalytic activity. Here, we show that H3K4 methylation is dynamically regulated during prolonged alteration of neuronal activity. The perturbation of H3K4me by the H3.3K4M mutant blocks synaptic scaling, a form of homeostatic plasticity that buffers the impact of prolonged reductions or increases in network activity. Unexpectedly, we found that the six individual enzymes are all necessary for synaptic scaling and that the roles of KMT2 enzymes segregate into evolutionary-defined subfamilies; KMT2A and KMT2B (fly-Trx homologs) for synaptic downscaling, KMT2C and KMT2D (Trr homologs) for upscaling, and KMT2F and KMT2G (dSet homologs) for both directions. Selective blocking of KMT2A enzymatic activity by a small molecule and targeted disruption of the enzymatic domain both blocked the synaptic downscaling and interfered with the activity-dependent transcriptional program. Furthermore, our study revealed specific phases of synaptic downscaling, i.e., induction and maintenance, in which KMT2A and KMT2B play distinct roles. These results suggest that mammalian brains have co-opted intricate H3K4me installation to achieve stability of the expanding neuronal circuits.

overall_design: Bromouridine sequencing (BrU-seq) was conducted as previously described with modification (Garay et al., 2020). In brief, on DIV17, cortical cultures derived by CD1 mice were pretreated with either DMSO or 25 μM MM401. After 30min of preincubation with the reagents, cells were treated with bicuculline-methiodide (Abcam, ab120108, 40 μM) or vehicle (sterile water) for 1 h or 4 h. All cells were treated with 2 mM bromouridine (Bru, Sigma, 18670, dissolved in PBS) for the last 30 min of incubation. Cultures were lysed in Tri-reagent BD (Sigma, T3809) and frozen for future procedures. RNA was purified by phenol-chloroform extraction and isopropaonol precipitation, treated with DNase-I (NEB, M0303) then fragmented by high-magnesium, high-temperature incubation. One 1μg of Bru-containing  RNA was used for library preparation. The library was prepared in collaboration with the BrU-seq lab of the University of Michigan (Paulsen et al., 2013, 2014). Finally, samples were sequenced by 150 bp paired-end on Illumina Novaseq. Experiments were conducted in three biological replicates with mixed sex

first: Takao

last: Tsukahara

first: Saini

last: Kethireddy

first: Katherine

last: Bonefas

first: Alex

first: Brendan

last: Sutton

first: Kai

last: Ge

first: Yali

last: Dou

first: Michael


title: Molecular Mechanism of type 2 diabetes mellitus-mediated heart failure with preserved ejection fraction

city: Tucson

first: Sakthivel

last: Sadayappan

state: AZ

address: 1656 E Mabel Street, Medical Research Building, Rm 315, Cellular and Molecular Medicine

department: Cellular and Molecular Medicine

institute: University of Arizona College of Medicine

summary: Type 2 diabetes mellitus (T2DM) is a metabolic disease associated with several comorbidities, including cardiac dysfunction leading to heart failure with preserved ejection fraction (HFpEF), in turn resulting in T2DM-induced cardiomyopathy (T2DM-CM). However, the molecular mechanisms underlying the development of T2DM-CM are poorly understood. It is hypothesized that molecular alterations in myopathic genes induced by diabetes promote the development of HFpEF, whereas cardiac myosin inhibitors can rescue the resultant T2DM-induced cardiomyopathy. To test this hypothesis, a Leptin receptor-deficient db/db homozygous (Lepr db/db) mouse model was used to define the pathogenesis of T2DM-CM. Echocardiographic studies at 4 and 6 months revealed that Lepr db/db hearts started developing cardiac dysfunction by four months, and left ventricular hypertrophy with diastolic dysfunction was evident at 6 months. Strikingly, the level of cardiac myosin binding protein-C phosphorylation was significantly increased in Lepr db/db mouse hearts. RNA-seq data analysis, followed by functional enrichment, revealed the differential regulation of genes related to cardiac dysfunction in Lepr db/db heart tissues. Finally, using isolated skinned papillary muscles and freshly isolated cardiomyocytes, CAMZYOS (mavacamten, which is a prescription heart medicine used for symptomatic obstructive hypertrophic cardiomyopathy treatment (herein after denotes as MYK-461), was tested for its ability to rescue T2DM-CM. Compared with controls, MYK-461 significantly reduced force generation in papillary muscle fibers and cardiomyocyte contractility in the db/db group. This line of evidence shows that 1) T2DM-CM is associated with hyperphosphorylation of cardiac myosin binding protein-C and 2) MYK-461 significantly lessened disease progression, suggesting its promise as a therapeutic treatment for HFpEF.

overall_design: To investigate the molecular mechanism underlying the development of T2DM CM, 6 months old leptin receptor deficient db/db homozygous mouse models were employed to understand the development of diabetic cardiomyopathy using  in vivo echocardiographic features, phosphorylation status of Mybpc3 and high throughput RNA sequencing of cardiac tissues.

first: Darshini

last: Desai

first: Akhil

last: Baby

first: Kalyani

last: Ananthamohan

first: Lisa

last: Green

first: Mohammed

last: Arif

first: Brittany

last: Duncan

first: Mohit

last: Kumar

first: Rohit

last: Singh

first: Sheryl

last: Koch

first: Sankar

last: Natesan

first: Jack

last: Rubinstein

first: Anil

last: Jegga


title: HIV/HBV co-infection remodels the immune landscape and Natural Killer cell functional responses

city: London

first: Dimitra

last: Peppa

address: Gower St

country: United Kingdom

institute: University College London

summary: Background: Hepatitis B (HBV) and human immunodeficiency virus (HIV) co-infection is a common occurrence globally, with significant morbidity and mortality. Both viruses lead to dysregulated immune responses including changes in natural killer (NK) cells, a key component of antiviral defense and a promising target for HBV cure strategies. In this study we used high-throughput single cell analysis to explore the immune cell landscape in people with HBV mono-infection and HIV/HBV co-infection, on antiviral therapy, with emphasis on identifying the distinctive characteristics of NK cell subsets. Results:  Our data show striking differences in the transcriptional programs of NK cells.  HIV/HBV co-infection was characterized by an overrepresentation of adaptive, KLRC2 expressing NK cells, including a higher abundance of a chemokine enriched (CCL3/CCL4) adaptive cluster. The NK cell remodeling in HIV/HBV co-infection was reflected in enriched activation pathways shared with T cells, including CD3 phosphorylation and ZAP-70 translocation that can mediate stronger ADCC responses and a bias towards chemokine/cytokine signaling. By contrast HBV mono-infection imposed a stronger cytotoxic profile on NK cells and a more prominent signature of exhaustion with higher circulating levels of HBsAg. Mirroring the transcriptomic analysis, phenotypic alterations in the NK cell pool in co-infection were consistent with increased ‘adaptiveness’ and better capacity for ADCC compared to HBV mono-infection.  Overall an adaptive NK cell signature correlated inversely with circulating levels of HBsAg and HBV-RNA in our cohort. Conlcusions: This study provides new insights into the differential transcriptional signature and functional profile of NK cells in HBV and HIV/HBV co-infection, highlighting new pathways that can be manipulated to tailor NK cell-focused approaches to advance cure strategies in the different population groups.

overall_design: Peripheral blood mononuclear cells were harvested from 3 control subjects along with 5 HIV-HBV co-onfected and 5 HBV monoinfected subjects. Those with >95% viability were used for this study. Library construction was performed using the 10x next GEM Chips Chromium single cell library 5’ construction kit. cDNA libraries were prepared as per 10x Genomics Single Cell 5’ reagent kit user guide with calculations based on the amount of input cDNA. Purified libraries were analysed by Novogene.

first: Bo

last: Sun

first: Upkar

last: Gill


title: Transcriptomic analysis of gene diffrentially expressed after Pemafibrate treatment on the livers of mice overexpressing FAT10.

city: Lille

first: Lucie

last: Bernard

state: North

address: Boulevard du Professeur Jules Leclercq

country: France

summary: Livers from C57Bl6 male adult mice infected either with an adenovirus control (Ad-CTRL) or an adenovirus overexpressing FAT10 (Ad-FAT10) and treated or not with pemafibrate (Pema, vehicule CMC) were used to prepare RNA.

overall_design: Livers of 4 mice of each following group were used for the analysis: Ad-CTRL CMC; Ad-CTRL-Pema, Ad-FAT10 CMC and Ad-FAT10-Pema

first: Ludivine

last: Clavreul

first: Réjane

last: Paumelle-Lestrelin


title: Transcriptional Control of Cell Fate Within the MS lineage in C. elegans

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary:
Our primary goal is to find the network of transcription factors that control the formation of bodywall muscle and other cells from the time just after fertilization and throughout subsequent embryogenesis.
The process of cell fate determination typically involves a series of cell division in which totipotent stem cells become progressively restricted in fate potential. To understand bodywall muscle cell (analogous to skeletal muscle in vertebrates) fate specification, it is suitable to use C. elegans as a model system. The current study is primary focusing on bodywall muscle cell development from the anterior blastomere MS lineage and is found the network of transcription factors for bodywall muscle cell specification from transcriptional profiling from genetically manipulated embryo.

overall_design: Wild type (N2) hermaphrodite worms are injected with mex-1, lit-1 and pal-1 dsRNA (~300 ng/ml each) and incubated at room temprarture for >12 hours before collecting embryos.Embryos at embryonic two- to four-cell stages from dsRNA injected hermaphrodite are isolated and incubated to different time points (0, 1, 2, 3 and 4 hours post collection). A total 15 samples were analyzed. Triplicate, independent samples at each developmental time point were used for expression microarray analysis.

first: Tetsunari

last: Fukushige

first: Michael

middle: W

last: Krause


title: THAP1 is a master regulator of zinc finger transcription factors guiding gastrulation of murine embryos [ChIP-seq_SH]

city: Tuebingen

first: Fubo

last: Cheng

address: Calwerstrasse 7

department: Institute of Medical Genetics and Applied Genomics

country: Germany

institute: University of Tuebingen

summary: Gastrulation and early organogenesis are remarkable processes of early embryonic development. Our previous study showed that deletion of DYT6 gene product THAP1 leads to embryonic lethality at the stage of gastrulation and early organogenesis. However, the function of THAP1 in regulating gene expression, as well as its role in regulating embryo gastrulation and early organogenesis are not well characterized. In this study, we used different in vitro and in vivo models to characterize the function of THAP1 in regulating gene expression and in controlling embryonic development, which could help us to understand pathogenesis of THAP1-associated disorders and provide data to characterize the transcription regulation of gastrulation of murine embryo.

overall_design: THAP1 and CSNK2A1 knock-out SH-SY5Y cells were generated and CTCF and YY1 ChIP-seq were performed to analyze their genomic bindings

first: Olaf

last: Riess

first: Wenxu

last: Zheng


title: THAP1 is a master regulator of zinc finger transcription factors guiding gastrulation of murine embryos [ChIP-seq(mESC)]

overall_design: THAP1 knock-out mESCs were generated and ChIP-seq was performed to analyze genomic binding of different transcription factors in each cell line


title: THAP1 is a master regulator of zinc finger transcription factors guiding gastrulation of murine embryos [RNA-seq_SH]

overall_design: CTCF, PAF, and CSNK2A1 knock-out SH-SY5Y cells were generated and RNA-seq was performed to analyze gene expression changes in each cell line.


title: Notch signaling suppresses neuroendocrine differentiation and alters the tumor immune microenvironment in advanced prostate cancer

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: Neuroendocrine prostate cancer (NEPC) is an aggressive, androgen-independent variant of prostate cancer (PCa) that most commonly develops in patients as a mechanism of therapeutic resistance. The underlying mechanisms driving PCa lineage plasticity and trans-differentiation to a neuroendocrine lineage are not fully understood. Here, we identify Notch signaling as a key suppressor of neuroendocrine differentiation in PCa. Restoration of Notch signaling in NEPC models results in phenotypic conversion towards a non-neuroendocrine state with expression of prostate luminal cell markers and immunologic changes including up-regulation of MHC Class I and II and type I interferon signaling that correlate with changes in the tumor immune microenvironment. Overall, these data provide new insights into how Notch signaling influences PCa lineage plasticity and points to new therapeutic avenues to modulate it.

overall_design: murine prostate from 12-week-old TKO or TKO-Nicd1 mice and TKO or TKO-Nicd1 derived organoid transplant tumors were collected and subject to scRNAseq (3'GEX, 10x Genomics).

first: Goodrich

last: David W

first: Beltran

last: Himisha

first: Ku

last: Sheng-Yu

first: Wang

last: Yanqing

first: Long

last: Mark D


title: THAP1 is a master regulator of zinc finger transcription factors guiding gastrulation of murine embryos [RNA-seq_mESC]

overall_design: THAP1, ZFP764, ZFP524, and Zscan10 knock-out mESCs were generated and RNA-seq was performed to analyze gene expression changes in each cell line.


title: Degradome sequencing were performed on maize inbred lines Chang7-2 (resistant to SCMV) and Mo17 (susceptible to SCMV).

city: shenyang

first: jun

last: zhang

address: liaoning

institute: Shenyang Agricultural University

summary: The maize inbred lines Chang7-2 (resistant to SCMV) and Mo17 (susceptible to SCMV) were inoculated with SCMV (SC, SM) and phosphate buffer (MC, MM), respectively to subjected to degradome sequencing.

overall_design: The crude extracts were inoculated on the second leaves of six-day-old Chang7-2 and Mo17 maize seedlings, and buffer-inoculated plants were used as control. At 10 days post inoculation, the systemically infected leaves from mock (MM, MC) and SCMV (SM, SC) maize plants with typical disease symptoms were collected respectively. In each treatment, the leaves samples from at least 15 maize seedlings were collected for RNA extraction.Samples from both treatment and control groups were combined together to construct a mixed degradation library.

first: Xinran

last: Gao

first: Zhichao

last: Du

first: Sijia

last: Zhang

first: Zihao

last: Xia


title: Germline inheritance of H3K9me3 and its function in constitutive heterochromatin establishment.[CUT&Tag]

first: Yinxiu

last: Zhan

overall_design: different stages of embryos of control, single mutants and triple mutant were subjeted to Cut and tag for H3K9me2/3,  HP1a, and H3.

first: Nazerke

last: Atinbayeva

first: Nicola

last: Iovino


title: THAP1 is a master regulator of zinc finger transcription factors guiding gastrulation of murine embryos

first: Fubo

last: Cheng

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

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: CDK7 is a novel therapeutic vulnerability in Fibrolamellar cancer

city: Madison

first: Sean

last: Ronnekleiv-Kelly

state: Wisconsin

address: K3/705 CSC, 600 Highland Avenue

department: Surgery

institute: University of Wisconsin Madison School of Medicine and Public Health

summary:
To identify targets in Fibrolamellar cancer (FLC), we introduced the FLC driver gene mutation (DNAJB1-PRKACA) into HepG2 cells to engineer FLC cell lines.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different cell samples from HepG2, H33 (FLC cell line) and H12 (FLC cell line)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 (control, n = 6) vs H33 (n = 6) and HepG2 (control, n = 6) vs H12 (n = 6)


title: Whole-transcriptome RNA sequencing and degradome sequencing were performed on maize inbred lines Chang7-2 (resistant to SCMV) and Mo17 (susceptible to SCMV).

summary: The maize inbred lines Chang7-2 (resistant to SCMV) and Mo17 (susceptible to SCMV) were inoculated with SCMV (SC, SM) and phosphate buffer (MC, MM), respectively to subjected to whole-transcriptome RNA sequencing and degradome sequencing.

overall_design: The crude extracts were inoculated on the second leaves of six-day-old Chang7-2 and Mo17 maize seedlings, and buffer-inoculated plants were used as control. At 10 days post inoculation, the systemically infected leaves from mock (MM, MC) and SCMV (SM, SC) maize plants with typical disease symptoms were collected respectively. In each treatment, the leaves samples from at least 15 maize seedlings were collected for RNA extraction.


title: snRNAseq of human limbus tissue

city: Cambridge

first: Minkyung

last: Sung

address: 25 Cambridge Science Park Milton Rd, Milton

department: Cell informatics

institute: Mogrify

summary: LSCs have been clinically approved as a cell therapy to treat limbal stem cell deficiency (LSCD), however, there has yet to be a consensus on LSC markers that allow the isolation of LSCs, and their transcriptome profile is not fully understood. In this study, we addressed this problem by using single nuclei RNA sequencing (snRNAseq) on healthy human limbal tissue excised from cataract patients.

overall_design: Healthy human limbal tissue excised from cataract patients was analyzed using snRNAseq.

first: Kathryn

last: Davidson

first: Karl

last: Brown

first: Julian

last: Contet

first: Aida

last: Moreno-Moral

last: Gough

first: Jose

last: Polo

first: Geraint

last: Parfitt


title: M2-exo transfers funcional microRNA to IEC

city: Beijing

first: xinyuan

last: huang

address: Yongan Street 95

institute: Beijing Friendship Hospital affiliated Capital Medical University

summary: In our study, sequencing results revealed a miRNA-mRNA modulated network in M2-exo treated IEC. This suggested that M2 macrophages load multiple miRNAs into exosomes, which then resolve ulcerative colitis by activating or inhibiting signaling pathways associated with proliferation and inflammation.

overall_design: The microRNA in M0-exo and M2-exo were analyized. The mRNA profile were determined in untreated IEC and M2-exo treated IEC.

first: Xinyuan

last: Huang

first: Fanqi

last: Bu

first: Shutian


title: Gene expression changes in mouse breast cancer cells (4T1) after axitinib resistance and FACS isolation of SA-β-galHi (SM+) and SA-β-galLo (SM-) cells

first: Mark

last: Long

summary: RNA sequencing analysis was used to identify changes in mouse breast cancer cells (4T1) after axitinib resistance and FACS isolation of SA-β-galHi (SM+) and SA-β-galLo (SM-) cells

overall_design: Mouse breast cancer cells (4T1) resistant to axitinib were derived in vivo after continuous treatment with 100mg/kg/day axitinib from post-surgical lesions. Resistant cells were maintained in vitro with 0.5µM axitinib for more than 2 months. Resistant cells were stained for fluorescent SA-β-gal substrate C12FDG and fractioned into SA-β-galHi (SM+) and SA-β-galLo (SM-) populations

first: Melissa

last: Dolan

first: John

last: Ebos


title: Pneumonia-induced shedding of epithelial heparan sulfate inhibits the bactericidal activity of cathelicidin

city: Aurora

first: Christophe

last: Langouët-Astrié

state: CO

department: Pulmonary Sciences and Critical Care

institute: University of Colorado Denver, Anschutz

summary: Interrogating Staphylococcus aureus transcriptional changes in the presence or absence of glycosaminoglycans, specifically heparin.

sample_organism: Staphylococcus aureus subsp. aureus NCTC 8325

overall_design: USA400 bacterial suspensions were grown in the presence of unfractionated heparin (2 µg/mL ) or saline control. After 3 or 10 hours of incubation, bacterial RNA was isolated and sent for sequencing (n=3 per treatment group and time point).

first: Jakub

last: Kwiecinski

first: Wells

last: LaRiviere

first: Christopher

last: Erzen

last: Langouet-Astrie

first: Alex

last: Horswill

first: Eric

last: Schmidt

first: James

last: Colbert


title: Alteration of miRNA profiles between lung tumours from the KRASLSL-G12D/+ mice and the normal lung tissues

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

summary: Small RNA deep sequencing to determine the alteration of miRNA profiles in the lung tumours from the KRASLSL-G12D/+ mice compared with the normal lung tissues from the mice without Adeno-Cre treatment.

overall_design:
We performed miRNA profiling analysis using data obtained from 5 different lung tissues of 2 groups each.
Applying a stringent threshold of log2 (fold-change) > 1 and significance criterion of p < 0.05.

first: Huanhuan

last: Hu


title: Diverse druggabilities of p53 mutations underline individual allele-based targeted therapy

city: Shanghai

first: Huaxin

last: Song

address: Shanghai Jiao Tong University School of Medicine


title: RNAseq analysis for transcriptomes of ATO treated U937 cell lines expressing p53-R280I or p53 wild-type

institute: Shanghai Jiao Tong University School of Medicine

summary: To globally evaluate to what extend the p53 mutant transcription activity can be restored by arsenic trioxide (ATO), p53-null U937 cells introduced with p53-R280I or wild-type p53 were treated with or without 1 μg/mL ATO. mRNA was isolated and then subject to deep sequencing, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed using Cutadapt.

overall_design: RNAseq to evaluate mutant p53 transcriptional activity upon ATO treatment.

first: Min

last: Lu


title: Next Generation translatome Sequencing (Ribo-seq) of Papillary Thyroid Carcinoma tissue sample and adjacent normal tissue

first: lv

last: chengzhou

state: liaoing

address: nanjingbeijie 155

department: thyroid surgery

institute: the first hospital of china medical university

summary:
Through the translatome sequencing (Ribo-seq) of clinically obtained papillary thyroid carcinoma and its paired adjacent tissues, we tried to find the differences in the translation of various genes and evaluate the translation function of circular RNAs in the two tissues.
We then performed gene expression profiling analysis using data obtained from Ribo-seq of 4 different pairs of Papillary Thyroid Carcinoma tissue sample and adjacent normal tissue. At the translatome level, we screened out 247 circRNAs with translation ability.

overall_design: Comparative gene expression profiling analysis of Ribo-seq data in 4 pairs of Papillary Thyroid Carcinoma tissue sample and adjacent normal tissue.

first: Chengzhou

last: Lv

first: Hao

last: Zhang


title: High-throughput microarray reveals the epitranscriptome-wide landscape of m6A-circRNA in large for gestational age placental tissues.

city: Shenyang

first: Dan

last: Wang

state: Liaoning Province, China

address: No.16, Puhe Avenue, Shenbei New District

department: Department of Obstetrics and Gynecology

institute: Shengjing Hospital of China Medical University

summary: We report an epitranscriptome-wide mapping of m6A-modified circRNAs (m6A-circRNA) in large for gestational age(LGA) placental tissues versus normal gestational age (NGA). Utilizing the data of m6A-circRNAs epitranscriptomic microarray analysis, we found that m6A-circRNAs exhibited their particular modification style in LGA.

overall_design:
Three NGA and four LGA placental tissues were used in m6A-circRNA microarray.
Note: These are two channel arrays that have been analyzed with a single-channel method. Each sample/GSM represents a sample and dye.


title: Regulation of pyroptosis in radiation induces mouse intestine cells

first: Changhui

last: Ge

email: chge502@163.com, chge88@sina.com

address: 27 Taiping Rd., Haidian Dist.

department: Department of Experimental Hematology and Biochemistry

institute: Beijing institute of Radiation Medicine

summary: Pyroptosis is a recently discovered form of lytic cell death that is characterized by cell swelling and formation of pores and large bubbles on the plasma membrane. We find radiation could induce pyroptosis in human colorectal cancer HCT116 cells, and irradiation induces pyroptosis in mouse normal intestine MODEK cells only after 36 hours and over 8.0 Gy. In view of the significant pyroptosis effect of MODE-K cells, we selected 4Gy and 12Gy, 24h and 48h for experiments. After ONT full-length transcriptome sequencing, the cell pyroptosis model can screen out the differential genes related to cell pyroptosis, which is helpful to further explore the mechanism of pyroptosis of MODE-K cells.

overall_design: Mouse intestine MODEK cells were cultured and divided into four groups, then irradiated with 0Gy/0h (ie.0 Gy at 0 hour), 4Gy/48h, 12Gy/24h and 12Gy/48h, then cells were harvested and performed RNA sequencing.

first: Junzhao

last: Duan

first: Hanjiang

last: Fu

first: Xiaofei

last: Zheng


title: Gene expression profile at single cell level of cardiomyocyte and non cardiomyocyte from the heart of pressure-overload model mice.

city: Bunkyo-ku

first: Manami

last: Katoh

state: Tokyo

address: 7-3-1 Hongo

department: Department of Cardiovascular Medicine

institute: The University of Tokyo

summary: The heart is composed of many cell types. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of cell types contained in the heart.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Cardiomyocyte and non cardiomyocyte from the heart of pressure-overload model mice were isolated by the Langendorff technique and analyzed using scRNAseq.


title: Transcriptomic analysis of RNases knockdown in A549 cells.

summary: The function of biomolecules is essential for maintaining homeostasis. The RNA and RNase regulatory system in maintaining cellular homeostasis is not clear. To investigate the effects of RNase on gene expression and biological functions, we respectively knocked down Ago2, ANG, DICER, DROSHA, RNase L, and RNase T2 in A549 cells and performed RNA sequencing.

overall_design: RNase L, ANG, Dicer, Drosha, AGO2, and RNase T2 were knocked down by siRNA transfection in A549 cells, respectively. These cells were harvested 48h after siRNA transfection, and total RNA was extracted for RNA sequencing analyses.


title: Gene expression profiling in Indolocarbazole alkaloid Loonamycin A treated MDA-MB-231 cells

first: wen

middle: wen

last: xue

address: 22 Han Kou Road, Nanjing

department: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences

summary: In triple negative breast cancer (TNBC), aberrant activation of Notch signaling plays an important role for the maintenance of cancer stem cell (CSC) stemness. Targeting CSCs via inhibition of Notch signaling can be a potential therapeutic option for this incurable disease. We previously used genome mining strategy to discover a new indolocarbazole alkaloid loonamycin A (Loo A). In this study, we demonstrate that Loo A has stronger cytotoxicity toward TNBC cells than its structural analog rebeccamycin. Apart from inhibition of TNBC cell proliferation and migration, Loo A reduced CD44high/CD24low/- sub-population, mammosphere formation, as well as the expression of stemness-associated genes. Co-administration of Loo A enhanced antitumor effects of paclitaxel by inducing apoptosis. RNA sequencing result showed that Loo A treatment caused the inhibition of Notch signaling, accompanied by the decreased expression of Notch1 and its targeted genes in TNBC cells. These results reveal a novel bioactivity of indolocarbazole-type alkaloids and provide promising Notch-inhibiting small molecular candidates for TNBC therapy.

overall_design: Total RNA was extracted from MDA-MB-231 cells treated or not with Indolocarbazole alkaloid Loonamycin A

first: Wenwen

last: Xue

first: Wuhao

last: Li

first: Qiang

last: Xu

first: Yan

last: Shen


title: Oncolytic biomineralized bacteria for tumor immunotherapy

city: suzhou

first: Chenya

institute: Soochow University

summary: Bacteria-based cancer immunotherapy, dated back to Coley’s toxins (inactivated bacteria) in 1893, has recently regained substantial attentions, usually by using attenuated bacteria to transform immune-silent “cold” tumors into immune-inflamed “hot” ones. However, while inactivated bacteria showed limited antitumor efficacy, attenuated live bacteria often possessed significant safety risks. Herein, by biomineralizing growth of manganese dioxide on the surface of paraformaldehyde-fixed gram-negative Salmonella typhimurium (S. typhimurium), we obtained MnO2-coated fixed S. typhimurium (M@F.S), which showed potent immune-stimulating effects via activating multiple pathways including Toll-like receptors (TLRs), cyclic GMP-AMP Synthase (cGAS)-stimulator of interferon genes (STING) and nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs). Single intratumoral administration of M@F.S at safe doses resulted in surprisingly strong efficacies in suppressing various types of mouse tumor models and a rabbit cancer model, and the cured mice and rabbits gained immune memory to reject re-challenged tumors. An abscopal antitumor effect was also observed, suggesting systemic antitumor immunity triggered by local injection of M@F.S. The antitumor mechanisms of M@F.S were preliminarily demonstrated to be innate immune activation initiated by multiple signaling pathways, followed by subsequent activation of tumor-specific immune responses, together with the modulation of immunosuppressive tumor microenvironment. We further demonstrated the efficacy of biomineralized bacteria in inhibiting an orthotopic breast tumor model established on tree shrews, an alternative animal model to primates with better clinical relevance. Such oncolytic biomineralized bacteria could be a potent yet safe immunotherapeutic agent for treatment of various solid tumors.

overall_design: 6 mouse tumor tissues (3 mice each in the blank and M@F.S-treated groups) on Day 3 post-treatment.


title: Transcriptome and metabolome analysis of walnuts in response to Phompsis capsici infection

city: sichuan

first: leming

last: zhou

address: chengdu

institute: Reference transcriptome

summary: By analyzing the transcriptome and metabolome data of walnut infected by phompsis capsici to study the changes of differentially expressed genes and secondary metabolites,Exploring the molecular mechanism of walnut phompsis capsici.

overall_design: With walnut annual branches as experimental materials, the transcriptome sequencing samples were divided into experimental group and control group, with 3 biological replicates in each group. Metabolome sequencing samples were also divided into experimental and control groups with 6 biological replicates in each group.

first: Leming

last: Zhou

first: Tianhui

last: Zhu


title: Transcriptomic analysis of non-coding RNAs reveals the regulatory network of testicular fusion in Spodoptera litura

city: Guangzhou

first: Chen

last: Yaqing

state: Guangdong

address: South China Normal University

department: School of Life Sciences

institute: South China Normal University

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of non-coding RNAs reveals the regulatory network of testicular fusion in Spodoptera litura [miRNA-seq]

summary: Spodoptera litura (Lepidoptera: Noctuidae), which has a strong and rapid reproductive capacity, is a polyphagous pest with great destruction to many crops, causing economic loss to agricultural production worldwide. Its two testes began to fuse into a single one during the larva-to-pupa metamorphosis, which was favorable to the sperms development in our previous study. But the mechanism of testicular fusion is still unknown. In this study, we analyzed long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in the testes by high-throughout RNA-seq to explore the mechanism of testicular fusion in S. litura. In total, 2,150 lncRNAs, 2,742 target mRNAs and 347 miRNAs were identified in the testes from 4-day-old sixth instar larvae (L6D4) (before fusion), 6-day-old sixth instar larvae (L6D6, prepupae) (on fusing) and 0-day-old pupae (P0D) (after fusion). It was found that a large number of DElncRNAs, DEmRNAs and a little number of DEmiRNAs were up-regulated from L6D4 to L6D6 when the testes began to fuse, a little number of DElncRNAs, DEmRNAs and a large number of DEmiRNAs were down-regulated from L6D6 to P0D after the testicular fusion. The GO terms and KEGG pathway enrichment analysis of DElncRNAs target DEmRNAs showed that ECM remodeling enzymes: stromelysin, A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTs) and inducible metalloproteinase inhibitor protein (IMIPs), ECM-intergrin interaction pathway and cell adhesion molecules (integrin, cadherin) may be involved in the testicular fusion. The DElncRNA-DEmiRNA-DEmRNA regulatory network related to ECM remodeling enzymes and its signal pathway may play important roles in cell adhesion when the testicular fusion occured. Our study will provide comprehensive information to study the mechanism of testicular fusion, and especially, will promote the functional study of non-coding RNAs (lncRNAs and miRNAs) during the testicular fusion in S. litura.

overall_design: To study the mechanism of testicular fusion in Spodoptera litura, the testes from from 4-day-old sixth instar larvae (L6D4) (before fusion), 6-day-old sixth instar larvae (L6D6, prepupae) (on fusing) and 0-day-old pupae (P0D) (after fusion) were collected for RNA-sequencing.Long non-coding RNA and mRNA were studied and analyzed during the testicular fusion in S. litura.

first: Yaqing

last: Chen

first: Yu

first: Xiao-qiang

last: Yu

first: Qili

last: Feng

first: Xiaoyun

first: Lin

last: Liu


title: Spermidine augments salt stress resilience in rice roots potentially by enhancing OsbZIP73’s RNA binding capacity

city: Zhanjiang

first: Mingming

address: Haida Street No.1

institute: Guangdong Ocean University

summary:
Background: Rice is a staple crop for over half of the global population, but soil salinization poses a significant threat to its production. As a type of polyamine, spermidine (Spd) has been shown to reduce stress-induced damage in plants, but its specific role and mechanism in protecting rice roots under salt stress require further investigation.
Results: This study suggested spermidine (Spd) mitigates salt stress on rice root growth by enhancing antioxidant enzyme activity and reducing peroxide levels. Transcriptomic analysis showed that salt stress caused 333 genes to be upregulated and 1,765 to be downregulated. However, adding Spd during salt treatment significantly altered this pattern: 2,298 genes were upregulated and 844 were downregulated, which indicated Spd reverses some transcriptional changes caused by salt stress. KEGG pathway analysis suggested that Spd influenced key signaling pathways, including MAPK signaling, plant hormone signal transduction, and phenylalanine metabolism. Additionally, the bZIP transcription factor OsbZIP73 was upregulated after Spd treatment, which is confirmed by Western blot. Further insights into the interaction between OsbZIP73 and Spd were gained through fluorescence polarization experiments, showing that Spd enhances protein OsbZIP73's affinity for RNA. Functional enrichment analyses revealed that OsPYL1, OsSPARK1, and various SAUR family genes involved in Spd-affected pathways. The presence of G/A/C-box elements in these genes suggests they are potential targets for OsbZIP73.
Conclusions: Our findings suggest a strategy of using spermidine as a chemical alleviator for salt stress and provide insights into the regulatory function of OsbZIP73 in mitigating salt stress in rice roots.

overall_design: RNA sequencing of rice root following treatment with Spermidine, NaCl or Spermidine+NaCl for 72hrs


title: Understanding the transcriptional consequences of the Progeria LmnaG609G mutation within the immune compartment of the lung using single cell RNA sequencing.

city: Paris

first: Kevin

last: De Azevedo

address: 12 rue Lhomond

institute: Institut Curie

summary: To understand the transcriptional consequences of Progeria LmnaG609G mutation within the immune compartment of the lung we conducted single cell RNA sequencing on sorted immune cells from WT vs. LmnaG609G/G609G mice (in duplicate, 2 mice per group).

overall_design: WT and LmnaG609G/G609G lung immune cells were subjected to single cell RNA sequencing.

first: Nilushi

last: De Silva

last: de Azevedo

first: Francesca

last: Nadalin

first: Nicolas

last: Manel


title: Identification of arsenic trioxide (ATO)-rescuable p53 mutations and temperature-sensitive p53 mutations in p53-null U937 cells using a patient-derived 800 p53 mutation library

first: Huaxin

last: Song

summary: Thousands of diverse p53 mutations have been identified in cancer. The leukemia-treating drug arsenic trioxide (ATO) rescues a part of p53 mutations with high potency. To repurpose ATO in personalized p53-targeted therapy, here we quantitatively determined the frequent 800 p53 mutations, covering 95.8% p53 missense-mutation cases in cancer, for their rescue potencies of cell growth inhibitory activity and mouse tumor suppressive activity by ATO. Furthermore, we determined the temperature sensitivity of 800 mutations in mammalian U937 cells and founded that ATO preferentially rescued temperature-sensitive subtype of structural p53 mutants.

overall_design: The most frequent 800 p53 missense variants recorded in IARC (R20), covering 95.8% p53 missense mutation cases, were cloned. The 800 variants, together with 5 frequent cancer-associated nonsense variants and 5 silent variants were then balanced mixed to generate the patient-derived plasmid library. The plasmid library was then packed into retroviral for p53-null U937 cell infection at a low multiplicity of infection so that the most of the infected cells expresses one p53 variant. The infected cells were then sorted by fluorescence activating cell sorter based on the co-expressed GFP, finally generating a balanced and abundant cell library. Cell growth inhibitory activities and mouse tumor suppressive activities were evaluated by the decreases of abundance for each variant in U937 cell library, as determined by the next-generation sequencing, in cultured cells and xenografted mice, respectively. To dissect the relationship between ATO-rescuable mutations and temperature-sensitive mutations, the cell library was cultured at either 32 or 37 °C for 7 days, followed by p53 variants abundance determination to determine the temperature-sensitive mutations.

first: Min

last: Lu


title: The Circulating Exosomal Long RNAs Expression Reveals T Cell Mediated Inflammatory Response and The Potential Clinical Value Analysis in Ischemic Stroke

first: guodong

last: he

address: zhongshan road No.102

institute: Guangdong Provincial People's Hospital

summary: This was a case-control study conducted from August 2020 to January 2021, in which 9 ischemic stroke and 2 healthy individuals (healthy control group) attending the Guangdong Provincial People's Hospital were recruited for plasma exoLRs sequencing. The other 10 normal samples from a previous study published in the Gene Expression Omnibu (GEO) database (Accession No. GSE159657) were used as part of healthy control group to analyzed the expression profile together.  30 ischemic stroke patients and 30 healthy individuals were also recruited for validation of the expression of exoLRs. Ischemic stroke diagnosis was performed according to World Health Organization guidelines and validated using computed tomography or magnetic resonance imaging. The ischemic stroke must have lasted not more 48 hours prior to recruitment. The participants ranged between 18–75 years old and were from either gender. To be included in this study, healthy individuals had to have displayed normal renal and liver function, and with no history of smoking, malignancy, recent cardiovascular or cerebrovascular events, rheumatologic disorders, chronic heart failure, diabetes, acute or chronic infectious disease, aortic dissection, pulmonary embolism, myocarditis, pericarditis or congenital heart disease.Blood samples were collected immediately at admission before thrombolytic therapy. For each patient, 2 ml of venous blood was collected in ethylene diamine tetraacetic acid routine blood tubes. In order to extract plasma, the blood was centrifuged at 3000×g for 10 min at 4 °C and the supernatant was carefully transferred to a new tube for repeated centrifugation. Then the plasma was stored in cryogenic vials at −80 °C till further use. Total RNA in exosomal vesicles was extracted using the exoRNeasy Serum/Plasma kit (Qiagen), following the manufacturer’s protocol. The RNA-seq libraries were constructed using SMART technology (Clontech). RNA sequencing was performed by the illumine Nova-Seq 6000 System.

overall_design: RNA-seq of plasma exosome from healthy controls and patients with ischemic stroke

first: Guo-dong

last: He

first: Jie

last: Li

first: Zhi-qiang

last: Nie

first: Shuo

last: Sun

first: Ying-qing

first: Yu-qing

last: Huang


title: Influenza-induced activation of recruited alveolar macrophages during the early inflammatory phase drives lung injury and lethality

city: Chicago

first: kishore

last: Anekalla

state: IL

address: 303 E. Superior

department: Pulmonary and Critical Care

institute: Northwestern University

summary: we identify gene expression patterns associated with three distinct phases (Infiltrating, Early Inflammatory, Late Inflammatory) in the influenza A virus response of recruited alveolar macrophages. In the Early Inflammatory phase, recruited macrophages begin expressing pro-inflammatory genes, driving cytokine-mediated lung damage and contributing to the morbidity observed in influenza-infected wild-type mice. In mice lacking vimentin (Vim-/-), genes associated with the Early Inflammatory phase are suppressed, while the expression of the Infiltrating Phase genes is maintained, which is associated with protection from influenza-induced injury. Using a bone-marrow chimera mouse model, we validate that Vim-/- recruited alveolar macrophages are sufficient to confer protection from influenza-induced mortality. Our results define the temporal dynamics of gene expression in recruited alveolar macrophages, which shape the host response to infection with respiratory viruses.

overall_design: RNA-seq on MoAMs over a 6-day time-course following IAV infection to characterize the immune response

first: Clarissa

last: M Koch

first: Kishore

first: Deborah

last: R Winter

first: Karen

last: M Ridge


title: RNAseq analysis for transcriptomes of ATO treated U937 cell lines expressing 10 type 1 p53 mutants, type-3 p53-R273H, p53 null, or p53 wild-type

summary: To globally evaluate to what extend type-1 p53 mutant transcription activity can be restored by arsenic trioxide (ATO) (compared to wild-type p53), p53-null U937 cells introduced with 10 frequent type-1 p53, type-3 p53-R273H (negative control), empty vector or wild-type p53 were treated with or without 1 μg/mL ATO. mRNA was isolated and then subject to deep sequencing, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed using Cutadapt.   Results and conclusions: The type-1 p53 mutants are the major cellular targets of ATO in the current cell contexts. The expression profiles of well-established p53 targets in cells expressing wild-type p53 highly correlated with the ones in cells expressing ATO-rescued type-1 mutants, but not those in cells expressing ATO-treated R273H. In cells harboring type-1 mutants, the median expression levels of these targets were elevated by ATO to extents comparable to wild-type p53.


title: Human melanoma Cells (A2058): Control interference fragment transfected vs. PARP1 interference fragment transfected

city: Xi`an

first: Rui

last: Ge

address: YAN TA WEST ROAD N0.277

department: Department of Dermatology

institute: First Affiliated Hospital，Xi’an Jiaotong University

summary: Human melanoma A2058 cells were transfected with PARP1 siRNA or control siRNA for 48 and 72 h. Goal was to determine the effects of PARP1 on global A2058 gene expression by comparing the changes in the expression profile of melanoma cells after PARP1 interference.

overall_design: Two-condition experiment, Ctrl siRNA transfected A2058 cells vs. PARP1 siRNA transfected cells. Cells were extracted at 48 hours and 72 hours after transfection, respectively.

first: Kuanhou

last: Mou

first: Lijuan

last: Wang

first: Xin

last: Mu

first: Yan

last: Zhou

first: Jian

last: Zhang


title: RNA-seq and Ribo-Seq of human iPSC-ECs treated with DMSO or sunitinib for 24 hours

first: Soroush

last: Tahmasebi

address: 909 S Wolcott, Chicago, IL 60607

institute: University of Illinois

summary: Sunitinib is a receptor tyrosine kinase (RTK) inhibitor that is widely used for treatment of various types of cancer. Vascular toxicity represents a debilitating side-effect of sunitinib which impends its application in some patients. Study of sunitinib has been primarily focused on transcriptional control, and there is an important gap in our understanding of its impact on translation. To interrogate the role of mRNA translation in mediating the effect of sunitinib on endothelial cells (ECs) we performed ribosome footprinting.

overall_design: Ribosome footprinting was performed on two healthy human induced pluripotent stem cell-derived endothelial cells (hiPSC-ECs) that were treated with DMSO or sunitinib (2ÂµM) for 24 hours."

first: Mehdi

last: Amiri

first: Stephen

last: Kiniry

first: Negar

last: Tabatabaei

first: Sang-Ging

last: Ong


title: Expression data from Hela cells stably expressing the wild-type preS and the three mutant preS

first: Shiliang

last: Cai

address: 800 Xiangyin Road

institute: Second Military Medical University

summary:
In large cohort studies, several preS mutants were identified as independent risk factors for HCC risk.In order to study the carcinogenic mechanism between different mutants, HeLa cell lines expressing wild type and different mutated preS proteins were constructed.
We used microarrays to describe gene expression in HeLa cells  stably expressing the wild-type preS and the three mutant preS, and to identify distinct classes of up-regulated genes.

overall_design: HBV DNA extracted from HCC patients was used as a template to amplify preS gene fragments and construct corresponding lentiviruses. Lentiviral vectors expressed different preS mutant proteins in Hela cells. Microarray analysis was performed on the constructed cells.

last: Pu

first: Wenbin

last: Liu

first: Xiaomei

last: Hou


title: Lacking all seven TRPC proteins accelerates DSS-induced colitis

first: Xinghua

last: Gao

address: #639 Longmian Dadao

institute: China Pharmaceutical University

summary: Analysis of colitic tissues of TRPC-hepta knockout mice. Results provide insight into the role of TRPC-hepta knockout in colitis.

overall_design: Colon Tissues mRNA profiles of TRPC-hepta knockout and TRPC-hepta control mice were generated by deep sequencing, in duplicate.

first: Yong

last: Yang

first: Yanting

last: Lin


title: Role of the STAR proteins in early mammalian development [RNA-seq]

city: Barcelona

first: Elias

last: Bechara

address: Dr Aiguader 88

country: Spain

institute: CRG

summary: RNA binding proteins (RBPs), are emerging as important master regulators of the biology of stem cells in both pluripotency and differentiation. The Signal transduction and activation of RNA (STAR) is family of proteins shown to be involved in mammalian development. We characterized the role of two members of the family, Sam68 and Quaking (QKI), in pluripotency and differentiation of mouse embryonic stem cells (mESCs) by making use of CRISPR-Cas9 generated knock-out (KO) cell lines along with RNA-sequencing, ribosome profiling and RNA crosslinking followed by immunoprecipitation (iCLIP2). Our results indicate that both proteins are important in the regulation of mESCs cell cycle and self-renewal and are indispensable for proper cardiomyocyte differentiation by regulating expression, alternative splicing and translation of the cardiogenic  factors GATA4. This work highlights the importance of the RBPs during the differentiation of mESCs.

overall_design: 9 samples in biological triplicate: a wild type E14 cell line of reference and KO lines (Sam68 or Qauking ) of the same genetic background. Each line was analyzed in 3 time points: day 0, day3 and day 10 of Embryoid body differentiation

first: Alessandro

last: Dasti

first: Maria

last: Antonelli


title: Nitrogen fertilizer reduces salicylic acid-mediated immunity  by activating gibberellin signaling in rice

first: xiaohan

last: zhang

address: Weigang

institute: Nanjing Agricultural University

summary: The environment plays important role in the interaction between plant hosts and pathogens. The application of chemical fertilizer is a crucial breeding technology to enhance crop yield since last century. As the most abundant fertilizer, nitrogen often increases disease susceptibility for crop plants. The underlying mechanism for nitrogen induced disease susceptibility is elusive. Here we found that nitrogen application activate gibberellin signaling by degradation of SLR1, the repressor protein in gibberellin signaling, which result in simultaneously promoting plant growth and disease susceptibility. SLR1, physically interacts with OsNPR1 and consequently facilitate OsNPR1 mediated defense responses. Transcriptome analysis showed that OsNPR1-SLR1 module plays a vital role in transcriptional reprogramming for both disease resistance and plant growth. Increase of SLR1 protein level in gibberellin deficient rice plants neutralizes disease susceptibility but sacrifice yield enhancement under high nitrogen supply. Mutation in SD1, encoding OsGA2ox2, produced more grains than WT，and maintains disease resistance under high nitrogen supply. Taken together, our work reveals the molecular mechanism underlying nitrogen-induced disease susceptibility, and demonstrates that the application of sd1 rice varieties prevent the tradeoff between disease susceptibility and yield increase under high nitrogen supply.

overall_design: Given OsNPR1 physically interacting with SLR1, it is possible OsNPR1-SLR1 protein complex co-regulate transcription.We used WT, OsNPR1-OE,   OsNPR1-OE/slr1-1, slr1-1 to conduct RNA-seq to examine common targets of OsNPR1 and SLR1.

first: Xiaohan

first: Dong-Lei


title: Development of serum exosomal miRNA signatures for persistent organ failures in early-phase of acute pancreatitis

first: Xiangyu

last: Kong

address: 168 Changhai Road

department: Gastroenterology

institute: Changhai Hospital

summary: To identify and assess exosomal miRNA signatures with potential to predict individuals with persistent organ failure (POF) at early phase of acute pancreatitis. We analyzed serum collected from 790 AP patients. In discovery cohort, we profiled exosomal miRNAs in sera sampled from AP patients with or without POF (5 vs. 5) using microarrays and identified a list of miRNAs with increased expression pattern. Of notes, 10 AP samples with/without POF are collected within 24 hours after AP onset and later did/didn’t develop POF. We further constructed a miRNA classifier (Cmi) through logistic regression and identified certain individual miRNAs (OR>2) as candidate predictive markers in the training cohort of 227 AP samples. Predictive performance of these markers were validated in three independent cohorts (255, 226 and 78 AP samples respectively).

overall_design: Ten serum samples were collected from AP patients within 24 hours after AP onset. Five cases later developed POF (POF group), while the other five did not (No POF group). Exosomal miRNAs were extracted and quantified in each group for potential markers for POF prediction.

first: Kong

last: Xiangyu

first: Du

last: Yiqi


title: RNA-sequence data of mouse hepatocytes with or without shear stress stimulation

first: Li

last: Wang

address: No.15, Beisihuan Road

institute: Institute of Mechanics

summary: Liver regeneration starting from hepatocyte proliferation was reported to be correlated with blood flow changes after partial hepatectomy (PHx). However, the regulatory effects of flow-induced shear stress on initiating hepatocyte proliferation have not been elucidated. Thus, the isolated hepatocytes were exposed to shear stress to identify their transcriptome changes.

overall_design: mRNA profiles of shear stress and static control group were generated by RNA sequencing, in quadruplicate, using DNBSEQ.

first: Wang

last: Li

first: Ning

first: Mian

last: Long